title: PD sample 6

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19
Supplementary_files_format_and_content: couts,FPKM,TPM

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 500-ng total RNA (Illumina) and by the Lexogen SENSE Total RNA-Seq Library Prep Kit using 500-ng total RNA (Lexogen). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

tag: disease

value: Parkinson's Disease


title: Brain endothelial cell 148

status: Public on Dec 21 2020

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain endothelial cell 148

library_source: transcriptomic

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Pdgfb ret mice were crossed with Cldn5-GFP; Cspg4-DsRed mice for endothelial cell (positive for GFP, negative for dsRed) isolation based on fluorescence-activated cell sorting (FACS),  followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: brain

tag: age

value: adult mice

tag: genotype

value: Pdgfb ret/+

tag: cell type

value: endothelial cell


title: PD sample 5

organism: Homo sapiens


title: Whole_Blood_GR04_V7

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

data_processing:
Reads were checked for quality using FastQC v0.11.7
Reads were aligned to the reference genome using STAR v2.5.4b
Reads were counted using HTSeq v0.10.0
Quality metrics were summarized using MultiQC v1.0
Genome_build: Ensembl Genome Build GRCh38 v91
Supplementary_files_format_and_content: Tab-delimited text files containing gene counts for each sample

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
PAXGene RNA purification kit was used on collected whole blood as per manufacturer's instructions
KAPA stranded RNA-Seq library preparation kit was used as per manufacturer's guidelines

value: Whole Blood

tag: Sex

value: Female

tag: participant id

tag: visit


title: Brain endothelial cell 173

description: Brain endothelial cell 173


title: PD sample 4


title: Brain endothelial cell 144

description: Brain endothelial cell 144


title: Brain endothelial cell 147

description: Brain endothelial cell 147


title: PD sample 3


title: Brain endothelial cell 143

description: Brain endothelial cell 143


title: Brain endothelial cell 141

description: Brain endothelial cell 141


title: Brain endothelial cell 140

description: Brain endothelial cell 140


title: Brain endothelial cell 139

description: Brain endothelial cell 139


title: Whole_Blood_GR04_V5


title: Whole_Blood_GR04_V3


title: PD sample 2


title: Brain endothelial cell 142

description: Brain endothelial cell 142


title: Whole_Blood_GR04_V4


title: Brain endothelial cell 138

description: Brain endothelial cell 138


title: Brain endothelial cell 137

description: Brain endothelial cell 137


title: Whole_Blood_GR04_V6


title: Brain endothelial cell 135

description: Brain endothelial cell 135


title: Brain endothelial cell 134

description: Brain endothelial cell 134


title: CTRL sample 10

value: Helathy Control


title: Brain endothelial cell 136

description: Brain endothelial cell 136


title: Brain endothelial cell 154

description: Brain endothelial cell 154


title: CTRL sample 11


title: Brain endothelial cell 145

description: Brain endothelial cell 145


title: Brain endothelial cell 146

description: Brain endothelial cell 146


title: Brain endothelial cell 133

description: Brain endothelial cell 133


title: PD sample 1


title: Brain endothelial cell 132

description: Brain endothelial cell 132


title: CTRL sample 8


title: Whole_Blood_GR03_V5


title: Brain endothelial cell 131

description: Brain endothelial cell 131


title: CTRL sample 9


title: Brain endothelial cell 130

description: Brain endothelial cell 130


title: Brain endothelial cell 129

description: Brain endothelial cell 129


title: Brain endothelial cell 128

description: Brain endothelial cell 128


title: Whole_Blood_GR03_V3


title: CTRL sample 6


title: Brain endothelial cell 126

description: Brain endothelial cell 126


title: CTRL sample 7


title: Brain endothelial cell 127

description: Brain endothelial cell 127


title: Brain endothelial cell 125

description: Brain endothelial cell 125


title: Whole_Blood_GR03_V6


title: CTRL sample 5


title: Whole_Blood_GR03_V7


title: Whole_Blood_GR02_V7


title: Brain endothelial cell 124

description: Brain endothelial cell 124


title: CTRL sample 4


title: Brain endothelial cell 121

description: Brain endothelial cell 121


title: Whole_Blood_GR02_V6


title: Brain endothelial cell 120

description: Brain endothelial cell 120


title: CTRL sample 3


title: Brain endothelial cell 119

description: Brain endothelial cell 119


title: Whole_Blood_GR02_V5


title: CTRL sample 2


title: Brain endothelial cell 118

description: Brain endothelial cell 118


title: CTRL sample 1


title: Whole_Blood_GR02_V4


title: Whole_Blood_GR03_V4


title: Whole_Blood_GR02_V3


title: Brain endothelial cell 117

description: Brain endothelial cell 117


title: Brain endothelial cell 116

description: Brain endothelial cell 116


title: Whole_Blood_GR01_V7


title: Brain endothelial cell 115

description: Brain endothelial cell 115


title: AD sample 6

value: Alzheimer’s Disease


title: Whole_Blood_GR01_V6


title: AD sample 5


title: Brain endothelial cell 114

description: Brain endothelial cell 114


title: Brain endothelial cell 112

description: Brain endothelial cell 112


title: Brain endothelial cell 110

description: Brain endothelial cell 110


title: Brain endothelial cell 111

description: Brain endothelial cell 111


title: Brain endothelial cell 123

description: Brain endothelial cell 123


title: Brain endothelial cell 122

description: Brain endothelial cell 122


title: Brain endothelial cell 109

description: Brain endothelial cell 109


title: AD sample 3


title: Brain endothelial cell 108

description: Brain endothelial cell 108


title: Brain endothelial cell 107

description: Brain endothelial cell 107


title: Whole_Blood_GR01_V5


title: AD sample 4


title: Whole_Blood_GR01_V3


title: Whole_Blood_GR01_V4


title: AD sample 1


title: Brain endothelial cell 104

description: Brain endothelial cell 104


title: Brain endothelial cell 103

description: Brain endothelial cell 103


title: AD sample 2


title: Brain endothelial cell 102

description: Brain endothelial cell 102


title: Brain endothelial cell 101

description: Brain endothelial cell 101


title: 17DMAG_4

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
raw paired-end reads were mapped by STAR_2.5.3a(parameters "--outFilterMultimapNmax 20   --outFilterMismatchNmax 10   --alignIntronMax 500000   --chimSegmentMin 20   --chimJunctionOverhangMin 20")
reads were counted using St Jude Cloud RNAseq pipeline (WARDEN, https://platform.stjude.cloud/workflows/warden)
hg19(GRCh37)
Genome_build: gene-based raw counts txt file

extract_protocol:
Xenografts were removed, flash frozen on dry ice, and RNA was harvested Qiagen RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocol with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA)

treatment_protocol: Mice were treated with  vehicle, 17-DMAG(25mg/kg), 17-AAG (50mg/kg), twice daily, via IP injection, on every Monday and Thursady.

tag: treatment


title: 17AAG_2


title: 17AAG_1


title: Brain endothelial cell 100

description: Brain endothelial cell 100


title: 4W VPA3

city: Seoul

first: SeungEun

address: 1 Gwanak-Ro, Gwanak-gu

department: Veterinary

country: South Korea

institute: Seoul National University

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes. Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed based on quantile normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor (Gentleman et al.,2004). Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: Quantile normalizatioin using EdgeR

source_name: 4W NPC+VPA brain organoid

growth_protocol: induced neual stem cells was cultured in neural stem cell maintenance media

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100  bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands),  and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
The library was amplified to add the complete  adapter sequences required for cluster generation. The finished library is purified from PCR  components. High-throughput sequencing was performed as single-end 75 sequencing using  NextSeq 500 (Illumina, Inc., USA).
QuantSeq 3` mRNA-Seq

treatment_protocol: VPA treatment to the NPC brain organoids at day21

value: induced neural stem cells

value: NPC1 mutant


title: 17DMAG_3


title: 4W VPA1


title: Brain endothelial cell 98

description: Brain endothelial cell 98


title: 17DMAG_2


title: Brain endothelial cell 97

description: Brain endothelial cell 97


title: 4W NPC3

source_name: 4W NPC brain organoid


title: Brain endothelial cell 105

description: Brain endothelial cell 105


title: Brain endothelial cell 95

description: Brain endothelial cell 95


title: Brain endothelial cell 96

description: Brain endothelial cell 96


title: 17DMAG_1


title: Brain endothelial cell 94

description: Brain endothelial cell 94


title: 4W NPC2


title: Veh_3

value: Vehicle


title: Brain endothelial cell 93

description: Brain endothelial cell 93


title: Brain endothelial cell 92

description: Brain endothelial cell 92


title: Brain endothelial cell 91

description: Brain endothelial cell 91


title: Brain endothelial cell 90

description: Brain endothelial cell 90


title: Brain endothelial cell 99

description: Brain endothelial cell 99


title: Veh_1


title: 4W VPA2


title: Brain endothelial cell 89

description: Brain endothelial cell 89


title: Sonicated 3 (Tn5 5x)

city: St Louis

first: Ricardo

last: D'Oliveira Albanus

state: MO

address: 4370 Duncan Avenue, Suite 6306D, Jeffrey T. Fort Neuroscience Bdg.

department: Neurology

institute: Washington University School of Medicine

library_source: genomic

data_processing:
Reads were trimmed for barcodes and aligned to the hg19 reference human genome using BWA (v. 0.7.15) similarly to our previous study (Scott et al., Nat Comm 2016), with additional parameters -I 200,200,5000 to avoid larger ATAC-seq fragments being discarded.
We removed duplicate alignments using Picard and retained properly paired and uniquely mapped alignments with high mapping quality (MAPQ ≥ 30). We called broad and narrow peaks using MACS2 (v. 2.1.1.20160309) with flags -g hs --nomodel --shift -100 --extsize 200 -B [--broad] --keep-dup all and kept peaks that were both outside blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) and reached 5% FDR.
Sample QC was determined using ataqv (https://github.com/ParkerLab/ataqv).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BedGraph files from MACS2.

molecule: genomic DNA

source_name: GM12878 lymphoblastoid cell line

growth_protocol: We cultured GM12878 cells following the ENCODE GM12878 cell culture protocol (https://www.encodeproject.org/documents/1bb75b62-ac29-4368-9855-68d410e1963a/), except that we added plasmocin (Invivogen, San Diego, CA; 50 ug/mL) to the growth media to prevent mycoplasma contamination.

