title: Non-operated tail, biological replicate 4

city: Fitzroy

first: Yinan

last: Yuan

address: 9 Princes St

institute: St. Vincent's Institute of Medical Research

hyb_protocol: Lablled cRNA samples were bybridized to MouseRef-8 c2.0 Expression BeadChips (Illumina, Inc., Sandiego, CA) in accoradance with Illumina's starndard protocol.

scan_protocol: MouseRef-8 c2.0 Expression BeadChips were imaged in accordance with Illumina's starndard protocol.

data_processing:
The microarray data was log2 transformed  and quantile normalized using Partek Genomic Suite®. Significantly differentially expressed transcripts were identifed with a cutoff at p-value ≤ 0.05 and a fold change ≥ 1.2 (Pollack JR et al., Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12963-8, Wang Y et al. BMC Genomics. 2006 Mar 21;7:59.)
Quantile normlized.

label: Biotin

source_name: Mouse tail skin

label_protocol: Biotinylated cRNA was synthesized using Illumina® at Australian Genome Research Facility.

extract_protocol: RNA was extracted from frozen tail skins using QIAGEN RNeasy mini kit® accoridng to the manufacture's protocol. Quality control was performed with Agilent RNA 6000 Nano kit according to the manufacture's protocol.

value: 6 weeks

tag: gender

value: Female

tag: source

value: Tail skin


title: Vec2-m6AIP

status: Public on Feb 19 2025

type: SRA

city: Milwaukee

first: Tongjun

last: Gu

address: 8727 W Watertown Plank Rd

country: USA

institute: VERSITI WISCONSIN, INC.

library_source: transcriptomic

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 92.8 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1

molecule: total RNA

organism: Homo sapiens

source_name: human lung cancer cell line

growth_protocol: NCI-H522 cells stably expressing pCDH-Vector and pCDH-strep-KRAS G12V were cultured in RPMI-1640 mediun supplemented with 10% FBS+ 1% P.S. + 1 ug/mL puromycin

extract_protocol:
Total RNAs were extracted by Trizol reagent
The libraries for RNA-seq and m6A-seq were constructed by using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB, Cat#E7760L).
The libraries for both RNA-seq and m6A-seq were sequenced by using Nova-seq X with 150 bp of paired-end.

treatment_protocol:
NCI-H522 cells were infected with pCDH-Vector lenti-virus twice. The infected cells were selected by using a final concentration of 1 ug/mL puromycin for three days.
1 mg/mL puromycin, 1:1000 dilution
NCI-H522 cells stably expressing pCDH-Vector and pCDH-strep-KRAS G12V were selected by 1 ug/mL puromycin (Final concentration).

tag: cell line

tag: cell type

value: lung cancer cell line

tag: genotype

value: KRAS wild-type


title: Sample27

type: protein

city: New York

first: Joseph

last: Castellano

state: NY

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: Plasma protein data is reported as SOMAmer reagent abundance in relative fluorescence units (RFU) with reagent abundance indicating protein concentration within the sample

hyb_protocol: Raw data were processed for hybridization normalization to adjust for individual sample variance according to manufacturer recommendations.

data_processing: Median signal normalization was performed to adjust sample-to-sample differences in RFU brightness. Calibration normalization was applied to all samples in the plate to remove variance due to assay run according to manufacturer recommendations.

label: Slow Offrate Modified Aptamer (SOMAmer) reagents

molecule: protein

source_name: plasma

extract_protocol: Whole blood samples were drawn from fasted subjects into 10 mL syringes pre-coated with 0.5 M EDTA and transferred to 15 mL polypropylene tubes containing 120 µL of 0.5 M EDTA. Samples were kept on ice until centrifugation (<2 hours) at 2,000 g x 17 minutes, allowing separation of plasma from the cellular fraction. Plasma was pooled and aliquoted into new polypropylene tubes (300-500 µL) prior to storage at -80°C.

tag: Sex

value: M

value: positive

tag: age

tag: subarray


title: MLO-Y4 cells, HICA1, 24h

city: Suzhou

first: Yujiang

last: Liu

address: Yangsu Road No.18

country: China

institute: Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine

data_processing:
The raw data were processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, snoRNA) (http://rfam.sanger.ac.uk/), repeats (http://www.girinst.org/repbase), and sequences <18 nt or >26 nt in length.
Subsequently, the unique sequences with a length of 18~26 nt were mapped to miRNA sequences in miRBase 22.0 (http://www.mirbase.org/). Mapping was also performed on pre-miRNA against mice genomic data (https://www.ncbi.nlm.nih.gov/genome/52?genome_assembly_id=992563).
The unique sequences that aligned to the known miRNAs sequences in miRBase 22.0 were identified as known miRNA. Secondary structure of pre-miRNAs was presented as a hairpin, including 5p- and 3p- derived miRNA.
The unique sequences mapping to the other arm of the pre-miRNAs sequences, which were not annotated in the miRBase 22.0, were considered to be 5p- or 3p- derived miRNA candidates. The remaining unmapped sequences were matched to the mice genomic sequences in search of candidate novel miRNAs.
To identify the results of putative miRNAs in mice, all the obtained miRNAs were used to predict the secondary structures using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi).
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FRKM and count values for eachi Sample

organism: Mus musculus

source_name: MLO-Y4 cells

extract_protocol:
Total RNA was extracted from the exosomes using an Exosome RNA Purification Kit (System Biosciences Inc., Mountain View, CA, USA) according to the manufacturer’s protocol. The concentration and integrity of isolated RNA were evaluated with a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA). Total exosome RNAs extracted were polyadenylated and reverse-transcribed with a poly (T) adapter into cDNAs. Only high-quality RNA sample (OD260/280 = 1.8∼2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0, >10 μg) was used to construct sequencing library.
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation kit from Illumina (San Diego, CA, USA) using 5 μg of total RNA. And then we performed the single-end sequencing (1x50bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

value: MLO-Y4 cells

value: osteocyte-like cells

tag: treatment

value: 10 uM ICA(HICA) for 24h


title: Non-operated tail, biological replicate 3

type: RNA

state: VIC

country: Australia

tag: strain


title: Non-operated tail, biological replicate 2


title: Sample7


title: SK-MEL-28siNC

city: Guangzhou

first: can

last: li

address: Southern Medical University

institute: Southern Medical University

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample.

source_name: melanoma tissues

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 and SK-MEL-28 cells were treated with siNC or siLINC00622 with transfection reagent when the cells were about 70% confluency and then cells were incubate in non-serum DMEM at 37°C with 5% CO2 for 6 hour，respectly. After 6h change the medium with 10% serum DMEM and continuously incubate  24h.

tag: tissue

value: melanoma tissues

value: siNC


title: Sample26


title: Sample28

value: negative


title: G12V2-Input

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 62 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1

treatment_protocol:
NCI-H522 cells were infected with pCDH-Flag-KRAS G12V lenti-virus twice. The infected cells were selected by using a final concentration of 1 ug/mL puromycin for three days.
1 mg/mL puromycin, 1:1000 dilution
NCI-H522 cells stably expressing pCDH-Vector and pCDH-strep-KRAS G12V were selected by 1 ug/mL puromycin (Final concentration).

value: KRAS mutant


title: Vec1-m6AIP

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 105 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1


title: Sample41


title: Sample13


title: Sample9


title: Non-operated tail, biological replicate 1


title: MLO-Y4 cells, LICA1, 24h

value: 0.1 uM ICA(LICA) for 24h


title: Sample6


title: G12V1-Input

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 58 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1


title: Chronic tail, biological replicate 4


title: MLO-Y4 cells, PBS3, 24h

value: PBS for 24h


title: Vec2-Input

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 65 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1


title: Sample16


title: MLO-Y4 cells, LICA3, 24h


title: Chronic tail, biological replicate 2


title: Chronic tail, biological replicate 3


title: MLO-Y4 cells, PBS2, 24h


title: Vec1-Input

data_processing:
The library was sequenced by using Nova-seq X with a paired-end 150bp. 63 millions reads has been collected.
RNA reads were aligned to hg38 human genome using STAR V2.7.11b and quantified using Salmon V1.10.2.
m6A reads were aligned to hg38 human genome using Hisat2 V2.2.1 and peaks were called using Macs2 V2.2.7.1.
Assembly: hg38
Supplementary files format and content: The processed data for RNAseq are in the format of txt file and contains the gene expression values in the format of raw counts and TPM (Transcription per Million).
Supplementary files format and content: The processed data for m6A are in the format of txt and contains the narrow peaks for each m6A region called by Macs2 V2.2.7.1


title: Chronic tail, biological replicate 1


title: MLO-Y4 cells, PBS1, 24h


title: Sample1


title: P57055, WT, YPD, R2

status: Public on Feb 18 2025

city: Pittsburgh

first: Charles

middle: Joel

last: McManus

state: Pennsylvania

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description:
Library name: P57055-WT-YPD-Rep2
P57055-WT-YPD-Rep2

data_processing:
Libraries were sequenced on the Illumina NovaSeq X-Plus Platform and basecalling was performed using the Illumina basespace platform
RNA-seq reads were aligned to the diploid C. albicans genome release 22 using HISAT2 version 2.2.1 with known splice junctions and no denovo splice junction calling.  Because this is a diploid genome, most read pairs aligned to two alleles. The primary (best) alignments were extracted from the resulting bam files using SAMTools version 1.15.1
Assembly: C. albicans SC5314 Assembly 22
Supplementary files format and content: Processed data files are provided as comma separated value format (csv) and contain the C. albicans gene identifies in the first column and raw read pairs aligned to each gene from each experimental sample.

molecule: polyA RNA

organism: Candida albicans

growth_protocol: Candida albicans strains were grown in YPD at 30C overnight and restarted at OD600 = 0.2 the next morning in fresh YPD. Strains were grown to OD600 = 0.8 at 30C. 20 mL of culture was centrifuged and frozen in liquid nitrogen for YPD yeast samples.

extract_protocol:
Frozen cells were resuspended in 1 mL of ice cold RNA buffer (4M NaCl, 1MTris-HCl pH7.5, EDTA). 500 uL of resuspended cells were mixed with 250 uL of zirconia beads and 500 uL of Acid-Phenol-CHCl3 ph 4.5) in 2mL eppendorf tubes. Cells were disrupted by 10 cycles of vortexing 1 minute and chilling 1 minute on ice. Samples were centrifuged for 2 minutes at room temperature and the aqueous phase was removed and back-extracted with an equal volume of CHCl3-Isoamyl alcohol. The subsequent aqueous phase was removed and three volumes of ethanol were added to precipitate the total RNA at -80C overnight. The pellet was washed with ice-cold ethanol and resuspended in 100 uL of ultrapure water. 5 ug of total RNA was treated with TurboDNA-free kit according to manufacturer specifications. The resulting RNA was extracted with Trizol to remove DNase and the aqueous phase was purified using the RNA Clean & Concentrator kit (Zymo Research). RNA was eluted in 60 uL of ultrapure water.
Strand-specific RNA-seq libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) to isolate mRNA and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L).

