title: NOD.GW_SN_S1_10x_scRNA-seq

status: Public on Nov 30 2021

type: SRA

city: Los Angeles

first: Maureen

last: Su

state: California

address: 615 Charles E Young Dr S

country: USA

institute: UCLA

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #1

library_source: transcriptomic

data_processing:
Single cell feature counts were generated by aligning sequencing data with the mm10 mouse reference genome (version 2020-A) using 10x Cell Ranger software (5.0.1)
Filtered output matrices and barcodes were analyzed with SEURAT 4.0 on R studio (version 1.2.5033) using the Read10X function to return a unique molecular identified (UMI) count matrix for creation of a Seurat object
Cells with fewer than 200 RNA count, more than 3000 unique genes and more than 12.5% mitochondria gene counts were excluded from the analysis.
Samples were integrated and then raw counts and metadata files were generated as the processed data files.
Cells were then clustered as described.
Genome_build: mm10
Supplementary_files_format_and_content: gw_integrated_counts.csv

molecule: polyA RNA

organism: Mus musculus

source_name: NOD.GW Sciatic Nerves

extract_protocol:
Chromium Single Cell GEM, Library & Gel Bead Kit
10x Genomics single cell RNA-Seq

treatment_protocol: Fresh sciatic nerves were removed after cardiac perfusion. Nerves were minced with a razor blade and digested in DPBS containing collagenase with 10% FBS. A 20-gauge needle was then used to triturate the nerve fragments to further aid in digestion. The further digested nerves were then filtered through a 40 μm mesh and washed to generate a single-cell suspension for flow cytometry analysis.

tag: cell type

value: NOD.GW Sciatic Nerves

tag: genotype

value: NOD.AIRE GW/+

tag: cell number

tag: age

value: 15 weeks

tag: sequencing method

value: 3' sequencing


title: Control_H3K4me1_rep6-1

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: Input DNA

library_source: genomic

data_processing:
Reads were aligned to the mm10 genome using Bowtie2(v2.3.4.1; --very-sensitive).
Reads were filtered to remove reads with low mapping quality (≤30 MapQ), those that align to the mitochondrial genome, and duplicates (Picard v2.5.0).
Aligned files were then converted to  bigwig files for viewing on the UCSC Genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: Files contain the alignment of reads to the mm10 genome

molecule: genomic DNA

source_name: whole placenta

extract_protocol:
Placenta were microdissected from e9.5 timed-pregnant mice and collected in cold dPBS. Three placentas were combined per biological replicate for chromatin isolation and ChIP was performed as previously described by Starks et al. (2019) for H3k27me3 with 10ug of chromatin and 4ug of H3k27me3 antibody (Millipore 17-622, lot:3070997) for a total of 4 biological replicates. H3k4me1 and H3k4me3 ChIPs were performed as previously described by Tuteja et al. (2008)  with the following modifications: 2.5ug of chromatin was precleared with 80ul of Protein G-agarose (Thermofisher 20422) in 1ml of ChIP dilution buffer and incubated overnight with 2ug of H3k4me1 antibody (Abcam ab8895, lot: GR3264996-2) or 0.5ug of H3k4me3 antibody (Abcam ab8580, lot: GR3264593-1), generating 6 biological replicates for each antibody. Input DNA (control) was simultaneously prepared from chromatin for each replicate.
ChIP-seq libraries were generated as previously described by Tuteja et al. (2009) with the following modifications: 40ul (80%) of the purified ChIP DNA was used for library preparation of each biological replicate and gel size selection was performed by excising DNA fragements between 250bp – 350bp. 5ng of input sample libraries were also prepared simultaneously as controls.

tag: tissue

value: placenta

tag: Stage

value: Embryonic day 9.5

tag: strain


title: Control_H3K27me3_rep4-1

description: Input DNA


title: Control_H3K4me1_rep6-3

description: Input DNA


title: Control_H3K4me1_rep5-2

description: Input DNA


title: Control_H3K27me3_rep1-1

description: Input DNA


title: Control_H3K4me1_rep5-1

description: Input DNA


title: Control_H3K27me3_rep3-1

description: Input DNA


title: Control_H3K4me1_rep4-2

description: Input DNA


title: Control_H3K4me1_rep6-2

description: Input DNA


title: Control_H3K4me1_rep4-1

description: Input DNA


title: Control_H3K27me3_rep2-1

description: Input DNA


title: Control_H3K4me1_rep4-3

description: Input DNA


title: Control_H3K4me1_rep3-3

description: Input DNA


title: Control_H3K4me1_rep3-1

description: Input DNA


title: Control_H3K4me1_rep3-2

description: Input DNA


title: Control_H3K4me1_rep2-2

description: Input DNA


title: Control_H3K4me3_rep6-3

description: Input DNA


title: Control_H3K4me1_rep2-3

description: Input DNA


title: Control_H3K4me1_rep2-1

description: Input DNA


title: Control_H3K4me1_rep5-3

description: Input DNA


title: Control_H3K4me3_rep5-2

description: Input DNA


title: Control_H3K4me3_rep4-3

description: Input DNA


title: Control_H3K4me3_rep5-1

description: Input DNA


title: Control_H3K4me3_rep5-3

description: Input DNA


title: Control_H3K4me3_rep6-1

description: Input DNA


title: Control_H3K4me3_rep3-3

description: Input DNA


title: Control_H3K4me3_rep4-2

description: Input DNA


title: Control_H3K4me3_rep2-3

description: Input DNA


title: Control_H3K4me3_rep3-1

description: Input DNA


title: Control_H3K4me3_rep6-2

description: Input DNA


title: Control_H3K4me3_rep3-2

description: Input DNA


title: Control_H3K4me3_rep2-1

description: Input DNA


title: Control_H3K4me3_rep2-2

description: Input DNA


title: Control_H3K4me1/H3K4me3_rep1-2

description: Input DNA


title: Control_H3K4me1/H3K4me3_rep1-3

description: Input DNA


title: Control_H3K4me1/H3K4me3_rep1-1

description: Input DNA


title: H3K27me3_rep4-1

description: H3K27me3 ChIP


title: H3K27me3_rep3-1

description: H3K27me3 ChIP


title: H3K4me1_rep6-2

description: H3K4me1 ChIP


title: H3K27me3_rep2-1

description: H3K27me3 ChIP


title: H3K27me3_rep1-1

description: H3K27me3 ChIP


title: H3K4me1_rep6-3

description: H3K4me1 ChIP


title: Control_H3K4me3_rep4-1

description: Input DNA


title: H3K4me1_rep5-2

description: H3K4me1 ChIP


title: H3K4me1_rep5-3

description: H3K4me1 ChIP


title: H3K4me1_rep6-1

description: H3K4me1 ChIP


title: H3K4me1_rep4-3

description: H3K4me1 ChIP


title: H3K4me1_rep5-1

description: H3K4me1 ChIP


title: H3K4me1_rep3-2

description: H3K4me1 ChIP


title: H3K4me1_rep4-2

description: H3K4me1 ChIP


title: H3K4me1_rep3-3

description: H3K4me1 ChIP


title: H3K4me1_rep3-1

description: H3K4me1 ChIP


title: H3K4me1_rep4-1

description: H3K4me1 ChIP


title: H3K4me1_rep2-2

description: H3K4me1 ChIP


title: H3K4me1_rep1-3

description: H3K4me1 ChIP


title: H3K4me1_rep1-1

description: H3K4me1 ChIP


title: H3K4me3_rep5-2

description: H3K4me3 ChIP


title: H3K4me3_rep5-3

description: H3K4me3 ChIP


title: H3K4me1_rep2-1

description: H3K4me1 ChIP


title: H3K4me3_rep6-1

description: H3K4me3 ChIP


title: H3K4me3_rep6-2

description: H3K4me3 ChIP


title: H3K4me3_rep4-3

description: H3K4me3 ChIP


title: H3K4me3_rep6-3

description: H3K4me3 ChIP


title: H3K4me3_rep4-2

description: H3K4me3 ChIP


title: H3K4me3_rep5-1

description: H3K4me3 ChIP


title: H3K4me3_rep3-1

description: H3K4me3 ChIP


title: H3K4me3_rep2-3

description: H3K4me3 ChIP


title: H3K4me3_rep2-2

description: H3K4me3 ChIP


title: H3K4me3_rep3-3

description: H3K4me3 ChIP


title: H3K4me3_rep4-1

description: H3K4me3 ChIP


title: H3K4me3_rep1-2

description: H3K4me3 ChIP


title: H3K4me3_rep1-3

description: H3K4me3 ChIP


title: H3K4me3_rep2-1

description: H3K4me3 ChIP


title: H3K4me1_rep2-3

description: H3K4me1 ChIP


title: H3K4me3_rep1-1

description: H3K4me3 ChIP


title: H3K4me1_rep1-2

description: H3K4me1 ChIP


title: genomic DNA from brain 217

type: genomic

city: Erlangen

first: Katja

last: Kobow

state: Deutschland

address: Schwabachanlage 6

department: Neuropathology

country: Germany

institute: Universitätsklinikum Erlangen

description: structural brain lesion and epilepsy

hyb_protocol: Following FFPE restoration bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation 850K Beadchip using standard Illumina protocol

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

data_processing:
Differential DNA methylation analysis was performed with a self-customized Python wrapped cross R package pipeline, utilizing 'Champ,' 'watermelon,' 'DNAMarray,' and 'minfi' as R packages. 'MethQC' and 'Pymethylarray' were used as Python-based array analysis packages. Additional own implementations of lacking functionality were used where needed. All these packages were wrapped by using 'rpy2', an interface to R running embedded in a Python process.
Data was stratified quantile normalized using the ‘minfi‘ ‘preprocessQuantile‘ function

label: Cy5 and Cy205

organism: Homo sapiens

source_name: Cortex

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE tissue punches using Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

tag: sample type

value: Test


title: WT_SP1

city: Chengdu

first: Qiang

last: Liu

address: Guoxue street 37

country: China

institute: West China Hospital, Sichuan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. aureus USA300_FPR3757 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: S. aureus USA300_FPR3757
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM value for every gene and every sample

molecule: total RNA

organism: Staphylococcus aureus

source_name: S. aureus USA300_FPR3757 wild-type in stationary phase 1

growth_protocol: S. aureus USA300_FPR3757 grow in TSB medium

extract_protocol:
RNA extraction was performed using an RNApure Bacteria Kit (CwBIO, Jiangsu, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bacterial cells were collected in dfferent growth phases

tag: phase

value: stationary


title: genomic DNA from brain 216

description: structural brain lesion and epilepsy

label: Cy5 and Cy204


title: WT_SP2

source_name: S. aureus USA300_FPR3757 wild-type in stationary phase 2


title: genomic DNA from brain 215

description: structural brain lesion and epilepsy

label: Cy5 and Cy203


title: WT_EP1

source_name: S. aureus USA300_FPR3757 wild-type in exponentional phase 1

value: exponentional


title: WT_EP2

source_name: S. aureus USA300_FPR3757 wild-type in exponentional phase 2


title: WT_LP1

source_name: S. aureus USA300_FPR3757 wild-type in lag phase 1

value: lag


title: WT_LP2

source_name: S. aureus USA300_FPR3757 wild-type in lag phase 2


title: genomic DNA from brain 214

description: structural brain lesion and epilepsy

label: Cy5 and Cy202


title: genomic DNA from brain 213

description: structural brain lesion and epilepsy

label: Cy5 and Cy201


title: Acinetobacter, 4 hr, rep C, batch 4

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description:
AB4C4
Acinetobacter baumannii, 4 hours, batch 4
A_S3.csv

