title: DMI_Quercetin3

city: Zhenjiang

first: Jue

last: Jia

address: No.438, Jiefang Road

institute: the Affiliated Hospital of Jiangsu University

description:
3T3-L1 adipocyte D6 quercetin re3
B3_count

data_processing:
Illumina pipeline CASAVA v1.8.2 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster  Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to  the manufacturer’s instructions. After cluster generation, the library preparations were  sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were  generated
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and iscurrently the most commonly used method for estimating gene expression levels
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

source_name: 3T3-L1 cells

growth_protocol: 3T3-L1 cells  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol agent (Invitrogen). ≥1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra TM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 0.5mM IBMX，1uM Dexamethasone and 10ug/ml Insulin.0.5mM IBMX，1uM Dexamethasone and 10ug/ml Insulin in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: cell line

value: 3T3-L1 cells

value: murine (3T3-L1) preadipocyte cells

value: WT


title: plasma, subject b7c69374T4

status: Public on Dec 01 2023

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

country: USA

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

organism: Homo sapiens

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: age

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: CON_SOL_1

type: SRA

city: Fayetteville

first: Kevin

last: Murach

state: AR

address: 155 Stadium Dr.

department: Health, Human Performance, and Recreation

institute: University of Arkansas

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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.

tag: tissue

value: Skeletal Muscle

tag: conditions

value: Control


title: plasma, subject b7c739c9T12

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 b7c69374T12

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 b7c69374T13


title: plasma, subject b7c69374T1


title: DMI_Quercetin1

country: China

description:
3T3-L1 adipocyte D6 quercetin re1
B1_count

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: genotype

tag: treatment


title: plasma, subject b77aa144T12


title: plasma, subject b77aa144T1


title: DMI_Luteolin3

description:
3T3-L1 adipocyte D6 luteolin re3
A3_count


title: E11.5 Pitx2KO Dental Lamina 1

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

value: Pitx2 Knockout


title: plasma, subject b7c69374T8


title: E11.5 Wild Type Posterior Epithelium 4

value: Wild Type


title: E11.5 Wild Type Posterior Epithelium 3


title: plasma, subject b7726c1aT4

value: Female


title: E11.5 Pitx2KO Dental Lamina 2


title: DMI_Luteolin2

description:
3T3-L1 adipocyte D6 luteolin re2
A2_count


title: plasma, subject b7726c1aT1


title: plasma, subject b6d73287T4


title: DMI_Quercetin2

description:
3T3-L1 adipocyte D6 quercetin re2
B2_count


title: plasma, subject bbf5be7bT1


title: DMI_Luteolin1

description:
3T3-L1 adipocyte D6 luteolin re1
A1_count


title: plasma, subject b5095d08T8


title: E11.5 Wild Type Posterior Epithelium 1


title: plasma, subject b5095d08T4


title: plasma, subject b5095d08T1


title: E11.5 Wild Type Posterior Epithelium 2


title: E11.5 Wild Type Dental Lamina 8


title: plasma, subject b4cf1b9dT20


title: plasma, subject b4cf1b9dT1


title: DMI2

description:
3T3-L1 adipocyte D6 control re2
DMI2_count


title: E11.5 Wild Type Dental Lamina 7


title: DNA methylation data PDXO D61 suspension ICB984

type: genomic

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina HumanMethylation450 BeadChip or Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.26.0)

label: Cy5 and Cy3

source_name: Patient-derived xenograft organoids D61 suspension ICB984

label_protocol: Standard Illumina Protocol

growth_protocol: For PDO and PDXO generation, fresh surgically resected tumor samples were disgregated within 24 hours of surgical resection and culured in PDO medium in a 37°C, 5% CO2 incubator (see Methods section for further details)

extract_protocol: Genomic DNA was extracted from FFPE samples using Resnova MagPurix FFPE DNA Extraction Kit according to standard instructions; while PDOs/PDXOs were lysed in lysis buffer (20 mM EDTA, 10 mM Tris, 200 mM NaCl, 0.2% Triton X-100, 100 µg/ml Proteinase K, pH 8.0) for 1h at 37°C under agitation. Genomic DNA was extracted with phenol-chloroform and precipitated with isopropanol.

tag: sample type

value: fresh-frozen


title: DNA methylation data PDXO D120 suspension HT028

source_name: Patient-derived xenograft organoids D120 suspension HT028


title: plasma, subject b43f71cbT4


title: DMI1

description:
3T3-L1 adipocyte D6 control re1
DMI1_count


title: E11.5 Wild Type Dental Lamina 6


title: DMI3

description:
3T3-L1 adipocyte D6 control re3
DMI3_count


title: plasma, subject b43f71cbT1


title: plasma, subject b358e077T1


title: NC3

description:
3T3-L1 preadipocyte D6 re3
NC3_count

value: untreated


title: E11.5 Wild Type Dental Lamina 5


title: plasma, subject b18b35ecT8


title: DNA methylation data PDXO D28 96well plate ICB984

source_name: Patient-derived xenograft organoids D28 96well plate ICB984


title: DNA methylation data PDO T#21 D14

source_name: Patient-derived organoid from tumor T#21


title: plasma, subject b18b35ecT4


title: MECLP5

city: Yangling

first: Zhenliang

last: Zhu

address: 3 Taicheng Road

institute: Northwest A&F University

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke with parameters: filter -l 5 -q 0.5 -n 0.1 -Q 2 -5 1 -c 50.  Cleaned reads were mapped to the reference genome using Bowtie2 (version: 2.2.5).
MACS2 was used (version: 2.1.2) to call peaks (open chromatin regions), in which '--bw 200 -s 50 -p 1e-5 -m 10 30 --broad -B --trackline' was used. With which the IDR (v2.0.4) was applied to measure the reproducibility of findings identified from replicate sample.
The different enrichment peaks from different sample was plotted by MAnorm (v1.1), the significant regions were picked up if |M|≥ 1 and p-value ≤10-5.
To identify the position of nucleosomes, broad peaks called by MACS2 were analyzed using NucleoATAC (v0.3.4)
Assembly: Capra hircus (assembly ARS1.2)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: bigWig, xls

organism: Capra hircus

source_name: mammary gland

extract_protocol:
The cell preparation was begin with harvesting and counting intact and homogenous cell, which followed by centrifuging those 50,000 cells for about 5min at 500g, 4°C. Washing those cells once with 50μl of cold PBS buffer and centrifuging them again under the same condition after removing and discarding supernatant. Removing and discarding supernatant again, and pipetted up and down to resuspend the cell pellet in 50μl of cold lysis buffer gently, which also obey centrifuge but for 10 min this time.
After discarding the supernatant, the resuspension of the nuclei pellet we obtained should be carried out immediately in the prepared transposition reaction mix which contained Nextera Tn5 Transposase from Nextera kit. Incubated the transposition reaction at 37°C for 30 min. A Qiagen MinElute PCR Purification Kit is used to transposition, purify instantly, following by which the 10μl elution buffer (Buffer EB from the MinElute kit consisting of 10 mM Tris·Cl, pH 8) was applied to elute transposed DNA. Finally the PCR amplification was performed to amplify transposed DNA fragments, combine the following in a 0.2 ml PCR tube with enough thermal cycle. Prior to amplification, adapters have to be completed with a 72°C extension step, as well as the qPCR and library quality control using gel electrophoresis is provided. Libraries were pooled at equimolar ratios with barcodes and sequenced on the BGISEQ-500 platform.

value: mammary gland

value: mammary epithelial cell

value: lactation period


title: E11.5 Wild Type Dental Lamina 4


title: NC1

description:
3T3-L1 preadipocyte D6 re1
NC1_count

value: 3T3-L1 cells

value: murine (3T3-L1) preadipocyte cells

value: WT


title: E11.5 Wild Type Dental Lamina 3


title: plasma, subject b18b35ecT1

value: Male

value: Positive

value: No


title: E11.5 Wild Type Dental Lamina 2


title: plasma, subject b0d5ae31T8

value: Yes

value: Somascan discovery platform v4


title: MECLP1


title: KO1

city: Beijing

first: Anna

address: Beijing Normal University

institute: BNU

data_processing:
Clean data were filtered and quality controlled from raw data, then alignment step was performed.
Novel transcripts prediction
Gene expression analysis
Differential expression analysis
Gene Ontology enrichment analysis and pathway enrichment analysis
Assembly: mm10
Supplementary files format and content: excel files include FPKM values of gene for each sample
Supplementary files format and content: excel files include FPKM values of transcript for each sample

source_name: bone marrow

growth_protocol: Granulocyte monocyte progenitor sorted from mouse bone marrow were placed in 1640 medium containing 10% serum.