treatment_protocol: For hyphal samples, 80 mL of yeast culture (OD600 = 0.8, YPD 30C) were collected by centrifugation, washed with PBS, and resuspended in 20 mL of pre-warmed filamentation medium (RPMI + serum, 37C) and grown for four hours. Cells were recovered by vacuum filtration. washed twice with 5 mL of ice-cold RNA buffer (4M NaCl, 1MTris-HCl pH7.5, EDTA) and frozen in liquid nitrogen for RPMI hyphae samples.

value: Yeast

value: WT

value: YPD 30C


title: P57055, WT, YPD, R1

description:
Library name: P57055-WT-YPD-Rep1
P57055-WT-YPD-Rep1


title: P57055, Dhh1-deletion, YPD, R2

description:
Library name: P57055-DHH1-YPD-Rep2
P57055-DHH1-YPD-Rep2


title: MLO-Y4 cells, LICA2, 24h


title: P57055, WT, RPMI, R1

description:
Library name: P57055-WT-RPMI-Rep1
P57055-WT-RPMI-Rep1

value: Hyphae

value: RPMI + serum 37C


title: P57055, WT, YPD, R3

description:
Library name: P57055-WT-YPD-Rep3
P57055-WT-YPD-Rep3


title: P57055, Dhh1-deletion, RPMI, R2

description:
Library name: P57055-DHH1-RPMI-Rep2
P57055-DHH1-RPMI-Rep2


title: Bovine Mammosphere-Derived Epithelial Cells

city: Ithaca

first: Gerlinde

middle: R.

last: Van de Walle

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation using cellranger v6.1.1
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Tab separated values and matrices

organism: Bos taurus

source_name: Mammary Gland

growth_protocol: Dulbecco’s Modified Eagle Medium (DMEM)/F12 (50/50), supplemented with 10% FBS, 2% B27, 10 ng/mL basic-fibroblast growth factor (bFGF) , 10 ng/mL epidermal growth factor (EGF) and 2% Antibiotic/Antimycotic, 37C, 5% CO2

extract_protocol:
Parenchymal tissue of a non-lactating cow (B. taurus) was isolated by means of a biopsy and was dissociated into single cells. MDECs were isolated using previously established protocols.  Upon isolation of colonies and formation of a monolayer, the cells were analyzed using scRNA-seq. Protocol described in "Ledet, M.M., Vasquez, A.K., Rauner, G. et al. The secretome from bovine mammosphere-derived cells (MDC) promotes angiogenesis, epithelial cell migration, and contains factors associated with defense and immunity. Sci Rep 8, 5378 (2018). https://doi.org/10.1038/s41598-018-23770-z"
According to manufacturer instructions, single cell 3' v3.1 protocol (10X Genomics)

value: Mammary Gland

value: MDEC

value: Mammosphere-derived epithelial cells


title: P57055, Dhh1-deletion, YPD, R1

description:
Library name: P57055-DHH1-YPD-Rep1
P57055-DHH1-YPD-Rep1


title: Sample33

value: M

value: positive


title: Sample11


title: P57055, WT, RPMI, R3

description:
Library name: P57055-WT-RPMI-Rep3
P57055-WT-RPMI-Rep3


title: P57055, Dhh1-deletion, YPD, R3

description:
Library name: P57055-DHH1-YPD-Rep3
P57055-DHH1-YPD-Rep3


title: P57055, WT, RPMI, R2

description:
Library name: P57055-WT-RPMI-Rep2
P57055-WT-RPMI-Rep2


title: SC5314, Dhh1-deletion, RPMI, R2

description:
Library name: DHH1-RPMI-Rep2
DHH1-RPMI-Rep2


title: SC5314, Dhh1-deletion, RPMI, R3

description:
Library name: DHH1-RPMI-Rep3
DHH1-RPMI-Rep3


title: SC5314, WT, YPD, R2

description:
Library name: WT-YPD-Rep2
WT-YPD-Rep2


title: SC5314, Dhh1-deletion, YPD, R1

description:
Library name: DHH1-YPD-Rep1
DHH1-YPD-Rep1


title: SC5314, WT, YPD, R1

description:
Library name: WT-YPD-Rep1
WT-YPD-Rep1


title: P57055, Dhh1-deletion, RPMI, R3

description:
Library name: P57055-DHH1-RPMI-Rep3
P57055-DHH1-RPMI-Rep3


title: SC5314, Dhh1-deletion, YPD, R3

description:
Library name: DHH1-YPD-Rep3
DHH1-YPD-Rep3


title: SC5314, Dhh1-deletion, YPD, R2

description:
Library name: DHH1-YPD-Rep2
DHH1-YPD-Rep2


title: P57055, Dhh1-deletion, RPMI, R1

description:
Library name: P57055-DHH1-RPMI-Rep1
P57055-DHH1-RPMI-Rep1


title: SC5314, WT, RPMI, R1

description:
Library name: WT-RPMI-Rep1
WT-RPMI-Rep1


title: SC5314, WT, RPMI, R2

description:
Library name: WT-RPMI-Rep2
WT-RPMI-Rep2


title: SC5314, Dhh1-deletion, RPMI, R1

description:
Library name: DHH1-RPMI-Rep1
DHH1-RPMI-Rep1


title: SC5314, WT, RPMI, R3

description:
Library name: WT-RPMI-Rep3
WT-RPMI-Rep3


title: SC5314, WT, YPD, R3

description:
Library name: WT-YPD-Rep3
WT-YPD-Rep3


title: sidouble_16h_flow_5/5

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

description:
Library name: P3253_RNA_45
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample

data_processing:
RNA-Seq reads were mapped to the human genome (GRCh38.p7) using STAR (version 2.7.3a). The reads were assigned to genes with FeatureCounts (version 2.0.3) using Gencode version 25 (Ensembl 85) annotation and the following parameters “ -t exon -g gene_id -s 2 -p”. Differential expression analysis was carried out using DESeq2 (version 1.38) using default parameters. Only genes with at least 5 reads in at least 3 samples were considered for the analysis.
Assembly: GRCh38.p7
Supplementary files format and content: Gene expression matrix, comma separated file with gene counts per sample

source_name: HUVECs

growth_protocol: HUVECs were grown in cell culture flasks in commerically available MV2 media (Promocell) in 37C, 5% CO2 incubator

extract_protocol:
Media is aspirated from flow slide. Monolayer is gently washed with PBS once. Two rounds of 200ul RLT buffer (Qiagen RNAesy kit) are used to lyse and collect the cells into tubes. Samples were kept in -80C until all experiments were concluded and extracted together in mixed batches to minimize variability.
mRNA-Seq libraries were constructed using NEBNext Ultra II RNA Poly(A) kit (NEB #E7765L)

treatment_protocol: siRNA protocol: on 70% confluent cells, using 10nM final concentration and RNAiMax transfection reagent for 5h. The following day, cells were seeded into flow slides (ibidi) at concentration of 2 million cells/ml. The following day, laminar shear stress was applied using the ibidi pump for 4h and 16h.

value: HUVECs

value: Human umbilical venous endothelial cells

value: siDouble

value: 16h laminar shear stress


title: sidouble_4h_flow_5/5

description:
Library name: P3253_RNA_42
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample

value: 4h laminar shear stress


title: sidouble_4h_flow_12/4

description:
Library name: P3253_RNA_41
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_flow_16h_13/4

description:
Library name: P3253_RNA_36
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: sidouble_16h_flow_30/3

description:
Library name: P3253_RNA_43
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: sidouble_16h_flow_12/4

description:
Library name: P3253_RNA_44
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: sidouble_stat_12/4

description:
Library name: P3253_RNA_38
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample

value: static


title: sidouble_stat_5/5

description:
Library name: P3253_RNA_39
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: sidouble_4h_flow_30/3

description:
Library name: P3253_RNA_40
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_flow_16h_10/3

description:
Library name: P3253_RNA_34
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: sidouble_stat_30/3

description:
Library name: P3253_RNA_37
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_flow_4h_17/3

description:
Library name: P3253_RNA_32
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_flow_4h_9/3

description:
Library name: P3253_RNA_31
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_flow_16h_17/3

description:
Library name: P3253_RNA_35
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_stat_13/4

description:
Library name: P3253_RNA_30
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_flow_4h_13/4

description:
Library name: P3253_RNA_33
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_stat_9/3

description:
Library name: P3253_RNA_28
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siSMAD4_16h_flow_13/4

description:
Library name: P3253_RNA_27
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siSMAD4_16h_flow_10/3

description:
Library name: P3253_RNA_25
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siSMAD4_16h_flow_17/3

description:
Library name: P3253_RNA_26
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siSMAD4_4h_flow_13/4

description:
Library name: P3253_RNA_24
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siSMAD4_4h_flow_9/3

description:
Library name: P3253_RNA_22
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siSMAD4_stat_13/4

description:
Library name: P3253_RNA_21
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siSMAD4_stat_17/3

description:
Library name: P3253_RNA_20
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siCtr_16h_flow_13/4

description:
Library name: P3253_RNA_18
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample

value: siCTRL


title: siSMAD4_stat_9/3

description:
Library name: P3253_RNA_19
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siCtr_16h_flow_17/3

description:
Library name: P3253_RNA_17
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siCtr_4h_flow_13/4

description:
Library name: P3253_RNA_15
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siCtr_4h_flow_17/3

description:
Library name: P3253_RNA_14
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siCtr_16h_flow_10/3

description:
Library name: P3253_RNA_16
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siCtr_4h_flow_9/3

description:
Library name: P3253_RNA_13
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siCtr_stat_13/4

description:
Library name: P3253_RNA_12
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: WT_16h_flow_10/3

description:
Library name: P3253_RNA_07
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample

value: wildtype


title: siCtr_stat_9/3

description:
Library name: P3253_RNA_10
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: WT_4h_flow_17/3

description:
Library name: P3253_RNA_05
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: siAlk1_stat_17/3

description:
Library name: P3253_RNA_29
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: WT_stat_9/3

description:
Library name: P3253_RNA_01
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: WT_stat_17/3

description:
Library name: P3253_RNA_02
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: WT_16h_flow_5/5

description:
Library name: P3253_RNA_09
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: WT_16h_flow_17/3

description:
Library name: P3253_RNA_08
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: WT_4h_flow_5/5

description:
Library name: P3253_RNA_06
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: male_CTRL

city: Freiburg

first: Achim

last: Lother

state: --- Select One ---

address: Albertstr. 25

department: Institute of experimental and clinical Pharmacology and Toxicology,

institute: University of Freiburg

description:
Library name: LA_2115_LIB-00052
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

data_processing:
We ran cellranger using following specifications: Cellranger Version:cellranger-7.0.0; transcriptome:mm10-2020-A; chemistry:SC3Pv3; include-introns=TRUE
R package SoupX (SoupX_1.6.2 ) was used with custom contamination fractions (LA_2109:0.15; LA_2111:0.05; LA_2112:0.05; LA_2115:0.1)  to remove ambient RNA signal.
Doublets were called using R package single cell doublet finder (scDblFinder_1.16.0) and removed from analysis.
Seurat pipeline was used for clustering, DEG analysis and data manipulation (Seurat_5.1.0;  SeuratObject_5.0.2). R package Harmony (harmony_1.2.1) was used for integration of data.
Cell-cell interactions were inferred with R package CellChat (CellChat_1.6.1)
Assembly: mm10-2020-A
Supplementary files format and content: fastq files contain demultiplexed raw fw and rv reads. rds file contains the final seurat object

molecule: nuclear RNA

source_name: heart, left atrium

extract_protocol:
The protocol is based on published work (Hocker, Sci. Adv. 2021 May;7(20)). In short, flash frozen tissue is homogenized via gentleMACS without enzymatic digestion at 4°C. Nuclei are filtered/centrifuged to remove debris and FAN-sorted to further purify the nuclei. Trypan blue staining was used to determine nuclei concentration, and adjusted to load 15,000 nuclei per sample onto the 10x Chromium Controller.
Single-nucleus GEM reactions and libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 kit (10x Genomics) as per manufacturer specifications (v3.1_User_Guide). Samples were amplified during cDNA preparation and library amplification for 12 cycles.