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings.
Sequencer.bcl basecall files were demultiplexed and formatted into fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl
Reads were aligned to the Lucilia sericata transcriptome using kallisto v0.44.0
Genome_build: Lucilia sericata transcriptome assembly 25_5 (Sze et al. 2012) with annotated effector transcripts added (Poppel et al. 2015)
Supplementary_files_format_and_content: Tab delimited file with read counts per transcript
Supplementary_files_format_and_content: DifferentialExpressionFile

organism: Lucilia sericata

source_name: second instar larvae

growth_protocol: second instar larvae were orded from Monarch Labs (Irvine, CA), separately for each experimental batch

extract_protocol:
RNA was extracted from 5 larvae from each sample. First, whole RNA was extracted using TriReagent, according to manufacturer’s protocols. Each sample was macerated in 1 mL of cold TriReagent. Following this, 50 mL of ice-cold BAN reagent was added and the solution was vigorously mixed. Next, the tubes were centrifuged at 14,000 G at 4°C for 15 min to isolate the RNA from the DNA and proteins. Approximately 500 μL of the top clear layer was carefully removed with a pipet and added to 500 μL of ice-cold 100% isopropanol. The tubes were mixed via inversion three times and allowed to rest on ice for 10 min to precipitate the RNA. The precipitate was then centrifuged at 14,000 G at 4°C for 15 min. Next, the supernatant was completely removed, 1 mL of ice-cold 70% ethanol was used to wash the RNA pellet, and the pellet was centrifuged at 4°C for 5 min at 14,000 G. The ethanol was eluted, and any remaining ethanol was allowed to completely evaporate. The RNA was then dissolved in a 10μL mixture of 99 μL of DNase/RNase/Nucleotide-free water and 1 μL of SUPERase•In™ (Invitrogen). The extracted RNA was further purified using a Qiagen RNeasy Micro Kit and on-column DNase treatment following manufacturer protocols. RNA was eluted again into a fresh 1:100μL mixture of SUPERase•In and DNase/RNase/Nucleotide-free water and stored at -80°C until sequencing.
TruSeq stranded mRNA-seq

treatment_protocol: feeding on a slant of 2 mL of TSA in a 5 mL tube, treated with 10 uL of bacterial inoculum or PBS

tag: bacterial treatment

value: Acinetobacter baumannii

tag: time

value: 4 hours

tag: experimental batch

value: batch 4


title: H3K4me3_rep3-2

description: H3K4me3 ChIP


title: genomic DNA from brain 211

description: structural brain lesion and epilepsy

label: Cy5 and Cy199


title: genomic DNA from brain 209

description: structural brain lesion and epilepsy

label: Cy5 and Cy197


title: genomic DNA from brain 210

description: structural brain lesion and epilepsy

label: Cy5 and Cy198


title: Acinetobacter, 4 hr, rep D, batch 4

description:
AB4D4
Acinetobacter baumannii, 4 hours, batch 4
A_S3.csv


title: genomic DNA from brain 208

description: structural brain lesion and epilepsy

label: Cy5 and Cy196


title: Acinetobacter, 4 hr, rep B, batch 4

description:
AB4B4
Acinetobacter baumannii, 4 hours, batch 4
A_S3.csv


title: genomic DNA from brain 207

description: structural brain lesion and epilepsy

label: Cy5 and Cy195


title: genomic DNA from brain 212

description: structural brain lesion and epilepsy

label: Cy5 and Cy200


title: Pseudomonas, 4 hr, rep C, batch 4

description:
PA4C4
Pseudomonas aeruginosa, 4 hours, batch 4
P_S2.csv

value: Pseudomonas aeruginosa


title: Pseudomonas, 4 hr, rep D, batch 4

description:
PA4D4
Pseudomonas aeruginosa, 4 hours, batch 4
P_S2.csv


title: Acinetobacter, 4 hr, rep A, batch 4

description:
AB4A4
Acinetobacter baumannii, 4 hours, batch 4
A_S3.csv


title: genomic DNA from brain 206

description: structural brain lesion and epilepsy

label: Cy5 and Cy194


title: genomic DNA from brain 204

description: structural brain lesion and epilepsy

label: Cy5 and Cy192


title: genomic DNA from brain 205

description: structural brain lesion and epilepsy

label: Cy5 and Cy193


title: Control, 4 hr, rep D, batch 4

description:
C4D4
Control (PBS), 4 hours, batch 4
P_S2.csv
A_S3.csv

value: Control (PBS)


