title: GD590-Robinson_L_WT5_Ec_S28_L001_R1_001

status: Public on May 31 2025

type: SRA

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

country: USA

institute: West Virginia University

library_source: transcriptomic

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1)+0.0001 for each samples.

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
The tissues  were homogenized in TRI Reagent® (Molecular Research Center, Cincinnati, OH). Using the commercial product protocol, the upper aqueous layer following phase separation was mixed with an equal volume of 75% ethanol and transferred to EZNA RNA isolation columns (Omega Biotek, Norcross, GA). The manufacturer’s instructions were followed to complete the tissue RNA isolation. RNA isolation from approximately 7.5x104 splenic myeloid cells was conducted with the RNeasy Plus Mini Kit (Qiagen, cat#74134) according to the manufacturer’s instructions.
RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems,Wilmington MA) with 100-500 ng of total RNA according to manufacturer’s recommendation.

tag: tissue

value: Liver

tag: strain

tag: genotype

value: IL-27R WT

tag: treatment

value: E. coli infection 24 h


title: GD591-Robinson_L_WT6_Ec_S29_L001_R1_001


title: GD587-Robinson_L_WT2_Control_S25_L001_R1_001

value: no E. coli infection


title: GD585-Robinson_L_KO6_Ec-low_S35_L001_R1_001

value: IL-27R KO


title: GD589-Robinson_L_WT4_Ec_S27_L001_R1_001


title: GD586-Robinson_L_WT1_Control_S24_L001_R1_001


title: GD583-Robinson_L_KO4_Ec-low_S33_L001_R1_001


title: GD584-Robinson_L_KO5_Ec-low_S34_L001_R1_001


title: GD581-Robinson_L_KO2_Control_S31_L001_R1_001


title: GD580-Robinson_L_KO1_Control_S30_L001_R1_001


title: GD578-Robinson-HM-WT5-EC_S2_L001_R1_001

source_name: Hindlimb muscle

value: Hindlimb muscle


title: GD576-Robinson-HM-WT3-control_S1_L001_R1_001


title: GD575-Robinson_HM_WT2_Control_S2_L001_R1_001


title: GD577-Robinson_HM_WT4_Ec_S4_L001_R1_001


title: GD574-Robinson_HM_WT1_Control_S1_L001_R1_001


title: GD571-Robinson_HM_KO3_Control_S9_L001_R1_001


title: GD573-Robinson_HM_KO6_Ec-low_S11_L001_R1_001


title: GD1847-KO-Ec3_S11_L001_R1_001

source_name: Pancreas

value: Pancreas


title: GD1843-KO-C2_S7_L001_R1_001


title: GD570-Robinson_HM_KO2_Control_S8_L001_R1_001


title: GD1839-WT-C3_S3_L001_R1_001


title: GD1846-KO-Ec2_S10_L001_R1_001


title: GD569-Robinson_HM_KO1_Control_S7_L001_R1_001


title: GD572-Robinson_HM_KO4_Ec-low_S10_L001_R1_001


title: GD1838-WT-C2_S2_L001_R1_001


title: GD1840-WT-Ec1_S4_L001_R1_001


title: GD1842-KO-C1_S6_L001_R1_001


title: GD582-Robinson_L_KO3_Control_S32_L001_R1_001


title: GD1841-WT-Ec2_S5_L001_R1_001


title: GD588-Robinson_L_WT3_Control_S26_L001_R1_001


title: GD1844-KO-C3_S8_L001_R1_001


title: chemoresistant tumors, ID8 model, scRNAseq

city: Guangzhou

first: Chaoyun

last: Pan

address: 74 Zhongshan Er Lu

country: China

institute: Sun Yat-sen University

description:
Library name: Sample 2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software  (version 8.0.1) (https://www.10xgenomics.com/support/software/cell-ranger/8.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: solid tumor

extract_protocol:
Freshly harvested ovarian tumor tissue was minced into ~2 mm³ pieces and gently crushed with the barrel of a syringe. Tissue fragments were digested with Type II collagenase (2.5 mg/mL, Thermo Fisher) in RPMI-1640 medium containing 10% FBS, 1% penicillin-streptomycin, 1× GlutaMAX, and 1% HEPES at 37°C for 25 min. The digested suspension was filtered through a 70-μm strainer, treated with ACK lysis buffer for erythrocyte removal, and washed with RPMI-1640 to generate a single-cell suspension.
Tumor single cell suspensions were pooled and processed using Chromium microfluidic chips with 3' v3 chemistry (10X Genomics). Cellular barcoding was performed using the 10X Chromium Controller, followed by reverse transcription and library preparation according to the manufacturer's protocol (Chromium Single Cell 3' v3 reagent kit). The resulting libraries were sequenced on an Illumina HiSeq 2000 platform following standard procedures.

value: solid tumor

value: cisplatin


title: primary tumors, ID8 model, scRNAseq

description:
Library name: Sample 1
10x Genomics

value: treatment naïve


title: GD1837-WT-C1_S1_L001_R1_001


title: GD1845-KO-Ec1_S9_L001_R1_001


title: recovered_6

city: Jongno-gu

first: Yoon Ji

last: Bang

state: --- Select One ---

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

data_processing:
FASTQ files were converted to DCC files.
Assembly: hg38
Supplementary files format and content: DCC: digital count conversion
Library strategy: Spatial Transciptomics

organism: Macaca mulatta

source_name: liver

extract_protocol:
FFPE sections of each biopsy were sectioned in 5 μm.
Spatial Transciptome sequencing libraries were prepared with DSP GeoMX according to manufacturer's construction.

value: liver

tag: cell type

value: recovered


title: GD579-Robinson_HM_WT6_Ec_S6_L001_R1_001


title: recovered_5


title: recovered_4


title: recovered_1


title: recovered_3


title: non-steatohepatitic_3

value: non-steatohepatitic


title: non-steatohepatitic_4


title: recovered_2


title: non-steatohepatitic_5


title: non-steatohepatitic_2


title: non-steatohepatitic_1


title: Ulcerative Colitis Sample Number 73

type: genomic

city: London

first: Laurence

middle: Bruce

last: Lovat

address: 43-45 Foley Street

department: Division of Surgery & Interventional Science

country: United Kingdom

institute: University College London

description:
Saliva Sample from Ulcerative Colitis Patient
UC073

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

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

data_processing:
raw .idat files were read via the minfi package in the R programming environment, data was normalised using Functional Normalisation in R
Average Beta value and detection P-values
Summarisd and normalised beta intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Saliva samples were collected using the Oragene DNA OG/600 saliva collection kit (DNAGenotek, Ottawa, Canada). All participants were required to fast for a minimum of one hour prior to sample collection.

tag: disease

value: Ulcerative Colitis

tag: age

tag: Sex

value: Male


title: steatohepatitic_2

value: steatohepatitic


title: Ulcerative Colitis Sample Number 75

description:
Saliva Sample from Ulcerative Colitis Patient
UC075

value: Female


title: Ulcerative Colitis Sample Number 70

description:
Saliva Sample from Ulcerative Colitis Patient
UC070


title: Ulcerative Colitis Sample Number 74

description:
Saliva Sample from Ulcerative Colitis Patient
UC074


title: steatohepatitic_6


title: steatohepatitic_5


title: steatohepatitic_1


title: steatohepatitic_4


title: steatohepatitic_3


title: Ulcerative Colitis Sample Number 72

description:
Saliva Sample from Ulcerative Colitis Patient
UC072


title: Ulcerative Colitis Sample Number 68

description:
Saliva Sample from Ulcerative Colitis Patient
UC068


title: Ulcerative Colitis Sample Number 71

description:
Saliva Sample from Ulcerative Colitis Patient
UC071


title: Ulcerative Colitis Sample Number 67

description:
Saliva Sample from Ulcerative Colitis Patient
UC067


title: Ulcerative Colitis Sample Number 66

description:
Saliva Sample from Ulcerative Colitis Patient
UC066


title: non-steatohepatitic_6


title: Ulcerative Colitis Sample Number 65

description:
Saliva Sample from Ulcerative Colitis Patient
UC065


title: primary_cultured_pre_treatment_brain_tumor_cell

type: RNA

city: Seoul

first: Sun Ha

last: Paek

address: 101, Daehak-ro, Jongno-gu

department: Neurosurgery

institute: Seoul National University College of Medicine

description: Gene expression before treatment

hyb_protocol: Hybridization were performed using Agilent’s LowInput QuickAmp Labeling Kit (Agilent)

scan_protocol: The acquired hybridization images were then analyzed by Agilent DNA microarray Scanner and the data quantification was performed using Agilent Feature Extraction software 10.7

data_processing: Normalization process of all data and selection of fold-changed genes were carried out using GeneSpringGX 7.3.1

source_name: primary cultured cell of pre-treatment tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1650ng of RNA and labeled cRNA target was then quantified using ND-1000 spectrophotometer

extract_protocol: Total RNA was extracted from GBM primary cells (< 5 passages) using a TRIzol reagent following manufacturer's instructions and its quantity and quality were assessed using Nanodrop

treatment_protocol: Human primary glioblastoma cell lines, GBM-28 and GBM-37, were maintained in DMEM (Gibco) containing 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37°C and 5% CO2.

