title: T+N_49F_3

city: Guangzhou

first: An

last: Xiao

state: Guangdong

address: JingXi street

department: Division of Nephrology

institute: Nanfang Hospital

description:
T+N_49F_3_count
Ncls_NRK49F_all sample Matrix_Count.xlsx

data_processing:
The high-quality reads were aligned to the mouse reference genome (mm10) via Hisat2. FeatureCounts was utilized to tally uniquely mapped reads. Differential expression analysis was conducted using the DESeq2 algorithm.
Assembly: An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome(mm10) using HISAT2 2.1.0 and other parameters set as a default.
Supplementary files format and content: Excel(xlsx.) file includes raw count for each sample.

organism: Rattus norvegicus

source_name: kidney

growth_protocol: Cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS). Once cell confluency reached approximately 70%, the cells were subjected to serum starvation in serum-free DMEM/F12 medium for 6 hours prior to drug treatment.

extract_protocol:
Total RNA was extracted from mouse primary TECs or NRK49F employing Trizol reagent (Vazyme) as per the guidelines provided by the manufacturer.RNA quality was assessed on an Agilent 2100 Bioanalyzer(Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China)

treatment_protocol: Ncls was diluted to a final concentration of 20 nM in serum-free DMEM/F12 medium. TECs or NRK49F were pre-incubated in this solution for 2 hours. Subsequently, TGF-β1 was added to achieve a concentration of 5 ng/ml in the medium, and the cells were co-stimulated with Ncls for 24 hours.

value: kidney

value: rat kidney fibroblast cell line

value: Ncls+TGF-β1 cotreated


title: Female Inha Het, corn oil, rep 1

status: Public on Jun 12 2025

type: SRA

city: Clayton

first: Kate

last: Loveland

state: Victoria

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

library_source: transcriptomic

data_processing:
Parsing and base calling performed using Dragen BCLConvert 3.10.11
Data processed using nf-core/rnaseq 3.0.1 pipeline
Assembly: Reference genome: Mus musculus/Ensembl/GRCm39.release-109
Supplementary files format and content: Excel file containing raw counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: Female E15.5 placenta

extract_protocol:
RNA for all samples extracted using the RNeasy mini kit (Qiagen), 25ng of RNA from each sample used for library preparation
Novel RNA-Seq pipeline (version 01/09/2021) developed by the MHTP Genomics facility

treatment_protocol: 500 mg/kg/day of DEHP dissolved in corn oil, or equivalent volume of corn oil, delivered orally to pregnant dams from E12.5-14.5

tag: tissue

value: Female E15.5 placenta

tag: genotype

value: Inha Het

tag: treatment

value: Corn oil


title: T+N_49F_1

country: China

description:
T+N_49F_1_count
Ncls_NRK49F_all sample Matrix_Count.xlsx

tag: cell line

tag: cell type


title: ko2_3

city: Bethesda

first: Ayden

last: Case

state: MD

address: 10 Center Dr

country: USA

institute: NHLBI

description: Library name: ps6201_7

data_processing:
Raw data quality were checked with FastQC (v0.12.1) and summarised with multiqc (v1.20)
Data were merged across lanes with cat
Alignment was performed using STAR (v2.7.11b)
Quantification was performed with featureCounts (subread v2.0.3)
Downstream analysis was performed in R (v4.3) using edgeR (v3.42.4) for filtering, normalisation and statistical analysis
Assembly: mm10
Supplementary files format and content: ptgir_ko_counts.txt contains the raw output from featureCounts
Supplementary files format and content: ptgir_ko_normalised_data.csv contains filtered and TMM-CPM normalised data

molecule: polyA RNA

source_name: Spleen

extract_protocol:
RNA was extracted from activated or non-activated CD4T cells (human or mouse) with the RNAqueous Micro Kit (Invitrogen, # AM1931,) followed by DNase digestion (TURBO DNA-free™ Kit, # AM1907)
RNA was quantified and applied to the TapeStation (Agilen) for quality assessment. RNA was subjected to library preparation using poly(A) mRNA capture (NEB, # E7770 and #E7490) according to manufacturer’s protocol

value: Spleen

tag: stimulation

value: CD4 T cell

value: ko


title: ko2_4

description: Library name: ps6201_8


title: wt0

description: Library name: ps6201_9

value: wt


title: T+N_49F_2

description:
T+N_49F_2_count
Ncls_NRK49F_all sample Matrix_Count.xlsx


title: Male Inha WT, corn oil, rep 1

source_name: Male E15.5 placenta

value: Male E15.5 placenta

value: Inha WT


title: Male Inha WT, corn oil, rep 2


title: AB6589_SB180

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

organism: Homo sapiens

extract_protocol:
Synovial fluid mononuclear cells and blood mononuclear cells were isolated within maximum 4 hours of sample collection. Synovial fluid samples were first filtered by 100-micron strainer into 50 ml tube and diluted 1:1 with ice cold FACS buffer (2mM EDTA, Ph 8.0, 0.5% bovine serum albumin in PBS). Blood samples were diluted 1:1 with ice cold FACS buffer. Synovial fluid and blood mononuclear cell separation was performed using density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with the diluted synovial fluid or blood sample. Centrifugation (460g, 25min) was performed at 10◦C and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After a short centrifuge (360g, 5min), we resuspended the cell pellet in cryopreservation media (FCS+10%DMSO) and stored the samples in cryotube at -80◦C. Prior to single-cell sorting, samples were quickly defrosted at 37◦C bath and washed with heated (37 ◦C) RPMI-1640. We resuspended the cells in FACS buffer for staining and sorting.
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)

tag: gating

tag: diagnosis

value: PsA

value: Synovial fluid (SF)

tag: pid


title: Tgfb_49F_2

description:
Tgfb_49F_2_count
Ncls_NRK49F_all sample Matrix_Count.xlsx

value: TGF-β1 treated


title: EC, 131 WT_Sham, 4 weeks

city: Boston

first: Erin

last: Sanders

state: MA

address: 150 Harrison Ave

institute: Tufts University

description:
Library name: 1_131_Sham
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:1_131_Sham

data_processing:
The resulting reads in fastq format were mapped to the mouse reference genome (UCSC mm10) using HISAT2 (Version2.1.0). The resulting alignment file in BAM format was used as input to generate a raw count matrix using FeatureCounts (Subread package), with USCS mm10 GTF as the annotation. The raw read count matrix was then used as input for downstream analyses using Qlucore Omics Explorer.  The normalization, quantification, different expression analysis, and visualization were all performed using Qlucore Omics Explorer following manufacturer recommendations.
Assembly: mm10
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Heart

extract_protocol:
RNA was extracted using Quigen RNAEasy Plus kit. XXμg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNASeq were prepared using TrueSeq Library Prep kit according the manufacturers instructions.

value: Heart

value: Endothelial Cells

value: WT

value: Sham

tag: batch


title: AB6587_SB180


title: AB6586_SB180


title: ko2_1

description: Library name: ps6201_5


title: wt2_4

description: Library name: ps6201_4


title: Female Inha WT, corn oil, rep 2


title: AB6585_SB180


title: Tgfb_49F_1

description:
Tgfb_49F_1_count
Ncls_NRK49F_all sample Matrix_Count.xlsx

value: kidney

value: rat kidney fibroblast cell line


title: AB6590_SB180


title: Con_49F_3

description:
Con_49F_3_count
Ncls_NRK49F_all sample Matrix_Count.xlsx

value: Control


title: Female Inha WT, corn oil, rep 1

value: Female E15.5 placenta

value: Corn oil


title: AB6584_SB180


title: ko2_2

description: Library name: ps6201_6

value: Spleen

value: CD4 T cell


title: AB6588_SB180


title: Con_49F_2

description:
Con_49F_2_count
Ncls_NRK49F_all sample Matrix_Count.xlsx


title: Male Inha KO, no treatment, rep 3

value: Inha KO


title: Tgfb_49F_3

description:
Tgfb_49F_3_count
Ncls_NRK49F_all sample Matrix_Count.xlsx


title: ko24_4

description: Library name: ps6201_18

value: ko


title: Con_49F_1

description:
Con_49F_1_count
Ncls_NRK49F_all sample Matrix_Count.xlsx


title: Female Inha WT, corn oil, rep 3

value: Inha WT


title: Male Inha KO, no treatment, rep 2

value: Male E15.5 placenta


title: ko24_3

description: Library name: ps6201_17


title: amiR-SYD-2, control, biol rep 2

city: La Jolla

first: Po-Kai

last: Hsu

state: CA

address: 9500 Gilman Dr

department: Cell and Developmental Biology

institute: UC San Diego

description:
Library name: amiR-SYD-2_CTRL2
column name in raw_counts_all_sample.csv: amiR-SYD-2_CTRL2

data_processing:
Low quality reads were processed by Trimmomatic_v0.39 (LEADING:20 TRAILING:20 SLIDINGWINDOW:4:28 MINLEN:30).
Sequencing reads were aligned to the reference genome using STAR (v2.7.10a) with default parameters. Gene-level read counts were generated during the alignment process.
genome build: TAIR10 assembly for Arabidopsis thaliana
processed data files format and content: Comma-Separated Values (CSV) file includes raw counts per gene ID from each sample

organism: Arabidopsis thaliana

source_name: Seed

growth_protocol: Surface-sterilized seeds from each genotype were sown  on ½ MS medium containing either 2 μM (±)-ABA or 0.002% EtOH (control condition). Following a 4 °C treatment in the dark for 3 days, the seeds were germinated under long-day conditions (16-hour light and 8-hour dark)with temperatures ranging from 22°C to 24°C and light intensity ~120 μmol·m-2·s-1 for 24 hrs.

extract_protocol:
Total RNA isolated by the Spectrum Plant Total RNA Kit (Sigma-Aldrich)
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep kit according to the manufacturer’s protocol. Libraries were sequenced as 100 bp paired-end reads on an Illumina NovaSeq 6000 platform.

value: Seed


title: AB6580_SB180

value: PsA

value: Synovial fluid (SF)


title: AB6581_SB180


title: Female Inha KO, no treatment, rep 3


title: Male Inha KO, no treatment, rep 1


title: ko24_1

description: Library name: ps6201_15


title: ko24_2

description: Library name: ps6201_16


title: wt2_3

description: Library name: ps6201_3

value: wt


title: amiR-SYD-2, ABA, biol rep 2

description:
Library name: amiR-SYD-2_ABA2
column name in raw_counts_all_sample.csv: amiR-SYD-2_ABA2

value: 2 μM (±)-ABA, 24hr


title: AB6582_SB180


title: amiR-SYD-2, control, biol rep 1

description:
Library name: amiR-SYD-2_CTRL1
column name in raw_counts_all_sample.csv: amiR-SYD-2_CTRL1


title: AB6579_SB180


title: Female Inha KO, no treatment, rep 1


title: amiR-SYD-2, ABA, biol rep 1

description:
Library name: amiR-SYD-2_ABA1
column name in raw_counts_all_sample.csv: amiR-SYD-2_ABA1


title: Female Inha KO, no treament, rep 2


title: wt24_4

description: Library name: ps6201_14


title: AB6578_SB180


title: wt2_2

description: Library name: ps6201_2


title: AB6583_SB180


title: wt24_2

description: Library name: ps6201_12


title: amiR-SYD-1, control, biol rep 1

description:
Library name: amiR-SYD-1_CTRL1
column name in raw_counts_all_sample.csv: amiR-SYD-1_CTRL1


title: Male Inha WT, no treatment, rep 3


title: AB6576_SB180


title: wt24_3

description: Library name: ps6201_13


title: amiR-SYD-1, control, biol rep 2

description:
Library name: amiR-SYD-1_CTRL2
column name in raw_counts_all_sample.csv: amiR-SYD-1_CTRL2