title: Pseudomonas, 4 hr, rep A, batch 4

description:
PA4A4
Pseudomonas aeruginosa, 4 hours, batch 4
P_S2.csv


title: genomic DNA from brain 202

description: structural brain lesion and epilepsy

label: Cy5 and Cy190


title: genomic DNA from brain 203

description: structural brain lesion and epilepsy

label: Cy5 and Cy191


title: Control, 4 hr, rep C, batch 4

description:
C4C4
Control (PBS), 4 hours, batch 4
P_S2.csv
A_S3.csv


title: Control, 4 hr, rep A, batch 4

description:
C4A4
Control (PBS), 4 hours, batch 4
P_S2.csv
A_S3.csv


title: Control, 4 hr, rep B, batch 4

description:
C4B4
Control (PBS), 4 hours, batch 4
P_S2.csv
A_S3.csv


title: genomic DNA from brain 198

description: structural brain lesion and epilepsy

label: Cy5 and Cy186


title: genomic DNA from brain 197

description: structural brain lesion and epilepsy

label: Cy5 and Cy185


title: genomic DNA from brain 200

description: structural brain lesion and epilepsy

label: Cy5 and Cy188


title: Acinetobacter, 1 hr, rep D, batch 4

description:
AB1D4
Acinetobacter baumannii, 1 hour, batch 4
A_S3.csv

value: 1 hour


title: genomic DNA from brain 199

description: structural brain lesion and epilepsy

label: Cy5 and Cy187


title: genomic DNA from brain 201

description: structural brain lesion and epilepsy

label: Cy5 and Cy189


title: Acinetobacter, 1 hr, rep B, batch 4

description:
AB1B4
Acinetobacter baumannii, 1 hour, batch 4
A_S3.csv


title: genomic DNA from brain 195

description: structural brain lesion and epilepsy

label: Cy5 and Cy183


title: genomic DNA from brain 196

description: structural brain lesion and epilepsy

label: Cy5 and Cy184


title: genomic DNA from brain 194

description: structural brain lesion and epilepsy

label: Cy5 and Cy182


title: Acinetobacter, 1 hr, rep C, batch 4

description:
AB1C4
Acinetobacter baumannii, 1 hour, batch 4
A_S3.csv


title: Pseudomonas, 1 hr, rep D, batch 4

description:
PA1D4
Pseudomonas aeruginosa, 1 hour, batch 4
P_S2.csv


title: Acinetobacter, 1 hr, rep A, batch 4

description:
AB1A4
Acinetobacter baumannii, 1 hour, batch 4
A_S3.csv


title: Pseudomonas, 4 hr, rep B, batch 4

description:
PA4B4
Pseudomonas aeruginosa, 4 hours, batch 4
P_S2.csv


title: Pseudomonas, 1 hr, rep C, batch 4

description:
PA1C4
Pseudomonas aeruginosa, 1 hour, batch 4
P_S2.csv


title: Pseudomonas, 1 hr, rep B, batch 4

description:
PA1B4
Pseudomonas aeruginosa, 1 hour, batch 4
P_S2.csv


title: genomic DNA from brain 193

description: structural brain lesion and epilepsy

label: Cy5 and Cy181


title: genomic DNA from brain 192

description: structural brain lesion and epilepsy

label: Cy5 and Cy180


title: genomic DNA from brain 191

description: structural brain lesion and epilepsy

label: Cy5 and Cy179


title: Pseudomonas, 1 hr, rep A, batch 4

description:
PA1A4
Pseudomonas aeruginosa, 1 hour, batch 4
P_S2.csv


title: Control, 1 hr, rep D, batch 4

description:
C1D4
Control (PBS), 1 hour, batch 4
P_S2.csv
A_S3.csv


title: genomic DNA from brain 190

description: structural brain lesion and epilepsy

label: Cy5 and Cy178


title: genomic DNA from brain 189

description: structural brain lesion and epilepsy

label: Cy5 and Cy177


title: genomic DNA from brain 188

description: structural brain lesion and epilepsy

label: Cy5 and Cy176


title: genomic DNA from brain 187

description: structural brain lesion and epilepsy

label: Cy5 and Cy175


title: genomic DNA from brain 184

description: structural brain lesion and epilepsy

label: Cy5 and Cy172


title: Acinetobacter, 4 hr, rep C, batch 3

description:
AB4C3
Acinetobacter baumannii, 4 hours, batch 3
A_S3.csv

value: batch 3


title: genomic DNA from brain 185

description: structural brain lesion and epilepsy

label: Cy5 and Cy173


title: Acinetobacter, 4 hr, rep D, batch 3

description:
AB4D3
Acinetobacter baumannii, 4 hours, batch 3
A_S3.csv


title: genomic DNA from brain 186

description: structural brain lesion and epilepsy

label: Cy5 and Cy174


title: Acinetobacter, 4 hr, rep B, batch 3

description:
AB4B3
Acinetobacter baumannii, 4 hours, batch 3
A_S3.csv


title: Control, 1 hr, rep A, batch 4

description:
C1A4
Control (PBS), 1 hour, batch 4
P_S2.csv
A_S3.csv


title: genomic DNA from brain 182

description: structural brain lesion and epilepsy

label: Cy5 and Cy170


title: genomic DNA from brain 183

description: structural brain lesion and epilepsy

label: Cy5 and Cy171


title: genomic DNA from brain 180

description: structural brain lesion and epilepsy

label: Cy5 and Cy168


title: genomic DNA from brain 179

description: structural brain lesion and epilepsy

label: Cy5 and Cy167


title: genomic DNA from brain 181

description: structural brain lesion and epilepsy

label: Cy5 and Cy169


title: Pseudomonas, 4 hr, rep B, batch 3

description:
PA4B3
Pseudomonas aeruginosa, 4 hours, batch 3
P_S2.csv


title: Acinetobacter, 4 hr, rep A, batch 3

description:
AB4A3
Acinetobacter baumannii, 4 hours, batch 3
A_S3.csv


title: Pseudomonas, 4 hr, rep D, batch 3

description:
PA4D3
Pseudomonas aeruginosa, 4 hours, batch 3
P_S2.csv


title: Pseudomonas, 4 hr, rep C, batch 3

description:
PA4C3
Pseudomonas aeruginosa, 4 hours, batch 3
P_S2.csv


title: Pseudomonas, 4 hr, rep A, batch 3

description:
PA4A3
Pseudomonas aeruginosa, 4 hours, batch 3
P_S2.csv


title: genomic DNA from brain 178

description: structural brain lesion and epilepsy

label: Cy5 and Cy166


title: genomic DNA from brain 177

description: structural brain lesion and epilepsy

label: Cy5 and Cy165


title: genomic DNA from brain 176

description: structural brain lesion and epilepsy

label: Cy5 and Cy164


title: Control, 4 hr, rep B, batch 3

description:
C4B3
Control (PBS), 4 hours, batch 3
P_S2.csv
A_S3.csv


title: Control, 4 hr, rep C, batch 3

description:
C4C3
Control (PBS), 4 hours, batch 3
P_S2.csv
A_S3.csv


title: genomic DNA from brain 175

description: structural brain lesion and epilepsy

label: Cy5 and Cy163


title: Control, 1 hr, rep B, batch 4

description:
C1B4
Control (PBS), 1 hour, batch 4
P_S2.csv
A_S3.csv


title: Control, 4 hr, rep A, batch 3

description:
C4A3
Control (PBS), 4 hours, batch 3
P_S2.csv
A_S3.csv


title: Control, 1 hr, rep C, batch 4

description:
C1C4
Control (PBS), 1 hour, batch 4
P_S2.csv
A_S3.csv


title: Acinetobacter, 1 hr, rep D, batch 3

description:
AB1D3
Acinetobacter baumannii, 1 hour, batch 3
A_S3.csv


title: genomic DNA from brain 174

description: structural brain lesion and epilepsy

label: Cy5 and Cy162

value: Reference


title: genomic DNA from brain 173

description: structural brain lesion and epilepsy

label: Cy5 and Cy161


title: Acinetobacter, 1 hr, rep C, batch 3

description:
AB1C3
Acinetobacter baumannii, 1 hour, batch 3
A_S3.csv


title: Acinetobacter, 1 hr, rep B, batch 3

description:
AB1B3
Acinetobacter baumannii, 1 hour, batch 3
A_S3.csv


title: Acinetobacter, 1 hr, rep A, batch 3

description:
AB1A3
Acinetobacter baumannii, 1 hour, batch 3
A_S3.csv


title: genomic DNA from brain 171

description: structural brain lesion and epilepsy

label: Cy5 and Cy159


title: genomic DNA from brain 172

description: structural brain lesion and epilepsy

label: Cy5 and Cy160


title: Pseudomonas, 1 hr, rep D, batch 3

description:
PA1D3
Pseudomonas aeruginosa, 1 hour, batch 3
P_S2.csv


title: genomic DNA from brain 168

description: structural brain lesion and epilepsy

label: Cy5 and Cy156


title: genomic DNA from brain 170

description: structural brain lesion and epilepsy

label: Cy5 and Cy158


title: Control, 4 hr, rep D, batch 3

description:
C4D3
Control (PBS), 4 hours, batch 3
P_S2.csv
A_S3.csv


title: Pseudomonas, 1 hr, rep C, batch 3

description:
PA1C3
Pseudomonas aeruginosa, 1 hour, batch 3
P_S2.csv


title: genomic DNA from brain 165

description: structural brain lesion and epilepsy

label: Cy5 and Cy153


title: Control, 1 hr, rep D, batch 3

description:
C1D3
Control (PBS), 1 hour, batch 3
P_S2.csv
A_S3.csv


title: genomic DNA from brain 164

description: structural brain lesion and epilepsy

label: Cy5 and Cy152


title: Pseudomonas, 1 hr, rep A, batch 3

description:
PA1A3
Pseudomonas aeruginosa, 1 hour, batch 3
P_S2.csv


title: genomic DNA from brain 166

description: structural brain lesion and epilepsy

label: Cy5 and Cy154


title: genomic DNA from brain 167

description: structural brain lesion and epilepsy

label: Cy5 and Cy155


title: Control, 1 hr, rep B, batch 3

description:
C1B3
Control (PBS), 1 hour, batch 3
P_S2.csv
A_S3.csv


title: Pseudomonas, 1 hr, rep B, batch 3

description:
PA1B3
Pseudomonas aeruginosa, 1 hour, batch 3
P_S2.csv


title: Control, 1 hr, rep C, batch 3

description:
C1C3
Control (PBS), 1 hour, batch 3
P_S2.csv
A_S3.csv


title: genomic DNA from brain 160

description: structural brain lesion and epilepsy

label: Cy5 and Cy148


title: genomic DNA from brain 163

description: structural brain lesion and epilepsy

label: Cy5 and Cy151


title: genomic DNA from brain 161

description: structural brain lesion and epilepsy

label: Cy5 and Cy149


title: Acinetobacter, 4 hr, rep C, batch 1

description:
AB4C1
Acinetobacter baumannii, 4 hours, batch 1
A_S3.csv

value: batch 1


title: genomic DNA from brain 159

description: structural brain lesion and epilepsy

label: Cy5 and Cy147


title: Acinetobacter, 4 hr, rep D, batch 1

description:
AB4D1
Acinetobacter baumannii, 4 hours, batch 1
A_S3.csv


title: Control, 1 hr, rep A, batch 3

description:
C1A3
Control (PBS), 1 hour, batch 3
P_S2.csv
A_S3.csv


title: genomic DNA from brain 162

description: structural brain lesion and epilepsy

label: Cy5 and Cy150


title: Acinetobacter, 4 hr, rep B, batch 1

description:
AB4B1
Acinetobacter baumannii, 4 hours, batch 1
A_S3.csv


title: genomic DNA from brain 158

description: structural brain lesion and epilepsy

label: Cy5 and Cy146


title: Pseudomonas, 4 hr, rep C, batch 1

description:
PA4C1
Pseudomonas aeruginosa, 4 hours, batch 1
P_S2.csv


title: genomic DNA from brain 156

description: structural brain lesion and epilepsy

label: Cy5 and Cy144


title: Pseudomonas, 4 hr, rep B, batch 1

description:
PA4B1
Pseudomonas aeruginosa, 4 hours, batch 1
P_S2.csv


title: genomic DNA from brain 155

description: structural brain lesion and epilepsy

label: Cy5 and Cy143


title: genomic DNA from brain 153

description: structural brain lesion and epilepsy

label: Cy5 and Cy141


title: Pseudomonas, 4 hr, rep A, batch 1

description:
PA4A1
Pseudomonas aeruginosa, 4 hours, batch 1
P_S2.csv


title: Control, 4 hr, rep C, batch 1

description:
C4C1
Control (PBS), 4 hours, batch 1
P_S2.csv
A_S3.csv


title: genomic DNA from brain 152

description: structural brain lesion and epilepsy

label: Cy5 and Cy140


title: genomic DNA from brain 154

description: structural brain lesion and epilepsy

label: Cy5 and Cy142


title: Control, 4 hr, rep B, batch 1

description:
C4B1
Control (PBS), 4 hours, batch 1
P_S2.csv
A_S3.csv


title: Control, 4 hr, rep D, batch 1

description:
C4D1
Control (PBS), 4 hours, batch 1
P_S2.csv
A_S3.csv


title: genomic DNA from brain 150

description: structural brain lesion and epilepsy

label: Cy5 and Cy138


title: Acinetobacter, 1 hr, rep D, batch 1

description:
AB1D1
Acinetobacter baumannii, 1 hour, batch 1
A_S3.csv


title: Acinetobacter, 1 hr, rep C, batch 1

description:
AB1C1
Acinetobacter baumannii, 1 hour, batch 1
A_S3.csv


title: genomic DNA from brain 149

description: structural brain lesion and epilepsy

label: Cy5 and Cy137


title: genomic DNA from brain 147

description: structural brain lesion and epilepsy

label: Cy5 and Cy135


title: Acinetobacter, 1 hr, rep B, batch 1

description:
AB1B1
Acinetobacter baumannii, 1 hour, batch 1
A_S3.csv


title: genomic DNA from brain 145

description: structural brain lesion and epilepsy

label: Cy5 and Cy133


title: genomic DNA from brain 146

description: structural brain lesion and epilepsy

label: Cy5 and Cy134


title: genomic DNA from brain 144

description: structural brain lesion and epilepsy

label: Cy5 and Cy132


title: Pseudomonas, 1 hr, rep C, batch 1

description:
PA1C1
Pseudomonas aeruginosa, 1 hour, batch 1
P_S2.csv


title: Acinetobacter, 1 hr, rep A, batch 1

description:
AB1A1
Acinetobacter baumannii, 1 hour, batch 1
A_S3.csv


title: genomic DNA from brain 143

description: structural brain lesion and epilepsy

label: Cy5 and Cy131


title: Acinetobacter, 4 hr, rep A, batch 1

description:
AB4A1
Acinetobacter baumannii, 4 hours, batch 1
A_S3.csv


title: Pseudomonas, 1 hr, rep D, batch 1

description:
PA1D1
Pseudomonas aeruginosa, 1 hour, batch 1
P_S2.csv


title: genomic DNA from brain 157

description: structural brain lesion and epilepsy

label: Cy5 and Cy145


title: Pseudomonas, 4 hr, rep D, batch 1

description:
PA4D1
Pseudomonas aeruginosa, 4 hours, batch 1
P_S2.csv


title: genomic DNA from brain 142

description: structural brain lesion and epilepsy

label: Cy5 and Cy130


title: genomic DNA from brain 151

description: structural brain lesion and epilepsy

label: Cy5 and Cy139


title: Control, 4 hr, rep A, batch 1

description:
C4A1
Control (PBS), 4 hours, batch 1
P_S2.csv
A_S3.csv


title: Control, 1 hr, rep C, batch 1

description:
C1C1
Control (PBS), 1 hour, batch 1
P_S2.csv
A_S3.csv


title: genomic DNA from brain 139

description: structural brain lesion and epilepsy

label: Cy5 and Cy127


title: genomic DNA from brain 138

description: structural brain lesion and epilepsy

label: Cy5 and Cy126


title: Control, 1 hr, rep A, batch 1

description:
C1A1
Control (PBS), 1 hour, batch 1
P_S2.csv
A_S3.csv


title: genomic DNA from brain 137

description: structural brain lesion and epilepsy

label: Cy5 and Cy125


title: Control, 1 hr, rep B, batch 1

description:
C1B1
Control (PBS), 1 hour, batch 1
P_S2.csv
A_S3.csv


title: genomic DNA from brain 135

description: structural brain lesion and epilepsy

label: Cy5 and Cy123


title: genomic DNA from brain 133

description: structural brain lesion and epilepsy

label: Cy5 and Cy121


title: U247B3

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

description:
Test, Mixed Co-Transcriptome
both rawCounts.xlsx

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence files were trimmed with TrimGalore version 0.6.2 using parameters --trim-n --trim1 --nextseq 20 --fastqc_args
Trimmed sequence reads were aligned with STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the alignment files using HTSeq-Count version 0.11.3 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 version 1.24.0 was used with default setting following their vignete to normalize and calculate differential expression
Genome_build: Gencode GRCh38 p13 Release 32 & Strep agalactiae strain 874391
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

organism:
Streptococcus agalactiae
Homo sapiens

source_name: Moncytes infected with Bacteria

growth_protocol: U937 monocytes (100,000/ml) were infected with Sa in wells of 6-well culture plates at a MOI of 100-200 for 6h prior to RNA extraction. Extensive optimizations were performed to validate these assay conditions to achieve sufficient yield and quality of Sa RNA from infected monocytes.

extract_protocol: Promega SV Total RNA Isolation System kit to extract RNA. Cell pellets (infected monocytes) resuspended in 100µl RNase-free TE Buffer containing 30mg/ml lysozyme. Five replicates were combined to a final volume of 500µl in 2ml tubes containing 50mg acid-washed glass beads. The suspensions were subject to bead-beating (10s), and 50µl (500U) of mutanolysin was added prior to incubation (90min at 37C). Digests were transferred 15ml tubes and lysis buffer was added at a ratio of 175µl per 5x1,000,000 viable monocytes in the initial cell pellet. The mixture was passed through a 20 gauge needle ten times to shear genomic DNA. Twice the volume of dilution buffer (to lysis buffer) was added and the mixture was inverted before aliquoting into four 2ml tubes for incubation (3min at 70C). After centrifuging (10min at 13000 x g, 4C), supernatants were combined into a 15ml tube and cold ethanol was added at a ratio of 200µl per 500µl supernatant. Ten spin columns for RNA isolation. DNA removed using Turbo DNAfree Ambion.

treatment_protocol: Media used was RPMI 1640 supplemented with 1mM sodium pyruvate, 1X non-essential amino acids, 25mM HEPES, 25μM beta-mercaptoethanol and 1% FBS to limit the growth of Sa. Gentamicin (50µg/ml) and penicillin-streptomycin (250 U/ml) were added to the infected cultures at 1h into the 6h incubation period to kill extracellular Sa (killed at efficiency >99.99%), as established in assay optimizations.

value: Wild-type strain 874391

tag: cell line

value: Mixed culture

tag: culture

value: Equivalent culture conditions


title: U237A1


title: genomic DNA from brain 132

description: structural brain lesion and epilepsy

label: Cy5 and Cy120


title: genomic DNA from brain 131

description: structural brain lesion and epilepsy

label: Cy5 and Cy119


title: Deo_6_1

city: Beijing

first: Jing

last: Wang

address: Shuguanghuayuan middle road #9, Haidian district

department: Institute of Animal Husbandry and Veterinary Medicine

institute: Beijing Academy of Agriculture and Forestry Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Sus scrofa

