title: WT

city: Daejeon

first: Jihyun

last: Yu

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description: 10X genomics

data_processing:
Raw sequencing files were initially processed with the Cell Ranger (v.4.0.0) pipeline, and down stream analysis was conducted based on the Scanpy (v.1.8.2) pipeline. Predicted doublets were identified from the Scrublet (v.0.2.2) package.
Assembly: mm10
Supplementary files format and content: h5ad file for Whole cells
Supplementary files format and content: h5ad file for neutrophil cluster
Supplementary files format and content: h5ad file for T cell cluster

source_name: Lung

extract_protocol:
To isolate asthmatic lung cells, lungs were chopped into small fragments and enzymatically digested with Collagenase D and DNase I at 37 °C for 30 minutes. The enzyme reaction was stopped by adding EDTA. After vigorous resuspension, cells were filtered through 100 µm strainers, and red blood cells were lysed with ACK lysis buffer. The dead cells and FSC(hi)SSC(hi) cells were removed by fluorescence-activated cell sorting (FACS). To synthesize scRNA-seq libraries, cells were suspended in PBS containing 0.04% BSA and loaded into Chromium-controller (10X Genomics)
scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v 3.1 (10X Genomics) according to the manufacturer’s protocol

value: Lung

value: Immune cells

value: Epx-Cre/+

value: HDM-induced asthma


title: Renca cells, passage 3, rep1

status: Public on Sep 24 2025

type: SRA

city: Shenzhen

first: Wei

last: Yang

address: Shenzhen 6082 longgang Road

country: China

institute: Shenzhen Longgang Central Hospital

description: Library name: Renca-P3-1

library_source: transcriptomic

data_processing:
Raw reads were processed with fastp to remove low-quality reads, adapter contaminants, and reads with excessive N content, yielding clean reads.
rRNA contamination was eliminated by aligning reads to an rRNA database using bowtie2.
The remaining reads were mapped to the reference genome using HISAT2, and mapping efficiency was calculated.
Gene expression levels (FPKM and TPM) were estimated with StringTie and RSEM.
Assembly: GRCh38 for Homo sapiens; GRCm39 for Mus musculus
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Renca

extract_protocol:
Total RNA was extracted using Trizol reagent. RNA purity was assessed with a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), concentration was measured using a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA), and integrity (RIN value) was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). After quality control, mRNA was enriched using Oligo(dT) magnetic beads, and first-strand cDNA was synthesized with M-MuLV Reverse Transcriptase. RNA templates were degraded by RNase H, and second-strand cDNA was synthesized. Subsequent steps included end repair, poly-A tailing, adapter ligation, and size selection (~200 bp) using AMPure XP beads, followed by PCR amplification for library construction.
RNA libraries for RNA-seq were prepared using New England Biolabs (#E7530 ) following manufacturer's protocols.

tag: cell line

value: Renca

tag: cell type

value: Renal Cell Adenocarcinoma Cell

tag: genotype

value: WT

tag: treatment

value: Routine Passaging


title: patient1_pre

type: RNA

city: Houston

first: Oluwadara

last: Coker

state: Texas

address: 6767 Bertner Ave

department: GI Medical Oncology

country: USA

institute: MD Anderson Cancer Center

description: Fresh frozen parafilm embedded spatial transcriptome imaging. 10X Genome Analyzer was used to process the samples. Xenium Explorer was used to analyze the imaging and Xenium data of these files. All the files in the processed folder were loaded into the Seurat object using LoadXenium function

hyb_protocol: Automated imaging and cyclic probe hybridization were performed on the Xenium Analyzer across 15 hybridization cycles. Fluorescent-labeled detection probes were hybridized, imaged, and removed sequentially in each cycle. Z-stack images were acquired at 0.75 µm step size to cover the entire tissue thickness for each round of imaging, across four fluorescent channels.

