title: bulk RNA-Seq C7d_rep2

city: beijing

first: xu

last: jie

state: beijing

address: No. 35 Qinghua East Road, Haidian District

institute: Beijing Forestry University

data_processing:
The clean reads were mapped to the Pinus taeda reference genome (v.1.01; https://treegenesdb.org/FTP/Genomes/Pita/v1.01/) using Spliced Transcripts Alignment to a Reference (version 2.5.0) software.
The clean reads were mapped to the Pinus taeda reference genome (v.1.01; https://treegenesdb.org/FTP/Genomes/Pita/v1.01/) (Kovach et al., 2010) using Spliced Transcripts Alignment to a Reference (version 2.5.0) software (Dobin et al., 2013). FeatureCounts (version 1.5.3) (Liao et al., 2014) was used in the process of quantifying gene expression, and the counts were then normalized to the TPM (transcripts per million) values.
Supplementary_files_format_and_content: raw counts, FASTA of transcript sequences is available on the series record.

organism: Pinus tabuliformis

source_name: Foliage of Pinus tabuliformis

growth_protocol: To be more specific, we used 2.5-year-old P. tabuliformis seedlings which were arranged in two rows in a greenhouse setting on cultivation shelves. Seedlings were grown in 1.5L pots filled with peat/perlite/vermiculite mixture (3:1:1), and maintained under the following growth conditions: 25℃ constant temperature and ~50% air relative humidity, 12-hr light (8:00 to 20:00) followed by a 12-hr darkness. Light was provided by common fluorescent lamps (wavelengths of 380-700nm and peaking at λ=540nm, provided by T5 28W fluorescence lamps, Hengxing, Zhengzhou, China) with 10cm distance from the top of the seedlings, reaching the foliage with 1,300μmol*m-2*s-1 irradiance.

extract_protocol:
Messenger RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module. RNA quality was determined using an Agilent 2100 BioAnalyzer. Sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit (Illumina Inc., San Diego, CA, USA).
The cDNA library was pair-end sequenced on Illumina HiSeq 2500 at 2×150 bp read length. Adapters and low-quality sequence reads were removed using Trimmomatic (version 0.36).

treatment_protocol: In our greenhouse experiments, we used 180 P. tabuliformis seedlings, randomly and equally divided into different treatment groups with 20 individuals/group: i) one control group (0h: no UV-B or UV-C irradiation), ii) four treatment groups with each group exposed to a different UV-B irradiation duration [4 hours (B4h), 1 day (B1d), 3 days (B3d), and 7 days (B7d)], and iii) four treatment groups exposed to four different UV-C durations [4 hours (C4h), 1 day (C1d), 3 days (C3d), and 7 days (C7d)] (Figure 1A). UV-B or UV-C was added to original illumination, and for the different treatment groups, seedlings were exposed to UV-B and UV-C radiation intensities of 280μW/cm2 (280-320nm; peaking at 306nm) and 28μW/cm2 (230–270 nm; peaking at 254nm), respectively, provided by UV-B lamps (FLB4T5E/5D 40W, Huaqiang, Jiangsu, China) and UV-C lamps (UV40W15-S1194, Liangyueliang, Guangzhou, China), respectively.

value: replicate = Irradiated by ultraviolet C radiation for 7 d 1

value: leaves

value: 2.5 years


title: bulk RNA-Seq C7d_rep3

status: Public on Oct 10 2022

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

tag: treatment

value: replicate = Irradiated by ultraviolet C radiation for 7 d 2

tag: tissue

tag: age


title: bulk RNA-Seq C3d_rep3

value: replicate = Irradiated by ultraviolet C radiation for 3 d 2


title: bulk RNA-Seq C3d_rep1

value: Irradiated by ultraviolet C radiation for 3 d


title: bulk RNA-Seq C3d_rep2

value: replicate = Irradiated by ultraviolet C radiation for 3 d 1


title: cHL biopsy, 14D

type: RNA

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

hyb_protocol: In brief, 5 μL of each sample were mixed with 8 μL of the hybridization cocktail (4 μL of the reporter codeset and 4 μL of hybridization buffer).Two μL of the capture codeset were added; the solution was mixed and spun down. It was then hybridized in a 65°C thermocycler (Veriti Thermal Cycler, Applied Biosystems, Foster City, CA, USA) for 16 hours.

scan_protocol: Hybridized samples were analyzed on the nCounter NanoString Preparation Station us-ing the high-sensitivity protocol, whereby excess capture and reporter probes were washed away and ternary target probe complexes were immobilized on a streptavidin-coated cartridge. Samples were scanned at maximum resolution on the nCounter Dig-ital Analyzer (NanoString Technologies, Seattle, WA).

data_processing:
Data were analyzed using ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, identity heatmaps, and sample Multidimensional Scaling (MDS) plots were generated as part of the QC step. Housekeeping probes used for normalization were se-lected based on the geNorm algorithm as implemented in the NormqPCR R library. Fold changes and p-values were calculated using nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment was performed using the Benjamini-Hochberg method of es-timating false discovery rates (FDR). Hypergeometric distribution was used to analyze the enrichment of pathways. The topGO R library was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including REACTOME. Further analyzes were performed and figures were generated with Graphpad Prism 9.0.0 and R v3.6.3, using Rstudio v1.2.5033. Hierarchical clustering and heatmaps were generated with the pheatmap package. Volcano plots were obtained using the EnhancedVolcano package. Lastly, the correlation matrix was created with the corrplot package.
normalized count after housekeeping genes normalization

label: biotin tag

molecule: total RNA

organism: Homo sapiens

source_name: lymph node

label_protocol: biotin tag

extract_protocol: RNA from each sample was extracted using the High Pure FFPET RNA Isolation Kit (Roche), following the manufacturer’s protocol. For each RNA extraction, the tumor con-tent was confirmed through histopathological evaluation performed by a certified pathologist. All 66 biological samples passed quantification and quality controls (QC) using the Agilent Bioanalyzer (BA) (2100 Bioanalyzer Instrument, Santa Clara, CA, USA).

tag: individual

value: patient 14

value: lymph node

value: other

value: EBVneg

tag: prognosis

value: relapse

value: DIAG

tag: ann arbor stage


title: bulk RNA-Seq C1d_rep2

value: replicate = Irradiated by ultraviolet C radiation for 1 d 1


title: bulk RNA-Seq C1d_rep3

value: replicate = Irradiated by ultraviolet C radiation for 1 d 2


title: cHL biopsy, 7R

value: patient 7

value: BEACOPP


title: bulk RNA-Seq B7d_rep3

value: replicate = Irradiated by ultraviolet radiation for 7 d 2


title: bulk RNA-Seq C7d_rep1

value: Irradiated by ultraviolet C radiation for 7 d

value: leaves


title: bulk RNA-Seq B7d_rep2

value: replicate = Irradiated by ultraviolet radiation for 7 d 1

value: 2.5 years


title: bulk RNA-Seq C1d_rep1

value: Irradiated by ultraviolet C radiation for 1 d


title: bulk RNA-Seq B7d_rep1

value: Irradiated by ultraviolet radiation for 7 d


title: bulk RNA-Seq B1d_rep2

value: replicate = Irradiated by ultraviolet radiation for 1 d 1


title: bulk RNA-Seq B1d_rep3

value: replicate = Irradiated by ultraviolet radiation for 1 d 2


title: bulk RNA-Seq B3d_rep2

value: replicate = Irradiated by ultraviolet radiation for 3 d 1


title: bulk RNA-Seq B1d_rep1

value: Irradiated by ultraviolet radiation for 1 d


title: bulk RNA-Seq B3d_rep3

value: replicate = Irradiated by ultraviolet radiation for 3 d 2


title: bulk RNA-Seq 0h_rep2

value: replicate = Irradiated by ultraviolet radiation for 0 h 1


title: bulk RNA-Seq 0h_rep3

value: replicate = Irradiated by ultraviolet radiation for 0 h 2


title: bulk RNA-Seq B3d_rep1

value: Irradiated by ultraviolet radiation for 3 d


title: bulk RNA-Seq 0h_rep1

value: Irradiated by ultraviolet radiation for 0 h


title: GRO_kap120_merged_replicates

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: GRO labelling for kap120 sample. Replicates 1-3

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.

organism: Saccharomyces cerevisiae

source_name: kap120 deletion strain

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC for at least 15 hours to reach early exponential phase at 0.4-0.5 OD600. Then, cells were spun-down, collected and frozen in liquid Nitrogen. Each sample was done in triplicate.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: strain

tag: genotype


title: MAT1

city: Shanghai

first: hui

last: pan

address: Zhizaoju Road No.639, Huangpu District

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

library_source: genomic

data_processing:
The data was filtered and removed low quality reads, N reads and adaptor sequences.
SOAPnuke was used for data filtering
ChIP-seq reads were aligned to the UCSC hg19 genome using bwa-mem0.7.17-r1188.
Duplicated reads are removed using picard2.22.2.jar
Peaks were called uing MACS v2 2.2.7.1 with the significance cut-off p-value <=0.001
To create ChIRP-seq coverage plots, the locations of the mapped ChIRP-seq reads were normalized to RPKM in the bigWig file format.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: ChIRP-Seq

molecule: genomic DNA

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated.
DNA was quantified by BioAnalyzer 2100 and Qubit fluorimeter. Then performed DNA-end repair and ligation of sequencing adaptor. Then DNA was amplified by PCR and selected size at 100-300bp. Finally, prepared libraries were  was sequenced by BGISEQ-500.

tag: cell line

tag: cell type

value: uveal melanoma cell line

tag: chip antibody


title: Input


title: cDNA_kap120_merged_replicates

description: cDNA labelling for kap120 sample. Replicates 1-3


title: cDNA_wt_merged_replicates

description: cDNA labelling for wt sample. Replicates 1-3

source_name: wild type

value: wt


title: GRO_wt_merged_replicates

description: GRO labelling for wt sample. Replicates 1-3


title: SCC13Ctr

city: Charlestown

first: Sandro

last: Goruppi

state: Massachusetts

address: 13th Street

department: CBRC

country: USA

institute: MGH-Partners Healthcare

description: Human squamous cell carcinoma cells - shControl

hyb_protocol: 4.7ug of cRNA was hybridized for 16h at 45C. Arrays were washed and stained on GenChip Fluidics Stations 450 (Thermo Fisher Scientific) according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on GS300 scanner (Thermo Fisher Scientific) with AGCC Scan Control Software.