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: treatment

value: deoxyshikonin 6h


title: Deo_6_2


title: Pseudomonas, 1 hr, rep B, batch 1

description:
PA1B1
Pseudomonas aeruginosa, 1 hour, batch 1
P_S2.csv


title: Deo_24_3

value: deoxyshikonin 24h


title: Pseudomonas, 1 hr, rep A, batch 1

description:
PA1A1
Pseudomonas aeruginosa, 1 hour, batch 1
P_S2.csv


title: genomic DNA from brain 140

description: structural brain lesion and epilepsy

label: Cy5 and Cy128


title: Control, 1 hr, rep D, batch 1

description:
C1D1
Control (PBS), 1 hour, batch 1
P_S2.csv
A_S3.csv


title: genomic DNA from brain 141

description: structural brain lesion and epilepsy

label: Cy5 and Cy129


title: genomic DNA from brain 128

description: structural brain lesion and epilepsy

label: Cy5 and Cy116


title: genomic DNA from brain 127

description: structural brain lesion and epilepsy

label: Cy5 and Cy115


title: Con_6_3

value: control 6h


title: genomic DNA from brain 126

description: structural brain lesion and epilepsy

label: Cy5 and Cy114


title: Deo_24_1


title: U237A3


title: Deo_24_2


title: genomic DNA from brain 125

description: structural brain lesion and epilepsy

label: Cy5 and Cy113


title: genomic DNA from brain 134

description: structural brain lesion and epilepsy

label: Cy5 and Cy122


title: genomic DNA from brain 136

description: structural brain lesion and epilepsy

label: Cy5 and Cy124


title: U237A2


title: Deo_6_3


title: Con_24_3

value: control 24h


title: genomic DNA from brain 130

description: structural brain lesion and epilepsy

label: Cy5 and Cy118


title: genomic DNA from brain 123

description: structural brain lesion and epilepsy

label: Cy5 and Cy111


title: Con_6_1


title: genomic DNA from brain 124

description: structural brain lesion and epilepsy

label: Cy5 and Cy112


title: Con_24_2


title: Con_24_1


title: genomic DNA from brain 120

description: structural brain lesion and epilepsy

label: Cy5 and Cy108


title: genomic DNA from brain 129

description: structural brain lesion and epilepsy

label: Cy5 and Cy117


title: genomic DNA from brain 122

description: structural brain lesion and epilepsy

label: Cy5 and Cy110


title: genomic DNA from brain 121

description: structural brain lesion and epilepsy

label: Cy5 and Cy109


title: genomic DNA from brain 119

description: structural brain lesion and epilepsy

label: Cy5 and Cy107


title: genomic DNA from brain 118

description: structural brain lesion and epilepsy

label: Cy5 and Cy106


title: Con_6_2


title: genomic DNA from brain 116

description: structural brain lesion and epilepsy

label: Cy5 and Cy104


title: genomic DNA from brain 117

description: structural brain lesion and epilepsy

label: Cy5 and Cy105


title: genomic DNA from brain 115

description: structural brain lesion and epilepsy

label: Cy5 and Cy103


title: E12.5 in vivo_A7

city: Madrid

first: Priscila

last: Ramos-Ibeas

address: Avda. Puerta de Hierro, 12, local 10

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

data_processing:
Paired-end read fastq files were quality checked with FastQC (Andrews, 2010) and preprocessed with fastp (Chen et al., 2018). Resulting files were pseudoaligned and quantified using kallisto (Bray et al., 2016) against the reference transcriptome of Ovis aries Rambouillet breed v1.0 (Ensembl release 104).
To perform gene annotation the R package biomaRt (Durinck et al., 2009) was used, and completed with the eggNOG mapper (Huerta-Cepas et al., 2019; Cantalapiedra et al., 2021) deploying blastx-like searches against a DIAMOND (Buchfink et al., 2015) database comprised of curated mammalian proteins.
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: TPMs_sheep_genes

organism: Ovis aries

source_name: E12.5 in vivo embryo_A7

growth_protocol: In vivo embryos were obtained from 3 years old Merino ewes superovulated with flugestone acetate (Sincropart® sponges, CEVA), PGF2α analog (Cloprostenol, Estrumate®, MSD) and follicle-stimulating hormone (Folltropin-V, Vetoquinol). Ewes were mated (day 0 PM and day 1 AM) and slaughtered at days 11 and 12.5 post-coitus. Embryos were recovered by uterine flushing with warmed recovery medium (Euroflush, IVM Technologies).

extract_protocol:
Embryos were snap-frozen in liquid nitrogen, and total RNA was extracted using MagMAXTM mirVanaTM Total RNA Isolation kit according to the manufacturer´s protocol. cDNA was synthetized with SMART-Seq™ v4 Ultra™ Low Input RNA Kit (Clontech) and amplified ds-cDNA was purified with AMPure XP beads (Beckman Coulter) and quantified with Qubit (Life Technologies). Libraries were prepared using Covaris shearing system and a size selection of 200 bp was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Merino

tag: developmental stage

value: Embryonic day 12.5

tag: origin

value: in vivo


title: genomic DNA from brain 113

description: structural brain lesion and epilepsy

label: Cy5 and Cy101


title: E11 in vivo_A6

source_name: E11 in vivo embryo_A6

value: Embryonic day 11


title: E12.5 in vivo_A8

source_name: E12.5 in vivo embryo_A8


title: D14 in vitro_A2

source_name: D14 in vitro embryo_A2

growth_protocol: In vitro embryo production procedures were performed as previously described (Cocero et al., 2019). D6/7 blastocysts were transferred to agarose-coated four-well dishes in N2B27 medium supplemented with 10 μM ROCK inhibitor and 20 ng/ml activin A (Stem Cell Technologies). AEmbryos were cultured at 38.5 ºC in a water saturated atmosphere of 5 % CO2, 5 % O2, and 90 % N2 and half of the culture medium was replaced every other day, until D14 when they were collected.

value: Day 14

value: in vitro


title: D14 in vitro_A3

source_name: D14 in vitro embryo_A3


title: E11 in vivo_A4

source_name: E11 in vivo embryo_A4


title: E11 in vivo_A5

source_name: E11 in vivo embryo_A5


title: E12.5 in vivo_A9

source_name: E12.5 in vivo embryo_A9


title: genomic DNA from brain 109

description: structural brain lesion and epilepsy

label: Cy5 and Cy97

source_name: Cortex


title: genomic DNA from brain 103

description: structural brain lesion and epilepsy

label: Cy5 and Cy91


title: genomic DNA from brain 107

description: structural brain lesion and epilepsy

label: Cy5 and Cy95


title: genomic DNA from brain 100

description: structural brain lesion and epilepsy

label: Cy5 and Cy88


title: genomic DNA from brain 108

description: structural brain lesion and epilepsy

label: Cy5 and Cy96


title: genomic DNA from brain 99

description: structural brain lesion and epilepsy

label: Cy5 and Cy87


title: genomic DNA from brain 102

description: structural brain lesion and epilepsy

label: Cy5 and Cy90


title: genomic DNA from brain 112

description: structural brain lesion and epilepsy

label: Cy5 and Cy100


title: genomic DNA from brain 110

description: structural brain lesion and epilepsy

label: Cy5 and Cy98


title: genomic DNA from brain 111

description: structural brain lesion and epilepsy

label: Cy5 and Cy99


title: genomic DNA from brain 101

description: structural brain lesion and epilepsy

label: Cy5 and Cy89


title: D14 in vitro_A1

source_name: D14 in vitro embryo_A1


title: genomic DNA from brain 97

description: structural brain lesion and epilepsy

label: Cy5 and Cy85


title: genomic DNA from brain 98

description: structural brain lesion and epilepsy

label: Cy5 and Cy86


title: K1_SR1_3

city: Changchun

first: Feng

last: Guan

state: China

address: Department of Nuclear Medicine, The First Hospital of Jilin University

institute: The First Hospital of Jilin University

data_processing:
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM, log2FoldChange

source_name: thyroid cancer

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

tag: cell type

value: AhR antagonist （StemRegenin 1）

tag: molecule subtype

value: circRNA


title: k1_control_3

value: DMSO


title: genomic DNA from brain 114

description: structural brain lesion and epilepsy

label: Cy5 and Cy102

value: Reference


title: k1_control_2


title: k1_control_1


title: K1_SR1_2


title: genomic DNA from brain 94

description: structural brain lesion and epilepsy

label: Cy5 and Cy82


title: genomic DNA from brain 95

description: structural brain lesion and epilepsy

label: Cy5 and Cy83


title: genomic DNA from brain 96

description: structural brain lesion and epilepsy

label: Cy5 and Cy84


title: genomic DNA from brain 105

description: structural brain lesion and epilepsy

label: Cy5 and Cy93


title: genomic DNA from brain 104

description: structural brain lesion and epilepsy

label: Cy5 and Cy92


title: genomic DNA from brain 106

description: structural brain lesion and epilepsy

label: Cy5 and Cy94


title: IV90 THC/SIV

type: RNA

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

data_processing:
QuantStudio run files representing all treatment groups and timepoints were analyzed using ExpressionSuite Software (Life Tech). The results from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the Omics Office StatMiner qPCR analysis software, TIBCO Spotfire, (Perkin Elmer, Waltham, MA). Omics Office StatMiner Software utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative gene expression across many genes and samples.
miRNA expression data was normalized using the global normalization method.
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Due to the small sample size and exploratory nature of the study multiple comparisons correction was not applied. However, differentially expressed miRNAs were confirmed using RT-qPCR.
ExpressionSuite v1.0.3 software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio data files.
Matrix normalized worksheet reports normalized signal (Normalization using global normalization method).
Fold Change worksheet reports test-1/control (i.e., VEH/SIV vs Uninfected control) and test-1 vs test-2 (THC/SIV vs VEH/SIV) ratios.

organism: Macaca mulatta

source_name: Gingiva

label_protocol: microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 100 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 10 animals were infected intravenously with 100 TCID50 SIVmac251 and 5 remained uninfected. Three SIV infected rhesus macaques were administered delta-9-tetrahydrocannabinol at 0.18 mg/kg one month before SIV Infection and increased to 0.32 mg/kg on the day of SIV infection until 6 months post SIV infection.