title: Male Inha WT, no treatment, rep 2


title: wt24_1

description: Library name: ps6201_11


title: amiR-SYD-1, ABA, biol rep 2

description:
Library name: amiR-SYD-1_ABA2
column name in raw_counts_all_sample.csv: amiR-SYD-1_ABA2


title: AB6575_SB180


title: amiR-SYD-1, ABA, biol rep 1

description:
Library name: amiR-SYD-1_ABA1
column name in raw_counts_all_sample.csv: amiR-SYD-1_ABA1


title: ko0

description: Library name: ps6201_10


title: Female Inha WT no treatment, rep 3


title: amiR-HsMYO (WT control), control, biol rep 2

description:
Library name: amiR-HsMYO_CTRL2
column name in raw_counts_all_sample.csv: amiR-HsMYO_CTRL2

value: amiR-HsMYO


title: Female Inha WT no treatment, rep 2


title: wt2_1

description: Library name: ps6201_1


title: AB6573_SB180


title: amiR-HsMYO (WT control), ABA, biol rep 2

description:
Library name: amiR-HsMYO_ABA2
column name in raw_counts_all_sample.csv: amiR-HsMYO_ABA2


title: AB6571_SB180


title: amiR-HsMYO (WT control), control, biol rep 1

description:
Library name: amiR-HsMYO_CTRL1
column name in raw_counts_all_sample.csv: amiR-HsMYO_CTRL1


title: Female Inha WT no treatment, rep 1


title: AB6572_SB180

value: OA


title: Echinococcus multilocularis infected liver, rep3

city: Vienna

first: Manuel

last: Salzmann

address: Lazarettgasse 14

department: Department of Medicine II, Division of Cardiology

country: Austria

institute: Medical University of Vienna

data_processing:
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403) incl. trimming of the sequencing adapters.
Reads in fastq format were aligned to a composite reference genome containing the mouse reference genome version GRCm38 with Gencode mV23 annotations and the Echinococcus multilocularis reference EMULTI002 from WormBase using STAR aligner  version 2.6.1a in 2-pass mode. Raw reads per gene were counted by STAR.
Differential gene expression was analysed using DESeq2 (6) version 1.43.5
Assembly: GRCm38 and EMULTI002
Supplementary files format and content: plain text, raw counts per gene, one file for all samples

source_name: liver

extract_protocol:
RNA was isolated from right middle lung lobe using Maxwell® RSC simplyRNA Tissue Kit (Promega, AS1340) in combination with a ball mill (Retsch)
Sequencing libraries were be prepared at the Core Facility Genomics, Medical University of Vienna, using the NEBNext UltraExpress rRNA Depletion Kit (NEB #E3330) according to manufacturer's protocols. Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen). Pooled libraries were sequenced on a P3 flowcell on a NextSeq2000 instrument (Illumina) in 1x50bp single-end sequencing mode.

treatment_protocol: Oral infection with 1000 E. multilocularis eggs.

value: liver

tag: strain

value: Wild type

value: infected with E. multilocularis


title: AB6577_SB180


title: amiR-HsMYO (WT control), ABA, biol rep 1

description:
Library name: amiR-HsMYO_ABA1
column name in raw_counts_all_sample.csv: amiR-HsMYO_ABA1


title: CUT&RUN for H3K4me3 in N2a cells after transfection with the Bahcc1 OE vector, replicate 2

first: Igor

last: Ulitsky

address: Hertzl St.

library_source: genomic

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples
CUT&RUN: CUT&RUN reads were mapped to the mouse genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, and MACS2/epic2-called peaks are provided for the CUT&RUN data.
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: N2a cells

growth_protocol:
Neuro2a (N2a) cells were cultured in DMEM supplemented with 4.5 g/L of glucose, 4 mM L-Glutamine, 10% FBS, 1% PenStrep solution, grown in incubators maintained at 37°C with 5% CO2, and were routinely passaged by gentle dissociation using a Trypsin (0.05%) – EDTA (0.02%) solution. DNA plasmid transfections were performed by using Lipofectamine 3000 (ThermoFisher Scientific), according to the respective protocols. For each transfection, the optimal DNA concentration and amount of transfection reagents were empirically determined to minimize cellular stress and maximize efficiency, to eventually ensure clean readouts. SiRNAs were transfected using DharmaFECT reagents (DharmaFECT 2), at a final concentration of 25 µM concordantly to the manufacturer’s protocol. GapmeRs were transfected at the final concentration of 50 µM with Lipofectamine 3000, following the manufacturer’s guidelines. In all cases, cells were plated the day before the transfection in an antibiotic-free medium which was subsequently changed prior to adding the transfection mix, and again after 24h to minimize cell death. Finally, transfections were carried out for 72h, unless stated otherwise.
Primary neuronal culture Embryonic cortices (embryonic day 16.5–17) were dissected from 5–6 embryos of mixed sex and pooled for a single replicate culture. Trypsin (0.25%) was used to dissociate tissue through a 10 minutes incubation at 37°C. Digestion was terminated with the addition of ovomucoid (trypsin inhibitor, Worthington). Digested tissue was gently triturated through a P1000 pipette to release cells and passed through a 40 µm filter. After trituration, the cell suspension was transferred to a 15 mL Falcon tube and centrifuged for 5 minutes at RT / 154×g. After centrifugation, the cloudy supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 10 mL DMEM medium and added to uncoated 90 mm Petri dishes. The plates were incubated at 37°C, 5% CO2 humidified incubator for 30 minutes. During this incubation, glial cells and other unwanted debris adhere to the bottom of the plate while cortical cells are retained in the media and recover from the trituration. The supernatant was carefully removed, without disturbing attached glial cells and unwanted cell debris at the bottom of the plate, and moved into a new 15 mL Falcon tube using a pipette. The collected supernatant was then centrifuged for 5 minutes at RT / 154×g. Neurons were plated onto cell culture dishes pre-coated overnight with poly-d-lysine (20 µg/mL) and laminin (4 µg/mL) and were grown in neurobasal medium (Gibco) containing B27 supplement (2%), 1% PenStrep solution and glutaMAX (1 mM). Neurons were grown in incubators maintained at 37°C with a CO2 concentration of 5%. GapmeRs for unassisted uptake were added directly to the culture medium at a final concentration of 500 nM.

extract_protocol:
CUT&RUN reactions were performed as previously described (Meers et al., 2019), with the addition of 20mM sodium butyrate when profiling BAHCC1, SIN3A and H3K27ac
RNA-seq libraries were prepared using the CORALL mRNA-Seq Kit V2 (Lexogen), following the manufacturer’s instructions. CUT&RUN libraries were prepared as described previously (Meers et al., 2019)

treatment_protocol: Sodium Butyrate (Sigma) was diluted in sterile H2O at a stock concentration of 1M and added to the cell culture media at a final concentration of 5µM. As a control, cells were supplemented with an equal volume of H2O. All treatments were performed for 24h in order to minimize indirect effects due to the extensive inhibition of deacetylation. Retinoic Acid (Sigma) was diluted in DMSO at a stock concentration of 0.01M, and added to a complete media with reduced (1%) serum concentration at a final concentration of 10µM, with equal volumes of DMSO serving as vehicle controls. After three days of treatment, cells were transfected with GapmeRs as previously described, and incubated for three additional days in the retinoic acid medium.

value: N2a cells

tag: cut&run antibody

value: untreated


title: W-10-F-4-RVL

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description: RNA-seq from tissue punches of brainstem regions

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

data_processing: Total count normalization was calculated so that the the ith miRNA in the jth sample was calculated as: expij= (Countij/TotalCountj) * 100,000  where Countij is the raw count for a given ith miRNA in jth sample and TotalCountj represents the sum of counts for all endogenous miRNAs in the jth sample while 100,000 is a normalization factor. Data was log2 normalized and low abundance miRNAs were filtered out using the negative controls as a minimum threshold. miRNAs were filtered out if more than 25% of samples had a normalized expression level of 4.5 or lower.

source_name: RVL of 10 weeks WKY rat rep4

label_protocol: Nanostring protocol

extract_protocol: Brainstems were frozen in OCT and sectioned at 200um. Three regions of the brainstem, the NTS, CVLM, and RVLM were extracted with a micropunch and total RNA from each sample was extracted using Zymo Direct-Zol micropep kit

tag: Sex

value: Female

value: RVLM of brainsstem

value: WKY

tag: age

value: 10 weeks

tag: region

value: RVLM


title: Echinococcus multilocularis infected liver, rep1


title: AB6569_SB180


title: CUT&RUN for H3K4me3 in N2a cells after transfection with the EV, replicate 3 (Bahcc1 OE control)


title: Echinococcus multilocularis infected liver, rep2


title: W-10-F-3-RVL

source_name: RVL of 10 weeks WKY rat rep3


title: CUT&RUN for H3K4me3 in N2a cells after transfection with the Bahcc1 OE vector, replicate 3


title: CUT&RUN for H3K4me3 in N2a cells after transfection with the Bahcc1 OE vector, replicate 1


title: AB6570_SB180


title: AB6568_SB180


title: Male Inha WT, no treatment, rep 1

value: Male E15.5 placenta

value: Inha WT


title: CUT&RUN for H3K4me3 in N2a cells after transfection with the EV, replicate 1 (Bahcc1 OE control)


title: Not infected control liver, rep3

value: untreated controls


title: AB6574_SB180

value: PsA

value: Synovial fluid (SF)


title: CUT&RUN for H3K4me3 in N2a cells after transfection with the EV, replicate 2 (Bahcc1 OE control)


title: W-10-F-2-RVL

source_name: RVL of 10 weeks WKY rat rep2


title: Not infected control liver, rep2


title: W-10-F-1-RVL

source_name: RVL of 10 weeks WKY rat rep1


title: CUT&RUN for H3K27ac in N2a cells after transfection with the Bahcc1 OE vector, replicate 3


title: AB6567_SB180


title: AB6566_SB180


title: Not infected control liver, rep1


title: AB6565_SB180


title: CUT&RUN for H3K27ac in N2a cells after transfection with the Bahcc1 OE vector, replicate 2


title: CUT&RUN for H3K27ac in N2a cells after transfection with the Bahcc1 OE vector, replicate 1


title: W-08-F-5-RVL

source_name: RVL of 8 weeks WKY rat rep4

value: 8 weeks


title: W-08-F-4-RVL

source_name: RVL of 8 weeks WKY rat rep3


title: pol III inhibitor + biol rep3

first: Katherine

last: McJunkin

state: Maryland

address: 50 South Dr

institute: NIDDK/ NIH

description: Library name: sRT28

data_processing:
Libraries were adaptor trimmed then de-multiplexed with CutAdapt 5.0. UMIs were trimmed with UMI-tools 11.5 before mapping to Homo_sapiens_NCBI_GRCh38 genome using Bowtie2 2.5.3. The resulting bam files were sorted and indexed using samtools 1.21. Reads were assigned to miRNAs using htseq 2.04. Analysis of miRNA expression was performed with DEseq2 including spike-in size factors.
Assembly: Homo_sapiens_NCBI_GRCh38
Supplementary files format and content: Excel
Supplementary files format and content: counts

source_name: RKO

growth_protocol: RPMI 1640 (Gibco) supplemented with 10% FBS, L-glutamine (4 mM), sodium pyruvate (1 mM) and penicillin/streptomycin (100 U ml−1/100 μg ml−1). 37C w/ 5% CO2

extract_protocol:
cell pellets were re-suspended in Trizol (Fischer Scientific) then immediately frozen in dry ice and stored in -80C until extraction. Once all samples were collected, then RNA extraction was performed with manufacturer instructions with the modification of supplementing isopropanol and 80% ethanol with 0.2mM DTT. Finally, purified RNA was resuspended in water supplemented with 0.1Mm DTT.
Small RNA libraries were prepped as described previously with minor modifications.2-3 Briefly, total RNA was mixed with spike-ins. smRNAs were enriched using the RNA Clean and Concentrator kit 5 (Zymo Research) before ligation to 3’ barcoded linker DNA. To minimize ligation bias, linkers contain degenerate bases at the 5’ or 3’ end and are performed overnight at 4ºC. Ligation products were pooled appropriately based on their barcode then purified via precipitation. Pooled ligation products were mixed with RNA loading dye (Thermo Fisher Scientific) at a 1:1 ratio then boiled at 95ºC for 5 minutes before being loaded on to a 15% Urea- polyacrylamide gel. As a reference, 18-mer and 30-mer long RNAs were also ligated to a 3’ linker thus allowing 18 – 30nt long RNA to be excised from each pooled sample. Excised gels were eluted, purified via precipitation, then subjected to 5’ linker ligation overnight at 4 ºC. Ligated products were purified using the RNA Clean and Concentrator 5 kit (Zymo Research) before subjection to reverse transcription (RT) using SuperScript III (Invitrogen). RT products were PCR amplified with KAPA HIFI HotStart Readymix (Roche) supplemented with 1uM Evagreen (Biotium) using 2.5uM NEBNEXT Multiplex Oligos for Illumina dual barcodes (NEB). Samples were monitored so that the PCR reaction can be terminated before overamplification. PCR products were loaded onto a 3% low melt agarose gel, then were excised and subjected to purification using Zymoclean Gel DNA Recovery kit (Zymo Research). Library preps were pooled then sequenced on NEBNext 2000 with 60 single end settings.

