title: bladder cell_Untreated_4 hours_replicate 3

city: Auckland

first: Priscila

middle: Pamela

last: Dauros-Singorenko

state: Auckland

address: 85 Park road, Grafton

country: New Zealand

institute: University of Auckland

description: gene expression data from bladder cells untreated

hyb_protocol: Arrays were hybridized for 16hrs at 45°C, then washed and stained using the fluidics protocol FS450_0007 using the Affymetrix GeneChip Fluidics Station 450

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000.

data_processing: The data was analyzed with Transcriptome Analysis Console (TAC) 4.0, using Affymetrix default analysis settings and Gene Level - SST-RMA as normalization method.

label: biotin

source_name: bladder cells untreated

label_protocol: RNA was  fragmented  and labelled according to Affymetrix protocol for Human Clariom S Array (GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays)

growth_protocol: Bladder cells were seeded at density of 50000 cells/cm in tissue culture treated 24 well plates and incubated at 37ᵒC and 5% CO2.

extract_protocol: After incubation of 4 hours, supernatant was removed and 500 μL of TRIzol was added to adherent cells, resuspended and stored at -80ᵒC for RNA extraction. TRIzol mixture was mixed with 50 ul of miRNA Homogenate Additive (mirVana RNA isolation kit), 100 μL of chloroform and 2 μL of 5 mg/mL glycogen. Samples were vortexed and incubated for 10 minutes in ice to continue with total RNA extraction with mirVana™ miRNA Isolation Kit. RNA yields were determined by Qubit 2.0 fluorometer using Qubit RNA HS assay kit

treatment_protocol: Forty-eight hours later, 2 ng/mL of EV-RNA or 1000 ng/mL of LPS mixed with Lipofectamine were added onto triplicate bladder cell wells along with reduced serum medium Opti-MEM. Control wells contained only media.

value: cultured bladder cells (5637)


title: Riboseq_12hr_Rep1

status: Public on Jul 08 2020

type: SRA

city: Ames

first: Wyatt

middle: Allen

last: Miller

state: IA

address: 2213 Pammel Dr

department: Plant Pathology & Microbiology

country: USA

institute: Iowa State University

description: Ribosome profiling data

library_source: transcriptomic

data_processing:
de-multiplexed sequenced data (fastq) files were obtained from the DNA facility at Iowa State University. The quality of raw sequencing reads was assessed using FastQC. Cutadapt 1.16 was used to remove adapters from raw sequencing reads using the following parameters: “ -a TGGAATTCTCGGGTGCCAAGG --discard-untrimmed --minimum-length 23.” Adapter trimmed reads were further processed to trim the four random bases, that were added to both ends of riboseq and RNAseq reads during library preparation, using cutadapt 1.16 with the following parameters: “-u 4 -u -4”. Subsequently, riboseq reads that were 27 nt to 32 nt in length and RNAseq reads from 25 nt to 40 nt were retained, and the rest were filtered out.
Subsequently, noncoding RNA (rRNA, snoRNA and tRNA) was depleted by mapping the reads to the maize ncRNA reference file (ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/fasta/zea_mays/ncrna/) using bowtie 1.2 with the following parameters: “-n 0 -l 23” and retaining only the unmapped reads. ncRNA depleted reads were subsequently mapped to maize cDNA and CDS reference transcriptomes (ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/fasta/zea_mays) using bowtie 1.2 with following parameters: “-l 23 -v 2 -m 20 --best -k 1” and only aligned reads were retained. cDNA and CDS aligned files were converted from sam to bam, sorted, indexed and read counts were extracted from CDS-aligned files using samtools view, sort, index and idxstats tools respectively. All transcriptome-level read counts were consolidated as gene-level read counts.
For gene-expression analysis, CDS-aligned read count table was used that is attached as the PROCESSED DATA FILES.
Genome_build: Zea_mays.AGPv4.ncrna.fa.gz
Genome_build: Zea_mays.AGPv4.cdna.all.fa.gz
Genome_build: Zea_mays.AGPv4.cds.all.fa.gz
Supplementary_files_format_and_content: excel sheet (.xlsx)  consisting of raw count data of CDS-aligned riboseq and RNAseq reads

molecule: total RNA

organism: Zea mays

source_name: maize seedling roots

growth_protocol: sterile maize B73 seeds were placed in sterile Sigma bottles (Cat No V8630-E100) with two layers of wet filter paper. The seeds were incubated at 30°C for two days then transferred to an illuminated incubator at 23°C for 7 days.

extract_protocol:
For RPF generation, the remaining lysate was adjusted to A254 = ~10  (Lysate - PEB) with PEB. 600 ul of the adjusted lysate were digested with 15 ul RNase1 (Ambion AM2295) for 30 min at 28 ˚C on a shaker with slow speed. To terminate RNase digestion, 15 ul superase-IN (Ambion AM2696) were added. For each sample, two-aliquots of 600 ul (technical reps) were used and pooled after ultracentrifugation. The RNAse-digested lysate was layered on a precooled 330 ul sucrose cushion (1M sucrose, 40 mM Tris-acetate (pH 8), 100 mM KCl, 15 mM MgCl2, 100 ug/mL cycloheximide, 100 ug/mL chloramphenicol, 10 mM B-mercaptoethanol) in ultracentrifuge tubes (ThermoScientific #45237) and subjected to ultracentrifugation at 131k g (57000 rpm) for 90 minutes at 4˚ C in a Sorvall mini ultracentrifuge (Discovery M150) with S150-AT fixed angle rotor (ThermoScientific 45582). The pellet was resuspended in 150 uL ribosome dissociation buffer (10 mM Tris-HCl (pH 7.5), 10 mM EDTA (pH 8), 5 mM EGTA (pH 8), 100 mM NaCl).   RNA was purified by Trizol extraction method until the phase separations step followed by addition of an equal volume of ice cold 100% ethanol to the aqueous phase and further purification using Zymo RNA Clean & ConcentratorTM-5 columns (Zymo R1016) according to manufacturer’s protocol and quantified using a Nanodrop spectrophotometer. Quality of RPFs was assessed by electrophoresis of denatured RNA in a 15% TBE-Urea gel (Invitrogen EC6885BOX) at 120V for 5 minutes and 200V for 55 minutes, staining the gel with SYBR gold (Invitrogen S11494) and determining the sharpness of the RPF band between the 28 nt and 34 nt RNA size markers. If the RPF bands appeared sharp for all samples, the RNAs from two technical duplicates were pooled for each sample. Subsequently, 10 ug RNA were treated with 1 uL Turbo DNase (Ambion AM2238) in a 50 uL reaction with 1x Turbo DNase buffer at 37 ˚C for 30 min followed by addition of 1 uL more Turbo DNase and incubation at 37 ˚C for additional 30 min, purification by Zymo RNA clean & concentrator -5 columns (Zymo R1016) and quantification with a Nanodrop spectrophotometer. Quality of the DNase-treated RNA was assessed as above. rRNA depletion was carried out using a half reaction of Ribo-Zero for plant seed/root kit (Illumina MRZSR116) per ~5-10 ug of DNAse treated RNA sample followed by RNA clean up using Zymo RNA clean & concentrator -5 columns (Zymo R1016) according to the Illumina TruSeq Ribo Profile kit protocol (Illumina 15066016). RNA was quantified using a Qubit RNA HS kit (Invitrogen Q32852) yielding ~20% recovery from the input.   For size-selecting the RPFs, denatured rRNA-depleted RNA was subjected to electrophoresis on a 15% TBE-Urea gel (Invitrogen EC6885BOX) at 120V for 5 min and 170V for 85 min, stained in the gel with SYBR gold (Invitrogen S11494), and visualized on a blue light transilluminator.  The gel region between 28 nt and 34 nt RNA size markers was excised and transferred to a 0.5 ml tube with a hole at the bottom made by a 18 G syringe needle, and the tube was placed a 2 mL microfuge tube.  The tube was then centrifuged at 21k g for 2 min at 4˚ C to crush the gel slice and transfer its contents to the 2 mL microfuge tube. 500 uL RNA gel extraction buffer (0.3 M NaOAc (pH5.5), 1 mM EDTA (pH 8), 10 mM Tris-HCl (pH 7.5), 0.25% (w/v) SDS) was added and incubated overnight at 4 ˚C on a shaker. Eluted RPFs were filtered through 0.22 µ SpinX cellulose acetate filter columns (Sigma-Aldrich CL8161). 2 uL Glyco Blue (Ambion AM9516) and equal volume of ice cold 100% isopropanol were added to the supernatant, and RPFs were precipitated at -80 ˚C for 3 hours followed by centrifugation for 45 min at 21k g at 4 ˚C, washing with ice cold 80% ethanol and resuspending the pellet in 3.5 uL water.  Prior to library preparation, RPF ends were repaired as follows using T4PNK kit (ThermoScientific EK0031): incubate 3.25 uL RNA at 70˚ C for 3 min, transfer to ice and centrifuge, add 0.5 uL 10 x T4 PNK buffer A (no ATP), 0.25 uL superase-IN, 0.5 uL T4PNK enzyme, incubate at 37 ˚C for 30 min, add 0.5 uL 10 mM ATP, incubate at 37 ˚C for 1 hr, add 5.5 uL water, deactivate the reaction by incubating at 75 ˚C for 10 min and transfer to ice.
250 mg of 10-day old maize B73 seedling roots (in biological duplicates) were ground with liquid N2 in 2.5 mL of polysome extraction buffer (PEB; 50 mM Tris-Acetate (pH 8), 200 mM KCl, 15 mM MgCl2, 1% (v/v) Triton X-100, 2% (v/v) polyoxyethelene 10-tridecylether, 200 mM sucrose, 100 g/mL cycloheximide, 100 g/mL chloramphenicol, 20 mM -mercaptoethanol). The crude lysate was filtered through a 40 µm cell strainer (Falcon 08-771-1) by centrifugation at 4000 g for 2 minutes. The flow through supernatant was further clarified by centrifugation at 21k g for 15 min. 300 l of clarified lysate were aliquoted for total RNA extraction.  Subsequent steps for ribosome profiling and RNAseq are described above in SAMPLES section
cDNA libraries were prepared using Nextflex small RNA-Seq kit v3 (Bioo Scientific 5132-05) according to manufacturer’s protocol and 12 cycles of PCR. Quality of the libraries was assessed using an Agilent bioanalyzer high sensitivity DNA Assay kit. Libraries were quantified using Qubit dsDNA HS Assay kit (Invitrogen Q32854) and diluted to same concentration. The riboseq and RNAseq libraries were pooled together for multiplexing and sequenced in two lanes using an Illumina HiSeq 3000 to yield single-end 50 bp reads. Because of low depth of riboseq sequences, riboseq samples were pooled and resequenced in additional two lanes using Illumina HiSeq 3000 to yield single-end 50 bp reads.
Ribo-seq and RNA-seq