value: SIV infected and THC treated


title: JT80 THC/SIV


title: KM98 VEH/SIV

value: SIV Infected and Vehicle treated


title: JI45 THC/SIV


title: genomic DNA from brain 91

description: structural brain lesion and epilepsy

label: Cy5 and Cy79


title: genomic DNA from brain 90

description: structural brain lesion and epilepsy

label: Cy5 and Cy78


title: genomic DNA from brain 89

description: structural brain lesion and epilepsy

label: Cy5 and Cy77


title: LF29 VEH/SIV


title: LB49 VEH/SIV


title: JD66 VEH/SIV


title: genomic DNA from brain 92

description: structural brain lesion and epilepsy

label: Cy5 and Cy80


title: JH47 VEH/SIV


title: genomic DNA from brain 86

description: structural brain lesion and epilepsy

label: Cy5 and Cy74


title: LB06 VEH/SIV


title: genomic DNA from brain 88

description: structural brain lesion and epilepsy

label: Cy5 and Cy76


title: genomic DNA from brain 85

description: structural brain lesion and epilepsy

label: Cy5 and Cy73


title: JB61 Uninfected Controls

description: Control

value: Untreated/uninfected


title: genomic DNA from brain 93

description: structural brain lesion and epilepsy

label: Cy5 and Cy81


title: JB84 Uninfected Controls

description: Control


title: II28 Uninfected Controls

description: Control


title: genomic DNA from brain 82

description: structural brain lesion and epilepsy

label: Cy5 and Cy70


title: genomic DNA from brain 84

description: structural brain lesion and epilepsy

label: Cy5 and Cy72


title: IG78 Uninfected Controls

description: Control


title: genomic DNA from brain 83

description: structural brain lesion and epilepsy

label: Cy5 and Cy71


title: genomic DNA from brain 81

description: structural brain lesion and epilepsy

label: Cy5 and Cy69


title: genomic DNA from brain 77

description: structural brain lesion and epilepsy

label: Cy5 and Cy65


title: genomic DNA from brain 79

description: structural brain lesion and epilepsy

label: Cy5 and Cy67


title: genomic DNA from brain 78

description: structural brain lesion and epilepsy

label: Cy5 and Cy66


title: genomic DNA from brain 76

description: structural brain lesion and epilepsy

label: Cy5 and Cy64


title: genomic DNA from brain 87

description: structural brain lesion and epilepsy

label: Cy5 and Cy75


title: genomic DNA from brain 80

description: structural brain lesion and epilepsy

label: Cy5 and Cy68


title: genomic DNA from brain 75

description: structural brain lesion and epilepsy

label: Cy5 and Cy63


title: genomic DNA from brain 72

description: structural brain lesion and epilepsy

label: Cy5 and Cy60


title: genomic DNA from brain 74

description: structural brain lesion and epilepsy

label: Cy5 and Cy62


title: genomic DNA from brain 70

description: structural brain lesion and epilepsy

label: Cy5 and Cy58


title: genomic DNA from brain 69

description: structural brain lesion and epilepsy

label: Cy5 and Cy57


title: genomic DNA from brain 71

description: structural brain lesion and epilepsy

label: Cy5 and Cy59


title: genomic DNA from brain 68

description: structural brain lesion and epilepsy

label: Cy5 and Cy56


title: genomic DNA from brain 66

description: structural brain lesion and epilepsy

label: Cy5 and Cy54


title: genomic DNA from brain 63

description: structural brain lesion and epilepsy

label: Cy5 and Cy51


title: genomic DNA from brain 61

description: structural brain lesion and epilepsy

label: Cy5 and Cy49


title: genomic DNA from brain 60

description: structural brain lesion and epilepsy

label: Cy5 and Cy48


title: genomic DNA from brain 65

description: structural brain lesion and epilepsy

label: Cy5 and Cy53


title: genomic DNA from brain 67

description: structural brain lesion and epilepsy

label: Cy5 and Cy55


title: genomic DNA from brain 64

description: structural brain lesion and epilepsy

label: Cy5 and Cy52


title: genomic DNA from brain 58

description: structural brain lesion and epilepsy

label: Cy5 and Cy46


title: genomic DNA from brain 57

description: structural brain lesion and epilepsy

label: Cy5 and Cy45


title: genomic DNA from brain 56

description: structural brain lesion and epilepsy

label: Cy5 and Cy44


title: WT 26 somite

city: Bunkyo

first: Ryuichi

last: Yamada

state: Tokyo

address: Yayoi 1-1-1

department: Veterinary Anatomy

country: Japan

institute: The Univerisity of Tokyo

description:
Chromium Single Cell 3’ Reagent Kits v3
scRNA-seq

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The cDNA insert was aligned to the mm10/GRCm38 reference genome.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: There are three files generated using the Cell Ranger Single-Cell Software. matrix.mtx: This file contains the gene-barcode matrix. barcodes.tsv: This file contains the barcodes represented in the mtx file. genes.tsv: This file contains all annotated genes.

source_name: 26 somite stage ocular area

extract_protocol:
A single embryo was dissected under a stereomicroscope, and a pair of optic areas was dissected manually using a fine needle (Austerlitz Insect Pins with a diameter of 0.1 mm). The dissected tissues were incubated with 0.05% Trypsin-EDTA for 3 min at 37°C. Then, 10% fetal calf serum/minimal essential medium was added to stop the proteinase reaction. The cells were dissociated by gentle pipetting and suspended in 0.04% bovine serum albumin/phosphate-buffered saline (PBS). The number of cells was counted using the Countess II FL automated cell counter (Invitrogen, Carlsbad, CA, USA).
2,000 cells/sample were then prepared as scRNA-seq library using Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics, Pleasanton, CA, USA).

value: ocular area

tag: genotype

value: wild type

value: 26 somite stage (E9.25)


title: genomic DNA from brain 62

description: structural brain lesion and epilepsy

label: Cy5 and Cy50


title: KO 26 somite

tag: tissue


title: genomic DNA from brain 55

description: structural brain lesion and epilepsy

label: Cy5 and Cy43


title: genomic DNA from brain 59

description: structural brain lesion and epilepsy

label: Cy5 and Cy47


title: genomic DNA from brain 54

description: structural brain lesion and epilepsy

label: Cy5 and Cy42


title: HSA-NRTN 2

city: Stockholm

first: Jorge

middle: C.

last: Correia

address: Biomedicum - Solnavägen 9

department: Dept. Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using HISAT2 with default parameters.
Normalized gene counts were obtained from bam files using HTSEQ-count (--stranded reverse; mus_musculus.GRCm38.93.gtf) and differential expression was performed using DESeq2. All other parameters were kept as default.
Genome_build: GRCm38
Supplementary_files_format_and_content: Standard cufflinks/cuffdiff output in tar.gz archive
Supplementary_files_format_and_content: Tab delimited text files containing raw counts

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscles were harvested and snap-frozen in liquid nitrogen. Total RNA was extracted using TRI reagent, according to the manufacturer's instructions.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: HSA-NRTN

value: Gastrocnemius muscle


title: genomic DNA from brain 73

description: structural brain lesion and epilepsy

label: Cy5 and Cy61


title: HSA-NRTN 3


title: genomic DNA from brain 53

description: structural brain lesion and epilepsy

label: Cy5 and Cy41


title: HSA-NRTN 1


title: genomic DNA from brain 52

description: structural brain lesion and epilepsy

label: Cy5 and Cy40


title: UL_Rep2

city: Singapore

first: Chin Tong

last: Ong

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: control sibling

data_processing:
Raw fastq reads (without adapter sequences) were aligned to Drosophila reference genome (BDGP6.22.98)  using STAR (v2.5). HTSeq-count was used to identify read counts per gene. Differentially expressed genes (DEGs) were determined using DESeq2 (v1.22.1) on Galaxy platform. The data was visualised by Heatmap2 (v3.0.1) and Volcano Plot (v0.0.3). Gene Ontology analysis was performed using DAVID Functional Annotation Bioinformatics (v6.8).
Genome_build: Drosophila melanogaster reference genome (BDGP6.22.98)
Supplementary_files_format_and_content: Tab-delimited raw count contains the raw gene count matrix for all samples and genes.
Supplementary_files_format_and_content: Tab-delimited Deseq output contains the differentially expressed genes for overexpression and control flies.

organism: Drosophila melanogaster

source_name: Drosophila head

growth_protocol: Drosophila melanogaster were cultured in standard fly media (6% cornmeal, 5% dextrose, 2.4% brewer’s yeast, 0.8% agarose and 0.3% nipagin) at 25◦C with 12-hour light/dark cycle.

extract_protocol:
Fly heads were dissected and frozen by liquid nitrogen. Total RNA was isolated from the pooled fly heads at the age of day 30 using RNAzol®RT (Sigma).
RNA-sequencing was carried at BGI (Hong Kong) according to company’s protocol. RNA quality was assessed with Agilent 2100 bioanalyzer. Following DNAse I treatment, mRNA enriched by magnetic beads coupled to Oligo-dT was fragmented and used as template for cDNA library construction. Short DNA fragments were then subjected to end-repair, A-tailing, adaptor ligation, size selection and sequenced on BGISEQ PE100.

treatment_protocol: Twenty flies were housed in one vial (diameter of 2.5 cm, height of 9.5 cm) and the food was changed every two days until the desired age of day 30.

value: +/+; +/UAS-LamB.GFP

tag: age

value: Day 30 adult

value: Head


title: Wild-type 3

value: WT


title: genomic DNA from brain 51

description: structural brain lesion and epilepsy

label: Cy5 and Cy39


title: genomic DNA from brain 50

description: structural brain lesion and epilepsy

label: Cy5 and Cy38


title: genomic DNA from brain 49

description: structural brain lesion and epilepsy

label: Cy5 and Cy37


title: UL_Rep1

description: control sibling


title: Wild-type 2


title: genomic DNA from brain 47

description: structural brain lesion and epilepsy

label: Cy5 and Cy35


title: HL_Rep2

description: lamin-B overexpression

value: Hsp70-Gal4/+; +/UAS-LamB.GFP


title: genomic DNA from brain 44

description: structural brain lesion and epilepsy

label: Cy5 and Cy32


title: genomic DNA from brain 46

description: structural brain lesion and epilepsy

label: Cy5 and Cy34


title: Rod photoreceptors

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Sequencing quality was checked using fastqc. Fastq files were processed usinig HiCUP to generate a bam of valid iiniteractions mapped on GRCm38.
Valid interactions from the bam file were converted to a .hic file using hicup2homer conversion tool, a homemade bash script and juicer tool pre.
Genome_build: GRCm38

source_name: Retina

extract_protocol:
Retinas were dissected in HBSS media and digested in a buffered solution containing Papain for 30 minutes at 8°C followed by 15 min at 28°C. Dissociated cells were crosslinked in 1% formaldehyde/HBSS followed by the addition of 125 mM Glycine for 5 min. Fixed cells were pelleted, resuspended in HBSS and subjected to Fluorescence-activated cell sorting.
HiC libraries were prepared using 2M purified rods following instructions from Arima HiC kit.

tag: strain

value: Nrlp-EGFP; C57BL/6

value: Purified rod photoreceptors

value: 2 months

value: Nrlp-EGFP KI


title: genomic DNA from brain 42

description: structural brain lesion and epilepsy

label: Cy5 and Cy30

tag: sample type

value: Reference


title: genomic DNA from brain 41

description: structural brain lesion and epilepsy

label: Cy5 and Cy29


title: genomic DNA from brain 43

description: structural brain lesion and epilepsy

label: Cy5 and Cy31


title: Wild-type 1


title: genomic DNA from brain 40

description: structural brain lesion and epilepsy

label: Cy5 and Cy28


title: HL_Rep1

description: lamin-B overexpression


title: genomic DNA from brain 38

description: structural brain lesion and epilepsy

label: Cy5 and Cy26


title: genomic DNA from brain 37

description: structural brain lesion and epilepsy

label: Cy5 and Cy25


title: genomic DNA from brain 36

description: structural brain lesion and epilepsy

label: Cy5 and Cy24


title: genomic DNA from brain 35

description: structural brain lesion and epilepsy

label: Cy5 and Cy23


title: genomic DNA from brain 32

description: structural brain lesion and epilepsy

label: Cy5 and Cy20


title: genomic DNA from brain 31

description: structural brain lesion and epilepsy

label: Cy5 and Cy19


title: genomic DNA from brain 30

description: structural brain lesion and epilepsy

label: Cy5 and Cy18


title: genomic DNA from brain 33

description: structural brain lesion and epilepsy

label: Cy5 and Cy21


title: K1_SR1_1

value: AhR antagonist （StemRegenin 1）

value: circRNA


title: genomic DNA from brain 29

description: structural brain lesion and epilepsy

label: Cy5 and Cy17


title: genomic DNA from brain 48

description: structural brain lesion and epilepsy

label: Cy5 and Cy36


title: genomic DNA from brain 27

description: structural brain lesion and epilepsy

label: Cy5 and Cy15


title: genomic DNA from brain 28

description: structural brain lesion and epilepsy

label: Cy5 and Cy16


title: genomic DNA from brain 45

description: structural brain lesion and epilepsy

label: Cy5 and Cy33


title: genomic DNA from brain 39

description: structural brain lesion and epilepsy

label: Cy5 and Cy27


title: genomic DNA from brain 25

description: structural brain lesion and epilepsy

label: Cy5 and Cy13


title: genomic DNA from brain 26

description: structural brain lesion and epilepsy

label: Cy5 and Cy14


title: genomic DNA from brain 23

description: structural brain lesion and epilepsy

label: Cy5 and Cy11


title: genomic DNA from brain 24

description: structural brain lesion and epilepsy

label: Cy5 and Cy12


title: genomic DNA from brain 22

description: structural brain lesion and epilepsy

label: Cy5 and Cy10


title: genomic DNA from brain 21

description: structural brain lesion and epilepsy

label: Cy5 and Cy9


title: genomic DNA from brain 19

description: structural brain lesion and epilepsy

label: Cy5 and Cy7


title: genomic DNA from brain 18

description: structural brain lesion and epilepsy

label: Cy5 and Cy6


title: genomic DNA from brain 17

description: structural brain lesion and epilepsy

label: Cy5 and Cy5


title: genomic DNA from brain 16

description: structural brain lesion and epilepsy

label: Cy5 and Cy4


title: genomic DNA from brain 20

description: structural brain lesion and epilepsy

label: Cy5 and Cy8


title: genomic DNA from brain 15

description: structural brain lesion and epilepsy

label: Cy5 and Cy3


title: genomic DNA from brain 14

description: structural brain lesion and epilepsy


title: genomic DNA from brain 13

description: structural brain lesion and epilepsy


title: genomic DNA from brain 12

description: structural brain lesion and epilepsy


title: genomic DNA from brain 34

description: structural brain lesion and epilepsy

label: Cy5 and Cy22


title: genomic DNA from brain 10

description: structural brain lesion and epilepsy


title: genomic DNA from brain 9

description: structural brain lesion and epilepsy


title: genomic DNA from brain 11

description: structural brain lesion and epilepsy


title: genomic DNA from brain 8

description: structural brain lesion and epilepsy


title: genomic DNA from brain 6

description: structural brain lesion and epilepsy


title: genomic DNA from brain 7

description: structural brain lesion and epilepsy


title: genomic DNA from brain 5

description: structural brain lesion and epilepsy


title: genomic DNA from brain 4

description: structural brain lesion and epilepsy


title: genomic DNA from brain 2

description: structural brain lesion and epilepsy


title: genomic DNA from brain 3

description: structural brain lesion and epilepsy


title: genomic DNA from brain 1

description: structural brain lesion and epilepsy


title: EtOH.72hr.untreated 4_11

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
EtOH.72hr.untreated
Male Sprague-Dawley rats