value: RKO

value: 24 hour Pol III inhibitor


title: pol III inhibitor + biol rep2

description: Library name: sRT27


title: CUT&RUN for H3K27ac in N2a cells after transfection with the EV, replicate 2 (Bahcc1 OE control)


title: pol III DMSO control biol rep3

description: Library name: sRT23

value: 24 hour DMSO


title: pol III inhibitor + biol rep1

description: Library name: sRT25


title: CUT&RUN for H3K27ac in N2a cells after transfection with the EV, replicate 3 (Bahcc1 OE control)


title: AB6563_SB180


title: S-10-F-4-RVL

source_name: RVL of 10 weeks SHR rat rep4

value: SHR


title: S-10-F-5-RVL

source_name: RVL of 10 weeks SHR rat rep5


title: AB6562_SB180


title: S-10-F-3-RVL

source_name: RVL of 10 weeks SHR rat rep3


title: CUT&RUN for SIN3A in N2a cells after transfection with control siRNAs, replicate 3

value: N2a cells

value: SIN3A (abcam, ab3479)


title: AB6550_SB180


title: pol III DMSO control biol rep1

description: Library name: sRT21


title: CUT&RUN for SIN3A in N2a cells after transfection with control siRNAs, replicate 2

value: untreated


title: W-08-F-6-RVL

source_name: RVL of 8 weeks WKY rat rep5

value: Female

value: RVLM of brainsstem


title: AB6549_SB180


title: CUT&RUN for SIN3A in N2a cells after transfection with control siRNAs, replicate 1


title: DGCR8-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 4

description: Library name: sRT20

value: iCas9, DGCR8 -/-

value: 4 day Doxycyclin


title: S-10-F-2-RVL

source_name: RVL of 10 weeks SHR rat rep2

value: 10 weeks

value: RVLM


title: DGCR8-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 3

description: Library name: sRT19


title: CUT&RUN for H3K27me3 in N2a cells after transfection with control siRNAs, replicate 2


title: AB6564_SB180


title: CUT&RUN for H3K27ac in N2a cells after transfection with the EV, replicate 1 (Bahcc1 OE control)


title: W-10-F-3-CVL

source_name: CVL of 10 weeks WKY rat rep3

value: CVLM of brainsstem

value: WKY

value: NTS


title: DGCR8-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 2

description: Library name: sRT18


title: pol III DMSO control biol rep2

description: Library name: sRT22


title: W-10-F-2-CVL

source_name: CVL of 10 weeks WKY rat rep2


title: DGCR8-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 1

description: Library name: sRT17


title: W-10-F-4-CVL

source_name: CVL of 10 weeks WKY rat rep4


title: AB6547_SB180

value: PsA

value: Synovial fluid (SF)


title: AB6561_SB180


title: CUT&RUN for H3K27me3 in N2a cells after transfection with siRNAs targeting Bahcc1, replicate 2


title: Dicer-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 4

description: Library name: sRT16

value: RKO

value: iCas9,Dicer -/-


title: Dicer-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 3

description: Library name: sRT15


title: W-10-F-1-CVL

source_name: CVL of 10 weeks WKY rat rep1


title: S-10-F-1-RVL

source_name: RVL of 10 weeks SHR rat rep1

value: SHR


title: AB6544_SB180


title: W-08-F-5-CVL

source_name: CVL of 8 weeks WKY rat rep4

value: 8 weeks


title: AB6543_SB180


title: AB6548_SB180


title: W-08-F-6-CVL

source_name: CVL of 8 weeks WKY rat rep5


title: CUT&RUN for H3K4me3 in N2a cells after transfection with control siRNAs, replicate 1

source_name: N2a cells

value: N2a cells


title: Dicer-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 1

description: Library name: sRT13


title: CUT&RUN for H3K27me3 in N2a cells after transfection with control siRNAs, replicate 1

value: untreated


title: CUT&RUN for H3K4me3 in N2a cells after transfection with siRNAs targeting Bahcc1, replicate 2


title: AB6545_SB180


title: W-08-F-4-CVL

source_name: CVL of 8 weeks WKY rat rep3

value: Female


title: AB6542_SB180


title: AB6541_SB180


title: wildtype + doxycycline for 4 days biol rep 4

description: Library name: sRT12


title: AB6540_SB180


title: wildtype + doxycycline for 4 days biol rep 3

description: Library name: sRT11


title: S-10-F-5-CVL

source_name: CVL of 10 weeks SHR rat rep5

value: CVLM


title: CUT&RUN for H3K27ac in N2a cells after transfection with control siRNAs, replicate 2


title: CUT&RUN for H3K4me3 in N2a cells after transfection with siRNAs targeting Bahcc1, replicate 1


title: S-10-F-4-CVL

source_name: CVL of 10 weeks SHR rat rep4


title: Dicer-mCherry-Puro dgRNA transducted cells + Doxycycline for 4 days biol rep 2

description: Library name: sRT14

source_name: RKO


title: AB6539_SB180


title: S-10-F-3-CVL

source_name: CVL of 10 weeks SHR rat rep3


title: CUT&RUN for H3K27ac in N2a cells after transfection with control siRNAs, replicate 1


title: wildtype + doxycycline for 4 days biol rep 2

description: Library name: sRT10


title: AB6538_SB180


title: CUT&RUN for H3K27ac in N2a cells after transfection with siRNAs targeting Bahcc1, replicate 2


title: S-10-F-2-CVL

source_name: CVL of 10 weeks SHR rat rep2


title: AB6537_SB180


title: Unexposed, CD13-EGFP-, donor 0801

city: Utrecht

first: Carla

last: Pou Casellas

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
FASTQ files were mapped using STAR mapping software
Readcounts were assigned using FeatureCounts
Assembly: hg38
Supplementary files format and content: The processed data file infection_readcounts_raw.csv contains read counts for all conditions

source_name: Tissue-derived SMG organoids

extract_protocol:
Transwell cultures were washed with DPBS and digested with TrypLE (Thermo Fisher Scientific) for 15 minutes, achieving single-cell suspensions through repeated pipetting. The cells were resuspended in culture medium supplemented with Y-27632 dihydrochloride (10 µM, Abmole Bioscience) and stained with CD13-APC antibody (1:250, BioLegend) for 20 minutes at 4 °C. Subsequently, the cells were washed, stained with DAPI (Sigma-Aldrich), and filtered through a cell strainer (Falcon) for sorting.Cells were sorted into 500 µL of TRIzol (Thermo Fisher Scientific) using different gating settings. A range of 25,000 to 150,000 cells were collected and subjected to RNA isolation. For library preparation of bulk RNA sequencing, a minimum of 100 ng of total RNA per condition was utilized.
Library construction was performed by USEQ (Utrecht, the Netherlands) using a TruSeq Stranded mRNA library kit

treatment_protocol: Human SMG organoids were dissociated into single cells and plated on coated transwells. After 7-10 days of continuous medium replenishment, upon cell confluency, the medium in the upper transwell chambers was replaced with DPBS (Thermo Fisher Scientific). On Day 21-28, the transwell cultures were exposed to hCoV-229E-EGFP for 16 hours.

value: Tissue-derived SMG organoids

value: CD13- cells

tag: donor

value: Unexposed to CoV-229E-EGFP


title: CUT&RUN for H3K27ac in N2a cells after transfection with siRNAs targeting Bahcc1, replicate 1


title: S-10-F-1-CVL

source_name: CVL of 10 weeks SHR rat rep1

value: 10 weeks


title: Unexposed, CD13+EGFP-, donor 0801

value: CD13+ cells


title: AB6536_SB180


title: S-24-F-6-RVL

source_name: RVL of 24 weeks SHR rat rep6

value: RVLM of brainsstem

value: 24 weeks

value: RVLM


title: AB6535_SB180

value: PsA

value: Synovial fluid (SF)


title: S-24-F-6-NTS

source_name: NTS of 24 week SHR rat rep6

value: NTS of brainstem

value: NTS


title: CUT&RUN for H3K4me3 in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 3


title: AB6534_SB180


title: Exposed, CD13+EGFP-, donor 0801

value: Exposed to CoV-229E-EGFP


title: wildtype + doxycycline for 4 days biol rep 1

description: Library name: sRT9

value: RKO

value: 4 day Doxycyclin


title: CUT&RUN for H3K4me3 in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 2

value: N2a cells

value: untreated


title: CUT&RUN for H3K4me3 in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 1


title: Exposed, CD13+EGFP+, donor 0801

value: Tissue-derived SMG organoids


title: AB6533_SB180


title: S-12-F-6-RVL

source_name: RVL of 12 weeks SHR rat rep6

value: Female

value: SHR

value: 12 weeks


title: S-24-F-6-CVL

source_name: CVL of 24 weeks SHR rat rep6

value: CVLM of brainsstem

value: CVLM


title: Exposed, CD13-EGFP-, donor 0801

value: CD13- cells


title: CUT&RUN for H3K4me3 in N2a cells after transfection with control GapmeRs, replicate 3


title: Unexposed, CD13-EGFP-, donor 0620

value: Unexposed to CoV-229E-EGFP


title: CUT&RUN for H3K4me3 in N2a cells after transfection with control GapmeRs, replicate 1


title: S-12-F-6-NTS

source_name: NTS of 12 week SHR rat rep6


title: Mammary tumor, MMTV-PyMT, rep 13

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

country: United Kingdom

institute: CRUK Scotland Institute

description: Library name: CCR20190325_S13_CC25_11_1e

data_processing:
Quality Control with FastQC and FastQ Screen. Aligned to genome with version 2.1 of HiSat2 and sorted with Samtools version 1.2 using code following the format of `hisat2 -x path/to/index_hisat2/ --known-splicesite-infile path/to/mouse_38.95_splice_sites.txt --rna-strandness RF -1 path/to/{read1} -2 path/to/{read2} | samtools sort -o path/to/{samplename}.bam`. Counts tables for each bam file produced with version 0.11.2 of HTSeq Count. Format of code `htseq-count /path/to/{sample name}.bam -s reverse --mode=intersection-nonempty --type=exon --idattr=gene_id -f bam /path/to/Mus_musculus_GeneAnnot.GRCh38.95.gtf '>' tables/{sample name}.tsv`. Individual tables merged using base Linux commands.
Assembly: Ensemble 38.95 Mus Musculus.
Supplementary files format and content: raw_count_table.tsv file is a tab separated flat text file table of the counts for each sample of the Ensembl IDs.

