title: MASK2

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
The Space Ranger software pipeline (version 1.0.0) provided by 10×Genomics was used to process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads using the STAR aligner, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.1).
We first normalized the data with sctransformin order to account for variance in sequencing depth across data points, detecting high-variance features, and stores the data in the SCT assay.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: tumor

growth_protocol: 4-week-old C57BL/6 mice was subcutaneously inoculated with B16-F10-Luciferase cells

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

treatment_protocol: C57BL/6 mice subcutaneously inoculated with B16-F10-Luciferase cells were randomly divided into two groups: PBS and MASK. Magnet processing group according to the previous method. Sample MASK1 was collected on the 7 days after MASK vaccine treatment,  Sample MASK2 was collected on the 13 days after MASK vaccine treatment. After the treatment periods, tumor samples were collected, and spatial transcriptomics was performed.

value: tumor

value: melanoma

value: MASK vaccine

tag: time point

value: 13 days


title: Relapse_2

status: Public on Dec 01 2023

type: SRA

city: Erlangen

first: Mathias

last: Linnerbauer

address: Schwabachanlage 6

department: Neurology

country: Germany

institute: University Hospital Erlangen

library_source: transcriptomic

data_processing:
Filtering: This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:    1) Remove the reads containing the adaptor(adaptor pollution);    2) Remove reads whose N content is greater than 5%;    3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).    The filtered "Clean Reads" are saved in FASTQ format. Software Information    SOAPnuke:    Version v1.5.2    Parameters -l 15 -q 0.2 -n 0.05    Official Websitehttps://github.com/BGI-flexlab/SOAPnuke    References    [1]Cock P., et al.(2010). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38(6): 1767-1771.
Alignment: Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) is software for mapping RNA-seq reads. Software Information    HISAT2:    Version：v2.0.4    Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8    Official Website：http://www.ccb.jhu.edu/software/hisat    References：    [1] Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357-360 (2015). Bowtie2 was used to get the alignment result.
Assembly: Mus_musculus_NCBI_GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited file includes normalized count values

molecule: total RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Mice were perfused with cold 1× PBS and the CNS was isolated and mechanically diced using sterile razors. Cortices were transferred into 5 ml of enzyme digestion solution consisting of 35.5 µl papain suspension (Worthington, #LS003126) diluted in enzyme stock solution (ESS) and equilibrated to 37 °C. ESS consisted of 10 ml 10× EBSS (Sigma-Aldrich, #E7510), 2.4 ml 30% D(+)-glucose (Sigma-Aldrich, #G8769), 5.2 ml 1 M NaHCO3 (VWR, #AAJ62495-AP), 200 µl 500 mM EDTA (Thermo Fisher Scientific, #15575020), and 168.2 ml ddH2O, filter-sterilized through a 0.22-µm filter. Samples were shaken at 80 rpm for 30–40 min at 37 °C. Enzymatic digestion was stopped with 1 ml of 10× hi ovomucoid inhibitor solution and 20 µl 0.4% DNase (Worthington, #LS002007) diluted in 10 ml inhibitor stock solution (ISS). 10× hi ovomucoid inhibitor stock solution contained 300 mg BSA (Sigma-Aldrich, #A8806) and 300 mg ovomucoid trypsin inhibitor (Worthington, #LS003086) diluted in 10 ml 1× PBS and filter sterilized using a 0.22-µm filter. ISS contained 50 ml 10× EBSS (Sigma-Aldrich, #E7510), 6 ml 30% D(+)-glucose (Sigma-Aldrich, #G8769), and 13 ml 1 M NaHCO3 (VWR, #AAJ62495-AP) diluted in 170.4 ml ddH2O and filter-sterilized through a 0.22-µm filter. Tissue was mechanically dissociated using a 5-ml serological pipette and filtered through a 70-µm cell strainer (Fisher Scientific, #22363548) into a fresh 50-ml conical tube. Tissue was centrifuged at 600g for 5 min and resuspended in 10 ml of 30% Percoll solution (9 ml Percoll (GE Healthcare Biosciences, #17-5445-01), 3 ml 10× PBS, 18 ml ddH2O). Percoll suspension was centrifuged at 600g for 25 min with no breaks. Supernatant was discarded and the cell pellet was washed once with 1× PBS, centrifuged at 500g for 5 min and prepared for downstream applications. Astrocytes were isolated using the Anti-ACSA-2 MicroBead Kit (Miltenyi, #130-097-678) and the pellets flash frozen in liquid nitrogen.
RNA isolation, and library preparation using Single Primer Isothermal Amplification (SPIA) was performed by BGI Tech Solutions.
Library preparation using Single Primer Isothermal Amplification (SPIA) and library pooling was performed by BGI Tech Solutions.

tag: tissue

value: cortex

tag: cell type

value: ACSA2 astrocyte

tag: genotype

value: wild type

tag: strain background

value: late stage worsening of EAE


title: Relapse_1


title: MASK1

country: China

tag: cell line

tag: strain

tag: treatment

value: 7 days


title: Control

value: PBS


title: Relapse_3


title: Peak_3

value: peak of EAE


title: Peak_2


title: Peak_1


title: Dictyostelium discoideum, Inoculum, Biol rep. 4

city: Geneva

first: Thierry

last: Soldati

address: 30 quai Ernest Ansermet, Sciences II

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
Quality control, alignment with Bowtie2, filtering out of non-transposon reads, PCR amplicon deduplication
Evaluation of TA sites & TA sites within annotated genes with TRANSIT HMM (default parameters); Hierarchical clustering of gene profiles (Manhattan distance, ward.D linkage)
Comparison of insertion frequency per gene to the reference condition using the TRANSIT resampling methods
Overrepresentation analysis with the GO and KEGG database with R
Assembly: NC_010612.1, NC_010604.1
Supplementary files format and content: FileS1.pdf, contains key parameters of all analyzed genes such as insertion sites, number, essentiality call, profile across experimental conditions
Supplementary files format and content: Table_S1_transposons_counts_per_Tasite.xlsb, contains information about insertion sites
Supplementary files format and content: Table_S2_Counts_per_gene.xlsx, contains information about insertion sites per gene
Supplementary files format and content: Table_S3_Conditional_essentiality.xlsx, contains information from the TRANSIT resampling method, comparisons of experimental conditions to the reference condition
Supplementary files format and content: Table_S4_Enrichment_analyses.xlsx, contains information about GO and KEGG enrichment analyses
Library strategy: Tn-Seq

molecule: genomic DNA

organism: Mycobacterium marinum

source_name: Mycobacterium marinum M strain

extract_protocol:
M. marinum gDNA was extracted following an adapted protocol from Belisle et Sonnenberg (Belisle & Sonnenberg, 1998). Briefly, M. marinum mutant pools were centrifuged and resuspended in breaking buffer (50 mM Tris, 10 mM EDTA, 100 mM NaCl, pH8). Mechanical lysis was performed with the Fastprep homogenizer during 30 s, this step was repeated three times. The upper phase was chemically lysed with RNase (200 µg/mL) and Lysozyme (100 µg/mL) 1h at 37°C. Then, 0.1 volume of SDS 10% and 0.01 volume of Proteinase K (100 µg/mL) were added for 1 h at 55°C.  Extraction steps were realized with equal volume of phenol:chlorophorm:isopropanol 25:24:1 for 30 min followed by chlorophorm:isopropanol during 5 min.  Precipitation was performed with 3 M sodium acetate pH 5.2 and 1 volume of isopropanol 100 %, gDNA was pelleted and washed with ethanol 70%. The extracted gDNA was quantified using Qubit (Invitrogen) and its quality was checked with the TapeStation system (Agilent).
A 2 µg aliquot of gDNA in Tris Buffer (10 mM Tris, 0.1 mM EDTA, pH8) was sheared in a Covaris S2 machine following these parameters: Intensity 4, Duty cycle 10%, cycles 200 and time 65 s. After purification with AMPure XP purification kit (Agencourt), 1000 ng of sheared DNA fragment ends were repaired, blunt ended and a d-A Tail added following NEBNextEnd/d A-Tailing module protocol. Specific adapters 1 and 2 described in Table B were self-hybridized and then ligated to the ‘A’ tail ends by T4 ligase (Promega). After purification with AMPure XP purification kit (Agencourt), 40 ng of libraries were amplified by PCR using KAPA polymerase with the following parameters: 95°C 3 min; 98°C 20 s, 60°C 15 s, 72°C 15 s (repeated for 25 cycles); 72°C 1 min for elongation. Transposon junctions were amplified with the IS6 primer: 5’ CAAGCAGAAGACGGCATACGA 3’ and specific primers MarA to MarP described in Table B. PCR products were purified with AMPure XP purification kit and Sixteen-plexed samples were pooled in approximately equimolar amounts of 5 nM and run in a single and double index reads on a Hiseq 4000 (Illumina).

value: Mycobacterium marinum M strain

tag: biological replicate

tag: sample condition

value: Inoculum

tag: passaged in

value: Dictyostelium discoideum


title: Dictyostelium discoideum, Inoculum, Biol rep. 2


title: N2 sqd-1 RNAi rep 3

city: BLOOMINGTON

first: Emily

middle: Ann

last: Erdmann

state: IN

address: 1001 E Third Street

department: Biology

country: USA

institute: Indiana University

data_processing:
Reads were aligned to C. elegans reference genome using STAR (v.2.7.10b)
Differential gene expression analysis was performed using Feature counts and DeSeq2
Assembly: C. elegans WS275
Supplementary files format and content: .csv files include DeSeq2 analysis with normalized read counts