extract_protocol:
Trizol and 0.2-fold volume of trichloromethane were added to the cells, and isopropanol and absolute ethanol were added to precipitate the extracted RNA. The RNA was dissolved with water and the RNA concentration and purity were detected with nano drop.
RNA was enriched with magnetic beads with oligo (DT), then cDNA was synthesized using mRNA as a template, double stranded cDNA was purified and amplified by PCR.

treatment_protocol: Mouse granulocyte-monocyte progenitor were not subjected to any drug treatment.

value: bone marrow

value: granulocyte-monocyte progenitor

value: MST1 deficient mice


title: MECDP3

value: dry period


title: MECDP2


title: DNA methylation data PDO T#1 D61

source_name: Patient-derived organoid from tumor T#1

value: fresh-frozen


title: MECLP2


title: NC2

description:
3T3-L1 preadipocyte D6 re2
NC2_count

value: untreated


title: E11.5 Wild Type Anterior Epithelium 5

value: Mandibular Epithelium

value: Wild Type


title: WT2

value: wild type


title: DNA methylation data PDO T#9 D14

source_name: Patient-derived organoid from tumor T#9


title: plasma, subject b0d5ae31T13


title: plasma, subject b0d5ae31T4


title: plasma, subject b0d5ae31T12


title: C57 allele SNP Bulk RNAseq

city: Wuhan

first: Weize

last: Xu

state: Hubei

address: shizishan street No.1

institute: Huazhong Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome using hisat2.
SNPs in the exon of expressed gene were called with GATK4.0, allele and reference of each SNP were counted with optional commands mpileup in samtools.
Supplementary_files_format_and_content: RNA-seq count matrix for each samples
Supplementary_files_format_and_content: Haplo-type SNP list for C57

source_name: Brain/PVN

extract_protocol:
C6 cell lines or the PVN of C57 was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. mRNA-seq Lib Prep Kit for Illumina (RK20302) used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain/PVN

value: 2 Day

value: Female C57BL/6 mice were crossed with male BALB/c mice. The PVN of mouse brain which from the offspring mice


title: DNA methylation data primary T#1

source_name: Primary tumor T#1

value: FFPE


title: DNA methylation data primary T#21

source_name: Primary tumor T#21


title: E11.5 Wild Type Anterior Epithelium 4


title: WT1


title: E11.5 Wild Type Anterior Epithelium 3


title: plasma, subject b0d5ae31T1

value: Male

value: Positive


title: Effector_T_4

first: Yang

last: Liu

address: Yiheyuan Road, No. 5

institute: School of life sciences, Peking University

description: cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted and transcfected into Rag1-/- recipient mice, after 21 days,recipients were sacrificed and inflammentory T cells from gut were sorted by CD90.1 and extract DNA

data_processing:
Illumina RTA software used for basecalling.
Both Illumina adapter sequences and ending low quality sequences (QC < 30) were trimmed by cutadapt (http://cutadapt.readthedocs.io/en/stable/); remaining reads shorter than 25bp were discarded.
The reported pipeline used in PEM-seq, termed superQ, was applied to perform reads alignment and translocation break point detection.
The reported pipeline, superQ, was applied to perform duplicates identification.
Break-site and neighbor ±5bp region was analyzed for indels; reads containing large deletions resulting from resection and rejoining in the break-site ±250kb region were also categorized as indels (I). Reads without any detected mutations around break point were identified as germline (G). Genome-wide translocation (T) was identified as described in PEM-seq.
Genome_build: mm10
Supplementary_files_format_and_content: tab files generated by superQ

source_name: gut

growth_protocol: T cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, 100 mM non-essential amino acids (NEAA), 50 U/mL penicillin, 50 mg/mL streptomycin, and 50 mM b-mercaptoethanol without further indication. For retroviral vector (RV) experiment, TCR transgenic naïve CD4+ T cells were sorted from a HH7-2tg Cas9 mouse, then activated under TH0 condition with plated coated a-mouse CD3e (0.25 mg/mL, BioXcell) and a-mouse CD28 (1 mg/mL, BioXcell) for 2 days, the medium was supplemented with 1 mg/mL a-mouse IFNg (BioXcell), 1 mg/mL a-mouse IL-4 (BioXcell), 20 U/mL hIL-2 (Peprotech) and 1 mg/ml a-TGFβ (BioXcell) to prevent TH1, TH2 or TH17 polarization.

extract_protocol:
Intestinal tissues were washed by PBS with 1 mM DTT for 10 min, followed by 5 mM EDTA for 20 min to remove epithelial cells, then treated by RPMI with collagenase (1 mg/mL collagenase; Roche), DNase I (100 μg/mL; Sigma), dispase (0.05 U/mL; Worthington) and 10% FBS at 37ºC for 60 min with constant mixing. Leukocytes were collected by 40-80% Percoll gradient. Inflammatory T cells were sorted with CD45.1+ and CD90.1+. Genomic DNA was extracted by the standard protocols with proteinase K treatment.
Genomic DNA was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced

treatment_protocol: Activated T cells were transfected with pST-sgRNA RV in the presence of 8 mg/mL polybrene during spin infection (2,000 g for 120 min at 33 ºC) and then rested for 3 days in medium containing 20 U/mL hIL-2 (Peprotech), 1 mg/mL a-TGFβ (BioXcell), 5 ng/mL mouse IL-7 (Sinobio), 1 mg/mL a-mouse IFNg (BioXcell) and 1 mg/mL a-mouse IL-4 (BioXcell). CD90.1 positive activated T cells were sorted and transferred into Rag1–/– recipient mice, with 300,000 cells for 1 recipient through i.v. tail. After 21 days, recipients were sacrificed and dissected to get intestinal tissues.

tag: strain

tag: transfection

value: pST-sgRNA

value: Rag1-/- NM


title: plasma, subject b0b02bb8T12

value: Female

value: Yes

value: No

value: Somascan discovery platform v4


title: Effector_T_3


title: BC01

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

department: Biology department

institute: Brandeis University

data_processing:
Data was aligned using minimap2
Visualization in IGV
Genome_build: dm6
Supplementary_files_format_and_content: TDF IGV format

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Total RNA was extracted using Trizol reagent (Sigma). Probes complementary to mbl-exon2 were denatured at 85°C for 3 minutes, and placed on ice immediately. Probes mixture was added to total RNA, mixed well and Incubated for 3h at 37°C rotating. Streptavidin C1 beads from NEB (CAT# S1420S) were prepared following manufacturer instructions. 50µl of resuspended beads were added to the sample, and Incubate for 1h at 37°C rotating. Magnetically separated the beads from samples, and then washed 5X in 8X bead volume (800µl) of 1X Hybridization buffer. For elution we added 100µl of elution buffer and then incubated for 10 min at 95°C. Magnetically separated the elutent from beads, and transferred to fresh tube and extract RNA using TRI reagent (Sigma). Samples were treated with DNaseI (NEB). Magnetically separated the elutent from beads, and transferred to fresh tube and extract RNA using TRI reagent (Sigma). Samples were treated with DNaseI (NEB) and performed the nanopore sequencing as instructed in the manual from oxford nanopore technology kit.
Libraries preparation was done following Nanopore technology manufacturer instruction for PCR-cDNA Sequencing Kit (SQK-PCS109)
Long reads Nanopore technology.

value: Canton S


title: E11.5 Wild Type Anterior Epithelium 2


title: Skin, susceptible, after infestation, bovine 19

city: Bagé

first: Robert

last: Domingues

state: Rio Grande do Sul

address: Av. General Osório 1737/302

department: Animal health

country: Brazil

institute: Embrapa

data_processing:
Sample RNA quality check was performed with the FastQC (v. 0.11.8)
Reads were aligned to the bovine reference genome using Hisat2 (v. 2.1.0), with the annotation from RefSeq assembly accession GCF_002263795.1
Sample counts were sorted using Samtools v 1.9 and grouped with the FeatureCounts (v. 1.6.4)
Using DESEQ2 (v. 4.0.3), gene counts were normalized and differential expression analyzes at the gene level were performed using the generalized linear model: Yijkl = TIMEj + TYPEk + TIME*TYPE(jk) + TYPE*ANIMAL(kl) + eijkl.
The 237preIA sample was removed from the final analysis due to its discrepancy with the other data, when the PCA and heatmap analysis was performed
Assembly: bovine reference genome (ARS-UCD1.2, GCA_002263795.2; 2018
Supplementary files format and content: featureCounts_total.txt - table with gene counts per sample
Supplementary files format and content: normalized_counts.txt - table with gene counts normalized according to the generalized linear model used

organism: Bos taurus

source_name: skin

extract_protocol:
Skin biopsies were mechanically crushed with 7 mm metallic beads in the TissueLyser equipment (Qiagen), and total RNA harvested using the RNeasy Fibrous Tissue kit (Qiagen)
Sequencing libraries were prepared individually using TruSeq RNA Sample Preparation kit v2 guide (Illumina, San Diego, CA) with standard protocols, clustered using TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina, San Diego, CA)
Sequencing libraries were sequenced in a paired-end mode (2 x 100 bp) on a HiSeq1500 equipment (Illumina, San Diego, CA)

treatment_protocol: Thirty-nine Braford cattle were artificially infected with approximately 20,000 cattle tick larvae (Rhipicephalus microplus). Skin biopsy samples were collected before infestation and 24 hours after infestation.