treatment_protocol: Adult male and female C57BL/6N wildtype mice were treated with aldosterone plus salt (ALDO, 500 µg/kg/d from osmotic minipumps, 1 % NaCl with drinking water)

value: heart, left atrium

value: male

value: aldosterone infusion


title: siSMAD4_4h_flow_17/3

description:
Library name: P3253_RNA_23
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: male_ALDO

description:
Library name: LA_2112_LIB-00051
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

value: untreated control


title: CD19_mock_5

city: Palo Alto

first: Michelle

last: Monje

state: California

address: 265 Campus Dr.

institute: Stanford University

description:
Library name: M6_S16_R1_001.fastq.gz
M6_S16.genes.results

data_processing:
Reads were mapped to mm38 annotation using STAR alignment (version 2.5.4b) and raw transcript expression was quantified as transcripts per million (tpm). Differential gene expression and log2 fold change calculations were determined using the DESeq2 (v.1.36.0) package in R. Volcano plot analysis was conducted using the R-based EnhancedVolcano (v1.14.0) package (https://github.com/kevinblighe/EnhancedVolcano).
Assembly: mm38
Supplementary files format and content: Raw TPM counts of gene abundance for murine microglia in csv format
Supplementary files format and content: Metadata table with sample key in csv format

source_name: Brain

extract_protocol:
cerebrum (whole brain minus the cerebellum) was dissected out and the tissue was digested and processed using the Multi Tissue Dissociation Kit (Miltenyi Biotech) followed by debris removal (Miltenyi Biotech).  Mouse F4/80+ cell selection was performed using F4/80+ selection kit (Biolegend). The viability of cells after the isolation process was typically over 90%.
F4/80+ cells were then processed with the Nextera XT Library Prep Kit (Illumina) to generate sequencing libraries following the manufacturer’s instructions.

treatment_protocol: Mice were treated with either tumor-clearing CD19 CAR T cells or mock T cell controls, and microglia was extacted from full cerebrum of mice at endpoint

value: Brain

value: Murine Microglia

value: Mock T cells


title: female_ALDO

description:
Library name: LA_2111_LIB-00050
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

value: female


title: CD19_treated_5

description:
Library name: L4_S14_R1_001.fastq.gz
L4_S14.genes.results

value: CD19- CAR T cells


title: CD19_treated_4

description:
Library name: L3_S13_R1_001.fastq.gz
L3_S13.genes.results


title: CD19_treated_3

description:
Library name: L2_S12_R1_001.fastq.gz
L2_S12.genes.results


title: CD19_treated_2

description:
Library name: L1_S11_R1_001.fastq.gz
L1_S11.genes.results


title: CD19_mock_4

description:
Library name: K9_S17_R1_001.fastq.gz
K9_S17.genes.results


title: CD19_mock_3

description:
Library name: K11_S19_R1_001.fastq.gz
K11_S19.genes.results


title: siCtr_stat_17/3

description:
Library name: P3253_RNA_11
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample

value: HUVECs


title: CD19_treated_1

description:
Library name: I4_S15_R1_001.fastq.gz
I4_S15.genes.results


title: CD19_mock_2

description:
Library name: K10_S18_R1_001.fastq.gz
K10_S18.genes.results


title: WT_stat_5/5

description:
Library name: P3253_RNA_03
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample

value: Human umbilical venous endothelial cells


title: WT_4h_flow_9/3

description:
Library name: P3253_RNA_04
B10 flowcell, 3 lanes, PE mode, 50mln reads per sample


title: TDP-43_Mid-Age_MouseBrain_IP_1

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

data_processing:
eCLIP data was analyzed using Skipper with default settings. The kDa of each ORF was matched to the closest input sample beginning at that range; for example, a 78 kDa ORF would be paired with the input sample covering the range of 75 to 150 kDa.
Assembly: hg38/mm10
Supplementary files format and content: Reproducible enriched peaks output by Skipper

source_name: Cerebellum

growth_protocol: DMEM, 15% FBS, 1X MEM NEAA for fibroblast culturing; mTeSR Plus for iPSC culturing; F12/Neurobasal, dox, db-cAMP, laminin, BDNF, GDNF, NT-3 for iPSC-derived neurons, F12/Neurobasal, dox, db-cAMP, laminin, DMH1, CHIR, SB, A83-01, forskolin for transdifferentiated neurons

extract_protocol: eCLIP experiments were performed as previously described using the antibodies indicated above in the "treatment" entry; see Blue et al. 2022 doi:10.1038/s41596-022-00680-z

treatment_protocol: Cells were either used as-is or treated for 1 h with 0.5 mM sodium arsenite; the RNA-binding protein in the file title was immuoprecipitated using the antibody listed in the "treatment" section prior to library preparation

value: Cerebellum

value: Neurons

value: Bethyl #A303-223A


title: TDP-43_Mid-Age_MouseBrain_IP_2


title: Cortex nuclei, GD2 CAR T treated, DIPG donor CART_D

description:
Library name: CART_D
Library names can be found in the "sampleid" observations column in the AnnData object contained in the "human_adata_object_filtered.h5ad" processed data file.

data_processing:
Preprocessing, alignment, and cell-by-gene matrix generation from FASTQ files was performed with Cell Ranger v7.0.1 (10X Genomics) using the prebuilt GRCh38-2024-A reference from 10X Genomics with the ‘--include-introns’ flag.
CellBender version 0.3.0 was used for ambient RNA removal with default parameters.
Resultant count matrices were aggregated into a single AnnData object using Scanpy v1.9.8.
Cells with less than 100 unique genes for which at least 1 UMI was detected and cells with fewer than 200 total UMIs were removed using Scanpy v1.9.8.
Doublets and multiplets were removed with scDoubletFinder v1.16.0.
Scater v1.30.1 was used to remove cells with total UMI counts or number of detected genes exceeding ±3 MADs, or a mitochondrial UMI percentage exceeding +3 MAD, from the within-sample and the across-sample medians.
Cells passing the above thresholds were additionally filtered to remove any remaining low complexity cells with fewer than 1000 total UMIs and 500 genes detected using Scanpy v1.9.8.
Assembly: GRCh38
Supplementary files format and content: hdf5 file storing AnnData object containing cell-level expression and metadata for all single cells (nuclei) from the aggregation of all samples

source_name: Brain cortex

extract_protocol:
Tissues were mechanically dissociated a Dounce pestle. Nuclei was pelleted and resuspended in resuspension buffer and centrifuged at 900g for another 15 minutes to pellet the nuclei. Supernatant was removed and nuclei were then stained by adding 1 mL of resuspension buffer containing 0.1 µg mL−1 of DAPI. Afterwards, nuclei were filtered through a 40 μm cell strainer into FACS tubes immediately prior to FACS sorting using a Sony MA900 sorter with a 70 µm chip. Single nuclei were sorted into chilled PCR tubes containing 10 µL of resuspension buffer. Nuclei were verified under microscope where counts were verified using a Fuchs-Rosenthal counting chamber.
Libraries were constructed using 10X Chromium Next GEM Single Cell 3′ HT Kits v.3.1.

treatment_protocol: DIPG patients received either CAR T cell therapy or not

value: Brain cortex

tag: diagnosis

value: DIPG

value: GD2 CAR T

tag: batch

value: B

value: Male


title: Cortex nuclei, no CAR T, DIPG donor Control_B

description:
Library name: Control_B
Library names can be found in the "sampleid" observations column in the AnnData object contained in the "human_adata_object_filtered.h5ad" processed data file.

value: No CAR T


title: TDP-43_Young-Age_MouseBrain_IP_3


title: TDP-43_Old-Age_MouseBrain_IP_1


title: TDP-43_Young-Age_MouseBrain_IP_2


title: TDP-43_Young-Age_MouseBrain_IP_1


title: Cortex nuclei, GD2 CAR T treated, DIPG donor CART_C

description:
Library name: CART_C
Library names can be found in the "sampleid" observations column in the AnnData object contained in the "human_adata_object_filtered.h5ad" processed data file.

value: A

value: Female


title: female_CTRL

description:
Library name: LA_2109_LIB-00049
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

value: heart, left atrium

value: untreated control


title: Cortex nuclei, no CAR T, DIPG donor Control_A

description:
Library name: Control_A
Library names can be found in the "sampleid" observations column in the AnnData object contained in the "human_adata_object_filtered.h5ad" processed data file.


title: Cortex nuclei, no CAR T, DIPG donor Control_C

description:
Library name: Control_C
Library names can be found in the "sampleid" observations column in the AnnData object contained in the "human_adata_object_filtered.h5ad" processed data file.


title: Cortex nuclei, GD2 CAR T treated, DIPG donor CART_B

description:
Library name: CART_B
Library names can be found in the "sampleid" observations column in the AnnData object contained in the "human_adata_object_filtered.h5ad" processed data file.


title: Cortex nuclei, GD2 CAR T treated, DIPG donor CART_A

description:
Library name: CART_A
Library names can be found in the "sampleid" observations column in the AnnData object contained in the "human_adata_object_filtered.h5ad" processed data file.


title: IMR90 cells, siZC3HC1 replicate 2

city: Edinburgh

first: Bethany

middle: M

last: Bartlett

address: Crewe Road South

country: United Kingdom

institute: University of Edinburgh

description:
Library name: siZC3HC1_2
SZ2

data_processing:
Reads were trimmed to remove adaptor sequences with cutadapt.
Raw Fastq files for each sample were merged and aligned to the human genome assembly hg19 using HISAT2 (Kim et al., 2019) with default parameters
Reads were assigned to genomic features using the featureCounts tool from the subread package (Liao et al., 2014).
Assembly: hg19
Supplementary files format and content: tab-delimited text format
Supplementary files format and content: RNA-seq feature counts per gene