data_processing:
the analysis was performed with Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).
#%result_name=Analysis_4
#%array_type=Clariom_D_Human
#%annotation=Clariom_D_Human.na36.hg38.transcript.csv

label: biotin

label_protocol: samples were labelled with biotin

growth_protocol: Human SCC13 cells were cultured in serum-free keratinocyte medium (Gibco) supplemented with antibiotics, Bovine Pituitary Extract and EGF. Cells were harvested at 60-65% confluency and lysed in Tri-reagent (Sigma-Aldrich)

extract_protocol: RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo research)

treatment_protocol: Cells were infected with either three diffent lentivirus silencing ULK3 or control, selected with puromycin and then harvested 10 days post infection

value: squamous cell carcinoma

tag: genotype/variation

value: Control


title: SCC13shULK3_3

description: Human squamous cell carcinoma cells silencing shULK3 #3

value: ULK3 silenced


title: SCC13shULK3_1

description: Human squamous cell carcinoma cells silencing shULK3 #1


title: SAMHD1_MDA5_DKO_2 (dataset 2)

city: Bonn

first: Rayk

last: Behrendt

state: North Rhine-Westphalia

address: Venusberg-Campus 1, 53127 Bonn

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: Universitätsklinikum Bonn

data_processing:
Whole Transcriptome:
The processing of the whole transcript RNA-seq data was carried-out using the nf-core RNA-seq pipeline v3.8.1 (Ewels et al., 2020).
Mapping of the raw reads to the reference genome (GRCm38.94) and quantification of aligned reads were done by STAR and Salmon, respectively.
Statistical analysis
The statistical analysis of both datasets was performed in R environment v4.1.2 with the Bioconductor R-package DESeq2. The Benjamini-Hochberg method was used to calculate multiple testing adjusted p-values. the downstream analysis was performed on the genes with a minimum expression level of 10 in at least 3 samples.
Data visualization, such as PCA and heatmaps, were generated upon variance stabilized  transformed data, using the R-packages FactoMineR and ComplexHeatmap, respectively, and the volcano plots were made using  ggplot2.
Assembly: mm10

organism: Mus musculus

source_name: peritoneal Macrophages

extract_protocol:
Rneasy mini plus kit (Qiagen).
pBWA version 0.5.9-r32-MPI-patch2 against mm10
Reads per exon were computed using bedtools version 2.16.2, summarized per gene based on Ensembl Gene 61 annotation.

value: peritoneal Macrophages

value: SAMHD1, MDA5 DKO

value: not treated

tag: time

value: Day 0


title: MDA5_KO_2 (dataset 2)

value: MDA5 KO


title: SAMHD1_MDA5_DKO_1 (dataset 2)


title: SAMHD1_DEL_3 (dataset 2)

value: SAMHD1 KO


title: SAMHD1_MDA5_DKO_3 (dataset 2)


title: WT_3 (dataset 2)

value: WT


title: SCC13shULK3_2

description: Human squamous cell carcinoma cells silencing shULK3 #2


title: HKCshULK2_3

description: Human keratinoctes silencing shULK3 #2 - strain #3

data_processing:
the analysis was performed with Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).
#%result_name=Analysis_6
#%array_type=Clariom_D_Human
#%annotation=Clariom_D_Human.na36.hg38.transcript.csv

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - shULK3 #2 - strain #3

growth_protocol: Human Primary Keratinocytes were cultured in serum-free keratinocyte medium (Gibco) supplemented with antibiotics, Bovine Pituitary Extract and EGF. Cells were harvested at 60-65% confluency and lysed in Tri-reagent (Sigma-Aldrich)

treatment_protocol: Cells were infected with either two diffent lentivirus silencing ULK3 or control, selected with puromycin and then harvested 7days post infection


title: SAMHD1_DEL_2 (dataset 2)


title: HKCshULK2_1

description: Human keratinoctes silencing shULK3 #2 - strain #1

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - shULK3 #2 - strain #1


title: SAMHD1_DEL_1 (dataset 2)


title: HKCCtl_2

description: Human keratinoctes - shControl -strain #2

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry -shControl #2


title: WT_2 (dataset 2)


title: HKCshULK2_2

description: Human keratinoctes silencing shULK3 #2 - strain #2

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - shULK3 #2 - strain #2


title: WT_5 (dataset 1)


title: HKCshULK1_3

description: Human keratinoctes silencing shULK3 #1 - strain #3

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - shULk3 #1 - strain #3


title: WT_4 (dataset 1)


title: HKCCtl_1

description: Human keratinoctes - shControl -strain #1

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry -shControl #1


title: MDA5_KO_3 (dataset 2)


title: HKCshULK1_2

description: Human keratinoctes silencing shULK3 #1 - strain #2

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - shULk3 #1 - strain #2


title: WT_3 (dataset 1)


title: HKCshULK1_1

description: Human keratinoctes silencing shULK3 #1 - strain #1

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - shULk3 #1 - strain #1


title: HKCCtl_3

description: Human keratinoctes - shControl -strain #3

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry -shControl #3


title: WT_1 (dataset 2)


title: WT_1 (dataset 1)


title: SAMHD1_RIG-I_DKO_3 (dataset 1)

value: SAMHD1, RIG-I DKO


title: SAMHD1_MDA5_DKO_4 (dataset 1)


title: SAMHD1_RIG-I_DKO_4 (dataset 1)


title: SAMHD1_MDA5_DKO_2 (dataset 1)


title: SAMHD1_MDA5_DKO_3 (dataset 1)


title: SAMHD1_MDA5_DKO_1 (dataset 1)


title: SAMHD1_RIG-I_DKO_2 (dataset 1)


title: RIG-I_KO_4 (dataset 1)

value: RIG-I KO


title: SAMHD1_KO_2 (dataset 1)


title: SAMHD1_DEL_1 (dataset 1)


title: SAMHD1_DEL_4 (dataset 1)


title: SAMHD1_RIG-I_DKO_1 (dataset 1)


title: WT_2 (dataset 1)


title: SAMHD1_KO_3 (dataset 1)


title: RIG-I_KO_3 (dataset 1)


title: MDA5_KO_1 (dataset 2)


title: RIG-I_KO_2 (dataset 1)


title: MDA5_KO_4 (dataset 1)


title: RIG-I_KO_1 (dataset 1)


title: MDA5_KO_3 (dataset 1)


title: MDA5_KO_2 (dataset 1)


title: PD1Int P14 cells from TdLN-rep1 (D23)

city: Chongqing

first: lilin

last: ye

address: Gaotanyan Street, Shapingba District

department: Institute of Immunology

institute: Third Military Medical University

data_processing:
Reads were aligned to the mm10 genome assembly using bwa version 0.7.15 with “mem” algorithm
Mapped reads were filtered for mapping quality (-q 20), and duplicates were removed using MarkDuplicates tool in Picard
Peaks were called using MACS2 with the following setting: --call-summits --nomodel --shift -100 --extsize 200 –keep-dup all
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using deepTools version 2.0 with the following setting: --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: bigwig files were generated using deepTools version 2.0
Supplementary files format and content: peak text files

source_name: Lymphocytes

growth_protocol: Firstly, 5x10^5 CD44-GFP+ naïve P14 cells bearing transgenic TCR specific for H-2Db LCMV-GP33-41 epitope that were isolated from TCF-1-GFP reporter P14 mice were transferred into C57BL/6J mice. Then, these mice were subcutaneously engrafted with half million of B16.F10 cells expressing the lymphocytic choriomeningitis virus (LCMV) glycoprotein (hereafter referred as B16.Gp) as a surrogate TSA to generate a mouse melanoma model.  To define the molecular basis for memory-like CD8+ T cells in TdLN, we performed ATAC-seq on antigen specific CD8+ T cells originated from TdLNs of melanoma tumor model at D23 post P14 cell transfer, including TdLN-TTSM (CD45.1+CD44+GFP+PD1lo) and TdLN-TPEX (CD45.1+CD44+GFP+PD1int) cells.

extract_protocol:
Briefly, 50,000 target cells were washed with PBS and then treated with lysis buffer, followed by labeling with the Nextera enzyme according to standard Illumina protocols (15027865; Illumina).
The labeled samples were immediately amplified by 9–10 cycles of polymerase chain reaction (PCR) with barcoded primers and sequenced with a NovaSeq 6000 instrument in a 150 bp/150 bp paired-end run using standard Illumina protocols.

tag: cell sorting stratergy

value: CD45.1+CD44+PD1+CD8 T cells


title: PD1lo P14 cells from TdLN-rep1 (D23)

value: CD45.1+CD44+PD1loCD8 T cells


title: PD1Int P14 cells from TdLN-rep2 (D23)


title: PD1lo P14 cells from TdLN-rep2 (D23)

value: CD45.1+CD44+PD-1loCD8 T cells


title: PD1lo P14 cells from TdLN-rep3 (D23)


title: Non-responder-Spleen-1-GEX

city: Pittsburgh

first: Jing

middle: Hong

last: Wang

email: jhw51@pitt.edu, wangj28@upmc.edu

state: PA

address: 5117 Centre Avenue, Suite 2.35

department: Department of Medicine

institute: University of Pittsburgh

description:
10x Genomics
polyA RNA 5' capture GEX

data_processing:
RNA-seq reads were mapped to mm10 (mouse reference genome) using 10× Genomics CellRanger (version 4.0.0) count pipeline and VDJ sequencing reads were mapped to the GRCm38 reference dataset using CellRanger VDJ (version 4.0.0).
Assembly: mm10 (mouse reference genome), GRCm38 reference.
Supplementary files format and content: 10× Genomics CellRanger output files.
Supplementary files format and content: tar archives for GEX Samples include h5 and barcodes.tsv/features.tsv/matrix.mtx files.
Supplementary files format and content: tar archives for VDJ Samples include clonotypes.csv, contig, and vloupe files.

source_name: Spleen

extract_protocol:
Tumors and spleens were harvested from responders (n=4) and non-responders (n=4) and single-cell suspensions were prepared. Single-cell suspensions of tumor and spleen from the first cohort (Responder-1, Non-responder-1) were flow sorted for alive CD8 T cells. Single-cell suspensions from the second, third and fourth cohort (Responder-2-4 and Non-responder-2-4) were subjected to EasySep™ Mouse CD8a Positive Selection Kit II (StemCell Technologies, Catalog#18953) according to manufacturer’s instructions to purify CD8 T cells. Sorted or purified samples were submitted for single cell capture and library preparation.
Cells were loaded into 10× Genomics Chromium Next GEM Chip K (Catalog#1000286) for the 5’ captures. Single-cell gene expression libraries were prepared using Chromium Next GEM Single Cell 5' Kit v2, (Catalogue#1000265) according to the manufacturer’s instructions. 5' libraries were split in half, one for RNA-seq and another half was enriched for TCR sequencing using the Chromium Single Cell Mouse TCR Amplification Kit (Catalogue#1000254).
Samples were sequenced on the Illumina NovaSeq 6000 platform for an estimated read depth of 50,000 reads per cell (5' expression), or 5,000 reads per cell (TCR VDJ).

treatment_protocol: A223 tumors were injected into C57BL/6J mice. When tumor size reached ~250-350mm3, tumor-bearing mice were randomized into two groups: control vs. anti-PD-L1, treated with PBS or anti-PD-L1 monoclonal antibody (mAb), respectively. Tumors and spleens were collected from responding and non-responding mice for CD8 T cell isolation followed by single-cell sequencing.