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Embryos were hatched on NGM plates seeded with RNAi vectors and allowed to develop 72 hrs

extract_protocol:
Worms were collected in Trizol (Invitogen) and purified using TURBO Dnase(Ambion) followed by Rneasy extraction kit (Qiagen)
Poly-A selected mRNA library preparation was done using KAPA HyperPrep stranded library preparation kit

value: Whole worm

tag: developmental stage

value: Young Adult

value: Wildtype

value: sqd-1 RNAi


title: N2 sqd-1 RNAi rep 2


title: N2 ctrl RNAi rep 3

value: empty vector RNAi


title: adr-2(-) ctrl RNAi rep 1


title: adr-2(-) sqd-1 RNAi rep 2


title: adr-2(-) sqd-1 RNAi rep 3


title: adr-2(-) ctrl RNAi rep 3


title: adr-2(-) sqd-1 RNAi rep 1


title: N2 sqd-1 RNAi rep 1


title: B.thetaiotaomicron, corn fiber, R2

city: JOUY EN JOSAS

first: paul

last: Biscarrat

state: ile de france

address: 4 AVENUE JEAN JAURES-DOMAINE VILVERT

country: France

institute: INRAE

description:
BT_M_R2
counts_BT.csv
BT_fibre_mais_vs_controle1_DESeq_results.csv

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 3.2 (adapter trimming)
FastQC v0.11.5 (quality control)
Assembly: B.xylanisolvens:NZ_JH724294,NZ_JH724295,NZ_JH724296,NZ_JH724297,NZ_JH724298,NZ_JH724299,NZ_JH724300,NZ_JH724301,NZ_JH724302,NZ_JH724303,NZ_JH724304,NZ_JH724305,NZ_JH724306/B;thetaiotaomicron:NC_004663.1/R.intestinalis:NZ_LR027880.1/S.variabile:NZ_GG704769,NZ_GG704770,NZ_GG704771,NZ_GG704772,NZ_GG704773,NZ_GG704774,NZ_GG704775,NZ_GG704776,NZ_GG704777,NZ_GG704778,NZ_GG704779
Supplementary files format and content: Table xxxx_DESeq_results.csv contains the raw, unfiltered results. There is one gene per row and in columns the metrics calculated by DEseq2 during the analysis: ID: gene name//baseMean: average of normalized counts for all samples/replicates involved in the comparison/log2FoldChange: log2 of the ratio of counts between the 2 conditions/lfcSE: standard error of this fold change/stat: the value of the statistical (Wald) test, used to calculate the pvalue. It is the ratio between log2FoldChange and lfcSE./pvalue: This value determines the significance of the statistical value or test. It indicates the probability that an observed fold change could be due to chance. The closer the p-value is to 0, the more significant the test, and the more real the differential in expression observed between the 2 conditions./- padj: adjusted (or corrected) pvalue, which takes into account multiple tests. As the statistical test is performed on each gene and each test is associated with a possible error, accumulating tests increases this error. We need to take this into account and make a correction for the number of tests performed. DEseq2 uses the Benjamini-Hochberg method./- then normalized counts for the samples involved in the comparison

organism: Bacteroides thetaiotaomicron

source_name: Bacteria

growth_protocol: Bacteria were cultured in Hungate tubes with a containing 90 % N2, 5 % CO2, 5 % H2 atmosphere. Cultures were performed in a minimum medium adapted from YCFA medium supplemented with 0.5 % or 0.1% carbohydrate. Cultures were stopped 12 h after inoculation.

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen)
Directional RNA-Seq Libraries were constructed using the TruSeq Stranded Total RNA library prep kit, with bacteria Ribo-Zero reagents (Illumina), following the manufacturer’s instructions. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.
Libraries were pooled in equimolar proportions and sequenced on a single read 75pb run, on an Illumina NextSeq500 instrument.

value: Bacteria

value: Corn Fiber


title: N2 ctrl RNAi rep 2


title: N2 ctrl RNAi rep 1


title: WT_b_noglu

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University

data_processing:
Merged FASTQ files for samples that were loaded onto multiple lanes of a given flowcell, respecting read pair assignment. Ex) cat *_L001_R1_001.fastq.gz *_L002_R1_001.fastq.gz
Adapter sequences were removed with Trim_galore! 0.4.3, cutadapt 2.3, and and sample quality assessed with FastQC 0.11.7 using default parameters.
Reads were aligned to the Haloferax volcanii DS2 reference genome (GCA_000025685.1, accessed 2023-09-11) with Bowtie2 2.3.5.1. Alignment by Bowtie2 required stand-specific read orientation for libraries constructed in the 2021 experiment. Only pairs aligning concordantly in the --rf orientation were considered.
Aligned sequence files were converted to binary format, sorted, and indexed using samtools 1.10.
Reads (for samples from 2019) or read paris (2021 samples) aligning to ORFs were counted using featureCounts 2.0.1 with arguments -p -B -s 2 and the DS2 reference genome  annotation (GCA_000025685.1, accessed 2023-09-11). For 2021 samples, fragments were required to align concordantly in the correct strand orientation (reverse) to be tallied.
In R, counts from 2019 and 2021 experiments were normalized relative to library size and batch corrected with DeSeq2 1.34.0. Pairwise correlations were computed using normalized counts for samples within each genotype+condition group, and samples with average R < 0.7  were considered outliers and were not used in downstream analyses.
Assembly: GCA_000025685.1
Supplementary files format and content: Text file of fragments mapping to genes. Each column is a sample, and rows are counts mapping to a given gene.

organism: Haloferax volcanii DS2

source_name: H26 ∆pyrE2

growth_protocol: Four single colonies of DF60 and ASK133 or AKS319 from 10-day old plates were inoculated in 5 mL YPC23 medium supplemented with 0.1% glucose and grown aerobically (250 rpm shaking) at 37C to stationary phase (optical density at 600nm ~ 4). Cells were washed twice with Hh-CA medium without glucose and transferred into fresh 50 mL Hh-CA with or without 0.1\% glucose at an initial optical density of ~ 0.4. After 24 hours cultures were collected and flash frozen with liquid nitrogen.

extract_protocol:
After 24 hours storage in -80C, RNA was extracted from cell pellets using Absolutely RNA Miniprep kit (Agilent Technologies, Santa Clara, CA).  For all samples, the absence of DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR and total RNA was quantified using Agilent Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Santa Clara, CA). For 2019 samples,  ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit (now discontinued, Illumina, San Diego, CA). For 2021 samples, extraction was followed by additional DNAse treatment with Turbo DNAse (Invitrogen), and ribosomal RNA was removed from total RNA with the PanArchaea riboPOOL kit according to the manufacturer protocol (siTOOLs Biotech, Germany) and checked for depletion using Agilent Bioanalyzer RNA Nano 6000 chip as described as described in Pastor et al. 2022.
For 2019 samples, rRNA-depleted RNA was used to construct the sequencing libraries with KAPA Stranded RNA-seq Library preparation (Kapa Biosystems) following manufacturer protocol. Fragment size of final libraries was measured using Agilent Bioanalyzer DNA 1000 chip and then pooled and sequenced on Illumina HiSeq4000 at the Duke Sequencing and Genomic Technologies Core Facility at Duke University (Durham, NC). For 2021 samples, sequencing libraries were constructed with NEBNext UltraII Directional RNA Library Preparation Kit (New England BioLabs, #E7760). The fragment size of all libraries was measured using Agilent Bioanalyzer DNA 1000 chip and then pooled and sequenced on NovaSeq6000 at the Center for Genomic and Computational Biology at Duke University (Durham, NC).

value: H26 {delta}pyrE2

value: archaeal cell culture

value: HvCA + uracil

tag: time

tag: year-flowcell


title: WT_c_glu

value: HvCA + uracil + 0.1% glucose (w/v)


title: WT_d_noglu


title: WT_d_glu


title: WT_glu_2


title: WT_glu_4


title: tbsP_glu_2

source_name: H26 ∆pyrE2∆tbsP (HVO_2861)

value: H26 {delta}pyrE2{delta}tbsP (HVO_2861)


title: WT_b_glu


title: adr-2(-) ctrl RNAi rep 2


title: WT_a_glu


title: trmB_b_noglu

source_name: H26 ∆pyrE2∆trmB

value: H26 {delta}pyrE2{delta}trmB


title: trmB_a_glu


title: trmB_c_noglu


title: Dictyostelium discoideum, Inoculum, Biol rep. 1


title: WT_a_noglu


title: tbsP_b_noglu


title: tbsP_e_noglu


title: tbsP_c_glu


title: tbsP_d_noglu


title: tbsP_d_glu


title: deltadelta_a_noglu

source_name: H26 ∆pyrE2∆trmB∆tbsP

value: H26 {delta}pyrE2{delta}trmB{delta}tbsP


title: tbsP_b_glu


title: tbsP_c_noglu


title: tbsP_a_glu


title: tbsP_a_noglu


title: trmB_a_noglu


title: deltadelta_d_noglu


title: deltadelta_c_glu


title: deltadelta_d_glu


title: deltadelta_b_glu


title: deltadelta_b_noglu


title: R1wtDnmt1 neurons

type: genomic

city: Hyderabad

first: Sumana

last: Choudhury

address: Dept of Biological Sciences

country: India

institute: Birla Institute of Technology and Sciences

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium mouse methylation Beadchip using standard Illumina protocol

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

data_processing: Standard Illumina software

label: Cy5 and Cy3

source_name: transgenic wild-type DNMT1 expressing neurons

label_protocol: Standard Illumina Protocol

growth_protocol: ESCs (mESCs) were grown in ESC medium (Knockout DMEM/F12: ThermoFisher, Cat. no. 12660012; 15% ESC-grade fetal bovine serum: HiMedia, Cat. no. RM10435; 1X Glutamax: ThermoFisher, Cat. no. 35050061; 1X Antibiotic/Antimycotic: HiMedia, Cat. no. A002A; 1X Non-Essential Amino Acids: ThermoFisher, Cat. no. 11140050, 1X β-Mercaptoethanol: ThermoFisher, Cat. no. 21985023 and 1X Leukemia Inhibitory Factor: a gift from Dr. Chandrasekhar’s lab, CCMB-Hyderabad). The ESCs were plated at a density of 50,000 cells/cm2 in a tissue culture treated dish coated with 0.1% sterile gelatin (Sigma, Cat. no. G1890). After reaching confluence, the ESCs were treated with 1X Trypsin-EDTA solution (HiMedia, Cat. no. TCL034) for further passaging. ESCs were differentiated into embryoid bodies in non adherent dishes with ESC medium without LIF and then in neural stem cell media (Knockout DMEM/F12: ThermoFisher, Cat. no. 12660012 with 1X Antibiotic/Antimycotic: HiMedia, Cat. no. A002A; 20ng/ml of basic fibroblast growth factor (bFGF): ThermoFisher, Cat. no. PHG0261; 20 ng/ml epidermal growth factor (EGF): ThermoFisher, Cat. no. PHG0315; 2% StemProTM Neural Supplement: ThermoFisher, Cat. no. A1050801; 6 units/ml Heparin Solution: STEMCELL Technologies, Cat. no. 07980; 200 mM Ascorbic acid: Merck, Cat. no. A8960 and 1X Glutamax) for a week with media changes on alternate days. One day prior to differentiation, adherent tissue culture dishes were coated with 20 µg/ml laminin (ThermoFisher, Cat. no. 23017015) in DMEM high glucose medium (HiMedia, Cat. no. AL007A) with 1X Antibiotic/Antimycotic. The resultant neurospheres were plated in the laminin coated dishes in presence of NDiff-227 (Takara Bio, Cat. no. Y40002), 1X CultureOne® Supplement (ThermoFisher, Cat. no. A3320201) and 1X Antibiotic/Antimycotic media to induce neuronal differentiation. Half of the differentiation media were replenished every alternate day for a total of 10 days. At the end of 10 days, well-differentiated neurons were obtained.