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen).
Libraries were prepared from 500ng of each RNA sample using the NEBNext Ultra II Directional RNA library kit with PolyA enrichment module (New England Biolabs).  Libraries were assessed for quality and fragment size using the Agilent Bioanalyser and sequenced on NextSeq-2000 platform

treatment_protocol: Cells were transfected with a 30nM final concentration of predesigned control or ZC3HC1 siRNAs (Dharmacon). Transfections were carried out on day 0 (day of plating) and day 3.


title: IMR90 cells, siCTRL replicate 1

description:
Library name: siCTRL_1
SC1

value: siCTRL


title: IMR90 cells, siCTRL replicate 2

description:
Library name: siCTRL_2
SC2


title: CD19_mock_1

description:
Library name: H14_S20_R1_001.fastq.gz
H14_S20.genes.results

value: Brain

value: Murine Microglia

value: Mock T cells


title: IMR90 cells, siZC3HC1 replicate 1

description:
Library name: siZC3HC1_1
SZ1


title: Psoriasis34_preTx_LS_01

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

data_processing:
CellRanger version 3.1 (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v4.0).
Seurat R package (version 4.0, https://satijalab.org/seurat/) was used for the single-cell data integration. We first merged single-cell data of samples with the common sequencer and the identical reagent kit version. To harmonize merged groups into a single dataset without batch effects, correspondences between cells in three merged datasets were identified by the FIndIntegrationAnchors function, and used for data integration with the IntegratedData function in Seurat R package.
Principal component analysis and graph-based clustering analysis were performed with Seurat R package (version 4.0, https://satijalab.org/seurat/). Sixty principal components (PCs) were selected for Uniform Manifold Approximation and Projection (UMAP) for Dimension Reduction. With a resolution of 0.8, cells were clustered by the FindClusters function. Then, differentially expressed genes of each cluster compared to all other cells were found by the FindAllMarkers function. Differentially expressed genes between psoriasis and control within each cluster were found by the FindMarkers function. The average gene expression of psoriasis vs. control cells within a cluster was calculated by the AverageExpression function.
Assembly: GRCh38
Supplementary files format and content: barcode table, gene table and gene expression matrix files generated by Cell Ranger version 3.1.

source_name: Skin

extract_protocol:
6 mm punch skin biopsy tissues from human skin were bisected, and one of the two bisected skin tissues was incubated in culture medium for harvesting emigrating cells. Harvested skin tissue was immediately placed in 0.2% Dispase II (Sigma-Aldrich) and incubated in a humidified incubator at 37 Celsius and 5% CO2 for 3 hours. Then, epidermis and dermis were separated with forceps and sliced into small pieces with #10 blade scalpels. Epidermis and dermis were separately cultured in RPMI-1640 medium with L-glutamine (Cytiva) supplemented with 10% human albumin serum (Sigma-Aldrich) and without any enzyme or antibiotic agent in a humidified incubator at 37 Celsius and 5% CO2. Nonplastic adherent cells that had emigrated out of epidermis and dermis were harvested after 48 hours. The harvested cells from epidermis and dermis were filtered through a 40-µm cell strainer (Corning) and stored on ice.
The 10x Genomics Chromium Single Cell 3′ Reagents Kit user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep) was used to prepare the single cell suspension. The appropriate volume of each sample was diluted to recover 10,000 cells. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell chip. After droplet generation, samples were transferred into PCR tubes and we performed reverse transcription using a ProFlex PCR Thermocycler System (Applied Biosystems). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide.

value: Skin

tag: tissue type

value: LS

tag: timeline

value: Baseline


title: TDP-43_Old-Age_MouseBrain_IP_2

value: Cerebellum

value: Neurons

value: Bethyl #A303-223A


title: Psoriasis33_preTx_LS_01


title: TDP-43_Young-Age_MouseBrain_IP_4


title: Psoriasis31_preTx_NL_01

value: NL


title: Psoriasis32_preTx_LS_01


title: Psoriasis30_preTx_NL_01


title: Psoriasis33_preTx_NL_01


title: Psoriasis32_preTx_NL_01


title: Psoriasis30_preTx_LS_01


title: Psoriasis31_preTx_LS_01


title: Psoriasis29_preTx_NL_01


title: Psoriasis28_preTx_LS_01


title: Psoriasis27_preTx_NL_01


title: Psoriasis34_preTx_NL_01


title: Psoriasis27_preTx_LS_01


title: Psoriasis27_postTx_risankizumab_week28_LS_01

value: 7 months after the first risankizumab injection


title: Psoriasis26_postTx_risankizumab_week28_LS_01


title: Psoriasis26_preTx_LS_01


title: Psoriasis24_preTx_NL_01


title: Psoriasis29_preTx_LS_01


title: Psoriasis28_postTx_risankizumab_week28_LS_01


title: Psoriasis28_preTx_NL_01


title: Psoriasis25_preTx_LS_01


title: Psoriasis23_postTx_risankizumab_week28_LS_01


title: Psoriasis24_preTx_LS_01


title: Psoriasis22_postTx_risankizumab_week28_LS_01


title: Psoriasis23_preTx_LS_01


title: Psoriasis22_preTx_NL_01


title: Psoriasis23_preTx_NL_01


title: Psoriasis20_preTx_NL_01


title: Psoriasis19_preTx_NL_02


title: Psoriasis21_preTx_LS_01


title: Psoriasis21_postTx_risankizumab_week28_LS_01


title: Psoriasis22_preTx_LS_01


title: Psoriasis20_preTx_LS_01


title: Psoriasis19_preTx_NL_01


title: Psoriasis19_preTx_LS_01


title: Psoriasis18_preTx_LS_02


title: Psoriasis18_preTx_NL_02


title: Psoriasis18_preTx_NL_01


title: Psoriasis20_preTx_NL_02


title: Psoriasis13_preTx_NL_01


title: Psoriasis13_preTx_LS_01


title: Psoriasis13_postTx_risankizumab_week28_LS_01


title: Psoriasis18_preTx_LS_01


title: Psoriasis13_preTx_LS_02


title: Psoriasis21_preTx_NL_01


title: Psoriasis19_preTx_LS_02


title: Psoriasis10_postTx_risankizumab_week28_LS_02


title: Psoriasis10_postTx_risankizumab_week28_LS_01


title: Psoriasis10_preTx_LS_03


title: Psoriasis10_preTx_NL_01


title: Psoriasis13_postTx_risankizumab_week28_LS_02


title: Psoriasis10_preTx_LS_02


title: Psoriasis07_postTx_risankizumab_week28_LS_01


title: Psoriasis13_preTx_NL_02


title: Psoriasis07_preTx_NL_04


title: Psoriasis07_preTx_NL_03


title: Psoriasis07_preTx_LS_04


title: TransdifferentiatedNeurons_pre-stress_3

description:
featurecounts_recoveryRNA-Seq.txt
NK_U_C

data_processing:
RNA-Seq data was processed using the NF-Core architecture, which compiles several RNA-seq processing steps into a single executable command
Assembly: hg38
Supplementary files format and content: Feature counts for all detected transcripts in .csv format

extract_protocol:
RNA was extracted using Trizol and then further purified using the RNA Clean&Concentrator kit
Libraries were constructed using the Illumina Stranded mRNA Prep with IDT for Illumina adaptors

treatment_protocol: Cells were either used as-is, treated for 1 h with 0.5 mM sodium arsenite, or arsenite-treated and recovered for 24 h

value: Transdifferentiated cortical neurons


title: TransdifferentiatedNeurons_pre-stress_2

description:
featurecounts_recoveryRNA-Seq.txt
NK_U_B


title: Psoriasis07_preTx_LS_03


title: TransdifferentiatedNeurons_24h_recovery_2

description:
featurecounts_recoveryRNA-Seq.txt
NK_24_B

value: 0.5 mM sodium arsenite for 1 h, recovery for 24 h


title: TransdifferentiatedNeurons_24h_recovery_1

description:
featurecounts_recoveryRNA-Seq.txt
NK_24_A


title: TransdifferentiatedNeurons_0h_recovery_3

description:
featurecounts_recoveryRNA-Seq.txt
NK_0_C

value: 0.5 mM sodium arsenite for 1 h


title: Psoriasis10_preTx_NL_02


title: TransdifferentiatedNeurons_0h_recovery_1

description:
featurecounts_recoveryRNA-Seq.txt
NK_0_A


title: iPSC-DerivedNeurons_24h_recovery_3

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_24_C

value: iPSC-derived cortical neurons


title: iPSC-DerivedNeurons_pre-stress_2

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_U_B


title: iPSC-DerivedNeurons_24h_recovery_2

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_24_B


title: TransdifferentiatedNeurons_24h_recovery_3

description:
featurecounts_recoveryRNA-Seq.txt
NK_24_C


title: TransdifferentiatedNeurons_0h_recovery_2

description:
featurecounts_recoveryRNA-Seq.txt
NK_0_B


title: TransdifferentiatedNeurons_pre-stress_1

description:
featurecounts_recoveryRNA-Seq.txt
NK_U_A


title: iPSC-DerivedNeurons_pre-stress_1

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_U_A


title: iPSC-DerivedNeurons_24h_recovery_1

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_24_A


title: iPSC-DerivedNeurons_0h_recovery_1

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_0_A


title: iPSC-DerivedNeurons_pre-stress_3

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_U_C


title: iPSC-DerivedNeurons_0h_recovery_2

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_0_B


title: G3BP1_Old-Age_HumanBrain_IP_1

source_name: Frontal cortex

value: Frontal cortex

value: MBLI #RN048PW


title: G3BP1_Old-Age_HumanBrain_IP_3


title: Psoriasis07_postTx_risankizumab_week28_LS_02


title: G3BP1_Old-Age_HumanBrain_IP_2


title: G3BP1_Mid-Age_HumanBrain_IP_2


title: iPSC-DerivedNeurons_0h_recovery_3

description:
featurecounts_recoveryRNA-Seq.txt
Ngn2_0_C


title: G3BP1_Mid-Age_HumanBrain_IP_3


title: G3BP1_Mid-Age_HumanBrain_IP_1


title: HE_IL1aO2

city: Minato-ku

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

country: Japan

institute: The University of Tokyo

description: Library name: SAMPLE3

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary files format and content: Comma-delimited text files include RPM values for each sample.

source_name: Organoid-derived cell

extract_protocol:
Organoid dissociation was done by adding collagenase, pronase, and DNase at 37°C for 40 minutes in a water bath. Pipetting was carried out every ten minutes. RNA was extracted with PureLink™ RNA Micro Scale Kit (Invitrogen, Waltham, Massachusetts, USA) was used for RNA extraction from sorted cells.
RNA libraries were prepared using total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific).