scan_protocol: Z-stack images from all cycles and channels were stitched, aligned to DAPI counterstains, and used to construct spatial maps of transcript localization within each region of interest. Transcript puncta were identified as fluorescent spots quantified by photon counts, and their spatial registration across cycles was achieved using Gaussian fitting. Each transcript was assigned a unique optical signature based on the combined fluorescence intensities across cycles and channels. A Phred-scaled quality score (Q-score) was calculated for each decoded transcript, and only transcripts with Q ≥ 20 were retained for downstream spatial gene expression analysis

data_processing: Cell segmentation was performed using a nuclear (DAPI-based) seed expansion algorithm, where cell boundaries were defined by expanding 15 µm radially from the nucleus or until adjacent cell boundaries were encountered. The Xenium Onboard Analysis (XOA) pipeline generated output files including the feature-cell expression matrix, transcript spatial coordinates, and cell boundary files (CSV format).

label: DAPI

organism: Homo sapiens

label_protocol: Nuclei was counterstained with DAPI

growth_protocol: Patient samples in the form of FFPE were obtained from ITB at MDA with approval from the IRB and with written consent from patients

extract_protocol: FFPE tissue sections were cut (5uM thick) from tumor biopsies and mounted onto Xenium slides. Sections then underwent deparaffinization, antigen retrieval, and permeabilization steps to expose RNA transcripts.

treatment_protocol: These samples came from patients who were treated with G12Ci/EGFRi during clinical trials

tag: tissue


title: wild-type, cerebellum, 3 months, sample 3

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
FastQC for raw read quality
Trimmomatic for trimming reads and adapters
STAR for read alignment to MM10 genome
DESeq2 analysis for DEGs
GO analysis using ToppFunn and SynGO
Assembly: MM10
Supplementary files format and content: TXT, Count table

molecule: polyA RNA

source_name: cerebellum

extract_protocol:
RNA extraction
150 bp paired end reads

value: cerebellum

value: 3 months


title: patient2_pre

source_name: Bone

value: Bone


title: Heart_tissue_TOF_6

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

description: Library name: TOF_6

data_processing:
RNA-Seq reads were mapped to the mm10 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000)
Samples were quantified using featureCounts with the default setting.
Assembly: hg38
Supplementary files format and content: Excel file include genename, gene length, row counts

source_name: RV Heart

extract_protocol:
Total RNA was isolated using the RNeasy Plus Universal Mini kit from Qiagen. RNA quality were performed by BGI. Only qualified samples were used for library construction.
RNA libraries were prepared by BGI for sequencing using standard DNBSEQ protocols

value: RV Heart


title: Eosinophil_specific_GPR43_KO

description: 10X genomics

library_source: transcriptomic single cell


title: wild-type, cerebellum, 3 months, sample 2


title: wild-type, cerebellum, 3 months, sample 1


title: Heart_tissue_TOF_2

description: Library name: TOF_2


title: wild-type, cerebellum, 3 months, sample 5


title: mESC , Dppa4 KO, UNC0638, rep1

status: Public on Sep 23 2025

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

description: Library name: Sample 10

data_processing:
Reads were trimmed to remove adapter sequences using trim galore v0.6.7 with parameters: --phred33 --quality 0 --stringency 10 --length 20
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
TE Counts v2.2.3 was used to assign mapped reads to genes and repeats with default parameters. GTFs from GENCODE (vM25) and a repeat file from TE Counts were used.
Bigwigs were made from bed files using deeptools v3.5.1 using parameters: -p 10 --binSize 10 --ignoreForNormalization chrX chrM --normalizeUsing RPGC --effectiveGenomeSize  2652783500 --extendReads 200 --ignoreDuplicates --blackListFileName mm10-blacklist.v2_highSignalRegions.bed
Differential gene expression was performed in R v4.1.0 using DESeq2 v1.34.0 with parameters: geneField = 'ensembl'
Assembly: mm10
Supplementary files format and content: Bigwigs normalized to sequencing depth for read 1 and read 2
Supplementary files format and content: CSVs of DESeq2 normalized counts for each round of RNAseq
Supplementary files format and content: CSVs of DESeq2 normalized counts for transposable elements (TEs) for each round of RNAseq
Supplementary files format and content: CSV of DESeq2 results of 7d bulk RNAseq projected onto the Dppa4 and WT UNC treated cells.