extract_protocol: We conducted ATAC-seq as described in Buenrostro et al. (2015) using a home-made Tn5 that we synthesized as described in Picelli et al. (2014). For each replicate we incubated 250,000 cells with three different concentrations of enzyme (0.2X, 1X, and 5X; 1X corresponds to 2.5 uL of Tn5 that carry 5-methylC-MEDS-A oligos) at 37℃ for 30 minutes in a 50 uL reaction. We column-purified the tagmented DNA using the Zymo DNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA), and sonicated to ~350 bp using the Covaris M220 sonicator (peak incident power - 50W; duty factor - 20%; cycles per burst - 200; treatment time - 60 sec). We constructed Illumina sequencing library using the ACCEL-NGS Methyl-seq DNA Library kit (Swift Biosciences #DL-ILMMS-12; revision 160106) with the following exceptions to the manufacturer’s protocol: 1) We skipped “Ligation” and “Post-ligation SPRI” steps (pg. 10-11), as 5’ end had already been tagged by Tn5 during the transposition step. Accordingly, we eluted DNA with 20 uL of TTE8 (10 mM Tris-HCl, 0.1 mM EDTA, 0.05% Tween-20, pH 8) for Post-Extension SPRI step (pg. 10), instead of 15 uL, to make up the difference in volume before proceeding to the “Indexing PCR” step (pg. 11); 2) We used 2:1 beads:sample ratio for “Post-Extension SPRI” step (pg. 10) and 1.8:1 beads:sample ratio for “Post-PCR SPRI” step (pg. 12); and 3) For indexing PCR, we used the Kitzman lab custom primers (barcode plate #5) to prime the P5 end and the “IndexD7XX” primers (Swift Biosciences #DI-ILMMS-48) to prime the P7 end. We PCR-amplified a total of 14 cycles for 0.2X, 1X samples and 16 cycles for 5X samples until amplification curve reached its mid-log phase (⅓ to ½ of max signal), and then purified the products using SPRI beads prepared as in (Rohland and Reich, 2012) and eluted in 22 uL of TTE8 buffer.

tag: cell line

value: Lymphoblastoid cell line

value: Sonicated

tag: tn5 concentration


title: 4W WT5

source_name: 4W wild type brain organoid

value: Wild-type


title: Brain endothelial cell 87

description: Brain endothelial cell 87


title: Brain endothelial cell 88

description: Brain endothelial cell 88


title: Brain endothelial cell 86

description: Brain endothelial cell 86


title: Sonicated 2 (Tn5 1x)


title: 4W WT4


title: AC16-CAR_rep2

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description:
Quiescent AC16-CAR cells, replicate 2
AC16 and AC16-CAR TPM.tsv

data_processing:
Adapters were trimmed using fastq-mcf (1.1.2) with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Reads were aligned to the human genome (GRCh38) using HISAT2 (2.1.0) with the following options: --dta --rna-strandness RF.
Output SAM files were converted to BAM files using samtools (1.4.1).
Aligned reads were assembled using StringTie (2.0.6) with the following options: -e -B
Genome_build: GRCh38 + SV40 + CVB3
Supplementary_files_format_and_content: AC16 and AC16-CAR TPM.tsv: Output file is a TSV with TPM-normalized read counts for each gene.

source_name: left ventricle

growth_protocol: DMEM/F12 medium (Gibco Cat#11330-032) + 12.5% fetal bovine serum + 1% pen/strep.

extract_protocol:
Cells were lysed in Buffer RLT and mRNA was extracted using the RNeasy kit (Qiagen #74104).
TruSeq stranded mRNA library prep kit per manufacturer's recommendations (RS-122-2101 Illumina).

treatment_protocol: AC16 or AC16-CAR cells (70,000 per well) were plated on a 12-well dish precoated with 0.02% gelatin for 1–2 hours at 37ºC. After 24 hours, cells were washed with PBS and the culture medium was changed to differentiation medium: DMEM/F12 (Gibco) + 2% horse serum (ThermoFisher) + 1x Insulin-Transferrin-Selenium supplement (ThermoFisher) + 1% penicillin–streptomycin (Gibco). After 24 hours, cells were washed with PBS and transduced with shSV40 lentivirus (125 µl per well) + 8 µg/ml polybrene in a total volume of 500 µl. After 18–21 hours, cells were washed with PBS and refed with differentiation medium. After another 24 hours, cells were washed with PBS and refed with differentiation medium again, and cells were lysed 24 hours after the final refeed.

tag: genotype/variation

value: ectopic CAR overexpression

value: shSV40+low serum


title: Brain endothelial cell 85

description: Brain endothelial cell 85


title: Brain endothelial cell 84

description: Brain endothelial cell 84


title: Brain endothelial cell 83

description: Brain endothelial cell 83


title: 4W NPC1


title: AC16-CAR_rep1

description:
Quiescent AC16-CAR cells, replicate 1
AC16 and AC16-CAR TPM.tsv


title: Brain endothelial cell 82

description: Brain endothelial cell 82


title: Veh_2


title: Brain endothelial cell 81

description: Brain endothelial cell 81


title: Sonicated 1 (Tn5 0.2x)

extract_protocol: We conducted ATAC-seq as described in Buenrostro et al. (Curr. Protoc. Mol. Biol. 2015) using a home-made Tn5 that we synthesized as described in Picelli et al. (Genome Res. 2014). For each replicate we incubated 250,000 cells with three different concentrations of enzyme (0.2X, 1X, and 5X; 1X corresponds to 2.5 uL of Tn5 that carry 5-methylC-MEDS-A oligos) at 37℃ for 30 minutes in a 50 uL reaction. We column-purified the tagmented DNA using the Zymo DNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA), and sonicated to ~350 bp using the Covaris M220 sonicator (peak incident power - 50W; duty factor - 20%; cycles per burst - 200; treatment time - 60 sec). We constructed Illumina sequencing library using the ACCEL-NGS Methyl-seq DNA Library kit (Swift Biosciences #DL-ILMMS-12; revision 160106) with the following exceptions to the manufacturer’s protocol: 1) We skipped “Ligation” and “Post-ligation SPRI” steps (pg. 10-11), as 5’ end had already been tagged by Tn5 during the transposition step. Accordingly, we eluted DNA with 20 uL of TTE8 (10 mM Tris-HCl, 0.1 mM EDTA, 0.05% Tween-20, pH 8) for Post-Extension SPRI step (pg. 10), instead of 15 uL, to make up the difference in volume before proceeding to the “Indexing PCR” step (pg. 11); 2) We used 2:1 beads:sample ratio for “Post-Extension SPRI” step (pg. 10) and 1.8:1 beads:sample ratio for “Post-PCR SPRI” step (pg. 12); and 3) For indexing PCR, we used the Kitzman lab custom primers (barcode plate #5) to prime the P5 end and the “IndexD7XX” primers (Swift Biosciences #DI-ILMMS-48) to prime the P7 end. We PCR-amplified a total of 14 cycles for 0.2X, 1X samples and 16 cycles for 5X samples until amplification curve reached its mid-log phase (⅓ to ½ of max signal), and then purified the products using SPRI beads prepared as in (Rohland and Reich, Genome Res. 2012) and eluted in 22 uL of TTE8 buffer.


title: mDC-Tcell 10

city: Badalona

first: Eva

middle: M

last: Martínez-Cáceres

state: Barcelona

address: Campus Can Ruti, Carretera de Can Ruti s/n

department: Immunology

country: Spain

institute: Germans Trias i Pujol University Hospital and Research Institute

data_processing:
BCL basecall files were converted to FASTQ per sample using CASAVA v1.8.2 (Illumina) with default parameters to generate demultiplexed per sample fastq raw sequencing data files.
Per sample read quality was assessed using the fastx_quality stats software (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
We used Tophat v2.1.0 (http://ccb.jhu.edu/software/tophat/index.shtml) [3], which uses Bowtie v2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), to map RNA-seq reads to the reference genome.
Using BAM files obtained from mapping all reads per sample and the GTF file with the annotation of exons and ERCC Spikes, we applied featureCounts (http://bioinf.wehi.edu.au/featureCounts/) [4] to count how many reads map to each feature.
Statistically significant differences in miRNA expression were determined both by DESeq2 (Love, 2014) with multiple testing adjustment.
Trimming of Illumina reads was performed using the tool Trimmomatic V0.30 (http://www.usadellab.org/cms/?page=trimmomatic).
Genome_build: Ensembl release 78 (Homo_sapiens.GRCh38.dna.primary_assembly) human reference genome.
Supplementary_files_format_and_content: Processed RNA expression profiling (human gene symbol HGNC_Id from ENSEMBL) data table is provided as a supplementary file in excel workbook (.xlsx) format. It includes normalized read counts derived from DESeq2 for all samples.

source_name: T CD4+ lymphocytes

growth_protocol: Dendritic cell (DC) growth conditions: monocytes were cultured for 6 days in 24-well plates at 37ºC at a density of 1 million cells/mL in X‑VIVO 15 medium, in the presence of 400 U/mL granulocyte macrophage colony-stimulating factor (GM‑CSF) and 500 U/mL IL‑4 (both from Peprotech, London, UK). On day 3, 0.1 µg/mL of whole tetanus toxin (Sigma-Aldrich, St. Louis, MO, USA) were added to all the culture conditions. Whole volume of medium and cytokines was replenished on day 4. Subsequently, we added a maturation cocktail, containing 1000 U/mL IL‑1b, 1000 U/mL TNF‑a (both from Peprotech) and 1 µM prostaglandin E2 (PGE2) (Pfizer, New York, NY, USA) on day 4. If no further treatment was applied, TT-loaded mature DC (mDC-TT) were obtained. For the generation of TT-loaded vitamin D3-generated tolerogenic DC (vitD3-tolDC-TT), we added 1 nM vitamin D3 (Calcijex, Abbott, Chicago, IL, USA) on days 0 and 4 of the culture. On day 6, cells were harvested after an accutase (Invitrogen, Carlsbad, CA, USA) detaching treatment for 30 min, and washed twice. T cell growth conditions: whole peripheral blood mononuclear cells (PBMC) of the same healthy donors were cultured on 96-well plates for 6 days at 37ºC at a density of 1 million cells/mL in RPMI medium. Cells were harvested on day 6.

extract_protocol:
Total RNA of CD3+CD4+ T cells was isolated using the automated Maxwell 16 LEV simplyRNA Purification Kit (Promega Biotech, Madison, WI, USA), including a DNAse I digestion step, according to manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, San Diego, CA, USA) with 200 ng of total RNA per sample.

treatment_protocol: The PBMC harvested from the cultures after 6 days were later co-cultured with autologous either mDC-TT (mDC-Tcell) or vitD3-tolDC-TT (vitD3-Tcell) at a 1:20 DC:PBMC ratio in 96-well plates for 114 hours at 37ºC. Cells were then harvested and CD3+CD4+ cells were isolated using flow cytometry cell sorting.

value: Flow cytometry-sorted T CD4+ lymphocytes

tag: co-culture condition

value: Autologous tetanus toxin-loaded mDC


title: vitD3-Tcell 10

value: Autologous tetanus toxin-loaded vitD3-tolDC


title: Brain endothelial cell 80

description: Brain endothelial cell 80

value: brain

value: adult mice

value: Pdgfb ret/+


title: 4W WT3


title: AC16 parental_rep1

description:
Quiescent AC16 cells, replicate 1
AC16 and AC16-CAR TPM.tsv

value: wild type


title: AC16 parental_rep2

description:
Quiescent AC16 cells, replicate 2
AC16 and AC16-CAR TPM.tsv


title: Brain endothelial cell 78

description: Brain endothelial cell 78

value: endothelial cell


title: Brain endothelial cell 79

description: Brain endothelial cell 79


title: vitD3-Tcell 09


title: mDC-Tcell 09


title: Brain endothelial cell 77

description: Brain endothelial cell 77


title: Brain endothelial cell 76

description: Brain endothelial cell 76


title: H3K4me3 ChIP-seq in MET5A cell line [MET5A.H3K4me3]