tag: breed

value: Braford

value: skin

tag: tick resistance_phenotype

value: susceptible

tag: time point

value: After infestation


title: Skin, susceptible, after infestation, bovine 18


title: E11.5 Wild Type Anterior Epithelium 1

value: Mandibular Epithelium

value: Wild Type


title: plasma, subject b0b02bb8T1

source_name: serum

tag: subject id

tag: blood sample id

tag: Sex


title: Effector_T_2


title: E11.5 Wild Type Aboral Epithelium 8


title: DNA methylation data PDXO D28 96well plate HT028

source_name: Patient-derived xenograft organoids D28 96well plate HT028

value: fresh-frozen


title: MECDP1

value: mammary gland

value: mammary epithelial cell

value: dry period


title: BC03


title: Effector_T_1

value: pST-sgRNA


title: plasma, subject b061d79cT4

tag: age

tag: days since first sample

tag: patient classification at first sample

value: Positive


title: DNA methylation data primary T#9

source_name: Primary tumor T#9

value: FFPE


title: E11.5 Wild Type Aboral Epithelium 7

source_name: Mandibular Epithelium

tag: tissue


title: plasma, subject b061d79cT1

value: Female

tag: covid-19 status

value: Yes

tag: instrument model


title: plasma, subject af7e42f1T1

value: Negative

value: No

value: Somascan discovery platform v4


title: Activated_T

description: cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted, and extract DNA

source_name: spleen

value: Activated by a-CD3/CD28, a-IFNg, and a-IL-4

tag: genotype

value: HH7-tg Cas9 CD45.1


title: Skin, susceptible, after infestation, bovine 17

value: Braford

value: skin

value: susceptible

value: After infestation


title: E11.5 Wild Type Aboral Epithelium 5

value: Mandibular Epithelium

value: Wild Type


title: plasma, subject af4f750aT8


title: NAT_LN_3

first: Shanqing

last: Li

address: No.1 Shuaifuyuan, Wangfujing Street

department: Department of Thoracic Surgery

institute: Peking Union Medical College Hospital

data_processing:
SOAPnuke (v1.5.2)
We used SOAPnuke(v1.5.2) to filter the raw reads, the filtering rules were as follows: 1) Removed reads containing adapters, 2) Removed reads with N ratio greater than 5%, 3) Removed low-quality reads (the number of bases with quality value Q<=15 accounts for more than 20% of the entire read).
We used CIRI(v2.0.5) and find_circ(v1.2) to predict circRNA, and integrate the results of the two software according to the start and end positions of circRNA. CircRNAs that satisfied both starting and ending positions within 10 bases before and after were merged into one class. The known circRNAs were identified according to the circBase database, and the source genes of the circRNAs were determined according to the location information of the reference genome and functional annotations were performed on the source genes (3 error bases were allowed for both the start and end positions).
We calculated the expression of circRNA according to the number of back-spliced reads aligned to both ends of the circRNA. Since two software CIRI and find_circ were used for prediction, the final number of back-spliced reads was the average of the prediction results of the two softwares.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Normal adjacent tissue to non-small cell lung cancer

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). Then, 3μg of total RNA was treated with DNase I which degraded double-stranded and single-stranded DNA presenting in RNA samples. And the ribosomal RNA was removed using the Ribo-off rRNA Depletion Kit (Vazyme, Inc.). Linear RNA was removed using RNase R (Epicentre, lnc). Purification was performed using Agencourt RNAClean XP magnetic beads. All other steps were performed according to the manufacturer's protocols. The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using BMG (OMEGA).
RNA libraries were prepared for sequencing using standard DNBSEQ protocols
RNase R degrades the abundant linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method. Double-stranded cDNA fragments are subjected to end-repair and A-tailing. After amplification by PCR, the reaction system and program for circularization are configured and set up. The concentration and specific activity of circRNAs were measured by DNBSEQ-G400.

value: female

tag: pair

value: pair 6


title: Skin, susceptible, after infestation, bovine 13


title: E11.5 Wild Type Aboral Epithelium 4


title: E11.5 Wild Type Aboral Epithelium 3


title: NAT_3

value: Normal adjacent tissue to non-small cell lung cancer

value: pair 5


title: E11.5 Wild Type Dental Lamina 1


title: NAT_LN_2

value: male

value: pair 4


title: plasma, subject af4f750aT4

value: Female

value: Positive

value: Yes


title: Skin, susceptible, after infestation, bovine 14


title: Skin, susceptible, after infestation, bovine 11


title: E11.5 Wild Type Aboral Epithelium 2


title: plasma, subject af4f750aT12

value: No

value: Somascan discovery platform v4


title: Skin, susceptible, after infestation, bovine 12

value: Braford


title: NAT_2

value: pair 3


title: Skin, susceptible, after infestation, bovine 15

value: skin

value: susceptible


title: E11.5 Wild Type Aboral Epithelium 1

value: Mandibular Epithelium


title: Skin, susceptible, after infestation, bovine 10

value: After infestation


title: E11.5 Wild Type Aboral Epithelium 6

value: Wild Type


title: Naïve_T_primer_control

description: cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, and extract DNA

tag: treatment

value: HH7-tg Cas9 CD45.1


title: plasma, subject af4f750aT1


title: Skin, susceptible, after infestation, bovine 16


title: NAT_LN_1

value: Normal adjacent tissue to non-small cell lung cancer

value: female

value: pair 2


title: plasma, subject af4f750aT0


title: NAT_1

value: pair 1


title: Skin, susceptible, after infestation, bovine 9


title: plasma, subject af4f750aT13

value: Female


title: Tumor_LN_3

source_name: Non-small cell lung cancer tissue

value: Non-small cell lung cancer tissue

value: pair 6


title: mouse CCS, Input-4

city: Salt Lake City

first: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

data_processing:
Sequencing was performed on an Illumina NovaSeq instrument using the 2 x 50 bp protocol to a depth of approximately 30 million reads per sample. ChIP-seq reads were aligned to the mm10 using BWA-MEM (version 0.7.10-r789) for paired-end reads
Assembly: mm10
Supplementary files format and content: Bigwig files are generated with MACS2 and bdg2bigwig and  Peaks were called from each aligned bam file against input reads using MACS2 version 2.2.6

source_name: Tumor

extract_protocol:
Tumor samples from mouse models were processed by cryogenic grinding, fixed with formaldehyde, and quenched with glycine. Nuclei were extracted via lysis and douncing, followed by lysis of nuclear pellets. The chromatin was fragmented by sonication, then incubated with primary antibodies (anti-V5, anti-RNAPOL2, or anti-H3K27ac) and DynaBeads, subsequently eluted and purified for DNA analysis using a commercial kit.(Zymo )
Libraries were constructed with the NEBNext ChIP-seq Library Prep kit with Unique Dual Index Primers (New England Biolabs).

value: Tumor

tag: antibody


title: plasma, subject ae4eb9bdT4

value: Male

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: Tumor_3

value: pair 5


title: Skin, susceptible, after infestation, bovine 8

value: Braford

value: skin

value: susceptible

value: After infestation


title: plasma, subject ae4eb9bdT8


title: mouse CCS, Input-3


title: Tumor_LN_2

value: male

value: pair 4


title: plasma, subject ae4eb9bdT1


title: Skin, susceptible, after infestation, bovine 7


title: plasma, subject b6d73287T1


title: mouse CCS, H3k27ac-4


title: mouse CCS, Input-1


title: plasma, subject adb5713dT1

value: Negative


title: Skin, susceptible, after infestation, bovine 5


title: Skin, susceptible, after infestation, bovine 4


title: plasma, subject acc5de3cT4


title: mouse CCS, pol2-4


title: Tumor_2

value: pair 3


title: mouse CCS, V5-4


title: Tumor_LN_1

value: Non-small cell lung cancer tissue

value: female

value: pair 2


title: Skin, susceptible, after infestation, bovine 3


title: Tumor_1

value: pair 1


title: mouse CCS, Input-2

value: Tumor


title: mouse CCS, H3k27ac-3


title: plasma, subject aba21b12T1

value: Female

value: Positive


title: plasma, subject aae65065T1

value: Yes

value: Somascan discovery platform v4


title: Skin, susceptible, after infestation, bovine 6

value: Braford


title: mouse CCS, pol2-3


title: plasma, subject aa853c05T8


title: Skin, susceptible, after infestation, bovine 2

value: skin


title: ESG3, replicate 1, scRNAseq

city: Kyoto

first: DUERNA

last: TIE

state: Kyoto

address: 54 Shogoin Kawara-machi, Sakyo

country: Japan

institute: Kyoto University Faculty of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Isolated eccrine sweat gland