treatment_protocol: 7-day old seedlings were treated with 5ug/ml tunicamycin in DMSO for 0, 6 and 12 hours

tag: tissue

value: seedling roots

tag: treatment

value: 12 hour tunicamycin treatment

tag: cultivar


title: Control (mock-infected) 2

city: Bethesda

first: Eytan

last: Ruppin

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome and the annotated transcripts using STAR (v2.7.3a).
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools (v1.3.2).
Genome_build: Chlorocebus sabaeus genome (https://useast.ensembl.org/Chlorocebus_sabaeus/Info/Annotation); SARS-CoV-2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_045512).
Supplementary_files_format_and_content: The RSEM result for each sample is given in a separate file, containing the expected read count, TPM and FPKM across genes and transcripts

organism: Chlorocebus sabaeus

source_name: Vero E6 cells

growth_protocol: Vero E6 cells were maintained in Dulbecco’s modified eagle medium (DMEM, Gibco) supplemented with 10 % heat-inactivated fetal bovine serum (FBS, Gibco), 50 U/mL penicillin, 50 μg/mL streptomycin, 1 mM sodium pyruvate (Gibco), 10 mM 4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid (HEPES, Gibco), and 1X MEM non-essential amino acids solution (Gibco).

extract_protocol:
Cells were harvested, and total RNA was extracted using the Qiagen RNeasy Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Vero E6 cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI = 0.3) for 24 hours.

tag: cell

value: Vero E6 cells

value: Control (mock infection)

tag: time


title: 4 Gy 48h rep3

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

data_processing:
Novogene Standard RNA-Seq pipeline
Genome_build: Homo_sapiens_hg38
Supplementary_files_format_and_content: counts

organism: Homo sapiens

growth_protocol: well density in a 6-well plate with complete media.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) colimns for RNA isolation by following manufacturer's protocol.
uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: min. The X-ray beam was operated at 300 kV and hardened using a 4 mm Be, a 3 mm Al, and a 1.5 mm cu filter and calibrated using NIST-traceable dosimetry). Corresponding control cells were sham irradiated. The cells were then incubated and the RNA samples extracted at 48 hours post irradiation.

tag: condition

value: Glioblastoma

tag: sample type

value: patient-derived


title: Riboseq_6hr_Rep2

description: Ribosome profiling data

value: 6 hour tunicamycin treatment


title: HIV2

city: Bronx

first: Rosiris

last: León-Rivera

state: NY

address: 1300 Morris Park Ave, Forchheimer 727

department: Pathology

institute: Albert Einstein College of Medicine

description: single cell RNA-seq

data_processing: The CellRanger analysis pipeline (10X Genomics; V3.0.0), to a combined human genome (hg19) and the HIV genome (NCBI Reference Sequence: NC_001802.1) subdivided into 5 transcripts, as described in the results section “Novel method for detection of HIV-1 transcripts using scRNAseq”. Downstream analyses of the datasets were performed using Seurat (v3.1.4) (101) R package (v3.6.1).

source_name: mature monocytes

growth_protocol: Monocytes were matured in vitro nonadherently in Teflon-coated flasks with M-CSF as described in (Veenstra et al., 2017)

extract_protocol:
Frozen mature monocytes were thawed by placing in a 37o C water bath without agitation until only a small ice crystal was left in the vial. One ml of pre-warmed DNase supplemented media (RPMI supplemented with 20% FBS and 1% DNase I (Sigma, Cat# 10104159001)) was then added using filtered tips. The samples were gently mixed by pipetting and allowed to rest for 5 minutes at room temperature. After the 5 minutes, the contents of each vial were transferred to 10mL of pre-warmed DNase supplemented media and incubated for an additional 5 minutes at room temperature. Cells were then centrifuged, supernatant was aspirated, and the mature monocytes were resuspended in 1 mL of RPMI supplemented with 20% FBS and incubated for 15 minutes at 37o C with 5% CO2. After incubation cells were counted, centrifuged, and divided into two subsets, one used for staining post-freeze/thawing to verify viability on the day of scRNAseq and the other for scRNAseq.
The scRNAseq cDNA libraries were prepared following the user guide manual provided by the 10X Genomics and Chromium Single Cell 3’ Reagent Kits (v2 for HIV-infected ART-treated mature monocytes and v3 for HIV-infected mature monocytes). The libraries for the three HIV-infected ART-treated independent biological samples were run each individually on four lanes of sequencing on an Illumina Nextseq 550 instrument. For the HIV-infected independent biological samples, they were each divided in half for library preparation. The pooled libraries for one of the two HIV-infected independent biological samples were run on four lanes for sequencing on an Illumina Nextseq 550, and the pooled libraries for the second HIV-infected independent biological sample were run on two lanes on an Illumina Novaseq instrument. For the uninfected independent biological samples, they were each divided in half for library preparation. The pooled libraries were run on two lanes for sequencing on an Illumina Novaseq instrument.

treatment_protocol: After 2 days of culturing the monocytes, they were then divided to either be left uninfected, infected with HIV, or infected with HIV and subsequently treated with ART. Cells that were to be infected with HIV, with and without subsequent treatment with ART, were resuspended to 10 x 106 cells/ml in fresh monocyte media, inoculated with 1 ug p24/mL of HIVADA stock, and cultured non-adherently in Teflon-coated flasks for 8h. After 8h, virus was removed by centrifugation of the cells, and monocytes were resuspended to 2 x 106 cells/ml in fresh monocyte media and cultured non-adherently in Teflon-coated flasks. Uninfected cells were resuspended to 10 x 106 cells/ml in fresh monocyte media and cultured non-adherently in Teflon-coated flasks for 8h. The uninfected and the HIV-infected mature monocytes that did not receive subsequent ART treatment were cultured for an additional 64h. The subset of HIV-infected monocytes used for ART treatment were cultured for an additional 18h to facilitate viral replication and infection before the addition of ART. After the 18h, ART (15 M Emtricitabine (NIH AIDS Reagent Program; Cat# 10071) and 15 uM Tenofovir (NIH AIDS Reagent Program; Cat# 10199) were added to the media of these HIV-infected mature monocytes and cells were then cultured non-adherently in the Teflon-coated flasks for an additional 46h.

tag: cell type

value: mature monocytes

value: HIV-infected


title: Control (mock-infected) 1


title: Control 48h rep1


title: Uninfected2

description: single cell RNA-seq

value: uninfected


title: Riboseq_0hr_Rep2

description: Ribosome profiling data

value: 0 hour tunicamycin treatment


title: Riboseq_0hr_Rep1

description: Ribosome profiling data


title: Riboseq_6hr_Rep1

description: Ribosome profiling data


title: Control 48h rep3


title: HIVandART2

description: single cell RNA-seq

value: HIV-infected ART-treated


title: 4B4 rep1

city: NewDelhi

first: Krishna

middle: Jyoti

last: Mukherjee

state: Delhi

address: Behind administration building

department: SBT

country: India

institute: JNU

data_processing:
Illumina HiSeq 2500 reads were trimmed for removing adapter sequences using Trimmomatic(v.0.36). Reads quality was checked for each sample using FastQC v0.10.1. Reference genome (Fasta) and annotation file (Gff) of L. lactis NZ9000 was procurred from Ensembl and Gff annotation file was converted to Gtf using "Gffread" from Cufflinks Suite and then reference indices were created using Bowtie2. BAM files generated by Bowtie2  tool alfter alignment were then used to calculate mapped reads abundance using RSEM. Normalization was done to rule out the effect of library size and reads length by estimating FPKM values for paired-end reads for each sample.  Differential expression was performed using edgeR, which is based on negative binomial distribution. We selected the genes having at least two log fold change values and false-discovery-rate (FDR) corrected P value < 0.05 to be considered as differentially expressed genes.
Genome_build: Lactococcus_lactis_subsp_cremoris_nz9000.ASM14320v1
Supplementary_files_format_and_content: Exp_sample.genes.results represents output generated from RSEM. The abundance of each transcript is represented by its corresponding FPKM values.

organism: Lactococcus cremoris

source_name: bacterial cell

growth_protocol: 4B4 was grown in GM17 media (containing 4% isobutanol) in 30 degrees incubator under static conditions to late log phase, cells were arrested and proceeded for RNA isolation

extract_protocol:
Total RNA was isolated by slight modification of the method described by(Dijkstra et al., 2016)  for L. lactis. Cells from the late-log phase were snap frozen and harvested at (5000 x g, 10 mins, 4 degrees). Cell pellets were resuspended in 500ul of ice-cold TE buffer pH 7.5 and transferred to ice-cold 2ml microfuge tube (Eppendorf), after which 500 μl phenol/chloroform mixture (1:1), 30 μl 10% SDS, 30 μl 3 M sodium acetate (pH 5.2), and 500 mg glass-beads (150-212 μm, Sigma-Aldrich, St. Louis, USA) were added. The mixture was vortexed for 4 minutes at maximum speed and then 400 μl of chloroform isoamyl alcohol (24 :1) was added. The mixture was spun at 10000 x g at 20 degrees for 2 minutes. The supernatant was transferred to fresh microfuge tube and equal volume of RNAzol (Sigma) was added and steps were followed according to manufacturer’s protocol. The total RNA concentration and quality was determined by Agilent bioanalyzer 2100 expert.
Illumina HiSeq 2000/2500 Paired end run; 2 X 100 bp 30 million reads (3GB) per sample. ~3 ug of total RNA was used to prepare the RNA seq library. In short, mRNA molecules were purified using magnetic beads. Folllowing purification, mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were used to synthesize first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA polymeraseI and RNase H. These cDNA fragments were used to generate RNA libraries. Bioanalyzer plots were used at every step to assess mRNA quality, enrichment success, fragmentation sizes,and final library sizes. The size distribution of the sequencing library was determined by AgilentTapestation or Bioanalyzer. After the libraries were constructed, paired end run were performed on Illumina’s HiSeq 2500 platform to obtain 2 x100bp reads.