value: brain

tag: cell line


title: Ulcerative Colitis Sample Number 63

description:
Saliva Sample from Ulcerative Colitis Patient
UC063


title: Ulcerative Colitis Sample Number 64

description:
Saliva Sample from Ulcerative Colitis Patient
UC064


title: control_cell

description: Gene expression of normal cell

source_name: normal brain tissue


title: primary_cultured_post_treatment_brain_tumor_cell

description: Gene expression after treatment

source_name: primary cultured cell of post-treatment tumor


title: Ulcerative Colitis Sample Number 69

description:
Saliva Sample from Ulcerative Colitis Patient
UC069


title: Ulcerative Colitis Sample Number 59

description:
Saliva Sample from Ulcerative Colitis Patient
UC059


title: Ulcerative Colitis Sample Number 61

description:
Saliva Sample from Ulcerative Colitis Patient
UC061


title: Ulcerative Colitis Sample Number 62

description:
Saliva Sample from Ulcerative Colitis Patient
UC062


title: Ulcerative Colitis Sample Number 57

description:
Saliva Sample from Ulcerative Colitis Patient
UC057


title: Ulcerative Colitis Sample Number 58

description:
Saliva Sample from Ulcerative Colitis Patient
UC058


title: Ulcerative Colitis Sample Number 50

description:
Saliva Sample from Ulcerative Colitis Patient
UC050


title: Ulcerative Colitis Sample Number 54

description:
Saliva Sample from Ulcerative Colitis Patient
UC054


title: Ulcerative Colitis Sample Number 55

description:
Saliva Sample from Ulcerative Colitis Patient
UC055


title: Ulcerative Colitis Sample Number 47

description:
Saliva Sample from Ulcerative Colitis Patient
UC047


title: Ulcerative Colitis Sample Number 45

description:
Saliva Sample from Ulcerative Colitis Patient
UC045


title: Ulcerative Colitis Sample Number 53

description:
Saliva Sample from Ulcerative Colitis Patient
UC053


title: Ulcerative Colitis Sample Number 43

description:
Saliva Sample from Ulcerative Colitis Patient
UC043


title: Ulcerative Colitis Sample Number 46

description:
Saliva Sample from Ulcerative Colitis Patient
UC046


title: Ulcerative Colitis Sample Number 42

description:
Saliva Sample from Ulcerative Colitis Patient
UC042


title: Ulcerative Colitis Sample Number 41

description:
Saliva Sample from Ulcerative Colitis Patient
UC041


title: Ulcerative Colitis Sample Number 38

description:
Saliva Sample from Ulcerative Colitis Patient
UC038


title: Ulcerative Colitis Sample Number 60

description:
Saliva Sample from Ulcerative Colitis Patient
UC060


title: Ulcerative Colitis Sample Number 37

description:
Saliva Sample from Ulcerative Colitis Patient
UC037


title: Ulcerative Colitis Sample Number 49

description:
Saliva Sample from Ulcerative Colitis Patient
UC049


title: Ulcerative Colitis Sample Number 48

description:
Saliva Sample from Ulcerative Colitis Patient
UC048


title: Ulcerative Colitis Sample Number 40

description:
Saliva Sample from Ulcerative Colitis Patient
UC040


title: Ulcerative Colitis Sample Number 25

description:
Saliva Sample from Ulcerative Colitis Patient
UC025


title: Ulcerative Colitis Sample Number 39

description:
Saliva Sample from Ulcerative Colitis Patient
UC039


title: Ulcerative Colitis Sample Number 56

description:
Saliva Sample from Ulcerative Colitis Patient
UC056


title: Ulcerative Colitis Sample Number 21

description:
Saliva Sample from Ulcerative Colitis Patient
UC021


title: Ulcerative Colitis Sample Number 20

description:
Saliva Sample from Ulcerative Colitis Patient
UC020


title: Ulcerative Colitis Sample Number 36

description:
Saliva Sample from Ulcerative Colitis Patient
UC036


title: Ulcerative Colitis Sample Number 34

description:
Saliva Sample from Ulcerative Colitis Patient
UC034


title: Ulcerative Colitis Sample Number 18

description:
Saliva Sample from Ulcerative Colitis Patient
UC018


title: Ulcerative Colitis Sample Number 52

description:
Saliva Sample from Ulcerative Colitis Patient
UC052


title: Ulcerative Colitis Sample Number 35

description:
Saliva Sample from Ulcerative Colitis Patient
UC035


title: Ulcerative Colitis Sample Number 51

description:
Saliva Sample from Ulcerative Colitis Patient
UC051


title: Ulcerative Colitis Sample Number 17

description:
Saliva Sample from Ulcerative Colitis Patient
UC017


title: Ulcerative Colitis Sample Number 29

description:
Saliva Sample from Ulcerative Colitis Patient
UC029


title: Ulcerative Colitis Sample Number 44

description:
Saliva Sample from Ulcerative Colitis Patient
UC044


title: Ulcerative Colitis Sample Number 16

description:
Saliva Sample from Ulcerative Colitis Patient
UC016


title: Ulcerative Colitis Sample Number 28

description:
Saliva Sample from Ulcerative Colitis Patient
UC028


title: Ulcerative Colitis Sample Number 27

description:
Saliva Sample from Ulcerative Colitis Patient
UC027


title: Ulcerative Colitis Sample Number 30

description:
Saliva Sample from Ulcerative Colitis Patient
UC030


title: Ulcerative Colitis Sample Number 32

description:
Saliva Sample from Ulcerative Colitis Patient
UC032


title: Ulcerative Colitis Sample Number 24

description:
Saliva Sample from Ulcerative Colitis Patient
UC024


title: Ulcerative Colitis Sample Number 31

description:
Saliva Sample from Ulcerative Colitis Patient
UC031


title: Ulcerative Colitis Sample Number 14

description:
Saliva Sample from Ulcerative Colitis Patient
UC014


title: Ulcerative Colitis Sample Number 26

description:
Saliva Sample from Ulcerative Colitis Patient
UC026


title: Ulcerative Colitis Sample Number 22

description:
Saliva Sample from Ulcerative Colitis Patient
UC022


title: Ulcerative Colitis Sample Number 13

description:
Saliva Sample from Ulcerative Colitis Patient
UC013


title: Ulcerative Colitis Sample Number 12

description:
Saliva Sample from Ulcerative Colitis Patient
UC012


title: Ulcerative Colitis Sample Number 9

description:
Saliva Sample from Ulcerative Colitis Patient
UC009


title: Ulcerative Colitis Sample Number 19

description:
Saliva Sample from Ulcerative Colitis Patient
UC019


title: Ulcerative Colitis Sample Number 23

description:
Saliva Sample from Ulcerative Colitis Patient
UC023


title: Ulcerative Colitis Sample Number 33

description:
Saliva Sample from Ulcerative Colitis Patient
UC033


title: Ulcerative Colitis Sample Number 15

description:
Saliva Sample from Ulcerative Colitis Patient
UC015


title: Ulcerative Colitis Sample Number 11

description:
Saliva Sample from Ulcerative Colitis Patient
UC011


title: Ulcerative Colitis Sample Number 6

description:
Saliva Sample from Ulcerative Colitis Patient
UC006


title: Ulcerative Colitis Sample Number 5

description:
Saliva Sample from Ulcerative Colitis Patient
UC005


title: Ulcerative Colitis Sample Number 3

description:
Saliva Sample from Ulcerative Colitis Patient
UC003


title: Ulcerative Colitis Sample Number 4

description:
Saliva Sample from Ulcerative Colitis Patient
UC004


title: Ulcerative Colitis Sample Number 2

description:
Saliva Sample from Ulcerative Colitis Patient
UC002


title: Crohn's Disease Sample Number 221

description:
Saliva Sample from Crohn's Patient
CROHNS221

value: Crohn's Disease


title: Crohn's Disease Sample Number 220

description:
Saliva Sample from Crohn's Patient
CROHNS220


title: Crohn's Disease Sample Number 226

description:
Saliva Sample from Crohn's Patient
CROHNS226


title: Ulcerative Colitis Sample Number 1

description:
Saliva Sample from Ulcerative Colitis Patient
UC001


title: Crohn's Disease Sample Number 223

description:
Saliva Sample from Crohn's Patient
CROHNS223


title: Crohn's Disease Sample Number 224

description:
Saliva Sample from Crohn's Patient
CROHNS224


title: Crohn's Disease Sample Number 225

description:
Saliva Sample from Crohn's Patient
CROHNS225


title: Crohn's Disease Sample Number 227

description:
Saliva Sample from Crohn's Patient
CROHNS227


title: Crohn's Disease Sample Number 214

description:
Saliva Sample from Crohn's Patient
CROHNS214


title: Crohn's Disease Sample Number 213

description:
Saliva Sample from Crohn's Patient
CROHNS213


title: Crohn's Disease Sample Number 211

description:
Saliva Sample from Crohn's Patient
CROHNS211


title: Ulcerative Colitis Sample Number 7

description:
Saliva Sample from Ulcerative Colitis Patient
UC007


title: Crohn's Disease Sample Number 216

description:
Saliva Sample from Crohn's Patient
CROHNS216


title: Crohn's Disease Sample Number 218

description:
Saliva Sample from Crohn's Patient
CROHNS218


title: Crohn's Disease Sample Number 217

description:
Saliva Sample from Crohn's Patient
CROHNS217


title: Ulcerative Colitis Sample Number 10

description:
Saliva Sample from Ulcerative Colitis Patient
UC010


title: Crohn's Disease Sample Number 209

description:
Saliva Sample from Crohn's Patient
CROHNS209


title: Crohn's Disease Sample Number 205

description:
Saliva Sample from Crohn's Patient
CROHNS205


title: Ulcerative Colitis Sample Number 8

description:
Saliva Sample from Ulcerative Colitis Patient
UC008


title: Crohn's Disease Sample Number 210

description:
Saliva Sample from Crohn's Patient
CROHNS210


title: Crohn's Disease Sample Number 207

description:
Saliva Sample from Crohn's Patient
CROHNS207


title: Crohn's Disease Sample Number 212

description:
Saliva Sample from Crohn's Patient
CROHNS212


title: Crohn's Disease Sample Number 204

description:
Saliva Sample from Crohn's Patient
CROHNS204


title: Crohn's Disease Sample Number 203

description:
Saliva Sample from Crohn's Patient
CROHNS203


title: Crohn's Disease Sample Number 219

description:
Saliva Sample from Crohn's Patient
CROHNS219


title: Crohn's Disease Sample Number 200

description:
Saliva Sample from Crohn's Patient
CROHNS200


title: Crohn's Disease Sample Number 201

description:
Saliva Sample from Crohn's Patient
CROHNS201


title: Crohn's Disease Sample Number 222

description:
Saliva Sample from Crohn's Patient
CROHNS222


title: Crohn's Disease Sample Number 215

description:
Saliva Sample from Crohn's Patient
CROHNS215


title: Crohn's Disease Sample Number 202

description:
Saliva Sample from Crohn's Patient
CROHNS202


title: Crohn's Disease Sample Number 198

description:
Saliva Sample from Crohn's Patient
CROHNS198


title: Crohn's Disease Sample Number 195

description:
Saliva Sample from Crohn's Patient
CROHNS195


title: Crohn's Disease Sample Number 194

description:
Saliva Sample from Crohn's Patient
CROHNS194


title: Crohn's Disease Sample Number 193

description:
Saliva Sample from Crohn's Patient
CROHNS193


title: Crohn's Disease Sample Number 196

description:
Saliva Sample from Crohn's Patient
CROHNS196


title: Crohn's Disease Sample Number 192

description:
Saliva Sample from Crohn's Patient
CROHNS192


title: Crohn's Disease Sample Number 208

description:
Saliva Sample from Crohn's Patient
CROHNS208


title: Crohn's Disease Sample Number 206

description:
Saliva Sample from Crohn's Patient
CROHNS206


title: Crohn's Disease Sample Number 190

description:
Saliva Sample from Crohn's Patient
CROHNS190


title: Crohn's Disease Sample Number 191

description:
Saliva Sample from Crohn's Patient
CROHNS191


title: Crohn's Disease Sample Number 189

description:
Saliva Sample from Crohn's Patient
CROHNS189


title: Crohn's Disease Sample Number 187

description:
Saliva Sample from Crohn's Patient
CROHNS187


title: Crohn's Disease Sample Number 188

description:
Saliva Sample from Crohn's Patient
CROHNS188


title: Crohn's Disease Sample Number 186

description:
Saliva Sample from Crohn's Patient
CROHNS186


title: Crohn's Disease Sample Number 185

description:
Saliva Sample from Crohn's Patient
CROHNS185


title: Crohn's Disease Sample Number 182

description:
Saliva Sample from Crohn's Patient
CROHNS182


title: Crohn's Disease Sample Number 181

description:
Saliva Sample from Crohn's Patient
CROHNS181


title: Crohn's Disease Sample Number 183

description:
Saliva Sample from Crohn's Patient
CROHNS183


title: Crohn's Disease Sample Number 180

description:
Saliva Sample from Crohn's Patient
CROHNS180


title: Crohn's Disease Sample Number 179

description:
Saliva Sample from Crohn's Patient
CROHNS179


title: Crohn's Disease Sample Number 197

description:
Saliva Sample from Crohn's Patient
CROHNS197


title: Crohn's Disease Sample Number 184

description:
Saliva Sample from Crohn's Patient
CROHNS184


title: Crohn's Disease Sample Number 176

description:
Saliva Sample from Crohn's Patient
CROHNS176


title: Crohn's Disease Sample Number 175

description:
Saliva Sample from Crohn's Patient
CROHNS175


title: Crohn's Disease Sample Number 178

description:
Saliva Sample from Crohn's Patient
CROHNS178


title: Crohn's Disease Sample Number 174

description:
Saliva Sample from Crohn's Patient
CROHNS174


title: Crohn's Disease Sample Number 173

description:
Saliva Sample from Crohn's Patient
CROHNS173


title: Crohn's Disease Sample Number 172

description:
Saliva Sample from Crohn's Patient
CROHNS172


title: Crohn's Disease Sample Number 199

description:
Saliva Sample from Crohn's Patient
CROHNS199


title: Crohn's Disease Sample Number 171

description:
Saliva Sample from Crohn's Patient
CROHNS171


title: Crohn's Disease Sample Number 169

description:
Saliva Sample from Crohn's Patient
CROHNS169


title: Crohn's Disease Sample Number 170

description:
Saliva Sample from Crohn's Patient
CROHNS170


title: Crohn's Disease Sample Number 168

description:
Saliva Sample from Crohn's Patient
CROHNS168


title: Crohn's Disease Sample Number 177

description:
Saliva Sample from Crohn's Patient
CROHNS177


title: Crohn's Disease Sample Number 167

description:
Saliva Sample from Crohn's Patient
CROHNS167


title: Crohn's Disease Sample Number 164

description:
Saliva Sample from Crohn's Patient
CROHNS164


title: Crohn's Disease Sample Number 162

description:
Saliva Sample from Crohn's Patient
CROHNS162


title: Crohn's Disease Sample Number 160

description:
Saliva Sample from Crohn's Patient
CROHNS160


title: Crohn's Disease Sample Number 161

description:
Saliva Sample from Crohn's Patient
CROHNS161


title: Crohn's Disease Sample Number 165

description:
Saliva Sample from Crohn's Patient
CROHNS165


title: Crohn's Disease Sample Number 166

description:
Saliva Sample from Crohn's Patient
CROHNS166


title: Crohn's Disease Sample Number 158

description:
Saliva Sample from Crohn's Patient
CROHNS158


title: Crohn's Disease Sample Number 159

description:
Saliva Sample from Crohn's Patient
CROHNS159


title: Crohn's Disease Sample Number 157

description:
Saliva Sample from Crohn's Patient
CROHNS157


title: Crohn's Disease Sample Number 156

description:
Saliva Sample from Crohn's Patient
CROHNS156


title: Crohn's Disease Sample Number 154

description:
Saliva Sample from Crohn's Patient
CROHNS154


title: Crohn's Disease Sample Number 155

description:
Saliva Sample from Crohn's Patient
CROHNS155


title: Crohn's Disease Sample Number 153

description:
Saliva Sample from Crohn's Patient
CROHNS153


title: Crohn's Disease Sample Number 152

description:
Saliva Sample from Crohn's Patient
CROHNS152


title: Crohn's Disease Sample Number 151

description:
Saliva Sample from Crohn's Patient
CROHNS151


title: Crohn's Disease Sample Number 150

description:
Saliva Sample from Crohn's Patient
CROHNS150


title: Crohn's Disease Sample Number 146

description:
Saliva Sample from Crohn's Patient
CROHNS146


title: Crohn's Disease Sample Number 148

description:
Saliva Sample from Crohn's Patient
CROHNS148


title: Crohn's Disease Sample Number 149

description:
Saliva Sample from Crohn's Patient
CROHNS149


title: Crohn's Disease Sample Number 147

description:
Saliva Sample from Crohn's Patient
CROHNS147


title: Crohn's Disease Sample Number 145

description:
Saliva Sample from Crohn's Patient
CROHNS145


title: Crohn's Disease Sample Number 140

description:
Saliva Sample from Crohn's Patient
CROHNS140


title: Crohn's Disease Sample Number 143

description:
Saliva Sample from Crohn's Patient
CROHNS143


title: Crohn's Disease Sample Number 139

description:
Saliva Sample from Crohn's Patient
CROHNS139


title: Crohn's Disease Sample Number 163

description:
Saliva Sample from Crohn's Patient
CROHNS163


title: Crohn's Disease Sample Number 142

description:
Saliva Sample from Crohn's Patient
CROHNS142


title: Crohn's Disease Sample Number 141

description:
Saliva Sample from Crohn's Patient
CROHNS141


title: Crohn's Disease Sample Number 138

description:
Saliva Sample from Crohn's Patient
CROHNS138


title: Crohn's Disease Sample Number 134

description:
Saliva Sample from Crohn's Patient
CROHNS134


title: Crohn's Disease Sample Number 133

description:
Saliva Sample from Crohn's Patient
CROHNS133


title: Crohn's Disease Sample Number 136

description:
Saliva Sample from Crohn's Patient
CROHNS136


title: Crohn's Disease Sample Number 130

description:
Saliva Sample from Crohn's Patient
CROHNS130


title: Crohn's Disease Sample Number 137

description:
Saliva Sample from Crohn's Patient
CROHNS137


title: Crohn's Disease Sample Number 131

description:
Saliva Sample from Crohn's Patient
CROHNS131


title: Crohn's Disease Sample Number 132

description:
Saliva Sample from Crohn's Patient
CROHNS132


title: Crohn's Disease Sample Number 128

description:
Saliva Sample from Crohn's Patient
CROHNS128


title: Crohn's Disease Sample Number 125

description:
Saliva Sample from Crohn's Patient
CROHNS125


title: Crohn's Disease Sample Number 126

description:
Saliva Sample from Crohn's Patient
CROHNS126


title: Crohn's Disease Sample Number 127

description:
Saliva Sample from Crohn's Patient
CROHNS127


title: Crohn's Disease Sample Number 129

description:
Saliva Sample from Crohn's Patient
CROHNS129


title: THP1, GUYDOS, 24hpi, Transwell, repIII

city: Midlothian

first: Musa

last: A Hassan

address: Easter Bush Campus

institute: University of Edinburgh

description: Library name: Transwell_GUYDOS_24hpi_repIII

data_processing:
Quantification was done using Kallisto and the transcripts were summed to gene-level counts
Assembly: GRCh38.p13, GENCODE, release 42 and TgondiiGT1, ToxoDB-61
Supplementary files format and content: txt. files containing count matrix

extract_protocol:
RNA was extracted using Qiagen RNA extraction kits
THP-1 cells were exposed for 12h to GFP-expressing RH parasites pre-labelled with pHrodo Red, a dye that fluoresces red in acidic conditions. 105 cells representing each of the three populations: uninfected cells (GFP- pHrodo-), cells infected through active invasion (GFP+), and cells infected via phagocytosis (GFP+ pHrodo+) were then sorted in cytometry. We also used naïve cells separated by a transwell membrane from cells exposed to Toxoplasma to generate true bystander cells that are neither infected nor injected with parasite effector proteins but still exposed to the host cell or parasite effectors secreted into the cell culture media. RNAs from naïve (unexposed), transwell, and sorted cell populations were separately extracted using RNA extraction kits (Qiagen) and processed for bulk RNA sequencing using ILLUMINA (NextSeq2000).