extract_protocol:
Healthy human skins were dissected and placed on a sterile 30-mm culture dish with ice-cold PBS. Tissues were then transferred into RPIM medium, minced with scissors, and placed in a 30-mm culture dish containing neutral red working buffer (10 uM neutral red). We isolated whole ESGs under a stereomicroscope using forceps and collected ESGs into a 12-well cell culture dish containing 2.5 mg/ml librease TL in RPIM medium and incubated at 37 ̊C for one night. The single-cell suspension was obtained the next day by repeatedly aspirating and dispensing the solution with a 10-ml pipette for 3 min with 3 ml warm 0.05% trypsin / 0.5M EDTA. Following tissue digestion, 40 ml of resuspension media (RIPM supplemented with 5% normal human serum and 1% pen/strep) was added to neutralize enzyme activity. The digestion mixture was passed through a 70 mm cell strainer and centrifuged at 150 x g for 8 min at 4 degrees. The pellet was resuspended and incubated in dead cell remove buffer to remove dead cells using the MS columns of the Dead Cell Removal Kit as per the manufacturer’s directions. Finally, the cell pellet was resuspended in 1 ml of 0.04% BSA in DPBS. This final cell suspension solution was passed through a 40 mm cell filter to discard debris. Cell number was counted using the automated cell counter Countess.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, ~8000 ESG cells for sample-1, ~10000 ESG cells for sample-2 and sample-3 were mixed with the retrotranscription reagents and pipetted into a Chip A Single Cell, also containing the Single Cell 3’ Gel Bead suspension and Partitioning Oil. The Chip was subsequently loaded into a Chromium Single Cell Controller. The cells were captured in nanoscale droplets containing the reagents needed for reverse transcription and a gel bead. Following the manufacturer's protocol, the resulting gel bead-in-emulsions (GEMs) were then transferred to a thermocycler to perform the retrotranscription. Each gel bead contained a specific 10X Genomics barcode, an Illumina R1 sequence, a Unique Molecular Identifier (UMI), and a poly-dT primer sequence. Following an amplification step, cDNA was further processed by fragmentation, end-repair, and A-tailing double-sided size selection. Finally, Illumina adaptors and a sample index were added through PCR using a total number of cycles adjusted to the cDNA concentration. After sample indexing, libraries were subjected to double-sided size selection, and quantification was carried out using the Qubit dsDNA HS Assay Kit, and cDNA integrity was assessed using D1000 ScreenTapes. Library quality control metrics were as follows: 550.19 pg/µl with an average size of ~454 bps. Paired-end sequencing (20,000 reads / cell) was finally performed with MGISEQ G400RS platform (MGI).

tag: cell type

value: eccrine sweat gland cells

value: Isolated eccrine sweat gland


title: ESG2, replicate 1, scRNAseq

description: 10x Genomics


title: Skin, susceptible, after infestation, bovine 1

tag: breed

value: susceptible

value: After infestation


title: plasma, subject aa853c05T4

value: No


title: Skin, resistant, after infestation, bovine 20

tag: tick resistance_phenotype

value: resistant


title: ESG1, replicate 1, scRNAseq

description: 10x Genomics


title: mouse CCS, H3k27ac-2


title: mouse CCS, V5-3


title: Skin, resistant, after infestation, bovine 19

tag: time point


title: UTX TCD - CD4+ T cell - 3

city: los angeles

first: Mandy

last: Cheng

state: CA

address: 615 Charles E Young Dr S

department: MIMG

institute: UCLA

data_processing:
fastq files were obtained and QC was performed using FASTQC.
Fastq files were then aligned to the mm10 genome using HiSat2.1.0.
HTSeq was then used to  extrapolate read counts.
Assembly: mm10
Supplementary files format and content: Tab delimited txt file contains raw counts for each sample

source_name: Spleen

growth_protocol: StemCell Naïve CD4+ T cell magnetic isolation kit was used to sort the cells from spleens of mice.

extract_protocol: RNA extraction was performed using Zymogen Quick-RNA Microprep kit using manufacturer's instructions.

treatment_protocol: Naïve CD4+ T cells were treated with platebound anti-CD3 and soluble anti-CD28 for 48 hours.

value: Spleen

tag: cell line

value: Primary

value: T Cell

value: UTX TCD

value: Anti-CD3/CD28 stimulation for 2 days


title: plasma, subject aa853c05T1

tag: subject id

tag: blood sample id

value: Female


title: mouse CCS, pol2-2

value: Tumor


title: plasma, subject aa499b5bT1

tag: Sex

tag: age

value: Positive

value: Yes


title: UTX TCD - CD4+ T cell - 2


title: Skin, resistant, after infestation, bovine 17

value: Braford


title: Skin, resistant, after infestation, bovine 18

value: skin


title: plasma, subject a9f46132T8

tag: days since first sample

tag: patient classification at first sample

value: Somascan discovery platform v4


title: UTX TCD - CD4+ T cell - 1

tag: tissue


title: mouse CCS, H3k27ac-1


title: plasma, subject a9f46132T4

tag: covid-19 status

tag: instrument model


title: Skin, resistant, after infestation, bovine 16


title: WT - CD4+ T cell - 3

tag: genotype

value: Wild Type


title: mouse CCS, pol2-1


title: plasma, subject a9f46132T0


title: WT - CD4+ T cell - 2

tag: treatment


title: Skin, resistant, after infestation, bovine 15


title: Skin, resistant, after infestation, bovine 14


title: plasma, subject a9e9e974T1


title: Skin, resistant, after infestation, bovine 13


title: WT - CD4+ T cell - 1


title: plasma, subject a8f43017T8

value: Male


title: WT

first: Mohamed

last: Omar

address: 413 East 69th Street

department: Department of Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

data_processing:
Sequencing libraries were demultiplexed with bcl2fastq (Illumina). Spatial transcriptomics libraries were processed and aligned to the mm10 mouse reference genome using the Space Ranger software (version 2.0.1), and tissue-associated barcodes were kept for further downstream analysis. The filtered UMI count matrices were merged to enable their joint analysis. Subsequently, the data was normalized (each cell was normalized by total counts over all genes) and log-scaled, then the top 4000 highly variable genes were identified (by model). The neighborhood graph was computed using the first 10 prinicipal components and 15 neighboring data points, then embedded using the UMAP algorithm. Spots were clustered using the Leiden algorithm with a resolution of 0.5, then marker genes were computed by comparing each cluster to the remaining clusters using a Student’s t-test. Spot annotation was performed using the clusters marker genes.
Assembly: mm10
Supplementary files format and content: Feature barcode matrix in HDF5 format. The matrix contains the number of unique molecular indeitifiers (UMIs) associated with a feature (row) and a barcode (column).
Library strategy: Spatial Transcriptomics

source_name: Prostate

extract_protocol:
One half of the prostate from GEMMs was utilized for scRNA-seq while the contralateral half was fixed in 10% buffered formalin and embedded in paraffin blocks and sliced into sections with a thickness of 10um thickness. dried at 42°C for 3 hrs and kept in a desiccator at room temperature overnight, before proceeding with the Visium CytAssist spatial protocol (guides CG000518, CG000520 and CG000495). Slides were deparaffinized, H&E stained and imaged using an EVOS M7000 Automated Imaging System (10x objective, 3.45µm/pixel -Thermo Fisher Scientific, CA). Slides were then de-coverslipped and tissues were hematoxylin destained, decrosslinked and hybridized overnight with the whole mouse transcriptome panel which contains pairs of specific probes for each targeted gene (PN-1000365). After hybridization, the probe pairs were ligated, the slides loaded on a Visium CytAssist instrument, ROIs adjusted and ligated probes transferred and captured on an 11 mm Visium CytAssist Spatial Gene Expression slide containing UMIs and barcoded oligos.
Spatially barcoded libraries were generated and sequenced with paired-end dual-indexing (28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2).

value: Prostate

value: C57BL6/129x1/SvJ) - littermates


title: Skin, resistant, after infestation, bovine 12

value: resistant

value: After infestation


title: PRN

value: Pb-Cre4 +/-;Pten f/f; LSL-MYCN +/+; Rb1 f/f


title: tbsPHA_4_input

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 4. Input sample.