tag: strain

value: 4% isobutanol tolerant

tag: culture

value: late log phase


title: Uninfected1

description: single cell RNA-seq


title: Nr4a-TKO Taive

type: RNA

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

country: Japan

institute: National Center for Global Health and Medicine

description: Gene expression of Nr4a-TKO naive CD4+ T cells.

hyb_protocol: Using Gene Expression Hybridiation kit (Agilent), 600 ng of Cy3-labelled cRNA (Cy3 incorporation > 6) was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, samples were hybridized to SurePrint G3 Mouse GE microarray kit 8x60k ver 2.0  (G4858A, Agilent) for 17 hours at 65°C, rotating in hybridization oven (G2545A , Agilent) at 10 rpm.  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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan (G4900DA) using a setting AgilentG3_GX_1color (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction 11.5.1.1 (Agilent) using default parameters (protocol GE１_1010_Sep10, QC metric GE１_QCMT_Sep10, and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Output data were further analyzed with GeneSpring GX 12.6.1 with a default setting, with Prcentile=75, to generate values of normalized signal intensity.

organism: Mus musculus

source_name: Naive CD4+T cells from Nr4a-TKO mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mni kit purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNAiso PLUS (TAKARA). Samples were further cleaned using an NucleoSpin RNA Clean-up XS (MACHEREY-NAGEL). RNA was quantified using a Quantus fluorometer (Promega) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Naive CD4+T cells were obtained by sorting spleen and lymph nodes with the surface expression profiles of: CD4+, CD25low, CD44low, CD62L-high, and Foxp3-. To obtain iTreg 3 h cells, Primary naïve CD4+ T cells were cultured for 3 h in RPMI1640 medium supplemented with plate-coated anti-CD3 (clone 2C11, 2 μg/ml), anti-CD28 (clone 57.31, 0.5 μg/ml) antibodies, 2-Mercaptoethanol (Invitrogen, 55 μM), 10% fetal bovine serum, and further supplemented with anti-IFN-γ (clone R4-6A2, 1 μg/ml), anti-IL-4 (clone 11B11, 1 μg/ml) antibodies, IL-2 (10 ng/ml, PeproTech) and recombinant human TGF-β1 (0.2 or 0.5 ng/ml, BioLegend).

tag: cell subset

value: Naive CD4+ T cells

tag: genotype

value: Nr4a triple knockout


title: bladder cell_Low dose LPS_4 hours_replicate 3

description: gene expression data from bladder cells exposed to LPS

source_name: bladder cells treated with Low dose LPS

value: cultured bladder cells (5637)


title: HIV1

description: single cell RNA-seq


title: 4B0 rep1

growth_protocol: Both wild type (WT) and isobutanol adapted cells (4B0) was cultured in GM17 media in 30 degrees incubator under static conditions to late log phase and arrested at the same specific growth rate.

extract_protocol:
Total RNA was isolated by slight modification of the method described by(Dijkstra et al., 2016)  for L. lactis. Cells from the late-log phase were snap frozen and harvested at (5000 x g, 10 mins, 40C) for the wild type and the adapted strains. Cell pellets were resuspended in 500ul of ice-cold TE buffer pH 7.5 and transferred to ice-cold 2ml microfuge tube (Eppendorf), after which 500 μl phenol/chloroform mixture (1:1), 30 μl 10% SDS, 30 μl 3 M sodium acetate (pH 5.2), and 500 mg glass-beads (150-212 μm, Sigma-Aldrich, St. Louis, USA) were added. The mixture was vortexed for 4 minutes at maximum speed and then 400 μl of chloroform isoamyl alcohol (24 :1) was added. The mixture was spun at 10000 x g at 20 degrees for 2 minutes. The supernatant was transferred to fresh microfuge tube and equal volume of RNAzol (Sigma) was added and steps were followed according to manufacturer’s protocol. The total RNA concentration and quality was determined by Agilent bioanalyzer 2100 expert.
Illumina HiSeq 2000/2500 Paired end run; 2 X 100 bp 30 million reads (3GB) per sample. ~3 ug of total RNA was used to prepare the RNA seq library. In short, mRNA molecules were purified using magnetic beads. Folllowing purification, mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were used to synthesize first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA polymeraseI and RNase H. These cDNA fragments were used to generate RNA libraries. Bioanalyzer plots were used at every step to assess mRNA quality, enrichment success, fragmentation sizes,and final library sizes. The size distribution of the sequencing library was determined by AgilentTapestation or Bioanalyzer. After the libraries were constructed, paired end run were performed on Illumina’s HiSeq 2500 platform to obtain 2 x100bp reads.


title: bladder cell_Low dose LPS_4 hours_replicate 2


title: Control 48h rep2


title: bladder cell_Untreated_4 hours_replicate 1


title: DGCR8 KO transfected with DGCR8 mut1 plasmid replicate 3

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The total RNAs were isolated from the DGCR8ΔCTT KO cells, which were transfected with pCK, pCK-DGCR8-WT, or pCK-DGCR8-mut1 plasmids. Next, the small RNA sequencing libraries were generated from these total RNAs using the TruSeq Small RNA Library Prep kit. The adapter sequences were trimmed from the raw reads using cutadapt (-a AGA TCG GAA GAG CAC ACG TC  -A GAT CGT CGG ACT GTA GAA CTC TGA AC) (Martin, 2011). The trimmed paired-end reads were then joined using fastq-join (default parameters) (Aronesty, 2013). Subsequently, the joined reads, which ranged from 18 nt to 26 nt, were selected. The low-quality reads were further removed (minimum quality score: 20, minimum percent of bases having the quality: 90) using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). The selected high-quality reads were then mapped to the human genome (hg38) using Bowtie2 (Langmead and Salzberg, 2012). The reads, which were mapped to miRNA loci (using the miRNA annotation obtained from miRBase v22; miRbase.org) and showed unambiguous alignments with no mismatches except for those at the 3′-ends were collected for subsequent analysis. The read counts of miRNAs were converted to reads per a million (rpm) and then normalized to the geometric mean of hsa-mir-320a and hsa-mir-320b, which were DROSHA-independent miRNAs. The normalized values were averaged for the three biological replicates.
Genome_build: GRCh38
Supplementary_files_format_and_content: rawcount.csv.gz containing the raw read counts.

source_name: DGCR8 KO HCT116 cells

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
Small RNA-seq libraries were generated with TruSeq Small RNA Sample Prep Kit (Illumina).

tag: disease state

value: colon carcinoma

tag: cell line

value: DGCR8 KO

tag: plasmid transfection

value: pCK-DGCR8 mut1 plamsid

tag: index

value: GATCAG


title: DGCR8 KO transfected with DGCR8 mut1 plasmid replicate 2

value: GCCAAT


title: HIVandART3

description: single cell RNA-seq


title: bladder cell_Untreated_4 hours_replicate 2


title: bladder cell_Low dose LPS_4 hours_replicate 1


title: DGCR8 KO transfected with DGCR8 mut1 plasmid replicate 1

value: TTAGGC


title: WTD/WT rep2

value: wild type


title: bladder cell_High dose LPS_4 hours_replicate 2

source_name: bladder cells treated with High dose LPS


title: bladder cell_High dose LPS_4 hours_replicate 1


title: HIVandART1

description: single cell RNA-seq

value: mature monocytes


title: bladder cell_High dose LPS_4 hours_replicate 3


title: DGCR8 KO transfected with DGCR8 WT plasmid replicate 1

value: pCK-DGCR8 WT plamsid

value: CGATGT


title: DGCR8 KO transfected with DGCR8 WT plasmid replicate 3

value: ACTTGA


title: Testicular tissue Zebu breed

city: Bangalore

first: Arumugam

last: Kumaresan

state: Karnataka

address: Hosur Road

department: Veterinary Gynaecology and Obstetrics

institute: National Dairy Research Institute

description: Gene expression testicular tissue – Zebu

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

organism: Bos taurus

source_name: Testis

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA was extracted using Qiagen Rneasy mini kit with Dnase treatment as per the manufacturer’s protocol.

tag: Sex

value: Male

tag: age

value: Adult


title: bladder cell_Nissle EV-RNA_Iron restricted_4 hours_replicate 3

description: gene expression data from bladder cells exposed to RNA from E.coli Extracellular Vesicles

source_name: bladder cells treated with Nissle EV-RNA grown under Iron restricted media


title: bladder cell_Nissle EV-RNA_Iron restricted_4 hours_replicate 2


title: HEK293T_ATF6_ex8-14

city: La Jolla

first: R. Luke

last: Wiseman

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

data_processing:
Basescaling was performed by BGI
Single end, 50 bp-long reads from RNA Seq experiments were aligned to the GRCh37.p13 human genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Counts Data were analyzed using DESeq
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: XLSX files contain counts data for each sample and DESeq differential expression analysis of ATF6 variant vs. Non-transfected control.

source_name: human embryonic kidney cells

growth_protocol: HEK293 cells were transfected with ATF6 variants or empty vector using Lipofectamine 2000.

extract_protocol:
HEK293 cells expressing WT or mutant ATF6 were collected for RNA-Seq analysis. Cells were lysed and total RNA was collected using a Qiagen kit (RNeasy Mini Kit) in line with the manufacturer’s recommendations.
Libraries were constructed using standard protocols at BGI

value: human embryonic kidney


title: Testricular tissue crossbred

description: Gene expression in testicular tissue – Crossbred


title: DGCR8 KO transfected with DGCR8 WT plasmid replicate 2

value: ACAGTG


title: HEK293T_ATF6_N267star


title: DGCR8 KO transfected with pCK empty plasmid replicate 3

value: pCK empty plasmid

value: CAGATC


title: HEK293T_ATF6_M67V


title: Patient 2 scRNA-seq

city: Palo Alto

first: Themasap

middle: Ahmad

last: Khan

address: 318 Campus Drive

department: Psychiatry

institute: Stanford University

data_processing:
All data processing performed with Cell Ranger (v.3.0 with default settings)
Genome_build: Human: GRCh38
Supplementary_files_format_and_content: Count matrices, barcodes, and features were

molecule: polyA RNA

source_name: iPSC-derived cortical spheroid

extract_protocol:
Chromium Single cell 3’ GEM, Library & Gel Bead Kit v2
Illumina TruSeq Stranded mRNA library prep kit (Illumina)

tag: tissue

value: iPSC-derived cortical spheroid

tag: cell line identification number


title: bladder cell_Nissle EV-RNA_Iron sufficient_4 hours_replicate 1

source_name: bladder cells treated with Nissle EV-RNA grown under Iron sufficient media

value: cultured bladder cells (5637)


title: bladder cell_Nissle EV-RNA_Iron sufficient_4 hours_replicate 2


title: DGCR8 KO transfected with pCK empty plasmid replicate 2

value: colon carcinoma

value: DGCR8 KO

value: TGACCA


title: [BIG+] replicate 2

city: Eugene

first: David

middle: M

last: Garcia

state: OR

address: 1318 Franklin Blvd.,, Room 273 Onyx Bridge

department: Biology

institute: University of Oregon, Institute of Molecular Biology

description:
total RNA with rRNA depletion
YDJ1952_2

data_processing:
Pre-processing performed by Beijing Genomics Institute
Alignment was performed using Bowtie2 (Langmead and Salzberg, 2012)
HT-Seq (Anders et al., 2015) was used to prepare read counts.
DE-Seq2 (Love et al., 2014) was used in R to perform differential gene expression analysis
Genome_build: S. cerevisiae strain S288C reference genome R64-2-1
Supplementary_files_format_and_content: Genes (systematic name) are listed in rows, samples listed in columns, values are TPM (Transcirpts Per kilobase Million)