source_name: Mammary

extract_protocol:
RNA was prepared from ~25mg of frozen tissue using Trizol (ThermoFisher) as per manufacturer instructions. For PyMT+ cell lines, cells lines were previously generated by Gounis et al., (Gounis et al, 2024), and plated at 0.5x106 - 1x106 cells per 10cm dish, 37°C/5% CO2 for 24 hours to achieve 80% confluence the next day. Cells were washed twice in ice-cold PBS, lysed into 1mL Trizol, and RNA prepped as manufacturer instructions.
Illumina TruSeq RNA Library Prep kit v2

value: Mammary


title: CUT&RUN for H3K27ac in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 3


title: Unexposed, CD13+EGFP-, donor 0620

value: CD13+ cells


title: S-12-F-6-CVL

source_name: CVL of 12 weeks SHR rat rep6


title: AB5989_SB176

value: OA

value: Synovial fluid (SF)


title: CUT&RUN for H3K27ac in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 2


title: W-10-F-4-NTS

source_name: NTS of 10 week WKY rat rep4

value: NTS of brainstem

value: WKY

value: 10 1eeks

value: NTS


title: AB5988_SB176


title: CUT&RUN for H3K27ac in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 1

source_name: N2a cells

value: N2a cells

value: untreated


title: W-10-F-3-NTS

source_name: NTS of 10 week WKY rat rep3

value: Female


title: Exposed, CD13+EGFP-, donor 0620

value: Tissue-derived SMG organoids

value: Exposed to CoV-229E-EGFP


title: AB5986_SB176


title: W-10-F-2-NTS

source_name: NTS of 10 week WKY rat rep2


title: AB6531_SB180

value: PsA


title: W-10-F-1-NTS

source_name: NTS of 10 week WKY rat rep1


title: W-08-F-6-NTS

source_name: NTS of 8 week WKY rat rep5

value: 8 weeks


title: Exposed, CD13+EGFP+, donor 0620


title: AB6532_SB180


title: AB5985_SB176


title: AB5984_SB176


title: CUT&RUN for H3K27ac in N2a cells after transfection with control GapmeRs, replicate 2


title: CUT&RUN for H3K27ac in N2a cells after transfection with control GapmeRs, replicate 1


title: Unexposed, CD13-EGFP-, donor 0523

value: CD13- cells


title: W-08-F-5-NTS

source_name: NTS of 8 week WKY rat rep4


title: CUT&RUN for H3K27ac in N2a cells after transfection with control GapmeRs, replicate 3


title: Unexposed, CD13+EGFP-, donor 0523

value: Unexposed to CoV-229E-EGFP


title: AB5981_SB176


title: AB5980_SB176


title: Exposed, CD13-EGFP-, donor 0523


title: CUT&RUN for BAHCC1 in N2a cells, replicate 4

value: BAHCC1 (this study)


title: Exposed, CD13-EGFP-, donor 0620


title: W-08-F-4-NTS

source_name: NTS of 8 week WKY rat rep3


title: CUT&RUN for BAHCC1 in N2a cells, replicate 3


title: Exposed, CD13+EGFP-, donor 0523

source_name: Tissue-derived SMG organoids

value: CD13+ cells


title: AB5979_SB176


title: Exposed, CD13+EGFP+, donor 0523


title: S-10-F-5-NTS

source_name: NTS of 10 week SHR rat rep5

value: SHR

value: 10 weeks


title: CUT&RUN for BAHCC1 in N2a cells, replicate 2


title: AB5978_SB176

value: Synovial fluid (SF)


title: CUT&RUN for BAHCC1 in N2a cells, replicate 1


title: CD13+, TNFa, rep2

data_processing:
FASTQ files were mapped using STAR mapping software
Readcounts were assigned using FeatureCounts
Assembly: hg38
Supplementary files format and content: The processed data file cytokines_readcounts_raw.csv contains read counts for all conditions

extract_protocol:
Organoids were removed from BME (R&D Systems) and digested with TrypLE (Thermo Fisher Scientific) for 5 minutes to dissociate them into single cells using glass Pasteur pipettes. After washing with ice-cold AdDMEM/F12 (Thermo Fisher Scientific), the cells were resuspended in culture medium supplemented with Y-27632 dihydrochloride (10 µM, Abmole Bioscience) and stained with CD13-APC antibody (1:250, BioLegend) for 20 minutes at 4 °C. Subsequently, the cells were washed, stained with DAPI (Sigma-Aldrich), and filtered through a cell strainer (Falcon) for sorting. Cells were sorted into 500 µL of TRIzol (Thermo Fisher Scientific) using different gating settings. A range of 25,000 to 150,000 cells were collected and subjected to RNA isolation. For library preparation of bulk RNA sequencing, a minimum of 100 ng of total RNA per condition was utilized.
Library construction was performed by USEQ (Utrecht, the Netherlands) using a TruSeq Stranded mRNA library kit

treatment_protocol: SMG organoids were treated with either IL-1B, IL-13, or TNFa (all at 10 ng/mL) for 7 days

value: TNFa


title: AB5977_SB176


title: CD13+, TNFa, rep1


title: CUT&RUN for BAHCC1 in N2a cells after transfection with the Bahcc1 OE vector, replicate 2


title: S-10-F-3-NTS

source_name: NTS of 10 week SHR rat rep3

value: NTS of brainstem


title: S-10-F-1-NTS

source_name: NTS of 10 week SHR rat rep1

value: NTS


title: CUT&RUN for BAHCC1 in N2a cells after transfection with the Bahcc1 OE vector, replicate 1

value: N2a cells


title: CD13-, TNFa, rep2


title: W-24-F-3-CVL

source_name: CVL of 24 weeks WKY rat rep3

value: CVLM of brainsstem

value: WKY

value: 24 weeks


title: CUT&RUN for HA in N2a cells after transfection with the Bahcc1 OE vector, replicate 3

value: HA (BioLegend, #901514)

value: untreated


title: AB5974_SB176

value: PsA


title: AB5975_SB176


title: W-24-F-2-CVL

source_name: CVL of 24 weeks WKY rat rep2

value: Female


title: CD13-, TNFa, rep1

value: Tissue-derived SMG organoids

value: CD13- cells


title: CUT&RUN for HA in N2a cells after transfection with the Bahcc1 OE vector, replicate 2


title: AB5973_SB176


title: CD13+, IL-13, rep2

value: CD13+ cells


title: AB6546_SB180


title: CUT&RUN for HA in N2a cells after transfection with the Bahcc1 OE vector, replicate 1


title: W-16-F-3-CVL

source_name: CVL of 16 weeks WKY rat rep3

value: 16 weeks


title: CD13-, IL-13, rep2


title: RNA-seq in N2a cells after H2O treatment, replicate 3

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples
CUT&RUN: CUT&RUN reads were mapped to the mouse genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, and MACS2/epic2-called peaks are provided for the CUT&RUN data.


title: S-10-F-4-NTS

source_name: NTS of 10 week SHR rat rep4

value: SHR

value: 10 weeks


title: W-16-F-2-CVL

source_name: CVL of 16 weeks WKY rat rep2


title: AB5972_SB176

value: Synovial fluid (SF)


title: AB5971_SB176


title: AB5976_SB176


title: W-16-F-1-CVL

source_name: CVL of 16 weeks WKY rat rep1


title: AB5970_SB176


title: RNA-seq in N2a cells after H2O treatment, replicate 2

source_name: N2a cells


title: CD13+, IL-1B, rep2


title: W-12-F-3-CVL

source_name: CVL of 12 weeks WKY rat rep3

value: 12 weeks


title: RNA-seq in N2a cells after H2O treatment, replicate 1


title: CD13-, IL-13, rep1


title: W-12-F-2-CVL

source_name: CVL of 12 weeks WKY rat rep2

value: NTS


title: CD13+, IL-1B, rep1


title: AB5968_SB176


title: RNA-seq in N2a cells after NaB treatment, replicate 2

value: N2a cells

value: Sodium Butyrate


title: CD13+, IL-13, rep1


title: CD13-, IL-1B, rep2


title: AB5969_SB176


title: S-16-F-6-CVL

source_name: CVL of 16 weeks SHR rat rep6

value: CVLM of brainsstem

value: CVLM


title: AB5967_SB176


title: CD13-, IL-1B, rep1


title: S-16-F-5-CVL

source_name: CVL of 16 weeks SHR rat rep5


title: RNA-seq in N2a cells after NaB treatment, replicate 1


title: AB5966_SB176


title: CUT&RUN for H3K27me3 in N2a cells after transfection with siRNAs targeting Bahcc1, replicate 1


title: S-16-F-4-CVL

source_name: CVL of 16 weeks SHR rat rep4


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 3 (siHdac1/siSin3b experiment)


title: AB5965_SB176


title: CD13+, Control, rep1

value: Untreated


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 2 (siHdac1/siSin3b experiment)

value: untreated


title: S-16-F-3-CVL

source_name: CVL of 16 weeks SHR rat rep3


title: CD13+, Control, rep2

source_name: Tissue-derived SMG organoids


title: S-16-F-1-CVL

source_name: CVL of 16 weeks SHR rat rep1


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 1 (siHdac1/siSin3b experiment)


title: CD13-, Control, rep1


title: AB5964_SB176

value: PsA


title: RNA-seq in N2a cells after NaB treatment, replicate 3


title: CD13-, Control, rep2


title: AB5963_SB176


title: RNA-seq in N2a cells after transfection with siRNAs against Sin3b, replicate 3


title: RNA-seq in N2a cells after transfection with siRNAs against Sin3b, replicate 1


title: W-08-F-3-CVL

source_name: CVL of 8 weeks WKY rat rep2

value: Female

value: WKY

value: 8 weeks


title: AB5961_SB176


title: RNA-seq in N2a cells after transfection with siRNAs against Sin3b, replicate 2


title: S-12-F-4-CVL

source_name: CVL of 12 weeks SHR rat rep4


title: W-08-F-2-CVL

source_name: CVL of 8 weeks WKY rat rep1


title: AB5960_SB176


title: RNA-seq in N2a cells after transfection with siRNAs against Hdac1, replicate 3


title: AB5958_SB176


title: S-12-F-3-CVL

source_name: CVL of 12 weeks SHR rat rep3


title: LC_40

city: Hong Kong

first: Mengsu

last: Yang

address: City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Kowloon

country: Hong Kong

institute: City University of Hong Kong

description: plasma miRNA profiling in HCC patients and LC patients

hyb_protocol: Hybridization was performed following the miRNA Complete Labeling & Hybridization Kit (Agilent Technologies).

scan_protocol: The arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version 10.7.1.1, Agilent Technologies) was used to extract the data from the scanned images. The raw data was normalized with the quantile algorithm.

source_name: Human plasma

label_protocol: Labelling was performed following the miRNA Complete Labeling & Hybridization Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from 400 µl plasma using mirVana miRNA Isolation Kit (Thermo Scientific) following the manufacturer’s instructions.