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to hg19 or mm10 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: cell line/tissue

value: cell line

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: Brain endothelial cell 75

description: Brain endothelial cell 75

tag: strain


title: Brain endothelial cell 74

description: Brain endothelial cell 74

tag: tissue


title: INPUT library in MET5A cell line [MET5A.INPUT]


title: Brain endothelial cell 73

description: Brain endothelial cell 73

tag: age


title: Brain endothelial cell 106

description: Brain endothelial cell 106

tag: genotype


title: Brain endothelial cell 72

description: Brain endothelial cell 72

tag: cell type


title: mDC-Tcell 08


title: SMARCA2 ChIP-seq in MET5A cell line [MET5A.SMARCA2]

value: Active Motif


title: INPUT library in MRC5 fibroblasts [MRC5.INPUT]

value: INPUT


title: Brain endothelial cell 70

description: Brain endothelial cell 70


title: vitD3-Tcell 07


title: Brain endothelial cell 69

description: Brain endothelial cell 69


title: Brain endothelial cell 68

description: Brain endothelial cell 68


title: H3K4me3 ChIP-seq in MRC5 fibroblasts [MRC5.H3K4me3]


title: SMARCA2 ChIP-seq in MRC5 fibroblasts [MRC5.SMARCA2]


title: Brain endothelial cell 67

description: Brain endothelial cell 67


title: mDC-Tcell 07


title: Brain endothelial cell 66

description: Brain endothelial cell 66


title: vitD3-Tcell 06


title: mDC-Tcell 06


title: Brain endothelial cell 64

description: Brain endothelial cell 64


title: Brain endothelial cell 62

description: Brain endothelial cell 62


title: Brain endothelial cell 63

description: Brain endothelial cell 63


title: vitD3-Tcell 05


title: MDM cornea without endothelium sample 5

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode release 33) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode annotation file (Gencode 33)
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL release 99 (Human genes, GRCh38.p13, download on 02/29/2020). Genes without ENTREZID were removed from analysis. Only genes with at least one raw read in each donor and in each stimulation group were considered for further analysis. Principal component analysis (PCA) was applied to check for potential batch effects, which were removed by the limma function remove-BatchEffect and by considering in the linear model of DESeq2. Another PCA subsequently confirmed the correct adjustment of the batch effect. Differential gene expression was analyzed using the R package DESeq2 Version 1.22.2 with default parameters (Benjamini-Hochberg adjusted p-values). Transcripts with log2 fold change (log2 FC) > 1 or < -1 and adjusted p-value < 0.05 were considered as differentially expressed genes (DEG).
Genome_build: hg38
Supplementary_files_format_and_content: normalized reads

source_name: MDM cornea without endothelium

extract_protocol:
After stimulation, stimuli were removed by gently washing tissue culture plates thoroughly with HBSS for three times. MDM samples were carefully collected using a cell scraper and removing adherent MDM from the tissue culture plate. RNA was extracted using an RNA purification kit (Quick-RNA MicroPrep; Zymo Research Corp., Irvine, CA, USA) according to the manufacturer's instructions.
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3’ RNA sequencing method as previously described. Briefly, 25 barcoded libraries (5 different stimuli in 5 experiments) were sequenced simultaneously on the NextSeq 500 (Illumina). PCR bias was removed based on unique molecular identifiers encoded in the library barcodes.

value: monocyte-derived macrophages


title: vitD3-Tcell 08


title: MDM cornea without endothelium sample 4


title: Brain endothelial cell 60

description: Brain endothelial cell 60


title: MDM cornea without endothelium sample 3


title: mDC-Tcell 05


title: Brain endothelial cell 71

description: Brain endothelial cell 71


title: MDM cornea without endothelium sample 2


title: Brain endothelial cell 59

description: Brain endothelial cell 59


title: Brain endothelial cell 58

description: Brain endothelial cell 58


title: Brain endothelial cell 57

description: Brain endothelial cell 57


title: vitD3-Tcell 04


title: mDC-Tcell 04


title: Brain endothelial cell 56

description: Brain endothelial cell 56


title: Brain endothelial cell 54

description: Brain endothelial cell 54


title: Brain endothelial cell 55

description: Brain endothelial cell 55


title: MDM cornea with endothelium sample 5

source_name: MDM cornea with endothelium


title: Brain endothelial cell 53

description: Brain endothelial cell 53


title: Brain endothelial cell 65

description: Brain endothelial cell 65


title: vitD3-Tcell 03


title: MDM cornea with endothelium sample 4


title: MDM cornea with endothelium sample 3


title: Brain endothelial cell 50

description: Brain endothelial cell 50


title: Brain endothelial cell 61

description: Brain endothelial cell 61


title: Brain endothelial cell 49

description: Brain endothelial cell 49


title: vitD3-Tcell 02


title: Brain endothelial cell 48

description: Brain endothelial cell 48


title: Brain endothelial cell 47

description: Brain endothelial cell 47


title: Brain endothelial cell 46

description: Brain endothelial cell 46


title: MDM cornea with endothelium sample 1


title: Brain endothelial cell 45

description: Brain endothelial cell 45


title: MDM cornea without endothelium sample 1


title: vitD3-Tcell 01


title: MDM IFNg sample 5

source_name: MDM IFNg

tag: agent

value: IFNg


title: MDM cornea with endothelium sample 2


title: Brain endothelial cell 44

description: Brain endothelial cell 44


title: MDM IFNg sample 4


title: Brain endothelial cell 43

description: Brain endothelial cell 43


title: Brain endothelial cell 113

description: Brain endothelial cell 113


title: Brain endothelial cell 52

description: Brain endothelial cell 52


title: Brain endothelial cell 42

description: Brain endothelial cell 42


title: MDM IFNg sample 3


title: Brain endothelial cell 41

description: Brain endothelial cell 41


title: mDC-Tcell 01


title: Brain endothelial cell 51

description: Brain endothelial cell 51


title: Brain endothelial cell 40

description: Brain endothelial cell 40


title: Tr1_Tbx21_Ctrl2

first: Vijay

last: Kuchroo

address: 60 Fenwood Road

institute: Brigham & Women's Hospital

description: bulk RNA-seq

data_processing:
Tophat
RSEM RNA Quantification
Genome_build: mm9

source_name: Tr1 cells derived in vitro with IL-27

growth_protocol: Naïve CD4 T cells were polarized to Tr1 cells with anti-CD3 (1ug/ml) and anti-CD8 (1ug/ml) stimulation in the presence of IL-27 (25ng/ml) for 72h

extract_protocol:
2000 cells were lysed in 2ul of RLT buffer
library was constructed using an adaptation of the SMART-Seq 2 protocol (Tirosh et al., 2016)

tag: time point

value: WT


title: Tr1_Tbx21_Ctrl1

description: bulk RNA-seq


title: Brain endothelial cell 37

description: Brain endothelial cell 37


title: Tr1_Tbx21_KO2

description: bulk RNA-seq

value: Tbx21 KO


title: mDC-Tcell 02


title: Tr1_Tbx21_KO1

description: bulk RNA-seq


title: MDM IFNg sample 2


title: MDM IFNg sample 1


title: Brain endothelial cell 32

description: Brain endothelial cell 32


title: Tr1_Stat3_KO1

description: bulk RNA-seq

value: CD4 Cre(+/-); Stat3 f/f


title: MDM LPS sample 4

source_name: MDM LPS

value: LPS


title: Brain endothelial cell 36

description: Brain endothelial cell 36


title: Brain endothelial cell 33

description: Brain endothelial cell 33


title: Brain endothelial cell 34

description: Brain endothelial cell 34


title: MDM LPS sample 5


title: Brain endothelial cell 35

description: Brain endothelial cell 35


title: Tr1_Nfil3_Ctrl3

description: bulk RNA-seq

value: Nfil3 f/f


title: MDM LPS sample 3


title: Brain endothelial cell 31

description: Brain endothelial cell 31


title: Brain endothelial cell 30

description: Brain endothelial cell 30


title: Brain endothelial cell 29

description: Brain endothelial cell 29


title: Brain endothelial cell 28

description: Brain endothelial cell 28


title: Brain endothelial cell 27

description: Brain endothelial cell 27


title: Brain endothelial cell 38

description: Brain endothelial cell 38


title: Tr1_Nfil3_Ctrl2

description: bulk RNA-seq


title: MDM LPS sample 1


title: Brain endothelial cell 26

description: Brain endothelial cell 26


title: Tr1_Nfil3_KO2

description: bulk RNA-seq

value: CD4 Cre(+/-); Nfil3 f/f


title: Brain endothelial cell 25

description: Brain endothelial cell 25

value: brain


title: mDC-Tcell 03

value: Flow cytometry-sorted T CD4+ lymphocytes

value: Autologous tetanus toxin-loaded mDC


title: Brain endothelial cell 24

description: Brain endothelial cell 24

value: adult mice

value: Pdgfb ret/+


title: Brain endothelial cell 23

description: Brain endothelial cell 23

value: endothelial cell


title: Tr1_Nfil3_KO1

description: bulk RNA-seq


title: MDM unstimulated sample 5

source_name: MDM unstimulated

value: unstimulated


title: MDM unstimulated sample 4


title: Brain endothelial cell 22

description: Brain endothelial cell 22


title: Brain endothelial cell 21

description: Brain endothelial cell 21


title: Brain endothelial cell 39

description: Brain endothelial cell 39


title: Brain endothelial cell 20

description: Brain endothelial cell 20


title: MDM unstimulated sample 3


title: Brain endothelial cell 18

description: Brain endothelial cell 18


title: Tr1_Irf9_Ctrl2

description: bulk RNA-seq

value: BALB/c


title: MDM unstimulated sample 2


title: Brain endothelial cell 19

description: Brain endothelial cell 19


title: Tr1_Irf9_Ctrl3

description: bulk RNA-seq


title: MDM unstimulated sample 1


title: Tr1_Nfil3_Ctrl1

description: bulk RNA-seq


title: MDM LPS sample 2


title: Brain endothelial cell 16

description: Brain endothelial cell 16


title: Tr1_Irf9_Ctrl1

description: bulk RNA-seq


title: Tr1_Irf9_KO4

description: bulk RNA-seq

value: Irf9 KO


title: Brain endothelial cell 14

description: Brain endothelial cell 14


title: Brain endothelial cell 15

description: Brain endothelial cell 15


title: Brain endothelial cell 13

description: Brain endothelial cell 13


title: Tr1_Irf9_KO3

description: bulk RNA-seq


title: Brain endothelial cell 12

description: Brain endothelial cell 12


title: Tr1_Irf9_KO2

description: bulk RNA-seq


title: Tr1_Irf9_KO1

description: bulk RNA-seq


title: Brain endothelial cell 9

description: Brain endothelial cell 9


title: Brain endothelial cell 11

description: Brain endothelial cell 11


title: Donor4_Day9_rna

city: Nijmegen

first: Hendrik

middle: G.