value: Spleen

value: CD8 T cells

value: 6-8 weeks

tag: tumor state

value: Non-responder


title: Non-responder-Spleen-2-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Responder-Spleen-4-GEX

description:
10x Genomics
polyA RNA 5' capture GEX

value: Responder


title: Responder-Spleen-2-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Responder-Spleen-1-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Non-responder-Spleen-4-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Non-responder-TIL-4-GEX

description:
10x Genomics
polyA RNA 5' capture GEX

source_name: Tumor

value: Tumor


title: Non-responder-Spleen-3-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Responder-TIL-1-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Non-responder-TIL-2-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Responder-TIL-3-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Responder-TIL-4-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Responder-TIL-2-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Non-responder-TIL-3-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Non-responder-TIL-1-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Non-responder-Spleen-3-VDJ

description:
10x Genomics
polyA RNA 5' capture VDJ enriched

data_processing:
RNA-seq reads were mapped to mm10 (mouse reference genome) using 10× Genomics CellRanger (version 4.0.0) count pipeline and VDJ sequencing reads were mapped to the GRCm38 reference dataset using CellRanger VDJ (version 4.0.0).
Assembly: mm10 (mouse reference genome), GRCm38 reference.
Supplementary files format and content: 10× Genomics CellRanger output files.
Supplementary files format and content: tar archives for GEX Samples include h5 and barcodes.tsv/features.tsv/matrix.mtx files.
Supplementary files format and content: tar archives for VDJ Samples include clonotypes.csv, contig, and vloupe files.
Library strategy: TCR VDJ-Seq


title: Non-responder-Spleen-1-VDJ


title: Responder-Spleen-4-VDJ


title: MDA5_KO_1 (dataset 1)

value: peritoneal Macrophages


title: Non-responder-Spleen-2-VDJ


title: Non-responder-Spleen-4-VDJ


title: Responder-Spleen-3-VDJ


title: Responder-Spleen-2-VDJ


title: Responder-Spleen-3-GEX

description:
10x Genomics
polyA RNA 5' capture GEX


title: Responder-Spleen-1-VDJ


title: Non-responder-TIL-1-VDJ


title: Non-responder-TIL-4-VDJ


title: Non-responder-TIL-2-VDJ


title: Non-responder-TIL-3-VDJ


title: Responder-TIL-2-VDJ


title: KΔY75_5XFAD3

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

data_processing:
Cell Ranger Software Suite (v5.0.0) from 10xGenomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cellranger count was used to align samples to the reference genome GRCm39, quantify reads, and filter reads and barcodes. Only protein-coding genes, with the exception of Clec7a, were retained in the analysis.
Assembly: custom-build GRCm39_genome to include Clec7a
Supplementary files format and content: raw aligned barcode and feature count matrices from cellranger count (.h5)

source_name: brain

extract_protocol:
After perfusion with cold PBS, cortices were dissociated, and CD45+ cells were sorted using FACS into 0.04% BSA.
All CD45+ cell libraries were prepared using the 10× Genomics Chromium Single Cell 3′ v3 Gene Expression Kit

value: cortex

value: 6 months

value: sorted CD45+ cells


title: WT_5XFAD1


title: Responder-TIL-3-VDJ


title: KΔY75_5XFAD4


title: Responder-TIL-1-VDJ


title: KΔY75_5XFAD1


title: KΔY75_5XFAD2


title: Mouse retina cell layers, pooled library

city: Boston

first: Emma

last: West

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
LS8 Pooled
ReorderedLightSeq_RetinaLayers.csv
Contains pooled data ReorderedLightSeq_RetinaLayers.csv
See our README file on our GitHub which will be linked in the publication.
Barcodes for each cell population are: TATGGA = ONL; GTTAGG = BCL; AGGGTA = GCL

data_processing:
Assembly: mm39
Extracted Light-Seq DNA barcodes (corresponding to different cell populations) using UMI-tools 1.1.1
Aligned to genome with STAR aligner 2.7.9a
Used featureCounts (subread) 2.0.1 to assign mapped reads to genes
Deduplicated reads based on UMIs + mapped gene pairs (samtools 1.9, 1.12)
Supplementary files format and content: CSV file containing Light-Seq read counts per gene. Rows are genes, columns are replicates for each cell population

source_name: Retina

extract_protocol:
Light-Seq
Nextera tagmentation

value: Retina

value: Mixed retinal layer cells

value: pooled library

tag: genome build


title: Mouse retina cell layers, Rep3

description:
LS8C
ReorderedLightSeq_RetinaLayers.csv
RGC_3/BP_3/ONL_3 in ReorderedLightSeq_RetinaLayers.csv
Barcodes for each cell population are: TATGGA = ONL; GTTAGG = BCL; AGGGTA = GCL

data_processing:
Assembly: mm39
'Merged_R1.fastq.gz' files were merged for lanes 1 and 2 based on the i7 index sequence
Extracted Light-Seq DNA barcodes (corresponding to different cell populations) using UMI-tools 1.1.1
Aligned to genome with STAR aligner 2.7.9a
Used featureCounts (subread) 2.0.1 to assign mapped reads to genes
Deduplicated reads based on UMIs + mapped gene pairs (samtools 1.9, 1.12)
Supplementary files format and content: CSV file containing Light-Seq read counts per gene. Rows are genes, columns are replicates for each cell population

value: WT


title: WT_5XFAD3


title: Mouse retina cell layers, Rep1

description:
LS8A
ReorderedLightSeq_RetinaLayers.csv
RGC_1/BP_1/ONL_1 in ReorderedLightSeq_RetinaLayers.csv
Barcodes for each cell population are: TATGGA = ONL; GTTAGG = BCL; AGGGTA = GCL


title: Islets, Control, rep1

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Reads were splice-aligned to a mouse genome (GRCm39) using HiSat2
FeatureCounts was used to assign reads to exons thus eventually getting counts per gene.
Assembly: GRCm39
Supplementary files format and content: comma-separated file (csv) includes count values for each Sample

source_name: pancreatic islets

growth_protocol: Wild-type and Tspan7 knockout mice (Tspan7y/-). Tspan7 KO mice were gifts from Dr Luca Murru (CNR Institute of Neuroscience, Milano, Italy)

extract_protocol:
Mouse islets were isolated as described in doi:10.1113/jphysiol.2003.059675 and doi:10.1038/s41467-018-03034-0. Islets were preserved in Trizol before their total RNA was extracted using Quick-RNA MicroPrep kit (R1050 Zymo Research).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: pancreatic islets


title: J7 MLKL 2

city: Paris

first: Jeremie

last: Gautheron

address: 27 rue chaligny

institute: Sorbonne Universite - Centre de Recherche Saint-Antoine

data_processing:
Illumina NOVAseq 6000 plateform and 150bp paired-end reads sequencing
Sequencing depth ranged from 26’310’118 to 46’400’698 reads per samples
Reads quality check was examined using FastQC v0.11.9. Clean reads were obtained using Fastp v0.20.1 to remove low-quality reads and read adapters
Clean reads were mapped on the USCS Mus musculus mm10 reference genome using HISAT2. v2.0.5
Transcripts’ abundance was quantified using feature Counts v1.5.0-p3. The differential expression analysis was performed using the DEseq2 package. Genes with an adjusted P-value <0.05 were further used for analysis
Assembly: mm10
Supplementary files format and content: Table with raw gene counts for every gene and every sample and associated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation

source_name: 3T3-L1 cells

extract_protocol:
Samples were extracted with machrey naget RNA axtraction kit and are diluted in ddH2O
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 3T3-L1 cells

value: Differentiated cells


title: J7 MLKL 3


title: Islets, TSPAN7-KO, rep2

value: TSPAN7 KO


title: Mouse retina cell layers, Rep2

description:
LS8B
ReorderedLightSeq_RetinaLayers.csv
RGC_2/BP_2/ONL_2 in ReorderedLightSeq_RetinaLayers.csv
Barcodes for each cell population are: TATGGA = ONL; GTTAGG = BCL; AGGGTA = GCL


title: Mouse retina cell layers, Rep4

description:
LS8D
ReorderedLightSeq_RetinaLayers.csv
RGC_4/BP_4/ONL_4 in ReorderedLightSeq_RetinaLayers.csv
Barcodes for each cell population are: TATGGA = ONL; GTTAGG = BCL; AGGGTA = GCL


title: Islets, Control, rep2


title: J7 MLKL 1


title: J7RIPK3 3

value: MLKL-/-


title: J7RIPK3 2


title: J7CTL 3

value: CTL


title: J7CTL 1


title: Responder-TIL-4-VDJ

value: CD8 T cells

value: 6-8 weeks


title: Islets, TSPAN7-KO, rep1


title: WT_5XFAD2


title: J0RIPK3 3

value: Untreated


title: J0RIPK3 2


title: J0RIPK3 1


title: J0MLKL 3


title: J0MLKL 2


title: J0CTL 2


title: J0CTL 1


title: J0MLKL 1


title: KOC3

source_name: AML-12 cells

value: AML-12 cells

value: Untraited


title: KOC4


title: KOPA3

value: Traited with 125µM palmitate-bovine serum albumin (PA) for 24h


title: KOC2


title: KOPA5


title: KOC1


title: KOPA2


title: KOPA4


title: KOC5


title: J7RIPK3 1


title: WTPA4


title: WTPA5


title: WTPA3


title: J7CTL 2


title: WTC4


title: WTPA2


title: WTPA1


title: WTC3


title: J0CTL 3


title: WTC2


title: lacZ

value: uveal melanoma cell line


title: WTC5


title: KOPA1


title: Trem2 KO 5XFAD 3

description: sorted CD45+ cells from cortex

data_processing:
Cell Ranger Software Suite (v6.0.0) from 10xGenomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cellranger count was used to align samples to the reference genome GRCm39, quantify reads, and filter reads and barcodes. Only protein-coding genes, with the exception of Clec7a, were retained in the analysis.
The Seurat (v4.0) package in R (v4.1.0) was used for downstream analysis (Hao et al., 2021). For quality control, cells with mitochondrial content 7.5% were removed. Cells with low UMI and gene number per cell were filtered out. Cutoffs for UMI and gene number were empirically determined on the basis of histograms showing cell density as a function of UMI per gene counts. Cutoffs of UMI greater than 2000 and less than 20000, and genes greater than 1000 were applied. Genes expressed in fewer than 10 cells were removed from the dataset. Microglia clusters were digitally isolated and further filtered for clusters containing doublets, stress genes, and apoptotic cells. After filtering, the dataset from Sykfl/fl, SykDMG, Sykfl/fl-5xFAD 32 and SykDMG-5xFAD mice (n = 3 for each genotype) showed in the Figure 5 and S3 (refer to as SYK ONLY) contained a total of 57,830 microglia cells with a median 5871 UMI and median 2537 genes and the integration dataset from Sykfl/fl-, SykDMG-, Trem2+/+- and Trem2-/- -5xFAD mice (n = 3 for each genotype) showed in the Figure 6 (refer to as SYKTREM2) contained a total of 38,404 microglia cells remained with a median 5483 UMI and median 2359 genes per cell. Clustering and differential expression analysis For both SYK ONLY and SYK-TREM2 datasets, data were normalized using the SCTransform method regressed on mitochondrial gene percentage and integrated using FindIntegrationAnchors function and Canonical Correlation Analysis (CCA) (Hafemeister and Satija, 2019; Stuart et al., 2019). Principle component analysis was performed, and the top 30 principal components were selected for dimensionality reduction using the Uniform Approximation and Projection (UMAP) algorithm. Clustering was performed using the FindNeighbors and FindClusters functions using a resolution of 0.6 or 0.4. Marker genes were identified by comparing each cluster against all other clusters using the FindAllMarkers function with default settings (log-fold change threshold of 0.25 and >10% cells expressing the gene). Cell clusters from each tissue were annotated based on marker gene expression. For data visualization and figure preparation, the scRNA-Seq data was also analyzed with BBrowser version 2.7.5 (SingleCell). Pseudotime trajectory analysis. 33 Single-cell pseudotime trajectories were inferred using the R package slingshot (v2.1.0) (Street et al., 2018). Normalized values resulting from batch integration were used as input for the calculation of cell lineages and pseudotime. Genes which were significantly differentially expressed along pseudotime were identified using the R package tradeSeq (v1.6) (Van den Berge et al., 2020). A negative binomial generalized additive model was fit to the identified lineages using the fitGAM function using the top 3000 variable features. Genes which changed significantly along the DAM trajectory were identified using associationTest. Microglia from SykDMG-5xFAD were then compared against Trem2-/- - 5xFAD microglia along the DAM trajectory using the conditionTest function. DE genes (FDR < 0.05) were further filtered by selecting those which overlapped with those that changed significantly along the DAM trajectory.
Genome_build: mm39
Supplementary_files_format_and_content: .h5 files containing Cellranger-filtered matrices