value: plasma

tag: disease state

value: liver cirrhosis


title: LC_39

tag: tissue


title: RNA-seq in N2a cells after transfection with siRNAs against Hdac1, replicate 1


title: W-12-F-1-CVL

source_name: CVL of 12 weeks WKY rat rep1


title: AB5957_SB176


title: S-12-F-1-CVL

source_name: CVL of 12 weeks SHR rat rep1

value: SHR


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 3 (siSin3a/siFam60a experiment)


title: AB5962_SB176


title: AB5956_SB176


title: S-08-F-5-CVL

source_name: CVL of 8 weeks SHR rat rep5

value: 10 weeks


title: LC_37


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 2 (siSin3a/siFam60a experiment)

source_name: N2a cells


title: LC_36


title: AB5955_SB176

value: Synovial fluid (SF)


title: LC_35


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 1 (siSin3a/siFam60a experiment)


title: AB5959_SB176


title: LC_34


title: RNA-seq in N2a cells after transfection with siRNAs against Hdac1, replicate 2


title: S-08-F-3-CVL

source_name: CVL of 8 weeks SHR rat rep3


title: RNA-seq in N2a cells after transfection with siRNAs against Fam60a, replicate 3


title: LC_38


title: S-12-F-2-CVL

source_name: CVL of 12 weeks SHR rat rep2

value: 12 weeks


title: AB5954_SB176


title: AB5953_SB176


title: CUT&RUN for H3K4me3 in N2a cells after transfection with control siRNAs, replicate 2


title: AB5952_SB176


title: LC_33


title: S-08-F-2-CVL

source_name: CVL of 8 weeks SHR rat rep2


title: LC_32


title: RNA-seq in N2a cells after transfection with siRNAs against Fam60a, replicate 2


title: LC_31


title: S-08-F-1-CVL

source_name: CVL of 8 weeks SHR rat rep1


title: RNA-seq in N2a cells after transfection with siRNAs against Fam60a, replicate 1


title: RNA-seq in N2a cells after transfection with siRNAs against Sin3a, replicate 3


title: AB5951_SB176


title: LC_30


title: AB5950_SB176


title: W-24-F-2-RVL

source_name: RVL of 24 weeks WKY rat rep2

value: RVLM of brainsstem

value: 24 weeks

value: RVLM


title: S-08-F-4-CVL

source_name: CVL of 8 weeks SHR rat rep4

value: CVLM of brainsstem


title: AB5949_SB176


title: RNA-seq in N2a cells after transfection with siRNAs against Sin3a, replicate 1

value: N2a cells


title: LC_29


title: AB5895_SB175

value: OA


title: W-24-F-1-RVL

source_name: RVL of 24 weeks WKY rat rep1


title: LC_27


title: RNA-seq in N2a cells after transfection with the Reno1 OE vector, replicate 3

value: untreated


title: AB5894_SB175

value: PsA


title: W-24-F-1-CVL

source_name: CVL of 24 weeks WKY rat rep1

value: Female

value: NTS


title: LC_26


title: RNA-seq in N2a cells after transfection with the Reno1 OE vector, replicate 2


title: AB5893_SB175


title: RNA-seq in N2a cells after transfection with the Reno1 OE vector, replicate 1


title: RNA-seq in N2a cells after transfection with the EV, replicate 3 (Reno1 OE control)


title: W-24-F-3-RVL

source_name: RVL of 24 weeks WKY rat rep3

value: WKY


title: S-24-F-5-RVL

source_name: RVL of 24 weeks SHR rat rep5


title: AB5892_SB175


title: S-24-F-4-RVL

source_name: RVL of 24 weeks SHR rat rep4


title: RNA-seq in N2a cells after transfection with siRNAs against Sin3a, replicate 2


title: S-24-F-4-CVL

source_name: CVL of 24 weeks SHR rat rep4

value: CVLM


title: S-24-F-3-RVL

source_name: RVL of 24 weeks SHR rat rep3


title: LC_24

source_name: Human plasma

value: plasma

value: liver cirrhosis


title: AB5891_SB175


title: AB5890_SB175


title: RNA-seq in N2a cells after transfection with the EV, replicate 2 (Reno1 OE control)


title: LC_28


title: S-24-F-3-CVL

source_name: CVL of 24 weeks SHR rat rep3

value: SHR


title: RNA-seq in N2a cells after transfection with the EV, replicate 1 (Reno1 OE control)


title: AB5889_SB175

value: Synovial fluid (SF)


title: RNA-seq in N2a cells after transfection with the Bahcc1 OE vector, replicate 3


title: LC_22


title: S-24-F-2-CVL

source_name: CVL of 24 weeks SHR rat rep2


title: LC_21


title: AB5888_SB175


title: RNA-seq in N2a cells after transfection with the Bahcc1 OE vector, replicate 2

source_name: N2a cells


title: LC_25


title: LC_20


title: AB5887_SB175


title: LC_19


title: LC_23


title: LC_18


title: RNA-seq in N2a cells after transfection with the EV, replicate 3 (Bahcc1 OE control)


title: AB5886_SB175


title: W-16-F-2-RVL

source_name: RVL of 16 weeks WKY rat rep2

value: 16 weeks


title: W-16-F-3-RVL

source_name: RVL of 16 weeks WKY rat rep3

value: RVLM of brainsstem


title: RNA-seq in N2a cells after transfection with the EV, replicate 2 (Bahcc1 OE control)


title: AB5885_SB175


title: W-08-F-3-RVL

source_name: RVL of 8 weeks WKY rat rep2

value: 8 weeks


title: AB5747_SB174


title: W-08-F-2-RVL

source_name: RVL of 8 weeks WKY rat rep1

value: RVLM


title: RNA-seq in N2a cells after transfection with the EV, replicate 1 (Bahcc1 OE control)


title: AB5746_SB174


title: RNA-seq in differentiated N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 3

value: Retinoic Acid


title: LC_16


title: S-24-F-1-CVL

source_name: CVL of 24 weeks SHR rat rep1

value: CVLM of brainsstem

value: 24 weeks


title: S-24-F-2-RVL

source_name: RVL of 24 weeks SHR rat rep2


title: AB5745_SB174


title: S-24-F-1-RVL

source_name: RVL of 24 weeks SHR rat rep1


title: AB5744_SB174


title: LC_14


title: RNA-seq in differentiated N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 2

value: N2a cells


title: RNA-seq in differentiated N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 1


title: RNA-seq in N2a cells after transfection with the Bahcc1 OE vector, replicate 1

value: untreated


title: S-16-F-6-RVL

source_name: RVL of 16 weeks SHR rat rep6

value: Female


title: AB5743_SB174

value: PsA


title: RNA-seq in differentiated N2a cells after transfection with control GapmeRs, replicate 3


title: RNA-seq in differentiated N2a cells after transfection with control GapmeRs, replicate 2


title: LC_13


title: LC_12


title: AB5742_SB174


title: S-08-F-5-RVL

source_name: RVL of 8 weeks SHR rat rep5


title: LC_17


title: S-08-F-4-RVL

source_name: RVL of 8 weeks SHR rat rep4


title: LC_11


title: AB5741_SB174


title: RNA-seq in differentiated N2a cells after transfection with control GapmeRs, replicate 1


title: S-08-F-3-RVL

source_name: RVL of 8 weeks SHR rat rep3


title: LC_15


title: AB5740_SB174


title: RNA-seq in N2a cells after transfection with control GapmeRs and DMSO, replicate 3

value: DMSO


title: W-24-F-3-NTS

source_name: NTS of 24 week WKY rat rep3

value: NTS of brainstem

value: WKY

value: 24 1eeks

value: NTS


title: LC_08

value: plasma

value: liver cirrhosis


title: S-08-F-2-RVL

source_name: RVL of 8 weeks SHR rat rep2

value: RVLM of brainsstem

value: SHR


title: LC_09

source_name: Human plasma


title: AB5739_SB174

value: Synovial fluid (SF)


title: AB5738_SB174


title: RNA-seq in N2a cells after transfection with control GapmeRs and DMSO, replicate 1


title: W-24-F-2-NTS

source_name: NTS of 24 week WKY rat rep2


title: AB5737_SB174


title: LC_07


title: RNA-seq in N2a cells after transfection with control GapmeRs, replicate 3


title: LC_10


title: AB5736_SB174


title: W-24-F-1-NTS

source_name: NTS of 24 week WKY rat rep1


title: W-16-F-3-NTS

source_name: NTS of 16 week WKY rat rep3

value: 16 1eeks


title: RNA-seq in N2a cells after transfection with control GapmeRs, replicate 1

source_name: N2a cells


title: RNA-seq in N2a cells after transfection with control GapmeRs, replicate 2


title: AB5734_SB174


title: S-24-F-5-NTS

source_name: NTS of 24 week SHR rat rep5


title: S-24-F-4-NTS

source_name: NTS of 24 week SHR rat rep4


title: RNA-seq in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 3


title: AB5733_SB174


title: S-24-F-3-NTS

source_name: NTS of 24 week SHR rat rep3


title: RNA-seq in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 1


title: RNA-seq in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 2


title: LC_03


title: LC_04


title: LC_02


title: S-24-F-2-NTS

source_name: NTS of 24 week SHR rat rep2


title: LC_06


title: S-24-F-1-NTS

source_name: NTS of 24 week SHR rat rep1


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 3 (siBahcc1 experiment)


title: LC_05


title: LC_01


title: AB5735_SB174


title: S-16-F-6-NTS

source_name: NTS of 16 week SHR rat rep6

value: 16 weeks


title: RNA-seq in N2a cells after transfection with control GapmeRs and DMSO, replicate 2


title: AB5729_SB174


title: AB5731_SB174


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 1 (siBahcc1 experiment)


title: Health_08

value: healthy control


title: S-16-F-5-NTS

source_name: NTS of 16 week SHR rat rep5


title: AB5728_SB174


title: Health_09


title: AB5730_SB174


title: RNA-seq in N2a cells after transfection with siRNAs against Bahcc1, replicate 3

value: N2a cells


title: AB5732_SB174


title: Health_07


title: S-16-F-4-RVL

source_name: RVL of 16 weeks SHR rat rep4

value: RVLM


title: Health_10


title: Health_06


title: AB5727_SB174


title: W-12-F-1-RVL

source_name: RVL of 12 weeks WKY rat rep1

value: Female

value: 12 weeks


title: W-08-F-3-NTS

source_name: NTS of 8 week WKY rat rep2

value: 8 weeks


title: AB5726_SB174

value: PsA


title: RNA-seq in N2a cells after transfection with siRNAs against Bahcc1, replicate 1

value: untreated


title: Health_04


title: AB5725_SB174


title: Health_05


title: RNA-seq in N2a cells after transfection with control siRNAs, replicate 2 (siBahcc1 experiment)


title: W-08-F-2-NTS

source_name: NTS of 8 week WKY rat rep1

value: NTS of brainstem

value: WKY


title: AB5724_SB174


title: brain6

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description: FFPE Cytassist Visium spatial

data_processing:
10X Space Ranger pipeline
Data processed with Seurat
Assembly: 10 mm
Supplementary files format and content: counts matrix
Supplementary files format and content: * images.tar contain the cytassist images, scalefactor json files, fiducials, position lists, * .h5 files
Supplementary files format and content: annotations
Library strategy: spatial transcriptomics

source_name: brain hz_Celsr3.1

extract_protocol:
Dissected brains were trimmed so coronal sections containing striatum was visable. Brains were formalin fixed and parafin embedded so that the coronal sections could be cut for spatial transcriptomics
10X Genomics Visium CytAssist Spatial Gene Expression for FFPE v2

treatment_protocol: no treatments - different genotypes

value: brain hz_Celsr3.1

tag: genotype

value: Celsr3 heterozygous biol rep 2


title: S-12-F-5-NTS

source_name: NTS of 12 week SHR rat rep5

value: NTS


title: AB5723_SB174


title: brain5

description: FFPE Cytassist Visium spatial

source_name: brain control.1

value: brain control.1

value: wild type biol rep 2


title: S-12-F-3-RVL

source_name: RVL of 12 weeks SHR rat rep3

value: RVLM of brainsstem

value: SHR


title: Health_02

source_name: Human plasma

value: plasma

value: healthy control


title: brain2

description: FFPE Cytassist Visium spatial

source_name: brain hz_Celsr3

value: brain hz_Celsr3

value: Celsr3 heterozygous biol rep 1


title: Health_03


title: AB5722_SB174

value: Synovial fluid (SF)


title: brain1

description: FFPE Cytassist Visium spatial

source_name: brain control

value: brain control

value: wild type biol rep 1


title: RNA-seq in N2a cells after transfection with siRNAs against Bahcc1, replicate 2

source_name: N2a cells

value: N2a cells

tag: treatment

value: untreated


title: S-12-F-2-RVL

source_name: RVL of 12 weeks SHR rat rep2

value: Female

value: 12 weeks

value: RVLM


title: AB5721_SB174

value: PsA


title: Health_01


title: HCC_50

value: hepetocellular carcinoma


title: dmm surgery, scRNAseq

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

description: CD45-Ter119-CD31-DAPI-CalceinAM+ articular superficial cells from 3 DMM surgery mice.