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University Nijmegen

description:
RNA-seq of Monocytes from volunteer isolated by CD14 positive selection on day 9 after controlled plasmodium infection (During inflammatory state)
Raw_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx
Normalized_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx

data_processing:
To infer gene expression levels, RNA-seq reads were aligned to the hg38 human reference transcriptome using STAR alignment tool. Genes with fewer than 50 reads on average in all time points (baseline, day9 and day36) were excluded from downstream analysis.
Utilizing DESeq2 libraries normalized and differentially expressed genes determined. Genes with more than two-fold change between at least two time points and less that 0.05 padj value were designated as significant differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx, Raw or Normalized Count table of Gene Expression from all samples

source_name: Adult Human Peripheral Blood

growth_protocol: No Growth of the cells (Primary Monocytes isolated by positive CD14 selection over the time course)

extract_protocol:
Total RNA was extracted from positively selected monocytes using the QIAGEN RNeasy RNA extraction kit (QIAGEN, Netherlands), using on-column DNaseI treatment.
Utilizing riboZero rRNA removal kit (Illumina) ribosomal RNA was removed from total RNA. RNA was then fragmented into approximately 200bp fragments by incubation for 3 min at 95C in fragmentation buffer (200 mM Tris-acetate, 500 mM Potassium Acetate, 150 mM Magnesium Acetate [pH 8.2]). First strand cDNA synthesis was performed using SuperScript III (Life Technologies), followed by synthesis of the second cDNA strand, recruiting DNA polymerase and DNA ligase (NEB). Libraries for RNA-sequencing were prepared using the KAPA hyperprep kit (KAPA Biosystems), according to the manufacturer’s protocol. Libraries were sequenced in Nextseq 500 illumina machine.

treatment_protocol: No Treatment

value: Monocyte

value: day 9


title: Donor1_Day36_rna

description:
RNA-seq of Monocytes from volunteer isolated by CD14 positive selection on day 36 after controlled plasmodium infection (During trained state)
Raw_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx
Normalized_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx

value: day 36


title: Brain endothelial cell 8

description: Brain endothelial cell 8


title: Brain endothelial cell 17

description: Brain endothelial cell 17


title: Donor3_Day36_rna


title: Tr1_Irf8_KO2

description: bulk RNA-seq

value: dLck Cre(+/-); Irf8 f/f


title: Donor3_Day9_rna

description:
RNA-seq of  Monocytes from volunteer isolated by CD14 positive selection on day 9 after controlled plasmodium infection (During inflammatory state)
Raw_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx
Normalized_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx


title: Brain endothelial cell 5

description: Brain endothelial cell 5


title: Donor4_Day36_rna


title: Brain endothelial cell 4

description: Brain endothelial cell 4


title: Tr1_Irf8_KO1

description: bulk RNA-seq


title: Brain endothelial cell 6

description: Brain endothelial cell 6


title: Donor2_Day9_rna


title: Tr1_Irf4_Ctrl2

description: bulk RNA-seq

value: WT


title: Brain endothelial cell 1

description: Brain endothelial cell 1


title: Donor1_Day9_rna


title: Brain endothelial cell 2

description: Brain endothelial cell 2


title: Brain endothelial cell 3

description: Brain endothelial cell 3


title: Donor4_Day0_rna

description:
RNA-seq of Monocytes from healthy volunteer isolated by CD14 positive selection on day 0 (Before start of the controlled plasmodium infection)
Raw_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx
Normalized_Count_RNA_Expr_Malaria_Trained_Immunity.xlsx

value: day 0


title: Brain endothelial cell 10

description: Brain endothelial cell 10


title: Donor2_Day36_rna


title: Tr1_Irf4_KO2

description: bulk RNA-seq

value: Irf4 KO


title: Donor3_Day0_rna


title: Tr1_Irf4_KO1

description: bulk RNA-seq


title: Tr1_Irf4_Ctrl3

description: bulk RNA-seq


title: Tr1_Irf1_Ctrl2

description: bulk RNA-seq


title: Donor1_Day0_rna


title: Donor2_Day0_rna


title: Donor4_Day36_h3k4me3_chip

description:
H3K4me3 Histone ChIP-Seq of Monocytes from volunteer isolated by CD14 positive selection on day 36 after controlled plasmodium infection (During trained state)
Raw_Peaks_H3K4me3_ChIP_Malaria_TRIM.xlsx
Normalized_H3K4me3_ChIP_Malaria_TRIM.xlsx

data_processing:
Reads from NGS results were mapped to hg38 human reference genome using bowite2. Duplicated fragments were excluded from further analyses steps.
Utilizing MACS2 software ChIP peaks were called on remaining reads with the pvalue of 1e-8.
Called peaks across all samples were merged and reads aligning within merged peaks from each sample were counted using peakstats.
Quantified ChIP-seq data were normalized using DESeq2. Peaks with more than 1.5 fold change and padj < 0.05 between at least two of time points were identified as significant differential peaks.
For the intersection analysis of ChIP and RNA-seq data, H3K4me3 peaks near the promoter regions of differentially expressed gene were extracted.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx, Raw or Normalized Peak Count Table of H3K4me3 ChIP from All Samples

extract_protocol:
Positively selected CD14+ monocytes were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells per ml. Fixed cell preparations were sonicated for 7 cycles (30 sec on, 30 sec off) using a Diagenode Bioruptor Pico sonicator. Around 1 million cells were mixed with dilution buffer, protease inhibitor cocktail (Roche) and 1mg of H3K4me3 antibody (Diagenode) and incubated overnight at 4C with rotation. Pre-washed protein A/G magnetic beads mixture, diluted in 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and incubated for 60 min at 4C. Beads were washed with 400µl wash buffer for 5 min at 4C (with rotation). Five rounds of washes were done. After washing, chromatin was eluted using elution buffer. Eluted chromatin mixed with 8 µl 5M NaCl, 3µl proteinase K, and samples were incubated for 4 hours at 65C with rotation. De-crosslinked samples were purified using Qiaquick MinElute PCR purification Kit (Qiagen) and eluted in 20 µl EB. Purified immunoprecipitated chromatin was used for library preparation.
Illumina libraries for next generation sequencing was done using the Kapa Hyper Prep Kit (Roche), according to the manufacturer’s protocol. Briefly, for end repair and A-tailing double stranded DNA, was incubated with end repair and A-tailing buffer and enzyme for 30 min at 20C and then for 30 min at 65C. Subsequently, adapters were ligated using DNA ligase, and Illumina NextFlex adapters, specific for each sample, for 15 min at 20C. Post-ligation cleanup was performed using Agencourt AMPure XP reagent and adapter-ligated samples were eluted in 20 ml elution buffer. Libraries were amplified by mixing 2x KAPA HiFi Hotstart ReadyMix and 10x Illumina library amplification primer mix and using PCR for 10 cycles. Amplified PCR products were purified using the QIAquick MinElute PCR purification kit (Qiagen). Utilizing E-gel, 300bp fragments selected from each sample. Correct size selection was approved by BioAnalyzer analysis. Sequencing experiments were performed in Illumina NextSeq 500 machine.

tag: antibody


title: Tr1_Irf1_KO2

description: bulk RNA-seq

value: Irf1 KO


title: Tr1_Irf1_KO3

description: bulk RNA-seq


title: Tr1_Irf4_Ctrl1

description: bulk RNA-seq


title: Donor3_Day36_h3k4me3_chip


title: Tr1_Irf1_KO1

description: bulk RNA-seq


title: Donor2_Day36_h3k4me3_chip


title: rsfG mutant - sample1

city: Porto

first: Marta

middle: V.

last: Mendes

address: Rua Alfredo Allen, 208

country: Portugal

institute: i3S - Instituto de Investigação e Inovação em Saúde

data_processing:
Trimming_The analysis of the generated sequence raw data was carried out using CLC Genomics Workbench 12.0.3 (Qiagen). Bioinformatic analysis started with trimming of raw sequences to generate high quality data. For each original read, the regions of the sequence to be removed were determined independently for each type of trimming operation based on the following parameters: a) Ambiguous limit – 2 nucleotides; b) Quality limit – 0.01 (error probability); c) Minimum number of nucleotides in reads – 15 nucleotides; d) Discard short reads.
Mapping_The high-quality sequencing reads were mapped against the S. tsukubaensis reference genome using length and similarity fractions of 0.8.
Gene expression_The result of mapping served to determine the gene expression levels based on the TPM (Trancripts per Million), which is a variation of the RPKM method. RPKM is defined as the Reads per Kilobase of exon model per Million mapped reads. In other words, and in this case, it is given by dividing the total number of reads from a particular gene by the number of total mapped reads of the transcriptome (in Millions), times the length (kb) of that gene (Mortazavi et al., 2008, Nat. Methods).
Genome_build: NZ_AJSZ00000000.1
Supplementary_files_format_and_content: Tab-delimited excel file includes annotated transcripts, transcript length, total transcript reads and associated TPM and RPKM values for each sample.

organism: Streptomyces tsukubensis NRRL18488

source_name: Liquid culture-grown bacteria

growth_protocol: S. tsukubaensis grown for 72h in liquid MGm-2.5 medium

extract_protocol:
Total RNA was isolated using the RNeasy® Mini kit (Quiagen) as in Beites et al. (2011) .
TruSeq Stranded Total RNA with Ribozero Library Preparation Kit was used for the construction of sequencing cDNA libraries. The generated DNA fragments were sequenced in the Illumina Novaseq 4000 platform, using 150bp paired-end sequencing reads.

tag: developmental stage

value: exponential phase

value: rsfG mutant


title: sigG1 mutant - sample2

value: sigG1 mutant


title: Tr1_Hif1a_Ctrl2

description: bulk RNA-seq

value: Hif1a f/f


title: sigG1 mutant - sample1


title: Tr1_Hif1a_Ctrl1

description: bulk RNA-seq


title: rsfG mutant - sample2


title: Tr1_Hif1a_KO2

description: bulk RNA-seq

value: CD4 Cre(+/-); Hif1a f/f


title: Wild type - sample2

value: Wild type


title: Tr1_Hif1a_KO1

description: bulk RNA-seq


title: Wild type - sample1


title: Donor1_Day36_h3k4me3_chip


title: Donor2_Day9_h3k4me3_chip

description:
H3K4me3 Histone ChIP-Seq of Monocytes from volunteer isolated by CD14 positive selection on day 9 after controlled plasmodium infection (During inflammatory state)
Raw_Peaks_H3K4me3_ChIP_Malaria_TRIM.xlsx
Normalized_H3K4me3_ChIP_Malaria_TRIM.xlsx


title: Donor3_Day9_h3k4me3_chip


title: Donor4_Day9_h3k4me3_chip


title: Tr1_Fosl2_Ctrl2

description: bulk RNA-seq

value: Fosl2 f/f


title: Donor1_Day9_h3k4me3_chip


title: A549 cells, Module 3 Time End Untreated replicate 3

city: Cambridge

first: Zi Peng

last: Fan

address: 88 Sidney Street

institute: Agios Pharmaceuticals

data_processing:
The constant fixed sequence immediately before and after the 20-nucleotide CRISPR sgRNA sequence was first removed before read mapping using AWK command in Unix.
To determine the read count value for each sgRNA, the trimmed reads were mapped to a custom sgRNA reference library using Bowtie2 (version 2.1.0) with option -L 20 -N 0 -k 1. These criteria retained only the perfectly matched reads for downstream analysis.
The raw read count from each of three separate Cellecta Human Genome-Wide CRISPR modules was used to calculate gene level statistics using Mageck (version 0.5.4) and DrugZ (version 1.1.0.2) with default options.
Genome_build: Cellecta CRISPR Human Genome Knockout Library, Modules 1, 2, & 3, Catalog #: KOHGW-M123-P
Supplementary_files_format_and_content: Tab-delimited text files include the read count of each sgRNA construct values for each sample.