source_name: Mouse embryonic stem cell

growth_protocol: Cells were cultured in FBS/LIF conditions at 37C at 5%CO2.

extract_protocol:
RNA was extracted using the  Trizol extraction method and then purified using the Zymo Rna Clean and concentrator kit.
RNA libraries (polyA enrichment) were prepped by Novogene and sequenced libraries at PE x150 on a Novaseq 6000.

treatment_protocol: Three independent clones of WTJ1 and DPPA4KO mESCs were treated with DMSO or UNC0638 for 48 hours

value: Mouse embryonic stem cell

value: ESC

value: Depleted of DPPA4 by CRISPR/Cas9 technology


title: mESC , Dppa4 KO, UNC0638, rep2

description: Library name: Sample 11


title: mESC , Dppa4 KO, DMSO, rep1

description: Library name: Sample 7

value: DMSO


title: mESC , Dppa4 KO, DMSO, rep2

description: Library name: Sample 8


title: mESC , WT, UNC0638, rep3

description: Library name: Sample 6

value: WT mESC


title: mESC , WT, UNC0638, rep2

description: Library name: Sample 5


title: mESC , Dppa4 KO, UNC0638, rep3

description: Library name: Sample 12


title: Human tissue sample C20

city: yinchuan

first: wang

last: linan

state: ningxia

address: ictory Street, Yinchuan, Ningxia

institute: Department of Orthopedics, General Hospital of Ningxia Medical University

description: Circular RNA (circRNA) enrichment and microarray profiling: Total RNA was extracted from human tissue samples. To enrich for circular RNAs, total RNA was treated with RNase R (Epicentre, Inc.) to degrade linear RNAs. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA using a random priming method (Arraystar Super RNA Labeling Kit). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After hybridization, the arrays were washed and scanned using the Agilent Scanner G2505C.  Data processing: Raw data were extracted using Agilent Feature Extraction software (v11.0.1.1). Quantile normalization and subsequent data analysis were performed using the R software limma package. circRNAs with flags in 'P' or 'M' in at least 3 out of 6 samples were retained for further analysis. Differential expression analysis was performed using a t-test; circRNAs with a fold change ≥ 2.0 and a p-value ≤ 0.09 were considered significantly differentially expressed.

hyb_protocol: For hybridization, 1 μg of each labeled cRNA was fragmented by adding 5 μl of 10× Blocking Agent and 1 μl of 25× Fragmentation Buffer, followed by incubation at 60°C for 30 minutes. The fragmented cRNA was then diluted with 25 μl of 2× Hybridization Buffer to form the final hybridization solution. A volume of 50 μl of this solution was dispensed onto the gasket slide and assembled with the Arraystar Human circRNA Array V2 (8x15K) slide. The assembled slides were hybridized for 17 hours at 65°C in an Agilent Hybridization Oven with rotation. Following hybridization, the arrays were washed according to the Agilent standard protocol for gene expression arrays (likely involving Gene Expression Wash Buffer 1 and 2 at specific temperatures). The hybridized arrays were then scanned immediately using the Agilent Scanner G2505C. No additional staining or post-processing steps were performed, as the direct detection of the Cy3 fluorophore was used.

scan_protocol: The hybridized arrays were scanned using the Agilent DNA Microarray Scanner (Model: G2505C). The scanning was performed according to the manufacturer's default settings for gene expression arrays. The scanning parameters were likely set to a resolution of 3 μm with the Green PMT gain set to 100% for the Cy3 channel. The resulting images (TIFF files) were acquired and analyzed using Agilent Feature Extraction Software (Version: 11.0.1.1). This software was used for grid alignment, feature (spot) finding, fluorescence intensity extraction, and background subtraction to generate the final raw data output files.