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Five independent colonies of naïve and [BIG+] cells were grown in 5 mL YPD cultures on a culture roller drum wheel overnight at 30°C. Saturated cultures were added to 700 mL YPD cultures in 2 L narrow mouthed baffled flasks, pre-incubated to 30°C. These were grown until a cuvette reading of OD 1.0. (700 mL cultures were used to provide enough material for other sample-intensive experiments done in parallel).

extract_protocol:
Cultures were pelleted in large table-top centrifuge with swing-bucket rotor at 4300 x g at 4°C for 20 minutes, washing once with ice-cold 1X TBS. RNA was harvested as described in (Carlile et al., 2015). Total RNA was treated with RiboZero (Illumina, San Diego, CA) to remove most rRNAs but retain mRNAs and other ncRNAs. RNA was fragmented and submitted for Illumina sequencing
Library preparation and Illumina sequencing was performed at the Beijing Genomics Institute in late 2017.

tag: strain background

value: WT

tag: prion

value: [BIG+]


title: HEK293T_ATF6_ex2-3


title: DGCR8 KO transfected with pCK empty plasmid replicate 1

value: ATCACG


title: WT/rep1

value: wild type

value: late log phase


title: HEK293T_ATF6_WT


title: bladder cell_Nissle EV-RNA_Iron sufficient_4 hours_replicate 3


title: HEK293T_ATF6_NT

value: non-transfected control


title: bladder cell_UPEC EV-RNA_Iron restricted_4 hours_replicate 3

source_name: bladder cells treated with UPEC EV-RNA grown under Iron restricted media


title: ZSlg01 [miRNA-seq]

city: Lanzhou

first: Qianyun

last: Ge

state: Gansu

address: NO.1 yingmen village, Anning district

country: China

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Remove the 3’ linker sequence, remove the sequence containing the fuzzy base N; 2) Remove low-quality reads so that at least 95% of the bases have a quality score of not less than 20; 3) Remove reads containing polyA/polyT, remove reads outside the miRNA length range (15-34nt).
Pipette 1µL library to Qubit Fluorometer (Invitogen) for detection. The library concentration, greater than 1.0ng/µL is qualified library.
Use Bio-Q100 to detect library length distribution and concentration.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: lung tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A small RNA library of about 150 bp was recovered using PAGE (polyacrylamide) gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: altitude

value: lung tissue

tag: breed

value: cattle


title: bladder cell_UPEC EV-RNA_Iron restricted_4 hours_replicate 2

tag: sample type


title: ZSlg02 [RNA-seq]

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: lung tissues

extract_protocol:
Retinas 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


title: Control 2 scRNA-seq


title: bladder cell_UPEC EV-RNA_Iron restricted_4 hours_replicate 1


title: ZSlg01 [RNA-seq]


title: Control 1 scRNA-seq


title: ZSlg02 [miRNA-seq]


title: bladder cell_UPEC EV-RNA_Iron sufficient_4 hours_replicate 3

source_name: bladder cells treated with UPEC EV-RNA grown under Iron sufficient media


title: Patient 1 scRNA-seq


title: 10938438_12

status: Public on Jul 07 2020

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

data_processing:
Fastq files were obtained from the sequencing facility (running Illumina NextSeq550 with HighOutput75cycles) after demultiplexing with bcl2fastq.
To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Quality control was performed to remove poor quality cells. Cells with less than 250 genes detected were removed. We further excluded cells with values below 3 median absolute deviations (MADs) from the median for UMI counts, for the number of genes detected, or for ERCC accuracy, and cells with values above 3 MADs from the median for ERCC transcript percentage.
Genome_build: GRCm38 with additional artificial chromosomes including for the YFP sequence and for 92 ERCC spike-in genes.
Supplementary_files_format_and_content: txt file containing gene UMI counts and csv file containing additional cell-specific metadata (index sorting parameters) for each filtered cell identified by a UniqueCellID.

source_name: plasmacytoid dendritic cells

extract_protocol:
Single cells were FACS sorted into ice-cold 96-well PCR plates (Thermofisher) containing 2 µl lysis mix per well. The lysis mix contained 0.5 µl 0.4% (v/v) Triton X-100 (Sigma-Aldrich), 0.05 µl 40 U/µl RnaseOUT (Thermofisher), 0.08 µl 25 mM dNTP mix (Thermofisher), 0.5 µl 10 µM (dT)30_Smarter primer (Table S3), 0.05 µl 0.5 pg/µl External RNA Controls Consortium (ERCC) spike-ins mix (Thermofisher), and 0.82 µl PCR-grade H20 (Qiagen). Immediately after cell sorting, each plate was covered with adhesive film (Thermofisher), briefly spun down in a benchtop plate centrifuge, and frozen on dry ice. Plates containing single cells in lysis mix were stored at -80°C and shipped on dry ice (only T cells) until further processing. The plate containing single cells in lysis mix was thawed on ice, briefly spun down in a benchtop plate centrifuge, and incubated in a thermal cycler for 3 minutes at 72°C (lid temperature 72°C). Immediately after, the plate was placed back on ice and 3 µl RT mastermix was added to each well. The RT mastermix contained 0.25 µl 200 U/µl SuperScript II (Thermofisher), 0.25 µl 40 U/µl RnaseOUT (Thermofisher), and 2.5 µl 2x RT mastermix. The 2x RT mastermix contained 1 µl 5x SuperScript II buffer (Thermofisher), 0.25 µl 100 mM DTT (Thermofisher), 1 µl 5 M betaine (Sigma-Aldrich), 0.03 µl 1 M MgCl2 (Sigma-Aldrich), 0.125 µl 100 µM well-specific template switching oligonucleotide TSO_BCx_UMI5_TATA (Table S3 and Table S4), and 0.095 µl PCR-grade H2O (Qiagen). Reverse transcription was performed in a thermal cycler (lid temperature 70°C) by 90 min at 42°C, followed by 10 cycles of 2 min at 50°C and 2 min at 42°C, then 15 min at 70°C. Plates with single-cell cDNA were stored at -20°C until further processing. For cDNA amplification, 7.5 µl LD-PCR mastermix were added to each well. The LD-PCR mastermix contained 6.25 µl 2x KAPA HiFi HotStart ReadyMix (Roche Diagnostics), 0.125 µl 20:µM PCR_Satija forward primer (Table S3), 0.125 µl 20 µM SmarterR reverse primer8 (Table S3), and 1 µl PCR-grade H2O (Qiagen). The amplification was performed in a thermal cycler (lid temperature 98°C) by 3 min at 98°C, followed by 22 cycles of 15 sec at 98°C, 20 sec at 67°C, 6 min at 72°C, then a final elongation for 5 min at 72°C. Plates with amplified single-cell cDNA were stored at -20°C until further processing.
For library preparation, 5 µl amplified cDNA from each well of a 96-well plate were pooled and completed to 500 µl with PCR-grade H2O (Qiagen). Two rounds of 0.6X solid-phase reversible immobilization beads (AmpureXP, Beckman, or CleanNGS, Proteigene) cleaning were used to purify 100 µl pooled cDNA with final elution in 15 µl PCR-grade H2O (Qiagen). After quantification with Qubit dsDNA HS assay (Thermofisher), 800 pg purified cDNA pool were processed with the Nextera XT DNA sample Preparation kit (Illumina), according to the manufacturer’s instructions with modifications to enrich 5’-ends of tagmented cDNA during library PCR. After tagmentation and neutralization, 25 µl tagmented cDNA was amplified with 15 µl Nextera PCR Mastermix, 5 µl Nextera i5 primer (S5xx, Illumina), and 5 µl of a custom i7 primer mix (0.5 µM i7_BCx + 10 µM i7_primer, Table S3). The amplification was performed in a thermal cycler (lid temperature 72°C) by 3 min at 72°C, 30 sec at 95°C, followed by 12 cycles of 10 sec at 95°C, 30 sec at 55°C, 30 sec at 72°C, then a final elongation for 5 min at 72°C. The resulting library was purified with 0.8X solid-phase reversible immobilization beads (AmpureXP, Beckman, or CleanNGS, Proteigene).
Libraries generated from multiple 96-well plates of single cells and carrying distinct i7 barcodes were pooled for sequencing on an Illumina NextSeq550 platform, with High Output 75 cycles flow cells,  targeting  5x105 reads per cell in paired-end single-index mode with the following primers (Table S3) and cycles: Read1 (Read1_SP, 67 cycles), Read i7 (i7_SP, 8 cycles), Read2 (Read2_SP, 16 cycles).