extract_protocol: Genomic DNA was extracted and purified from ESC and neuron samples using Qiagen AllPrep DNA/RNA Kit according to standard instructions

tag: gender

value: male

value: Differentiated neurons

value: transgenic wild-type DNMT1 expressing


title: R1wtDnmt1 mESC

source_name: transgenic wild-type DNMT1 overexpressing mESC

value: embryonic stem cells


title: R1 mESC

source_name: wild-type mESC

value: wild-type


title: R1Dnmt1Y495C mESC

source_name: transgenic mutant Y495C DNMT1 overexpressing mESC


title: trmB_c_glu


title: UBQ10::mCherry-GR-WUS,Dex,Input,Rep2

city: Heidelberg

first: Jian

last: Zeng

address: Im Neuenheimer Feld 230

department: Department of Stem Cell Biology

institute: Heidelberg University

data_processing:
Quality control: FastQC
Mapping: Burrow-Wheeler Aligner
Peak Calling: MACS2
Assembly: Assembly: TAIR10
Supplementary files format and content: BigWig files include reads coverage for each Sample

organism: Arabidopsis thaliana

source_name: 7 DAG seedlings

growth_protocol: 21°C; 65% humidity; 16h light/8h dark

extract_protocol:
Seedlings were fixed with 1% formaldehyde for 15 min. After quenching and cell lysis, chromatin was sonicated using a BioRad solicator.
Libraries were generated using a kit.

treatment_protocol: 1/2 MS with and without 10uM Dex,  4 hours

value: 7 DAG seedlings

tag: ecotype

value: pUBI10::mCherry-GR-linker-WUS (WUS-GR)

value: Dex 4h


title: UBQ10::mCherry-GR-WUS,Dex,Input,Rep1


title: ap1/cal,SNP,Rep3 [S12]

data_processing:
Quality control: FastQC
Read alignment: STAR
DEG calling: DESeq2
Assembly: Assembly: TAIR10
Supplementary files format and content: text files include raw counts values for each Sample

extract_protocol:
RNAeasy plant mini kit according to manufacturer instructions (Qiagen, Hilden, Germany)
The RNA were poly A selected using the NEB Poly (A) Magnetic isolation module (7490), then the NEBnext Ultra Direction RNA Prep Kit (E7420) for Illumina with the NEBnext Multiplex Oligo's for Illumina (E7335). For RNA 1 µg input was used.

treatment_protocol: 1/2 MS plates with and without 1mM SNP, 24 hours

value: 1mM SNP 24h


title: Col-0,Mock,Rep3 [S3]

value: Mock 24h


title: UBQ10::mCherry-GR,Dex,eChIP,Rep1


title: Col-0,SNP,Rep3 [S6]


title: UBQ10::mCherry-GR-WUS,Dex,eChIP,Rep1


title: Col-0,SNP,Rep2 [S5]


title: ap1/cal,Mock,Rep2 [S8]


title: R1Dnmt1Y495C neurons

source_name: transgenic mutant Y495C DNMT1 expressing neurons


title: R1 neurons

source_name: wild-type neurons


title: UBQ10::mCherry-GR,Dex,Input,Rep1


title: ap1/cal,Mock,Rep3 [S9]


title: ap1/cal,SNP,Rep2 [S11]


title: ap1/cal,Mock,Rep1 [S7]


title: ap1/cal,SNP,Rep1 [S10]


title: Col-0,SNP,Rep1 [S4]


title: deltadelta_a_glu


title: Col-0,Mock,Rep2 [S2]


title: UBQ10::mCherry-GR-WUS,Dex,eChIP,Rep2


title: ubp5_4

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
In our sequencing strategy, read 21nt R1 of pooled library contains two parts of UMI splitted by barcode. We move UMI sequences to be next to each other and remove additional nucleotide. For this we use awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq file for read 55 nt R2 of pooled library was demultiplexed into separate fastq files for each replica using BRBseqTools (v 1.6) and R1. Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each library was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 54 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

source_name: seedlings

growth_protocol: Seeds were imbibed at 4 degree celsius on MS medium agar plates for 3 days  and then transferred to long day conditions. Seedlings were collected 12 days after germination and frozen for RNA isolation.

extract_protocol:
Total RNA was isolated using E.Z.N.A. Plant RNA Kit (OMEGA biotek) following manufacturer instructions.
500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. cDNA pool was purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reaction was purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reaction was mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, sample was purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reaction with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Library was Illumina Nova-seq sequenced to obtain two reads: R1 (contain barcode and UMI) and R2 (contain mRNA sequence).

value: seedlings

tag: age

value: 12 DAG


title: ubp5_3


title: Col-0,Mock,Rep1 [S1]


title: ubp5_1


title: Col0_3


title: Col0_4


title: Col0_1


title: B.xylanisolvens, inulin, R3

description:
BX_I_R3
counts_BX.csv
BX_inuline_vs_controle2_DESeq_results.csv

organism: Bacteroides xylanisolvens

value: Bacteria

value: Inulin


title: B.xylanisolvens, corn fiber, R3

description:
BX_M_R3
counts_BX.csv
BX_fibre_mais_vs_controle2_DESeq_results.csv

value: Corn Fiber


title: B.xylanisolvens, inulin, R1

description:
BX_I_R1
counts_BX.csv
BX_inuline_vs_controle2_DESeq_results.csv


title: B.xylanisolvens, inulin, R2

description:
BX_I_R2
counts_BX.csv
BX_inuline_vs_controle2_DESeq_results.csv


title: B.xylanisolvens, glucose, R3

description:
BX_G_R3
counts_BX.csv

value: Glucose


title: Sample09, Pt : Edge

type: RNA

city: San Francisco

first: Saket

last: Jain

state: CA

address: 1450 3rd Street, HD 415

institute: University of California San Francisco

hyb_protocol: RNA (100 ng) was used for the Metabolic Pathways Panel. RNA from each sample was hybridized with the codeset for 18 hours, and 30 μL of the reaction was loaded into the nCounter cartridge and run on  the nCounter SPRINT Profiler.

data_processing: Raw RCC files were processed using nanostring Nsolver software to generate the Raw counts. These raw counts were used to perform a differential gene expression analysis between groups using the DESeq2 algorithm in R

organism: Homo sapiens

source_name: Glioblastoma

extract_protocol: RNA was extracted using RNAeasy mini kit by qiagen as per the manufractures protocol

value: Glioblastoma patient tissue

tag: sample type

value: Pt :Edge


title: B.xylanisolvens, corn fiber, R2

description:
BX_M_R2
counts_BX.csv
BX_fibre_mais_vs_controle2_DESeq_results.csv


title: B.xylanisolvens, glucose, R2

description:
BX_G_R2
counts_BX.csv


title: Sample10, Pt : Core

tag: tissue

value: Pt :Core


title: ubp5_2


title: Sample07, Pt : Edge


title: B.xylanisolvens, corn fiber, R1

description:
BX_M_R1
counts_BX.csv
BX_fibre_mais_vs_controle2_DESeq_results.csv

tag: cell type


title: Sample06, Device : Core

value: Glioblastoma GBM43 cell line

value: 3d invasion model

value: Device :Core


title: Sample12, Pt : Core


title: Sample08, Pt : Edge


title: Sample05, Device : Edge

value: Device :Edge


title: Sample04, Device : Core


title: B.xylanisolvens, glucose, R1

description:
BX_G_R1
counts_BX.csv


title: S.variabile, inulin, R2

description:
SV_I_R2
counts_SV.csv
SV_inuline_vs_controle4_DESeq_results.csv

organism: Subdoligranulum variabile


title: S.variabile, inulin, R3

description:
SV_I_R3
counts_SV.csv
SV_inuline_vs_controle4_DESeq_results.csv


title: Sample03, Device : Core


title: S.variabile, inulin, R1

description:
SV_I_R1
counts_SV.csv
SV_inuline_vs_controle4_DESeq_results.csv


title: Sample02, Device : Edge


title: Col0_2

tag: genotype


title: Sample01, Device : Edge


title: S.variabile, pectin, R2

description:
SV_P_R2
counts_SV.csv
SV_pectine_vs_controle4_DESeq_results.csv

value: Pectin


title: S.variabile, pectin, R3

description:
SV_P_R3
counts_SV.csv
SV_pectine_vs_controle4_DESeq_results.csv


title: S.variabile, pectin, R1

description:
SV_P_R1
counts_SV.csv
SV_pectine_vs_controle4_DESeq_results.csv


title: tbsP_e_glu

value: H26 {delta}pyrE2{delta}tbsP (HVO_2861)

value: archaeal cell culture

value: HvCA + uracil + 0.1% glucose (w/v)


title: Sample11, Pt : Core


title: S.variabile, glucose, R3

description:
SV_G_R3
counts_SV.csv


title: S.variabile, glucose, R2

description:
SV_G_R2
counts_SV.csv


title: plasma, subject ff852327T4

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

hyb_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

molecule: protein

source_name: serum

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: subject id

tag: blood sample id

tag: Sex

value: Male

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: No

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: plasma, subject ff852327T21