growth_protocol: A549 cells were cultured in vendor-recommended media. Additional uridine was provided in the medium at a concentration of 5 µM.

extract_protocol:
Genomic DNA was extracted using phenol:chloroform followed by ethanol precipitation.
sgRNAs were amplified by PCR using primers specific for the regions of the plasmid flanking the sgRNA (FwdU6-1: 5’-CAAGGCTGTTAGAGAGATAATTGG-3’ R2: 5’-CGACAACAACGCAGAAATTTTGAAT-3’). The PCR product was sequenced with 80–100 million single-end 50 base pair reads.
Crispr Knock-out screen

treatment_protocol: A VSV-G pseudotype lentiviral plasmid library containing single guide RNAs (sgRNAs) was generated using the Cellecta Three-Module Human Genome-Wide CRISPR construct library with the pRSG16-U6-sg-HTS6C-UbiC-TagRFP-2A-Puro plasmid. A lentiviral plasmid encoding stable Cas9 from Cellecta (pR-CMV-Cas9-2A-Blast) was introduced into A549 cells. The sgRNA library was introduced into the Cas9-expressing cells at a multiplicity of infection of 0.3 and selected under antibiotics for 48 hours. A sample of cells was collected and then 1 µM AG-636 or 0.05% DMSO was added. Cell culture medium was changed every 2 days until the cells completed 12 doublings.

tag: cell line

tag: crispr ko library

value: Module 3

tag: treatment

value: vehicle control


title: Tr1_Fosl2_Ctrl1

description: bulk RNA-seq


title: Donor4_Day0_h3k4me3_chip

description:
H3K4me3 Histone ChIP-Seq of Monocytes from healthy volunteer isolated by CD14 positive selection on day 0 (Before start of the controlled plasmodium infection)
Raw_Peaks_H3K4me3_ChIP_Malaria_TRIM.xlsx
Normalized_H3K4me3_ChIP_Malaria_TRIM.xlsx

value: Monocyte


title: IL27-72 [HT_MG-430A]

type: RNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. GenePattern ExpressionFileCreator v. 12

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Naïve CD4 T cells were polarized to Tr1 cells with anti-CD3 (1ug/ml) and anti-CD8 (1ug/ml) stimulation in the presence of IL-27 (25ng/ml)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: timepoint


title: A549 cells, Module 3 Time End Untreated replicate 2


title: Tr1_Fosl2_KO2

description: bulk RNA-seq

value: CD4 Cre(+/-); Fosl2 f/f


title: ctrl-72d [HT_MG-430A]


title: A549 cells, Module 3 Time End Untreated replicate 1


title: ctrl-60 [HT_MG-430A]


title: IL27-72d [HT_MG-430A]


title: IL27-54 [HT_MG-430A]


title: ctrl-48 [HT_MG-430A]


title: ctrl-54d [HT_MG-430A]


title: Donor3_Day0_h3k4me3_chip


title: IL27-36 [HT_MG-430A]


title: ctrl-42 [HT_MG-430A]


title: Tr1_Fosl2_KO1

description: bulk RNA-seq


title: IL27-54d [HT_MG-430A]


title: ctrl-36 [HT_MG-430A]


title: A549 cells, Module 3 Time End Treated replicate 3


title: IL27-42d [HT_MG-430A]


title: IL27-48 [HT_MG-430A]


title: Donor2_Day0_h3k4me3_chip


title: ctrl-72 [HT_MG-430A]


title: ctrl-54 [HT_MG-430A]


title: IL27-42 [HT_MG-430A]


title: ctrl-42d [HT_MG-430A]


title: IL27-30 [HT_MG-430A]


title: ctrl-30d [HT_MG-430A]


title: A549 cells, Module 3 Time End Treated replicate 2


title: Tr1_Ets1_Ctrl2

description: bulk RNA-seq


title: Tr1_Ets1_Ctrl1

description: bulk RNA-seq


title: Donor1_Day0_h3k4me3_chip


title: IL27-30d [HT_MG-430A]


title: Tr1_Ets1_KO2

description: bulk RNA-seq

value: Ets1 KO


title: Tr1_Ets1_KO1

description: bulk RNA-seq


title: A549 cells, Module 3 Time 0 replicate 2


title: A549 cells, Module 2 Time End  Untreated replicate 3

value: Module 2


title: A549 cells, Module 3 Time 0 replicate 3


title: Tr1_Cebpb_Ctrl1

description: bulk RNA-seq

value: Cebpb f/f


title: A549 cells, Module 2 Time End  Untreated replicate 2


title: sg-ftsH r3

city: Muenster

first: Anne-Sophie

last: Stolle

address: Von-Esmarch-Str. 56

institute: Institut für Infektiologie

description: ftsH r3

data_processing:
Sequncing of the Illumina cDNA libraries was performed by Biopolymers facility at Harvard Medical School. RNA-sequencing was performed on NextSeq Mid Output by 100 bp single end high-throughput sequencing.
The raw reads in FastQ format were aligned to P. aeruginosa PAO1 genome (RefSeq accession number NC_002516) using the bowtie2 algorithm on Geneious 10.0 (http://www.geneious.com).
Differential expression analysis was performed on Geneious using Deseq2
Genome_build: NC_002516
Supplementary_files_format_and_content: RPKM and TPM values of each sample
Supplementary_files_format_and_content: differential expression analysis compared to sg-CTRL

organism: Pseudomonas aeruginosa

source_name: total cell lysate

growth_protocol: over night cultures were grown in LB + 5 ug/ml irgasan & 30 ug/ml gentamycin at 37°C shaking, cultures were backdiluted to fresh LB + antibiotics and 0.2% arabinose to an OD of 0.05 and cultured for 3h. 2 ml of culture were harvested.

extract_protocol:
bacterial pellets were resuspended in 1ml Tri Reagent (Sigma Aldrich T9424) and incubated for 5 min. 200 ul Chloroform were added, vortexed and incubated for 5 min. Samples were centrifuged for 10 min at 4°C and the aqueous phase was mixed with 200 ul 100% EtOH and transferred to PureLink RNAMini Columns (Invitrogen). Subsequent washing and elution was performed following manufactorer's instructions. Contaminating DNA was removed using DNA-free kit (Apllied Bioystems). RNA was stored at -80 °C.
Libraries were constructed using NuGEN Ovation Complete Prokaryotic RNA-Seq DR Multiplex Systems kit. Preparation was performed following manufactorer's instructions

tag: growth phase

value: exponential

tag: guide rna target

value: ftsH


title: sg-CTRL r3

description: CTRL r3

value: CTRL


title: sg-lptD r3

description: lptd r3

value: lptD


title: A549 cells, Module 2 Time End  Untreated replicate 1


title: Tr1_Cebpb_KO2

description: bulk RNA-seq

value: Lck Cre(+/-); Cebpb f/f


title: sg-lptD r2

description: lptd r2


title: sg-bamA r3

description: bamA r3

value: bamA


title: A549 cells, Module 3 Time End Treated replicate 1


title: Tr1_Cebpb_KO1

description: bulk RNA-seq


title: A549 cells, Module 2 Time End  Treated replicate 3


title: Brain endothelial cell 7

description: Brain endothelial cell 7

source_name: Brain

extract_protocol:
Pdgfb ret mice were crossed with Cldn5-GFP; Cspg4-DsRed mice for endothelial cell (positive for GFP, negative for dsRed) isolation based on fluorescence-activated cell sorting (FACS),  followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: brain

value: adult mice

value: Pdgfb ret/+

value: endothelial cell


title: A549 cells, Module 2 Time End  Treated replicate 2


title: sg-bamA r2

description: bamA r2


title: ctrl-30 [HT_MG-430A]


title: sg-ftsH r2

description: ftsH r2


title: Tr1_Cebpb_Ctrl2

description: bulk RNA-seq


title: sg-CTRL r1

description: CTRL r1


title: A549 cells, Module 2 Time End  Treated replicate 1


title: Tr1_Ctrl1_for_Batf_KO2_Irf8_KO2_Stat3_KO1

description: bulk RNA-seq

value: WT


title: Tr1_Ctrl_for_Batf_KO1_Irf1_KO1_Tr1_Irf8_KO1

description: bulk RNA-seq


title: Tr1_Batf_KO2

description: bulk RNA-seq

value: Batf KO


title: sg-lptD r1

description: lptd r1


title: sg-bamA r1

description: bamA r1


title: ctrl-20d [HT_MG-430A]


title: ctrl-20 [HT_MG-430A]


title: IL27-20d [HT_MG-430A]


title: IL27-25 [HT_MG-430A]


title: A549 cells, Module 2 Time 0 replicate 3


title: A549 cells, Module 2 Time 0 replicate 2


title: Tr1_Ctrl2_for_Batf_KO2_Irf8_KO2_Stat3_KO1

description: bulk RNA-seq


title: Tr1_Batf_KO1

description: bulk RNA-seq


title: sg-ftsH r1

description: ftsH r1


title: Tr1_Atf3_Ctrl2

description: bulk RNA-seq

value: Atf3 f/f


title: IL27-20 [HT_MG-430A]


title: ctrl-25 [HT_MG-430A]


title: A549 cells, Module 1 Time End Untreated replicate 2

value: Module 1

value: vehicle control


title: A549 cells, Module 1 Time End Untreated replicate 3


title: A549 cells, Module 1 Time End Untreated replicate 1


title: IL27-16 [HT_MG-430A]


title: Tr1_Atf3_KO2

description: bulk RNA-seq

value: Actin Cre(+/-); Atf3 f/f


title: A549 cells, Module 1 Time End Treated replicate 3


title: Tr1_Atf3_KO1

description: bulk RNA-seq


title: IL27-18 [HT_MG-430A]


title: ctrl-18 [HT_MG-430A]


title: Tr1_Ahr_Ctrl2

description: bulk RNA-seq


title: ctrl-16d [HT_MG-430A]


title: A549 cells, Module 1 Time End Treated replicate 1


title: SAMPLE 8: db kidney total 4

city: Saitama

first: Hiroki

last: Ishii

address: 1-847 Amanuma-cho, Omiya-ku

department: First Department of Integrated Medicine

country: Japan

institute: Jichi Medical University Saitama Medical Center

hyb_protocol: The hybridization mixture was denatured at 100°C for 5 minutes in a reaction volume of 45 ul containing 2x Agilent GE hybridization buffer HI-RPM and 10x Agilent blocking agent following the manufacturers instructions and immediately transferred to ice water bath. Each sample was hybridized to SurePrint G3 Mouse miRNA microarray 8 x 60K Rel.21.0 (Agilent, G4859C) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using miRNA setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters(protocol miRNA_1200_Jun14 and Grid 070155_D_F_20141006). The 90th percentile shift normalization was performed by the GeneSpring GX software using Agilent.miRNA.70155_v21_0 technology. Data were baseline shifted to the median of all samples.