tag: mouse genotype

tag: cell type

value: pDC LIFRlo/neg

value: spleen

tag: infection time

tag: plate


title: 10938438_11


title: 10938438_10

value: pDC total


title: 10938438_13


title: 10938438_7


title: 10938438_9


title: 10938438_15


title: 10938438_8


title: 10938438_6


title: 10938438_4


title: 10938438_5


title: bladder cell_Nissle EV-RNA_Iron restricted_4 hours_replicate 1


title: bladder cell_UPEC EV-RNA_Iron sufficient_4 hours_replicate 2


title: bladder cell_UPEC EV-RNA_Iron sufficient_4 hours_replicate 1


title: 10938438_3


title: 10938438_2


title: 10633848_S7

data_processing:
Fastq files were obtained from the sequencing facility (running Illumina NextSeq550 with HighOutput75cycles) after demultiplexing with bcl2fastq.
To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Quality control was performed to remove poor quality cells. Cells with less than 250 genes detected were removed. We further excluded cells with values below 3 median absolute deviations (MADs) from the median for UMI counts, for the number of genes detected, or for ERCC accuracy, and cells with values above 3 MADs from the median for ERCC transcript percentage.
Genome_build: GRCm38 with additional artificial chromosomes for 92 ERCC spike-in genes.
Supplementary_files_format_and_content: txt file containing gene UMI counts and csv file containing additional cell-specific metadata (index sorting parameters) for each filtered cell identified by a UniqueCellID.

source_name: pDC sorted from wt C57Bl/6 mice

value: WT C57Bl/6

value: pDC enriched for LIFRlo cells


title: 10633846_S5


title: 10633847_S6


title: 10633844_S3


title: 10633845_S4


title: 10633842_S1


title: 10633843_S2


title: 10938438_1


title: TW2.6-NOG09

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

description:
Sample 8
Experiment 2

data_processing:
Partek Flow  was used for base calling, trimming, filtering of quality <20 and adaptor sequences
Clean reads were aligned to the hg38 and mm10 genomes, respectively
for each sample, hg38.bam and mm10.bam files were subjected to XenofilteR (pmid 30286710)  to remove ambiguous reads
XenofilteR-processed hg38.bam and mm10.bam were subjected to Parktek Flow for gene count quantitation (Partek E/M GRCh38 and mm10, respectively)
abundance measurements (cpm) for each gene in each sample were used to construct the expression matrix (OSCC_CDX_hg38_cpm and OSCC_CDX_mm10_cpm)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Tab-delimited text files include cpm values for each sample.

organism:
Homo sapiens
Mus musculus

source_name: OSCC cell line TW2.6

extract_protocol:
The tumors of xenografts were removed and RNA was extracted using TRIZOL reagent. Illumina TruSeq RNA Sample Prep Kit (for samples 1 to 9) and TruSeq Rapid PE Cluster Kit V2 (for samples 10 and 11) were used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

value: NOG

value: xenograft tumor

tag: day of collection

tag: batch

tag: library preparation

value: TruSeq Stranded mRNA

tag: core lab

value: AS IMB, TW


title: TW2.6-NOG07

description:
Sample 6
Experiment 2

tag: cell line


title: OC3-NOG05

description:
Sample 4
Experiment 2

source_name: OSCC cell line OC3

tag: tissue


title: OC3-NOG06

description:
Sample 5
Experiment 2


title: OC3-NOG01

description:
Sample 1
Experiment 2


title: OC3-NOG04

description:
Sample 3
Experiment 2


title: TW2.6-NOG08

description:
Sample 7
Experiment 2


title: TW2.6-NOG10

description:
Sample 9
Experiment 2


title: OC3-NOG03

description:
Sample 2
Experiment 2


title: SE-14000 stimulated Human keratinocyte cells vs. control 3

city: Tokyo

first: noriko

middle: muto

last: matsumoto

address: 1-1-5 Sendagi, Bunkyo-ku

department: Department of Plastic, Reconstructive and Regenerative Surgery

institute: Nippon Medical School

description: Biological replicate 3 of 3. Control Human keratinocyte cells, untreated, harvested after several passages.

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies SureScan G4900DA at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 11.5.1.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Human keratinocyte cells, 14000V/3days

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: cells were kept in medium with 2% Fetal calf serum

extract_protocol: Total RNA extracted using RNeasy Mini Kit following manufacturer's instructions

treatment_protocol: cells were treated by 3hrs stimulation of 14000V and 90Hz for three days by SE-14000

value: Human keratinocyte cells

value: HaCaT (Human keratinocyte cell line, cryopreserved in CM-2)

source_name: Human keratinocyte cells, untreated control


title: SE-14000 stimulated Human keratinocyte cells vs. control 2

description: Biological replicate 2 of 3. Control Human keratinocyte cells, untreated, harvested after several passages.


title: SE-14000 stimulated Human keratinocyte cells vs. control 1

description: Biological replicate 1 of 3. Control Human keratinocyte cells, untreated, harvested after several passages.


title: WT mTEC 3

city: San Francisco

first: Anthony

last: Shum

address: 555 Mission Bay Blvd South

department: Pulmonary

institute: University of California San Francisco

description: WT 3

data_processing:
Sequencing reads were then aligned to the mouse reference genome and the ensemble annotation build (GRCm38.78) using STAR (v2.4.2a)
Read counts per gene were used as input to DESeq2 (v1.26.0) to test for differential gene expression between conditions using a Wald test.
At least one condition in a given pairwise comparison must have greater than zero read counts in all three samples
Genes passing a multiple testing correct p-value of 0.1 (FDR method) were considered significant.
Genome_build: GRCm38.78
Supplementary_files_format_and_content: txt and xlsx. Raw counts and DESeq2 results, respectively.

growth_protocol: Thymi were isolated from mice euthanized at post natal 4 weeks of age.

extract_protocol:
RNA was isolated using EZNA Total RNA kit from Omega Bio-tek. Complimentary DNA was created with Nugen Ovation method.
Sequencing library was created from cDNA using Illumina Nextera XT method, following manufacturer's protocol.

treatment_protocol: Medullary thymic epithelial cells were isolated following: Miller CN, Proekt I, von Moltke J, et al. Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development. Nature. 2018;559(7715):627-631. doi:10.1038/s41586-018-0345-2

tag: genotype

value: Copa+/+

tag: strain

tag: age

value: post natal 4 weeks

value: Medullary thymic epithelial cell


title: MUT mTEC 2

description: MUT 2


title: MUT mTEC 3

description: MUT 3


title: WT mTEC 1

description: WT 1


title: MUT mTEC 1

description: MUT 1


title: WT mTEC 2

description: WT 2


title: SE-14000 stimulated Human Microvascular Endotheilal Cells vs. control 3

description: Biological replicate 3 of 3. Control Human Microvascular Endotheilal Cells, untreated, harvested after several passages.

source_name: Human Microvascular Endotheilal Cells, 14000V/3days

value: Human Microvascular Endotheilal Cells

value: HMEC-1 (ATCC CRL-3243)

source_name: Human Microvascular Endotheilal Cells, untreated control


title: SE-14000 stimulated Human Microvascular Endotheilal Cells vs. control 2

description: Biological replicate 2 of 3. Control Human Microvascular Endotheilal Cells, untreated, harvested after several passages.


title: SE-14000 stimulated Human Microvascular Endotheilal Cells vs. control 1

description: Biological replicate 1 of 3. Control Human Microvascular Endotheilal Cells, untreated, harvested after several passages.


title: SST-TdT-X94_P97_tdt

city: Padova

first: Davide

last: Risso

address: Via C. Battisti, 241

country: Italy

institute: University of Padova

data_processing: The libraries were processed with the 10X Genomics Cell Ranger (v. 2.0.0) pipeline. In particular, `cellranger mkfastq` with `--ignore-dual-index` was used, followed by cellranger count with default parameters and GRCm38 genome annotation

source_name: triple transgenic SST-TdT-X94

extract_protocol: cDNA libraries were prepared from the isolated cells using the Chromium Single Cell 3’ System according to manufacturer’s instructions, with the sole following modification: The quantified cell suspension was directly added to the reverse transcription master mix, along with the appropriate volume of water to achieve the approximate cell capture target. We omitted the 0.04% weight/volume BSA (400 µg/ml) washing step to avoid inevitable cell loss. 2470 tdT +and 1100 GFP +cells were applied to individual channels of the Single Cell 3’ Chip. The completed libraries were sequenced an Illumina HiSeq4000 to produce paired-end 100nt reads.

value: Background:Crl:CD1(ICR); Transgenes from JAX013044, JAX006334, JAX007909

value: Somatosensory Cortex

tag: sorting

value: tdTomato+ sorted cells


title: SST-TdT-X94_P97_gfp-tdt

value: GFP+, tdTomato+ sorted cells


title: SST-TdT-X94_P45_tdt1


title: SE-14000 stimulated Normal Human Dermal Fibroblasts vs. control 3

description: Biological replicate 3 of 3. Control Normal Human Dermal Fibroblasts, untreated, harvested after several passages.

source_name: Normal Human Dermal Fibroblasts, 14000V/3days

value: Normal Human Dermal Fibroblasts

value: Normal Human Dermal Fibroblasts TAKARA C-12302

source_name: Normal Human Dermal Fibroblasts, untreated control


title: SE-14000 stimulated Normal Human Dermal Fibroblasts vs. control 1

description: Biological replicate 1 of 3. Control Normal Human Dermal Fibroblasts, untreated, harvested after several passages.


title: SE-14000 stimulated Normal Human Dermal Fibroblasts vs. control 2

description: Biological replicate 2 of 3. Control Normal Human Dermal Fibroblasts, untreated, harvested after several passages.


title: sample384_S434

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were mapped to mouse genome GRCm38 using STAR version 2.2.1 with default parameters except --sjdbOverhang 49 --outSAMstrandField intronMotif --outFilterMultimapNmax 1 (The max number of multiple alignments allowed for a read is 1. if exceeded, the read is considered unmapped).
Read counting was performed using HTSeq-Count (version 0.9.1) with parameters --stranded=no -m union, and using the annotations of mouse genome GRCm38 release 94 downloaded from the ENSembl website. In short, our RNA-Seq data has not been made with a strand-specific protocol. When a read was mapped to more than one gene, it was considered as ambiguous and assigned to none of them.
Genome_build: GRCm38 with an additional artificial chromosome for the YFP sequence
Supplementary_files_format_and_content: Text files with tab delimiters including raw gene counts and metadata (including index sorting information) for each sample

source_name: splenic plasmacytoid dendritic cells

extract_protocol:
Single cells were FACS sorted into 96-well PCR plates (Eppendorf), each well containing 10 µl of TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol. Plates were spun down at 800g for 1 min, flash frozen on dry ice and stored at -80°C until further processing (Villani and Shekhar, 2017).
Single cell RNA-sequencing libraries were generated using an adaptation of Smart-Seq2 (Villani and Shekhar, 2017).
Full-length RNA-sequencing was performed.