value: Monocytic cell


title: THP1, GUYDOS, 24hpi, Transwell, repII

description: Library name: Transwell_GUYDOS_24hpi_repII


title: Crohn's Disease Sample Number 144

description:
Saliva Sample from Crohn's Patient
CROHNS144


title: Crohn's Disease Sample Number 124

description:
Saliva Sample from Crohn's Patient
CROHNS124


title: Crohn's Disease Sample Number 123

description:
Saliva Sample from Crohn's Patient
CROHNS123


title: Crohn's Disease Sample Number 122

description:
Saliva Sample from Crohn's Patient
CROHNS122


title: Crohn's Disease Sample Number 121

description:
Saliva Sample from Crohn's Patient
CROHNS121


title: THP1, RH1, 24hpi, Transwell, repIII

description: Library name: Transwell_RH1_24hpi_repIII


title: THP1, RH1, 24hpi, Transwell, repII

description: Library name: Transwell_RH1_24hpi_repII


title: Crohn's Disease Sample Number 119

description:
Saliva Sample from Crohn's Patient
CROHNS119


title: Crohn's Disease Sample Number 135

description:
Saliva Sample from Crohn's Patient
CROHNS135


title: THP1, RH1, 24hpi, Transwell, repI

description: Library name: Transwell_RH1_24hpi_repI


title: Crohn's Disease Sample Number 120

description:
Saliva Sample from Crohn's Patient
CROHNS120


title: THP1, GUYDOS, 8hpi, Transwell, repIII

description: Library name: Transwell_GUYDOS_8hpi_repIII


title: THP1, GUYDOS, 8hpi, Transwell, repII

description: Library name: Transwell_GUYDOS_8hpi_repII


title: Crohn's Disease Sample Number 116

description:
Saliva Sample from Crohn's Patient
CROHNS116


title: Crohn's Disease Sample Number 118

description:
Saliva Sample from Crohn's Patient
CROHNS118


title: THP1, GUYDOS, 8hpi, Transwell, repI

description: Library name: Transwell_GUYDOS_8hpi_repI


title: THP1, RH1, 8hpi, Transwell, repII

description: Library name: Transwell_RH1_8hpi_repII


title: Crohn's Disease Sample Number 117

description:
Saliva Sample from Crohn's Patient
CROHNS117


title: THP1, RH1, 8hpi, Transwell, repIII

description: Library name: Transwell_RH1_8hpi_repIII


title: Crohn's Disease Sample Number 115

description:
Saliva Sample from Crohn's Patient
CROHNS115


title: Crohn's Disease Sample Number 114

description:
Saliva Sample from Crohn's Patient
CROHNS114


title: THP1, RH1, 8hpi, Transwell, repI

description: Library name: Transwell_RH1_8hpi_repI


title: THP1, GUYDOS, 24hpi, GFP, repI

description: Library name: Exposed_GFP_GUYDOS_24hpi_repI


title: Crohn's Disease Sample Number 113

description:
Saliva Sample from Crohn's Patient
CROHNS113


title: THP1, RH1, 24hpi, GFP, repII

description: Library name: Exposed_GFP_RH1_24hpi_repII


title: THP1, GUYDOS, 24hpi, Transwell, repI

description: Library name: Transwell_GUYDOS_24hpi_repI


title: Crohn's Disease Sample Number 112

description:
Saliva Sample from Crohn's Patient
CROHNS112


title: THP1, RH1, 24hpi, GFP, repI

description: Library name: Exposed_GFP_RH1_24hpi_repI


title: THP1, RH1, 8hpi, GFP, repIII

description: Library name: Exposed_GFP_RH1_8hpi_repIII


title: Crohn's Disease Sample Number 111

description:
Saliva Sample from Crohn's Patient
CROHNS111


title: Crohn's Disease Sample Number 110

description:
Saliva Sample from Crohn's Patient
CROHNS110


title: Crohn's Disease Sample Number 108

description:
Saliva Sample from Crohn's Patient
CROHNS108


title: THP1, GUYDOS, 8hpi, GFP, repI

description: Library name: Exposed_GFP_GUYDOS_8hpi_repI


title: Crohn's Disease Sample Number 107

description:
Saliva Sample from Crohn's Patient
CROHNS107


title: Crohn's Disease Sample Number 109

description:
Saliva Sample from Crohn's Patient
CROHNS109


title: THP1, RH1, 8hpi, GFP, repI

description: Library name: Exposed_GFP_RH1_8hpi_repI


title: THP1, GUYDOS, 24hpi, DoublePos, repIII

description: Library name: Exposed_DoublePositive_GUYDOS_24hpi_repIII


title: Crohn's Disease Sample Number 105

description:
Saliva Sample from Crohn's Patient
CROHNS105


title: THP1, RH1, 8hpi, GFP, repII

description: Library name: Exposed_GFP_RH1_8hpi_repII


title: Crohn's Disease Sample Number 103

description:
Saliva Sample from Crohn's Patient
CROHNS103


title: THP1, GUYDOS, 24hpi, DoublePos, repI

description: Library name: Exposed_DoublePositive_GUYDOS_24hpi_repI


title: Crohn's Disease Sample Number 106

description:
Saliva Sample from Crohn's Patient
CROHNS106


title: THP1, RH1, 24hpi, DoublePos, repIII

description: Library name: Exposed_DoublePositive_RH1_24hpi_repIII


title: Crohn's Disease Sample Number 102

description:
Saliva Sample from Crohn's Patient
CROHNS102


title: THP1, GUYDOS, 24hpi, DoublePos, repII

description: Library name: Exposed_DoublePositive_GUYDOS_24hpi_repII


title: Crohn's Disease Sample Number 101

description:
Saliva Sample from Crohn's Patient
CROHNS101


title: THP1, RH1, 24hpi, DoublePos, repII

description: Library name: Exposed_DoublePositive_RH1_24hpi_repII


title: Crohn's Disease Sample Number 100

description:
Saliva Sample from Crohn's Patient
CROHNS100


title: Crohn's Disease Sample Number 104

description:
Saliva Sample from Crohn's Patient
CROHNS104


title: THP1, RH1, 24hpi, DoublePos, repI

description: Library name: Exposed_DoublePositive_RH1_24hpi_repI


title: THP1, GUYDOS, 8hpi, DoublePos, repIII

description: Library name: Exposed_DoublePositive_GUYDOS_8hpi_repIII


title: Crohn's Disease Sample Number 99

description:
Saliva Sample from Crohn's Patient
CROHNS099


title: THP1, GUYDOS, 8hpi, DoublePos, repII

description: Library name: Exposed_DoublePositive_GUYDOS_8hpi_repII


title: THP1, GUYDOS, 8hpi, DoublePos, repI

description: Library name: Exposed_DoublePositive_GUYDOS_8hpi_repI


title: Crohn's Disease Sample Number 98

description:
Saliva Sample from Crohn's Patient
CROHNS098


title: Crohn's Disease Sample Number 97

description:
Saliva Sample from Crohn's Patient
CROHNS097


title: THP1, RH1, 8hpi, DoublePos, repIII

description: Library name: Exposed_DoublePositive_RH1_8hpi_repIII


title: Crohn's Disease Sample Number 96

description:
Saliva Sample from Crohn's Patient
CROHNS096


title: Crohn's Disease Sample Number 95

description:
Saliva Sample from Crohn's Patient
CROHNS095


title: THP1, RH1, 8hpi, DoublePos, repI

description: Library name: Exposed_DoublePositive_RH1_8hpi_repI


title: THP1, RH1, 8hpi, DoublePos, repII

description: Library name: Exposed_DoublePositive_RH1_8hpi_repII


title: Crohn's Disease Sample Number 94

description:
Saliva Sample from Crohn's Patient
CROHNS094


title: THP1, GUYDOS, 24hpi, DoubleNeg, repIII

description: Library name: Exposed_DoubleNegative_GUYDOS_24hpi_repIII


title: THP1, GUYDOS, 24hpi, DoubleNeg, repII

description: Library name: Exposed_DoubleNegative_GUYDOS_24hpi_repII


title: Crohn's Disease Sample Number 93

description:
Saliva Sample from Crohn's Patient
CROHNS093


title: Crohn's Disease Sample Number 92

description:
Saliva Sample from Crohn's Patient
CROHNS092


title: THP1, GUYDOS, 24hpi, DoubleNeg, repI

description: Library name: Exposed_DoubleNegative_GUYDOS_24hpi_repI


title: THP1, RH1, 24hpi, DoubleNeg, repIII

description: Library name: Exposed_DoubleNegative_RH1_24hpi_repIII


title: Crohn's Disease Sample Number 91

description:
Saliva Sample from Crohn's Patient
CROHNS091


title: Crohn's Disease Sample Number 90

description:
Saliva Sample from Crohn's Patient
CROHNS090


title: THP1, RH1, 24hpi, DoubleNeg, repI

description: Library name: Exposed_DoubleNegative_RH1_24hpi_repI


title: THP1, RH1, 24hpi, DoubleNeg, repII

description: Library name: Exposed_DoubleNegative_RH1_24hpi_repII


title: THP1, GUYDOS, 8hpi, DoubleNeg, repIII

description: Library name: Exposed_DoubleNegative_GUYDOS_8hpi_repIII


title: Crohn's Disease Sample Number 88

description:
Saliva Sample from Crohn's Patient
CROHNS088


title: Crohn's Disease Sample Number 86

description:
Saliva Sample from Crohn's Patient
CROHNS086


title: Crohn's Disease Sample Number 87

description:
Saliva Sample from Crohn's Patient
CROHNS087


title: THP1, GUYDOS, 8hpi, DoubleNeg, repII

description: Library name: Exposed_DoubleNegative_GUYDOS_8hpi_repII


title: Crohn's Disease Sample Number 85

description:
Saliva Sample from Crohn's Patient
CROHNS085


title: THP1, RH1, 8hpi, DoubleNeg, repI

description: Library name: Exposed_DoubleNegative_RH1_8hpi_repI


title: P2 resect C57/BL6 mouse ventricles

city: Cambridge

first: Richard

last: Lee

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description:
Library name: P2_C57/BL6_resect
thoracotomy + apical resection

data_processing:
Processed feature matrices were generated from raw FASTQ files via the Cell Ranger pipeline
Assembly: GRCm38
Supplementary files format and content: filtered_feature_bc_matrix.h5: processed feature matrices generated via the Cell Ranger pipeline

source_name: Neonatal Mouse Left and Right Ventricles

extract_protocol:
Fresh samples were perfused with PBS, and pooled by surgical condition. Ventricles were minced and 1200μL of dissociation media (RPMI 1640 media (Gibco 1187503), 0.04U/mL Dispase II in DMEM/F-12 (STEMCELL Technologies 07923), 2μg/mL Collagenase D (Roche 11088858001), 32U/mL DNase I (NEB M0303S)) were added. Samples were incubated (30min, 37°C) before deactivating the enzymes with cold 5% FBS in PBS. Samples were filtered through a 40μm cell strainer (Pluriselect 43-10040), centrifuged (300g, 5min, 4°C), resuspended in 2mL ACK lysing buffer (Gibco A10492-01), and incubated (5min, 37°C). Samples were centrifuged, washed (5% FBS in PBS), and recentrifuged. Live cells were enriched through dead cell removal (Miltenyi Biotech 130-090-101) and miniMACS separators. The suspension was washed and pelleted (400g, 5min, 4°C). Pellets were resuspended in 0.04% BSA in PBS at 1000 cells/μL and viability was determined through the LUNA-FL (Logos Biosystems).