data_processing:
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 in single-end mode.
Aligned sequence files were converted to binary format, sorted, and indexed using samtools 1.9.
Aligned and sorted BAM files were imported in to R coding environment and fragment length was optimized for each IP and input (WCE) sample using ChIPQC 1.30.
Peaks were called using Mosaics 2.32 in R 4.1.2 using the estimated fragment lengths from ChIPQC and FDR < 0.01.
For per base coverage plots, BAM files were extended in the 3' direction to 150 bps with samtools 1.10 and converted to BEDGRAPH format using bedtools 2.30.0 as described in Grünberger et al. 2020.
Assembly: GCA_000025685.1
Supplementary files format and content: BED files with mosaics called peaks (except for input (WCE) samples)
Supplementary files format and content: bedgraph files with per base read coverage, generated from extended .bam files.

organism: Haloferax volcanii DS2

source_name: H26 ΔpyrE2 ΔtbsP::tbsP-HA

growth_protocol: Strains H26 and AK239 were struck from freezer stocks onto YPC18+uracil plates and incubated at 42C until single colonies formed. Independent colonies were used to start 2 cultures of H26 and 4 cultures AKS239 in 5 mL YPC18+uracil. Precultures were grown at 42C with 250 rpm shaking until average optical density at 600nm reached ~1. Cells were transferred to fresh 100 mL HvCa with or without 0.1% glucose and harvested at exponential phase (OD600 ~ 0.3-0.5).

extract_protocol:
Samples were processed as described in Wilbanks et al. (2012) using anti-HA polyclonal antibody (Abcam #ab9110) to immunoprecipitate cross-linked fragments.
Libraries were constructed by the Center for Genomic and Computational Biology at Duke University (Durham, NC) using KAPA Hyper Prep kit and Illumina TruSeq adapters, and the 50 bp, single-ended libraries were sequenced on an Illumina HiSeq 4000

tag: strain

value: {delta}pyrE2 tbsP::HA cell culture

value: H26 {delta}pyrE2 {delta}tbsP::tbsP-HA

value: HvCA + uracil

tag: chip antibody


title: mouse CCS, V5-2

tag: antibody


title: plasma, subject a8f43017T12


title: tbsPHA_3_input

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 3. Input sample.

tag: cell type


title: plasma, subject a8f43017T4

value: No


title: Skin, resistant, after infestation, bovine 10

tag: breed

tag: tick resistance_phenotype

tag: time point


title: tbsPHA_2_input

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 2. Input sample.


title: Skin, resistant, after infestation, bovine 11


title: tbsPHA_1_input

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 1. Input sample.


title: plasma, subject a8f43017T1

tag: subject id

tag: blood sample id


title: Skin, resistant, after infestation, bovine 9


title: plasma, subject a7d130f6T8

tag: Sex

value: Female

tag: age


title: H26_2_input

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 2. Input sample.

source_name: DS70 ∆pyrE2

value: {delta}pyrE2 cell culture

value: DS70 {delta}pyrE2


title: Skin, resistant, after infestation, bovine 8

value: Braford


title: AOC11-LN

city: Suwon-si

first: Ji-Hye

last: Choi

state: Gyeonggi-do

address: World cup-ro

country: South Korea

institute: Ajou university

description: metastatic lymph node tumor cell line

data_processing:
Low-quality sequence reads with PHRED scores < 30 and adapter sequences were trimmed using the Trim Galore tool and then mapped to the mouse reference genome (mm10). RNA abundance was estimated as the FPKM values using TopHat2/Cufflinks according to the GENCODE database (version M21) with default parameters.
Assembly: mm10
Supplementary files format and content: comma-deliminated txt file includes FPKM values for each sample

source_name: oral cavity

extract_protocol:
RNA was isolated from the cells using TRIzol reagent (Invitrogen).
mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA), according to the manufacturer’s protocols. Briefly, mRNA was purified and fragmented from 2 μg total RNA. The libraries were sequenced as paired-end reads (2 × 100 bp) using NovaSeq 6000 (Illumina).

value: oral cavity

tag: cell line

value: lymph node metastatic cancer


title: mouse CCS, V5-1

tag: tissue

value: Tumor


title: H26_1_input

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 1. Input sample.


title: KO2

source_name: bone marrow

value: bone marrow

value: granulocyte-monocyte progenitor

value: MST1 deficient mice


title: AOC11

description: head and neck cancer cell line

value: oral cancer


title: plasma, subject a7d130f6T4

first: Pushkala

address: 1 Gustave Levy Pl

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.

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

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: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

value: Somascan discovery platform v4


title: tbsPHA_4_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 4. Immuno-precipitated sample.

value: {delta}pyrE2 tbsP::HA cell culture

tag: genotype

value: H26 {delta}pyrE2 {delta}tbsP::tbsP-HA

tag: treatment

value: Abcam #ab9110


title: AOC3-LN

description: metastatic lymph node tumor cell line


title: AOC3

description: head and neck cancer cell line


title: plasma, subject a6f6c40cT20

value: Male

value: No

tag: instrument model


title: Skin, resistant, after infestation, bovine 6

value: skin

value: resistant

value: After infestation


title: tbsPHA_3_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 3. Immuno-precipitated sample.

tag: strain

value: HvCA + uracil

tag: chip antibody


title: plasma, subject a6f6c40cT1


title: tbsPHA_2_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 2. Immuno-precipitated sample.

tag: cell type


title: Skin, resistant, after infestation, bovine 4

tag: breed

value: Braford

tag: tick resistance_phenotype


title: tbsPHA_1_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 1. Immuno-precipitated sample.


title: plasma, subject a63504b7T1

tag: subject id

value: Female

value: Negative


title: plasma, subject a62483bbT1

tag: blood sample id


title: OGdelta#59MCSF

city: Indianapolis

first: Yasuyoshi

last: Ueki

state: IN

address: 635 N. Barnhill Dr.

institute: Indiana University

data_processing:
The sequence reads were mapped to the designated reference geneome using STAR (Spliced Transcripts Alignment to a Reference)(Dobin et al. 2012).
To evaluate the quality of the RNA-seq data, number of reads that fall into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes were determined with bamUtils(Breese and Liu 2013).
Assembly: UCSC mm10
Supplementary files format and content: excel file with raw counts for each sample

source_name: Bone marrow-derived M-CSF-dependent macrophages

growth_protocol: Non-adherent bone marrow cells were seeded on 6-well plates (5.0 × 105 cells/well) and cultured with M-CSF (25 ng/mL, Peprotech) for 4 days to expand bone marrow-derived M-CSF-dependent macrophages (BMMs).

extract_protocol:
Total RNA samples were isolated by phase separation method using Ribozol RNA reagent
KAPA mRNA Hyper Prep Kit

value: M-CSF


title: OGdelta#50MCSF

value: Bone marrow-derived M-CSF-dependent macrophages


title: OGdelta#57MCSF


title: WT (jawbone)

description: 10x Genomics

data_processing:
CellRanger 6.1.1 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
Briefly, cellranger mkfastq was implemented to demultiplex raw base sequence calls generated from the Illumina sequencer into sample-specific FASTQ files.
The FASTQ files were then aligned to the mouse reference genome mm10 with RNAseq aligner STAR.
The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell. The filtered feature-cell barcode matrices generated by CellRanger were used for further analysis.
Assembly: mouse reference genome mm10
Supplementary files format and content: compressed h5 file including tab-separated values files and matrix files

source_name: jawbone cells

extract_protocol:
Jawbone cells were desociated from the culture dishes using Tripsin EDTA. The obtained cells were suspended to 10% serum MEM and filtered with 70um cell strainer.
Chromium™ Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1

treatment_protocol: Cells isolated from mouse jawbones were seeded on type 1 coated culture dishes

value: jawbone cells

value: C57BL/6J wildtype


title: H26_2_IP

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 2. Immuno-precipitated sample.

value: {delta}pyrE2 cell culture

value: DS70 {delta}pyrE2


title: Skin, resistant, after infestation, bovine 2

source_name: skin

tag: time point


title: H26_1_IP

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 1. Immuno-precipitated sample.