value: pDC

value: spleen


title: SST-TdT-X94_P45_tdt2


title: sample382_S432


title: sample380_S430


title: sample379_S429


title: sample381_S431


title: sample377_S427


title: sample371_S421


title: sample378_S428


title: sample376_S426


title: sample372_S422


title: sample370_S420


title: sample369_S419


title: sample368_S418


title: sample367_S417


title: sample364_S414


title: sample363_S413


title: sample365_S415


title: sample366_S416


title: sample356_S406

value: LIFRLowYFPpos


title: sample361_S411


title: sample360_S410


title: sample359_S409


title: sample357_S407


title: sample358_S408


title: sample354_S404


title: sample383_S433


title: sample353_S403


title: sample352_S402


title: sample351_S401


title: sample350_S400


title: sample349_S399


title: sample348_S398


title: sample346_S396


title: sample347_S397


title: sample343_S393


title: sample345_S395


title: sample344_S394


title: sample362_S412


title: sample355_S405


title: sample341_S391

value: LIFRHigh


title: sample340_S390


title: sample337_S387


title: sample338_S388


title: sample339_S389


title: sample334_S384


title: sample333_S383


title: sample330_S380


title: sample329_S379


title: sample327_S377


title: sample326_S376


title: sample328_S378


title: sample325_S375


title: sample324_S374


title: sample323_S373


title: sample322_S372


title: sample321_S371


title: sample335_S385


title: sample342_S392


title: 10938438_14

value: pDC LIFRlo/neg


title: sample320_S370


title: sample319_S369


title: sample317_S367


title: sample318_S368


title: sample315_S365

value: LIFRHighYFPpos


title: sample316_S366


title: sample314_S364


title: sample336_S386


title: sample313_S363


title: sample331_S381


title: sample312_S362


title: sample310_S360


title: sample332_S382


title: sample308_S358


title: sample307_S357


title: sample311_S361


title: sample309_S359


title: sample305_S355


title: sample306_S356


title: sample304_S354


title: sample303_S353


title: sample302_S352


title: sample301_S351


title: sample300_S350


title: sample296_S346


title: sample295_S345


title: sample297_S347


title: sample298_S348


title: sample294_S344


title: sample293_S343


title: sample291_S341


title: sample290_S340


title: sample289_S339


title: sample288_S338


title: sample285_S335


title: sample286_S336


title: sample287_S337


title: sample283_S333


title: sample284_S334


title: sample276_S326


title: sample280_S330


title: sample281_S331


title: sample272_S322


title: sample274_S324


title: sample271_S321


title: sample273_S323


title: sample268_S318


title: sample269_S319


title: sample265_S315


title: sample264_S314


title: sample267_S317


title: sample292_S342


title: sample261_S311


title: sample262_S312


title: sample282_S332


title: sample275_S325


title: sample299_S349


title: sample254_S304


title: sample260_S310


title: sample255_S305


title: sample258_S308


title: sample259_S309


title: sample256_S306


title: sample253_S303


title: sample250_S300


title: sample252_S302


title: sample247_S297


title: sample248_S298


title: sample246_S296


title: sample245_S295


title: sample251_S301


title: sample244_S294


title: sample249_S299


title: sample266_S316


title: sample263_S313


title: sample242_S292


title: sample243_S293


title: sample241_S291


title: sample240_S290


title: sample239_S289


title: sample238_S288


title: sample237_S287


title: sample236_S286


title: sample234_S284


title: sample233_S283


title: sample230_S280


title: sample232_S282


title: sample235_S285


title: sample231_S281


title: sample229_S279


title: sample228_S278


title: sample226_S276


title: sample225_S275


title: sample227_S277


title: sample223_S273


title: sample221_S271


title: sample222_S272


title: sample215_S265


title: sample218_S268


title: sample217_S267


title: sample216_S266


title: sample219_S269


title: sample220_S270


title: sample211_S261


title: sample210_S260


title: sample209_S259


title: sample208_S258


title: sample213_S263


title: sample224_S274


title: sample207_S257


title: sample204_S254


title: sample200_S250


title: sample205_S255


title: sample202_S252


title: sample201_S251


title: sample206_S256


title: sample199_S249


title: sample198_S248


title: sample196_S246


title: sample197_S247


title: sample214_S264


title: sample194_S244


title: sample189_S239


title: sample191_S241


title: sample190_S240


title: sample192_S242


title: sample187_S237


title: sample188_S238


title: sample185_S235


title: sample184_S234


title: sample203_S253


title: sample179_S229


title: sample176_S226


title: sample174_S224


title: sample178_S228


title: sample177_S227


title: sample173_S223


title: sample175_S225


title: sample172_S222


title: sample169_S219


title: sample195_S245


title: sample170_S220


title: sample166_S216


title: sample167_S217


title: sample164_S214


title: sample163_S213


title: sample180_S230


title: sample186_S236


title: sample165_S215


title: sample160_S210


title: sample162_S212


title: sample161_S211


title: sample159_S209


title: sample157_S207


title: sample158_S208


title: sample155_S205


title: sample171_S221


title: sample156_S206


title: sample154_S204


title: sample153_S203


title: sample168_S218


title: sample150_S200


title: sample149_S199


title: sample151_S201


title: sample146_S196


title: sample147_S197


title: sample145_S195


title: sample143_S193


title: sample142_S192


title: sample141_S191


title: sample140_S190


title: sample138_S188


title: sample144_S194


title: sample137_S187


title: sample139_S189


title: sample134_S184


title: sample193_S243


title: sample133_S183


title: sample136_S186


title: sample130_S180


title: sample152_S202


title: sample128_S178


title: sample131_S181


title: sample129_S179


title: sample148_S198


title: sample127_S177


title: sample126_S176


title: sample123_S173


title: sample135_S185


title: sample122_S172


title: sample118_S168


title: sample115_S165


title: sample121_S171


title: sample119_S169


title: sample112_S162


title: sample120_S170


title: sample113_S163


title: sample117_S167


title: sample110_S160


title: sample111_S161


title: sample109_S159


title: sample108_S158


title: sample107_S157


title: sample270_S320


title: sample132_S182


title: sample124_S174


title: sample105_S155


title: sample104_S154


title: sample102_S152


title: sample125_S175


title: sample101_S151


title: sample103_S153


title: sample99_S149


title: sample100_S150


title: sample98_S148


title: sample97_S147


title: sample257_S307


title: sample95_S145


title: sample96_S146


title: sample94_S144


title: sample93_S143


title: sample116_S166


title: sample92_S142


title: sample90_S140


title: sample89_S139


title: sample114_S164


title: sample88_S138


title: sample106_S156


title: sample87_S137


title: sample84_S134


title: sample80_S130


title: sample83_S133


title: sample82_S132


title: sample78_S128


title: sample77_S127


title: sample79_S129


title: sample76_S126


title: sample81_S131


title: sample75_S125


title: sample73_S123


title: sample71_S121


title: sample72_S122


title: sample91_S141


title: sample70_S120


title: sample69_S119


title: sample74_S124


title: sample67_S117


title: sample61_S111

value: LIFRLow


title: sample65_S115


title: nPM_M4

city: San Diego

first: Amin

last: Haghani

address: 5510 Morehouse Dr

institute: Altos labs

data_processing:
Raw sequencing reads were quality checked with FastQC
adapter sequences were trimmed from the reads using Trimmomatic
Reads were aligned to the mm10 genome using the HISAT2 splice-aware aligner
alignments overlapping genes were counted using featureCounts version 1.5.0-p3 relative to Gencode version M11
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv files count values for each gene

source_name: Hippocampus

extract_protocol:
A random number of 5 young adults per sex of each group were selected for RNAseq analysis of hippocampus
Samples were homogenized and disrupted with pestles, 22-gauge needles, pipetting and QIA shredders (Qiagen #79654).  DNA was extracted using QIAzol (Qiagen #79306) from the organic layer for genotyping. RNA was extracted following the QIAGEN RNeasy plus universal protocol (Qiagen #73404). Extracted RNA was used to determine sex of mouse pups by qPCR for the Y-chromosome Sry gene.
RNA (600ng) was made into RNA-seq libraries using the Illumina RiboZero Gold library preparation kit and sequenced on an Illumina HiSeq 3000 sequencer at the Lieber Institute for Brain Development

treatment_protocol: Prenatal transcriptome changes of air pollution were examined by exposing pregnant C57BL/6 dams to 300 mg/m3 nano-sized particulate matter (nPM) for 5 hr/day, 3 days/weeks beginning at gestational day 2 until birth.

tag: Sex

value: M

value: Hippocampus

tag: treatment

value: nPM

tag: age (weeks)


title: sample66_S116

tag: mouse genotype

tag: cell type


title: sample63_S113

tag: infection time

tag: plate


title: nPM_M1


title: sample60_S110


title: sample59_S109


title: nPM_M2


title: sample64_S114


title: sample62_S112


title: nPM_M5


title: nPM_F4

value: F


title: nPM_M3


title: nPM_F5


title: nPM_F3


title: sample54_S104


title: nPM_F1


title: sample53_S103


title: sample212_S262


title: sample57_S107


title: sample56_S106


title: sample55_S105


title: sample52_S102


title: sample68_S118


title: sample58_S108


title: Ct_M5

value: Ctrl


title: Ct_M3


title: sample50_S100


title: Ct_M2


title: Ct_F5


title: sample51_S101


title: Ct_M1


title: Ct_F3


title: nPM_F2


title: bone marrow progenitors, dnmt1 mutant rep3 (EMSeq)

city: Freiburg im Breisgau

first: Thomas

last: Boehm

address: Stübeweg 51

department: Immunology

country: Germany

institute: MPI-IE Freiburg

description:
MUT3
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv

library_source: genomic

data_processing:
Library strategy: non-bisulfite EM-seq
Basecalling was performed with Illumina HiSeq Control Software/RTA version 2.7.6.
Raw sequencing reads were processed with the snakePipes version 1.2.0 WGBS workflow to produce bam files filtered for PCR duplicates, separately for reads obtained with each library preparation kit. The resulting bam files were merged per sample.
Merged bams from the previous step were processed with the snakePipes version 1.2.0 WGBS workflow using the –fromBam argument and providing a sample sheet. This produced a.o. a list of differentially methylated regions between the mutant and the wildtype sample groups filtered for FDR<2% and absolute methylation difference between groups of at least 20%.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated tables with methylation values aggregated over DMR intervals per sample are available, as well as tables with filtered hyper- and hypo-methylated DMRs annotated with statistical metrics and distance to nearest gene.