source_name: db/db mice

label_protocol: RNA labeling was performed using miRNA Complete Labeling Reagent & Hybridization Kit (Agilent, 5190-0456) following the Agilent protocols v.2.3. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. After adding DMSO, the reaction mixture was incubated at 100°C for 7 minutes and immediately transferred to ice water bath.Ligation was performed with pCp-Cy3 at 16 °C for 2 hours.The labeled RNA were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: To measure miRNA expression, kidney samples were homogenized using a glass homogenizer and a filter column shredder (Qiagen), then RNA was extracted using an miRNeasy Mini Kit (Qiagen).

value: kidney

tag: gender

value: male

value: C57BLKS/J Iar -+Leprdb/+Leprdb


title: sg-CTRL r2

description: CTRL r2

value: exponential

value: CTRL


title: SAMPLE 7: db kidney total 3


title: IL27-16d [HT_MG-430A]


title: SAMPLE 6: db kidney total 2


title: ctrl-16 [HT_MG-430A]


title: Tr1_Ahr_Ctrl1

description: bulk RNA-seq


title: Tr1_Atf3_Ctrl1

description: bulk RNA-seq


title: IL27-12 [HT_MG-430A]


title: ctrl-12 [HT_MG-430A]


title: ctrl-14 [HT_MG-430A]


title: IL27-14 [HT_MG-430A]


title: Tr1_Ahr_KO2

description: bulk RNA-seq


title: SAMPLE 4: dbm kidney total 4

source_name: control mice(m/m mice)

value: C57BLKS/J Iar -m+/m+


title: A549 cells, Module 1 Time End Treated replicate 2


title: A549 cells, Module 1 Time 0 replicate 2


title: SAMPLE 3: dbm kidney total 3


title: SAMPLE 5: db kidney total 1


title: IL27-60 [HT_MG-430A]


title: PBS_24

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

country: China

institute: sysu

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: C57BL/6J mice implanted subcutaneously in the right flank with B16F10 cells

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6J mice were implanted subcutaneously in the right flank with B16F10 cells at day 0 and treated intravenously with PBS(n=4) or M1 (n=4) (1x107 pfu) daily on day 6-10. Tumors were harvested on day 12, total RNA was extracted and then performed RNA-sequencing.

value: tumors

value: PBS


title: A549 cells, Module 1 Time 0 replicate 3


title: PBS_23


title: SAMPLE 2: dbm kidney total 2


title: Tr1_Ahr_KO1

description: bulk RNA-seq


title: Tr1_Prdm1/Maf_DKO1

description: bulk RNA-seq

value: CD4 Cre(+/-); Prdm1 f/f; Maf f/f


title: SAMPLE 1: dbm kidney total 1


title: PBS_21


title: SAMPLE 8: Akita4

source_name: Akita

value: C57BL/6-Ins2Akita/J mice


title: IL27-8 [HT_MG-430A]


title: SAMPLE 7: Akita3


title: ctrl-8d [HT_MG-430A]


title: Tr1_Maf_KO3

description: bulk RNA-seq

value: CD4 Cre(+/-); Maf f/f


title: C6V1_72


title: Tr1_Maf_KO2

description: bulk RNA-seq


title: ctrl-8 [HT_MG-430A]


title: IL27-4 [HT_MG-430A]


title: C6V1_88


title: IL27-8d [HT_MG-430A]


title: PBS_95


title: SAMPLE 5: Akita1


title: Tr1_Prdm1/Maf_DKO3

description: bulk RNA-seq


title: ctrl-4 [HT_MG-430A]


title: IL27-2d [HT_MG-430A]


title: SAMPLE 4: Mock4

source_name: control mice(C57BL/6J)


title: Tr1_Prdm1/Maf_DKO2

description: bulk RNA-seq


title: C6V1_26


title: C6V1_63


title: Tr1_Prdm1_KO3

description: bulk RNA-seq

value: CD4 Cre(+/-); Prdm1 f/f


title: ctrl-2d [HT_MG-430A]


title: SAMPLE 3: Mock3


title: Tr1_Maf_KO1

description: bulk RNA-seq


title: ctrl-2 [HT_MG-430A]


title: Tr1_Prdm1_KO2

description: bulk RNA-seq


title: Tr1_Prdm1_KO1

description: bulk RNA-seq


title: SAMPLE 6: Akita2


title: Hy_Jejunum_2

city: Qingdao

first: Shichao

last: Xing

address: No.167, Wutai Mountain Road,

institute: Affiliated Hospital of Qingdao University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: small intestine

extract_protocol:
Intestine were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jejunum

value: 15 weeks

value: UOX-/-


title: Hy_Jejunum_1


title: Tr1_Prdm1/Maf_Ctrl3

description: bulk RNA-seq

value: Prdm1/Maf control (Cre-)


title: Tr1_Prdm1/Maf_Ctrl2

description: bulk RNA-seq


title: WT_Jejunum_3

value: wild type


title: Hy_Jejunum_3


title: Tr1_Prdm1/Maf_Ctrl1

description: bulk RNA-seq


title: IL27-2 [HT_MG-430A]


title: SAMPLE 2: Mock2

value: kidney


title: WT_Jejunum_2


title: Tr1_18pos

description: bulk RNA-seq

data_processing:
RSEM RNA Quantification
Genome_build: mm10
Supplementary_files_format_and_content: TSV Gene Expression Matrix

source_name: IL-10 positive compartment of Tr1 cells derived in vitro

growth_protocol: naïve CD4+CD44-CD62L+GFP- cells were sorted from Foxp3-GFP; IL-10 -Thy1.1 double reporter mice using BD FACSAria sorter and were activated with irradiated splenocytes depleted of CD4 T cells (at the T: APC ratio of 1:6) and 2.5ug/ml soluble anti-CD3 in the presence of polarizing cytokines. Concentration of cytokines are as follows: 20ng/ml rmIL-12 (R & D systems) for Th1; 20ng/ml rmIL-4 (Miltenyi Biotec) for Th2; 2ng/ml of rhTGFb1 and 25ng/ml rmIL-6(both from Miltenyi Biotec) for non-pathogenic Th17; 20ng/ml rmIL-1β(Miltenyi Biotec), 25ng/ml rmIL-6 (Miltenyi Biotec), and 20ng/ml rmIL-23 (R & D systems) for pathogenic Th17; 25ng/ml of rmIL-27 (R & D systems) for Tr1. IL-10 positive (Thy1.1+) and negative (Thy1.1+) 7-AAD-TCRβ+CD4+GFP- cells were resorted at 72 hours.

value: Foxp3-GFP; IL-10 Thy1.1 double reporter


title: WT_Jejunum_1


title: IL27-1 [HT_MG-430A]


title: SAMPLE 1: Mock1

value: male


title: Hy_Ileum_4

value: Ileum


title: Tr1_17pos

description: bulk RNA-seq


title: ctrl-1 [HT_MG-430A]


title: SAMPLE 5: PEI-C1

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Ver.2.0 Microarray (Agilent, G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 074809_D_F_20171030). The 75th percentile shift normalization was performed by the GeneSpring GX software using Agilent.SingleColor.74809 technology. Data were baseline shifted to the median of all samples.

source_name: db/db mice administered control-miRNA-PEI-NPs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Kidney samples were homogenized using a glass homogenizer and a filter column shredder (Qiagen). RNA was isolated using an RNeasy Total RNA Isolation kit (Qiagen).

value: C57BLKS/J Iar -+Leprdb/+Leprdb


title: IL27-0.5 [HT_MG-430A]


title: SAMPLE 7: PEI-M1

source_name: db/db mice administered miRNA-181b-5p-mimic-PEI-NPs


title: Tr1_17neg

description: bulk RNA-seq

source_name: IL-10 negative compartment of Tr1 cells derived in vitro


title: Tr1_16pos

description: bulk RNA-seq


title: Hy_Ileum_1


title: SAMPLE 8: PEI-M2


title: Hy_Ileum_2


title: hESC_D6_10x

city: TianJin

first: Changlu

last: Xu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
10X Genomics CellRanger version 3.0.2 were used to the basecalling.
Cell Ranger (version 3.0.2) software from 10X Genomics (http://www.10xgenomics.com) was used to aligned and quantified sequencing raw data with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-Separated Values files include UMI for each cell

source_name: human embryonic stem cells

extract_protocol: The libraries were constructed and  sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner (sequenced by Novogene).

tag: tissue/cell type

value: hESC

tag: development stage


title: ctrl-0.5 [HT_MG-430A]

source_name: Tr1 cells derived in vitro with IL-27

tag: strain


title: Hy_Ileum_5

tag: tissue

tag: age


title: SAMPLE 6: PEI-C2


title: SAMPLE 4: dbdb2

source_name: untreated db/db mice


title: Tr1_16neg

description: bulk RNA-seq

tag: genotype


title: WT_Ileum_5


title: SAMPLE 3: dbdb1


title: pTh17_15pos

description: bulk RNA-seq

source_name: IL-10 positive compartment of pathogenic Th17 (IL-1b + IL-6 + IL-23) cells derived in vitro


title: MA2 cells transfected with negative control, 48h post-transfection, biological replicate 2 (CTR-48h-2)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

institute: University of Padova

description: Gene expression profiling of control cells 48h post-transfection (CTR-48h-2)

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed with Agilent Gene Expression wash buffers and Stabilization and Drying Solution as suggest by the supplier

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings. Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with quantile method (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) to correct for possible experimental distortions. A normalization function was applied to the expression data of all the experiments and the values of within-arrays replicate spots were then averaged. Feature Extraction Software, which provided spot quality measures, was used to evaluate the quality and reliability of the hybridization. In particular, the flag glsPosAndSignif (set to 1 if the spot had an intensity value significantly different from the local background and to 0 when otherwise) was used to filter out unreliable probes: the flag equal to 0 was noted as null. Probes with a high proportion of null values were removed from the dataset in order to carry out a more solid, unbiased, statistical analysis. 33%  of null was used as the threshold in the filtering process, and a total of 33,152  human transcripts were obtained.

source_name: MA2 melanoma cells

label_protocol: Eight hundred nanograms of total RNA were labelled with “Agilent One-Color Microarray-Based Gene Expression protocol” (Agilent) according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with RNeasy Mini columns (Qiagen). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurement (NanoDrop Technologies).

growth_protocol: MA-2 cells were provided by R.O. Hynes (Massachusetts Institute of Technology, Cambridge, MA) and maintained in Dulbecco’s Modified Eagle’s Medium containing 10mM Glutamax and 4.5 g/ml glucose (DMEM GlutamaxTM, GIBCO Invitrogen Life Technologies, Carlsbad, CA), supplemented with 10% heat-inactivated FCS (Seromed, GmbH), 1mM sodium pyruvate, 25mM HEPES pH 7.4, 1 MEM vitamin solution, 1X MEM non-essential amino acids and 100 mg/ml gentamicin (all from GIBCO Invitrogen Life Technologies).