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

data_processing: Raw expression of background probes were averaged and the mean + two standard deviations was calculated. Any probe whose average expression over half the samples was less than the mean+2sd of background probes was removed. The remaining samples were normalized by calculating normalization factors followed by voom transformation.

label: NanoString

organism: Rattus norvegicus

source_name: rat liver tissue

label_protocol: Nanostring protocol

extract_protocol: Total RNA from each sample was extracted from frozen liver samples using an Animal Tissue RNA Purification Kit (Norgen Biotek).

treatment_protocol: Locked nucleic acid (LNA)-modified oligo antisense to miR-21 (AM21, Exiqon) was used to inhibit miRNA in vivo, and rats were subjected to 70% PHx fed on either ethanol or control diet.

value: rat liver tissue

tag: diet

value: ethanol

value: untreated

tag: time point


title: EtOH.72hr.untreated 4_10


title: CHO.72hr.untreated 4_8

description:
CHO.72hr.untreated
Male Sprague-Dawley rats

value: carbohydrate


title: CHO.72hr.untreated 4_9


title: EtOH.6hr.untreated 4_5

description:
EtOH.6hr.untreated
Male Sprague-Dawley rats


title: CHO.6hr.untreated 4_3

description:
CHO.6hr.untreated
Male Sprague-Dawley rats


title: EtOH.24hr.AM21 3_12

description:
EtOH.24hr.AM21
Male Sprague-Dawley rats


title: CHO.72hr.untreated 4_7


title: CHO.6hr.untreated 4_1


title: CHO.6hr.untreated 4_2


title: EtOH.6hr.untreated 4_4


title: EtOH.6hr.untreated 4_6


title: EtOH.24hr.saline 3_11

description:
EtOH.24hr.saline
Male Sprague-Dawley rats

value: saline


title: CHO.24hr.untreated 3_7

description:
CHO.24hr.untreated
Male Sprague-Dawley rats


title: EtOH.24hr.untreated 3_10

description:
EtOH.24hr.untreated
Male Sprague-Dawley rats


title: SPL-MZ-3

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

description: splenic marginal zone B cell

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: Isotype_plasma_cells.normExp.txt.gz: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Isotype_plasma_cells.rawTPM.txt.gz: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Isotype_plasma_cells.noIg.normExp.txt.gz: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts
Supplementary_files_format_and_content: Isotype_plasma_cells.noIg.rawTPM.txt.gz: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts

source_name: Splenic B cell

growth_protocol: B6.Blimp1+/GFP,  B6.IgA-/- and C57BL/6 mice were bred and maintained in UPENN SPF facilities.

extract_protocol:
Bone marrow, small intestine lamina propria and spleens were harvested at time of saccrifice and lypmhocytes were stained and FACS sorted twice directly into TRIZOL reagent as follows: bone marrow plasma cell: Dump[CD4, CD8a, F4/80, Ter119]-, IgD-, GFP(Blimp1)+, CD138+, IgA+ or IgM+ or IgA/M-; siLP plasma cell Dump[CD4, CD8a, F4/80, Ter119]-, IgD-, GFP(Blimp1)+, IgA+;   follicular B cell: live, singlet, CD19+, CD93-, CD23+, CD21/35int.  marginal zone B cell: live, singlet, CD19+, CD93-, CD23-, CD21/35high.
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech SMART-Seq HT kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.

value: Spleen

value: 12 weeks


title: SPL-MZ-1

description: splenic marginal zone B cell


title: SPL-MZ-4

description: splenic marginal zone B cell


title: SPL-FO-2

description: splenic follicular B cell


title: SPL-MZ-2

description: splenic marginal zone B cell


title: EtOH.0hr.AM21 3_6

description:
EtOH.0hr.AM21
Male Sprague-Dawley rats


title: SPL-FO-3

description: splenic follicular B cell


title: EtOH.0hr.untreated 3_4

description:
EtOH.0hr.untreated
Male Sprague-Dawley rats


title: EtOH.0hr.saline 3_5

description:
EtOH.0hr.saline
Male Sprague-Dawley rats


title: SPL-FO-4

description: splenic follicular B cell


title: CHO.24hr.saline 3_8

description:
CHO.24hr.saline
Male Sprague-Dawley rats


title: CHO.24hr.AM21 3_9

description:
CHO.24hr.AM21
Male Sprague-Dawley rats


title: CHO.0hr.saline 3_2

description:
CHO.0hr.saline
Male Sprague-Dawley rats


title: CHO.0hr.AM21 3_3

description:
CHO.0hr.AM21
Male Sprague-Dawley rats


title: EtOH.72hr.untreated 4_12


title: SPL-FO-1

description: splenic follicular B cell


title: IgAKO5

description: siLP plasma cell from IgA-/-

source_name: small iintestine lamina propria plasma cell

value: small intestine laminia propria


title: IgAKO4

description: siLP plasma cell from IgA-/-


title: IgAKO3

description: siLP plasma cell from IgA-/-


title: CHO.0hr.untreated 3_1

description:
CHO.0hr.untreated
Male Sprague-Dawley rats


title: IgAKO2

description: siLP plasma cell from IgA-/-


title: EtOH.24hr.AM21 2_12

description:
EtOH.24hr.AM21
Male Sprague-Dawley rats


title: EtOH.24hr.untreated 2_10


title: EtOH.24hr.saline 2_11


title: EtOH.0hr.AM21 2_6

description:
EtOH.0hr.AM21
Male Sprague-Dawley rats


title: IgAKO1

description: siLP plasma cell from IgA-/-


title: LP-IgA-2

description: IgA+ siLP plasma cell


title: CHO.24hr.untreated 2_7


title: LP-IgA-3

description: IgA+ siLP plasma cell


title: LP-IgA-1

description: IgA+ siLP plasma cell


title: LP-IgA-4

description: IgA+ siLP plasma cell


title: EtOH.0hr.saline 2_5


title: EtOH.0hr.untreated 2_4


title: CHO.0hr.untreated 2_1


title: CHO.0hr.AM21 2_3

description:
CHO.0hr.AM21
Male Sprague-Dawley rats


title: CHO.0hr.saline 2_2

description:
CHO.0hr.saline
Male Sprague-Dawley rats


title: CHO.24hr.untreated 1_7


title: EtOH.24hr.AM21 1_12

description:
EtOH.24hr.AM21
Male Sprague-Dawley rats


title: EtOH.24hr.untreated 1_10


title: CHO.24hr.saline 1_8


title: EtOH.0hr.AM21 1_6

description:
EtOH.0hr.AM21
Male Sprague-Dawley rats


title: BM-IgA-4

description: IgA+ bone marrow plasma cell

source_name: Bone marrow plasma cell

value: bone marrow


title: EtOH.0hr.saline 1_5


title: BM-IgA-3

description: IgA+ bone marrow plasma cell


title: CHO.24hr.saline 2_8


title: EtOH.0hr.untreated 1_4


title: CHO.0hr.AM21 1_3

description:
CHO.0hr.AM21
Male Sprague-Dawley rats


title: BM-IgA-2

description: IgA+ bone marrow plasma cell


title: CHO.0hr.untreated 1_1


title: COVID-19 negative control [S003J-0060_S332]

city: Abu Dhabi

first: Habiba

last: Alsafar

address: Al Saada St. Muroor Road

department: Center of Biotechnology

country: United Arab Emirates

institute: Khalifa University

data_processing:
BCL files from sequencing were demultiplexed using Illumina's bcl2fastq tool. We subsequently describe the analysis pipeline for microbial communities based on Qiime2, which underwent the paradigm shift from operational taxonomic units (OTUs) to Amplicon sequence variants (ASV), as the latter exhibit several advantages over the former. After demultiplexing using Qiime demux, sequence quality control and feature table construction have been performed with DADA2.
Visual summaries are generated with qiime commands feature-table summarize and feature-table tabulateseqs. Subsequently, we generate a phylogeny for diversity analysis using qiime phylogeny. The resulting phylogeny qiime artifact, particularly the rooted phylogenetic tree, enables a range of diversity analyses using qiime diversity commands.
Alpha diversity commonly applied qualitative measure of community richness.
Compregenive diversity analysis is conducted with Qiime's command core-diversity-phylogenetic (https://view.qiime2.org/)
Phylogenetic investigation of communities by reconstructing unobserved states (PICRUSt) functional analyses based on 16 S rRNA gene abundance profiles was conducted. PICRUSt un-normalized output was also analyzed using the standard DESeq2 workflow. PICRUSt not only estimates full metagenomes from 16S rRNA data, but it also estimates for each sample what operational taxonomic unit contributed to each predicted gene.

source_name: Nasal and Fecal samples from COVID-19 negative control

extract_protocol:
Faecal samples were subjected to DNA extraction using DNeasy PowerLyzer PowerSoil Kit
The primer sequence design included overhang adapter sequences optimized for the Illumina Sequencing, which in turn were further processed by employing the 16 S Metagenomic Sequencing Library Preparation Protocol
16 S Metagenomic Sequencing

tag: group

value: COVID-19 negative control

tag: gender

value: Male

tag: bmi


title: COVID-19 negative control [S003J-0059_S331]

value: Female


title: EtOH.24hr.saline 1_11


title: BM-IgA-1

description: IgA+ bone marrow plasma cell


title: BM-IgG-4

description: IgG (IgM/A-) bone marrow plasma cell


title: BM-IgG-3

description: IgG (IgM/A-) bone marrow plasma cell


title: COVID-19 negative control [S003J-0054_S326]


title: COVID-19 negative control [S003J-0055_S327]


title: COVID-19 negative control [S003J-0053_S325]


title: COVID-19 negative control [S003J-0056_S328]


title: COVID-19 negative control [S003J-0051_S323]


title: COVID-19 negative control [S003J-0040_S312]


title: COVID-19 negative control [S003J-0052_S324]


title: COVID-19 negative control [S003J-0039_S311]


title: COVID-19 negative control [S003J-0058_S330]


title: BM-IgG-2

description: IgG (IgM/A-) bone marrow plasma cell


title: CHO.24hr.AM21 1_9

description:
CHO.24hr.AM21
Male Sprague-Dawley rats


title: CHO.0hr.saline 1_2

description:
CHO.0hr.saline
Male Sprague-Dawley rats


title: COVID-19 negative control [S003J-0049_S321]


title: CHO.24hr.AM21 2_9

description:
CHO.24hr.AM21
Male Sprague-Dawley rats


title: COVID-19 negative control [S003J-0038_S310]


title: BM-IgM-3

description: IgM+ bone marrow plasma cell


title: COVID-19 negative control [S003J-0037_S309]


title: BM-IgG-1

description: IgG (IgM/A-) bone marrow plasma cell


title: COVID-19 negative control [S003J-0034_S306]


title: COVID-19 negative control [S003J-0031_S303]


title: COVID-19 negative control [S003J-0035_S307]


title: COVID-19 negative control [S003J-0036_S308]


title: COVID-19 negative control [S003J-0029_S301]


title: COVID-19 negative control [S003J-0032_S304]


title: COVID-19 negative control [S003J-0030_S302]


title: COVID-19 negative control [S003J-0033_S305]


title: COVID-19 negative control [S003J-0027_S299]


title: COVID-19 negative control [S003J-0023_S295]


title: COVID-19 negative control [S003J-0028_S300]


title: COVID-19 negative control [S003J-0026_S298]


title: COVID-19 negative control [S003J-0022_S294]


title: COVID-19 negative control [S003J-0018_S290]


title: COVID-19 negative control [S003J-0019_S291]


title: BM-IgM-1

description: IgM+ bone marrow plasma cell


title: COVID-19 negative control [S003J-0020_S292]


title: COVID-19 negative control [S003J-0025_S297]


title: KO2

city: Daejeon

first: Haemin

last: Chon

address: Daehak-ro 291

department: Graduate school of medical science and engineering

country: South Korea

institute: KAIST

description:
Fyn_KO_GBM2_cancer_cell
tdTomato+

data_processing:
Trimming was done with > Average Q20 using BBDuk.
Mapping of reads were done using Bowtie2 to mm10 reference genome. Calculation of read counts were done using Bedtools.
Quality control of genes were done excluding of lowly expressed genes (< 10 counts).
Normalization of readcounts were done by log normalization.
Differentially expressed genes between WT and KO were extracted with DESeq2 (v1.32.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: modified_readcount.csv: Comma-separated text file.