title: OGdelta#42MCSF


title: plasma, subject a5dcbad9T4

source_name: serum

tag: Sex

tag: age

value: Positive

value: Yes

value: Somascan discovery platform v4


title: Skin, resistant, after infestation, bovine 1

tag: tissue


title: tbsPHA_4_glc_input

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 4. Input sample. Media supplemented with 0.1% glucose (w/v)

value: {delta}pyrE2 tbsP::HA cell culture

value: H26 {delta}pyrE2 {delta}tbsP::tbsP-HA

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


title: plasma, subject a7d130f6T1

tag: days since first sample

value: No


title: plasma, subject a5b7cb76T1

tag: patient classification at first sample


title: OGdelta#36MCSF


title: Skin, resistant, after infestation, bovine 7

value: skin

value: resistant

value: After infestation


title: plasma, subject a56fd839T4

value: Female

tag: covid-19 status


title: tbsPHA_3_glc_input

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 3. Input sample. Media supplemented with 0.1% glucose (w/v)

tag: genotype


title: OGdelta#27MCSF

tag: treatment

value: M-CSF


title: plasma, subject a56fd839T1

tag: instrument model


title: Skin, susceptible, before infestation, bovine 19

value: Braford

value: susceptible

value: Before infestation


title: Skin, susceptible, before infestation, bovine 18


title: Skin, resistant, after infestation, bovine 5


title: tbsPHA_2_glc_input

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 2. Input sample. Media supplemented with 0.1% glucose (w/v)

tag: strain


title: Skin, resistant, after infestation, bovine 3


title: OGdelta#25MCSF

value: Bone marrow-derived M-CSF-dependent macrophages


title: Skin, susceptible, before infestation, bovine 17


title: plasma, subject a4cb2478T12

value: Male


title: plasma, subject a4cb2478T1

value: Positive


title: Skin, susceptible, before infestation, bovine 15


title: Skin, susceptible, before infestation, bovine 16


title: H26_1_glc_input

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 1. Input sample. Media supplemented with 0.1% glucose (w/v)

value: {delta}pyrE2 cell culture

value: DS70 {delta}pyrE2

tag: chip antibody


title: WT

description: 10x Genomics

data_processing:
CellRanger 5.0.1 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
Briefly, cellranger mkfastq was implemented to demultiplex raw base sequence calls generated from the Illumina sequencer into sample-specific FASTQ files.
The FASTQ files were then aligned to the mouse reference genome mm10 with RNAseq aligner STAR.
The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell.
The filtered feature-cell barcode matrices generated by CellRanger were used for further analysis. Intronic reads were included in the analysis since this is snRNA-seq.
Assembly: mouse reference genome mm10
Supplementary files format and content: compressed h5 file including tab-separated values files and matrix files

source_name: Bone marrow cells

extract_protocol:
Bone marrow isolated from mouse femur/tibia was treated with RBC lysis buffer to remove red blood cells and then suspended in 10%FBS alpha-MEM
Chromium™ Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1

tag: cell type

value: Bone marrow cells

value: Ogfrl1 +/+


title: plasma, subject a4bf14dbT8

value: Yes

value: Somascan discovery platform v4


title: Skin, susceptible, before infestation, bovine 14

tag: breed

value: skin


title: H26_2_glc_input

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 2. Input sample. Media supplemented with 0.1% glucose (w/v)

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


title: plasma, subject a4bf14dbT4

value: No


title: murine primary VSMCs, siSirt7-2, 48hrs

city: Guangzhou

first: Dongxing

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online platform.
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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were  transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome  GrCM38/mm10.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Assembly: mm10
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: vascular smooth muscle cells

growth_protocol: Mouse primary VSMCs were isolated using a collagenase digestion method from 12*6-week-old C57BL/6 male mice. Mouse primary VSMCs were cultured in growth medium consisting of α-MEM supplemented with 10% FBS (Gibco, 16000-044), 100 U/ml of penicillin (HyClone, SH40003.01), and 100 mg/ml of streptomycin (Hyclone, SV30010)

extract_protocol:
Total RNA was extracted according to the instruction manual of the TRlzol Reagent (Lifetechnologies, California, USA).1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations

treatment_protocol: Scrambled siRNAs (siScrambled) or siRNAs targeting against the mouse Sirt7 gene  were obtained from Guangzhou RiboBio Co., Ltd, China. Mouse VSMCs were seeded at a density of 1.0*105 cells/well in 6-well plates, and transfected with siScarmbled or siSirt7 at a final concentration of 20 nM using Lipofectamine RNAiMAX (Invitrogen, 13778) according to the manufacturer’s instructions.

value: male

value: vascular smooth muscle cells

value: Sirt7 knockdown

value: Normal Growth Medium


title: tbsPHA_4_glc_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 4. Immuno-precipitated sample. Media supplemented with 0.1% glucose (w/v)

value: {delta}pyrE2 tbsP::HA cell culture

value: H26 {delta}pyrE2 {delta}tbsP::tbsP-HA

value: Abcam #ab9110


title: murine primary VSMCs, siSirt7-3, 48hrs


title: KO

description: 10x Genomics

value: Ogfrl1 -/-


title: Skin, susceptible, before infestation, bovine 13

value: Braford

tag: tick resistance_phenotype

value: susceptible

value: Before infestation


title: plasma, subject a4bf14dbT12

tag: subject id

value: Female

value: Positive


title: Skin, susceptible, before infestation, bovine 12


title: tbsPHA_3_glc_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 3. Immuno-precipitated sample. Media supplemented with 0.1% glucose (w/v)


title: tbsPHA_2_glc_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 2. Immuno-precipitated sample. Media supplemented with 0.1% glucose (w/v)


title: plasma, subject a4a38a22T8

tag: blood sample id

value: Yes

value: Somascan discovery platform v4


title: Skin, susceptible, before infestation, bovine 11

value: skin

tag: time point


title: murine primary VSMCs, siScarmbled-3, 48hrs

tag: Sex

value: WT


title: murine primary VSMCs, siSirt7-1, 48hrs

value: male


title: tbsPHA_1_glc_input

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 1. Input sample. Media supplemented with 0.1% glucose (w/v)

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


title: OGdelta#17MCSF

value: Bone marrow-derived M-CSF-dependent macrophages

value: M-CSF


title: tbsPHA_1_glc_IP

description:
∆pyrE2 tbsP::HA cell culture
TrmB:HA translational fusion. Replicate 1. Immuno-precipitated sample. Media supplemented with 0.1% glucose (w/v)

value: {delta}pyrE2 tbsP::HA cell culture


title: H26_2_glc_IP

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 2. Immuno-precipitated sample. Media supplemented with 0.1% glucose (w/v)

value: {delta}pyrE2 cell culture

value: DS70 {delta}pyrE2


title: Skin, susceptible, before infestation, bovine 10


title: plasma, subject a4a38a22T4

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

tag: age

value: No


title: murine primary VSMCs, siScarmbled-2, 48hrs

value: vascular smooth muscle cells

value: Normal Growth Medium


title: plasma, subject a4a38a22T1


title: H26_1_glc_IP

description:
∆pyrE2 cell culture
Parental, no-tag control. Replicate 1. Immuno-precipitated sample. Media supplemented with 0.1% glucose (w/v)

value: Abcam #ab9110


title: plasma, subject a48e192eT4

value: Female


title: plasma, subject a4bf14dbT1

value: Positive


title: trmB_glu_6

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.

source_name: H26 ∆pyrE2∆trmB

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{delta}trmB

value: archaeal cell culture

tag: time

tag: year-flowcell


title: murine primary VSMCs, siScarmbled-1, 48hrs


title: trmB_glu_5


title: trmB_glu_1


title: Skin, susceptible, before infestation, bovine 7

value: Braford

tag: tissue

value: skin

value: susceptible

value: Before infestation


title: plasma, subject a472cc4bT8

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Yes

value: Somascan discovery platform v4


title: plasma, subject a48e192eT1

tag: instrument model


title: A8

city: Erlangen

first: Mathias

last: Linnerbauer

address: Schwabachanlage 6

department: Neurology

country: Germany

institute: University Hospital Erlangen

description: PhIX spike in 30%

data_processing:
The Nf-core/methylseq bioinformatics pipeline was used to process raw fastq files with the following parameters: --clip_r1 10 --clip_r2 10 --three_prime_clip_r1 10 --three_prime_clip_r2 10 --non_directional --relax_mismatches.
Assembly: mm10
Supplementary files format and content: The processed files are coverage files containing genomic location (chromosome, start, stop), DNA methylation levels (%), C and T counts.

source_name: brain and spinal cord

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 by FACS and the pellets flash frozen in liquid nitrogen. Genomic DNA of FACS-sorted astrocytes was isolated using the QIAmp DNA Micro Kit (Qiagen, #56304) according to the manufacturers’ instruction. Genomic DNA was bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen, #59826) according to the manufacturers’ instruction.
Following bisulfite conversion, library preparation and amplification was performed using the QIAseq Methyl Library Kit (Qiagen, #180502) according to the manufacturers’ instruction. Libraries were analyzed on a Illumina Novaseq (PE 150 bp) in collaboration with BGI Tech 861 Solutions.