source_name: sorted CD45+ cells from cortex

extract_protocol:
6-month-old of Sykfl/fl, SykDMG, Sykfl/fl-5xFAD and SykDMG-5xFAD, as well as Trem2+/+- Trem2-/- -5xFAD female mice were sacrificed for the sample preparation. After perfusion with cold PBS, cortices were dissociated, and CD45+ cells were sorted using FACS.
All CD45+ cell libraries were prepared using the 10× Genomics Chromium Single Cell 3′ v3 Gene Expression Kit and sequenced on Illumina NovaSeq.

value: Trem2 KO 5XFAD


title: Trem2 KO 5XFAD 2

description: sorted CD45+ cells from cortex


title: Trem2 KO 5XFAD 1

description: sorted CD45+ cells from cortex


title: Cx3cr1-creER Syk fl/fl 5XFAD 3

description: sorted CD45+ cells from cortex

value: Cx3cr1-creER Syk fl/fl 5XFAD


title: Cx3cr1-creER Syk fl/fl 5XFAD 2

description: sorted CD45+ cells from cortex


title: Trem2 WT 5XFAD 1

description: sorted CD45+ cells from cortex

value: Trem2 WT 5XFAD


title: Trem2 WT 5XFAD 2

description: sorted CD45+ cells from cortex


title: Syk fl/fl 5XFAD 2

description: sorted CD45+ cells from cortex

value: Syk fl/fl 5XFAD


title: Syk fl/fl 5XFAD 3

description: sorted CD45+ cells from cortex


title: Cx3cr1-creER Syk fl/fl 5XFAD 1

description: sorted CD45+ cells from cortex


title: Cx3cr1-creER Syk fl/fl 2

description: sorted CD45+ cells from cortex

value: Cx3cr1-creER Syk fl/fl


title: Cx3cr1-creER Syk fl/fl 3

description: sorted CD45+ cells from cortex


title: Cx3cr1-creER Syk fl/fl 1

description: sorted CD45+ cells from cortex


title: Syk fl/fl 3

description: sorted CD45+ cells from cortex

value: Syk fl/fl


title: Propyzamide_induced_colitis

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description:
Propyzamide
Propyzamide Treated Mouse with colitis

data_processing:
The sample is aligned to GRCm38 transcriptome and quantified using cellranger
Genome_build: GRCm38
Supplementary_files_format_and_content: gzipped count files

extract_protocol:
N/A
Libraries were prepared by the Broad Institute according to the 10X multiplexed barcode protocol as described (https://pages.10xgenomics.com/rs/446-PBO-704/images/10x_LIT000117_CellPlex-Infographic_letter_digital.pdf).
single cell RNA-Seq

tag: Sex

value: male

value: 11 weeks


title: Syk fl/fl 1

description: sorted CD45+ cells from cortex


title: Syk fl/fl 2

description: sorted CD45+ cells from cortex


title: Vehicle_induced_colitis

description:
Vehicle
Vehicle Treated Mouse with colitis


title: WTC1

value: WT

tag: treatment


title: Vehicle_Naive

description:
Vehicle
Vehicle Treated Naïve Mouse


title: CEBPBKO_DC_2

description: Single Cell RNA-Seq samples from CEBPB knockout in Dendritic Cells mouse

source_name: CEBPBKO

extract_protocol:
N/A
Libraries were prepared by the Broad Institute according to the 10X multiplexed barcode protocol as described (https://pages.10xgenomics.com/rs/446-PBO-704/images/10x_LIT000117_CellPlex-Infographic_letter_digital.pdf).


title: WT_DC_1

description: Single Cell RNA-Seq samples from wild type mouse

source_name: WT


title: WT_DC_2


title: CEBPBKO_DC_1


title: WT_DC_4


title: WT_DC_3


title: WT_DC_5


title: Syk fl/fl 5XFAD 1

description: sorted CD45+ cells from cortex


title: Propyzamide_AntiCD3_24Hour Anti.CD3.TCGACGTC_TCTTACGC

description:
Propyzamide_AntiCD3_24Hour
Antigen-Stimulated Mouse Treated with Propyzamide
Antigen-Stimulated Mouse Treated with Propyzamide. Sample is collected at 24 hour after stimulation.

data_processing:
The sample is aligned to GRC.38 transcriptome and quantified using Kallisto
Genome_build: GRCm38
Supplementary_files_format_and_content: gzipped abundance.tsv output from Kallisto

extract_protocol:
N/A
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

value: Male

value: 11 weeks old


title: Propyzamide_AntiCD3_24Hour Anti.CD3.CCTAAGAC_TCTTACGC


title: Propyzamide_AntiCD3_24Hour Anti.CD3.CGATCAGT_TCTTACGC


title: Propyzamide_AntiCD3_3Hour Anti.CD3.CGGAGCCT_TCTTACGC

description:
Propyzamide_AntiCD3_3Hour
Antigen-Stimulated Mouse Treated with Propyzamide
Antigen-Stimulated Mouse Treated with Propyzamide. Sample is collected at 3 hour after stimulation.


title: Vehicle_AntiCD3_24Hour Anti.CD3.TACGCTGC_TCTTACGC

description:
Vehicle_AntiCD3_24Hour
Antigen-Stimulated Mouse Treated with empty vehicle
Antigen-Stimulated Mouse Treated with empty vehicle. Sample is collected at 24 hour after stimulation.


title: Vehicle_AntiCD3_24Hour Anti.CD3.ATGCGCAG_TCTTACGC


title: Vehicle_AntiCD3_24Hour Anti.CD3.TAGCGCTC_TCTTACGC


title: Propyzamide_AntiCD3_3Hour Anti.CD3.ACTCGCTA_TCTTACGC


title: Propyzamide_AntiCD3_3Hour Anti.CD3.GGAGCTAC_TCTTACGC


title: Propyzamide_AntiCD3_3Hour Anti.CD3.GCGTAGTA_TCTTACGC


title: Vehicle_AntiCD3_3Hour Anti.CD3.TCGACGTC_ACTCTAGG

description:
Vehicle_AntiCD3_3Hour
Antigen-Stimulated Mouse Treated with empty vehicle
Antigen-Stimulated Mouse Treated with empty vehicle. Sample is collected at 3 hour after stimulation.


title: Propyzamide_Naive

description:
Propyzamide
Propyzamide Treated Naïve Mouse


title: Propyzamide_Naive_None Anti.CD3.ACTGAGCG_ACTCTAGG

description:
Propyzamide_Naive_None
Naïve Mouse Treated with Propyzamide
Naïve Mouse Treated with Propyzamide


title: Propyzamide_Naive_None Anti.CD3.TAGCGCTC_ACTCTAGG


title: Vehicle_AntiCD3_3Hour Anti.CD3.CCTAAGAC_ACTCTAGG


title: Vehicle_AntiCD3_3Hour Anti.CD3.CGATCAGT_ACTCTAGG


title: Vehicle_AntiCD3_3Hour Anti.CD3.TGCAGCTA_ACTCTAGG


title: Propyzamide_Naive_None Anti.CD3.ATGCGCAG_ACTCTAGG


title: Vehicle_Naive_None Anti.CD3.CGGAGCCT_ACTCTAGG

description:
Vehicle_Naive_None
Naïve Mouse Treated with empty vehicle
Naïve Mouse Treated with empty vehicle


title: Propyzamide_AntiCD3_24Hour Anti.CD3.TGCAGCTA_TCTTACGC


title: Propyzamide_Naive_None Anti.CD3.TACGCTGC_ACTCTAGG


title: Vehicle_Naive_None Anti.CD3.GCGTAGTA_ACTCTAGG


title: Vehicle_Naive_None Anti.CD3.ACTCGCTA_ACTCTAGG


title: Vehicle_Naive_None Anti.CD3.GGAGCTAC_ACTCTAGG


title: MI rep 2

first: Yaozu

last: Xiang

address: 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
Illumina Casava v1.8 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.4.0j with parameters --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM --runThreadN 10
Transcripts per million (TPM) were evaluated by a statistical method RSEM (RNA-Seq by Expectation Maximization) using a generative model of RNA-seq reads and the EM algorithm, taking read mapping uncertainty into account and achieving the most accurate abundance estimates
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated from the bone marrow of mouse for analysis using the miRNeasy Mini Kit (1038703, QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were anesthetized by spontaneous inhalation and maintained under general anesthesia with 1–2% isoflurane. Animals were mechanically ventilated using a rodent ventilator (Harvard Apparatus) connected to an endotracheal tube. The heart was exposed by a left side limited thoracotomy and the LAD was ligated with a 6-0 polyester suture 1 mm from the apex of the normally positioned left auricle. Bone marrow of samples including Sham, Sham-E, MI and MI-E were analyzed.

tag: tissue

value: Bone marrow

value: MI


title: MI-E rep 3

value: MI with EMPA


title: MI rep 3


title: MI-E rep 1


title: Vehicle_AntiCD3_24Hour Anti.CD3.ACTGAGCG_TCTTACGC

tag: age


title: MI-E rep 2


title: MI rep 1


title: Sham-E rep 2

value: Sham with EMPA


title: Sham-E rep 1


title: Sham-rep 1

value: Sham


title: MI-E

description: Bone marrow purified using standard Ficoll-Paque gradient centrifugation

data_processing:
Raw data were demultiplexed using Cellranger (v5.0.1, 10x Genomics).
UCSC mm10 reference genome, provided by 10x Genomics, was used for alignment and unique molecular identifier (UMI) quantification.
Gene level quantification was completed using Cellranger count.
Raw counts data was imported into R for downstream processing.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw read count values for every gene and every cell.