value: Organoid-derived cell

value: hiPSC

value: HE

value: Control


title: HE_IL1a

description: Library name: SAMPLE2


title: HE_cont

description: Library name: SAMPLE1


title: 1K: 1749__11221_S11

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
1KCreMinus
processed data file: 1K_vs_2K.txt
processed data file: 1K_vs_2K_2.txt
processed data file: 1KcrePlus_vs_1KcreMinus.txt

data_processing:
Quality check of the Fastq files using FastQC v0.11.5.
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11.
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the mouse genome (mm10).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include the DESEQ2 output plus these columns: Symbol is the HUGO Gene symbols for Mus musculus; GeneID is the NCBI Gene ID; and Alias lists common aliases. Description is a brief description of the gene. The next columns represent raw read counts per gene labels come from the Sample Names. Briefly, these are 1KcreMinus vs. 1KcrePlus, 2KcreMinus vs. 2KcrePlus and 1K vs. 2K comparisons. 1K refers to unilateral nephrectomy, 2K refers to sham. Columns to the right of the Base Mean column represent DEseq2 output.

source_name: Kidney

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: 6-8 weeks old tamoxifen induced adult Pkd1 mice with and without cre (N=3 each) underwent unilateral nephrectomy (UNx) or sham and kidney was harvested 4 weeks later for RNA seq.

tag: mouse model

tag: genotype/variation

value: CreMinus

value: Kidney

value: Unilateral nephrectomy

value: Adult


title: 2K: 1748__11227_S10

description:
2KCrePlus
processed data file: 1K_vs_2K.txt
processed data file: 1K_vs_2K_2.txt
processed data file: 2KcrePlus_vs_2KcreMinus.txt
processed data file: 2KcrePlus_vs_2KcreMinus_2.txt
processed data file: 1KcrePlus_vs_2KcrePlus.txt

value: CrePlus

value: Sham nephrectomy


title: 1K: 1752__11224_S14


title: 1K: 1753__11225_S15

description:
1KCrePlus
processed data file: 1K_vs_2K.txt
processed data file: 1K_vs_2K_2.txt
processed data file: 1KcrePlus_vs_1KcreMinus.txt
processed data file: 1KcrePlus_vs_2KcrePlus.txt


title: 2K: 1744__11230_S6


title: 2K: 1755__2K-creplus_S1


title: 1K: 1750__11222_S12


title: 1K: 1751__11223_S13


title: 2K: 1747__11226_S9

description:
2KCreMinus
processed data file: 1K_vs_2K.txt
processed data file: 1K_vs_2K_2.txt
processed data file: 2KcrePlus_vs_2KcreMinus.txt
processed data file: 2KcrePlus_vs_2KcreMinus_2.txt


title: 2K: 1745__11220_S7


title: hiPSC-CM-D140, sample 2

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description: Library name: CMD140_2

data_processing:
Reads were mapped to human GRCh38 reference genome using STAR pipeline.
Then, for each gene, the count of transcripts for each sample was recorded via HtSeq.
Assembly: human GRCh38
Supplementary files format and content: Excel files, each file has the following columns: transcript ID (gene_ID), transcript count
Supplementary files format and content: See file RawCount.xlsx for all sample processed data.

source_name: Cardiac

growth_protocol: iPSC reprogramming was performed with a CytoTune™-iPS 2.0 Sendai Reprogramming Kit as directed by the manufacturer’s instructions. Briefly, cells were transduced with CytoTune™-iPS 2.0 Sendai reprogramming vectors and then transferred to feeder cells in fibroblast medium (DMEM supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids Solution, and 0.1% 2-mercaptoethanol). Putative hiPSC colonies were identified via Tra1-60 live staining, transferred into Matrigel-coated wells containing mTeSR medium, and expanded without feeder cells.

extract_protocol:
iPSC-CMs were trypsinized into single cells, fixed with fixation and permeabilization solution (51-2090KZ) for 30 minutes at 4 °C, and blocked in Human BD Fc Block (564219) at room temperature for 10 minutes. Cells were then incubated with primary antibodies and isotype control antibodies at room temperature for 40 minutes, incubated with corresponding fluorescently conjugated secondary antibodies for 30 minutes, and resuspended in wash buffer (554723). Flow cytometry was performed with an LSR Fortessa instrument (BD Biosciences, USA).
All cell lines RNA sequencing was performed by the Heflin Center for Genomic Sciences, the University of Alabama at Birmingham, using Illumina NextSeq500 platforms
RNA quality control was achieved by removing reads containing adapters, having more than 10% of undetermined bases, and low-quality reads. Less than 2% of these reads were removed in all samples.

value: Cardiac

value: human-induced pluripotent stem cell

value: iPS-CM

value: WT


title: hiPSC-CM-D140, sample 3

description: Library name: CMD140_3


title: hiPSC-CM-D16, sample 2

description: Library name: CMD16_2


title: hiPSC-CM-D16, sample 1

description: Library name: CMD16_1


title: 2K: 1746__11233_S8


title: hiPSC-CM-D16, sample 3

description: Library name: CMD16_3


title: B16-IFNA9 Tumours (Day 8) biol rep 10

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

institute: University of Western Australia

description: Library name: Sample_30

data_processing:
Read quality was assessed using FastQC (v0.11.3) followed by alignment to the mouse genome (mm11 reference) using HISAT2 (v2.0.4). Gene-level quantitation of aligned reads was calculated using SummerizeOverlaps (v1.7.2) and SAMStat (v1.5.2) used to perform post-alignment quality control.
Assembly: mm10
Supplementary files format and content: comma-delimited .csv file containing raw counts for each sample

source_name: Whole Tumour

extract_protocol:
Total RNA was extracted from whole tumours using TRIzol (Invitrogen, Waltham, USA) and purified using the RNEasy MinElute Kit (Qiagen, Hilden, Germany) according to manufacturers' instructions.
Sequencing libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit and 50 bp single-end read sequencing was performed using the Illumina HiSeq 2000 system (Illumina, San Diego, USA) according to manufacturer’s instructions.

value: Whole Tumour


title: B16-IFNA9 Tumours (Day 8) biol rep 8

description: Library name: Sample_28


title: B16-IFNA9 Tumours (Day 8) biol rep 9

description: Library name: Sample_29


title: B16-IFNA9 Tumours (Day 8) biol rep 7

description: Library name: Sample_27


title: hiPSC-CM-D140, sample 1

description: Library name: CMD140_1


title: B16-IFNA9 Tumours (Day 8) biol rep 3

description: Library name: Sample_23


title: B16-IFNA9 Tumours (Day 8) biol rep 4

description: Library name: Sample_24


title: B16-IFNA9 Tumours (Day 8) biol rep 5

description: Library name: Sample_25


title: B16-IFNA9 Tumours (Day 8) biol rep 2

description: Library name: Sample_22


title: B16-IFNA9 Tumours (Day 8) biol rep 6

description: Library name: Sample_26


title: 1K: 1754__11231_S16


title: B16-IFNA9 Tumours (Day 8) biol rep 1

description: Library name: Sample_21


title: B16-IFNA4 Tumours (Day 8) biol rep 9

description: Library name: Sample_19


title: B16-IFNA4 Tumours (Day 8) biol rep 4

description: Library name: Sample_14


title: B16-IFNA4 Tumours (Day 8) biol rep 5

description: Library name: Sample_15


title: B16-IFNA4 Tumours (Day 8) biol rep 6

description: Library name: Sample_16


title: B16-IFNA4 Tumours (Day 8) biol rep 3

description: Library name: Sample_13


title: B16-IFNA4 Tumours (Day 8) biol rep 7

description: Library name: Sample_17


title: B16-IFNA4 Tumours (Day 8) biol rep 8

description: Library name: Sample_18


title: B16-IFNA4 Tumours (Day 8) biol rep 1

description: Library name: Sample_11


title: Psoriasis20_preTx_LS_02

value: Skin

value: LS

value: Baseline


title: B16-GFP Tumours (Day 8) biol rep 10

description: Library name: Sample_10


title: B16-IFNA4 Tumours (Day 8) biol rep 2

description: Library name: Sample_12


title: B16-GFP Tumours (Day 8) biol rep 7

description: Library name: Sample_7


title: 577 Injured Zone (Infarct) Agrin Day 3

city: Rehovot

first: Shoval

last: Miyara

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
fastq files were generated by the usage bcl2fastq-v2.20.0.422 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the Sus scrofa genome build Sscrofa11 using STAR (2.7.3a)
Deduplication of reads with the same UMI (UMI is in read 2) was performed by PICARD (2.22.4) MarkDuplicate tool (using the BARCODE_TAG parameter)
Reads were counted using Ensembl annotations (release 103), using HTSeq-counts (version 0.11.2)
Normalization and differential expression analysis were performed using DESeq2 (1.26.0)
Assembly: Sscrofa11
Supplementary files format and content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary files format and content: Excel file includes the normalized counts (DESeq Normalization)

organism: Sus scrofa

source_name: Heart

extract_protocol:
Frozen samples were crushed into fine powder using a mortar and pestle and further processed using miRNeasy Mini Kit (Qiagen, Cat# 217004) according to manufacturer's guidelines.
Inhouse polyA based RNA seq.

value: Heart

tag: condition

value: Injured Zone (Infarct)

value: Agrin

tag: time

value: Day 3


title: B16-GFP Tumours (Day 8) biol rep 8

description: Library name: Sample_8


title: 577 Remote Zone (Healthy) Agrin Day 3

tag: cell line

value: Remote Zone (Healthy)


title: B16-GFP Tumours (Day 8) biol rep 9

description: Library name: Sample_9


title: 576 Remote Zone (Healthy) Agrin Day 3


title: B16-GFP Tumours (Day 8) biol rep 3

description: Library name: Sample_3


title: B16-GFP Tumours (Day 8) biol rep 4

description: Library name: Sample_4


title: 576 Injured Zone (Infarct) Agrin Day 3


title: B16-GFP Tumours (Day 8) biol rep 5

description: Library name: Sample_5


title: B16-GFP Tumours (Day 8) biol rep 2

description: Library name: Sample_2


title: 575 Injured Zone (Infarct) PBS Day 3

value: PBS


title: B16-GFP Tumours (Day 8) biol rep 1

description: Library name: Sample_1


title: Knockout

city: Omaha

first: Brian

last: North

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University School of Medicine