source_name: cancer cell

extract_protocol:
FACS-sorted tumor cells were lysed with Qiazol Lysis Reagent (79306, Qiagen Sciences) and RNA was extracted and purified with RNeasy mini plus kit (74134, Qiagen Sciences). Protocols were followed from user guides of products.
Using Lexogen QuantSeq 3' mRNA-seq Library Prep Kit (Lexogen), cDNA libraries were constructed.

value: FYN-KO

tag: disease

value: Glioblastoma

value: FACS-sorted tumor cells

value: Adult


title: KO1

description:
Fyn_KO_GBM1_cancer_cell
tdTomato+


title: KO4

description:
Fyn_KO_GBM4_cancer_cell
tdTomato+


title: BM-IgM-4

description: IgM+ bone marrow plasma cell


title: cd3_atnf_acd40l_1 (blocking)

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

department: Immunology

institute: Cincinnati Children's Hospital Medical Center

description:
cd3_atnf_acd40l_1
CD11c+ BMDCs, pretreated with anti-TNF and anti-CD40L blocking antibody, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-1
M6

data_processing:
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed on CLC Genomics Workbench 7 (Qiagen).
The expression of the genes in all samples was calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: xlsx, raw counts matrix that contains gene names and associated counts

source_name: CD11c+ BMDC

growth_protocol: Bone marrow progenitors were cultured with GMCSF for 7 days with media being replenished every 2 days. WT Th0 cells were differentiated on anti-CD3/anti-CD28 coated plates in the presence of IL-2 for 5 days then rested for 2 days in uncoated plates supplemented with low dose IL-2.

extract_protocol:
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using BioTek Take3 before samples were shipped and processed by BGI Genomics.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.

treatment_protocol: BMDCs were pretreated with 20ug/ml of indicated blocking antibody for 30min then cocultured with Th0 cells in the presence of soluble anti-CD3. BMDCs were then sorted by Moflo on the basis of CD45.2+ CD90.2- CD11c+.

tag: blockade

value: anti-TNFa + anti-CD40L


title: COVID-19 negative control [S003J-0024_S296]


title: COVID-19 negative control [S003J-0021_S293]


title: cd3_acd40l_2 (blocking)

description:
cd3_acd40l_2
CD11c+ BMDCs, pretreated with anti-CD40L blocking antibody, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-2
M11


title: KO3

description:
Fyn_KO_GBM3_cancer_cell
tdTomato+


title: COVID-19 negative control [S003J-0014_S286]


title: cd3_acd40l_1 (blocking)

description:
cd3_acd40l_1
CD11c+ BMDCs, pretreated with anti-CD40L blocking antibody, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-1
M5


title: cd3_atnf_acd40l_2 (blocking)

description:
cd3_atnf_acd40l_2
CD11c+ BMDCs, pretreated with anti-TNF and anti-CD40L blocking antibody, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-2
M12


title: COVID-19 negative control [S003J-0015_S287]


title: COVID-19 negative control [S003J-0012_S284]


title: COVID-19 negative control [S003J-0016_S288]


title: COVID-19 negative control [S003J-0011_S283]


title: COVID-19 negative control [S003J-0017_S289]


title: cd3_2 (blocking)

description:
cd3_2
CD11c+ BMDCs, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-2
M9


title: cd3_1 (blocking)

description:
cd3_1
CD11c+ BMDCs, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-1
M3


title: COVID-19 negative control [S003J-0010_S282]


title: COVID-19 negative control [S003J-0001_S273]


title: COVID-19 negative control [S003J-0003_S275]


title: COVID-19 negative control [S003J-0006_S278]


title: cd3_atnf_1 (blocking)

description:
cd3_atnf_1
CD11c+ BMDCs, pretreated with anti-TNF neutralizing antibody, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-1
M4

value: anti-TNFa


title: COVID-19 negative control [S003J-0008_S280]


title: COVID-19 negative control [S003J-0005_S277]


title: COVID-19 negative control [S003J-0004_S276]


title: plus_th0_2 (blocking)

description:
plus_th0_2
CD11c+ BMDCs, cocultured with Th0 cells, replicate-2
M8


title: COVID-19 positive case [BQ_ST127_COVID_663_18_S18]

source_name: Nasal and Fecal samples from COVID-19 positive case

value: COVID-19 positive case

value: female


title: COVID-19 positive case [BQ_ST129_COVID_665_13_S13]

value: male


title: COVID-19 negative control [S003J-0013_S285]


title: COVID-19 negative control [S003J-0002_S274]


title: unstimulated_2 (blocking)

description:
unstimulated_2
CD11c+ BMDCs, unstimulated, replicate-2
M7


title: COVID-19 positive case [BQ_ST126_COVID_662_14_S14]


title: COVID-19 positive case [BQ_ST124_COVID_660_11_S11]


title: plus_th0_1 (blocking)

description:
plus_th0_1
CD11c+ BMDCs, cocultured with Th0 cells, replicate-1
M2


title: COVID-19 positive case [BQ_ST110_COVID_658_23_S23]


title: unstimulated_1 (blocking)

description:
unstimulated_1
CD11c+ BMDCs, unstimulated, replicate-1
M1


title: COVID-19 positive case [BQ_ST123_COVID_659_49_S47]


title: plus_th0_cd3_3

description:
CD11c+ BMDCs, cultured with Th0 cells in the presence of soluble CD3, replicate-3
3-DC-plus-TC-plus-CD3

data_processing:
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed on CLC Genomics Workbench 7 (Qiagen).
The expression of the genes in all samples was calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: .txt, raw counts matrix that contains all gene names and counts for each sample

extract_protocol:
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using NanoDrop2000 for cDNA synthesis or Agilent Bioanalyzer 2100 before RNA-Seq Library preparation.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.

treatment_protocol: BMDCs were stimulated with LPS or cocultured with Th0 cells in the presence or absence of soluble anti-CD3. BMDCs were then sorted by Moflo on the basis of CD45.2+ CD90.2- CD11c+.

tag: treatment


title: COVID-19 negative control [S003J-0009_S281]


title: COVID-19 negative control [S003J-0007_S279]


title: COVID-19 positive case [BQ_ST106_COVID_621_16_S16]


title: COVID-19 positive case [BQ_ST105_COVID_620_25_S25]


title: plus_th0_cd3_1

description:
CD11c+ BMDCs, cultured with Th0 cells in the presence of soluble CD3, replicate-1
1-DC-plus-TC-plus-CD3


title: cd3_atnf_2 (blocking)

description:
cd3_atnf_2
CD11c+ BMDCs, pretreated with anti-TNF neutralizing antibody, cocultured with Th0 cells in the presence of soluble anti-CD3, replicate-2
M10


title: plus_th0_3

description:
CD11c+ BMDCs, cultured with Th0 cells, replicate-3
3-DC-plus-TC-NO-CD3


title: plus_th0_2

description:
CD11c+ BMDCs, cultured with Th0 cells, replicate-2
2-DC-plus-TC-NO-CD3


title: COVID-19 positive case [BQ_ST101_COVID_616_9_S9]


title: COVID-19 positive case [BQ_ST098_COVID_614_27_S85]


title: COVID-19 positive case [BQ_ST096_COVID_612_29_S27]


title: COVID-19 positive case [BQ_ST098_COVID_613_8_S8]


title: lps_3

description:
CD11c+ BMDCs, LPS, replicate-3
3-DC-plus-LPS

value: LPS


title: COVID-19 positive case [BQ_ST096_COVID_611_7_S7]


title: COVID-19 positive case [BQ_ST092_COVID_607_30_S28]


title: COVID-19 positive case [BQ_ST109_COVID_657_15_S15]


title: COVID-19 positive case [BQ_ST107_COVID_622_48_S46]


title: COVID-19 positive case [BQ_ST090_COVID_605_32_S30]


title: COVID-19 positive case [BQ_ST091_COVID_606_31_S29]


title: unstimulated_3

description:
CD11c+ BMDCs, unstimulated, replicate-3
3-DC-NO-LPS


title: COVID-19 positive case [BQ_ST095_COVID_610_28_S86]


title: COVID-19 positive case [BQ_ST089_COVID_604_6_S6]


title: COVID-19 positive case [BQ_ST088_COVID_603_17_S17]


title: lps_1

description:
CD11c+ BMDCs, LPS, replicate-1
1-DC-plus-LPS


title: COVID-19 positive case [BQ_ST087_COVID_602_5_S5]


title: COVID-19 positive case [BQ_ST085_COVID_600_22_S22]


title: plus_th0_cd3_2

description:
CD11c+ BMDCs, cultured with Th0 cells in the presence of soluble CD3, replicate-2
2-DC-plus-TC-plus-CD3


title: COVID-19 positive case [BQ_ST104_COVID_619_10_S10]


title: COVID-19 positive case [BQ_ST083_COVID_598_19_S19]


title: COVID-19 positive case [BQ_ST103_COVID_618_47_S45]


title: unstimulated_1

description:
CD11c+ BMDCs, unstimulated, replicate-1
1-DC-NO-LPS


title: COVID-19 positive case [BQ_ST081_COVID_596_67_S65]


title: plus_th0_1

description:
CD11c+ BMDCs, cultured with Th0 cells, replicate-1
1-DC-plus-TC-NO-CD3


title: COVID-19 positive case [BQ_ST077_COVID_592_4_S4]


title: COVID-19 positive case [BQ_ST079_COVID_594_21_S21]


title: COVID-19 positive case [BQ_ST078_COVID_593_51_S49]


title: lps_2

description:
CD11c+ BMDCs, LPS, replicate-2
2-DC-plus-LPS


title: COVID-19 positive case [BQ_ST076_COVID_591_44_S42]


title: COVID-19 positive case [BQ_ST075_COVID_590_34_S32]


title: COVID-19 positive case [BQ_ST074_COVID_589_3_S3]


title: MAMBO89NT241016 Untreated

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: established from FVBhuHER2 virgin female mice

data_processing:
Demultiplexing (bcl2fastq Illumina tool version 2.17.1.14-2)
counts  table generated using STAR (version 2.5) /RSEM (version 1.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited, raw counts

source_name: HER2 stable

growth_protocol: Cell lines were stabilized and cultured in DMEM (Thermo Fisher Scientific, Monza, Italy) that was supplemented with 20% fetal bovine serum (FBS, Thermo Fisher Scientific), 30 µg/ml bovine pituitary extract (Corning Life Sciences, Glendale, AZ, USA) and 0.5% v/v MITO Serum Extender (Corning). Cell cultures were maintained at 37°C in a humified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from cell pellets using Trizol Reagent (Thermo Fisher), according to the manufacturer’s instructions.
RNA-seq libraries were generated using TruSeq RNA Sample Prep Kit v2 (Illumina), according to the manufacturer’s recommendations