extract_protocol:
For 10X Genomics scRNA-seq, cells were isolated from femur and tibia of Sham, MI and MI-E, which were further purified via density gradient centrifugation using Ficoll-PaqueTM media. The barcoded libraries were prepared under Single Cell 3’ Reagents Kit v3.1 (10X Genomics) according to the manufacturer’s protocol. Single cell suspensions were loaded on Chromium Controller (10X Genomics) to form single cell gel beads in emulsion (GEMs). The libraries were further controlled via Agilent 2100 Bioanalyzer (Agilent Technologies). After passing quality control, the libraries were sequenced on NovaSeq 6000 (Illumina) to generate 150 bp paired-end reads.
The barcoded libraries were prepared under Single Cell 3’ Reagents Kit v3.1 (10X Genomics) according to the manufacturer’s protocol.

treatment_protocol: Mice were anesthetized by spontaneous inhalation and maintained under general anesthesia with 1–2% isoflurane. Animals were mechanically ventilated using a rodent ventilator (Harvard Apparatus) connected to an endotracheal tube. The heart was exposed by a left side limited thoracotomy and the LAD was ligated with a 6-0 polyester suture 1 mm from the apex of the normally positioned left auricle.


title: Sham-rep 2


title: P14 cells from PBMC

data_processing:
Raw single-cell RNA data was processed using 10X Genomics Cell Ranger Suite (v3.1.0), including aligning the demultiplexed FASTQ reads to the mouse reference genome (mm10, v3.0.0, from 10X Genomics)
Counting the unique molecular identifier (UMI) for each cell barcode by using the ‘cellranger count’ function
Data sets from individual libraries were aggregated using the ‘cellranger aggr’ function of Cell Ranger Suite without sequencing depth normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in every sample

growth_protocol: We first subcutaneously engrafted C57/B6 (B6) mice with half million of B16.F10 cells expressing the lymphocytic choriomeningitis virus (LCMV) glycoprotein (hereafter referred as B16.Gp) as a surrogate TSA to generate a mouse melanoma model. Then 5x105 CD44-GFP+ naïve P14 cells bearing transgenic TCR specific for H-2Db LCMV-GP33-41 epitope that were isolated from TCF-1-GFP reporter P14 mice were transferred into tumor-bearing mice at D8 post B16.Gp inoculation. To define the molecular basis for memory-like CD8+ T cells in TdLN, we performed single-cell RNA-sequencing (scRNA-seq) on antigen specific CD8+ T cells originated from TdLNs, TIL and PBMC of melanoma tumor model at D16 post P14 cell transfer, and memory (D200) T cells from acute LCMV infection.

extract_protocol:
Briefly, FACS-sorted CD8+ T cells were suspended in DPBS containing 0.04% BSA and captured in droplets using a Chromium Single Cell Controller instrument (10x Genomics). After reverse transcription and cell barcoding in droplets, cDNA was purified and PCR amplified, followed by fragmentation, end-repair, double-size selection and PCR amplification with sample-indexing primers.
The single-cell RNA-seq (scRNA-seq) libraries were prepared using Chromium Next GEM Single Cell 3’ reagent Kits (10x Genomics) according to the manufacturer’s instructions.

value: CD45.1+CD44+CD8 T cells


title: P14 cells from TdLN (D21) 3

description: P14 cells from TdLN (D21)

data_processing:
ATAC-seq reads were aligned to the mm10 genome assembly using bwa version 0.7.15 with “mem” algorithm
Mapped reads were filtered for mapping quality (-q 20), and duplicates were removed using MarkDuplicates tool in Picard
Peaks were called using MACS2 with the following setting: --call-summits --nomodel --shift -100 --extsize 200 –keep-dup all
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using deepTools version 2.0 with the following setting: --normalizeUsing RPKM.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools version 2.0
Supplementary_files_format_and_content: peak text files

growth_protocol: We first subcutaneously engrafted C57L/B6 (B6) mice with half million of B16.F10 cells expressing the lymphocytic choriomeningitis virus (LCMV) glycoprotein (hereafter referred as B16.Gp) as a surrogate TSA to generate a mouse melanoma model. Then 5x105 CD44-GFP+ naïve P14 cells bearing transgenic TCR specific for H-2Db LCMV-GP33-41 epitope that were isolated from TCF-1-GFP reporter P14 mice were transferred into tumor-bearing mice at day 8 (D8) post B16.Gp inoculation. To define the molecular basis for memory-like CD8+ T cells in TdLN, we performed ATAC-seq on antigen specific CD8+ T cells originated from TdLNs of melanoma tumor model at indicated timepoints post P14 cell transfer.

tag: time point


title: P14 cells from TdLN


title: P14 cells from TdLN (D8) 3

description: P14 cells from TdLN (D8)


title: P14 cells from TdLN (D21) 1

description: P14 cells from TdLN (D21)


title: P14 memory cells


title: P14 cells from TdLN (D4) 1

description: P14 cells from TdLN (D4)


title: P14 cells from TdLN (D8) 1

description: P14 cells from TdLN (D8)


title: P14 cells from TdLN (D8) 2

description: P14 cells from TdLN (D8)


title: P14 cells from TdLN (D4) 3

description: P14 cells from TdLN (D4)


title: P14 cells from TdLN (D4) 2

description: P14 cells from TdLN (D4)


title: Sham-E rep 3


title: P9-H09

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description: number of genes expressed: 3983

data_processing:
The fastq read-pairs were aligned to mouse reference genome (mm10) using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to mouse gene model by GENCODE (v19) using Cufflinks and HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for all genes

source_name: inner ear

extract_protocol:
RNA extraction from dissociated cells was done according to Smartseq2 protocol (Picelli et al., 2014)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: inner ear

value: Endolymphatic sac

value: Sox9Y440X/+ endolymphatic sacs


title: P9-H11

description: number of genes expressed: 4741


title: P9-H05

description: number of genes expressed: 4468


title: P9-H08

description: number of genes expressed: 3457


title: P9-H12

description: number of genes expressed: 3269

value: Wild-type


title: P9-H06

description: number of genes expressed: 3831


title: Sham-rep 3


title: P9-H10

description: number of genes expressed: 2490


title: P9-H04

description: number of genes expressed: 3051


title: Sham


title: MI


title: P9-H03

description: number of genes expressed: 1864


title: P9-H01

description: number of genes expressed: 3186


title: P14 cells from TdLN (D21) 2

description: P14 cells from TdLN (D21)


title: P9-G11

description: number of genes expressed: 2308


title: P9-G12

description: number of genes expressed: 7095


title: P9-G09

description: number of genes expressed: 3010


title: P9-G10

description: number of genes expressed: 3369


title: P9-G08

description: number of genes expressed: 4652


title: P9-G07

description: number of genes expressed: 1716


title: P9-F12

description: number of genes expressed: 8276


title: P9-G03

description: number of genes expressed: 2592


title: P9-G02

description: number of genes expressed: 3270


title: P9-G04

description: number of genes expressed: 3312


title: P9-G01

description: number of genes expressed: 2889


title: P9-H07

description: number of genes expressed: 3304


title: P9-F11

description: number of genes expressed: 4123


title: P9-H02

description: number of genes expressed: 4319


title: P9-F09

description: number of genes expressed: 3712


title: P9-F06

description: number of genes expressed: 5242


title: P9-F08

description: number of genes expressed: 5189


title: P9-F07

description: number of genes expressed: 4996


title: P9-F02

description: number of genes expressed: 3461


title: P9-E12

description: number of genes expressed: 4127


title: P9-F10

description: number of genes expressed: 2699


title: P9-F04

description: number of genes expressed: 4063


title: P9-F05

description: number of genes expressed: 5144


title: P9-F03

description: number of genes expressed: 2599


title: P9-F01

description: number of genes expressed: 4439


title: P9-G05

description: number of genes expressed: 3268


title: P9-E09

description: number of genes expressed: 4040


title: P9-E08

description: number of genes expressed: 3432


title: P9-E05

description: number of genes expressed: 3492


title: P9-E07

description: number of genes expressed: 2202


title: P9-E04

description: number of genes expressed: 3032


title: P9-E02

description: number of genes expressed: 6291


title: P9-G06

description: number of genes expressed: 3095


title: P9-E03

description: number of genes expressed: 3715


title: P9-D12

description: number of genes expressed: 3984


title: P9-D10

description: number of genes expressed: 2507


title: P9-D09

description: number of genes expressed: 4759


title: P9-D11

description: number of genes expressed: 3071


title: P9-E01

description: number of genes expressed: 3891


title: P9-D08

description: number of genes expressed: 3923


title: P9-C09

description: number of genes expressed: 3518


title: P9-D07

description: number of genes expressed: 4392


title: P9-C12

description: number of genes expressed: 4240


title: P9-D01

description: number of genes expressed: 2232


title: P9-D04

description: number of genes expressed: 3812


title: P9-D05

description: number of genes expressed: 3293


title: P9-D02

description: number of genes expressed: 3789


title: P9-C05

description: number of genes expressed: 4043


title: P9-B10

description: number of genes expressed: 3549


title: P9-E10

description: number of genes expressed: 4021


title: P9-D06

description: number of genes expressed: 4831


title: P9-C01

description: number of genes expressed: 3736


title: P9-D03

description: number of genes expressed: 3028


title: P9-C10

description: number of genes expressed: 4598


title: P9-B09

description: number of genes expressed: 1966


title: P9-C04

description: number of genes expressed: 2981


title: P9-C08

description: number of genes expressed: 3900


title: P9-C02

description: number of genes expressed: 4617


title: P9-B07

description: number of genes expressed: 3743


title: P9-B06

description: number of genes expressed: 4317


title: P9-C07

description: number of genes expressed: 3728


title: P9-C06

description: number of genes expressed: 4574


title: P9-C03

description: number of genes expressed: 4186


title: P9-B05

description: number of genes expressed: 4245


title: P9-E06

description: number of genes expressed: 3104


title: P9-B12

description: number of genes expressed: 3924


title: P9-B03

description: number of genes expressed: 1988


title: P9-B11

description: number of genes expressed: 3638


title: P9-B08

description: number of genes expressed: 3638


title: P9-B04

description: number of genes expressed: 4066


title: P9-A12

description: number of genes expressed: 4866


title: P9-A11

description: number of genes expressed: 3904


title: P9-B01

description: number of genes expressed: 3172


title: P9-A09

description: number of genes expressed: 3247


title: P9-A10

description: number of genes expressed: 3727


title: P9-A08

description: number of genes expressed: 3821


title: P9-B02

description: number of genes expressed: 4950


title: Puck_210119_20

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Demultiplexing, genome alignment and spatial matching was performed using Slide-seq tools github.com/MacoskoLab/slideseq-tools/releases/tag/0.1
Giotto (version 1.0.3) was used for data handling and RCTD (version 1.2.0) for the cell type deconvolution
Assembly: GRCh38 (hg38)
Supplementary files format and content: Giotto objects in RDS format containing bead location and count matrices and cell type weights after deconvolution; raw counts digital gene expression (DGE) matrix (.txt.gz) and a bead barcode locations file (.csv)

source_name: Kidney Cortex

extract_protocol:
Tissue pucks were prepared according to the step-by-step protocol: dx.doi.org/10.17504/protocols.io.bpgzmjx6
Sequencing libraries were prepared according to the step-by-step protocol: dx.doi.org/10.17504/protocols.io.bpgzmjx6