scan_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf


title: plasma, subject ff852327T8

label_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf


title: plasma, subject ff852327T12


title: plasma, subject fe62e57dT4

value: Negative


title: plasma, subject fe62e57dT8


title: plasma, subject fe62e57dT1


title: plasma, subject fe5b68f0T1

value: Female


title: plasma, subject ff852327T20


title: plasma, subject fd6471c1T4


title: plasma, subject fd6471c1T23


title: plasma, subject fe55679dT2


title: plasma, subject fde86321T4


title: plasma, subject fde86321T1


title: plasma, subject fd6471c1T22


title: plasma, subject fe55679dT3


title: plasma, subject fd6471c1T24


title: plasma, subject fd6471c1T1


title: plasma, subject fcf3089aT12


title: plasma, subject fc557f8fT8


title: plasma, subject fc557f8fT4


title: plasma, subject fc4918dcT1


title: plasma, subject fc557f8fT1


title: S.variabile, glucose, R1

description:
SV_G_R1
counts_SV.csv

tag: strain

value: Bacteria

tag: treatment

value: Glucose


title: plasma, subject fba056e9T1


title: plasma, subject fb907f4aT1


title: plasma, subject ff852327T1


title: plasma, subject fd6471c1T8


title: plasma, subject faaa2797T1


title: plasma, subject f8a8067cT1


title: plasma, subject f869206fT1


title: plasma, subject fd6471c1T20


title: plasma, subject f807b2c9T8


title: plasma, subject f84c1a76T1


title: plasma, subject f8a8067cT4


title: plasma, subject f807b2c9T1


title: plasma, subject f7199584T4


title: plasma, subject f7199584T3


title: plasma, subject fcc683b5T1


title: plasma, subject f807b2c9T4


title: plasma, subject f7c4a713T1


title: plasma, subject f5fc1a21T4


title: plasma, subject f6e2911eT1


title: plasma, subject f7199584T1


title: plasma, subject f6e2911eT4


title: plasma, subject f5259cc7T20


title: plasma, subject fbc1daadT1


title: plasma, subject f7199584T2


title: plasma, subject f5259cc7T4


title: plasma, subject f3900bdfT4


title: plasma, subject f5259cc7T1


title: plasma, subject f5fc1a21T20


title: plasma, subject f3900bdfT13


title: plasma, subject f874b0abT0


title: plasma, subject f3900bdfT1


title: plasma, subject f38e5dcaT1


title: plasma, subject f775557aT1


title: plasma, subject f32baa8fT4


title: plasma, subject f32baa8fT8


title: plasma, subject f32baa8fT12


title: plasma, subject f32baa8fT1


title: plasma, subject f229be6cT12


title: plasma, subject f229be6cT1


title: plasma, subject f28b1b6aT1


title: plasma, subject f0157e97T4


title: plasma, subject f0157e97T1


title: plasma, subject eed3d360T1


title: plasma, subject ee630923T13


title: plasma, subject ee630923T4


title: plasma, subject ed553ddbT1


title: plasma, subject efb76cb1T1


title: plasma, subject ee630923T8


title: plasma, subject ed914a91T1


title: plasma, subject ec1ef0e4T12


title: plasma, subject ed01a4e0T1


title: plasma, subject ebcaccc9T4


title: plasma, subject ec1ef0e4T1


title: plasma, subject eb4355e7T1


title: plasma, subject ea04d4fdT12


title: plasma, subject ea1d4510T20


title: plasma, subject ebcaccc9T1


title: plasma, subject ea1d4510T1


title: plasma, subject eb21880dT1


title: plasma, subject ea04d4fdT4


title: plasma, subject ea04d4fdT8


title: plasma, subject f3900bdfT12


title: plasma, subject f1d9c69fT1


title: plasma, subject ea04d4fdT1


title: plasma, subject e97b318fT1


title: plasma, subject e977aca1T1


title: plasma, subject f09c9d08T1


title: plasma, subject ecfd9917T1


title: plasma, subject ebcaccc9T8


title: plasma, subject ec1ef0e4T8


title: plasma, subject e90ecc64T1


title: plasma, subject e8116d96T8


title: plasma, subject e8b3f790T4


title: plasma, subject e8116d96T1


title: plasma, subject e8b3f790T1


title: plasma, subject e78f97d6T4


title: plasma, subject e78f97d6T12


title: plasma, subject e718d059T1


title: plasma, subject e78f97d6T1


title: plasma, subject e9ea305bT1A


title: plasma, subject e707a5caT1


title: plasma, subject e4729ab6T1


title: plasma, subject e4729ab6T20


title: plasma, subject e3dd4350T1


title: plasma, subject e5865047T1A


title: plasma, subject e3dd4350T20


title: plasma, subject e687040dT12


title: plasma, subject e4729ab6T4


title: plasma, subject e3d686b8T1


title: plasma, subject e34fa597T1


title: plasma, subject e33e989cT12


title: plasma, subject e33e989cT1


title: plasma, subject e28e61f1T1


title: plasma, subject e1e3b175T8


title: plasma, subject e8116d96T4


title: plasma, subject e78f97d6T8


title: plasma, subject e1e3b175T4


title: plasma, subject e1d859a9T1


title: plasma, subject e1e3b175T1


title: plasma, subject e1e3b175T12


title: plasma, subject e19edd6eT21


title: plasma, subject e19edd6eT20


title: plasma, subject e19edd6eT12


title: plasma, subject e1015f47T8


title: plasma, subject e687040dT1


title: plasma, subject e1015f47T4


title: plasma, subject e1015f47T1


title: plasma, subject e0e8f34bT8


title: plasma, subject e34fa597T4


title: plasma, subject e0e8f34bT4


title: A8-1 in MRS with  Na₂SeO3 at 22h replicate 2

city: Xi'an

first: Bei

last: Han

state: Shaanxi

address: NO 76 Yanta West Road

department: School of Public Health

institute: Xi'an Jiaotong University

description:
Biological replicate 2 of 3  Enterococcus durans A8-1 strain in MRS medium supplied with Na₂SeO3, 22h culture cells
A8_B_Se.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
The raw data passed the quality control and mapped to the reference genome, differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value<0.05 found by DESeq were assigned as differentially expressed. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression. For the differentially expressed genes, the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment were analyzed.
Genome_build: PRJNA769572(Enterococcus durans A8-1 )
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Enterococcus durans

source_name: collected the whole fermentation cells

growth_protocol: E. durans A8-1was inoculated into MRS medium  and incubated aerobically with constant temperature shaker at 37 °C

extract_protocol:
RNA was extracted from E. durans A8-1 grown in MRS broth containing 60 μg/ml selenite using a bacteria RNA kit (Tiangen Biotech Co. Ltd, Beijing, China). E. durans A8-1 grown in MRS broth without selenite was used as negative control, the control and treatment were all in triplicates. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Through qualified RNA samples, the cDNA library was constructed, and then transcriptome sequencing was performed at Novogen Co. Ltd (Beijing, China).

treatment_protocol: E. durans A8-1was inoculated into MRS medium with  60 μg/ml Na₂SeO3  and incubated aerobically with constant temperature shaker at 37 °C

value: wild type strain A8-1


title: plasma, subject de78995dT1


title: A8-1 in MRS with  Na₂SeO3 at 22h replicate 3

description:
Biological replicate 3 of 3  Enterococcus durans A8-1 strain in MRS medium supplied with Na₂SeO3, 22h culture cells
A8_B_Se.txt


title: plasma, subject e0e8f34bT12


title: plasma, subject e0e8f34bT1


title: plasma, subject df456dcbT1


title: plasma, subject de607d2bT1


title: plasma, subject de607d2bT4


title: plasma, subject de46f293T8


title: plasma, subject def9ce10T1


title: plasma, subject de607d2bT8


title: A8-1 in MRS with  Na₂SeO3 at 14h replicate 3

description:
Biological replicate 3 of 3  Enterococcus durans A8-1 strain in MRS medium supplied with Na₂SeO3, 14h culture cells
A8_A_Se.txt


title: A8-1 in MRS with  Na₂SeO3 at 14h replicate 1

description:
Biological replicate 1 of 3  Enterococcus durans A8-1 strain in MRS medium supplied with Na₂SeO3, 14h culture cells
A8_A_Se.txt


title: A8-1 in MRS at 22h replicate 3

description:
Biological replicate 3 of 3  Enterococcus durans A8-1 strain in MRS medium, 22h culture cells
A8_B.txt


title: plasma, subject de46f293T4


title: A8-1 in MRS with  Na₂SeO3 at 14h replicate 2

description:
Biological replicate 2 of 3  Enterococcus durans A8-1 strain in MRS medium supplied with Na₂SeO3, 14h culture cells
A8_A_Se.txt


title: plasma, subject de46f293T12


title: A8-1 in MRS at 14h replicate 3

description:
Biological replicate 3 of 3  Enterococcus durans A8-1 strain in MRS medium, 14h culture cells
A8_A.txt


title: A8-1 in MRS at 22h replicate 2

description:
Biological replicate 2 of 3  Enterococcus durans A8-1 strain in MRS medium, 22h culture cells
A8_B.txt


title: A8-1 in MRS at 14h replicate 2

description:
Biological replicate 2 of 3  Enterococcus durans A8-1 strain in MRS medium, 14h culture cells
A8_A.txt


title: plasma, subject de46f293T1


title: A8-1 in MRS at 14h replicate 1

description:
Biological replicate 1 of 3  Enterococcus durans A8-1 strain in MRS medium, 14h culture cells
A8_A.txt


title: plasma, subject dd383e46T12


title: RNA_F1_protoplast_P1

city: East Lasing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Rd.

department: Biochemistry and Molecular Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
Sample quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, V0.11.5). Adapters and low quality reads were trimmed with Trimmomatic (Bolger et al., 2014) using the following parameters: ILLUMINACLIP:Adapter.fastq:2:40:15 SLIDINGWINDOW:4:20 MINLEN:30
ChIP- and DAP-seq: Cleaned reads were mapped to the reference genome (AGPv4) using bowtie2 v2.3.4.1.
RNA-seq: Cleaned reads were mapped to the reference genome (AGPv4) using HISAT2 (2.0.4)
RNA-seq: Reads aligned to genes were counted with the R package Rsubread v1.32.2
Assembly: AGPv4
Supplementary files format and content: txt with raw counts
Supplementary files format and content: bed

organism: Zea mays

source_name: Protoplast

growth_protocol: DAP-seq: Plant materials were grown in the growth chamber for two weeks at 22 C and under 16:8 hrs light/dark cycles. A pool of eight seedlings were used for collection of leaf tissues from B73xMo17 F1 hybrids. RNA-seq:  For silk and pericarp, three biological replicates of tissues obtained from silks at silking stage (exposed silks are about 2-5 cm long), pericarp at 14 days after pollination (DAP)  were collected from P1-rr and P1-ww, B73, A632 and A632 x Mo17 F1 hybrid in the MSU fields in the summer of 2019. ChIP-seq For protoplast experiment, seeds were soaked in water overnight before sawing in soil. Plants were growing in dark at 26C for 12 days. The 2nd leaves were collected for 12 seedlines and pooled as one replicates. Transforamtion were done using electroporation.

extract_protocol:
DAP-seq: All the DNA protein interaction process was done as published (Bartlett, 2017).  RNA-seq: RNA extraction was conducted using Trizol (Invitrogen) following the company’s recommended procedure. The RNA integrity and concentration were checked on 1.5 % agarose gel and Qubit RNA HS assay, respectively.
DAP-seq: All the DNA protein interaction process was done as published (Bartlett, 2017) except for the following: Approximate 200 ng of DAP-seq gDNA library was added as an input for incubation with each pIX-HALO-TF protein extract. To perform double-size selection of 200-300 bp fragments for each sample, 0.8 volume of Agencout AMPure XP beads (40ul) to 1 volume of sample (50ul) were mixed for 5 minutes and the bead were discarded to remove fragments with size larger than 300 bp. Next, the supernatant (90 ul) contain < 300bp fragments were added to 0.2 volume of Agencout AMPure XP beads (10 ul) and mixed for 15 minutes. Bound DNA was eluted by adding 18 ul UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen). The DNA concentration of DAP-seq libraries was evaluated using Qubit HS dsDNA assay kit, and approximate 5-20 ng/μl final concentration were obtained. Fragment sizes were further examined by agarose gel electrophoresis after six cycles of PCR using 2ul of DAP-seq library in 20 ul total volume with library specific primer pairs. RNA-seq: Samples with sharp rRNA bands were used for RNA-seq library preparation using TruSeq RNA library pre kit v2 (Illumina) following the manufacturer instructions. The RNA libraries (in pools of 9 samples each using Illumina barcodes) were sent to the Genomic Core Facility at Michigan State University for 50 bp single-end sequencing on the Illumina Hiseq 4000. ChIP-seq: All ChIP-seq librares were made using NEBNext Ultra II DNA library Prep kit for Illumina (NEB#7645 S/L, $E7103 S/L). Hiseq4000 were used for all SE50 sequencing.