extract_protocol: Total RNA was isolated from 106 cells by using Trizol® Reagent (Thermo Fisher) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, were used for microarray analysis.

treatment_protocol: To obtain transient pre-miR expression, cells were plated in 6-well plates at 30–50% confluency and transfected 24 h later using RNAiFect (Qiagen, Stanford, CA) reagent, according to the manufacturer’s instructions, with 75nM pre-miR. For transient cDNA overexpression, cells were plated in 6-well plates at 90% confluency and transfected 24 h later using LipofectamineTM2000 (Invitrogen Life Technologies) reagent, according to the manufacturer’s instruction. Cells were tested for gene expression 48 or 72 h later.

tag: cell type

value: MA2 melanoma cells

tag: transfection

value: negative control

value: 48h post-transfection

tag: biological replicate


title: MA2 cells transfected with negative control, 72h post-transfection, biological replicate 3 (CTR-72h-3)

description: Gene expression profiling of control cells 72h post-transfection (CTR-72h-3)

tag: time point

value: 72h post-transfection


title: MA2 cells transfected with negative control, 72h post-transfection, biological replicate 1 (CTR-72h-1)

description: Gene expression profiling of control cells 72h post-transfection (CTR-72h-1)


title: hFetal_CS23_FL_10x

source_name: human embryonic cells

value: Fetal liver

value: CS 23


title: MA2 cells transfected with negative control, 72h post-transfection, biological replicate 2 (CTR-72h-2)

description: Gene expression profiling of control cells 72h post-transfection (CTR-72h-2)


title: WT_Ileum_1


title: WT_Ileum_4


title: SAMPLE 2: mm2

source_name: normal mice (m/m mice)

value: C57BLKS/J Iar -m+/m+


title: MA2 cells transfected with negative control, 48h post-transfection, biological replicate 1 (CTR-48h-1)

description: Gene expression profiling of control cells 48h post-transfection (CTR-48h-1)


title: MA2 cells transfected with negative control, 48h post-transfection, biological replicate 3 (CTR-48h-3)

description: Gene expression profiling of control cells 48h post-transfection (CTR-48h-3)


title: hEmbryo_CS11_YS_10x

value: Yolk sac

value: CS 11


title: pTh17_14neg

description: bulk RNA-seq

source_name: IL-10 negative compartment of pathogenic Th17 (IL-1b + IL-6 + IL-23) cells derived in vitro


title: pTh17_15neg

description: bulk RNA-seq


title: hEmbryo_CS10_YS_10x

value: CS 10


title: SAMPLE 1: mm1


title: MA2 cells transfected with precursor of miR-214, 48h post-transfection, biological replicate 3 (miR214-48h-3)

description: Gene expression profiling of miR-214 over-expressing cells 48h post-transfection (miR214-48h-3)

value: precursor of miR-214


title: Hy_Colon_5

value: Colon

value: 15 weeks

value: UOX-/-


title: pTh17_13pos

description: bulk RNA-seq

value: Foxp3-GFP; IL-10 Thy1.1 double reporter


title: MA2 cells transfected with precursor of miR-214, 72h post-transfection, biological replicate 3 (miR214-72h-3)

description: Gene expression profiling of miR-214 over-expressing cells 72h post-transfection (miR214-72h-3)


title: MA2 cells transfected with precursor of miR-214, 72h post-transfection, biological replicate 1 (miR214-72h-1)

description: Gene expression profiling of miR-214 over-expressing cells 72h post-transfection (miR214-72h-1)


title: Hy_Colon_3


title: hFetal_CS20_FL_10x

value: CS 20


title: pTh17_13neg

description: bulk RNA-seq


title: pTh17_14pos

description: bulk RNA-seq


title: Hy_Colon_1


title: MA2 cells transfected with precursor of miR-214, 48h post-transfection, biological replicate 2 (miR214-48h-2)

description: Gene expression profiling of miR-214 over-expressing cells 48h post-transfection (miR214-48h-2)


title: pre_trans_WT2_S2_R1_001.fastq.gz

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
Quantitation of transcripts against the mm9 reference genome was performed in Partek Flow (Partek Inc.) using the STAR aligner.
Differential expression analysis was performed in Partek Flow (Partek Inc.) using Partek GSA algorithm
Genome_build: mm9
Supplementary_files_format_and_content: Processed data contains normizied gene expression data in a .txt file format

source_name: Sorted T cells

growth_protocol: Sorted from fresh spleen

extract_protocol:
RNeasy Mini (Qiagen)
Illumina TruSeq

value: Sorted T cells

value: Pre transfer

value: WT

value: BALB/c


title: pre_trans_WT3_S3_R1_001.fastq.gz


title: pre_trans_WT1_S1_R1_001.fastq.gz


title: Th17_12pos

description: bulk RNA-seq

source_name: IL-10 positive compartment of non-pathogenic Th17 (TGFb + IL-6) cells derived in vitro


title: WT_Colon_5

value: wild type


title: Th17_12neg

description: bulk RNA-seq

source_name: IL-10 negative compartment of non-pathogenic Th17 (TGFb + IL-6) cells derived in vitro


title: WT_Colon_3


title: WT_G9_post_S5_R1_001.fastq.gz

value: Post transfer


title: Th17_11pos

description: bulk RNA-seq


title: WT_Colon_1


title: Th17_11neg

description: bulk RNA-seq


title: WT_G10_post_S6_R1_001.fastq.gz


title: WT_G8_post_S4_R1_001.fastq.gz


title: WT_Ileum_2

value: Ileum


title: Th17_10pos

description: bulk RNA-seq


title: WT_3_post_S8_R1_001.fastq.gz


title: WT_5_post_S9_R1_001.fastq.gz


title: MA2 cells transfected with precursor of miR-214, 72h post-transfection, biological replicate 2 (miR214-72h-2)

description: Gene expression profiling of miR-214 over-expressing cells 72h post-transfection (miR214-72h-2)

value: MA2 melanoma cells

value: 72h post-transfection


title: Th2_9pos

description: bulk RNA-seq

source_name: IL-10 positive compartment of Th2 cells derived in vitro


title: WT_2_post_S7_R1_001.fastq.gz


title: Th2_9neg

description: bulk RNA-seq

source_name: IL-10 negative compartment of Th2 cells derived in vitro


title: ITK_pre_6_S12_R1_001.fastq.gz

value: ITK KO


title: MA2 cells transfected with precursor of miR-214, 48h post-transfection, biological replicate 1 (miR214-48h-1)

description: Gene expression profiling of miR-214 over-expressing cells 48h post-transfection (miR214-48h-1)

value: 48h post-transfection


title: GFPN-48 [Mouse430A_2]


title: IL27-48 [Mouse430A_2]


title: GFPP-48 [Mouse430A_2]


title: ITK_pre_5_S11_R1_001.fastq.gz


title: IL27-16 [Mouse430A_2]


title: Th2_8pos

description: bulk RNA-seq


title: ctrl-48 [Mouse430A_2]


title: Th17_10neg

description: bulk RNA-seq


title: ctrl-16 [Mouse430A_2]


title: Th2_8neg

description: bulk RNA-seq


title: ITK_3_post_S15_R1_001.fastq.gz


title: Th2_7neg

description: bulk RNA-seq


title: ITK_pre_4_S10_R1_001.fastq.gz


title: Th1_6pos

description: bulk RNA-seq

source_name: IL-10 positive compartment of Th1 cells derived in vitro


title: ITK_2_post_S14_R1_001.fastq.gz


title: Th2_7pos

description: bulk RNA-seq


title: ITK_1_post_S13_R1_001.fastq.gz


title: ctrl-4 [Mouse430A_2]


title: IL27-4 [Mouse430A_2]


title: Th1_6neg

description: bulk RNA-seq

source_name: IL-10 negative compartment of Th1 cells derived in vitro


title: cLP_CD4_Prdm1/Maf DKO_2

description: single cell RNA-seq

data_processing:
10X Cellranger Count
Genome_build: mm10
Supplementary_files_format_and_content: H5

source_name: CD4 T cells from colonic lamina propria

extract_protocol:
Colons were first washed for 20min in RPMI medium (GIBCO) with 3% FBS (Sigma-Aldrich), 5mM EDTA (Invitrogen) and 1mM DTT (Sigma) in a shaking incubator at 400rpm at 37℃, followed by three other washes each for 30 seconds by vibrant vortexing in RPMI with 2mM EDTA. The tissue was then cut into little pieces and digested for 30min in RPMI with 100ug/mL Liberase TL (Sigma) and 500ug/mL DNase I (Sigma) Digestion in a shaking incubator at 400rpm at 37℃. Digestion was terminated by addition of ice-cold RPMI with 3% FCS. Cells were washed twice in RPMI with 3% FCS, passed through a 40µm cell strainer and resuspended in ice-cold RPMI with 3% FCS and 1mM EDTA. Live (7-AAD-) TCRβ+CD4+ cells were then sorted by FACS.
Cells were processed using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics). For each biological replicate, an input of 7,000 single cells was added to an individual channel with a recovery rate of approximately 1,300~2100 cells. The generated scRNA-seq libraries were sequenced using a 75 cycle Nextseq 500 high output V2 kit.

value: CD4 Cre(+/-); Prdm1 f/f; Maf f/f


title: cLP_CD4_Prdm1/Maf DKO_1

description: single cell RNA-seq


title: PANC-1_anlotinib_48h_rep3

city: Changsha

first: Zewen

last: Song

state: Hunan

address: 138 Tongzipo Road, Yuelu District

department: Oncology

institute: The Third Xiangya Hospital of Central South University

description: Gene expression data from PANC-1 cells treated with anlotinib

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: PANC-1 cells  treated with anlotinib(5.535 uM)

growth_protocol: cell were cultured in RPMI-1640 medium (Invitrogen, USA) supplemented with 10% fetal bovine serum (FBS, ExCell), and were incubated under humidified atmospheric conditions with 5% CO2 at 37℃.

treatment_protocol: PANC-1 cells were treated with anlotinib (5.535 uM) or DSMO as control for 48h and investigated by a microarray profiling

tag: cell line

value: anlotinib(5.535 uM)


title: hESC_D0_10x

source_name: human embryonic stem cells

value: hESC


title: PANC-1_anlotinib_48h_rep2


title: cLP_CD4_Maf cKO_2

description: single cell RNA-seq

value: CD4 Cre(+/-); Maf f/f


title: GR13_V7

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2 used to obtain betas, probe filtering completed, sample outliers removed, dansen normalization performed, ComBat used to remove known batch effects, invariable probes removed, predicted cell type proportional differences regressed out.