Libraries were constructed following the 10x Genomics Chromium pipeline


title: Crohn's Disease Sample Number 83

description:
Saliva Sample from Crohn's Patient
CROHNS083


title: Crohn's Disease Sample Number 82

description:
Saliva Sample from Crohn's Patient
CROHNS082


title: Crohn's Disease Sample Number 80

description:
Saliva Sample from Crohn's Patient
CROHNS080


title: Crohn's Disease Sample Number 89

description:
Saliva Sample from Crohn's Patient
CROHNS089


title: HG3 USP28 WT/KO Clone 2

city: Ulm

first: Alena

middle: Sophie

last: Ehrmann

address: Albert-Einstein-Allee 23

department: Internal Medicine III

country: Germany

institute: University Hospital Ulm

data_processing:
Paired-reads were mapped against the GRCh37 version of the human genome using the STAR aligner (v2.7.10a) and gene annotations from Ensembl (v85)
Gene level counts were obtained from the BAM files through the HTSeq package (v0.11.2) in its “union” mode
Low expressed genes across samples were removed so that only those genes with 5 or more assigned reads in at least two samples were considered for subsequent analyses
The resulting count matrix was normalized to the estimated size factors using the DESeq2 (v1.36.0) median of ratios method
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include normalized read counts per each sample

growth_protocol: HG3 cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% penicilin/streptomycin and 1% glutaMAX in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
5x10^6 cells per condition were suspended in RLT PLus buffer and stored at -80ºC. RNA was harvested using Rneasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA protocol (Illumina), following manufacturer's instructions.

value: B-cell chronic lymphocytic leukemia

value: Monoallelic USP28 knockout


title: P2 sham C57/BL6 mouse ventricles

description:
Library name: P2_C57/BL6_sham
thoracotomy only

value: Neonatal Mouse Left and Right Ventricles


title: HG3 USP28 WT/WT Clone 2

value: WT


title: Crohn's Disease Sample Number 78

description:
Saliva Sample from Crohn's Patient
CROHNS078


title: Crohn's Disease Sample Number 84

description:
Saliva Sample from Crohn's Patient
CROHNS084


title: THP1, GUYDOS, 8hpi, DoubleNeg, repI

description: Library name: Exposed_DoubleNegative_GUYDOS_8hpi_repI


title: Crohn's Disease Sample Number 77

description:
Saliva Sample from Crohn's Patient
CROHNS077


title: Crohn's Disease Sample Number 79

description:
Saliva Sample from Crohn's Patient
CROHNS079


title: Crohn's Disease Sample Number 81

description:
Saliva Sample from Crohn's Patient
CROHNS081


title: THP1, RH1, 8hpi, DoubleNeg, repII

description: Library name: Exposed_DoubleNegative_RH1_8hpi_repII


title: Crohn's Disease Sample Number 76

description:
Saliva Sample from Crohn's Patient
CROHNS076


title: rne delta CTD lysate rep2

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

description: Library name: GSF4134-RNE-NTD--Apex2-Lysate-Rep-2_S2

data_processing:
Reads were first stripped of adapters using a custom python script and aligned to rRNA and tRNA using bowtie.
all reads not aligning to rRNA and tRNA were then aligned to the NA1000 genome using bowtie.
RNA counts for each RNA species were calculated from the resulting map files, and the RPKM values for each sample were calculated for RNA species with >=50 reads.
The RPKM of the elution of each sample was then divided by the RPKM of the lysate, and the log2 ratio of elution/lysate was reported.
Assembly: NA1000
Supplementary files format and content: Summary.csv, CSV file of Log2 ratios (elution/lysate) for each gene in each biological sample.

organism: Caulobacter vibrioides NA1000

source_name: log-phase cells

growth_protocol: Caulobacter crescentus strains were grown in M2G mimimal medium to mid-log (OD600 0.3 to 0.6).

extract_protocol:
RNA extraction was performed via TRIZOL of pelleted cells.  An aliquote of the RNA from the lysate was saved as the lysate, and the proximity labeled RNA was purified via click chemistry of a biotin azide, followed by streptavidin purification.
Illumina Truseq kit was used to prepare the libraries from the IU CGM core facility.

treatment_protocol: Upon reaching mid-log, the cells were incubated with alkyne phenol for 30 minutes, and then hydrogen peroxide for 1 minute before harvesting the cells at max speed in an eppendorf microcentrifuge.

value: log-phase cells

value: NA1000 rne::rnedeltaCTD-APEX2


title: Crohn's Disease Sample Number 75

description:
Saliva Sample from Crohn's Patient
CROHNS075


title: rne delta CTD elution rep2

description: Library name: GSF4134-RNE-NTD--Apex2-Elution-Rep-2_S4


title: Crohn's Disease Sample Number 74

description:
Saliva Sample from Crohn's Patient
CROHNS074


title: rne delta CTD elution rep1

description: Library name: GSF4134-RNE-NTD--Apex2-Elution-Rep-1_S3


title: rne Full length elution rep2

description: Library name: GSF4134-RNE-FL--Apex2-Elution-Rep-2_S8

value: NA1000 rne::rne-APEX2


title: Crohn's Disease Sample Number 73

description:
Saliva Sample from Crohn's Patient
CROHNS073


title: rne Full length elution rep1

description: Library name: GSF4134-RNE-FL--Apex2-Elution-Rep-1_S7


title: Crohn's Disease Sample Number 72

description:
Saliva Sample from Crohn's Patient
CROHNS072


title: rne Full length lysate rep2

description: Library name: GSF4134-RNE-FL--Apex2-Lysate-Rep-2_S6


title: Crohn's Disease Sample Number 71

description:
Saliva Sample from Crohn's Patient
CROHNS071


title: Crohn's Disease Sample Number 70

description:
Saliva Sample from Crohn's Patient
CROHNS070


title: rne Full length lysate rep1

description: Library name: GSF4134-RNE-FL--Apex2-Lysate-Rep-1_S5


title: HG3 USP28 WT/KO Clone 1


title: acaule freeze rep3

city: Sainte-Anne-de-Bellevue

first: Juan Carlos

last: Camargo-Tavares

state: Quebec

address: 21111 Lakeshore Road

country: Canada

institute: McGill University

description:
acaule_TMM.txt
acaule_annotation.txt

data_processing:
Reads were trimmed and quality filtered with Trimmomatic v0.39 and then cleaned of viral sequences with custom pipeline.
De novo transcriptomes for each species were assembled by generating a de novo and a reference guided assemblies with Trinity and merging them with EvidentialGene.
Transcrpts were mapped
TMM files were generated with DESeq2 using a Trinity pipeline.
Assembly: Acaule: GenBank Biosample SAMN23440999; Atlantic: ATL_v2.0_asm.fasta https://doi.org/10.1016/j.molp.2022.01.003
Supplementary files format and content: There are two files per species: a TMM file with each colum representing each sample (2 conditions 3 replicates), and a annotation file pointing to respective reference genome gene and location. If there is no annotation

organism: Solanum acaule

source_name: shoot

extract_protocol:
Total RNA was extracted from shoot frozen samples using RNeasy Plant Mini Kit (Qiagen), according to the manufacturer’s instructions.
mRNA Stranded

value: shoot

value: freeze


title: HG3 USP28 WT/WT Clone 1


title: Crohn's Disease Sample Number 69

description:
Saliva Sample from Crohn's Patient
CROHNS069


title: acaule freeze rep2

description:
acaule_TMM.txt
acaule_annotation.txt


title: acaule freeze rep1

description:
acaule_TMM.txt
acaule_annotation.txt


title: Crohn's Disease Sample Number 68

description:
Saliva Sample from Crohn's Patient
CROHNS068


title: Crohn's Disease Sample Number 67

description:
Saliva Sample from Crohn's Patient
CROHNS067


title: Crohn's Disease Sample Number 66

description:
Saliva Sample from Crohn's Patient
CROHNS066


title: acaule control rep2

description:
acaule_TMM.txt
acaule_annotation.txt

value: control


title: acaule control rep3

description:
acaule_TMM.txt
acaule_annotation.txt


title: Crohn's Disease Sample Number 65

description:
Saliva Sample from Crohn's Patient
CROHNS065


title: Crohn's Disease Sample Number 63

description:
Saliva Sample from Crohn's Patient
CROHNS063


title: rne delta CTD lysate rep1

description: Library name: GSF4134-RNE-NTD--Apex2-Lysate-Rep-1_S1


title: 9_SMM_Rep1_S5

city: Brighton

first: Ruslan

last: Evans

state: East Sussex

address: Lewes Road

department: School of Applied Science

institute: University of Brighton

data_processing:
Reads were quantified against S. coelicolor transcriptome using kallisto quant version 0.46.2. Transcriptome gene annotations used from NCBI reference NC_003888.3 and sRNA annotations from 'The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)', Jeong et al. 2016 https://doi.org/10.1038/ncomms11605
Kallisto quantifications were converted to gene level by tximport version 1.20.0 then analysed for differential expression using DESeq2 version 1.32.0.
lfcShrink used to calculate differential expression contrasts with adaptive shrinkage (type='ashr').
Assembly: GCF_000203835.1_ASM20383v1  NC_003888.3
Supplementary files format and content: CSV-delimited text file. DE contrasts log2-fold changes and padj for contrasts cold-shock at 15, 30 and 60 min vs cold-shock at 5 min, and cold-shock vs control at 5 and 60 min by media type.
Supplementary files format and content: tab-delimited text files. Matrix table of counts for every gene and sRNA generated by kallisto quant.