tag: cultivar

value: 2nd leave of 12-day-old maize seedling


title: A8-1 in MRS at 22h replicate 1

description:
Biological replicate 1 of 3  Enterococcus durans A8-1 strain in MRS medium, 22h culture cells
A8_B.txt


title: plasma, subject dd383e46T1


title: plasma, subject dcce851fT1


title: plasma, subject dc557cb4T12


title: plasma, subject dc557cb4T1


title: RNA_F1_protoplast_DP611

value: Empty vector control


title: RNA_Prr_pericarp

source_name: Pericap

value: A619 inbred

value: 14 DAP kernals


title: plasma, subject dc31ed75T1


title: plasma, subject dc31ed75T0


title: plasma, subject dc0bc1f9T8


title: RNA_Pww_pericarp


title: RNA_Prr_silk

source_name: Silk

value: 0 DAP silk

value: Unfertilized silk


title: plasma, subject dc0bc1f9T4


title: RNA_F1_silk


title: TCRseq from Pat14, skin, Stage: nonlesional

city: Mainz

first: Philipp

last: Licht

address: Langenbeckstrasse 1

department: Dept. of Dermatology

institute: University Medical Center Mainz

description: T cell receptor

data_processing:
The sequencing data were uploaded to the Galaxy web platform and processed with the pRESTO toolkit implemented in a publicity available workflow at https://usegalaxy.org/u/bradlanghorst/w/presto-nebnext-immune-seq-workflow-v320. Subsequently, the R toolkit immunarch 0.7.0 was used to analyze the TCR repertoire and to visualize T cell clonotype tracking as well as TCR gene usage.
To investigate if TCRs recognize microbial epitopes, known S. aureus epitopes were downloaded from the IEDB database (https://www.iedb.org/). If an epitope of special interest (i.e. an epitope from a virulence factor we identified as being enriched in plaque-associated S. aureus strains) was not available, it was predicted with an online tool for both MHC-II and MHC-I (http://tools.iedb.org/main/tcell/). The 10 most abundant TCR clones in each sample were then paired with each epitope (downloaded from IEDB and predicted with the online tool). The online implementation of tool ERGO-II was used to calculate a binding score of a given pair of TCR and epitope. The higher the binding score, the higher the probability that the TCR recognizes and binds the epitope.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts of TCRs in AIRR (Adaptive Immune Receptor Repertoire) format.
Library strategy: TCR-seq

source_name: Skin

extract_protocol:
4 mm punch biopsies were obtained from the same lesions sampled for metagenomics and at the same visit. The punch biopsies were immediately shock frozen and kept in liquid nitrogen until processed. RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (74704, Qiagen, Germany) along with the TissueLyser II (85300, Qiagen, Germany) according to the manufacturer’s instruction. Peripheral blood mononuclear cells (PBMCs) were isolated from freshly drawn blood using density gradient centrifugation (Histopaque-1077, 10771, SIGMA-ALDRICH, Germany) and kept in liquid nitrogen until processed. PBMCs were thawed at 37° C, washed in pre-warmed RPMI 1640 medium (31870-025, Gibco, USA) including 10% FCS and counted using the Countess 3 machine (ThermoFisher Scientific, USA). To enrich the T cell population, the Pan T Cell Isolation Kit human (Miltenyi Biotec, Germany) was used according to the manufacturer's instructions. Directly thereafter total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen, Germany) according to the manufacturer's instructions.
Illumina sequencing libraries were constructed with the NEBNext Immune Sequencing Kit, human (E6320, New England Biolabs, USA) according to the manufacturer’s instructions with 200 ng total RNA as starting material. The optimal number of PCR cycles for target amplification were determined for each sample by RT-qPCR as outlined in the manual.
TCRseq, 300 bp PE using a 600-cycle V3 reagent kit

value: Skin

tag: condition

value: nonlesional

tag: individual


title: RNA_Pww_silk


title: TCRseq from Pat14, skin, Stage: Plaque

description: T cell receptor

value: Plaque


title: RNA_A632_silk

value: A632 inbred


title: RNA_B73_silk

value: B73 inbred


title: TCRseq from Pat12, skin, Stage: nonlesional

description: T cell receptor


title: plasma, subject db8b671fT21

value: Male

tag: age

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: plasma, subject dc0bc1f9T12


title: plasma, subject db8b671fT20


title: plasma, subject dc0bc1f9T1


title: plasma, subject db8b671fT12


title: plasma, subject db8b671fT13


title: TCRseq from Pat12, skin, Stage: Patch

description: T cell receptor

value: Patch


title: plasma, subject db8b671fT1


title: DAP_WRKY38_deM_SE50

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
Sample quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, V0.11.5). Adapters and low quality reads were trimmed with Trimmomatic (Bolger et al., 2014) using the following parameters: ILLUMINACLIP:Adapter.fastq:2:40:15 SLIDINGWINDOW:4:20 MINLEN:30
ChIP- and DAP-seq: Cleaned reads were mapped to the reference genome (AGPv4) using bowtie2 v2.3.4.1.
RNA-seq: Cleaned reads were mapped to the reference genome (AGPv4) using HISAT2 (2.0.4)
RNA-seq: Reads aligned to genes were counted with the R package Rsubread v1.32.2
Assembly: AGPv4
Supplementary files format and content: txt with raw counts
Supplementary files format and content: bed
Library strategy: DAP-Seq

source_name: Leave

value: 2 week old seedling

value: deMethylated


title: plasma, subject db803103T4


title: plasma, subject db803103T8


title: DAP_THX39_deM_SE50


title: TCRseq from Pat9, skin, Stage: Plaque

description: T cell receptor


title: TCRseq from Pat10, skin, Stage: Patch

description: T cell receptor


title: plasma, subject db803103T1


title: plasma, subject db3a573fT4


title: DAP_Orphan249_deM_SE50

description: ungenerated


title: TCRseq from Pat8, skin, Stage: Patch

description: T cell receptor


title: plasma, subject db8b671fT22


title: plasma, subject db3a573fT1


title: DAP_Orphan207_deM_SE50

description: ungenerated


title: plasma, subject db0ff43fT1


title: DAP_Orphan175_deM_SE50

description: ungenerated


title: DAP_bZIP76_deM_SE50

description: ungenerated


title: TCRseq from Pat7, skin, Stage: Plaque

description: T cell receptor


title: TCRseq from Pat7, skin, Stage: nonlesional

description: T cell receptor


title: plasma, subject db0ff43fT13


title: plasma, subject da24293eT8

value: Female


title: plasma, subject da3d1cb6T12


title: plasma, subject da3d1cb6T1


title: plasma, subject da24293eT4


title: DAP_NLP14_deM_SE50


title: plasma, subject da24293eT1


title: TCRseq from Pat6, skin, Stage: nonlesional

description: T cell receptor


title: TCRseq from Pat6, skin, Stage: Patch

description: T cell receptor


title: DAP_NAC102_deM_SE50

description: ungenerated


title: plasma, subject d9bb1b6aT4


title: DAP_MYBR78_deM_SE50

description: ungenerated


title: TCRseq from Pat5, skin, Stage: nonlesional

description: T cell receptor


title: plasma, subject d9bb1b6aT1


title: plasma, subject d8028ee0T4


title: DAP_MYB53_deM_SE50


title: TCRseq from Pat5, skin, Stage: Patch

description: T cell receptor


title: plasma, subject d8028ee0T1


title: plasma, subject db0ff43fT4


title: plasma, subject d7f3c9eeT4


title: DAP_MYB40_Met_SE150_SE50

value: Methylated


title: plasma, subject d7f3c9eeT1


title: TCRseq from Pat4, skin, Stage: nonlesional

description: T cell receptor


title: DAP_MYB100_deM_SE50


title: plasma, subject d7b2bc5eT2


title: plasma, subject d7b2bc5eT1


title: TCRseq from Pat1, skin, Stage: Plaque

description: T cell receptor


title: TCRseq from Pat4, skin, Stage: Plaque

description: T cell receptor


title: plasma, subject d78e965aT12


title: DAP_MBF1.3_deM_SE50

description: ungenerated


title: plasma, subject d7adaed4T12


title: TCRseq from Pat14, blood --> PBMC --> T cell enriched

description: T cell receptor

source_name: Blood

value: Blood

value: PBMC (T cell enriched)

value: Mycosis fungoides, blood


title: TCRseq from Pat12, blood --> PBMC --> T cell enriched

description: T cell receptor


title: DAP_F1_gDNA_library_03


title: plasma, subject d78e965aT1


title: plasma, subject d78770a0T8


title: plasma, subject d78770a0T4


title: DAP_F1_gDNA_library_02


title: plasma, subject d78770a0T1


title: plasma, subject d78770a0T12


title: TCRseq from Pat8, blood --> PBMC --> T cell enriched

description: T cell receptor


title: plasma, subject d764d5ebT1


title: DAP_F1_gDNA_library_01


title: plasma, subject d703e6aeT4


title: plasma, subject d703e6aeT1


title: TCRseq from Pat4, blood --> PBMC --> T cell enriched

description: T cell receptor


title: DAP_F1_P1_deM_SE50


title: plasma, subject d78e965aT20


title: DAP_JMJ13_deM_SE50

description: ungenerated


title: DAP_F1_Halo_deM_SE50


title: plasma, subject d683ade0T4


title: plasma, subject d6c2f748T4


title: plasma, subject d650fa11T8


title: plasma, subject d683ade0T1


title: plasma, subject d650fa11T4


title: DAP_EREB156_Met_SE150_SE50

description: ungenerated


title: plasma, subject d650fa11T12


title: plasma, subject d650fa11T1


title: DAP_EREB122_deM_SE50


title: plasma, subject d5ffe2b1T1


title: plasma, subject d55887ecT1

value: Negative


title: plasma, subject d50792d5T4


title: 500 μM_oleic_acid_rep2

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

hyb_protocol: Cy3-labeled cRNA (600 ng) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μL of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray 8×60K (G4851C) (Agilent Technologies) for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). After hybridization, microarrays were washed at room temperature for 1 min with GE Wash Buffer 1 (Agilent Technologies) and at 37°C for 1 min with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20200924) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The obtained data were normalized by quantile normalization using GeneSpring GX14.9 software (Agilent Technologies). In addition, the minimum expression value (raw signal) was set at 100 to filter by expression level. GeneSpring GX14.9 software was used to obtain expression data with more than 2.0-fold expression change in each treated group (50, 200, and 500 μM) compared to the control group (0 μM). Matrices were denoted with gProcessedSignal (raw).

source_name: 500 μM oleic acid, HepG2

label_protocol: Cyanine 3 (Cy3)-labeled cRNA was synthesized from 150 ng of total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer’s instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: In vitro adipogenesis used the liver cancer cell line, HepG2 cells. The Japanese Collection of Research Bioresources provided HepG2 cells (JCRB1054), and Dulbecco’s Modified Eagle Medium (Fujifilm wako) with 10% fetal bovine serum and antibiotics, including penicillin and streptomycin, cultured HepG2 cells. Cultures cultivated at 37°C under 5% CO2.

extract_protocol: Total RNAs were extracted using the RNeasy Mini kit (QIAGEN) following the manufacturer’s instructions. A NanoDrop spectrophotometer (NanoDrop Technologies) assessed the quality and concentration of total RNAs. All RNA samples demonstrated 260/280-nm absorbance ratios of 1.8–2.0. An Agilent 2100 Bioanalyzer and an Agilent RNA 6000 Pico Kit (Agilent Technologies) confirmed the peaks of total RNAs, following the manufacturer’s instructions.