data_processing:
For scRNA-seq, sequencing data from 10× Genomics were processed with CellRanger (version 3.0.1) for demultiplexing, barcode processing and single-cell 3′ gene counting. Human and mouse genome reference was used for sequence alignment. Only confidently mapped, non-PCR duplicates with valid barcodes and UMIs were used to generate the gene-barcode matrix. For quality control, only cells with more than 5000 reads and less than 10% of mitochondrial genes were retained for downstream analyses. Cell doublets were removed using Doublet Finder software implemented in R. The clustering and visualization were finished by Seurat. For RNA-seq data analysis, adapters were trimmed and the resulting data were mapped to mm10 genome using STAR. HtSeq was used to summarize read counts, and duplicated reads were removed by UMI information (in Read2) to obtain gene counts. DEGs were calculated by DESeq2. Normalized CPM value = gene counts/ total gene counts x 1,000,000.
Assembly: mm10
Supplementary files format and content: For  scRNA-seq data, we provided Tab-separated values files and matrix files. For RNA-seq data, we provided tab-delimited text files including raw count values for each sample.

source_name: knee joint cartilage

extract_protocol:
For scRNA-seq, intact long bones were isolated, and attached soft tissues were removed using forceps, and dissociated periosteum cells and epiphysis articular cartilage cells with enzymatic digestion solution: 3 mg/ml type I collagenase (Worthington, LS004197), 4 mg/ml Dispase II (Sigma, 04942078001) and 1 U/ml DNase I (Sigma, D4527) in HBSS with Ca2+ and Mg2+. After four rounds of enzymic digestion in 37°C water bath (20 min per round), cells were resuspended in staining buffer (Ca2+ and Mg2+ free HBSS with 2% FBS) with 2 mM EDTA to stop the digestion for flow cytometry. Dissociated cells were stained by standard protocols with the following antibodies (eBioscience, Shanghai, China). allophycocyanin (APC)-conjugated CD31 (390), CD45 (30F-11), Ter119 (TER-119). DAPI and CalceinAM were used for viable cell gating. For RNA-seq, Intact long bones were isolated, and attached soft tissues were removed using forceps, and dissociated epiphysis articular cartilage cells with enzymatic digestion solution: 3 mg/ml type I collagenase (Worthington, LS004197), 4 mg/ml Dispase II (Sigma, 04942078001) and 1 U/ml DNase I (Sigma, D4527) in HBSS with Ca2+ and Mg2+. After four rounds of enzymic digestion in 37°C water bath (20 min per round), cells were resuspended in staining buffer (Ca2+ and Mg2+ free HBSS with 2% FBS) with 2 mM EDTA to stop the digestion for flow cytometry. Dissociated cells were stained by standard protocols with the following antibodies (eBioscience, Shanghai, China). allophycocyanin (APC)-conjugated CD31 (390), CD45 (30F-11), Ter119 (TER-119), Procr (eBio1560), PE/Cy5-CD105 (MJ7/18). DAPI and CalceinAM were used for viable cell gating.
For scRNA-seq library construction, harvested cells were resuspended at 1 × 103 cells/mL and loaded on Chromium Controller to obtain single cells (10× Genomics) according to the manufacturer’s protocol of Beijing SeekGene BioSciences Co., Ltd (Beijing, China). Chromium Single cell 3’ Library and Gel Bead Kit V2 (10× Genomics, PN120237) was used to generate single cell gel beads in emulsion (GEM). The captured cells were lysed, and the released RNA was reverse-transcribed with primers containing poly-(d)T, barcode, Unique Molecular Identifiers (UMIs) and read 1 primer sequence in GEMs. Barcoded cDNA was purified and amplified by PCR. The adapter ligation reaction was performed to add sample index and read 2 primer sequence. After quality control, the libraries were sequenced on Illumina Novaseq 6000 platform in 150 bp pair-ended manner.

value: knee joint cartilage

value: superficial cells

value: WT


title: AB5720_SB174


title: S-12-F-1-RVL

source_name: RVL of 12 weeks SHR rat rep1

value: RVLM of brainsstem

value: SHR


title: S-08-F-5-NTS

source_name: NTS of 8 week SHR rat rep5

value: NTS of brainstem

value: 8 weeks

value: NTS


title: sham surgery, scRNAseq

description: CD45-Ter119-CD31-DAPI-CalceinAM+ articular superficial cells from 3 sham surgery mice.


title: AB5719_SB174

value: Synovial fluid (SF)


title: AB5718_SB174


title: S-08-F-3-NTS

source_name: NTS of 8 week SHR rat rep3


title: Liver Condition Comparison

city: Cambridge

first: Reuben

last: Saunders

address: 455 Main St

institute: Whitehead Institute

description: 10x Genomics Flex

library_source: other

data_processing:
cellranger-7.1.0 (Liver Condition Comparison) or cellranger-8.0.0 (Liver Perturb-seq)
Assembly: mm10
Supplementary files format and content: h5: 10X genomics cellranger-generated Hierarchical Data Format 5 file with filtered_feature_bc_matrix representing single-cell gene expression

molecule: other

source_name: Liver

extract_protocol:
Perfusion with PFA, dissociation with Miltenyi FFPE, 10x Genomics Flex according to manufacturer's instructions, or with an additional spikein targeting sgRNAs
Manufacturer's instructions, including Flex feature barcode kit
10x Genomics Flex (RNA-templated ligation + single-cell barcoding)

value: Liver

value: ad libitum, fasting, or high-fat


title: HCC_49

value: plasma


title: HCC_48


title: S-08-F-2-NTS

source_name: NTS of 8 week SHR rat rep2

value: Female


title: AB5717_SB174


title: HCC_47


title: WT Li-Deficient Rep 4

first: Jae Joon

last: Choi

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR aligner (STAR aligner options: --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --limitBAMsortRAM 40000000000).
Reads aligned to each genes were counted using htseq-count (default options, used mm10 gene annotation(.gtf) from NCBI RefSeq).
Assembly: mm10
Supplementary files format and content: htseq-count output file (.htseq). Tab-delimited files containing gene symbols and their supporting read counts.

source_name: Cortex, Hippocampus

extract_protocol:
Li-deficient or control WT and 3xTg mice were perfused transcardially using cold PBS. The cortex and hippocampus were quickly dissected and pooled, then minced using scalpel, before transferring to 5 ml cold dissection buffer (HBSS without calcium and magnesium, Protector RNase inhibitor (Sigma) in Dounce Homogenizer. Brain samples were dounced 20 times with a loose and 10 times with a tight pestle. The cell suspension was passed through a pre-wet 70-micron cell strainer into a pre-chilled 15 ml tube. Cells are then spun down at 300xg for 10 min at 4˚C. Cell pellets were resuspended in 10 ml ice cold 40% Percoll (GE Healthcare) and centrifuged at 800xg for 20 minutes at 4˚C. Myelin debris were removed by vacuum suction and the cell pellet was washed with 5 ml ice cold HBSS and spun again for 5 minutes at 300g, 4˚C. The pellets were then resuspended in 180 μl ice cold MACs buffer (0.5% BSA, 2mM EDTA, Protector RNase inhibitor in PBS) with 20 μL CD11b microbeads (Miltenyi Biotec, 130-049-601) and incubated on ice for 15 minutes. Following incubation, 1 ml of MACs buffer was added to samples and cells were centrifuged for 5 minutes at 300xg, 4˚C. Microglia were then isolated using LS columns with QuadroMACS™ Separator following to manufacturer’s instructions. Briefly, LS columns were pre-washed three times with 3 ml of MACs buffer. Samples were resuspended in 500 µl MACs buffer and transferred to LS columns, followed by three additional washes with 3 ml MACs buffer. Finally, microglia were released with 5 ml of MACs buffer (without EDTA). Total microglial RNA was extracted using RNAzol® RT (Sigma, R4533).
RNA extracted from each microglial preparation was quantified using an Agilent Tapestation 4200 instrument, with a corresponding Agilent Tapestation High Sensitivity RNA assay (catalog no. 5067-5579). The samples were normalized to 4 ng of input in 9.5 μl, and the polyadenylated mRNA was selected for using 3' SMART-Seq CDS Primer II A as part of the Takara SMART-Seq v4 Ultra Low Input RNA (Catalog No. 634894) workflow, which generated cDNA. From there, an Agilent Bioanalyzer High Sensitivity DNA assay (catalog no. 5067-4626) was used to quantify cDNA concentration. Libraries were obtained using the Illumina NexteraXT kit (catalog no. FC-131-1096). Adapter ligation, indexing, and amplification were conducted subsequently as part of the same workflow. Following amplification, residual primers were eluted away using KAPA Pure Beads (catalog no. 07983298001) in a 0.6x SPRI-based cleanup. The resulting purified libraries were run on an Agilent 4200 Tapestation instrument, with a corresponding Agilent D5000 ScreenTape assay (catalog no. 5067-5588, 5067-5589) to visualize the libraries and check the size and concentration of each library. Molarity values obtained from this assay were used to normalize all samples in equimolar ratio for one final pool. The pool was denatured and loaded onto an Illumina NovaSeq 6000 instrument, with a single lane of an S4 flowcell to obtain Paired-End 100bp reads. The pool was loaded at 200 pM (normalized to 1nM pre-denaturation), with 1% PhiX spiked in as a sequencing control. The basecall files were demultiplexed through the Harvard BPF Genomics Core pipeline, and the resulting fastq files were used in subsequent analysis.