tag: patient

tag: condition

value: Reference

value: Kidney Cortex

tag: tissue source

value: Nephrectomy

tag: project

value: HuBMAP

tag: raw data location

tag: raw data id

tag: assay


title: Puck_210119_09

value: Deceased Donor


title: P9-A07

description: number of genes expressed: 2909

tag: genotype


title: Puck_210119_18


title: Puck_210113_39

source_name: Kidney Medulla

value: Kidney Medulla


title: P9-A05

description: number of genes expressed: 3541


title: P9-A03

description: number of genes expressed: 4600


title: P9-A06

description: number of genes expressed: 3675


title: Puck_210113_40


title: P9-A04

description: number of genes expressed: 3602


title: P9-A01

description: number of genes expressed: 3426


title: P10-H04

description: number of genes expressed: 4898


title: Puck_210113_35


title: Puck_210113_34


title: Puck_210113_38


title: Puck_210113_36


title: P10-H02

description: number of genes expressed: 4996


title: Puck_210113_33


title: P9-A02

description: number of genes expressed: 5116


title: Puck_210113_32


title: P10-H03

description: number of genes expressed: 4045


title: P10-H01

description: number of genes expressed: 5063


title: P10-G04

description: number of genes expressed: 3879


title: P10-G03

description: number of genes expressed: 4553


title: Puck_210113_31


title: P10-G02

description: number of genes expressed: 4937


title: Puck_210113_29


title: Puck_210113_37


title: Puck_210113_28


title: Puck_210113_27


title: Puck_210113_30


title: Puck_210113_26


title: P10-G01

description: number of genes expressed: 3438


title: P10-F04

description: number of genes expressed: 4197


title: Puck_210113_23


title: Puck_210113_21


title: P10-F01

description: number of genes expressed: 3571


title: P10-D04

description: number of genes expressed: 3337


title: P10-F03

description: number of genes expressed: 3906


title: P10-E02

description: number of genes expressed: 4982


title: P10-D03

description: number of genes expressed: 4366


title: Puck_210113_22


title: P10-F02

description: number of genes expressed: 5067


title: KPMP, 20190829E, 10X-R

data_processing:
Basecalls were performed using NovaSeq Control Software v1.6.0
Sample demultiplexing, barcode processing, and gene expression quantifications were performed with the 10X Cell Ranger v3 pipeline using the GRCh38 (hg38) reference genome
Assembly: GRCh38 (hg38)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
Nuclei were isolated from cryosectioned tissues according to the following protocol: dx.doi.org/10.17504/protocols.io.ufketkw with the exception that 4',6-diamidino-2-phenylindole (DAPI) was excluded from the nuclear extraction buffer and only used to stain a subset of nuclei used for counting
10X single nucleus RNA sequencing was performed according to dx.doi.org/10.17504/protocols.io.86khzcw using the 10X Chromium Single-Cell 3’ Reagent Kit v3

value: Chronic Kidney Disease

value: KPMP

value: 10X snRNA-seq


title: P10-E04

description: number of genes expressed: 4192


title: BUKMAP, 20190822F, 10X-R


title: P10-E03

description: number of genes expressed: 2874


title: BUKMAP, 20190829B, 10X-R


title: KPMP, 20190829D, 10X-R


title: P10-D02

description: number of genes expressed: 5171


title: P10-D01

description: number of genes expressed: 4858


title: KPMP, 20190829C, 10X-R


title: P10-C02

description: number of genes expressed: 4113


title: P10-C04

description: number of genes expressed: 3585


title: Puck_210113_25


title: Puck_210113_24


title: P10-E01

description: number of genes expressed: 4546


title: P10-B03

description: number of genes expressed: 5296


title: P10-B01

description: number of genes expressed: 3920


title: HPK128_HPV16E7-3

city: Vienna

first: Anna

last: Obenauf

state: Vienna

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

data_processing:
library strategy: QUANT-seq
Reads were aligned against the human genome (hg38) with STAR.
Aligned reads in 3'-UTR region of each transcript were counted and collapsed to gene level using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: featureCount output files of 3'-UTR counts.

source_name: normal keratinocytes

growth_protocol: Cells were maintained in keratinocyte serum-free medium supplemented with recombinant human epidermal growth factor, bovine pituitary extract, and gentamycin.

extract_protocol:
Total RNA isolation from cells was performed with an in-house paramagnetic bead-based purification protocol.
3'UTR sequencing libraries were generated from 500ng total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).

value: skin

tag: cell type

value: normal keratinocytes


title: HPK128_HPV42E7-3


title: HPK128_mCherry-3

value: mCherry


title: P10-C03

description: number of genes expressed: 5401


title: HPK128_HPV16E7-1


title: P10-A03

description: number of genes expressed: 5287


title: HPK128_HPV16E7-2


title: P10-A02

description: number of genes expressed: 1714


title: P10-A01

description: number of genes expressed: 5589


title: HPK128_HPV42E7-2


title: HPK128_mCherry-2


title: HPK113_HPV42-2

tag: hpv genome


title: HPK128_mCherry-1


title: HPK113_HPV42-1


title: P10-C01

description: number of genes expressed: 4505


title: HPK128_HPV42E7-1


title: P10-A04

description: number of genes expressed: 4739


title: HPK113_HPV16E8m-3


title: HPK113_HPV42-3


title: HPK113_HPV16E8m-1


title: P10-B04

description: number of genes expressed: 3889


title: HPK113_EV-3

value: EV


title: HPK113_HPV16E8m-2


title: P10-B02

description: number of genes expressed: 4032

value: inner ear


title: HPK113_EV-2


title: WT-062

description:
number of genes expressed: 3801
innerEar.gene.expression.tables.FPKM.txt.gz

value: Endolymphatic sac


title: mutant-063c

description:
number of genes expressed: 4254
innerEar.gene.expression.tables.FPKM.txt.gz

value: Sox9Y440X/+ endolymphatic sacs


title: mutant-061c

description:
number of genes expressed: 4506
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-063

description:
number of genes expressed: 3993
innerEar.gene.expression.tables.FPKM.txt.gz

value: Wild-type


title: WT-061

description:
number of genes expressed: 2942
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-062c

description:
number of genes expressed: 5607
innerEar.gene.expression.tables.FPKM.txt.gz


title: VR236

source_name: DPA tumor sample

extract_protocol:
Total RNA was extracted from FFPE DPA tumor samples according to manufacturer instructions (A31881, Life Technologies Limited) and eluted in nuclease-free water.
3'UTR sequencing libraries were generated from 500ng total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).

value: tumor

tag: tissue type

value: digital papillary adenocarcinoma (DPA)


title: VR235


title: VR182


title: mutant-060c

description:
number of genes expressed: 6024
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-060

description:
number of genes expressed: 2223
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-059

description:
number of genes expressed: 3587
innerEar.gene.expression.tables.FPKM.txt.gz


title: VR188


title: mutant-059c

description:
number of genes expressed: 5079
innerEar.gene.expression.tables.FPKM.txt.gz


title: HPK113_EV-1


title: VR179


title: mutant-058c

description:
number of genes expressed: 3990
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-058

description:
number of genes expressed: 1973
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-057c

description:
number of genes expressed: 2560
innerEar.gene.expression.tables.FPKM.txt.gz


title: VR168


title: VR169


title: VR178


title: mutant-056c

description:
number of genes expressed: 3928
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-056

description:
number of genes expressed: 479
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-055c

description:
number of genes expressed: 3560
innerEar.gene.expression.tables.FPKM.txt.gz


title: hPSC-CM-NM-rep2

first: Mengying

last: Feng

address: no. 67 Chifeng road, Yangpu district

department: School of Life Sciences and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 or mm10 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S
Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
Genome_build: rn6 or hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human pluripotent stem cells derived cardiomyocytes

growth_protocol: Neonatal rat’s hearts were harvested from 1-day old SD rats. Next, the ventricles were separated and cut into pieces (1–3 mm2), then they were dissociated in 0.25% trypsin (Gibco, 15090046) at 4 °C overnight. Then the tissue was transferred to 0.1% collagenase type Ⅱ (Worthington, LS004176) to further digest at 37°C at 145 rpm, and the supernatant was collected into DMEM medium containing 10% FBS every 5 min. The digestion procedure was repeated 3-4 times. When the tissue was completely digested, the supernatant was centrifuged at 1500 rpm for 6 min. Then, the cells were plated in DMEM medium which containing 10% FBS, 100 unit/ml penicillin and 100 mg/ml streptomycin at 15 cm dishes at an atmosphere of 5% CO2 at 37℃ for 90 min, to remove cells that are easier attached the dishes than cardiomyocytes. Finally, the culture supernatant was collected, plated in the plates which were coated with collagen and then incubated 24 h in an atmosphere of 5% CO2 at 37 ℃ with the same medium. After 24 h, the medium was changed to cardiomyocyte medium: DMEM: F12 (1:1) medium containing 0.25% FBS, 3 mM sodium pyruvate, 0.1 mM Vitamin C and 2 mM L-Glu. hPSC-CMs were produced from ZSSY001 (Nuwacell) by regulating Wnt signaling pathway. hPSCs were grown on Matrigel (Corning, 354277) in Essential 8 TM Medium (Gibco, A15169-01, A15171-01). Cardiac differentiation was performed using dense monolayers of hPSCs treated with 6µM CHIR-99021 (Sellect, S1263) for 48 h and 5μM IWP-2 (Sellect, S7065) for 2 days in RPMI 1640 (Gibco, 11875-093)/B-27 minus insulin Medium (Gibco, A18956-01) previously described protocol . Spontaneously beating hPSC-CMs appeared after 7 days. Then the containing medium was replaced with RPMI 1640/B-27 Medium (Gibco, A17504-044). Metabolism selection was performed using Cardiomyocyte Selection Medium (ScienCell, 5911, 5962) for high purity cardiomyocytes.

extract_protocol:
The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NRVCs and hPSC-CMs were treated with NM for 12h.