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0  (https://cloud.10xgenomics.com/cloud-analysis).
Assembly: Mouse (mm10) 2020-A
Supplementary files format and content: Tab-separated  value files and matrix files

extract_protocol:
E10.5 embryos were dissected in cold PBS and the yolk sac was removed for genotyping. The embryos were stored in 1% FBS (Cytvia, SH30910.03) on ice for 3 hours during genotyping. The yolk DNA was extracted and processed for genotyping with QuickExtract DNA Extraction Solution (Epicentre, QE09050). Embryonic hearts from embryos with desired genotypes were further microdissected. Four embryonic hearts were pooled together for each group. The dissected tissue was incubated in 200 L TrypLE (ThermoFisher Scientific, 12563029) for 5 minutes. The samples were triturated with a 200 L pipette tip and incubated for 5 minutes. After the incubation period, 600 L of PBS/1% FBS was added, and the cells were strained through a 70 m cell strainer (BD Falcon, 352350) and subsequently centrifuged at 150 x g for 3 minutes, supernatant removed and pelleted cells resuspended in 35 L PBS/1% FBS as described previously (24). Cell viability was assessed with Cellometer Auto T4 (Nexcelom bioscience).
Samples were used to prepare single cell droplet libraries in the 10X Genomics Chromium controller according to the Chromium Single Cell 3’ Reagent Kit User Guide with reagents from Single Cell 3’ Reagent Kit v3.1 (201456), library construction kit (201781), dual index plate TT set A (163910), and Chromium next gem chip G single cell kit (201862). Libraries were sequenced on the Illumina NextSeq 2000 and P2 100 cycle kit. Libraries were sequenced to 100 bp read length and 500 million read number.

tag: cell type

value: Cardiac cells

value: BubR1fl/fl ; Nkx2.5-cre (het)


title: Wildtype

description: 10x genomics

tag: genotype

value: BubR1+/+ ; Nkx2.5-cre (het)


title: B16-IFNA4 Tumours (Day 8) biol rep 10

description: Library name: Sample_20


title: 573 Remote Zone (Healthy) PBS Day 3


title: OA3 cells, shPINK1, sh2, Replicate 2

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 12
Library name: Sample 12

data_processing:
Adapter sequences and low-quality bases from RNA-seq raw reads were removed using Trim-Galore. Clean reads were aligned to the GRCh38 human reference genome using the STAR aligner and further quantified by HTSeq to generate a raw count matrix, which was subsequently normalized to transcripts per million (TPM) using a custom script.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: shPINK1_Control_count.matrix.txt

source_name: Bone. Marrow

growth_protocol: MOLM13 and OA3cells were routinely maintained in RPMI-1640 medium (Gibco, Carlsbad, CA, USA), supplemented with 10% fetal bovine serum (FBS) (Gibco).

extract_protocol:
Total RNA from control and PINK1 knockdown MOLM13, OA3 cells were isolated using RNeasy Mini Kits, and cDNA was synthesized from the isolated mRNA using QuantiTect Reverse Transcription Kit in accordance with the manufacturer protocols.
RNA-sequencing libraries were prepared using Illumina Stranded Total RNA prep.

value: Bone. Marrow

value: Acute Myeloid Leukemia

value: PINK1 knock down


title: 572 Remote Zone (Healthy) Agrin Day 3

value: WT


title: 573 Injured Zone (Infarct) PBS Day 3


title: OA3 cells, shPINK1, sh1, Replicate 1

description:
Library name: Sample 9
Library name: Sample 9


title: OA3 cells, shPINK1, sh1, Replicate 2

description:
Library name: Sample 10
Library name: Sample 10


title: OA3 cells, shPINK1, sh2, Replicate 1

description:
Library name: Sample 11
Library name: Sample 11


title: OA3 cells, shControl, Replicate 2

description:
Library name: Sample 8
Library name: Sample 8

value: Scambled Control


title: OA3 cells, shControl, Replicate 1

description:
Library name: Sample 7
Library name: Sample 7


title: MOLM13 cells, shPINK1, sh2, Replicate 1

description:
Library name: Sample 5
Library name: Sample 5


title: B16-GFP Tumours (Day 8) biol rep 6

description: Library name: Sample_6

value: Whole Tumour


title: 575 Remote Zone (Healthy) PBS Day 3


title: 571 Injured Zone (Infarct) PBS Day 3


title: MOLM13 cells, shPINK1, sh1, Replicate 1

description:
Library name: Sample 3
Library name: Sample 3


title: MOLM13 cells, shControl, Replicate 2

description:
Library name: Sample 2
Library name: Sample 2


title: 570 Remote Zone (Healthy) Agrin Day 3


title: MOLM13 cells, shPINK1, sh1, Replicate 2

description:
Library name: Sample 4
Library name: Sample 4


title: 572 Injured Zone (Infarct) Agrin Day 3


title: Immunoprecipitated (IP) RNA-seq sample from THP-1 cells for MeRIP-seq analysis

first: Yin

last: Zhang

address: No. 135, Xingang Xi Road

institute: SYSU

description: Library name: IP

data_processing:
Base calling software: BCL convert
Data filter: FastQC(0.11.9)，adapter and low-quality read removal
reads alignment: STAR(2.7.6a)
Peak calling: R package: MetPeak (1.1.0)
Assembly: eg GRCH38
Supplementary files format and content: realdata_peak.xlsx,which contains the called peaks from MeRIP-seq data of the THP-1 cell line.
Supplementary files format and content: input_CleanData_RPM.bedgraph, RPM-normalized coverage data for the input RNA sample in BEDGRAPH format, including chromosome, start/end positions, and signal intensity.
Supplementary files format and content: IP_CleanData_RPM.bedgraph, RPM-normalized coverage data for the m6A IP sample, used for m6A peak identification, stored in BEDGRAPH format with genomic coordinates and signal intensity.

source_name: male

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: male

value: cell line


title: 570 Injured Zone (Infarct) Agrin Day 3

value: Heart


title: 548 Injured Zone (Infarct) Agrin Day 28

value: Injured Zone (Infarct)

value: Day 28


title: scARC library, group 70305, 6hr_GEX

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description:
Library name: GEX_scARC_Library_70305_6
Library 70305, 6 hr post stimulation, contains cell lines CD0000039, CW50037, CW70079, CW70305, CW70344

library_source: other

data_processing:
10x Genomics Chromium single cell Multiome sequencing libraries were sequenced at UMGC on Novaseq S4 platform targeting pair-end (2 x 150bp) 50k reads per nuclei for ATAC library and 25K reads per nuclei for gene expression library. Briefly, after raw data collection, Illumina’s BCL2FASTQ software was used to de-multiplex and assemble the fastq files corresponding to reads (R1/R2) and indices (i5/i7) for Cell Ranger ARC. The fastq files were subsequently processed by 10x Genomics Cell Ranger ARC (v2.0.2) and aligned twice to both the human GRCh38.p14 genome and a contingent of human GRCh38.p14 and mouse GRCm38 provided by 10x Genomics for efficient identification and removal of rodent astrocytes. For snATAC-seq, the per-library Transcription Start Sites (TSS) enrichment score is usually between 7-9 and the Fraction of high-quality Reads overlapping Peaks (FRiP) is usually between 40%-80%. We excluded cells with >15% of the reads mapped to mitochondrial genes, cells with > 8,000 or < 400 number of features, and cells with > 40,000 or <500 number of UMI counts (filtered by 400 < nCount < 8,000 using Seurat).
For each library that contains cells derived from 3-4 iPSC lines, barcode-level identification was performed separately for snRNA-seq (GEX) and snATAC-seq data with genotyping information of all donors. Briefly, the BAM files generated from GEX and ATAC assays (gex_possorted_bam.bam and atac_possorted_bam.bam) were processed by demuxlet (Kang et al., 2018) with known genotype information provided as .vcf files. Barcodes (cells) identified as singlets with P1 likelihood (p1LLK) < 1x10-8 were collected, and only barcodes positively identified in both GEX and ATAC assays were retained for downstream analysis.
snRNA-seq (GEX) data were processed by extracting gene expression data from the .h5 files generated by Cell Ranger ARC. Only barcodes (cells) confidently assigned to individual iPSC lines were retained. With Seurat 5.1.0(Hao et al., 2024), for cell type assignmentsTo assign cell type identity, Leiden clustering was performed at the library level based on the first 30 PCs (or appropriate as determined by the elbowplot) and subsequently by comparing cell clusters and their marker gene expressions (GAD1, GAD2, SLC17A6, SLC17A7, NEFM) and added as metadata. The library-level gene expression matrices were subsequently collated in Seurat 5.1.0(Hao et al., 2024) as one large object with cell line-specific metadata assigned. Harmony (Korsunsky et al., 2019) was used to integrate the library-level gene matrices and removed sequencing batch-derived effects.
For snATAC-seq data, the aggregation function of Cell Ranger ARC was used to merge and generate new fragment files for MACS2-based peak calling with the CallPeaks() function in Signac(Stuart et al., 2021) with default settings. We made two merged fragment files, one containing all libraries from batch 024 (18 cell lines) and the other from batch 018, 024, 025, and 029 (76 cell lines). From each fragment file, we iterated througugh the combinations of cell types (NEFM+ glut, NEFM- glut, GABA) and stimulation stages (0 hr, 1 hr, 6 hr), which generated nine peak sets (cell type x time). We further generated a union peak set from batch 024 by setting CallPeaks(combine.peaks = TRUE) for peak analysis across different cell types. Finally, peaks that fell within the ENCODE blacklisted regions were removed. We also removed peaks that fall within chromosomes X and Y and the mitochondrial genome regions.
Assembly: hg38/GRCh38
Supplementary files format and content: CellRanger 2.0.2 output directory sans .bam files
Supplementary files format and content: h5, count matrices snATAC and snRNA-seq
Supplementary files format and content: .cloupe, 10x Genomics Loupe data file

molecule: other

source_name: Neuron

growth_protocol: We differentiated iPSC lines into both excitatory and inhibitory neurons and co-cultured with rate glial cells. For excitatory neuron differentiation, we used the method to derive Ngn2-glutamatergic neuron {Zhang, 2013 #6824}  with minor modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 5 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor, together with appropriate amount of rtTA virus and Ngn2-puro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. On DIV2 - DIV4, cells were treated with neural culture media (Neuralbasal media with 1x B27Plus and 1x Glutamax) supplemented with 2g/ml puromycin, 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, puromycin was withdrawn and cells were treated with neural culture media with 2ug/ml doxycycline. On DIV7, cells would be ready for replating. For generating excitatory neurons, we used the method to derive Ascl1/Dlx2-GABAergic neurons {Yang, 2017 #7817} with minopr modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 7 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor together with rtTA virus, Ascl1-puro virus and Dlx2-hygro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. From DIV2 - DIV4, cells were treated with neural culture media supplemented with 2g/ml puromycin, 150g/ml hygromycin and 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, cells were treated with neural culture media with 2g/ml doxycycline and 2M AraC. Cells would be ready for replating on DIV7. To co-culture the excitatory and inhibitory neurons,  on DIV7, separately cultured Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and primary rat cortical astrocytes (Thermofisher; N7745100) were dissociated using accutase at 37C for 15-20min. Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and astrocytes were replated at 5:5:1 ratio onto Matrigel pre-coated 12-well plate in neural culture media supplemented with 2g/ml doxycycline, 10ng/ml BDNF, 10ng/ml GDNF, 10ng/ml NT-3 and 1% FBS. For each co-culture,  we pooled cells from 3-4 donor lines with equal proportion. On DIV8, we refilled cells with more media. From DIV9 – DIV33, media was refreshed every three days with half volume change. Doxycycline was withdrawn at DIV14 and 1uMµM AraC was added in the media from DIV8-DIV17 to ensure neuron purity. DIV33 neurons were used for KCI stimulation.