label: Cy5 and Cy3

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen DNeasy Kit according to standard instructions

tag: time

value: 14 days post vaccine

value: post-vaccine

tag: Sex

value: F

value: Normal whole blood sample

tag: individual


title: Th1_5neg

description: bulk RNA-seq

extract_protocol:
2000 cells were lysed in 2ul of RLT buffer
library was constructed using an adaptation of the SMART-Seq 2 protocol (Tirosh et al., 2016)

value: Foxp3-GFP; IL-10 Thy1.1 double reporter


title: PANC-1_anlotinib_48h_rep1

tag: treatment


title: GR10_V4

value: 1 days post vaccine


title: Th1_4pos

description: bulk RNA-seq


title: PANC-1_DSMO_48h_rep3

description: Gene expression data from PANC-1 cells treated with DSMO as control

source_name: PANC-1 cells  treated with DSMO

value: DMSO


title: cLP_CD4_Maf cKO_1

description: single cell RNA-seq


title: GR17_V6

value: 7 days post vaccine


title: Tr1_18neg

description: bulk RNA-seq

source_name: IL-10 negative compartment of Tr1 cells derived in vitro


title: Th1_4neg

description: bulk RNA-seq


title: PANC-1_DSMO_48h_rep2


title: cLP_CD4_Prdm1 cKO_2

description: single cell RNA-seq

value: CD4 Cre(+/-); Prdm1 f/f


title: Tr1_Prdm1/Maf DKO_3

description:
ATAC-seq
Tr1_70hr_20_22.R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig

data_processing:
ATAC-seq data were processed using a public pipeline  (Lee et al., 2016). Briefly, reads were aligned to the mm10 genome using Bowtie2 and filtered to remove duplicates and mitochondrial reads. Biological replicate for each group were merged peaking-calling using MACS2 (Zhang et al., 2008)
Genome_build: mm10
Supplementary_files_format_and_content: Format: bigwig, Content: signal track for fold change generated by Macs2

source_name: Tr1 cells derived in vitro with IL-27

extract_protocol:
6,000 viable Tr1 cells were sorted for each sample and frozen in BambankerTM cell freezing media (LYMPHOTEC Inc.) at -80℃.
For ATAC-seq library preparation, cells were thawed at 37℃, washed once with PBS, and lysed and tagmented in 1X TD Buffer, 0.2ml TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS in 40ml reaction volume following the protocol described by Corces at al. (Corces et al., 2016). The DNA was purified immediately with the MinElute PCR purification kit (QIAGEN),  and then PCR amplified and quantified as we previously described (Wallrapp et al., 2019). The library was sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.


title: GR19_V4

value: M


title: Th1_5pos

description: bulk RNA-seq


title: PANC-1_DSMO_48h_rep1


title: cLP_CD4_Prdm1 cKO_1

description: single cell RNA-seq


title: GR17_V4


title: Tr1_Prdm1/Maf DKO_2


title: GR19_V6


title: cLP_CD4_control_2

description: single cell RNA-seq

value: Prdm1/Maf control (Cre-)


title: ctrl-0 [Mouse430A_2]

tag: timepoint


title: Tr1_Prdm1/Maf DKO_1


title: GR18_V6


title: cLP_CD4_control_1

description: single cell RNA-seq


title: D8_E7386_50_4

city: Tsukuba-shi

first: Kazuhiko

last: Yamada

address: 5-1-3 Tokodai

institute: Eisai Co., Ltd.

data_processing:
Illumina bcl2fastq was used to de-multiplex and convert reads to FASTQ.
Sequencing data were processed by using Trimmomatic (version 0.36) to remove all Illumina adaptor sequences and bases with low quality scores.
Filtered reads were mapped to the mouse genome (Mm10 and Ensembl 84) by using STAR software (version 2.5.0c) .
Gene expression levels, in transcripts per million, were estimated for all samples by using RSEM software (version 1.2.31).
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file including TPM values for each sample

source_name: MMTV-Wnt1 tumor tissue

extract_protocol:
RNA was purified using RNeasy kit (Qiagen) following manufacturer’s instructions. SureSelect Strand Specific RNA Library Prep Kit (Agilent) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MMTV-Wnt1 tumors were collected Day4 and Day 8 after treatment with E7386 at 25, 50 mg/kg.

tag: agent


title: Tr1_Maf_cKO_2

description:
ATAC-seq
Tr1_70hr_96_12k_1b.R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig


title: GR17_V3

value: 0 days post vaccine

value: Baseline


title: D8_E7386_50_3


title: Tr1_Maf_cKO_1


title: GR04_V3


title: G-NEC1Li

city: Tokyo

first: Kohta

last: Toshimitsu

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University

description: Gene expression data of liver-metastatized gastric NEC organoid 1

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Raw expression data were normalized with RMA.

source_name: Liver-metastasized gastric NEC organoid 1

label_protocol: Standard Affymetrix procedures

growth_protocol: Organoids were maintained in a medium containing Wnt-3A, R-spondin, Noggin, A83-01, EGF, IGF-1 and FGF-2.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit according to the manufacturer's instructions.

value: Stomach


title: D8_E7386_50_2


title: G-NEC2

description: Gene expression data of gastric NEC organoid 2

source_name: Gastric NEC organoid 2


title: GR11_V3


title: GR13_V6


title: GR18_V3


title: GR04_V7


title: GR11_V4


title: C-NEC4

description: Gene expression data of colonic NEC organoid 4

source_name: Colonic NEC organoid 4

value: Colon


title: Tr1_Prdm1 cKO_4

description:
ATAC-seq
Tr1_70hr_98_16.R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig


title: D8_E7386_50_1


title: G-NEC1

description: Gene expression data of gastric NEC organoid 1

source_name: Gastric NEC organoid 1


title: Tr1_Prdm1 cKO_3


title: Larynx, LH32

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

data_processing:
Reads were aligned against Oryctolagus_cuniculus.OryCun2.0/ ENSEMBL 95 using STAR v. 2.5.4b with the following flags  --runThreadN 8 --runMode alignReads --outSAMunmapped Within --outSAMattrIHstart 0 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif --twopassMode Basic
Gene expression was quantitated using HTSeq (v 0.7.0) with the following flags for all libraries: -m union -s yes -t gene -i gene_id
Genome_build: Oryctolagus_cuniculus.OryCun2.0/ ENSEMBL 95
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

organism: Oryctolagus cuniculus

source_name: Larynx (vocal folds)

extract_protocol:
Total RNA of vocal folds (low humidity n=6, moderate humidity n=6) was extracted with commercial kit RNeasy Fibrous Tissue Mini Kit (QIAGEN).
Library construction was done using NuGEN's Universal Plus mRNA Kit. Each library was performed with 200 ng of RNA. Unique barcodes were used for each library.

treatment_protocol: Rabbits (n=6) were exposed to a low relative humidity environment for 8 hours. Control rabbits (n=6) were held in a moderate realtive humidity environment.

tag: breed

value: New Zealand White

value: Male

value: 7 months

value: low relative humidity

value: Larynx (vocal folds)


title: Tr1_Maf_cKO_3

city: Boston

value: CD4 Cre(+/-); Maf f/f


title: C-NEC5-N

description: Gene expression data of neuroendocrine carcinoma fractoion of colonic NEC organoid 5

source_name: Neuroendocrine carcinoma fraction of clonic NEC organoid 5


title: GR11_V6

value: post-vaccine

value: F

value: Normal whole blood sample


title: GR17_V5

value: 3 days post vaccine


title: Larynx, LH31


title: D8_E7386_25_3


title: GR15_V7

value: 14 days post vaccine


title: Larynx, LH30


title: D8_E7386_25_4


title: GR09_V7


title: GR15_V4

value: 1 days post vaccine


title: C-NEC5-A

description: Gene expression data of adenocarcinoma fraction of colonic NEC organoid 5

source_name: Adenocarcinoma fraction of clonic NEC organoid 5


title: Tr1_control_5

description:
ATAC-seq
Tr1_70hr_99_19.R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig

value: Prdm1/Maf control (Cre-)


title: D8_E7386_25_2


title: GR19_V7

value: M


title: D8_E7386_25_1


title: Larynx, LH29


title: Tr1_control_4


title: D8_Vehicle_4

value: Vehicle


title: Larynx, LH26


title: Tr1_Prdm1 cKO_1

value: CD4 Cre(+/-); Prdm1 f/f


title: Tr1_control_3


title: D8_Vehicle_3


title: GR09_V4


title: Tr1_control_2


title: D8_Vehicle_2


title: Tr1_control_1


title: Larynx, CH38

value: control


title: D8_Vehicle_1


title: TnSeq_WGS

city: Little Rock

first: Stephanie

middle: D

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

description: We processed data using long_read_TA_counts from bioinformatics pipeline on (github).

data_processing:
Reads were trimmed using fastp v0.19.5
Alignment to reference using bwa v0.7.17-r1188
Filtering for reads at TA sites and counting using bedtools v2.25.0
for ONT samples: Basecalling using Guppy v3.4.5; alignment using minimap2 v2.17-r941
Genome_build: (chromosome: CP055225; cryptic plasmid: CP055226)
Supplementary_files_format_and_content: All processed data files are in the BedGraph format. They detail the location of detected transposon insertions and number of reads mapped to each inserton.

organism: Staphylococcus aureus

source_name: Bacteria

growth_protocol: TnSeq libraries were grown in rich media (Tryptic Soy broth) to either exponential or stationary phase with constant aeration and agitation at 37C

extract_protocol:
Extracted gDNA from the TnSeq library was prepared for Flongle ONT sequencing using the Sequencing Ligation Kit (LSK-109). Here, the transposon insertions were not enriched but we did process the data and enumerate the mapped transposon insertions.
genomic DNA was extracted using the NucleoBond HMW DNA kit
Detailed in 'SAMPLES'

tag: growth phase

value: stationary

tag: number of pcr cycles

tag: sequencing platform

value: Oxford Nanopore Technologies -MinION


title: Larynx, CH37

value: New Zealand White

value: Male

tag: age

value: 7 months

tag: tissue


title: nCATRAs_S3

extract_protocol:
The previously published nCATS protocol was modified in this paper to enrich for the transposon-genomic insertions such that only one end of the region of interest was cleaved as opposed to excision of the region of interest as described in the nCATS protocol (PMID: 32042167). In our modified nCATRAs method, gDNA extracted from the TnSeq library was sheared using Covaris g-tubes to 6,000bps, which resulted in DNA fragments between 6kb to 10kb in size. Two samples each containing 6ug of fragmented gDNA were separately dephosphorylated using Quick CIP (NEB) and incubated at 37°C for 15 mins. Two crRNA probes targeting two sites on the 5’ end of the transposon were used to direct Cas9 to the region. Cas9-cleaved DNA fragments were ligated to the Oxford Nanopore adaptors and the Ligation Sequencing Kit (LSK-109) protocol was followed according to the manufacturer. The two starting samples were pooled in the final elution step prior to loading onto the MinION flow cell. One MinION flow cell was used per pool of two samples.
genomic DNA was extracted using the NucleoBond HMW DNA kit
Detailed in 'SAMPLES'


title: Tr1_Prdm1 cKO_2

first: Vijay

last: Kuchroo

address: 60 Fenwood Road

institute: Brigham & Women's Hospital

tag: strain

tag: genotype


title: Larynx, CH36

value: Larynx (vocal folds)


title: Larynx, LH28

value: low relative humidity


title: D4_E7386_50_3


title: nCATRAs_S2


title: Larynx, CH35


title: D4_E7386_50_2


title: GR15_V5

value: post-vaccine

value: F


title: GR09_V3

value: 0 days post vaccine

value: Baseline

value: Normal whole blood sample


title: nCATRAs_S1


title: D4_E7386_50_1


title: Larynx, CH34