organism: Streptomyces coelicolor A3(2)

source_name: bacterial cultures

growth_protocol: Rich liquid medium cultures were inoculated at a concentration of approx. 1,000,000 cfu / ml in 500 ml conical flasks containing springs and 120 ml yeast extract-malt extract (YEME) medium (Practical Streptomyces Genetics, Kieser et al. 2000, ISBN 9780708406236) and incubated for 19 h 19 min in a shaking incubator at 30°C and 250 rpm. Solid medium cultures were pre-germinated in 2 x YT medium (Kieser et al., 2000) for 9hrs at 30°C and 250 rpm then plated on supplemented minimal medium, solid (SMMS) media (Kieser et al., 2000) overlayed with cellophane discs at a concentration of approx 1,000,000 germ tubes per plate and incubated for 42 h at 30°C.

extract_protocol:
10 ml of bacterial cultures were resuspended in 200 µl of lysozyme dissolved in TE buffer at a concentration of 0.015 g per ml and incubated at room temperature for 15 min. 600 µl of RNeasy Lysis Buffer (RLT buffer, Qiagen #79216) containing 10 µl/ml b-mercaptoethanol was added and the mixture mixed by vortex mixer then transferred to a 2ml microfuge tube containing 5 mm stainless steel beads (Qiagen 69989) and placed in a Tissuelyser LT (Qiagen #85600) for efficient mechanical cell disruption / homogenisation for 2 min at 30 rpm. The suspension was then centrifuged at 16,627 RCF for 2 min, the supernatant was recovered and its volume estimated. One volume of neutral pH phenol:chloroform:isoamyl alcohol (25:24:1, Sigma #77617) was added, and the mixture mixed by vortex mixer for 30 seconds, then centrifuged at 4°C for 5 min at 16,627 RCF. The top phase containing the nucleic acids was removed and retained leaving the interface, and the phenol/chloroform extraction repeated twice more. Then one volume of chloroform was added, the mixture mixed by vortex mixer then centrifuged at 4°C for 2 min at 16,627 RCF, and the top phase was again transferred to a fresh RNase-free microfuge tube. From this point onward the standard manufacturer’s instructions were followed for the miRNAeasy RNA extraction kit (Qiagen #217004). The total RNA was then eluted in 30 µl of nuclease free water and stored at -80°C. Genomic DNA was removed using the Turbo DNA free kit (Invitrogen AM1907).
NEBNext® Ultra™II Directional  RNA Library Prep Kit for Illumina® (cat. E7760) according to manufacturer’s instructions

treatment_protocol: Liquid medium cultures were exposed to cold-shock by the addition of 3 volumes of fresh media at 4°C to reduce the temperature to 10°C, whilst control cultures had fresh media at 30°C added. Solid medium cultures were exposed to cold-shock by transfering the mycelium growing on cellophane discs to a fresh plate pre-chilled plates to 4°C, whilst control cultures were transferred to pre-warmed plates at 30°C.

value: bacterial cultures

tag: medium

value: SMMS

value: cold-shock

tag: time (min)

tag: replicate


title: 7_YEME_Rep1_S60

value: YEME


title: Crohn's Disease Sample Number 62

description:
Saliva Sample from Crohn's Patient
CROHNS062

value: Male


title: acaule control rep1

description:
acaule_TMM.txt
acaule_annotation.txt


title: Crohn's Disease Sample Number 61

description:
Saliva Sample from Crohn's Patient
CROHNS061

value: Crohn's Disease


title: Crohn's Disease Sample Number 64

description:
Saliva Sample from Crohn's Patient
CROHNS064

value: Female


title: Crohn's Disease Sample Number 60

description:
Saliva Sample from Crohn's Patient
CROHNS060


title: Crohn's Disease Sample Number 58

description:
Saliva Sample from Crohn's Patient
CROHNS058


title: Crohn's Disease Sample Number 59

description:
Saliva Sample from Crohn's Patient
CROHNS059


title: 5_YEME_Rep1_T60


title: 8_YEME_Rep2_S5


title: 4_YEME_Rep1_T5


title: 2_SMM_Rep2_T60


title: 6_YEME_Rep1_S5


title: 3_SMM_Rep2_S15


title: Crohn's Disease Sample Number 56

description:
Saliva Sample from Crohn's Patient
CROHNS056


title: Crohn's Disease Sample Number 57

description:
Saliva Sample from Crohn's Patient
CROHNS057


title: 27_YEME_Rep2_T60


title: Crohn's Disease Sample Number 54

description:
Saliva Sample from Crohn's Patient
CROHNS054


title: Crohn's Disease Sample Number 55

description:
Saliva Sample from Crohn's Patient
CROHNS055


title: 25_SMM_Rep1_T5


title: Crohn's Disease Sample Number 53

description:
Saliva Sample from Crohn's Patient
CROHNS053


title: 22_YEME_Rep1_S15


title: 23_YEME_Rep1_S30


title: Crohn's Disease Sample Number 51

description:
Saliva Sample from Crohn's Patient
CROHNS051


title: 20_SMM_Rep2_S30


title: Crohn's Disease Sample Number 50

description:
Saliva Sample from Crohn's Patient
CROHNS050


title: 21_SMM_Rep2_S60


title: 1_SMM_Rep1_T60


title: Crohn's Disease Sample Number 48

description:
Saliva Sample from Crohn's Patient
CROHNS048


title: Crohn's Disease Sample Number 49

description:
Saliva Sample from Crohn's Patient
CROHNS049


title: 19_SMM_Rep1_S60


title: Crohn's Disease Sample Number 46

description:
Saliva Sample from Crohn's Patient
CROHNS046


title: 18_SMM_Rep1_S30


title: 16_YEME_Rep2_S60


title: Crohn's Disease Sample Number 47

description:
Saliva Sample from Crohn's Patient
CROHNS047


title: Crohn's Disease Sample Number 45

description:
Saliva Sample from Crohn's Patient
CROHNS045


title: 14_YEME_Rep2_S15


title: 13_YEME_Rep2_T5


title: 12_SMM_Rep2_S5


title: Crohn's Disease Sample Number 42

description:
Saliva Sample from Crohn's Patient
CROHNS042


title: 11_SMM_Rep2_T5


title: Crohn's Disease Sample Number 41

description:
Saliva Sample from Crohn's Patient
CROHNS041


title: Crohn's Disease Sample Number 40

description:
Saliva Sample from Crohn's Patient
CROHNS040


title: Crohn's Disease Sample Number 39

description:
Saliva Sample from Crohn's Patient
CROHNS039


title: 10_SMM_Rep1_S15


title: Crohn's Disease Sample Number 52

description:
Saliva Sample from Crohn's Patient
CROHNS052


title: Wild Type Phenotype_19-0026

city: West Point

first: Zoltan

last: Erdos

state: PA

address: 770 Sumneytown Pike

institute: Merck

description: Library name: TT19-9913_19-0026_CRW

data_processing:
Reads were aligned to the Mouse.B39 (Ensembl.R96) genome reference using the OmicSoft Aligner (OSA4).
Assembly: Mouse.B39 (Ensembl.R96)
Supplementary files format and content: Tab delimited text

source_name: Thyroid

extract_protocol:
Extract RNA from mouse Thyrpoid with MagMax RNA 96 for microarrays kit (PN1839-4).
500ng of total RNA was used to build the library with the KAPA RNA HyperPrep kit with RiboErase (HMR) KR1351 – v1.16

value: Thyroid

tag: phenotype

value: Wild Type Phenotype


title: Wild Type Phenotype_19-0025

description: Library name: TT19-9913_19-0025_CRW


title: Wild Type Phenotype_19-0024

description: Library name: TT19-9913_19-0024_CRW


title: Crohn's Disease Sample Number 37

description:
Saliva Sample from Crohn's Patient
CROHNS037


title: Crohn's Disease Sample Number 35

description:
Saliva Sample from Crohn's Patient
CROHNS035


title: Wild Type Phenotype_19-0022

description: Library name: TT19-9913_19-0022_CRW


title: Wild Type Phenotype_19-0014

description: Library name: TT19-9913_19-0014_TCK


title: 15_YEME_Rep2_S30


title: Crohn's Disease Sample Number 32

description:
Saliva Sample from Crohn's Patient
CROHNS032


title: Crohn's Disease Sample Number 31

description:
Saliva Sample from Crohn's Patient
CROHNS031


title: Thyroid Dysplasia Phenotype_19-0005

description: Library name: TT19-9913_19-0005_TCW

value: Thyroid Dysplasia Phenotype


title: Thyroid Dysplasia Phenotype_19-0006

description: Library name: TT19-9913_19-0006_TCW


title: Crohn's Disease Sample Number 43

description:
Saliva Sample from Crohn's Patient
CROHNS043


title: Thyroid Dysplasia Phenotype_19-0003

description: Library name: TT19-9913_19-0003_TCW


title: Crohn's Disease Sample Number 28

description:
Saliva Sample from Crohn's Patient
CROHNS028


title: Thyroid Dysplasia Phenotype_19-0001

description: Library name: TT19-9913_19-0001_TCW


title: SLE_S1Pi_WB_20

city: Allschwil

first: Pijus

last: Brazauskas

address: Hegenheimermattweg 91

country: Switzerland

institute: Idorsia Pharmaceuticals

description: Library name: SLEACT-167994_S17

data_processing:
Sequenced reads were aligned with STAR v2.5 to the Mouse Reference genome (Mus_musculus_GRCm38_98), and alignments per gene (exons) quantified with featureCounts using Ensembl gene annotations.
Assembly: Mus_musculus_GRCm38_98
Supplementary files format and content: Text file of raw read counts

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
Individual tissue samples were lysed and homogenized in 850 µl of TRI Reagent (ThermoFisher Scientific) using the Tissue-Lyzer (Qiagen). Total RNA was isolated from the tissue lysate using MagMax 96 microarray kit (AM1839, Life Technologies) according to the manufacturer's instructions.
RNA from blood and kidney from cenerimod- and vehicle-treated mice was isolated and prepared for sequencing using NUGEN Universal Plus mRNA kit with PolyA select (and globin depletion for the blood samples) according to protocol