treatment_protocol: Control vs Lithium Deficient diet

value: Cortex, Hippocampus

value: Wildtype

value: Lithium Deficient


title: HCC_46

value: hepetocellular carcinoma


title: WT Li-Deficient Rep 3


title: AB5716_SB174

value: PsA


title: Liver Perturb-seq

description: 10x Genomics Flex Perturb-seq

value: transduction with lentivirus, transduction with AAV-Cre, ad libitum or fasting diet


title: S-08-F-1-NTS

source_name: NTS of 8 week SHR rat rep1


title: AB5715_SB174


title: W-12-F-3-RVL

source_name: RVL of 12 weeks WKY rat rep3

value: WKY

value: 12 weeks

value: RVLM


title: W-12-F-3-NTS

source_name: NTS of 12 week WKY rat rep3

value: NTS of brainstem

value: 12 1eeks


title: WT Li-Deficient Rep 2


title: AB5714_SB174


title: HCC_45


title: AB5713_SB174


title: W-12-F-2-RVL

source_name: RVL of 12 weeks WKY rat rep2

value: RVLM of brainsstem


title: HCC_44


title: WT Li-Deficient Rep 1


title: WT Control Rep 4

value: Control


title: S-08-F-4-NTS

source_name: NTS of 8 week SHR rat rep4

value: SHR

value: 8 weeks

value: NTS


title: HCC_42

source_name: Human plasma

value: plasma


title: HCC_43


title: WT Control Rep 3

value: Cortex, Hippocampus


title: W-12-F-2-NTS

source_name: NTS of 12 week WKY rat rep2

value: Female


title: HCC_41


title: AB5480_SB173

value: Synovial fluid (SF)


title: W-12-F-1-NTS

source_name: NTS of 12 week WKY rat rep1


title: WT Control Rep 2

value: Wildtype


title: HCC_40

value: hepetocellular carcinoma


title: WT Control Rep 1


title: AB5477_SB173

value: PsA


title: AB5481_SB173


title: HCC_38


title: HCC_39


title: S-12-F-5-RVL

source_name: RVL of 12 weeks SHR rat rep5


title: AB5476_SB173


title: 3xTG Li-Deficient Rep 4

value: Lithium Deficient


title: S-12-F-5-CVL

source_name: CVL of 12 weeks SHR rat rep5

value: CVLM of brainsstem

value: 12 weeks

value: CVLM


title: S-12-F-4-RVL

source_name: RVL of 12 weeks SHR rat rep4

value: RVLM


title: AB5471_SB173


title: 3xTG Li-Deficient Rep 2


title: AB5475_SB173


title: S-12-F-3-NTS

source_name: NTS of 12 week SHR rat rep3

value: NTS of brainstem


title: HCC_37


title: 3xTG Li-Deficient Rep 3


title: AB5712_SB174


title: AB5470_SB173


title: HCC_35


title: HCC_34


title: HCC_36


title: 3xTG Li-Deficient Rep 1


title: S-12-F-2-NTS

source_name: NTS of 12 week SHR rat rep2


title: 3xTG Control Rep 4

value: Control


title: S-12-F-1-NTS

source_name: NTS of 12 week SHR rat rep1

value: SHR


title: 3xTG Control Rep 3


title: AB5469_SB173


title: AB5468_SB173


title: W-16-F-2-NTS

source_name: NTS of 16 week WKY rat rep2

value: WKY

value: 16 1eeks


title: S-12-F-4-NTS

source_name: NTS of 12 week SHR rat rep4

value: NTS


title: 3xTG Control Rep 1

source_name: Cortex, Hippocampus

value: Cortex, Hippocampus


title: AB5466_SB173


title: AB5467_SB173


title: W-16-F-1-RVL

source_name: RVL of 16 weeks WKY rat rep1

value: Female

value: RVLM of brainsstem

value: 16 weeks


title: HCC_32

value: plasma

value: hepetocellular carcinoma


title: HCC_33


title: AB5465_SB173

value: PsA

value: Synovial fluid (SF)


title: HCC_31


title: HCC_30


title: S-16-F-5-RVL

source_name: RVL of 16 weeks SHR rat rep5


title: Alloxan (negative control, T=5), scRNAseq

city: Miami

first: Juan

last: Domínguez-Bendala

state: FL

address: 1450 NW 10th Ave

department: Diabetes Research Institute

institute: University of Miami Miller School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse reference genome, mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Seuratobject in RDS file format

source_name: Pancreas

extract_protocol:
Pancreatic slices are washed 3x with dPBS transferred into 15ml of prewarmed (37C) Dissociation solution- Triple-E. 10 minutes incubation at 37C follows. Brief vortex 5seconds bursts repeated 10x and additional 2min. incubation. The vortex step is repeated one more time.  Dissociated slices are immediately washed in 20ml of wash medium and spun down at 1500 RPM. Washing is repeated and cells are put through 40-micron strainer. The single cells are now washed one time with dPBS at 4 C resuspended in 1ml dPBS and 10 µl of single cell suspension is taken to control  number and viability with Trypan blue. After additional spin, the pellet is resuspended in 200 µl of ice cold dPBS. 800 µl of ice cold methanol is added dropwise with constant stirring to prevent clumping during fixation. Fixed cells are kept in-20C for 24 hrs and later in -80C.  Single cell suspension is taken to control  number and viability with Trypan blue .After additional spin, the pellet is resuspended in 200 µl of ice cold dPBS. 800 µl of ice cold methanol is added dropwise with constant stirring to prevent clumping during fixation. Fixed cells are kept in-20C for 24 hrs and later in -80C. Slices are washed 3x with dPBS transferred into 15ml of prewarmed (37C) Dissociation solution- Triple-E. 10 minutes incubation at 37C follows. Brief vortex 5 seconds bursts repeated 10x and additional 2min. incubation. The vortex step is repeated one more time.  Dissociated slices are immediately washed in 20ml of wash medium and spun down at 1500 RPM. Washing is repeated and cells are put through 40-micron strainer. The single cells are now washed one time with dPBS at 4 C resuspended in 1ml dPBS and 10 µl of single cell suspension is taken to control  number and viability with Trypan blue. After additional spin, the pellet is resuspended in 200 µl of ice cold dPBS. 800 µl of ice cold methanol is added dropwise with constant stirring to prevent clumping during fixation. Fixed cells are kept in-200C for 24 hrs and later in -80 C.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: THR-123 grsoup slices were treated with THR-123 for 5 days culture with 10nM THR-123

value: Pancreas


title: W-16-F-1-NTS

source_name: NTS of 16 week WKY rat rep1


title: S-16-F-4-NTS

source_name: NTS of 16 week SHR rat rep4


title: AB5464_SB173

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt


title: HCC_29

source_name: Human plasma


title: Non-diabetic Control (T=5), scRNAseq

description: 10x Genomics


title: THR-123 (treatment, T=5), scRNAseq

description: 10x Genomics

value: 10nM of THR-123 treatment


title: Spleen, CD30KO, D10, Py17XNL infection, rep3

city: Shenyang

first: Li

last: Zheng

state: Liaoning

address: No.77 Puhe Road

institute: China Medical University

data_processing:
Hisat2 v2.0.5.
Reference genome and gene model annotation files were downloaded  from genome website directly. Index of the reference genome was built using  Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference  genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that  Hisat2 can generate a database of splice junctions based on the gene model  annotation file and thus a better mapping result than other non-splice mapping  tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

growth_protocol: Six to eight-week-old, female and male C57BL/6J mice (B6, WT mice) were purchased from Beijing HFK Bioscience Co., Ltd. (Beijing, China). The generation and preliminary characterization of CD30L−/− and CD30−/− B6 mice were a kind gift from Dr. Sun at China Medical University. All mice were maintained with the same feeding conditions and a specific pathogen-free environment within a treatment room (12-h light/dark cycle, 22±2°C, 60–65% relative humidity).

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The WT and KO mice were bred in the animal facility, at China Medical University, Shenyang, China. Six to eight-week-old, female mice were used for infection. To begin infections, WT, CD30L−/−, or CD30−/− mice were inoculated intraperitoneally with 1×106 P. yoelii 17XNL parasitized red blood cells (pRBCs).

value: spleen

tag: cell line

value: splenocyte

value: CD30 knockdown

value: Py17XNL infection


title: S-16-F-3-RVL

source_name: RVL of 16 weeks SHR rat rep3

value: SHR

value: RVLM


title: HCC_28


title: HCC_27


title: AB5463_SB173

extract_protocol:
Synovial fluid mononuclear cells and blood mononuclear cells were isolated within maximum 4 hours of sample collection. Synovial fluid samples were first filtered by 100-micron strainer into 50 ml tube and diluted 1:1 with ice cold FACS buffer (2mM EDTA, Ph 8.0, 0.5% bovine serum albumin in PBS). Blood samples were diluted 1:1 with ice cold FACS buffer. Synovial fluid and blood mononuclear cell separation was performed using density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with the diluted synovial fluid or blood sample. Centrifugation (460g, 25min) was performed at 10◦C and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After a short centrifuge (360g, 5min), we resuspended the cell pellet in cryopreservation media (FCS+10%DMSO) and stored the samples in cryotube at -80◦C. Prior to single-cell sorting, samples were quickly defrosted at 37◦C bath and washed with heated (37 ◦C) RPMI-1640. We resuspended the cells in FACS buffer for staining and sorting.
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)


title: 3xTG Control Rep 2

value: Control


title: HCC_26


title: Spleen, CD30KO, D10, Py17XNL infection, rep2

tag: cell type


title: AB5462_SB173


title: S-16-F-3-NTS

source_name: NTS of 16 week SHR rat rep3

value: NTS of brainstem

value: NTS


title: AB5461_SB173

value: OA


title: Spleen, CD30KO, D10, Py17XNL infection, rep1


title: S-16-F-2-RVL

source_name: RVL of 16 weeks SHR rat rep2

value: Female

value: RVLM of brainsstem

value: 16 weeks


title: Spleen, CD30LKO, D10, Py17XNL infection, rep3

value: CD30L knockdown


title: AB5460_SB173

value: Synovial fluid (SF)


title: S-16-F-2-NTS

source_name: NTS of 16 week SHR rat rep2


title: S-16-F-2-CVL

source_name: CVL of 16 weeks SHR rat rep2

value: CVLM of brainsstem

value: CVLM


title: AB5459_SB173


title: Spleen, CD30LKO, D10, Py17XNL infection, rep2

value: spleen


title: HCC_23

value: plasma

value: hepetocellular carcinoma


title: HCC_25


title: HCC_24


title: S-16-F-1-RVL

source_name: RVL of 16 weeks SHR rat rep1


title: Spleen, CD30LKO, D10, Py17XNL infection, rep1

value: splenocyte

value: Py17XNL infection


title: HCC_22


title: AB5420_SB172

value: PsA


title: Spleen, WT, D10, Py17XNL infection, rep3

value: WT


title: Spleen, WT, D10, Py17XNL infection, rep2


title: AB5418_SB172


title: RIFr.4206_03

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude.
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Staphylococcus aureus subsp. aureus ATCC33591 genome (Reference genome downloaded from ATCC website: https://genomes.atcc.org/genomes/bfa4253471534524) using STAR2.5.3a and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 in the R statistical computing environment.
Assembly: Reference genome downloaded from ATCC website: https://genomes.atcc.org/genomes/bfa4253471534524
Supplementary files format and content: Binary Alignment Map (.bam) files include aligned reads to Staphylococcus aureus subsp. aureus ATCC33591 reference genome described above.
Supplementary files format and content: tab-delimitated text (.txt) files include raw counts for each Sample

organism: Staphylococcus aureus

source_name: Planktonic

growth_protocol: S. aureus subsp. aureus ATCC 33591 was cultured in tryptic soy broth shaking at 210 rpm at 37 °C.

extract_protocol:
After 30 minutes treatment, 5 mL of Bacterial RNAprotect (Qiagen) was added for 5 minutes at room temperature. The culture was then centrifuged at 3214 xg for 10 minutes at 4 °C and the supernatant discarded. An RNAeasy Plus Mini Kit (Qiagen; Cat. No. 74134) was used to extract the RNA following the manufacturer’s instructions utilizing mechanical lysis for Gram-positive bacteria.
Libraries were prepared from ribosomal RNA-depleted total RNA using Illumina Stranded Total RNA Prep, ligation with Ribo-Zero Plus mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20037135). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher). Paired-end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).

treatment_protocol: Five mL of mid-log cultures (OD600 0.4-0.6) were treated with 1/2 MIC of ARI-4206 (0.125 mg/L), ARI-5192 (0.5 mg/L), rifampin (0.004 mg/L), or equilalent vehicle control (DMSO) for 30 minutes shaking at 210 rpm at 37 °C.

value: ATCC 33591, rifampin resistant

value: Planktonic


title: HCC_20


title: HCC_21


title: AB10905_SB207

first: Ido

last: Amit

value: Control

value: Blood


title: HCC_19


title: T+N_TECs_3

city: Guangzhou

first: An

last: Xiao

address: JingXi street

institute: Nanfang Hospital

description:
T+N_TECs_3_count
Ncls_TECs_all sample Matrix_Count.xlsx

data_processing:
The high-quality reads were aligned to the mouse reference genome (mm10) via Hisat2. FeatureCounts was utilized to tally uniquely mapped reads. Differential expression analysis was conducted using the DESeq2 algorithm.
Assembly: An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome(mm10) using HISAT2 2.1.0 and other parameters set as a default.
Supplementary files format and content: Excel(xlsx.) file includes raw count for each sample.