value: brain and spinal cord

value: FACS-sorted astrocyte

tag: genotype

value: wild type (C57BL6)

tag: treatment

value: peak of EAE


title: Skin, susceptible, before infestation, bovine 8


title: Skin, susceptible, before infestation, bovine 6


title: Skin, susceptible, before infestation, bovine 4


title: Skin, susceptible, before infestation, bovine 5


title: trmB_noglu_5

tag: strain

tag: cell type

value: HvCA + uracil


title: plasma, subject a472cc4bT4

city: New York

last: Jayaraman

value: No


title: A5

description: PhIX spike in 30%


title: A6

description: PhIX spike in 30%


title: plasma, subject a472cc4bT1


title: plasma, subject a472cc4bT12


title: trmB_noglu_1


title: Skin, susceptible, before infestation, bovine 3

tag: breed

tag: tick resistance_phenotype


title: A4

description: PhIX spike in 30%

value: naive


title: Skin, susceptible, before infestation, bovine 9


title: tbsP_glu_5

source_name: H26 ∆pyrE2∆tbsP (HVO_2861)

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

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


title: A7

description: PhIX spike in 30%


title: plasma, subject a46725b1T1

tag: subject id

tag: blood sample id

value: Female

value: Positive


title: A2

description: PhIX spike in 30%


title: Skin, susceptible, before infestation, bovine 1

value: Braford

tag: time point


title: trmB_noglu_6

value: H26 {delta}pyrE2{delta}trmB

value: archaeal cell culture


title: A1

description: PhIX spike in 30%


title: OMI_C_1

city: 昆明市

first: Lin

last: dongdong

state: 云南

address: 云南省昆明市五华区茭菱路

institute: Peking Union Medical College

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of macaca mulatta from Mmul_8.0 using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Mmul_8.0

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Total RNAs were extracted from sample using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
digital RNA-seq

value: PBMC

value: Omicron control


title: OMI_1

address: 云南省昆明市五华区茭菱路

value: Omicron infection


title: Skin, resistant, before infestation, bovine 20

value: skin

value: resistant

value: Before infestation


title: plasma, subject a414431cT1

tag: Sex

value: Male

tag: age

value: Yes

value: Somascan discovery platform v4


title: plasma, subject a395f41cT1

value: Negative

value: No


title: Skin, resistant, before infestation, bovine 19


title: IND_C_3

address: 云南省昆明市五华区茭菱路

value: Delta control

tag: time


title: Skin, resistant, before infestation, bovine 18

tag: tissue


title: WT_AM6545_4

city: Barcelona

first: Andrés

last: Ozaita

address: Dr Aiguader, 88

department: Department of Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
Transcript abundances in Transcripts Per Million (TPM) were quantified with Salmon 1.5.2
Low counts reads were filtered out based on mean expression greater than 0
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for each sample
Supplementary files format and content: Matrix table with raw transcripts counts for each ample

source_name: Brain

extract_protocol:
Synaptoneurosomes were isolated from hippocampal tissue and total RNA were obtained using RNeasy mini kit (Qiagen)
Libraries were obtained using SMARTer Ultra Low Input kit according to the manufacturer’s instructions

value: Brain

tag: source

value: Hippocampal synaptoneurosomes


title: IND_C_2

address: 云南省昆明市五华区茭菱路


title: plasma, subject a2f4eb0bT8

tag: days since first sample

tag: patient classification at first sample

value: Positive


title: A3

description: PhIX spike in 30%

value: brain and spinal cord

value: FACS-sorted astrocyte

value: wild type (C57BL6)

value: naive


title: WT_AM6545_5


title: WT_AM6545_2


title: plasma, subject a2f4eb0bT1

tag: covid-19 status

tag: instrument model


title: IND_C_1

address: 云南省昆明市五华区茭菱路

value: PBMC

tag: treatment


title: IND_3

address: 云南省昆明市五华区茭菱路

value: Delta infection


title: Skin, resistant, before infestation, bovine 17

data_processing:
Sample RNA quality check was performed with the FastQC (v. 0.11.8)
Reads were aligned to the bovine reference genome using Hisat2 (v. 2.1.0), with the annotation from RefSeq assembly accession GCF_002263795.1
Sample counts were sorted using Samtools v 1.9 and grouped with the FeatureCounts (v. 1.6.4)
Using DESEQ2 (v. 4.0.3), gene counts were normalized and differential expression analyzes at the gene level were performed using the generalized linear model: Yijkl = TIMEj + TYPEk + TIME*TYPE(jk) + TYPE*ANIMAL(kl) + eijkl.
The 237preIA sample was removed from the final analysis due to its discrepancy with the other data, when the PCA and heatmap analysis was performed
Assembly: bovine reference genome (ARS-UCD1.2, GCA_002263795.2; 2018
Supplementary files format and content: featureCounts_total.txt - table with gene counts per sample
Supplementary files format and content: normalized_counts.txt - table with gene counts normalized according to the generalized linear model used

extract_protocol:
Skin biopsies were mechanically crushed with 7 mm metallic beads in the TissueLyser equipment (Qiagen), and total RNA harvested using the RNeasy Fibrous Tissue kit (Qiagen)
Sequencing libraries were prepared individually using TruSeq RNA Sample Preparation kit v2 guide (Illumina, San Diego, CA) with standard protocols, clustered using TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina, San Diego, CA)
Sequencing libraries were sequenced in a paired-end mode (2 x 100 bp) on a HiSeq1500 equipment (Illumina, San Diego, CA)

value: Braford

value: skin

value: resistant


title: Skin, susceptible, before infestation, bovine 2

value: susceptible

value: Before infestation


title: plasma, subject a2f4eb0bT4

value: Male

value: Yes

value: Somascan discovery platform v4


title: plasma, subject a46725b1T4

value: Female


title: Skin, resistant, before infestation, bovine 16


title: Skin, resistant, before infestation, bovine 15


title: WT_AM6545_1

value: Brain

value: Hippocampal synaptoneurosomes

tag: strain


title: IND_2

address: 云南省昆明市五华区茭菱路


title: plasma, subject a26c0556T1

value: Negative

value: No


title: Skin, resistant, before infestation, bovine 14


title: plasma, subject a103a05aT4

value: Positive


title: WT_VEH_5

value: Vehicle


title: IND_1

address: 云南省昆明市五华区茭菱路

value: PBMC


title: Skin, resistant, before infestation, bovine 13


title: WT_VEH_4


title: plasma, subject a103a05aT13


title: GD_C_3

address: 云南省昆明市五华区茭菱路

value: Prototype control


title: WT_VEH_3


title: WT_AM6545_3


title: plasma, subject a103a05aT12


title: Skin, resistant, before infestation, bovine 12

value: Braford


title: GD_C_2

address: 云南省昆明市五华区茭菱路


title: plasma, subject a03b4104T1


title: Skin, resistant, before infestation, bovine 10

value: skin


title: WT_VEH_1


title: Skin, resistant, before infestation, bovine 11

value: resistant


title: Skin, resistant, before infestation, bovine 9


title: WT_VEH_2


title: GD_C_1

address: 云南省昆明市五华区茭菱路


title: GD_3

address: 云南省昆明市五华区茭菱路

value: Prototype infection


title: plasma, subject a077aab0T1


title: Unpol, rep3 [M3_Up_S12]

city: Columbus

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
genome build/assembly: grcm38
Human data: Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0 [1]. Gene wise counts were generated with featureCounts from the subread package v1.5.1 [2] for genes annotated by ensembl Homo_sapiens.GRCh38.101, counting the primary alignment in the case of multimapped reads.
Mouse data: Individual FASTQ files were trimmed for adapter sequences and filtered using fastp v0.20.0. Mouse reference genome GRCm38.p6 and gene annotation described by Gene Transfer Format (GTF) were downloaded from Ensembl release 99 (January 2020). Reads alignment was performed against the reference genome using HISAT2 v2.1.0. Gene expression values for genes were quantified using the featureCounts tool of the Subread package v1.5.0-p2 in unstranded mode.
Supplementary files format and content: human_featurecounts.txt
Supplementary files format and content: mouse_counts.csv

source_name: Bone Marrow

extract_protocol:
RNA was harvested using total RNA purifcation plus kit (Biotek Corp). 200 ng per sample was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared using NEBNext Ultra II directional RNA library prep kit following manufacturer's instruction

treatment_protocol: Both mouse Ly6G+ neutrophils, and human CD34+, bone marrow cells were cultured with media and with cytokines IL-4 and/or G-CSF

value: Bone Marrow

tag: cell type

value: Neutrophil


title: GD_2

address: 云南省昆明市五华区茭菱路


title: plasma, subject 9f9eff0aT20

value: Yes


title: Skin, resistant, before infestation, bovine 8

tag: breed

value: Before infestation


title: plasma, subject 9f621c0fT4

value: Female

value: Somascan discovery platform v4


title: IL4, rep3 [M3_L4_S13]


title: Skin, resistant, before infestation, bovine 7

tag: tick resistance_phenotype


title: plasma, subject 9f621c0fT1

tag: subject id


title: SA_C_3

address: 云南省昆明市五华区茭菱路

value: Beta control


title: Skin, resistant, before infestation, bovine 6


title: IL4+GCSF, rep3 [M3_L4_G_S15]