treatment_protocol: HepG2 cells were seeded at 1 × 105 cells/well in 6-well plates and incubated at 37℃ under 5% CO2. The culture medium was replaced with 0, 50, 200, or 500 μM oleic acid after 72 h and was incubated for 24 h.

value: 500 uM oleic acid


title: DAP_E2F19_deM_SE50

description: ungenerated


title: plasma, subject d4a362f0T8


title: 500 μM_oleic_acid_rep1


title: 200 μM_oleic_acid_rep2

source_name: 200 μM oleic acid, HepG2

value: 200 uM oleic acid


title: 200 μM_oleic_acid_rep1


title: DAP_DOF3_deM_SE50


title: TCRseq from Pat1, blood --> PBMC --> T cell enriched

description: T cell receptor


title: DAP_DOF23_deM_SE50


title: plasma, subject d683ade0T13


title: 50 μM_oleic_acid_rep1

source_name: 50 μM oleic acid, HepG2

value: 50 uM oleic acid


title: plasma, subject d4a362f0T12


title: plasma, subject d4a362f0T4


title: 50 μM_oleic_acid_rep2


title: DAP_CPP8_deM_SE50


title: plasma, subject d4a362f0T1


title: plasma, subject d4840c8bT12


title: DAP_CAP5P9_deM_SE50

description: ungenerated


title: 0 μM_oleic_acid_rep2

source_name: 0 μM oleic acid, HepG2

value: 0 uM oleic acid


title: plasma, subject d4840c8bT1

value: Positive


title: plasma, subject d4782981T1

value: Male


title: plasma, subject d50792d5T5

value: No

value: Yes


title: 2-X-TOP_hmC_GC_IonTorrent_mESC_shallow

city: Vilnuis

first: Kotryna

last: Kvederaviciute

address: Universiteto str. 3

country: Lithuania

institute: Vilnius University

description:
GC_table.tsv
hmC_table.tsv

data_processing:
Raw data quality was evaluated using FASTQC. Reads were trimmed using cutadapt (v3.4) and in-house script.
Cleaned reads were mapped to the reference genome (mm10) using bwa (v0.7.17). Samtools (v1.9) were used to perform all manipulations with SAM/BAM files.
Each reads was assigned to a specific GC/CG target and coverage tables were generated using an in-house R (v.4.0.2) script. Open chromatin regions were identified using an in-house R script.
Assembly: mm10
Supplementary files format and content: Tab delimited table with target (5hmCG, uCG, GC) coverage per each sample.
Supplementary files format and content: Tab delimited table with identified coordinates of open chromatin regions.
Library strategy: TOP-Seq

source_name: Embryo blastocyst

growth_protocol: ESCs were cultured on feeder-free 0.15% gelatin-coated plates in DMEM medium supplemented with 15% embryonic stem-cell FBS, 50 µg/ml penicillin–streptomycin mix, 2 mM L-glutamine, 1 × non-essential amino acids, 1 mM 2-mercaptoethanol (all from Gibco) and 1000 units/mL ESGRO mLIF (Milipore).

extract_protocol:
Genomic DNA from nuclei was extracted by using standard phenol-chloroform extraction.
2-X-TOP Ion Torrent libraries - sonicated uCG- and GC- or 5hmC- and GC-azide labeled gDNA samples were used for the ligation of adaptors, as described in Gibas et al., 2020. After ligation, the alkyne-bearing oligodeoxyribonucleotide with biotin was attached to the azide moiety of the modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads and subsequently used in a DNA priming reaction from the tethered oligonucleotide. The primed DNA library was amplified, size-selected, and subjected to Ion Proton sequencing. 3-X-TOP Ion Torrent libraries - CG-, GC-alkyne, and 5hmC-azide labeled gDNA samples libraries were prepared using the same methodology as for 2-X-TOP Ion Torrent libraries, except that the biotinylated azide-containing and the biotinylated alkyne-containing oligonucleotides were click conjugated in two rounds. 3-X-TOP Illumina libraries - to CG-, GC-alkyne, and 5hmC-azide labeled gDNA samples adapters were attached by incubating the samples with hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. The library was then prepared using the same methodology as for 3-X-TOP Ion Torrent library preparation (without the click product enrichment) and was subjected to Illumina sequencing.

treatment_protocol: Differentiation of mouse ESCs to neurons was performed, as described in Bibel et al., 2007.

value: Embryo blastocyst

tag: cell line

value: Embryonic stem cells

value: WT

tag: modification

value: 5-hydroxymethylcytosine and GC


title: 0 μM_oleic_acid_rep1

tag: tissue


title: plasma, subject d463b069T8

value: Somascan discovery platform v4


title: DAP_C3H42_deM_SE50

description: ungenerated

value: 2 week old seedling

value: deMethylated


title: plasma, subject d463b069T4


title: DAP_BSD8_deM_SE50

description: ungenerated


title: plasma, subject d4626a9bT1


title: 2-X-TOP_uCG_GC_IonTorrent_mESC_shallow

description:
GC_table.tsv
uCG_table.tsv

tag: cell type

tag: genotype

value: GC and unmodified CG sites


title: plasma, subject d4a362f0T13

tag: subject id

tag: blood sample id

value: Female


title: 3-X-TOP_IonTorrent_mESC_shallow

description:
GC_table.tsv
hmC_table.tsv
uCG_table.tsv

value: 5-hydroxymethylcytosine, GC and unmodified CG sites


title: DAP_BAF60.21_deM_SE50

description: ungenerated


title: 3-X-TOP_IonTorrent_NC_deep

description:
GC_table.tsv
hmC_table.tsv
uCG_table.tsv
regions_idGC.tsv
regions_idT.tsv

value: Neuronal differentiation


title: plasma, subject d42085cfT8

tag: Sex

tag: days since first sample


title: ChIP_F1_Silk_P1

source_name: silk

value: silk from silking stage(2-5cm emerging)

value: P1 specific Ab (serum:344-3)


title: plasma, subject d42085cfT4

tag: patient classification at first sample

tag: covid-19 status

value: Positive


title: 3-X-TOP_IonTorrent_NPC_deep


title: plasma, subject d42085cfT20

value: Male

tag: instrument model


title: ChIP_Pww_Silk_Input

value: A619 inbred

tag: treatment

value: Input


title: plasma, subject d42085cfT13

value: Yes


title: plasma, subject ec1ef0e4T4

value: No


title: plasma, subject d42085cfT12


title: 3-X-TOP_IonTorrent_mESC_deep

value: Embryo blastocyst

value: Embryonic stem cells

value: WT


title: ChIP_F1_Protoplast_P1_Input

tag: cultivar

value: protoplast from the 2nd leave of 12-day-old maize seedling (etiolated)


title: plasma, subject d42085cfT1

value: Somascan discovery platform v4


title: plasma, subject d3aa54b3T8


title: RNAseq_NC_rep2

data_processing:
Quality of raw reads was evaluated using FASTQC and reads were trimmed using cutadapt (v3.4)
Cleaned reads were mapped to the reference Mus musculus genome (mm10) using STAR (v2.7.9a)
Expression quantification was performed using stringtie (v2.1.5). Statistical analysis was performed using R (v.4.0.3) and DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene ID, Symbo, coordinates, coverage, FPKM and TPM values.

extract_protocol:
Total RNA was isolated using RNAzol RT (Molecular Research Center) reagent according to the manufacturer’s instructions. mRNA was enriched from 7 μg of total RNA with Dynabeads mRNA Purification Kit (Thermo Fisher Scientific). Ribosomal RNA was depleted using RiboCop rRNA Depletion Kit (Lexogen) according to the manufacturer’s recommendations.
cDNA libraries for RNA sequencing were prepared with Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) in two biological replicates following the manufacturer’s protocol. Final libraries were subjected to Ion Proton (Thermo Fisher Scientific) sequencing.


title: plasma, subject d3aa54b3T4


title: ChIP_F1_Protoplast_35S_P1


title: plasma, subject d4626a9bT4


title: RNAseq_NC_rep1


title: plasma, subject d3aa54b3T1


title: Tnnt2a degron

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo
Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format.
Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 117 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 40%. Furthermore, we filtered 9060 genes if they were detected in less than 30 cells (<0.01%).
Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding (McInnes & Healy, https://arxiv.org/abs/1802.03426) and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: danRer11
Supplementary files format and content: starsolo outputs

organism: Danio rerio

source_name: Whole heart

extract_protocol:
The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 10000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics).
Library preparation was conducted according to the manufacturer indications.

value: Whole heart

value: Heart cells

tag: developmental stage

value: 72 hpf


title: plasma, subject d2b3daf4T12


title: plasma, subject d3aa54b3T0


title: plasma, subject d2b3daf4T1


title: plasma, subject d28718f3T12


title: RNAseq_NPC_rep1

value: Neuronal differentiation


title: plasma, subject d28718f3T1


title: Wild-type

description: 10x Genomics


title: RNAseq_mESC_rep2


title: plasma, subject d28718f3T0


title: plasma, subject d2649ca8T1


title: BMSC, TB4

city: Changsha

first: Qile

last: Gao

state: Hunan

address: 932, Lushan Nan Lu, Yuelu District

institute: Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, China.

data_processing:
lllumina bcl2fastq 2.0 software used for basecalling.
Raw data obtained by sequencing was filtered using SOAPnuke (v1.5.6) to filter out: 1) reads containing joints (joint contamination); 2) reads with unknown base N content greater than 5%; 3) clean data were obtained from low-quality reads (reads with a mass value of less than 15 bases accounting for more than 20% of the total base number of the reads). Subsequently, Dr. Tom Multiomics Data Mining system (https://biosys.bgi.com) was used for data analysis, mapping and mining.
Clean data was compared to the reference genome using HISTA2 (v2.1.0) software. Then, Ericscript (v0.5.5) was used for gene fusion detection and rMATS (V3.2.5) for variable splicing and differential variable splicing detection.
Clean data was compared to the reference gene set using Bowtie2(v2.3.4.3). The reference gene set was provided by the Dr. Tom Multiomics Data Mining System. RSEM (v1.3.1) software was used for gene expression quantification, and pheatmap (v1.0.8) was used to draw clustering heat maps of gene expression levels in different samples. Differential gene testing was performed using DESeq2 (v1.4.5) (or DEGseq[9] or PoissonDis) when Q value≤0.05 or FDR≤0.001.
To further explore gene function related to phenotypic change, we based on hypergeometric tests, Using Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) to GO (http://www.geneontology.org/) and KEGG genetic variations (https://www.kegg.jp/) For enrichment analysis, Qvalue≤0.05 was taken as the threshold, and those meeting this condition were defined as significant enrichment in candidate genes.
Assembly: hg19
Supplementary files format and content: read_counts, fpkms, tpms

source_name: mesenchymal stem cells

extract_protocol:
Total RNA was extracted from the BMSC of 4 STB patients and 4 controls. The DNBSEQ platform of BGISEQ-500 was used for RNA-seq.
RNA libraries was prepared for sequencing using standard lllumina protocols