extract_protocol:
After stimulation, cells were briefly washed with 1x PBS and dissociated in accutase at 37C for 40min with gentle shaking. After accutase incubation, we pipetted cells multiple times and filtered suspension twice with 40m tip filter (Sigma# BAH136800040-50EA) to obtain single cells. The washed cells were subjected to fresh nuclei isolation following 10x Genomics’ protocols (CG000365 and CG000338). For each library, around 15,000 freshly isolated nuclei were loaded for GEM capture targeting 10,000 nuclei recovery.
The pre-amplified DNAs (for snATAC-seq) and cDNAs (for snRNA-seq) were shipped to University of Minnesota Genomics Center  (UMGC) for sn-multiomics sequencing library construction following 10x Genomics’ standard protocol.

treatment_protocol: To model neuron activation, we followed previously used protocol to treat the cells with KCI {Boulting, 2021 #8234}. Briefly, 24hr before stimulation, old media was aspirated and DIV33 neuron co-culture were silenced in neural culture media supplemented with 1M TTX and 100M DL-AP5. The next day, we added fresh culture media with warmed depolarization solution (10mM HEPES, 170mM KCl, 1mM MgCl2, 2mM CaCl2) to initiate KCI stimulation. We prepared three conditions with different treatment duration (0hr, 1hr and 6hr). After stimulation, cells were dissociated for 10x Genomics’ sn-Multiomics sequencing library preparation.

value: Neuron

value: cultured glutamatergic and GABAergic neurons derived from iPS cells


title: 571 Remote Zone (Healthy) PBS Day 3

value: Remote Zone (Healthy)

value: PBS

value: Day 3


title: MOLM13 cells, shControl, Replicate 1

description:
Library name: Sample 1
Library name: Sample 1


title: scARC library, group 70305, 1hr_GEX

description:
Library name: GEX_scARC_Library_70305_1
Library 70305, 1 hr post stimulation, contains cell lines CD0000039, CW50037, CW70079, CW70305, CW70344


title: scARC library, group 70305, 0hr_GEX

description:
Library name: GEX_scARC_Library_70305_0
Library 70305, unstimulated, contains cell lines CD0000039, CW50037, CW70079, CW70305, CW70344


title: RNA-seq input sample from THP-1 cells for MeRIP-seq analysis

city: Guangzhou

description: Library name: input


title: scARC library, group 50094, 6hr_GEX

description:
Library name: GEX_scARC_Library_50094_6
Library 50094, 6 hr post stimulation, contains cell lines CW50021, CW50023, CW50094, CW50150, CW70282


title: 548 Remote Zone (Healthy) Agrin Day 28

value: Agrin


title: scARC library, group 50094, 1hr_GEX

description:
Library name: GEX_scARC_Library_50094_1
Library 50094, 1 hr post stimulation, contains cell lines CW50021, CW50023, CW50094, CW50150, CW70282


title: scARC library, group 50094, 0hr_GEX

description:
Library name: GEX_scARC_Library_50094_0
Library 50094, unstimulated, contains cell lines CW50021, CW50023, CW50094, CW50150, CW70282


title: MOLM13 cells, shPINK1, sh2, Replicate 2

description:
Library name: Sample 6
Library name: Sample 6

value: Bone. Marrow


title: 547 Injured Zone (Infarct) PBS Day 28


title: scARC library, group 20111, 6hr_GEX

description:
Library name: GEX_scARC_Library_20111_6
Library 20111, 6 hr post stimulation, contains cell lines CW20111, CW50059, CW50148, CW70030


title: scARC library, group 20063, 6hr_GEX

description:
Library name: GEX_scARC_Library_20063_6
Library 20063, 6 hr post stimulation, contains cell lines CW20063, CW20079, CW20112, CW20137


title: scARC library, group 20111, 1hr_GEX

description:
Library name: GEX_scARC_Library_20111_1
Library 20111, 1 hr post stimulation, contains cell lines CW20111, CW50059, CW50148, CW70030


title: scARC library, group 20111, 0hr_GEX

description:
Library name: GEX_scARC_Library_20111_0
Library 20111, unstimulated, contains cell lines CW20111, CW50059, CW50148, CW70030


title: 544 Remote Zone (Healthy) Agrin Day 28


title: scARC library, group 20063, 0hr_GEX

description:
Library name: GEX_scARC_Library_20063_0
Library 20063, unstimulated, contains cell lines CW20063, CW20079, CW20112, CW20137


title: 544 Injured Zone (Infarct) Agrin Day 28


title: scARC library, group 70305, 6hr_ATAC

description:
Library name: scARC_Library_70305_6
Library 70305, 6 hr post stimulation, contains cell lines CD0000039, CW50037, CW70079, CW70305, CW70344


title: 536 Remote Zone (Healthy) PBS Day 28


title: scARC library, group 70305, 0hr_ATAC

description:
Library name: scARC_Library_70305_0
Library 70305, unstimulated, contains cell lines CD0000039, CW50037, CW70079, CW70305, CW70344


title: 536 Injured Zone (Infarct) PBS Day 28


title: scARC library, group 70305, 1hr_ATAC

description:
Library name: scARC_Library_70305_1
Library 70305, 1 hr post stimulation, contains cell lines CD0000039, CW50037, CW70079, CW70305, CW70344


title: scARC library, group 50094, 6hr_ATAC

description:
Library name: scARC_Library_50094_6
Library 50094, 6 hr post stimulation, contains cell lines CW50021, CW50023, CW50094, CW50150, CW70282


title: scARC library, group 50094, 1hr_ATAC

description:
Library name: scARC_Library_50094_1
Library 50094, 1 hr post stimulation, contains cell lines CW50021, CW50023, CW50094, CW50150, CW70282


title: scARC library, group 50094, 0hr_ATAC

description:
Library name: scARC_Library_50094_0
Library 50094, unstimulated, contains cell lines CW50021, CW50023, CW50094, CW50150, CW70282


title: 523 Remote Zone (Healthy) PBS Day 28


title: scARC library, group 20063, 6hr_ATAC

description:
Library name: scARC_Library_20063_6
Library 20063, 6 hr post stimulation, contains cell lines CW20063, CW20079, CW20112, CW20137


title: scARC library, group 20111, 0hr_ATAC

description:
Library name: scARC_Library_20111_0
Library 20111, unstimulated, contains cell lines CW20111, CW50059, CW50148, CW70030


title: 522 Remote Zone (Healthy) Agrin Day 28


title: scARC library, group 20063, 0hr_ATAC

description:
Library name: scARC_Library_20063_0
Library 20063, unstimulated, contains cell lines CW20063, CW20079, CW20112, CW20137


title: 522 Injured Zone (Infarct) Agrin Day 28


title: scARC library, group 20063, 1hr_ATAC

description:
Library name: scARC_Library_20063_1
Library 20063, 1 hr post stimulation, contains cell lines CW20063, CW20079, CW20112, CW20137


title: 523 Injured Zone (Infarct) PBS Day 28


title: 547 Remote Zone (Healthy) PBS Day 28


title: scARC library, group 60060, 6hr_GEX

description:
Library name: GEX_scARC_Library_60060_6
Library 60060, 6 hr post stimulation, contains cell lines CW60060, CW70224, CW70316, CW70330


title: scARC library, group 60060, 1hr_GEX

description:
Library name: GEX_scARC_Library_60060_1
Library 60060, 1 hr post stimulation, contains cell lines CW60060, CW70224, CW70316, CW70330


title: 519 Injured Zone (Infarct) Agrin Day 28


title: scARC library, group 60060, 0hr_GEX

description:
Library name: GEX_scARC_Library_60060_0
Library 60060, unstimulated, contains cell lines CW60060, CW70224, CW70316, CW70330


title: 519 Remote Zone (Healthy) Agrin Day 28


title: scARC library, group 50040, 1hr_GEX

description:
Library name: GEX_scARC_Library_50040_1
Library 50040, 1 hr post stimulation, contains cell lines CW20080, CW20144, CW50040, CW50166


title: scARC library, group 20063, 1hr_GEX

description:
Library name: GEX_scARC_Library_20063_1
Library 20063, 1 hr post stimulation, contains cell lines CW20063, CW20079, CW20112, CW20137


title: scARC library, group 50040, 0hr_GEX

description:
Library name: GEX_scARC_Library_50040_0
Library 50040, unstimulated, contains cell lines CW20080, CW20144, CW50040, CW50166


title: Neuron_OX

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
Libray preparison:mRNA is enriched by using the oligo(dT) magnetic beads, following to be fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer and M-MuLV Reverse Transcriptase . Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with AMPure XP beads.  Remaining overhangs of the purified  cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system. Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.
Sequencing: The library products are ready for sequencing via Illumina HiSeq 2500.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.   The clean reads were mapped to human reference sequences and/or reference gene set using TopHat2(Kim et al, 2013). FPKM(Fragments Per Kilo bases per Million reads) is used to estimate gene expression level. Readcount was adjusted by TMM, then differential expression analysis was performed by using the DEGseq R package.
The software GOseq (Young et al., 2010) was used for Gene Ontology (OG) enrichment analysis.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample.

growth_protocol: iPS cells were generated from Primary fibroblasts with CytoTune®-iPS 2.0 Sendai Reprogramming Kit (Life Technologies) using a multiplicity of infection of 5:5:3 (KOS:c-Myc:Klf4). Individual colonies with typical morphology of human embryonic stem cells (hESC) were manually picked around 3-4 weeks after infection. The IPS were continuously cultured and expanded on Geltrex coated 6-well plates with Essential 8 medium. Differentiation of iPS towards neural lineage was performed as described by Mariani, J. et al 2015 (Cell 162) with modifications. Briefly, IPS were pretreated with 50 uM Y-27632 (Stemcell Technologies) for 1 h. Then the cells were dissociated with Accutase (Stemcell Technologies) and plated onto low attachment V-type 96-well plate at 20,000 cells per well or AggreWellTM800 plate (Stemcell Technologies) to form aggregates. The culture was maintained in neural induction medium consisting of DMEM/F12 supplemented with 2% B27 supplement without vitamin A, 1% N2 supplement, 200 nM Noggin (R & D Systems) and 10 uM Y-27632 for 48 h. Formed aggregates (Embryoid body, EB) were then transferred onto low attachment 6-well plates and continued culture for another 4 days. To induce neural rosette formation, the aggregates were transferred onto Geltrex coated 6-well plate and cultured for 4 days in neural induction medium supplemented with 200 ng/ml Noggin, 200 ng/ml DKK1 (R & D Systems) and 20 ng/ml bFGF (Life Technologies). Neural rosettes were picked and transferred onto low attachment 6-well plate in neural induction medium supplemented with 10 ng/ml bFGF and 10 ng/ml EGF to allow neuroepithelial sphere formation for five days. The NES were dissociated into single cells with Accutase and replated onto poly-D-lysine/laminin coated 24 or 48-well plates and cultured for 5 days with neural differentiation medium supplemented with 10 ng/ml BDNF, 10 ng/ml GDNF, 200 uM ascorbic acid, 500 uM cyclic AMP.