value: Whole Blood


title: Wild Type Phenotype_19-0021

description: Library name: TT19-9913_19-0021_CRW


title: Crohn's Disease Sample Number 38

description:
Saliva Sample from Crohn's Patient
CROHNS038


title: SLE_S1Pi_WB_19

description: Library name: SLEACT-167993_S16


title: Crohn's Disease Sample Number 44

description:
Saliva Sample from Crohn's Patient
CROHNS044


title: Crohn's Disease Sample Number 26

description:
Saliva Sample from Crohn's Patient
CROHNS026


title: Crohn's Disease Sample Number 36

description:
Saliva Sample from Crohn's Patient
CROHNS036


title: Wild Type Phenotype_19-0023

description: Library name: TT19-9913_19-0023_CRW


title: Crohn's Disease Sample Number 25

description:
Saliva Sample from Crohn's Patient
CROHNS025


title: Crohn's Disease Sample Number 24

description:
Saliva Sample from Crohn's Patient
CROHNS024


title: SLE_S1Pi_WB_18

description: Library name: SLEACT-167992_S15


title: Crohn's Disease Sample Number 34

description:
Saliva Sample from Crohn's Patient
CROHNS034


title: SLE_S1Pi_WB_16

description: Library name: SLEACT-167990_S13


title: Crohn's Disease Sample Number 33

description:
Saliva Sample from Crohn's Patient
CROHNS033


title: Crohn's Disease Sample Number 23

description:
Saliva Sample from Crohn's Patient
CROHNS023


title: SLE_S1Pi_WB_15

description: Library name: SLEACT-167989_S12


title: Crohn's Disease Sample Number 22

description:
Saliva Sample from Crohn's Patient
CROHNS022


title: SLE_S1Pi_WB_14

description: Library name: SLEACT-167988_S11_2


title: Crohn's Disease Sample Number 21

description:
Saliva Sample from Crohn's Patient
CROHNS021


title: Crohn's Disease Sample Number 30

description:
Saliva Sample from Crohn's Patient
CROHNS030


title: Thyroid Dysplasia Phenotype_19-0004

description: Library name: TT19-9913_19-0004_TCW


title: Crohn's Disease Sample Number 20

description:
Saliva Sample from Crohn's Patient
CROHNS020


title: SLE_S1Pi_WB_12

description: Library name: SLEACT-167986_S9


title: Crohn's Disease Sample Number 29

description:
Saliva Sample from Crohn's Patient
CROHNS029


title: Crohn's Disease Sample Number 27

description:
Saliva Sample from Crohn's Patient
CROHNS027


title: Crohn's Disease Sample Number 18

description:
Saliva Sample from Crohn's Patient
CROHNS018


title: Crohn's Disease Sample Number 19

description:
Saliva Sample from Crohn's Patient
CROHNS019


title: Crohn's Disease Sample Number 17

description:
Saliva Sample from Crohn's Patient
CROHNS017


title: SLE_S1Pi_WB_9

description: Library name: SLEACT-167983_S16


title: Crohn's Disease Sample Number 16

description:
Saliva Sample from Crohn's Patient
CROHNS016


title: SLE_S1Pi_WB_17

description: Library name: SLEACT-167991_S14


title: SLE_S1Pi_WB_7

description: Library name: SLEACT-167981_S14


title: SLE_S1Pi_WB_8

description: Library name: SLEACT-167982_S15


title: Crohn's Disease Sample Number 15

description:
Saliva Sample from Crohn's Patient
CROHNS015


title: SLE_S1Pi_WB_6

description: Library name: SLEACT-167980_S13


title: Crohn's Disease Sample Number 12

description:
Saliva Sample from Crohn's Patient
CROHNS012


title: SLE_S1Pi_WB_5

description: Library name: SLEACT-167979_S12


title: SLE_S1Pi_WB_10

description: Library name: SLEACT-167984_S17


title: Crohn's Disease Sample Number 11

description:
Saliva Sample from Crohn's Patient
CROHNS011


title: Crohn's Disease Sample Number 14

description:
Saliva Sample from Crohn's Patient
CROHNS014


title: SLE_S1Pi_WB_4

description: Library name: SLEACT-167978_S11


title: Crohn's Disease Sample Number 9

description:
Saliva Sample from Crohn's Patient
CROHNS009


title: Crohn's Disease Sample Number 10

description:
Saliva Sample from Crohn's Patient
CROHNS010


title: SLE_S1Pi_WB_2

description: Library name: SLEACT-167976_S9


title: SLE_S1Pi_WB_3

description: Library name: SLEACT-167977_S10


title: SLE_WB_14

description: Library name: SLE-167973_S7


title: Crohn's Disease Sample Number 8

description:
Saliva Sample from Crohn's Patient
CROHNS008


title: SLE_S1Pi_WB_13

description: Library name: SLEACT-167987_S10


title: SLE_WB_13

description: Library name: SLE-167972_S6


title: Crohn's Disease Sample Number 6

description:
Saliva Sample from Crohn's Patient
CROHNS006


title: SLE_WB_12

description: Library name: SLE-167971_S5


title: Crohn's Disease Sample Number 5

description:
Saliva Sample from Crohn's Patient
CROHNS005


title: SLE_S1Pi_WB_11

description: Library name: SLEACT-167985_S8


title: Crohn's Disease Sample Number 4

description:
Saliva Sample from Crohn's Patient
CROHNS004


title: SLE_WB_11

description: Library name: SLE-167970_S4_2


title: SLE_WB_10

description: Library name: SLE-167969_S3


title: Crohn's Disease Sample Number 3

description:
Saliva Sample from Crohn's Patient
CROHNS003


title: SLE_WB_9

description: Library name: SLE-167968_S2


title: Crohn's Disease Sample Number 2

description:
Saliva Sample from Crohn's Patient
CROHNS002


title: Crohn's Disease Sample Number 13

description:
Saliva Sample from Crohn's Patient
CROHNS013


title: SLE_WB_8

description: Library name: SLE-167967_S1


title: Control Sample number 250

description:
Saliva Sample from Control
CONTROL250

value: Control Sample number 250


title: Crohn's Disease Sample Number 1

description:
Saliva Sample from Crohn's Patient
CROHNS001


title: SLE_WB_6

description: Library name: SLE-167964_S6


title: SLE_WB_5

description: Library name: SLE-167961_S5


title: SLE_S1Pi_WB_1

description: Library name: SLEACT-167975_S8


title: Control Sample number 246

description:
Saliva Sample from Control
CONTROL246

value: Control Sample number 246


title: SLE_WB_4

description: Library name: SLE-167960_S4


title: Control Sample number 248

description:
Saliva Sample from Control
CONTROL248

value: Control Sample number 248


title: SLE_WB_3

description: Library name: SLE-167959_S3


title: Crohn's Disease Sample Number 7

description:
Saliva Sample from Crohn's Patient
CROHNS007


title: Control Sample number 247

description:
Saliva Sample from Control
CONTROL247

value: Control Sample number 247


title: Control Sample number 245

description:
Saliva Sample from Control
CONTROL245

value: Control Sample number 245


title: Control Sample number 244

description:
Saliva Sample from Control
CONTROL244

value: Control Sample number 244


title: SLE_WB_1

description: Library name: SLE-167957_S1_2


title: Control Sample number 242

description:
Saliva Sample from Control
CONTROL242

value: Control Sample number 242


title: NAIVE_WB_2

description: Library name: NV-168794_S18


title: Control Sample number 243

description:
Saliva Sample from Control
CONTROL243

value: Control Sample number 243


title: Control Sample number 240

description:
Saliva Sample from Control
CONTROL240

value: Control Sample number 240


title: SLE_S1Pi_Kidney_18

description: Library name: SLEACT-167992-38_S11

source_name: Kidney

value: Kidney


title: NAIVE_WB_1

description: Library name: NV-168793_S18


title: Control Sample number 249

description:
Saliva Sample from Control
CONTROL249

value: Control Sample number 249

value: Male


title: SLE_S1Pi_Kidney_20

description: Library name: SLEACT-167994-40_S12


title: Control Sample number 241

description:
Saliva Sample from Control
CONTROL241

value: Control Sample number 241

value: Female


title: Control Sample number 237

description:
Saliva Sample from Control
CONTROL237

value: Control Sample number 237


title: Control Sample number 238

description:
Saliva Sample from Control
CONTROL238

value: Control Sample number 238


title: SLE_S1Pi_Kidney_15

description: Library name: SLEACT-167989-35_S9


title: SLE_WB_7

description: Library name: SLE-167966_S7

value: Whole Blood


title: SLE_S1Pi_Kidney_17

description: Library name: SLEACT-167991_S12


title: Control Sample number 239

description:
Saliva Sample from Control
CONTROL239

value: Control Sample number 239


title: Control Sample number 236

description:
Saliva Sample from Control
CONTROL236

value: Control Sample number 236


title: SLE_S1Pi_Kidney_14

description: Library name: SLEACT-167988_S11


title: Control Sample number 235

description:
Saliva Sample from Control
CONTROL235

value: Control Sample number 235


title: SLE_WB_2

description: Library name: SLE-167958_S2


title: Control Sample number 234

description:
Saliva Sample from Control
CONTROL234

value: Control Sample number 234


title: SLE_S1Pi_Kidney_13

description: Library name: SLEACT-167987_S11


title: SLE_S1Pi_Kidney_16

description: Library name: SLEACT-167990-36_S10


title: Control Sample number 232

description:
Saliva Sample from Control
CONTROL232

value: Control Sample number 232


title: SLE_S1Pi_Kidney_12

description: Library name: SLEACT-167986-32_S8


title: SLE_S1Pi_Kidney_10

description: Library name: SLEACT-167984_S10


title: Control Sample number 231

description:
Saliva Sample from Control
CONTROL231

value: Control Sample number 231


title: SLE_S1Pi_Kidney_11

description: Library name: SLEACT-167985_S10


title: SLE_S1Pi_Kidney_19

description: Library name: SLEACT-167993_S12


title: SLE_S1Pi_Kidney_9

description: Library name: SLEACT-167983-29_S7


title: Control Sample number 230

description:
Saliva Sample from Control
CONTROL230

value: Control Sample number 230


title: SLE_S1Pi_Kidney_8

description: Library name: SLEACT-167982_S9


title: SLE_S1Pi_Kidney_6

description: Library name: SLEACT-167980-26_S6


title: Control Sample number 227

description:
Saliva Sample from Control
CONTROL227

value: Control Sample number 227


title: Control Sample number 226

description:
Saliva Sample from Control
CONTROL226

value: Control Sample number 226


title: SLE_S1Pi_Kidney_5

description: Library name: SLEACT-167979_S8

value: Kidney


title: SLE_S1Pi_Kidney_4

description: Library name: SLEACT-167978_S8


title: Control Sample number 229

description:
Saliva Sample from Control
CONTROL229

value: Control Sample number 229


title: Control Sample number 228

description:
Saliva Sample from Control
CONTROL228

value: Control Sample number 228


title: SLE_S1Pi_Kidney_7

description: Library name: SLEACT-167981_S9


title: Control Sample number 225

description:
Saliva Sample from Control
CONTROL225

value: Control Sample number 225


title: SLE_S1Pi_Kidney_3

description: Library name: SLEACT-167977-23_S5


title: Control Sample number 224

description:
Saliva Sample from Control
CONTROL224

value: Control Sample number 224

value: Male


title: Control Sample number 233

description:
Saliva Sample from Control
CONTROL233

value: Control Sample number 233

value: Female


title: Control Sample number 223

description:
Saliva Sample from Control
CONTROL223

value: Control Sample number 223


title: Control Sample number 222

description:
Saliva Sample from Control
CONTROL222

value: Control Sample number 222


title: SLE_S1Pi_Kidney_2

description: Library name: SLEACT-167976_S7


title: SLE_S1Pi_Kidney_1

description: Library name: SLEACT-167975_S7


title: Control Sample number 220

description:
Saliva Sample from Control
CONTROL220

value: Control Sample number 220


title: SLE_Kidney_12

description: Library name: SLE-167971-17_S4


title: Control Sample number 221

description:
Saliva Sample from Control
CONTROL221

value: Control Sample number 221


title: SLE_Kidney_14

description: Library name: SLE-167973_S5


title: SLE_Kidney_11

description: Library name: SLE-167970_S4


title: SLE_Kidney_13

description: Library name: SLE-167972_S5


title: Control Sample number 218

description:
Saliva Sample from Control
CONTROL218

value: Control Sample number 218


title: SLE_Kidney_10

description: Library name: SLE-167969_S4


title: Control Sample number 217

description:
Saliva Sample from Control
CONTROL217

value: Control Sample number 217


title: SLE_Kidney_9

description: Library name: SLE-167968-14_S3


title: SLE_Kidney_8

description: Library name: SLE-167967_S3


title: Control Sample number 216

description:
Saliva Sample from Control
CONTROL216

value: Control Sample number 216


title: Control Sample number 215

description:
Saliva Sample from Control
CONTROL215

value: Control Sample number 215


title: SLE_Kidney_7

description: Library name: SLE-167966_S3


title: Control Sample number 213

description:
Saliva Sample from Control
CONTROL213

value: Control Sample number 213


title: Control Sample number 214

description:
Saliva Sample from Control
CONTROL214

value: Control Sample number 214


title: Control Sample number 212

description:
Saliva Sample from Control
CONTROL212

value: Control Sample number 212


title: SLE_Kidney_5

description: Library name: SLE-167961_S2

value: Kidney


title: Control Sample number 210

description:
Saliva Sample from Control
CONTROL210

value: Control Sample number 210


title: SLE_Kidney_3

description: Library name: SLE-167959-5_S1


title: SLE_Kidney_2

description: Library name: SLE-167958_S1


title: Control Sample number 208

description:
Saliva Sample from Control
CONTROL208

value: Control Sample number 208


title: SLE_Kidney_1

description: Library name: SLE-167957_S1


title: Control Sample number 211

description:
Saliva Sample from Control
CONTROL211

value: Control Sample number 211


title: NAIVE_Kidney_2

description: Library name: NAIVE-168794_S6


title: Control Sample number 209

description:
Saliva Sample from Control
CONTROL209

value: Control Sample number 209


title: NAIVE_Kidney_1

description: Library name: NAIVE-168793_S6


title: Control Sample number 207

description:
Saliva Sample from Control
CONTROL207

value: Control Sample number 207

value: Female


title: Control Sample number 219

description:
Saliva Sample from Control
CONTROL219

value: Control Sample number 219


title: corin_PD1_3

city: Boston

first: Robert

last: Fisher

address: 609 Albany St

department: Dermatology

institute: Boston University

data_processing:
Transcriptomic data were mapped to the Mus musculus reference genome (GRCm39) and assigned to individual cells of origin using Cell Ranger software 8.0 (10X Genomics). Subsequent count matrices were read into Seurat (v5.0.11)96 for downstream analysis. Doublets were identified and removed for each sample individually using the DoubletFinder (v2.0.4)97 pipeline. The data were further filtered to exclude cells with high mitochondrial gene expression (>10%) and aberrant unique feature counts (<600, >4000) or contaminating non-immune cells. Samples were then merged together for normalization and identification of highly variable features using scTransform (v0.4.13)98. Dimensionality reduction was carried out via principal component analysis using 20 dimensions. The optimal number of clusters was identified using clustree (v0.5.1)99 and each cluster was annotated based on the top genes determined by FindAllMarkers function in Seurat and SingleR62 annotations. The T cell population was further subset based on Cd3e expression to determine effects of corin treatment.
Assembly: GRCm39
Supplementary files format and content: Outputs from CellRanger filtered_feature_bc_matrix  (barcodes, features, and matrix tsv's)