treatment_protocol: trastuzumab treated cells were kept in contact with 30 μg/ml of trastuzumab for 30 or 60 days

value: Untreated

tag: cell line


title: COVID-19 positive case [BQ_ST094_COVID_609_33_S31]


title: COVID-19 positive case [BQ_ST072_COVID_587_68_S66]


title: COVID-19 positive case [BQ_ST068_COVID_567_42_S40]


title: MAMBO89AG3241016 Untreated


title: MAMBO43TRT241016 Trastuzumab 30 µg/ml 60 days

source_name: HER2 labile

value: Trastuzumab 30 µg/ml 60 days


title: COVID-19 positive case [BQ_ST066_COVID_565_55_S53]


title: COVID-19 positive case [BQ_ST067_COVID_566_39_S37]


title: COVID-19 positive case [BQ_ST065_COVID_564_72_S70]


title: MAMBO43TRNT241016 Trastuzumab 30 µg/ml 30 days  then w/o 30 days


title: COVID-19 positive case [BQ_ST064_COVID_563_46_S44]


title: COVID-19 positive case [BQ_ST080_COVID_595_69_S67]


title: MAMBO38TRT190617 Trastuzumab 30 µg/ml 60 days

source_name: HER2 loss


title: MAMBO89TRT241016 Trastuzumab 30 µg/ml 60 days


title: MAMBO38TRNT190617 Trastuzumab 30 µg/ml 30 days then w/o 30 days


title: MAMBO89TRNT241016 Trastuzumab 30 µg/ml 30 days  then w/o 30 days


title: COVID-19 positive case [BQ_ST061_COVID_560_36_S34]


title: COVID-19 positive case [BQ_ST056_COVID_559_77_S75]


title: COVID-19 positive case [BQ_ST053_COVID_579_41_S39]


title: COVID-19 positive case [BQ_ST050_COVID_577_2_S2]


title: MAMBO38NT241016 Untreated


title: COVID-19 positive case [BQ_ST062_COVID_561_66_S64]


title: unstimulated_2

description:
CD11c+ BMDCs, unstimulated, replicate-2
2-DC-NO-LPS


title: COVID-19 positive case [BQ_ST047_COVID_574_40_S38]


title: COVID-19 positive case [BQ_ST070_COVID_569_65_S63]


title: COVID-19 positive case [BQ_ST046_COVID_573_35_S33]


title: MAMBO38NT190617 Untreated


title: COVID-19 positive case [BQ_ST045_COVID_572_73_S71]


title: COVID-19 positive case [BQ_ST044_COVID_571_81_S79]


title: COVID-19 positive case [BQ_ST048_COVID_575_63_S61]


title: NOD.GW_SN_S2_10x_scRNA-seq

city: Los Angeles

first: Maureen

last: Su

address: 615 Charles E Young Dr S

institute: UCLA

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #2

data_processing:
Single cell feature counts were generated by aligning sequencing data with the mm10 mouse reference genome (version 2020-A) using 10x Cell Ranger software (5.0.1)
Filtered output matrices and barcodes were analyzed with SEURAT 4.0 on R studio (version 1.2.5033) using the Read10X function to return a unique molecular identified (UMI) count matrix for creation of a Seurat object
Cells with fewer than 200 RNA count, more than 3000 unique genes and more than 12.5% mitochondria gene counts were excluded from the analysis.
Samples were integrated and then raw counts and metadata files were generated as the processed data files.
Cells were then clustered as described.
Genome_build: mm10
Supplementary_files_format_and_content: gw_integrated_counts.csv

source_name: NOD.GW Sciatic Nerves

extract_protocol:
Chromium Single Cell GEM, Library & Gel Bead Kit
10x Genomics single cell RNA-Seq

value: NOD.GW Sciatic Nerves

value: NOD.AIRE GW/+

tag: cell number

value: 15 weeks

tag: sequencing method

value: 3' sequencing


title: COVID-19 positive case [BQ_ST041_COVID_550_75_S73]


title: COVID-19 positive case [BQ_ST039_COVID_548_79_S77]


title: COVID-19 positive case [BQ_ST038_COVID_557_37_S35]


title: COVID-19 positive case [BQ_ST036_COVID_547_59_S57]


title: COVID-19 positive case [BQ_ST034_COVID_555_64_S62]


title: COVID-19 positive case [BQ_ST060_COVID_585_20_S20]


title: ELS2

city: Suita

first: Noriyoshi

last: Usui

address: 2-2 Yamadaoka

institute: Osaka University

data_processing:
Bulk RNA-seq reads were aligned with STAR v2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M17). Uniquely mapped reads were quantified using HTSeq v0.9.1 suite using protein coding genes by gene.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Input tables are included as tab separated files.

source_name: prefrontal cortex

extract_protocol:
Total RNA was extracted from prefrontal cortex (PFC) of male mice at 9 weeks with the AllPrep DNA/RNA Mini Kit (#80204, Qiagen, Hilden, Germany) according to the manufacturer’s instruction. RNA integrity number (RIN) of total RNA was quantified by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Pico Kit (#5067-1513, Agilent, Santa Clara, CA).
RNA-seq was performed as a service by Bioengineering Lab. Co., Ltd. (Kanagawa, Japan). Briefly, total RNA with RIN values of ≥8.8 were used for RNA-seq library preparation. mRNA was purified from 500 ng total RNA, and subjected to cDNA library making (fragmentation, first and second strand syntheses, adenylation, ligation and amplification) by TruSeq Stranded mRNA Library Prep (#20020594, Illumina, San Diego, CA) according to the manufacturer’s instruction. cDNA library quality was quantified by 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Library was sequenced as 151 bp paired-end on Illumina NextSeq 500.

value: PFC

value: ELS

tag: Sex

value: Male


title: ELS3


title: ELS1


title: MAMBO43NT241016 Untreated


title: CTL3

value: Control


title: CTL1


title: IHT-IP (VWF del4-34)_rep2

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

data_processing:
Trimming of first 8bp using cutadapt
Mapped against hg38 genome using miARma-seq pipeline
Mapped BAM files were read into Qlucore to convert mapped data into expression values
FPKM normalization was used
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: blood outgrowth endothelial cells (BOECs)

growth_protocol: Martin-Ramirez J, Hofman M, van den Biggelaar M, Hebbel RP, Voorberg J. Establishment of outgrowth endothelial cells from peripheral blood. Nat Protoc. 2012 Sep;7(9):1709-15. doi: 10.1038/nprot.2012.093. Epub 2012 Aug 23. PMID: 22918388.

extract_protocol:
RNeasy_ Mini kit (Qiagen)
QuantSeq 3´-mRNA Library Prep kit (Lexogen)
3' RNA-seq (Illumina HiSeq 2500 V4 platform)

treatment_protocol: No Treatment

tag: cell type

tag: disease state

value: type 3 von Willebrand disease


title: COVID-19 positive case [BQ_ST030_COVID_546_83_S81]

tag: age


title: COVID-19 positive case [BQ_ST028_COVID_544_70_S68]


title: COVID-19 positive case [BQ_ST027_COVID_543_80_S78]


title: COVID-19 positive case [BQ_ST029_COVID_545_57_S55]


title: COVID-19 positive case [BQ_ST032_COVID_526_53_S51]


title: Ribo_MsLV_M_Expr3

city: Worcester

first: Yue

last: Zhang

state: Massachusetts

address: GeneTherapyCenter, 368 Plantation st

institute: Umass medical school

description: ribosome proteced RNA fragments

data_processing:
Illumina bcl2fastq was used to convert base call (BCL) files into FASTQ files.
3′ adapter sequences were removed using Trimmomatic (with parameters ILLUMINACLIP, minlength, 10; seed mismatches, 2; palindrome clip threshold, 30; simple clip threshold, 5). Then 1 nucleotide from the 3' end of each read was trimmed using FASTX-Toolkit Trimmer.
The trimed reads that mapped to noncoding RNA sequences (rRNA, from RefSeq; Mt_rRNA, Mt_tRNA, rRNA, miRNA, scRNA, scaRNA, snoRNA, snRNA, sRNA, vaultRNA from GENCODE v30 were discarded. STAR8 was used for this alignment step with following parameters: --limitBAMsortRAM 20000000000 --outFilterMismatchNmax 1 --outFilterMultimapNmax 100 --alignIntronMax 1 --outWigType wiggle read1_5p.
The remaining reads were mapped to the hg38 human or mm10 mouse genome using annotations from GENCODE (v30) and (v25), respectively. For this step, STAR was used with following parameters to keep only uniquely mapped reads: --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterType BySJout --outFilterMultimapNmax 200 --outSAMmultNmax 1 --outMultimapperOrder Random --outWigType wiggle read1_5p.
Following alignment, reads were assigned to a custom transcriptome annotation  where single transcripts are selected for each protein-coding gene. Further data analysis was performed on the Ribosome-Profiling pipeline of the DolphinNext, available at https://dolphinnext.umassmed.edu/index.php?np=1&id=695.
Genome_build: hg38 human or mm10 mouse
Supplementary_files_format_and_content: csv files containing raw counts and FPKM values for each Sample

source_name: liver

growth_protocol: Patient and control fibroblasts were purchased from Coriell Institute and were maintained in EMEM supplemented with 15% (v/v) fetal bovine serum and antibiotics at 37 °C with 5% CO2.

extract_protocol:
PFB cells and ground  mouse livers powder were lysed on ice in the presence of cycloheximide.  Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation and purified by miRNeasy mini kit.
Ribosome proteced RNA fragments ranging from 26-34 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product  was followed by reverse transcription and gel purification. Then the RT product was circularized by CircLigase ssDNA ligase followed by rRNA depletion with biotinylated subtraction oligo pool. Libraries were then PCR-amplified, and gel-purified libraries were pooled in equimolar ratios and submitted for sequencing.
Ribosome profiling

treatment_protocol: Patient fibroblasts were infected with lentiviral vectors in the presence of 8 µg/mL polybrene. G418 was added to culture media to a final concentration of 0.1 mg/mL or 0.5 mg/mL as indicated 24 hours prior to harvest. 6-week old MPS1 KI male mice were injected with rAA9.2xsup-tRNATyr by IV. 10 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C.

tag: strain

tag: genotype

value: Idua-W401X KI/KI

tag: treat


title: COVID-19 positive case [BQ_ST019_COVID_537_76_S74]


title: COVID-19 positive case [BQ_ST020_COVID_554_56_S54]


title: COVID-19 positive case [BQ_ST017_COVID_553_52_S50]


title: IHT-IP (VWF del4-34)_rep1

value: blood outgrowth endothelial cells (BOECs)


title: Ribo_MsLV_M_Expr2

description: ribosome proteced RNA fragments


title: IHT-IR_rep2

value: Healthy

value: Female


title: IHT-IR_rep1


title: IHT-BP_rep2


title: CTL2

tag: tissue


title: IHT-BP_rep1


title: Ribo_MsLV_M_Ctrl2

description: ribosome proteced RNA fragments

value: untreat


title: COVID-19 positive case [BQ_ST013_COVID_535_1_S1]

tag: group

value: COVID-19 positive case

value: male


title: Ribo_MsLV_M_Expr1

description: ribosome proteced RNA fragments


title: COVID-19 positive case [BQ_ST010_COVID_534_45_S43]

tag: gender


title: Ribo_MsLV_M_Ctrl3

description: ribosome proteced RNA fragments


title: COVID-19 positive case [BQ_ST015_COVID_552_82_S80]

value: female

tag: bmi


title: COVID-19 positive case [BQ_ST024_COVID_540_78_S76]


title: COVID-19 positive case [BQ_ST007_COVID_531_54_S52]


title: COVID-19 positive case [BQ_ST006_COVID_530_61_S59]


title: COVID-19 positive case [BQ_ST005_COVID_529_71_S69]