source_name: kidney

extract_protocol:
Total RNA was extracted from mouse primary TECs or NRK49F employing Trizol reagent (Vazyme) as per the guidelines provided by the manufacturer.RNA quality was assessed on an Agilent 2100 Bioanalyzer(Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China)

value: kidney

value: primary cell

value: primary mouse tubular epithelial cell

value: Ncls+TGF-β1 cotreated


title: RIFr.5192_03


title: T+N_TECs_2

description:
T+N_TECs_2_count
Ncls_TECs_all sample Matrix_Count.xlsx


title: AB10884_SB207

address: 234 Herzl st.

institute: Weizmann Institute of Science


title: RIFr.DMSO_03

value: DMSO


title: HCC_18


title: AB10878_SB207


title: RIFr.RIF_02

value: Rifampin 0.004 mg/L


title: AB5458_SB173

value: OA

value: Synovial fluid (SF)


title: HCC_17

value: plasma

value: hepetocellular carcinoma


title: AB10877_SB207


title: T+N_TECs_1

description:
T+N_TECs_1_count
Ncls_TECs_all sample Matrix_Count.xlsx


title: AB10647_SB206


title: AB5419_SB172


title: RIFr.4206_02


title: S-16-F-1-NTS

source_name: NTS of 16 week SHR rat rep1

value: Female

value: NTS of brainstem

value: SHR

value: 16 weeks

value: NTS


title: RIFr.RIF_03

value: ATCC 33591, rifampin resistant

value: Planktonic


title: Tgfb_TECs_3

description:
Tgfb_TECs_3_count
Ncls_TECs_all sample Matrix_Count.xlsx

value: kidney

value: TGF-β1 treated


title: Spleen, WT, D10, Py17XNL infection, rep1

value: spleen

value: splenocyte

value: WT

value: Py17XNL infection


title: HCC_15


title: RIFr.5192_02


title: AB10627_SB206

value: Control

value: Blood


title: RIFr.DMSO_02

value: DMSO


title: Tgfb_TECs_1

description:
Tgfb_TECs_1_count
Ncls_TECs_all sample Matrix_Count.xlsx

value: primary cell

value: primary mouse tubular epithelial cell


title: AB10622_SB206


title: HCC_14

value: plasma

value: hepetocellular carcinoma


title: HCC_12


title: RIFr.RIF_01

value: Rifampin 0.004 mg/L


title: HCC_16


title: AB10621_SB206


title: Con_TECs_3

description:
Con_TECs_3_count
Ncls_TECs_all sample Matrix_Count.xlsx


title: Con_TECs_2

description:
Con_TECs_2_count
Ncls_TECs_all sample Matrix_Count.xlsx


title: AB10620_SB206


title: RIFr.5192_01


title: AB10612_SB206


title: Celsr3 heterozygous biol rep 3

description:
20681X6
10X genomics

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1)
Assembly: mm10, M_musculus_Jun_2020, GRCm38
Supplementary files format and content: csv - counts and metadata - xlsx

molecule: nuclear RNA

source_name: brain - striatum

extract_protocol:
Dissected striatum was flash frozen in LN2 and preserved in OCT compound until processing. Excess OCT was removed and the specimens were gently thawed in 2 ml of ice-cold phosphate-buffered saline (PBS, devoid of Ca2+ and Mg2+). This solution was supplemented with various compounds to preserve the quality of the sample: 0.54 μM Nectostatin (Inc. #J65341, ThermoFisher Scientific Chemicals, Waltham, MA), 1 μM HPN-07 (SML2163, Sigma-Aldrich), 0.32 μM sodium hydroxybutyrate (A1161314, ThermoFisher Scientific Chemicals), 78 nM Q-VD-Oph (SML0063, Sigma-Aldrich), and 0.2 U/ml of Ribolock RNase inhibitor (EO0381, Life Technologies Corporation, Carlsbad, CA). The tissue, held over dry ice in a 60-mm Petri dish, was methodically minced into fragments smaller than 2 mm using a razor blade. Subsequently, this tissue was transitioned to a 2 ml Dounce homogenizer containing 1.5 ml of nuclei extraction buffer (130-128-024, Miltenyi Biotec, Bergisch Gladbach, Germany) along with 0.2 U/ml Ribolock RNase inhibitor.  Samples were then centrifuged at 600×g for 5 min, resuspended in 400 μL of PBS enriched with 2% BSA, passed through a 70-μm FLOWMI for clarification, and strained via a 40-μm FLOWMI. Specimens were then entrusted to the Hunstman Cancer Institute High Throughput Genomics Core for 10X Genomics library construction and sequencing.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit v1.5_150x150 bp Sequencing (these six samples were sequenced on a lane of an S4 flowcell).
snRNA-seq

value: brain - striatum

value: Celsr3 heterozygous


title: HCC_10


title: Tgfb_TECs_2

description:
Tgfb_TECs_2_count
Ncls_TECs_all sample Matrix_Count.xlsx


title: HCC_13


title: AB10608_SB206


title: ARI-4206r.RIF_03

value: ATCC 33591, ARI-4206 resistant

value: Planktonic


title: Celsr3 heterozygous biol rep 2

description:
20681X5
10X genomics


title: AB10478_SB205


title: ARI-4206r.4206_03


title: AB10458_SB205


title: Celsr3 heterozygous biol rep 1

description:
20681X4
10X genomics


title: HCC_09


title: wild type biol rep 3

description:
20681X3
10X genomics

value: wild type


title: RIFr.4206_01

value: ATCC 33591, rifampin resistant


title: ARI-4206r.5192_03


title: AB10453_SB205


title: Con_TECs_1

description:
Con_TECs_1_count
Ncls_TECs_all sample Matrix_Count.xlsx

value: kidney


title: wild type biol rep 2

description:
20681X2
10X genomics


title: HCC_07


title: HCC_08


title: HCC_06


title: AB10452_SB205


title: HCC_11


title: HCC_05


title: RIFr.DMSO_01


title: wild type biol rep 1

description:
20681X1
10X genomics


title: ARI-4206r.RIF_02


title: AB10451_SB205


title: HCC_03


title: EAE Control and  Perampanel Tag 01-06

city: Mainz

first: Frauke

last: Zipp

address: Langenbeckstraße 1

department: Department of Neurology

country: Germany

institute: University Medical Center Mainz

data_processing:
Resulting raw data was preprocessed according to the Illumina standard protocol and transcript alignment, counting and demultiplexing was performed using the BD Rhapsody WTA analysis pipeline yielding 8,300 so-called putative cells overall with a mean of 88,500 aligned reads per cell. The outputs of the BD Rhapsody WTA Analysis Pipeline were used for single-cell downstream analysis.
Single-cell gene expression analysis and visualization were carried out using Seurat (Hao et al., 2021). High-quality cells with at least 500 UMIs, 250 genes, log10 genes per UMI over 0.8, and mitochondrial ratios under 20 percent were retrieved for further analysis. In addition, only genes expressed in more than 10 cells were kept.
After the log normalization, dimensionality reduction was carried out with 500 variable features and 50 principal components. The UMAP clusters were defined using the Louvain algorithm with multilevel refinement. The clusters were assigned to the different cell types using the gene markers. Cell type-specific differentially expressed genes were statistically identified using DESeq2 (Love et al., 2014).
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: inguinal lymph node

extract_protocol:
Inguinal lymph nodes were isolated on day 3 after EAE induction from 3 SJL mice therapeutically treated with perampanel as well as 3 control mice. Lymph nodes were meshed through a 100-µm cell strainer in order to create a single-cell suspension.
Single-cell capturing, isolation of RNA and synthesis of cDNA was performed according to the BD Rhapsody Single-Cell Analysis System (BD Rhapsody) following the manufacturer’s guidelines. Each sample was tagged with a unique sample tag in order to allow multiplexing of samples on the same cartridge.  Whole transcriptome libraries and sample tag libraries were prepared using BD WTA Amplification Kit (BD Rhapsody) with random primers followed by amplification and insertion of sequencing adaptors following the BD Rhapsody System mRNA WTA and Sample Tag Library Preparation Protocol (BD Biosciences). Quality and quantity of cDNA libraries was checked on a Bioanalyzer2100 (Agilent) and sequencing (150 PE reads aiming on 100,000 raw reads /cell) was performed on a NovaSeq 6000 (Illumina) at Novogene (Cambridge; UK).

value: inguinal lymph node

value: primary tissue

value: Lymphocytes

value: SJL


title: ARI-4206r.4206_02


title: HCC_04


title: EAE Perampanel 03

data_processing:
The raw sequencing reads (30 mio 150 PE reads per sample) of Illumina’s NovaSeq 6000 (Novogene; Cambridge, UK) were preprocessed according to the Illumina standard protocol.
Sequence reads were trimmed for adapter sequences and further processed using Qiagen’s software CLC Genomics Workbench (v21.0.5 with CLC’s default settings for RNA-Seq analysis).
Reads were aligned to GRCm38 genome. Unique gene counts from the CLC workbench were used to perform statistical differential expression analysis with DESeq2 (Love et al., 2014). Gene ontology analysis was performed for genes with adjusted p-values under 0.05 using clusterProfiler and DOSE (Yu et al., 2015). Network plots were generated with Enrichplot (Yu et al., 2015). Heatmaps were generated using the pheatmap R package (Kolde, 2019). Volcano plots were created with the ggplot2 (Wickham, 2016) and ggrepel (Slowikowski, 2021) R packages. The database org.Mm.eg.db was used for annotating genes (Carlson, 2019).
Unique gene counts from the CLC workbench were used to perform statistical differential expression analysis with DESeq2 (Love et al., 2014). Gene ontology analysis was performed for genes with adjusted p-values under 0.05 using clusterProfiler and DOSE (Yu et al., 2015).
Network plots were generated with Enrichplot (Yu et al., 2015). Heatmaps were generated using the pheatmap R package (Kolde, 2019). Volcano plots were created with the ggplot2 (Wickham, 2016) and ggrepel (Slowikowski, 2021) R packages. The database org.Mm.eg.db was used for annotating genes (Carlson, 2019).
Assembly: GRCm38
Supplementary files format and content: DESeq 2 output

extract_protocol:
RNA was purified immediately after with the RNeasy Plus Micro Kit according to the manufacturer’s protocol (Qiagen). RNA was quantified with a Qubit 2.0 fluorometer (Invitrogen) and the quality was assessed on a Bioanalyzer 2100 (Agilent) using a RNA 6000 Pico chip (Agilent). Samples with an RNA integrity number (RIN) of > 9 were used for library preparation.
Barcoded mRNA-seq cDNA libraries were prepared from 100 ng of total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual with a final amplification of 12 PCR cycles. Quantity was assessed using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: Inguinal lymph nodes were isolated on day 3 after EAE induction from 3 SJL mice therapeutically treated with perampanel as well as 3 control mice. Lymph nodes were meshed through a 100-µm cell strainer in order to create a single-cell suspension.

value: Perampanel


title: HCC_02


title: ARI-4206r.5192_02


title: AB10438_SB205

value: Control

value: Blood


title: EAE Perampanel 02


title: AB10442_SB205


title: EAE Perampanel 01


title: HCC_01

value: plasma


title: AB10067_SB202


title: ARI-4206r.DMSO_03

value: DMSO


title: EAE Control 03


title: AB10065_SB202


title: ARI-4206r.4206_01


title: EAE Control 01


title: AB10046_SB202


title: AB10063_SB202


title: ARI-4206r.DMSO_01


title: ARI-4206r.RIF_01

value: Rifampin 0.004 mg/L


title: EAE Control 02