source_name: CD45+ immune cells from B16-F10 melanoma xenograft in mouse

extract_protocol:
Minced tumor biopsies were incubated with 200uL 20mg/mL collagenase, 200uL 20mg/mL hyaluronidase, and 5uL DNase for 20 minutes to 1 hour with agitation until the tumor fully dissociated. Single-cell suspension was passed through a 100um strainer and washed with 1X PBS by centrifugation. Cells were resuspended in 1ml of freezing media frozen down. Cryopreserved single-suspension tumor samples were thawed and dead cells were removed using the Dead Cell Removal Kit (Miltenyi, 130-090-101) following manufacturer instructions. Live cells from the flow-though were used for CD45+ cell isolation using CD45 mouse MicroBeads (Miltenyi, 130-052-301) following the recommendations. CD45+ cells were counted and resuspended in PBS + 0.04% BSA at 1000 cells/µL for scRNA-seq.
About 23,000 cells were loaded onto a 10× Genomics ChromiumTM X instrument (10x Genomics) according to the manufacturer’s recommendations. The scRNAseq libraries were processed using Chromium GEM-X Single Cell 5' Kit v3 (10x Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq were normalized to 4nM concentration and pooled. The pooled sequencing libraries were sequenced on the Illumina NovaSeq S4 300 cycle platform. The sequencing parameters were: Read 1 of 28bp, Read 2 of 90bp, Index 1 of 10bp and Index 2 of 10bp.

treatment_protocol: 6-10 week-old female C57BL/6 female mice (Jackson Lab) were inoculated with 2.5x105 B16F10 cells. Mice were treated with 200 µg/mice of Corin (HY-111048, MedChemExpress) or 200 µl vehicle control (5% DMSO/PBS) by daily intraperitoneal (i.p.) injections starting from day 6 after the tumor injection. For Anti-PD1 treatment, mice were treated with 150 µg/mice anti-PD1 (clone 29F.1A12, BioLegend, 135248) or isotype control (clone RTK2758, BioLegend, 400566) 3 times/week starting from day 7 post-tumor grafts. 10 mice per treatment group were used.

value: corin + PD1


title: Control Sample number 204

description:
Saliva Sample from Control
CONTROL204

value: Control Sample number 204

value: Male


title: Control Sample number 205

description:
Saliva Sample from Control
CONTROL205

value: Control Sample number 205


title: corin_PD1_2

value: CD45+ immune cells from B16-F10 melanoma xenograft in mouse


title: Control Sample number 206

description:
Saliva Sample from Control
CONTROL206

value: Control Sample number 206


title: corinPD1_1


title: Control Sample number 202

description:
Saliva Sample from Control
CONTROL202

value: Control Sample number 202


title: Control Sample number 203

description:
Saliva Sample from Control
CONTROL203

value: Control Sample number 203


title: PD1_3


title: PD1_2


title: Control Sample number 201

description:
Saliva Sample from Control
CONTROL201

value: Control Sample number 201


title: PD1_1


title: SLE_Kidney_6

description: Library name: SLE-167964-10_S2

value: Kidney


title: Control Sample number 200

description:
Saliva Sample from Control
CONTROL200

value: Control Sample number 200


title: SLE_Kidney_4

description: Library name: SLE-167960_S2


title: Control Sample number 199

description:
Saliva Sample from Control
CONTROL199

value: Control Sample number 199


title: Chd4 cKO ATAC rep2

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

institute: OHRI

description: ATAC-seq, Chd4 cKO

library_source: genomic

data_processing:
FastQ Groomer: Fastq file reformatting
Trimmomatic: Read trimming
Bowtie2 (mapping to the mm9 genome)
Macs2 (peak calling)
Assembly: mm9
Supplementary files format and content: bigwig (data mapped to the mm9 genome), bed (called narrowpeaks)

source_name: P1 retina

extract_protocol:
mechanical trituration - P0 dissected murine retina
For ATAC-seq, we followed Buenrostro et al. [54]. Briefly, 75,000 cells were sorted from Chx10-Cre-YFP animals using YFP to purify RPCs. Cells were lysed in cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630). Lysed nuclei were tagmented using 6.5 µl of TDE1 transposase from the Nextera DNA Flex Library kit (Illumina). Samples were purified using Zymo-Spin IC columns (Zymo), and libraries constructed according to the Nextera workflow. Libraries were cleaned up using the AMPure XP kit (Beckman Coulter). PE 150 sequencing was performed using the NextSeq 500 platform.

value: P1 retina

value: Chd4 cKO


title: Control Sample number 198

description:
Saliva Sample from Control
CONTROL198

value: Control Sample number 198


title: Chd4 cKO ATAC rep1

description: ATAC-seq, Chd4 cKO


title: Control Sample number 197

description:
Saliva Sample from Control
CONTROL197

value: Control Sample number 197

value: Female


title: Control Sample number 196

description:
Saliva Sample from Control
CONTROL196

value: Control Sample number 196


title: Chd4 Ctl ATAC rep1

description: ATAC-seq, control

value: control


title: Control Sample number 195

description:
Saliva Sample from Control
CONTROL195

value: Control Sample number 195


title: Chd4 C&R Chd4 cKO

description: Cut&run-seq Chd4, Chd4 cKO

data_processing:
FastQ Groomer: Fastq file reformatting
Trimmomatic: Read trimming
Bowtie2 (mapping to the mm9 genome)
Macs2 (peak calling)
Assembly: mm9
Supplementary files format and content: bigwig (data mapped to the mm9 genome), bed (called narrowpeaks)
Library strategy: CUT&Run

source_name: P0 retina

extract_protocol:
mechanical trituration - P0 dissected murine retina
Cut&run-seq was performed using the Cutana cut&run kit (14-0500; Epicypher), following the manufacturer’s instructions. Briefly, P0 retinas were dissected. Cells were dissociated with mechanical trituration in order to retain the glycoproteins necessary for adhering to the concavanalin beads. 500 000 cells were used in each reaction. Cut&run seq was performed using antibodies against Chd4 (Abcam ab72418) or Mbd3 (Fortis A302-529A). Non-specific IgG was used as a negative control. Libraries were prepared using the NEBNext® UltraTM II Library Prep Kit (New England Biolabs). Paired-end 150 sequencing was performed using the NextSeq 500 platform (Illumina) to a read-depth of ~20-35 million reads per sample.

value: P0 retina


title: Control Sample number 191

description:
Saliva Sample from Control
CONTROL191

value: Control Sample number 191


title: Chd4 C&R Ctl

description: Cut&run-seq Chd4, control


title: Mbd3 C&R Ctl

description: Cut&run-seq Mbd3, control


title: Control Sample number 193

description:
Saliva Sample from Control
CONTROL193

value: Control Sample number 193

value: Male


title: Control Sample number 192

description:
Saliva Sample from Control
CONTROL192

value: Control Sample number 192


title: IgG C&R Ctl

description: Cut&run-seq negative control


title: Control Sample number 189

description:
Saliva Sample from Control
CONTROL189

value: Control Sample number 189


title: 3 months old, biol replicate1-3, HTO

city: LITTLE ROCK

first: Zijing

last: Zhang

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

description:
10x Genomics
hashtag library
filtered_feature_bc_y_matrix.mtx.gz
filtered_feature_bc_y_barcodes.tsv.gz
filtered_feature_bc_y_features.tsv.gz

data_processing:
Cell Ranger (v7.0.0)’s mkfastq tools is used to demultiplex raw binary base call (BCL) files, and transform them into FastQ files. Quality checking is performed using FastQC v0.11.4. Next, the Cell Ranger tool count is used to perform alignment, filtering, barcode counting, and UMI counting using the FastQ files as input. For experiments that include feature barcodes, this step is performed by the Cell Ranger tool multi instead.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files

source_name: ovary

extract_protocol:
Ovaries were harvested from 2-3 months old and 14-17 months old mice. For the 2-3 months old age group, ovaries from 6 animals were assigned to 3 replicates (ovaries from 2 animals per replicate), while for the 14-17 months old age group, ovaries from 5 animals were assigned to 3 replicates (2 replicates with ovaries from 2 animals and 1 replicate with ovary from 1 animal). All samples were dissociated into single cell suspension in digestion buffer (1x PBS, 5% FBS, 200U collagenase IV, 200U DNaseI) using gentleMacsTM dissociator with the program 37C_m_LDK1. The suspensions were washed with 5 mL 1x PBS 5% FBS 2 nM EDTA, and passed through 100µm cell strainer to remove debris.
Samples were processed using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) (NOTE 3) as described in the manufacturer’s instructions (10X Genomics) (Haque et al., 2017). In brief, aiming for 8000 cells per library (NOTE 4), single cell suspensions with more than 70% live cells (NOTE 5) were loaded onto Chromium Controller (10X Genomics) to generate gel beads-in-emulsions (GEMs). Then co-partitioned cells were lysed, primers were released from Gel Beads, and barcoded full-length cDNA was produced and amplified. 3’ Gene expression libraries were generated from cDNA by fragmentation, end repair, A-tailing, adaptor ligation and index PCR amplification. The concentration and size distribution of final libraries were assessed by Qubit™ 1X dsDNA HS Assay (Thermo Fisher Scientific, catalog # Q33231) and the Fragment Analyzer System (Agilent).

value: ovary

value: CD45+CD11b+ myeloid cells

value: 3 months

value: WT


title: Control Sample number 188

description:
Saliva Sample from Control
CONTROL188

value: Control Sample number 188


title: 15 months old, biol replicate 1-3, HTO

description:
10x Genomics
hashtag library
filtered_feature_bc_o_matrix.mtx.gz
filtered_feature_bc_o_barcodes.tsv.gz
filtered_feature_bc_o_features.tsv.gz

value: 15 months


title: Control Sample number 187

description:
Saliva Sample from Control
CONTROL187

value: Control Sample number 187


title: 15 months old, biol replicate 1-3, mRNA

description:
10x Genomics
mRNA library
filtered_feature_bc_o_matrix.mtx.gz
filtered_feature_bc_o_barcodes.tsv.gz
filtered_feature_bc_o_features.tsv.gz


title: 3 months old, biol replicate1-3, mRNA

description:
10x Genomics
mRNA library
filtered_feature_bc_y_matrix.mtx.gz
filtered_feature_bc_y_barcodes.tsv.gz
filtered_feature_bc_y_features.tsv.gz


title: Control Sample number 186

description:
Saliva Sample from Control
CONTROL186

value: Control Sample number 186


title: Chd4 Ctl ATAC rep2

description: ATAC-seq, control

value: P1 retina


title: Mbd3 C&R Chd4 cKO

description: Cut&run-seq Mbd3, Chd4 cKO

value: Chd4 cKO


title: Control Sample number 185

description:
Saliva Sample from Control
CONTROL185

value: Control Sample number 185


title: Ctrl-TAC-2

city: Beijing

first: li

middle: guo

last: qi

state: Chaoyang

address: Anzhen number 2 road

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: Con_TAC_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl 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.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts 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 readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: heart

growth_protocol: Heart tissue from mice (including Ctrl-TAC, VNS-TAC,) was collected for RNA extraction at 8 weeks post-TAC.