title: SA_C_2

address: 云南省昆明市五华区茭菱路


title: plasma, subject 9f1bc4a8T1

tag: blood sample id


title: SA_C_1

address: 云南省昆明市五华区茭菱路


title: plasma, subject 9e2d5ea6T1

value: Male


title: Skin, resistant, before infestation, bovine 5

tag: time point


title: Unpol, rep2 [M2_Up_S8]


title: plasma, subject 9de59036T1

tag: Sex


title: Skin, resistant, before infestation, bovine 3


title: SA-3

address: 云南省昆明市五华区茭菱路

value: Beta infection


title: SA-2

address: 云南省昆明市五华区茭菱路


title: BM, rep3 [M3_S3]


title: SA-1

address: 云南省昆明市五华区茭菱路


title: IL4, rep2 [M2_L4_S9]


title: GD_1

address: 云南省昆明市五华区茭菱路


title: Skin, resistant, before infestation, bovine 2


title: plasma, subject 9dae8071T4

tag: age

value: Positive


title: BM, rep2 [M2_S2]


title: Skin, resistant, before infestation, bovine 1


title: R.intestinalis, inulin, R3

city: JOUY EN JOSAS

first: paul

last: Biscarrat

state: ile de france

address: 4 AVENUE JEAN JAURES-DOMAINE VILVERT

country: France

institute: INRAE

description:
RI_I_R3
counts_RI.csv
RI_inuline_vs_controle3_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: Roseburia intestinalis

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: Inulin


title: IL4+GCSF, rep2 [M2_L4_G_S11]


title: 3-X-TOP_Illumina_NC_deep

city: Vilnuis

first: Kotryna

last: Kvederaviciute

address: Universiteto str. 3

country: Lithuania

institute: Vilnius University

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

tag: genotype

value: WT

value: Neuronal differentiation

tag: modification

value: 5-hydroxymethylcytosine, GC and unmodified CG sites


title: GCSF, rep2 [M2_G_S10]

tag: tissue

value: Bone Marrow


title: GCSF, rep3 [M3_G_S14]

value: Neutrophil


title: R.intestinalis, inulin, R2

description:
RI_I_R2
counts_RI.csv
RI_inuline_vs_controle3_DESeq_results.csv


title: Unpol, rep1 [M1_Up_S4]


title: R.intestinalis, inulin, R1

description:
RI_I_R1
counts_RI.csv
RI_inuline_vs_controle3_DESeq_results.csv


title: 3-X-TOP_Illumina_NPC_deep


title: Skin, resistant, before infestation, bovine 4

institute: Embrapa

value: Braford

value: skin

value: resistant


title: plasma, subject 9d7ef962T22

tag: days since first sample

tag: patient classification at first sample

value: Negative

value: No

value: Yes

value: Somascan discovery platform v4


title: BM, rep1 [M1_S1]


title: plasma, subject 9d7ef962T21

value: Male

tag: covid-19 status

tag: instrument model


title: 3-X-TOP_Illumina_mESC_deep

tag: treatment


title: plasma, subject 9d7ef962T20


title: plasma, subject 9dc56b1cT1

value: Positive


title: R.intestinalis, corn fiber, R3

description:
RI_M_R3
counts_RI.csv
RI_fibre_mais_vs_controle3_DESeq_results.csv

tag: strain

tag: cell type

value: Bacteria

value: Corn Fiber


title: IL4+GCSF, rep1 [M1_L4_G_S7]


title: IL4, rep1 [M1_L4_S5]


title: R.intestinalis, corn fiber, R2

description:
RI_M_R2
counts_RI.csv
RI_fibre_mais_vs_controle3_DESeq_results.csv


title: plasma, subject 9dae8071T20


title: R.intestinalis, corn fiber, R1

description:
RI_M_R1
counts_RI.csv
RI_fibre_mais_vs_controle3_DESeq_results.csv


title: plasma, subject 9d0c1107T1


title: R.intestinalis, glucose, R3

description:
RI_G_R3
counts_RI.csv

value: Glucose


title: GCSF, rep1 [M1_G_S6]


title: plasma, subject 9d0c1107T4


title: plasma, subject 9dae8071T1


title: R.intestinalis, glucose, R2

description:
RI_G_R2
counts_RI.csv


title: plasma, subject 9ca46218T4


title: KO M2 biol rep 4

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

data_processing:
Data was analyzed using Rosalind.
Reads were trimmed using catadapt. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel files with raw counts
Supplementary files format and content: excel files with normalized counts

molecule: polyA RNA

source_name: BMDM

growth_protocol: RPMI containing 10% FBS, 10 mM HEPES, and 100 U/ml penicillin/ streptomycin) supplemented with 10 ng/ml M-CSF

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: BMDM were stimulated with 10 ng/ml LPS and 25 ng/mL IFN-γ for M1-like polarization and 10 ng/mL IL-4 for M2-like macrophage polarization for 16 h prior to RNA isolation.

value: BMDM

value: mouse macrophage

tag: group


title: R.intestinalis, glucose, R1

description:
RI_G_R1
counts_RI.csv


title: KO M2 biol rep 3


title: KO M2 biol rep 2


title: plasma, subject 9ca46218T1

state: New York

tag: subject id


title: KO M1 biol rep 3


title: R22035324LR02-RKO-shPNP-CTRL-4h

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

data_processing:
In this project, PE 150 was applied to sequence the samples. However, the length of DNA segment may be less than 150 bp during library preparation, in results of adapter sequences (green region in the figure below) in the raw reads. fastp(v0.20.1) (Chen S, el at. 2018) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed. Then the selected reads, named as Clean reads, were used for downstream analysis.
Since mature RNA sequences are formed by concatenating different exons of a gene owing to alternative splicing, alignment gap will occur when genome is used as reference sequence. STAR (v2.7.8a) (Dobin A, et al. 2013) software can fastly and accurately align RNA sequences to gene regions (schematic maps below). The alignment analysis can basically be divided into two steps: 1) genemeGenerate Build an index; 2) Sequence alignment. In this project, clean reads of each sample were aligned to reference genome by using STAR software with default parameters.
RSEM (v1.3.3) (Li B, et al. 2011) can accurately quantify gene or transcript expression levels from RNA-seq data. In the analysis of this project, expression estimation of gene and transcript was performed by using RSEM with setting --estimate-rspd parameter to estimate the distribution of the starting position of the sequence (RSPD) and other parameters were set as defalut. Then edgeR (v3.28.1) package in R was used to perform TMM (trimmed mean of M values) (Robinson, MD, & Oshlack, A. 2010) and CPM (count per million) normalization for the the gene expression. TMM is mainly used to normalize the depth of sequencing in different samples and estimate the expression level for each sample. CPM is used to normalize the amount of read count expression between samples. TMM and CPM normalized read counts of genes were applied to compare between two samples in the downstream analysis. Further more, detected genes were annotated with Gene Ontology (gene2go.20141211), GenRef (gene_info.20141211), and GENCODE(v19), respectively.
EdgeR (Robinson, M.D., McCarthy et al. 2010) used the overdispersed Poisson model and empirical Bayes model to estimate the dispersion of all gene expression levels. In this project, raw read counts of gene expression were applied to estimate the differetiation between pair samples or groups by using edgeR package in R. Genes whose CPM and TMM value is greater than 1 in at least one sample were selected. The criteria for significantly differentially expressed genes was: padj < 0.05 and |FC| >= 2. The databases of Ensembl, GO, and KEGG were used to annotate differentially expression genes to illustrate the biological processes related to these differential genes.
Assembly: hg19
Supplementary files format and content: gene expression for each Sample

organism: Homo

source_name: colorectal

extract_protocol:
mRNA was extracted from total RNA using magnetic beads with oligo-dT then were fragmented randomly.
The first strand of cDNA and the second strand are then synthesized using reverse transcriptase. The reverse transcription product is subjected to terminal repair, followed by addition of an A base at the 3' end. Subsequently, the fragments were ligated with a Illumina universal adapter. After PCR amplified, the ligation products were purified in order to remove the incompletely ligated fragment and the self-ligated adapter.
Library sizes were detected using an Agilent 2100 Bioanalyzer and library concentrations were detected using Qubit 2.0. The RNA sequencing was performed according to Illumina's standard protocol.

treatment_protocol: 4 mM guanosine stimulation for 6 hours

value: colorectal

value: RKO

value: epithelial

value: shPNP

value: no treatment


title: R22035323LR02-RKO-NC-4G-4h

value: NC

value: guanosine stimulation


title: plasma, subject 9c3d28d3T1

tag: blood sample id


title: plasma, subject 9c5c5cb0T1

value: No


title: plasma, subject 9b9f2c91T1

value: Female

value: Yes


title: R22035322LR02-RKO-NC-CTRL-4h