molecule: genomic DNA

source_name: lin- bone marrow progenitors

extract_protocol:
NEBNext Enzymatic Methyl-Seq
Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
0.5mg and 0.1mg of DNA was used for  library construction using the TruSeq DNA Methylation kit (Illumina) and the  NEBNext Enzymatic Methyl-Seq (NEB), respectively. The fragments were sequenced in paired-end 100bp mode .

value: BALB/c

value: lin- bone marrow progenitors


title: Ct_F4


title: sample49_S99


title: Ct_F2


title: Ct_F1


title: sample48_S98


title: Ct_M4


title: bone marrow progenitors, dnmt1 mutant rep1 (EMSeq)

description:
MUT1
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv


title: bone marrow progenitors, control rep1 (EMSeq)

description:
WT1
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv

value: wt


title: bone marrow progenitors, control rep2 (EMSeq)

description:
WT2
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv


title: sample46_S96


title: cultured cells, reprogrammed

city: Milan

first: Mario

last: Barilani

address: Via F. Sforza 35

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

description:
StemMACS culture medium
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
Rnase R-treated total RNA

hyb_protocol: The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Raw data worksheet reports Agilent Feature Extraction file. Matrix worksheet reports after data processing as reported above.

source_name: human induced pluripotent stem cells from human cord blood mesenchymal stem cells

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: RNA extraction was performed on samples deriving from 80% confluent cell cultures

extract_protocol: Trizol extraction. Total RNA from each sample was quantified using the NanoDrop ND-1000. Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: Steady state

value: hiPSC


title: bone marrow progenitors, dnmt1 mutant rep2 (TruSeqMeth)

description:
Mut2
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv

data_processing:
Basecalling was performed with Illumina HiSeq Control Software/RTA version 2.7.6.
Raw sequencing reads were processed with the snakePipes version 1.2.0 WGBS workflow to produce bam files filtered for PCR duplicates, separately for reads obtained with each library preparation kit. The resulting bam files were merged per sample.
Merged bams from the previous step were processed with the snakePipes version 1.2.0 WGBS workflow using the –fromBam argument and providing a sample sheet. This produced a.o. a list of differentially methylated regions between the mutant and the wildtype sample groups filtered for FDR<2% and absolute methylation difference between groups of at least 20%.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated tables with methylation values aggregated over DMR intervals per sample are available, as well as tables with filtered hyper- and hypo-methylated DMRs annotated with statistical metrics and distance to nearest gene.

extract_protocol:
TruSeq DNA Methylation kit
Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
0.5mg and 0.1mg of DNA was used for  library construction using the TruSeq DNA Methylation kit (Illumina) and the  NEBNext Enzymatic Methyl-Seq (NEB), respectively. The fragments were sequenced in paired-end 100bp mode .


title: sample45_S95


title: bone marrow progenitors, dnmt1 mutant rep2 (EMSeq)

description:
MUT2
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv


title: bone marrow progenitors, dnmt1 mutant rep1 (TruSeqMeth)

description:
Mut1
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv


title: bone marrow progenitors, control rep3 (TruSeqMeth)

description:
WT3
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv


title: sample43_S93


title: bone marrow progenitors, control rep2 (TruSeqMeth)


title: sample44_S94


title: bone marrow progenitors, control rep3 (EMSeq)


title: Gastrocnemius, Wildtype control

city: Kyoto

first: Yasutomi

last: Kamei

address: 1-5 Shimogamo-Hangicho, Sakyo-ku

institute: Kyoto Prefectural University

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-028005 Whole Mouse Genome Microarray 8 × 60K G4858A was used.

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner to detect Cy3 fluorescence.

data_processing: The scanned images were analyzed using Feature Extraction Software 9.5 (Agilent) with default parameters (protocol: GE1_1100_Jul11 and Grid: 028005_D_F_20150604) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction Software as Non-uniform outliers were excluded.

label_protocol: Cy3-labeled cRNA (1.65 μg) was mixed and fragmented according to the Agilent Technologies protocol.

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of control mice (25 weeks of age) and FOXO1 Tg mice (25 weeks of age). RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany). Samples from wild-type　(N=6) and FOXO1 Tg (N=5) mice were pooled before use.

value: gastrocnemius skeletal muscle

tag: gender

value: male

value: Wildtype control


title: sample42_S92

value: pDC

value: spleen


title: sample47_S97


title: bone marrow progenitors, control rep1 (TruSeqMeth)


title: sample41_S91


title: MPP4 dnmt1 mutant rep2

description:
Sequencing batch B
MPP4.counts.tsv [MUT981_P11]
DESeq2.results.MPP4.tsv

data_processing:
Basecalling was performed with Illumina HiSeq Control Software/RTA version 2.7.6.
Raw sequencing reads were processed with the snakePipes version 0.5 scRNAseq-mapcount workflow to produce a count table per sample. Read trimming was enabled, and annotation was filtered to remove entries with keywords “decay” or “pseudogene” in biotype description.
Postprocessing and differential gene expression analysis were performed in R version 3.4.0. Counts were normalized by downscaling to 200.000 transcripts per sample with RaceID3 package and rounded to integer counts. Outlier samples were removed. Differentially expressed genes were called between Dnmt1 mutant and wildtype replicates in each cell population separately, using R packages zingeR and DESeq2. Sequencing batch was not included in the model.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated tables with downsampled integer counts for retained samples per cell population, as well as tables with DESeq2 results of differential gene expression analysis are provided.

extract_protocol:
No RNA extraction was performed. Cells were sorted into the lysis and reaction buffer.
Libraries were constructed with the CellSeq2 protocol.

tag: population


title: MPP4 dnmt1 mutant rep4

description:
Sequencing batch C
MPP4.counts.tsv [MUT_1175_P11]
DESeq2.results.MPP4.tsv


title: bone marrow progenitors, dnmt1 mutant rep3 (TruSeqMeth)

description:
Mut3
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv


title: Gastrocnemius, FOXO1 transgenic

source_name: Gastrocnemius_FOXO1 Tg

value: FOXO1 transgenic


title: Vanillin_1

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

description: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

hyb_protocol: Fluorescent targets were hybridized to Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that pass aforementioned criteria were normalized by R program in the limma package.

source_name: Mice were treated topically with IMQ and/or orally with 100 mg/kg vanillin for 7 consecutive days.

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

treatment_protocol: Mice were treated daily with Vaseline cream (mock) or IMQ on the shaved dorsal skin for 7 consecutive days. In vanillin groups, mice were applied topically with IMQ and given orally with 100 mg/kg vanillin.

value: Female

value: Skin

value: IMQ and 100 mg/kg vanillin


title: MPP4 control rep4

description:
Sequencing batch C
MPP4.counts.tsv [WT_1171_P11]
DESeq2.results.MPP4.tsv


title: Vanillin_3

extract_protocol: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).


title: MPP4 control rep3

description:
Sequencing batch C
MPP4.counts.tsv [WT_1156_P11]
DESeq2.results.MPP4.tsv


title: sample40_S90

value: LIFRLow


title: MPP4 dnmt1 mutant rep1

description:
Sequencing batch A
MPP4.counts.tsv [MUT996_9]
DESeq2.results.MPP4.tsv


title: sample39_S89


title: MPP4 control rep2

description:
Sequencing batch B
MPP4.counts.tsv [WT984_P11]
DESeq2.results.MPP4.tsv


title: Vanillin_2


title: MPP1 dnmt1 mutant rep2

description:
Sequencing batch C
MPP1.counts.tsv [MUT_1175_P10]
DESeq2.results.MPP1.tsv


title: MPP1 dnmt1 mutant rep1

description:
Sequencing batch C
MPP1.counts.tsv [MUT_1159_P10]
DESeq2.results.MPP1.tsv


title: sample38_S88


title: sample37_S87


title: MPP1 control rep2

description:
Sequencing batch C
MPP1.counts.tsv [WT_1171_P10]
DESeq2.results.MPP1.tsv


title: IMQ_1

source_name: Mice were treated daily with IMQ on the shaved dorsal skin for 7 consecutive days.

value: IMQ


title: sample36_S86

value: LIFRHigh


title: Mock_3

source_name: Mice were treated daily with Vaseline cream on the shaved dorsal skin for 7 consecutive days.

value: vaseline


title: Mock_1

value: BALB/c


title: Mock_2


title: HSC dnmt1 mutant rep2

description:
Sequencing batch C
HSC.counts.tsv [MUT_1175_P9]
DESeq2.results.HSC.tsv

value: HSC


title: HSC dnmt1 mutant rep3

description:
Sequencing batch C
HSC.counts.tsv [MUT_1159_P9]
DESeq2.results.HSC.tsv


title: HSC dnmt1 mutant rep1

description:
Sequencing batch A
HSC.counts.tsv [MUT996_7]
DESeq2.results.HSC.tsv


title: sample35_S85


title: HSC control rep3

description:
Sequencing batch C
HSC.counts.tsv [WT_1171_P9]
DESeq2.results.HSC.tsv

value: wt


title: IMQ_3


title: MPP4 control rep1

description:
Sequencing batch A
MPP4.counts.tsv [WT990_3]
DESeq2.results.MPP4.tsv


title: HSC control rep2

description:
Sequencing batch C
HSC.counts.tsv [WT_1156_P9]
DESeq2.results.HSC.tsv


title: sample34_S84


title: sample33_S83


title: HSC control rep1

description:
Sequencing batch A
HSC.counts.tsv [WT990_1]
DESeq2.results.HSC.tsv


title: MPP4 dnmt1 mutant rep3

description:
Sequencing batch C
MPP4.counts.tsv [MUT_1159_P11]
DESeq2.results.MPP4.tsv


title: TW2.6

description: Cell Line Ref PMID: 17070096

data_processing:
For alignment: raw reads with good quality are mapped to human reference genomes (hg19) using Tophat (2.0.0).
For quantification: aligned reads were performed gene quantification by calculating the number of reads that are mapped to individual genes. The gene assembly and quantification in TPM values were computed using Cufflinks (2.1.1) based on associated gene annotation files of homo sapiens.
For gene fusion: paired end reads were processed to identify any that either contained or spanned a fusion junction. Encompassing paired reads refer to those in which each read aligns to an independent transcript, thereby encompassing the fusion junction. Spanning mate pairs refer to those in which one sequence read aligns to a gene and its paired-end spans the fusion junction. Both categories undergo a series of filtering steps to remove false positives before being merged together to generate the final chimera nominations. Detailed method can be found in pmid: 23558953 (Identification of targetable FGFR gene fusions in diverse cancers)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements (tpm) for each gene (n=21916) in each sample (n=7) (text document)

source_name: oral squamous cell carcinoma cells

growth_protocol: CGHNK2, CGHNK6, CGHNC8, and CGHNC9 [pmid#22318752], OC3 [pmid#14720193], OEC-M1 [pmid#3254744], TW2.6 [pmid#17070096] were cultivated in specified media as described in each original literature.