extract_protocol:
We used optogenetics to specifically activate vagus pre-ganglionic neurones in the DVMN and evaluated the development of HF. A recombinant adeno-associated virus (rAVV) carrying the activator channel rhodopsin (ChR) 2 (H134R)-enhanced GFP under the control of the ChAT promoter (rAAV-ChAT-hChR2[H134R]-GFP) was injected into the DVMN of mice. Mice that received rAAV-ChAT-GFP served as the control (Ctrl).
Oligo-dT magnetic bead capture for eukaryotic mRNA enrichment

treatment_protocol: We performed bulk RNA-sequencing (RNA-seq) and single-cell RNA-sequencing (scRNA-seq) 8 weeks after TAC

value: heart

value: VNS

tag: batch

value: TAC 8Weeks


title: Ctrl-TAC-3

description: Library name: Con_TAC_3


title: Control Sample number 194

description:
Saliva Sample from Control
CONTROL194

value: Control Sample number 194

value: Female


title: Control Sample number 184

description:
Saliva Sample from Control
CONTROL184

value: Control Sample number 184


title: Ctrl-TAC-1

description: Library name: Con_TAC_1


title: Control Sample number 183

description:
Saliva Sample from Control
CONTROL183

value: Control Sample number 183

value: Male


title: VNS-TAC-3

description: Library name: X10Hz_TAC_6


title: VNS-TAC-2

description: Library name: X10Hz_TAC_5


title: Control Sample number 182

description:
Saliva Sample from Control
CONTROL182

value: Control Sample number 182


title: Control Sample number 181

description:
Saliva Sample from Control
CONTROL181

value: Control Sample number 181


title: VNS-TAC-1

description: Library name: X10Hz_TAC_4

value: WT


title: CKO-1

city: Hangzhou

first: Jian

last: Mao

address: 2318 Yuhangtang Rd

institute: Hangzhou Normal University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 and paired-end clean reads were aligned to the reference genome using Hisat2.
HTSeq was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: ear skin

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen). A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ear skin

tag: condition

value: CKO

value: Ufl1f/f  KRT14Cre/+


title: Control Sample number 178

description:
Saliva Sample from Control
CONTROL178

value: Control Sample number 178


title: CKO-3


title: Control Sample number 179

description:
Saliva Sample from Control
CONTROL179

value: Control Sample number 179


title: CKO-2


title: CTRL-3

value: CTRL

value: Ufl1f/+or Ufl1f/f


title: Control Sample number 180

description:
Saliva Sample from Control
CONTROL180

value: Control Sample number 180


title: Control Sample number 176

description:
Saliva Sample from Control
CONTROL176

value: Control Sample number 176


title: Control Sample number 177

description:
Saliva Sample from Control
CONTROL177

value: Control Sample number 177


title: CTRL-1


title: Control Sample number 175

description:
Saliva Sample from Control
CONTROL175

value: Control Sample number 175

value: Female


title: Control Sample number 173

description:
Saliva Sample from Control
CONTROL173

value: Control Sample number 173


title: Control Sample number 172

description:
Saliva Sample from Control
CONTROL172

value: Control Sample number 172

value: Male


title: Control Sample number 171

description:
Saliva Sample from Control
CONTROL171

value: Control Sample number 171


title: D2_H11_RNAseq

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: 2i_release_NMTSeq_RNAseq_filtered_normalized.txt

data_processing:
All sequencing was carried out on HiSeq instrument. RNA-seq libraries were pooled as 96-plex or 192-plex pools and sequenced using 75-bp paired-end reads.
scRNA-seq alignments were performed using Hisat 2 as described previously (Clark et al. Nature Communications, 2018).
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited file with Ensembl Gene IDs, quantified values show number of reads per gene per sample

growth_protocol: E14 mESC were cultured in 2i+LIF media consisting out of N2B27 medium, composed out of DMEM/F12 (Life Technologies, 12634010) and Neurobasal (Life Technologies, 21103049) in a volume/volume (v/v) ratio 1:1, 0.1 mM 2-mercaptoethanol, 2 mM L-Glutamine, 1:200 v/v N2 (Life Technologies, 17502048) and 1:100 v/v B27 supplement (Life Technologies, 17504044), supplemented with 3 µM CHIR99021, 1 µM PD0325901 and 20 ng/ml of leukemia inhibitory factor (LIF)  (all Department of Biochemistry, University of Cambridge). mESCs were cultured on tissue culture plastic pre-coated with 0.1 % gelatine in H2O. Cultures were passaged when approaching confluence (every 2 days). All cells were cultured in a humidified incubator at 37 °C in 5 % CO2 and 20 % O2. mESCs were subject to routine mycoplasma testing using the MycoAlert testing kit (Lonza) and tested negative. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium consisting of DMEM (Life Technologies, 10566-016), containing 15% Fetal Bovine Serum (FBS) (Gibco, 10270106), 1x non-essential amino acids (NEAA) (Life Technologies, 11140050), 0.1 mM 2-mercaptoethanol (Life Technologies, 31350-010), 2 mM L-Glutamine (Life Technologies, 25030-024), supplemented with 20 ng/ml of LIF (Department of Biochemistry, University of Cambridge).

extract_protocol:
0h, 24h, and 48h after induction of 2i-release  the cells been dissociated into single cells using accutase before flow sorting  (BD Influx) into 96-well plate containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL CA-630 (Sigma)). Samples were incubated for 15 min at 37 °C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at −80 °C before processing.
All downstream library preparation steps been performed as previously described by Clark et al. (Clark et al. Nature Communications, 2018).

value: embryonic stem cell


title: D2_H08_RNAseq


title: CTRL-2

value: ear skin


title: D2_H10_RNAseq


title: D2_H09_RNAseq


title: Control Sample number 170

description:
Saliva Sample from Control
CONTROL170

data_processing:
raw .idat files were read via the minfi package in the R programming environment, data was normalised using Functional Normalisation in R
Average Beta value and detection P-values
Summarisd and normalised beta intensities

extract_protocol: Saliva samples were collected using the Oragene DNA OG/600 saliva collection kit (DNAGenotek, Ottawa, Canada). All participants were required to fast for a minimum of one hour prior to sample collection.

value: Control Sample number 170


title: D2_H12_RNAseq


title: Control Sample number 169

description:
Saliva Sample from Control
CONTROL169

value: Control Sample number 169


title: D2_H07_RNAseq


title: D2_H06_RNAseq


title: Control Sample number 168

description:
Saliva Sample from Control
CONTROL168

value: Control Sample number 168


title: D2_H05_RNAseq


title: Control Sample number 167

description:
Saliva Sample from Control
CONTROL167

value: Control Sample number 167


title: D2_H04_RNAseq


title: D2_H03_RNAseq


title: Control Sample number 164

description:
Saliva Sample from Control
CONTROL164

value: Control Sample number 164


title: D2_H02_RNAseq


title: Control Sample number 165

description:
Saliva Sample from Control
CONTROL165

value: Control Sample number 165


title: Control Sample number 163

description:
Saliva Sample from Control
CONTROL163

value: Control Sample number 163


title: Control Sample number 162

description:
Saliva Sample from Control
CONTROL162

value: Control Sample number 162


title: D2_G12_RNAseq


title: D2_G11_RNAseq


title: Control Sample number 161

description:
Saliva Sample from Control
CONTROL161

value: Control Sample number 161


title: D2_G10_RNAseq


title: Control Sample number 160

description:
Saliva Sample from Control
CONTROL160

value: Control Sample number 160


title: Control Sample number 174

description:
Saliva Sample from Control
CONTROL174

value: Control Sample number 174


title: D2_G09_RNAseq


title: D2_G07_RNAseq


title: D2_G08_RNAseq


title: D2_G06_RNAseq


title: D2_G04_RNAseq


title: Control Sample number 155

description:
Saliva Sample from Control
CONTROL155

value: Control Sample number 155

value: Female


title: Control Sample number 157

description:
Saliva Sample from Control
CONTROL157

value: Control Sample number 157


title: Control Sample number 158

description:
Saliva Sample from Control
CONTROL158

value: Control Sample number 158


title: Control Sample number 159

description:
Saliva Sample from Control
CONTROL159

value: Control Sample number 159


title: D2_G03_RNAseq

value: embryonic stem cell


title: Control Sample number 153

description:
Saliva Sample from Control
CONTROL153

value: Control Sample number 153


title: Control Sample number 156

description:
Saliva Sample from Control
CONTROL156

value: Control Sample number 156


title: Control Sample number 166

description:
Saliva Sample from Control
CONTROL166

value: Control Sample number 166

value: Male


title: D2_G05_RNAseq


title: Control Sample number 154

description:
Saliva Sample from Control
CONTROL154

value: Control Sample number 154


title: Control Sample number 152

description:
Saliva Sample from Control
CONTROL152

value: Control Sample number 152


title: D2_G01_RNAseq


title: D2_F12_RNAseq


title: Control Sample number 150

description:
Saliva Sample from Control
CONTROL150

value: Control Sample number 150


title: Control Sample number 151

description:
Saliva Sample from Control
CONTROL151

value: Control Sample number 151


title: D2_F11_RNAseq


title: D2_G02_RNAseq


title: Control Sample number 149

description:
Saliva Sample from Control
CONTROL149

value: Control Sample number 149


title: D2_H01_RNAseq


title: D2_F10_RNAseq


title: D2_F09_RNAseq


title: Control Sample number 148

description:
Saliva Sample from Control
CONTROL148

value: Control Sample number 148


title: Control Sample number 147

description:
Saliva Sample from Control
CONTROL147

value: Control Sample number 147


title: Control Sample number 146

description:
Saliva Sample from Control
CONTROL146

value: Control Sample number 146


title: D2_F08_RNAseq


title: Control Sample number 145

description:
Saliva Sample from Control
CONTROL145

value: Control Sample number 145

value: Female


title: D2_F07_RNAseq


title: Control Sample number 143

description:
Saliva Sample from Control
CONTROL143

value: Control Sample number 143


title: D2_F06_RNAseq


title: Control Sample number 144

description:
Saliva Sample from Control
CONTROL144

value: Control Sample number 144


title: Control Sample number 142

description:
Saliva Sample from Control
CONTROL142

value: Control Sample number 142


title: D2_F05_RNAseq

value: embryonic stem cell


title: D2_F04_RNAseq


title: Control Sample number 141

description:
Saliva Sample from Control
CONTROL141

value: Control Sample number 141


title: D2_F03_RNAseq


title: D2_F02_RNAseq


title: Control Sample number 140

description:
Saliva Sample from Control
CONTROL140

value: Control Sample number 140


title: Control Sample number 139

description:
Saliva Sample from Control
CONTROL139

value: Control Sample number 139

value: Male


title: D2_F01_RNAseq


title: Control Sample number 138

description:
Saliva Sample from Control
CONTROL138

value: Control Sample number 138


title: Control Sample number 137

description:
Saliva Sample from Control
CONTROL137

value: Control Sample number 137


title: Control Sample number 136

description:
Saliva Sample from Control
CONTROL136

value: Control Sample number 136


title: D2_E11_RNAseq


title: D2_E12_RNAseq


title: Control Sample number 135

description:
Saliva Sample from Control
CONTROL135

value: Control Sample number 135


title: D2_E09_RNAseq


title: D2_E08_RNAseq


title: Control Sample number 134

description:
Saliva Sample from Control
CONTROL134

value: Control Sample number 134


title: Control Sample number 133

description:
Saliva Sample from Control
CONTROL133

value: Control Sample number 133


title: D2_E06_RNAseq


title: D2_E05_RNAseq


title: D2_E04_RNAseq


title: Control Sample number 130

description:
Saliva Sample from Control
CONTROL130

value: Control Sample number 130


title: Control Sample number 128

description:
Saliva Sample from Control
CONTROL128

value: Control Sample number 128


title: Control Sample number 131

description:
Saliva Sample from Control
CONTROL131

value: Control Sample number 131

value: Female


title: D2_E02_RNAseq


title: Control Sample number 126

description:
Saliva Sample from Control
CONTROL126

value: Control Sample number 126


title: D2_E01_RNAseq


title: D2_D11_RNAseq


title: D2_E03_RNAseq


title: D2_E10_RNAseq


title: Control Sample number 125

description:
Saliva Sample from Control
CONTROL125

value: Control Sample number 125


title: Control Sample number 124

description:
Saliva Sample from Control
CONTROL124

value: Control Sample number 124


title: Control Sample number 123

description:
Saliva Sample from Control
CONTROL123

value: Control Sample number 123


title: D2_D10_RNAseq

value: embryonic stem cell


title: Control Sample number 122

description:
Saliva Sample from Control
CONTROL122

value: Control Sample number 122


title: Control Sample number 121

description:
Saliva Sample from Control
CONTROL121

value: Control Sample number 121


title: D2_D09_RNAseq


title: D2_E07_RNAseq


title: D2_D07_RNAseq


title: D2_D06_RNAseq