value: cardiomyocytes

tag: agent

value: Nimodipine


title: WT-055

description:
number of genes expressed: 3155
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-054

description:
number of genes expressed: 4592
innerEar.gene.expression.tables.FPKM.txt.gz


title: hPSC-CM-Ctrl-rep3


title: hPSC-CM-Ctrl-rep2


title: mutant-054c

description:
number of genes expressed: 2262
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20200707C_10X-R

description:
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Metadata_Field_Descriptions.txt

data_processing:
Basecalls were performed using NovaSeq Control Software v1.6.0
Sample demultiplexing, barcode processing, and gene expression quantifications were performed with the 10X Cell Ranger v3 pipeline using the GRCh38 (hg38) reference genome
Mitochondrial transcripts (MT-*) were removed
Doublets were identified using the DoubletDetection software (v2.4.0) and removed
Cell barcodes having greater than 400 and less than 7500 genes detected were kept for downstream analyses
A gene UMI ratio filter (gene.vs.molecule.cell.filter) was applied using Pagoda2 (github.com/hms-dbmi/pagoda2)
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Seurat object in h5Seurat format, raw RNA counts provided in RDS format, sample metadata table in txt format, and metadata field descriptions in txt format

source_name: Kidney Papilla

value: Reference

value: Kidney Papilla

value: Biopsy

value: HuBMAP


title: mutant-053c

description:
number of genes expressed: 158
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-053

description:
number of genes expressed: 6236
innerEar.gene.expression.tables.FPKM.txt.gz


title: hPSC-CM-Ctrl-rep1


title: mutant-052c

description:
number of genes expressed: 3326
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20200702D_10X-R

value: 10X snRNA-seq


title: BUKMAP_20200702C_10X-R

value: Kidney Cortex


title: mutant-051c

description:
number of genes expressed: 2330
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-051

description:
number of genes expressed: 3022
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-050c

description:
number of genes expressed: 5352
innerEar.gene.expression.tables.FPKM.txt.gz


title: hPSC-CM-NM-rep3


title: WT-050

description:
number of genes expressed: 3188
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20200707A_10X-R


title: WT-052

description:
number of genes expressed: 4277
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200702B_10X-R

value: COVID-AKI

value: KPMP


title: KPMP_20200702A_10X-R


title: hPSC-CM-NM-rep1


title: KPMP_20200513A_10X-R


title: WT-048

description:
number of genes expressed: 3213
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20190607J-10X-R

value: Nephrectomy


title: KPMP_20190607I-10X-R


title: BUKMAP_20200707B_10X-R


title: mutant-047c

description:
number of genes expressed: 4863
innerEar.gene.expression.tables.FPKM.txt.gz

value: inner ear


title: BUKMAP_20200304F_10X-R

value: Deceased Donor


title: mutant-046c

description:
number of genes expressed: 2538
innerEar.gene.expression.tables.FPKM.txt.gz

value: Endolymphatic sac

value: Sox9Y440X/+ endolymphatic sacs


title: WT-046

description:
number of genes expressed: 3471
innerEar.gene.expression.tables.FPKM.txt.gz

value: Wild-type


title: BUKMAP_20200304B_10X-R


title: mutant-049c

description:
number of genes expressed: 4638
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200513B_10X-R


title: WT-045

description:
number of genes expressed: 1974
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20200205A_10X-R

value: Kidney Medulla


title: WT-044

description:
number of genes expressed: 2499
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-048c

description:
number of genes expressed: 4852
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-044c

description:
number of genes expressed: 1773
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20200205D_10X-R

description:
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Metadata_Field_Descriptions.txt


title: mutant-043c

description:
number of genes expressed: 3135
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-043

description:
number of genes expressed: 2877
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20191104A-10X-R


title: KPMP_20190607K-10X-R


title: BUKMAP_20200304A_10X-R


title: BUKMAP_20190829B_10X-R


title: mutant-045c

description:
number of genes expressed: 4897
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20190822F_10X-R


title: WT-042

description:
number of genes expressed: 1688
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20191010-10X-R


title: mutant-042c

description:
number of genes expressed: 5718
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20191009-10X-R


title: mutant-041c

description:
number of genes expressed: 5554
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-047

description:
number of genes expressed: 2727
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20190529L_10X-R


title: WT-041

description:
number of genes expressed: 1209
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20200205F_10X-R


title: mutant-040c

description:
number of genes expressed: 5555
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20190829E_10X-R

value: Chronic Kidney Disease


title: KPMP_20190829D_10X-R


title: WT-040

description:
number of genes expressed: 2361
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-039c

description:
number of genes expressed: 4542
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20190829C_10X-R


title: WT-039

description:
number of genes expressed: 3445
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200212G_10X-R

value: Diabetic Kidney DIsease (DKD)


title: mutant-038c

description:
number of genes expressed: 2670
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200212F_10X-R


title: WT-038

description:
number of genes expressed: 3314
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200212E_10X-R

value: Acute Kidney Injury (AKI)


title: WT-037

description:
number of genes expressed: 2015
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200212C_10X-R


title: mutant-036c

description:
number of genes expressed: 3727
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200212D_10X-R

description:
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_snCv3_Metadata_Field_Descriptions.txt


title: WT-036

description:
number of genes expressed: 1543
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200212B_10X-R

value: Hypertensive CKD (H-CKD)


title: KPMP_20200212A_10X-R

value: Biopsy


title: mutant-037c

description:
number of genes expressed: 3161
innerEar.gene.expression.tables.FPKM.txt.gz


title: BUKMAP_20190607L_10X-R

value: Reference

value: HuBMAP


title: mutant-034c

description:
number of genes expressed: 3593
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200115A_10X-R

value: Kidney Cortex

value: 10X snRNA-seq


title: KPMP_20200115B_10X-R

value: KPMP


title: WT-034

description:
number of genes expressed: 2700
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20191219C_10X-R


title: KPMP_20191219D_10X-R


title: KPMP_20191219B_10X-R


title: WT-033

description:
number of genes expressed: 2212
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-033c

description:
number of genes expressed: 6033
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-032c

description:
number of genes expressed: 6317
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-035c

description:
number of genes expressed: 3654
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20200212H_10X-R


title: KPMP_20191204B_10X-R

value: Diabetic Kidney Disease (DKD)


title: WT-032

description:
number of genes expressed: 3120
innerEar.gene.expression.tables.FPKM.txt.gz

value: inner ear


title: mutant-031c

description:
number of genes expressed: 5298
innerEar.gene.expression.tables.FPKM.txt.gz


title: KPMP_20191219A_10X-R


title: WT-031

description:
number of genes expressed: 2235
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-030c

description:
number of genes expressed: 1959
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-035

description:
number of genes expressed: 4684
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE46

description:
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_Field_Descriptions.txt

data_processing:
Basecalls were performed using NovaSeq Control Software v1.7.0
Sample demultiplexing, barcode processing, and gene expression quantifications were performed with the 10X Cell Ranger v3 pipeline using the GRCh38 (hg38) reference genome
A cutoff of < 50% mitochondrial reads per cell was applied
Ambient mRNA contamination was corrected using SoupX (v1.5.0)
Cell barcodes having greater than 500 and less than 5000 genes detected were kept for downstream analyses
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Seurat object in h5Seurat format, raw RNA counts provided in RDS format, sample metadata table in txt format, and metadata field descriptions in txt format

source_name: Kidney

extract_protocol:
Single cells were isolated from frozen tissues according to the following protocol: dx.doi.org/10.17504/protocols.io.7dthi6n
10X single cell RNA sequencing was performed according to dx.doi.org/10.17504/protocols.io.7dthi6n using the 10X Chromium Single-Cell 3’ Reagent Kit v3

value: Kidney

value: LivingDonor Biopsy

value: CZI-HCA

value: 10X scRNA-seq


title: PREMIERE47


title: PREMIERE48


title: KPMP_20191204A_10X-R

value: Kidney Medulla


title: WT-030

description:
number of genes expressed: 5304
innerEar.gene.expression.tables.FPKM.txt.gz

value: Endolymphatic sac

value: Wild-type


title: mutant-029c

description:
number of genes expressed: 4520
innerEar.gene.expression.tables.FPKM.txt.gz

value: Sox9Y440X/+ endolymphatic sacs


title: WT-029

description:
number of genes expressed: 3270
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE45


title: mutant-028c

description:
number of genes expressed: 4200
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE44


title: WT-028

description:
number of genes expressed: 5701
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-027c

description:
number of genes expressed: 2966
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE43


title: PREMIERE42


title: PREMIERE41


title: mutant-026c

description:
number of genes expressed: 4249
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE40


title: PREMIERE39


title: WT-025

description:
number of genes expressed: 2909
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-025c

description:
number of genes expressed: 6459
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-026

description:
number of genes expressed: 2614
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE49


title: PREMIERE38


title: PREMIERE37


title: mutant-024c

description:
number of genes expressed: 3369
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE36


title: mutant-023c

description:
number of genes expressed: 3543
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-022c

description:
number of genes expressed: 4717
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE32


title: CR013_Lund_CCmutComp_H3K9me3

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
library strategy: CUT&RUN-seq
Paired-end reads (2x150) were aligned to the hg38 genome using bowtie2 v. 2.3.4.2 (--local–very-sensitive-local --no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700)
Reads were trimmed and de-duplicated with Picard (http://broadinstitute.github.io/picard/)
SAM files were converted to bam files with samtools (Langmead and Salzberg, 2012; Li et al., 2009). The BAM files were filtered according to alignment quality (MAPQ>10) using samtools (samtools view -bq 10 {BAM} > {FILTERED_BAM}) (Langmead and Salzberg, 2012; Li et al., 2009).
Normalized bigwig coverage tracks were made with bamCoverage (deepTools)  (Ramirez et al., 2014), with RPKM normalization.
Assembly: GRCh38
Supplementary files format and content: Bigwigs of filtered alignments for genome browser visualization, normalized with RPKM

growth_protocol: 293 T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&RUN was done on 250,000 cells per condition following the protocol of Henikoff and colleagues (Skene et al, 2018). DNA was purified by the Nucleospin PCR clean-up kit (Macherey-Nagel). Antibodies were: rabbit anti-H3K9me3 (ab8898, 1:100 dilution) and guinea pig anti rabbit IgG (CSB-PA00150E1Gp, 1:100 dilution)
Illumina sequencing libraries were prepared using the Hyperprep kit (KAPA) with unique dual-indexed adapters (KAPA) following the manufacturer's instructions

treatment_protocol: Lentivirus for KAP1 complementation was produced by transfecting HEK23T cells in 6-well plates with 0.6 µg pMD2.G, 1.2 µg p8.91 and 1.2 µg KAP1 pHRSIN (WT or CCmut) using FuGENE 6 (Promega). Virus-containing supernatant was collected 48 h post-transfection, filtered through a 0.45 µm PVDF membrane and used to infect KAP1 KO HEK239T cells. Transduced cells were selected with 200 µg ml-1 hygromycin.