extract_protocol:
Total RNA was extracted from immortalized oral keratinocyates and oral cancer cells using Trizol reagent (Invitrogen), and further purified on RNeasy columns (QIAGEN) according to the manufacturer’s instructions. The quality of RNA was assessed with the Agilent Bioanalyzer 2100 using RNA Nano reagents (Agilent) to assure RIN>8.
Two rounds of polyA selection were performed using SeraMag oligo dT magnetic beads (SeraDyn) following the Illumina protocol. Transcriptome libraries from the mRNA fractions were generated following the RNA-SEQ protocol (Illumina) and size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN) with a gel melting temperature of 32oC. Libraries were quantified using the Bioanalyzer 2100 using the DNA 1000 protocol and reagents (Agilent). Each sample was sequenced in a single lane with the Illumina Genome Analyzer II (80 nucleotide read length).
stranded mRNA-Seq

treatment_protocol: not applicable

value: oral cancer

tag: origin

value: human oral cavity

tag: date

tag: machine

value: Illumina GAII

value: MCTP, University of Michigan, USA


title: MPP1 control rep1

description:
Sequencing batch C
MPP1.counts.tsv [WT_1156_P10]
DESeq2.results.MPP1.tsv


title: BMDM_ADP_rep3

city: Shanghai

first: Xiaoyu

last: Zhang

address: 500 Dongchuan Road

department: School of Life Sciences

institute: East China Normal University

description: Gene expression after 6hr ADP treatment in BMDMs

hyb_protocol: 1 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Microarrays 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C (Agilent) using one color scan setting for 8x60k array slides.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis.

source_name: BMDM, ADP, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using theTRIzol™ Reagent (Thermo Fisher Scientific) following the manufacturer's recommendations. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Murine bone marrow-derived macrophages were isolated and culturedin RPMI 1640 medium containing 10% FBS as well as 20% (v/v) L929-conditioned medium as a source of M-CSF, for 7 d with fresh medium that was changed every other day, and the cells were stimulated with 100μM ADP for 6 hours.

tag: tissue

value: Bone Marrow

value: bone marrow-derived macrophages (BMDM)

value: ADP


title: sample31_S81

value: pDC

value: spleen


title: OEC-M1

description: Cell Line Ref PMID: 3254744

tag: core lab


title: OC3

description: Cell Line Ref PMID: 14720193


title: sample30_S80


title: BMDM_ADP_rep2

source_name: BMDM, ADP, replicate 2

tag: strain


title: BMDM_CON_rep3

description: Gene expression after 6hr control treatment in BMDMs

source_name: BMDM, CON, replicate 3

value: control


title: CGHNC9

description: Cell Line Ref PMID: 22318752


title: sample29_S79


title: BMDM_CON_rep1

source_name: BMDM, CON, replicate 1


title: BMDM_ADP_rep1

source_name: BMDM, ADP, replicate 1


title: BMDM_CON_rep2

source_name: BMDM, CON, replicate 2


title: CGHNC8

description: Cell Line Ref PMID: 22318752


title: sample28_S78


title: sample32_S82


title: IMQ_2

description: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

value: Female

value: Skin


title: CGHNK6

description: Cell Line Ref PMID: 22318752

source_name: immortalized oral keratinocytes

value: grossly normal oral mucosa


title: sample26_S76

value: LIFRHigh


title: CGHNK2

description: Cell Line Ref PMID: 22318752


title: WAT_C-group5

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

hyb_protocol: cRNA 15µg were flagmentated, and hybridized for 16hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized using the statistical software R, and the qFARMS method.

organism: Rattus norvegicus

source_name: WAT_Control diet

label_protocol: Biotin-labeled cRNA was synthesized from 100ng total RNA according to the manufacture's protocol.

growth_protocol: The rats had paired feeding (control- or noodle-diet at about 60 g diet/kg BW x day) with water provided ad libitum for 4 weeks, and were kept in a 12 hour light/dark cycle.

extract_protocol: Total RNA was extracted from the brain sample using TRIzol Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol. The extracted total RNA was cleaned up with RNeasy Mini Kit (QIAGEN).

treatment_protocol: We fed rats a diet containing 30 wt.% instant noodle with a 26% fat-to-energy ratio for 30 days.

value: male

tag: age

value: 13 weeks old

tag: diet

value: control diet

value: WAT


title: WAT_C-group14


title: WAT_N-group4

source_name: WAT_Noodle diet

value: Noodle diet


title: WAT_C-group2


title: WAT_C-group8


title: WAT_N-group13


title: WAT_C-group11


title: Liver_C-group11

source_name: Liver_Control diet

value: liver


title: sample25_S75

source_name: splenic plasmacytoid dendritic cells


title: WAT_N-group10


title: Liver_C-group14


title: sample23_S73


title: sample24_S74


title: sample27_S77


title: WAT_N-group1


title: WAT_N-group7


title: Liver_C-group5


title: sample22_S72


title: Liver_C-group8


title: Liver_C-group2


title: Liver_N-group1

source_name: Liver_Noodle diet


title: Liver_N-group13


title: Liver_N-group7


title: Liver_N-group10


title: Liver_N-group4


title: hypothalamus_C-group11

source_name: hypothalamus_Control diet

value: hypothalamus


title: sample21_S71


title: sample20_S70


title: hypothalamus_C-group8


title: sample18_S68


title: hypothalamus_C-group2


title: hypothalamus_C-group14


title: sample17_S67


title: sample16_S66


title: sample14_S64


title: sample13_S63


title: sample19_S69


title: sample15_S65


title: hypothalamus_N-group13

source_name: hypothalamus_Noodle diet


title: sample12_S62

value: LIFRLow


title: sample11_S61


title: hypothalamus_N-group7


title: IN_CD86+YFP+, rep2

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G at a resolution of 0.7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. The data were RMA normalized in R and Bioconductor, using the oligo package.

source_name: Spleen

label_protocol: 3 to 20 ng of total RNA from each sample was used to synthesize biotinylated probes, using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit, according to NuGEN recommendations, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from sorted cells  with the Qiagen RNeasy PLUS Micro Kit, according to the manufacturer protocol.

treatment_protocol: Mice were untreated or infected for 1.5 days with a salivary gland stock of the Smith strain of MCMV that was administred through intraperitoneal injection.

tag: lineage

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high) CD86(pos)YFP(pos)

value: WT CD45.1 pDC

tag: mice

value: CD45.1 WT:CD45.2 Ifnar1-KO MBMC

value: d1.5 MCMV-infected


title: IN_CD86+YFP+, rep1

value: WT CD45.2 pDC

tag: treatment


title: IN_CD86+YFP-, rep2

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high) CD86(pos)YFP(neg)


title: hypothalamus_N-group1


title: IN_CD86-YFP-, rep2

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high) CD86(neg)YFP(neg)


title: hypothalamus_C-group5


title: IN_CD86+YFP-, rep1

value: Ifnar1-KO CD45.2 pDC


title: IN_CD86-YFP-, rep1


title: UN_CD86+YFP-, rep1

value: Uninfected


title: sample10_S60

tag: mouse genotype

value: pDC

value: spleen


title: sample9_S59

tag: cell type


title: CD49a+ hepatic NK cells

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

description: Whole Human Genome Microarray 4x44K

hyb_protocol: Gene ExpressionEach slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructionsHybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US),

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US)settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction

source_name: CD49+ hepatic NK cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,OneOne -Color(Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US)

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).


title: CD49a- hepatic NK cells

description: Whole Human Genome Microarray 4x44K

source_name: CD49- hepatic NK cells


title: sample8_S58

tag: infection time


title: UN_CD86-YFP-, rep2


title: hypothalamus_N-group4

value: male

value: 13 weeks old


title: GMSA_073_Vagina_Placebo

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

hyb_protocol: Standard as recommended by Illumina, except that the temperature was 48C

scan_protocol: Standard Illumina protocol using Illumina iScan system

data_processing:
The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.
Matrix normalized table: This table contains detection p-values and signal intensity data that were transformed with a variance stabilizing transformation and normalized with a robust spline normalization using the Bioconductor lumi package (version 2.34.0). The normalized data was filtered to only include probes with a detection threshold p value <0.05 in at least 10 samples. Matrix non-normalized table: This table contains raw signal intensity values and detection p-values for each sample.

source_name: Vagina from GMSA_073 treated with Placebo

label_protocol: 50 ng of total RNA was labeled using the Ovation PicoSL WTA System V2 kit and the Encore BiotinIL kit (both NuGEN)

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit

tag: ptid

tag: visit

tag: collectiondate

value: Vagina

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: oral

tag: birthcontrollab

value: NonDecided

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive

tag: rin

tag: inclusion

value: Included

tag: paired

value: Unpaired


title: sample7_S57

tag: mouse genotype

tag: cell type

tag: tissue

tag: infection time

value: LIFRLow

tag: plate


title: GMSA_072_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_072 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

value: Paired


title: GMSA_075_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_075 treated with TDF-OffTreatment

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: implant

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

value: unknown

tag: rin


title: GMSA_071_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_071 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

tag: tissue

value: Vagina

value: B

value: FTC/TDF

tag: inclusion

tag: paired


title: sample6_S56

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: plate


title: GMSA_074_Vagina_Placebo

source_name: Vagina from GMSA_074 treated with Placebo

tag: collectiondate

tag: age

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

value: NoHC


title: UN_CD86-YFP-, rep1

tag: lineage

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high) CD86(neg)YFP(neg)

value: WT CD45.2 pDC

tag: mice

value: CD45.1 WT:CD45.2 Ifnar1-KO MBMC

tag: treatment

value: Uninfected


title: UN_CD86+YFP-, rep2

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high) CD86(pos)YFP(neg)

value: WT CD45.1 pDC