tag: phenotype

value: OXR1 deficient patient

value: OXR1 mutation


title: scARC library, group 20088, 6hr_GEX

description:
Library name: GEX_scARC_Library_20088_6
Library 20088, 6 hr post stimulation, contains cell lines CW20058, CW20777, CW20088, CW60109


title: scARC library, group 50040, 6hr_GEX

description:
Library name: GEX_scARC_Library_50040_6
Library 50040, 6 hr post stimulation, contains cell lines CW20080, CW20144, CW50040, CW50166


title: scARC library, group 20088, 1hr_GEX

description:
Library name: GEX_scARC_Library_20088_1
Library 20088, 1 hr post stimulation, contains cell lines CW20058, CW20777, CW20088, CW60109


title: scARC library, group 20088, 0hr_GEX

description:
Library name: GEX_scARC_Library_20088_0
Library 20088, unstimulated, contains cell lines CW20058, CW20777, CW20088, CW60109


title: scARC library, group 20111, 1hr_ATAC

description:
Library name: scARC_Library_20111_1
Library 20111, 1 hr post stimulation, contains cell lines CW20111, CW50059, CW50148, CW70030


title: scARC library, group 20111, 6hr_ATAC

description:
Library name: scARC_Library_20111_6
Library 20111, 6 hr post stimulation, contains cell lines CW20111, CW50059, CW50148, CW70030


title: NA_OX

source_name: Neural aggregate

extract_protocol: mRNA is enriched by using the oligo(dT) magnetic beads, following to be fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer and M-MuLV Reverse Transcriptase . Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with AMPure XP beads.  Remaining overhangs of the purified  cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system. Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

value: Neural aggregate


title: scARC library, group 20087, 0hr_GEX

description:
Library name: GEX_scARC_Library_20087_0
Library 20087, unstimulated, contains cell lines CW20087, CW60134, CW70001, CW70177


title: scARC library, group 60060, 6hr_ATAC

description:
Library name: scARC_Library_60060_6
Library 60060, 6 hr post stimulation, contains cell lines CW60060, CW70224, CW70316, CW70330

library_source: genomic single cell

molecule: genomic DNA


title: scARC library, group 20087, 1hr_GEX

description:
Library name: GEX_scARC_Library_20087_1
Library 20087, 1 hr post stimulation, contains cell lines CW20087, CW60134, CW70001, CW70177


title: NA_WT

value: Healthy control

value: healthy control


title: scARC library, group 20087, 6hr_GEX

description:
Library name: GEX_scARC_Library_20087_6
Library 20087, 6 hr post stimulation, contains cell lines CW20087, CW60134, CW70001, CW70177


title: iPSC_OX

source_name: induced pluripotent stem cell

value: induced pluripotent stem cell


title: scARC library, group 60060, 1hr_ATAC

description:
Library name: scARC_Library_60060_1
Library 60060, 1 hr post stimulation, contains cell lines CW60060, CW70224, CW70316, CW70330


title: scARC library, group 60060, 0hr_ATAC

description:
Library name: scARC_Library_60060_0
Library 60060, unstimulated, contains cell lines CW60060, CW70224, CW70316, CW70330


title: scARC library, group 50040, 1hr_ATAC

description:
Library name: scARC_Library_50040_1
Library 50040, 1 hr post stimulation, contains cell lines CW20080, CW20144, CW50040, CW50166


title: scARC library, group 50040, 0hr_ATAC

description:
Library name: scARC_Library_50040_0
Library 50040, unstimulated, contains cell lines CW20080, CW20144, CW50040, CW50166


title: Urine cells, lupus nephritis patient, ADT

first: Jan

last: Klocke

address: Charitéplatz 1

department: Nephrology and Intesive Care

institute: Charité Universitätsmedizin Berlin

data_processing:
fastqc to check quality of sequencing reads
cellranger (v3.1) mkfastq to demultiplex fastq files
cellranger (v3.1) count to align sequencing files to a reference transcriptome
Assembly: Assembly: GRCh38
Supplementary files format and content: provide library.csv and feature_ref.csv for cellranger (v3.1) count of ADT samples
Supplementary files format and content: Tab-separated UMI counts in matrix.mtx. List of genes in features.tsv List of cell barcodes in barcodes.tsv
Library strategy: CITE-seq

source_name: urine

extract_protocol:
Samples were collected either as first morning void urine or via urinary catheter (using the pooled urine output of 4 hours) and stored on ice. Incubation with Actinomycin D for 30 min on ice was applied to prevent subsequent alteration of transcriptomes followed by blocking Fc receptors using human FcR blocking reagent (Miltenyi, Bergisch Gladbach, Germany). Cells were then incubated with fluorescent dyes and fluorochrome-conjugated monoclonal antibodies for fluorescence-activated cell sorting (FACS). The following antibodies and dyes were used for cell labeling: Calcein AM (BD Biosciences, San Jose, CA, USA, 564061), Hoechst 33342 (BD Biosciences, San Jose, CA, USA, 561908), AnnexinV-PE (Biolegend, San Diego, CA, USA, 640908), CD45-APC/Vio770 and CD66b-PE/Vio770 (both Miltenyi, 130-110-635 and 130-119-768). Cells were washed, filtered through a 70 µm cell strainer and labeled with To-Pro3 iodide (T3605, Life technologies, Eugene, Oregon) for dead cell discrimination immediately prior to sorting. Samples were sorted using a Sony MA900 (Sony, Tokyo, Japan) with a 100µm nozzle into phosphate buffered saline (PBS) / 1 % BSA gating To-Pro3-AnnexinV- Hoechst33342+CalceinAM+ singlets for obtaining single viable urinary cells. Urinary granulocytes, which make up a large fraction of the urinary cellular signal (median 58% in FACS gating) but for which a renal tissue origin is not verifiable, and which may interfere with downstream analysis, were excluded. Relative single cell counts in sorted suspensions were counted using a MACSQuant Analyzer (Miltenyi). Cells were centrifuged, resuspended, and re-counted on a hemocytometer. Cell suspensions were subjected to single-cell sequencing following the 10x Genomics protocol for Chromium Next GEM Single Cell  v3.1 chemistry targeting between 1000 - 10000 cells depending on sample cell count.
According to manufacturer recommendation of Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1

value: urine

tag: patient

value: lupus nephritis patient

tag: library type

value: adt

tag: adt

value: TotalSeq-B0062 anti-human CD10, TotalSeq-B0364 anti-human CD13, TotalSeq-B0180 anti-human CD24, TotalSeq-B0073 anti-human CD44, TotalSeq-B0952 Streptavidin (binding anti-human CD133 biotin (miltenyi 130-113-669), TotalSeq-B0123 anti-human CD326


title: iPSC_WT


title: scARC library, group 50040, 6hr_ATAC

description:
Library name: scARC_Library_50040_6
Library 50040, 6 hr post stimulation, contains cell lines CW20080, CW20144, CW50040, CW50166

value: Neuron


title: scARC library, group 20088, 6hr_ATAC

description:
Library name: scARC_Library_20088_6
Library 20088, 6 hr post stimulation, contains cell lines CW20058, CW20777, CW20088, CW60109

value: cultured glutamatergic and GABAergic neurons derived from iPS cells


title: Urine cells, pool of 2 AKI patients, ADT

value: pool of 2 AKI patients


title: scARC library, group 20088, 1hr_ATAC

description:
Library name: scARC_Library_20088_1
Library 20088, 1 hr post stimulation, contains cell lines CW20058, CW20777, CW20088, CW60109


title: scARC library, group 20088, 0hr_ATAC

description:
Library name: scARC_Library_20088_0
Library 20088, unstimulated, contains cell lines CW20058, CW20777, CW20088, CW60109


title: scARC library, group 20087, 1hr_ATAC

description:
Library name: scARC_Library_20087_1
Library 20087, 1 hr post stimulation, contains cell lines CW20087, CW60134, CW70001, CW70177


title: Urine cells,  membranous nephropathy patient, ADT

value: membranous nephropathy patient


title: scARC library, group 20087, 6hr_ATAC

description:
Library name: scARC_Library_20087_6
Library 20087, 6 hr post stimulation, contains cell lines CW20087, CW60134, CW70001, CW70177


title: scARC library, group 20087, 0hr_ATAC

description:
Library name: scARC_Library_20087_0
Library 20087, unstimulated, contains cell lines CW20087, CW60134, CW70001, CW70177


title: Neuron_WT


title: Urine cells, pool of 4 AKI patients, ADT

value: pool of 4 AKI patients


title: scARC library, group 63, 6 hr_GEX

description:
Library name: GEX_scARC_Library_63_6
Library 63, 6 hr post stimulation, contains cell lines CD0000004, CD0000063, CD0000064, CD0000065


title: scARC library, group 63, 1 hr_GEX

description:
Library name: GEX_scARC_Library_63_1
Library 63, 1 hr post stimulation, contains cell lines CD0000004, CD0000063, CD0000064, CD0000065


title: Urine cells, lupus nephritis patient, GEX

value: rna


title: scARC library, group 63, 0 hr_GEX

description:
Library name: GEX_scARC_Library_63_0
Library 63, unstimulated, contains cell lines CD0000004, CD0000063, CD0000064, CD0000065


title: scARC library, group 51, 1 hr_GEX

description:
Library name: GEX_scARC_Library_51_1
Library 51, 1 hr post stimulation, contains cell lines CD0000051, CD0000060, CD0000062, CD0000066


title: scARC library, group 51, 6 hr_GEX

description:
Library name: GEX_scARC_Library_51_6
Library 51, 6 hr post stimulation, contains cell lines CD0000051, CD0000060, CD0000062, CD0000066


title: Urine cells, pool of 2 AKI patients, GEX


title: scARC library, group 51, 0 hr_GEX

description:
Library name: GEX_scARC_Library_51_0
Library 51, unstimulated, contains cell lines CD0000051, CD0000060, CD0000062, CD0000066


title: scARC library, group 35, 1 hr_GEX

description:
Library name: GEX_scARC_Library_35_1
Library 35, 1 hr post stimulation, contains cell lines CD0000035, CD0000050,  CD0000056