tag: cell line

value: Human embryonic kidney cells

value: KO-CCmutant complement

tag: antibody


title: mutant-021c

description:
number of genes expressed: 460
innerEar.gene.expression.tables.FPKM.txt.gz

tag: tissue

tag: age


title: PREMIERE31

value: Reference


title: CR013_Lund_WTcomp_H3K9me3

value: KO-WTcomplement

value: rabbit anti-H3K9me3 (ab8898, 1:100 dilution)


title: WT-021

description:
number of genes expressed: 3603
innerEar.gene.expression.tables.FPKM.txt.gz

tag: organ


title: WT-027

description:
number of genes expressed: 4887
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE30

description:
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_Field_Descriptions.txt

tag: patient


title: CR013_Lund_KAP1KO_H3K9me3


title: CR013_Lund_HEK293_H3K9me3

value: WT


title: mutant-020c

description:
number of genes expressed: 3247
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE29

tag: condition

value: Hypertensive CKD (H-CKD)

value: Biopsy

value: KPMP


title: CR013_Lund_HEK293_IgG

value: guinea pig anti rabbit IgG (CSB-PA00150E1Gp, 1:100 dilution)


title: Mouse retinal amacrine cells, Rep5

description:
TLS23F
ReorderedLightSeq_RetinaAmacrines.csv
TH_5/Am_5 in ReorderedLightSeq_RetinaAmacrines.csv
Th represents TH+ Amacrine Cells, Am represents TH- AmacrineCells.
Barcodes for each cell population are: GTTAGG = TH+ amacrines; AGGGTA = TH- amacrines

data_processing:
Assembly: mm39
Extracted Light-Seq DNA barcodes (corresponding to different cell populations) using UMI-tools 1.1.1
Aligned to genome with STAR aligner 2.7.9a
Used featureCounts (subread) 2.0.1 to assign mapped reads to genes
Deduplicated reads based on UMIs + mapped gene pairs (samtools 1.9, 1.12)
Supplementary files format and content: CSV file containing Light-Seq read counts per gene. Rows are genes, columns are replicates for each cell population

extract_protocol:
Light-Seq
Nextera tagmentation

value: Retina

value: TH+ and TH- Amacrine Cells

tag: genome build


title: Mouse retinal amacrine cells, Rep4

description:
TLS23E
ReorderedLightSeq_RetinaAmacrines.csv
TH_4/Am_4 in ReorderedLightSeq_RetinaAmacrines.csv
Th represents TH+ Amacrine Cells, Am represents TH- AmacrineCells.
Barcodes for each cell population are: GTTAGG = TH+ amacrines; AGGGTA = TH- amacrines


title: Mouse retinal amacrine cells, Rep3

description:
TLS23D
ReorderedLightSeq_RetinaAmacrines.csv
TH_3/Am_3 in ReorderedLightSeq_RetinaAmacrines.csv
Th represents TH+ Amacrine Cells, Am represents TH- AmacrineCells.
Barcodes for each cell population are: GTTAGG = TH+ amacrines; AGGGTA = TH- amacrines


title: mutant-019c

description:
number of genes expressed: 3931
innerEar.gene.expression.tables.FPKM.txt.gz

value: inner ear


title: Mouse retinal amacrine cells, Rep2

description:
TLS23B
ReorderedLightSeq_RetinaAmacrines.csv
TH_2/Am_2 in ReorderedLightSeq_RetinaAmacrines.csv
Th represents TH+ Amacrine Cells, Am represents TH- AmacrineCells.
Barcodes for each cell population are: GTTAGG = TH+ amacrines; AGGGTA = TH- amacrines


title: PREMIERE28

value: Kidney

tag: tissue source

tag: project

value: 10X scRNA-seq


title: PREMIERE27

tag: raw data location


title: Mouse retinal amacrine cells, Rep1

description:
TLS23A
ReorderedLightSeq_RetinaAmacrines.csv
TH_1/Am_1 in ReorderedLightSeq_RetinaAmacrines.csv
Th represents TH+ Amacrine Cells, Am represents TH- AmacrineCells.
Barcodes for each cell population are: GTTAGG = TH+ amacrines; AGGGTA = TH- amacrines


title: WT-024

description:
number of genes expressed: 5367
innerEar.gene.expression.tables.FPKM.txt.gz

value: Endolymphatic sac

value: Wild-type


title: PREMIERE35

value: LivingDonor Biopsy

value: CZI-HCA

tag: raw data id

tag: assay


title: WT-022

description:
number of genes expressed: 4391
innerEar.gene.expression.tables.FPKM.txt.gz

tag: genotype


title: PREMIERE33

value: Reference


title: WT-019

description:
number of genes expressed: 3159
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE34


title: 102_4_DCA_FFPE

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

data_processing:
FASTQ files uploaded to PartekFlow (Partek build version 9.0.20.0202, St. OLouis, MO)
Reads mapped to mm10 using Star 2.6
Quantitation (Partek expectation maximization) to mm10 - RefSeq Transcripts 92
Raw gene counts were offset by a 0.0001 count, filtered to remove any gene feature with geometric mean across all samples <1, counts per million mapped reads (CPM) normalized and log2 transformed
Significant differentially expressed genes (DEGs) were identified using Partek Gene Specific Analysis (GSA) fit to multiple models (negative binomial, normal and log-normal). The lowest corrected Akaike Information Criterion (AIC) was used to select the gene model fit. Significant DEGs were defined as genes with false discovery rate (FDR) adjusted p-value <0.05 (Benjamini and Hochberg 1995) and absolute fold change > 2.
Genome_build: MM10
Supplementary_files_format_and_content: tab deliminated files with filtered, counts per million mapped reads normalized, and log2 transformed counts for all genes

source_name: formalin-fixed paraffin embedded left lateral and right media liver lobes

growth_protocol: Studies were conducted in 4 week-old male B6C3F1 mice maintained under standard housing conditions at the U.S. Environmental Protection Agency (US EPA) AAALAC-accredited animal facility (Research Triangle Park, NC). Animal care and procedures were conducted under protocols approved by the Institutional Animal Care and Use Committee of the USEPA.

extract_protocol:
RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome.
Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500  platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads.
Targeted RNA-seq

treatment_protocol: Dichloroacetic acid (CAS 79-43-6, Aldrich) was administered in the drinking water at doses of 0, 1.0, 2.0, and 3.5 g/L (as described in DeAngelo et al. 1991) for six days. Drinkin water consumption along with measured DCA dose-levels were converted to mg per kg bodyweight per day (mg/kg-d) as 0, 198, 313, and 427 mg DCA/kg-d

value: liver

tag: strain

value: 4 weeks

tag: Sex

value: male

tag: treatment

value: dichloroacetic acid (DCA)

tag: dose

value: 427 mg/kg-d


title: PREMIERE25

value: Diabetic Kidney Disease (DKD)

value: Biopsy

value: KPMP


title: 100_4_DCA_FFPE


title: mutant-018c

description:
number of genes expressed: 140
innerEar.gene.expression.tables.FPKM.txt.gz

value: Sox9Y440X/+ endolymphatic sacs


title: 101_4_DCA_FFPE


title: 99_4_DCA_FFPE


title: WT-018

description:
number of genes expressed: 5100
innerEar.gene.expression.tables.FPKM.txt.gz

value: inner ear


title: PREMIERE24

value: Kidney


title: 98_4_DCA_FFPE


title: 97_4_DCA_FFPE


title: mutant-017c

description:
number of genes expressed: 5237
innerEar.gene.expression.tables.FPKM.txt.gz


title: 78_3_DCA_FFPE

value: 313 mg/kg-d


title: PREMIERE23

value: 10X scRNA-seq


title: WT-017

description:
number of genes expressed: 5732
innerEar.gene.expression.tables.FPKM.txt.gz

value: Endolymphatic sac

value: Wild-type


title: WT-020

description:
number of genes expressed: 2557
innerEar.gene.expression.tables.FPKM.txt.gz


title: 77_3_DCA_FFPE


title: PREMIERE22


title: 75_3_DCA_FFPE


title: PREMIERE21


title: 73_3_DCA_FFPE


title: PREMIERE26


title: WT-016

description:
number of genes expressed: 4077
innerEar.gene.expression.tables.FPKM.txt.gz


title: mutant-016c

description:
number of genes expressed: 4909
innerEar.gene.expression.tables.FPKM.txt.gz


title: 54_2_DCA_FFPE

value: 198 mg/kg-d


title: PREMIERE20

description:
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Seurat_07302021.h5Seurat
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Counts_07302021.RDS
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_07302021.txt
Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_Field_Descriptions.txt


title: mutant-015c

description:
number of genes expressed: 5559
innerEar.gene.expression.tables.FPKM.txt.gz


title: PREMIERE19


title: 53_2_DCA_FFPE


title: 52_2_DCA_FFPE


title: PREMIERE18


title: WT-015

description:
number of genes expressed: 3070
innerEar.gene.expression.tables.FPKM.txt.gz


title: 50_2_DCA_FFPE


title: 51_2_DCA_FFPE


title: PREMIERE17


title: mutant-014c

description:
number of genes expressed: 2847
innerEar.gene.expression.tables.FPKM.txt.gz


title: WT-014

description:
number of genes expressed: 5992
innerEar.gene.expression.tables.FPKM.txt.gz


title: 8_1_control_FFPE

value: 0 mg/kg-d


title: 6_1_control_FFPE

value: liver


title: PREMIERE16


title: 7_1_control_FFPE

value: 4 weeks


title: mutant-013c

description:
number of genes expressed: 5579
innerEar.gene.expression.tables.FPKM.txt.gz


title: 5_1_control_FFPE

value: male


title: 76_3_DCA_FFPE

value: dichloroacetic acid (DCA)


title: 74_3_DCA_FFPE


title: PREMIERE15


title: PREMIERE14


title: TNBS_Propy_1uM_Myeloid TCGACGTC_TCGCATAA

description:
TNBS_Propy_1uM_Myeloid
Control and 4 uM of Propyzamide
Myeloid cells from TNBS-induced Zebrafish treated by 4 uM of Propyzamide

data_processing:
The sample is aligned to GRCz38 transcriptome and quantified using Kallisto
Genome_build: GRCz38
Supplementary_files_format_and_content: gzipped abundance.tsv output from Kallisto

organism: Danio rerio

value: AB


title: mutant-012c

description:
number of genes expressed: 1406
innerEar.gene.expression.tables.FPKM.txt.gz


title: 3_1_control_FFPE

source_name: formalin-fixed paraffin embedded left lateral and right medial liver lobes


title: PREMIERE13

value: Diabetic Kidney Disease (DKD)


title: 4_1_control_FFPE


title: WT-013

description:
number of genes expressed: 5233
innerEar.gene.expression.tables.FPKM.txt.gz


title: 102_4_DCA_FROZ

source_name: frozen liver (mixed lobes)

value: 427 mg/kg-d


title: TNBS_Propy_1uM_Myeloid TGCAGCTA_TCGCATAA


title: PREMIERE12

value: Acute Kidney Injury (AKI)

value: Biopsy

value: KPMP


title: WT-012

description:
number of genes expressed: 4998
innerEar.gene.expression.tables.FPKM.txt.gz

value: inner ear


title: mutant-011c

description:
number of genes expressed: 6323
innerEar.gene.expression.tables.FPKM.txt.gz

value: Sox9Y440X/+ endolymphatic sacs


title: 49_2_DCA_FFPE


title: TNBS_Propy_1uM_Myeloid CGATCAGT_TCGCATAA


title: PREMIERE11

value: Kidney

value: 10X scRNA-seq


title: WT-011

description:
number of genes expressed: 2658
innerEar.gene.expression.tables.FPKM.txt.gz

value: Endolymphatic sac

value: Wild-type


title: TNBS_Propy_1uM_Myeloid CCTAAGAC_TCGCATAA


title: PREMIERE10


title: 100_4_DCA_FROZ


title: 101_4_DCA_FROZ


title: mutant-010c

description:
number of genes expressed: 2970
innerEar.gene.expression.tables.FPKM.txt.gz


title: TNBS_Propy_20uM_Myeloid ACTGAGCG_TCGCATAA

description:
TNBS_Propy_20uM_Myeloid
Control and 20 uM of Propyzamide
Myeloid cells from TNBS-induced Zebrafish treated by 20 uM of Propyzamide


title: PREMIERE9


title: WT-010

description:
number of genes expressed: 5575
innerEar.gene.expression.tables.FPKM.txt.gz