value: BMSCs

tag: disease state

value: TB

tag: individual

value: Tuberculosis patient


title: BMSC, TB3


title: plasma, subject d15ed14dT1

value: Male

tag: age

value: Positive


title: BMSC, TB2


title: plasma, subject d0544d28T1


title: ES-2,60-day PtNPs exposed and evolved PAO1 (ES)

city: Hangzhou,Zhejiang

first: Yulu

last: Lian

state: Zhejiang

address: Hangzhou

institute: Zhejiang Gongshang University

data_processing:
SeqPrep gram (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) were used to filter the raw reads.
Clean data was mapped with the reference genome of P. aeruginosa (GCA_000006765.1) by Bowtie2
RSEM (http://deweylab.github.io/RSEM/) was utilized for quantification of transcripts expression, and DEseq2 (https://github.com/mikelove/DESeq2) was utilized for identification and analysis of differentially expressed genes (DEGs) among samples (log2FC ≥ 1 and p < 0.05)
Assembly: GCA_000006765.1
Supplementary files format and content: The mRNA abundance was determined by the number of uniquely mapped reads from a transcript per million reads (TPM)

organism: Pseudomonas aeruginosa

extract_protocol:
Total RNA was extracted using TruSeq™ Stranded Total RNA Library Prep Kit (Illumina, CA, USA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: strain

value: ES

value: 60-day PtNPs exposed and evolved

tag: time

value: Day 60


title: ES-3,60-day PtNPs exposed and evolved PAO1


title: plasma, subject d0544d28T0

value: No

value: Yes


title: ES-1, 60-day PtNPs exposed and evolved PAO1 (ES)


title: RNAseq_NPC_rep2

tag: tissue

value: Embryo blastocyst

tag: cell line

tag: cell type

value: Embryonic stem cells

value: WT


title: plasma, subject d01d4d62T4

tag: subject id

tag: blood sample id

value: Somascan discovery platform v4


title: plasma, subject d01d4d62T20

tag: Sex

tag: days since first sample


title: BMSC, N4

value: Control


title: tnnt2a mutant

description: 10x Genomics

value: Whole heart

value: Heart cells

tag: genotype

value: 72 hpf


title: BMSC, TB1

value: BMSCs

value: TB


title: BMSC, N3


title: plasma, subject cfa8b753T4

value: Male

tag: patient classification at first sample

tag: covid-19 status

tag: instrument model


title: CK-3, non-exposed but evolved PAO1

value: CK

tag: treatment

value: non-exposed but evolved PAO1


title: plasma, subject cfa8b753T1

value: Positive


title: plasma, subject d01d4d62T1


title: plasma, subject d1ea06c3T1

value: Female


title: BMSC, N2

tag: disease state


title: plasma, subject cfa8b753T0

value: No


title: CK-1, non-exposed but evolved PAO1

value: Day 60


title: RNAseq_mESC_rep1

value: Embryo blastocyst


title: CK-2, non-exposed but evolved PAO1


title: plasma, subject d1dc29d4T1

value: Yes


title: plasma, subject d1161d57T1


title: plasma, subject cecb13a2T2


title: BMSC, N1

value: WT

tag: individual


title: WT-3, wild-type strains

value: Day 0


title: plasma, subject d01d4d62T8

tag: age

value: Somascan discovery platform v4


title: plasma, subject cec04d04T1


title: Macrophage cells - anti-MAFB antibody_donor #2

city: Madrid

first: Miguel

middle: A

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

data_processing:
BGISEQ-500 platform
Sequenced single-end 50-bp reads were aligned to the genome assembly GRCh38 using BWA program
Homer software suite was used for peak calling, peak annotation and motif discovery
Genome_build: GRCh38
Supplementary_files_format_and_content: ChIP-seq reads were aligned to the GRCh38 genome using BWA (fq.gz files). The bed files include genomic peaks found for each ChIP-seq sample

source_name: Macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

extract_protocol:
Lysates were clarified from sonicated nuclei and MAFB-DNA complexes were isolated with antibody.
Libraries from genomic DNA were prepared for sequencing using standard BGI protocols

treatment_protocol: ChIP-Seq was performed essentially as described by Nowak et al. (Biotechniques 39: 715–724, 2005), using a Diagenode Bioruptor for sonication, DNA crosslinking using 1% formaldehyde and the rabbit anti-MAFB antibody (HPA005653, Sigma) for immunoprecipitation

tag: cell

value: Monocyte-derived M-CSF macrophages

value: anti-MAFB antibody


title: WT-2, wild-type strains

tag: strain

tag: time


title: plasma, subject ce7d0642T1

source_name: serum


title: plasma, subject cdff3cedT4


title: plasma, subject ce17b133T1


title: Macrophage cells - anti-MAFB antibody_donor #1


title: plasma, subject ce17b133T4


title: WT-1, wild-type strains


title: Macrophage cells -Input DNA_donor #2

value: untreated


title: plasma, subject cdff3cedT1


title: Macrophage cells -Input DNA_donor #1


title: Clone14.2(CD24-low)-2

city: Seoul

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

country: South Korea

institute: Yonsei University

hyb_protocol: Hybridization of probes was conducted by Agilent hybridization system according to the manufacturer's protocol.

scan_protocol: Sample cartridges were scaned and analyzed by Agilent scanner & Feature Extraction v10.7.3.1 (Agilent technologies, inc.)

data_processing:
The data were processed using variance stabilization normalization.
*** Submitter declares that the raw files cannot be submitted because the company that provided the microarray service is no longer operational ***

source_name: a primary ovarian cancer cell

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (Agilent technologies, inc.) were conducted according to the manufacturer's protocol.

growth_protocol: Ovarian cell lines and primary ovarian cancer cells were were cultured in the RPMI medium supplemented with 1% penicillin/streptomycin and 10% FBS at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from Caov3 and primary ovarian cancer cells using Rneasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

tag: tissue

value: primary ovarian cancer


title: plasma, subject cde00319T12


title: Clone14.2(CD24-low)-1


title: plasma, subject cde00319T4


title: plasma, subject cde00319T1


title: Clone4(CD24-high)-3


title: plasma, subject cecb13a2T1


title: plasma, subject cd79de3cT8


title: Clone4(CD24-high)-2


title: plasma, subject cd79de3cT4


title: plasma, subject cd79de3cT13


title: Clone14.2(CD24-low)-3


title: plasma, subject cd79de3cT12


title: plasma, subject cde00319T8


title: plasma, subject cd79de3cT1


title: plasma, subject ccd360dbT4


title: CD24-negative Caov3-3

source_name: Ovarian cancer cell line Caov-3

value: Caov-3 cell line


title: plasma, subject cde00319T13


title: plasma, subject ccd360dbT1

value: Male


title: CD24-negative Caov3-2


title: CTL ASO2 rep 2

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

hyb_protocol: Samples were hybridized to a Clariom_D array (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Relative expression changes assessed by Expression Console

label: Biotin

source_name: Deceased male individual

label_protocol: Standard Affymetrix protocol

growth_protocol: William's E, 10% serum, pen/strep and hepatocyte growth supplements (ThermoFisher)

extract_protocol: High Pure RNA isolation using Trizol and cartridges

treatment_protocol: Hepatocytes in 12 well plates were treated for 72 hwith 60 nM final of ASO1, ASO2 or a Non-target ASO.

tag: gender

value: male

tag: cell type

value: Primary hepatocyte cultures


title: ASO2 rep 2


title: CD24-negative Caov3-1


title: A8-1 in MRS with  Na₂SeO3 at 22h replicate 1

description:
Biological replicate 1 of 3  Enterococcus durans A8-1 strain in MRS medium supplied with Na₂SeO3, 22h culture cells
A8_B_Se.txt

source_name: collected the whole fermentation cells

value: wild type strain A8-1


title: plasma, subject ccce11a7T4

tag: subject id

tag: blood sample id

value: Positive


title: plasma, subject ccce11a7T1

tag: Sex

tag: days since first sample

value: No


title: plasma, subject cb70545dT1

value: Female

tag: patient classification at first sample


title: plasma, subject cda38947T1

tag: covid-19 status


title: plasma, subject cb3e883fT8

tag: instrument model


title: plasma, subject cb3e883fT4


title: Clone4(CD24-high)-1


title: CTL ASO2 rep 1


title: CD24-positive Caov3-2


title: plasma, subject cb3e883fT1


title: plasma, subject cb1296c7T8


title: plasma, subject ccce11a7T8


title: CD24-positive Caov3-1


title: plasma, subject cb1296c7T4


title: ASO2 rep 1


title: plasma, subject cb1296c7T1


title: CD24-positive Caov3-3


title: plasma, subject c927cf0eT1


title: plasma, subject c8719b33T8


title: ChIP-seq T7 RNAP of E coli: RSG_B012 - 2h arabinose + 10 min rifampicinHi-C (HpaII) of E coli: RSG_B212 - 2h arabinose

city: Paris

first: Amaury

last: Bignaud

address: 28 Rue du Docteur Roux

institute: Institut Pasteur

data_processing:
tinymapper ChIP mode v0.10.0 (https://github.com/js2264/tinyMapper)
Assembly: E. coli K12 MG1655 - https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3/
Supplementary files format and content: bigWig

organism: Escherichia coli

growth_protocol: All strains were grown in minimal media A (0.26 M KH2PO4, 0.06 M K2HPO4, 0.01 M tri sodium citrate, 2mM MgSO4, 0.04 M (NH4)2SO4) supplemented with 0.2% of casamino acids and 0.5% of glucose at 37°C. The strains were grown with 0.2% arabinose for 1h to induce T7 RNA polymerase expression under the control of the PBAD promoter.

extract_protocol:
Briefly, overnight cultures were diluted to OD600nm= 0.01, grown until OD600nm= ~0.2 - 0.25, diluted and crosslinked using formaldehyde (Sigma-Aldrich; final concentration of 1%) for 10 minutes at 22.5°C. Formaldehyde was then quenched by adding 2.5M glycine (final concentration: 0.5 M), for 10 minutes at room temperature (e.g. 19 - 22°C). Cells were collected by centrifugation at 1,500 x g for 10 minutes and washed three times in ice-cold 1X PBS. The pellets can be stored at -80 °C or used straight away.
A pellet was then resuspended into 500 μl of 1X TE buffer, supplemented with 5 μl of ready-lyse lysozyme, and incubated with shaking at 37 °C for 30 minutes. 500 μl of 2X ChIP buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate (DOC), 0.1% SDS 1X Roche Complete EDTA-free protease inhibitor cocktail) was then added and the sample transferred to ice. The sample was transferred to a pre-chilled 1 mL Covaris tube (Covaris), and sonicated using Covaris S220 for 7 min (settings as followed: target size, 200 - 700; PIP 140; DF 5%; CPB 200). 100 μl of the sample was removed as input and stored at 20. Immunoprecipitation was performed overnight under rotation at 4 using 1/100 T7RNA antibody (Biolabs CB MAB-0296MC) and antiflag (Sigma F1804 and F3165). Immunoprecipitated samples were incubated with Protein G Dynabeads (Invitrogen) with rotation for 2 min at room temperature. The tube was washed three times with 1X PBS with 0.02% Tween-20 using the Dynamag magnet setup. The beads were resuspended in 200 μl TE buffer with 1% SDS and 1 μl RNAseA (10 mg/ml) and 1 μl proteinase K (20 mg/ml). Samples were incubated at 65 for 10 h to reverse the formaldehyde crosslinking. The beads were removed using the Dynamag magnet and DNA of the supernatant purified using Qiagen Minelute PCR purification kit using two elution steps. DNA was eluted into a 50 μl TE buffer and stored at -20 until further processing.

tag: chip antibody

value: T7 RNA pol antibody (Biolabs CB MAB-0296MC)


title: plasma, subject c8719b33T1

value: Yes


title: plasma, subject c8719b33T4


title: plasma, subject ca128984T4

value: Negative


title: CTL ASO1 rep 3

source_name: Deceased female individual

value: female


title: plasma, subject ca128984T1

value: Somascan discovery platform v4


title: plasma, subject ca2561d8T1


title: plasma, subject c82d0824T1


title: ChIP-seq T7 RNAP of E coli: RSG_B012 - 2h arabinoseHi-C (HpaII) of E coli: RSG_B834 - 2h arab. + 10 min rifam/novob


title: CTL ASO1 rep 2


title: plasma, subject c7f7c7f5T1


title: plasma, subject c7ad26dbT4


title: ChIP-seq T7 RNAP of E coli: RSG_B012 - 2h glucoseHi-C (HpaII) of E coli: RSG_B834 - 2h arabinose + 10 min novobiocin


title: DAP_EREB7_deM_SE50

source_name: Leave

tag: cultivar

value: 2 week old seedling

tag: treatment

value: deMethylated


title: plasma, subject c78052ddT1

tag: age


title: plasma, subject c76458ceT1


title: CTL ASO1 rep 4


title: plasma, subject c7ad26dbT1


title: ASO1 rep 2


title: CTL ASO1 rep 1


title: ChIP-seq GapR of Escherichia coli: RSG_B789 - 2h arabinose + 10 min rifampicin

value: Antiflag (Sigma F1804 and F3165)


title: ChIP-seq GapR of Escherichia coli: RSG_B795 - 2h arabinose + 10 min rifampicin


title: plasma, subject c665f523T1


title: plasma, subject c59bd348T8


title: plasma, subject c65c02ddT1


title: plasma, subject c5988ee0T1


title: ChIP-seq GapR of Escherichia coli: RSG_B793 - 2h arabinose + 10 min rifampicin


title: plasma, subject c59bd348T4


title: ChIP-seq GapR of Escherichia coli: RSG_B792 - 2h arabinose + 10 min rifampicin


title: plasma, subject c58f203aT1


title: ChIP-seq GapR of Escherichia coli: RSG_B791 - 2h arabinose + 10 min rifampicin


title: plasma, subject c359e5caT1


title: ChIP-seq T7 RNAP of Escherichia coli: RSG_B229 - 2h arabinose + 10 min rifampicin


title: ASO1 rep 4


title: plasma, subject c2ab97d4T8


title: plasma, subject c34042b9T4


title: plasma, subject c3797258T1


title: plasma, subject c2ab97d4T13


title: ChIP-seq T7 RNAP of Escherichia coli: RSG_B838 - 2h arabinose + 10 min rifampicin


title: plasma, subject c2ab97d4T12


title: ChIP-seq GapR of Escherichia coli: RSG_B794 - 2h arabinose + 10 min rifampicin


title: ChIP-seq T7 RNAP of Escherichia coli: RSG_B837 - 2h arabinose + 10 min rifampicin


title: plasma, subject c24d17c6T1


title: ASO1 rep 1


title: plasma, subject c1d16ee5T1


title: plasma, subject c2ab97d4T1


title: ChIP-seq T7 RNAP of Escherichia coli: RSG_B836 - 2h arabinose + 10 min rifampicin


title: plasma, subject c12a975cT1


title: plasma, subject c12a975cT4


title: ChIP-seq T7 RNAP of Escherichia coli: RSG_B835 - 2h arabinose + 10 min rifampicin


title: plasma, subject c06f90b7T4


title: plasma, subject c06f90b7T8


title: ChIP-seq T7 RNAP of Escherichia coli: RSG_B834 - 2h arabinose + 10 min rifampicin


title: plasma, subject c1b7f5bdT1


title: CPF3

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline (CIRCexplorer2) is applied to detect circRNAs and identify alternative (back-)splicing in back-spliced circular RNAs (circRNAs)
The expression of circRNAs is usually represented by the fragments that are mapped to the back-spliced exon–exon junction sites. In addition to the raw fragment numbers, normalized RNA-seq fragments that are mapped to a specific back-spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM (Fragments mapped to back- spliced junction Per Million mapped fragments), circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology (GO) annotates genes to  biological processes, molecular functions, and cellular components in a directed acyclic graph structure, and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotates genes to  pathways. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level  information, especially large- scale molecular datasets generated by genome sequencing and other high- throughput experimental technologies (http://www.genome.jp/kegg/). We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways.
circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs, microRNA target site in exons of circRNA loci were identified using miRanda (animal species) or psRobot (plant species). software could be used to construct the circRNA-miRNA-gene networks.
Genome_build: UMD3.1

source_name: Brain tissue

extract_protocol:
Total RNA was isolated with Trizol from brain tissues
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

value: CPF toxication


title: CPF2


title: plasma, subject c06f90b7T12


title: plasma, subject c02cee4eT1

value: Male


title: plasma, subject bfb9f0d5T20


title: plasma, subject c02cee4eT4


title: plasma, subject bfb9f0d5T12


title: ASO1 rep 3


title: plasma, subject bf2bf92bT1


title: plasma, subject bfb9f0d5T1


title: CYP3

value: CYP toxication


title: CYP2


title: plasma, subject bf04cb82T13


title: plasma, subject bf04cb82T8


title: plasma, subject bf04cb82T4


title: plasma, subject bf04cb82T12


title: plasma, subject bf04cb82T1


title: plasma, subject c06f90b7T1


title: Cont3

value: No toxication


title: plasma, subject bece8414T1


title: Cont2


title: plasma, subject be3bd991T4


title: plasma, subject be3bd991T21


title: CPF1


title: Cont1


title: plasma, subject bdb8a81cT8


title: plasma, subject be3bd991T1


title: plasma, subject bdb8a81cT4


title: E11.5 Tfap2EDKO Aboral Epithelium 6

city: Iowa City

first: HUOJUN

last: CAO

state: IA

address: 801 Newton Road

institute: University of Iowa

data_processing:
RNA-seq reads were quality checked using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Low-quality and adapter sequences were removed using Trimmomatic. Expression of transcripts was quantified using Salmon, and estimates of transcript abundance for gene-level analysis were imported and summarized using the tximport package of the R/Bioconductor software suite.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts (gene level summarized with tximport) for each sample

source_name: Mandibular Epithelium

extract_protocol:
Tissues were dehydrated through a graded ethanol series, embedded in paraffin wax and sectioned (7 μm). Selected regions of tissue sections were microdissected with the Leica LMD7000 Laser Microdissection System, at 20× magnification while keeping laser power to a minimum. After cells were collected in cap, tubes were spun down quickly and 5 μl of Smart-seq2 lysis buffer (with 0.5% Triton X-100, 5μg Proteinase K and 2 U μl−1 RNase inhibitor) was added, followed by pipetting up and down to mix.
The Smart-seq2 protocol was followed for cDNA preparation, Tn5 Tagmentation, and library preparation for next generation sequencing. Quality of cDNA and sequencing libraries were determined using a Bioanalyzer system (Agilent) and real time PCR. The KAPA Library Quantification Kit (Roche) was used for quantification of RNA sequencing libraries.

value: Mandibular Epithelium

tag: genotype

value: Tfap2 EDKO


title: E11.5 Tfap2EDKO Aboral Epithelium 5


title: plasma, subject bdb8a81cT1

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

value: Positive

value: No


title: CYP1


title: plasma, subject bcc5d52bT1


title: plasma, subject bca30fbaT1

value: Female


title: plasma, subject bc367deaT1

value: Yes


title: E11.5 Tfap2EDKO Aboral Epithelium 4


title: plasma, subject bbe4f261T1

value: Negative


title: plasma, subject bbc4f6dfT1


title: E11.5 Tfap2EDKO Aboral Epithelium 3


title: MYC_SOL_4

city: Fayetteville

first: Kevin

last: Murach

state: AR

address: 155 Stadium Dr.

department: Health, Human Performance, and Recreation

institute: University of Arkansas

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Assembly: A custom genome assembly to interrogate both nuclear and rDNA methylation was generated by adding the consensus rDNA repeat sequences, BK000964.3, as a separate chromosome to the GRCm39 (GCA_000001635.9) mouse reference genome assembly.
Supplementary files format and content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome

source_name: soleus

extract_protocol:
DNA was isolated from the soleus tissue using the Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) as specified in the protocol.
“Classic” RRBS library preparation was performed by digesting genomic DNA with 30 units of MspI enzyme (New England BioLabs, R0106), and fragments were ligated to pre-annealed adapters containing 5’-methyl-cyotosine. Adapter-ligated fragments ≥50 base pairs were recovered using the DNA Clean & Concentrator Kit (Zymo Research, D4003) and bisulfite-converted using the EZ DNA Methylation-Lightning KitTM (Zymo Research, D5030) following the standard protocol. Preparative-scale PCR was performed, and the products were purified again using the Clean and Concentrator kit.

treatment_protocol: Soleus tissue and DNA were extracted and reduced representation bisulfite sequencing (RRBS) for whole-genome and ribosomal DNA-specific analysis.

value: Skeletal Muscle

tag: conditions

value: Myc overexpression


title: E11.5 Tfap2EDKO Aboral Epithelium 2


title: plasma, subject b9c7c078T1

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

value: Somascan discovery platform v4


title: plasma, subject b8a6551dT1


title: E11.5 Tfap2EDKO Aboral Epithelium 1


title: plasma, subject b974b122T4


title: MYC_SOL_3


title: E11.5 Pitx2KO Dental Lamina 8

value: Pitx2 Knockout


title: plasma, subject b8414bb0T8


title: MYC_SOL_2


title: plasma, subject b8414bb0T12


title: E11.5 Pitx2KO Dental Lamina 7


title: plasma, subject b8414bb0T1


title: plasma, subject b8414bb0T4


title: MYC_SOL_1


title: plasma, subject b8347125T4


title: plasma, subject b8347125T1


title: E11.5 Pitx2KO Dental Lamina 6


title: CON_SOL_3

value: Control


title: plasma, subject b82ddf4fT20


title: plasma, subject b82ddf4fT1


title: E11.5 Pitx2KO Dental Lamina 5


title: plasma, subject b7c739c9T8


title: plasma, subject b7c739c9T4


title: CON_SOL_2


title: E11.5 Pitx2KO Dental Lamina 4


title: plasma, subject b7c739c9T1


title: E11.5 Pitx2KO Dental Lamina 3