data_processing: The raw signal intensities were collected using Agilent Feature Extraction Software (v11.0.1.1). The resulting data files were then processed using the R software environment and the limma package. First, quantile normalization was applied to the raw data to remove technical variations and make the distributions of signal intensities comparable across all arrays. Following normalization, a low-intensity filtering step was performed: only circRNAs that had flags in P (Present) or M (Marginal) in at least 3 out of the 6 samples were retained for further analysis. The final output is the normalized signal intensity matrix, which is provided in the submitted dataset.

source_name: tissue

label_protocol: Total RNA was digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA (Cy3-labeled) using the Arraystar Super RNA Labeling Kit (Arraystar) based on a random priming method. The labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen). The concentration and specific activity (pmol Cy3 per μg cRNA) of the labeled cRNAs were measured using a NanoDrop ND-1000 spectrophotometer.

extract_protocol: Total RNA was isolated from human tissue samples using the TRIzol Reagent (Invitrogen) according to the manufacturer's protocol.

value: Lumbar intervertebral disc protrusion and intervertebral disc tissue


title: Human tissue sample T6

description: Circular RNA (circRNA) enrichment and microarray profiling: Total RNA was extracted from human tissue samples. To enrich for circular RNAs, total RNA was treated with RNase R (Epicentre, Inc.) to degrade linear RNAs. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA using a random priming method (Arraystar Super RNA Labeling Kit). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After hybridization, the arrays were washed and scanned using the Agilent Scanner G2505C.  Data processing: Raw data were extracted using Agilent Feature Extraction software (v11.0.1.1). Quantile normalization and subsequent data analysis were performed using the R software limma package. circRNAs with flags in 'P' or 'M' in at least 3 out of 6 samples were retained for further analysis. Differential expression analysis was performed using a t-test; circRNAs with a fold change ≥ 2.0 and a p-value ≤ 0.05 were considered significantly differentially expressed.

value: Spinal tuberculosis lesion of intervertebral disc tissue


title: mESC , WT, DMSO, rep3

description: Library name: Sample 3


title: mESC , WT, DMSO, rep2

description: Library name: Sample 2


title: mESC , Dppa4 KO, DMSO, rep3

description: Library name: Sample 9


title: mESC , WT, DMSO, rep1

description: Library name: Sample 1


title: Human tissue sample C23

description: Circular RNA (circRNA) enrichment and microarray profiling: Total RNA was extracted from human tissue samples. To enrich for circular RNAs, total RNA was treated with RNase R (Epicentre, Inc.) to degrade linear RNAs. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA using a random priming method (Arraystar Super RNA Labeling Kit). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After hybridization, the arrays were washed and scanned using the Agilent Scanner G2505C.  Data processing: Raw data were extracted using Agilent Feature Extraction software (v11.0.1.1). Quantile normalization and subsequent data analysis were performed using the R software limma package. circRNAs with flags in 'P' or 'M' in at least 3 out of 6 samples were retained for further analysis. Differential expression analysis was performed using a t-test; circRNAs with a fold change ≥ 2.0 and a p-value ≤ 0.10 were considered significantly differentially expressed.


title: AKK_1306

city: Fuzhou

first: Yijuan

last: Liu

address: First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China

description:
Library name: Sample16
FPKM.AKK_1306

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: FPKM, counts values for each Sample

source_name: Colon

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Colon

value: AKK


title: AKK_1310

institute: First Affiliated Hospital of Fujian Medical University

description:
Library name: Sample18
FPKM.AKK_1310


title: Human tissue sample T8

description: Circular RNA (circRNA) enrichment and microarray profiling: Total RNA was extracted from human tissue samples. To enrich for circular RNAs, total RNA was treated with RNase R (Epicentre, Inc.) to degrade linear RNAs. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA using a random priming method (Arraystar Super RNA Labeling Kit). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After hybridization, the arrays were washed and scanned using the Agilent Scanner G2505C.  Data processing: Raw data were extracted using Agilent Feature Extraction software (v11.0.1.1). Quantile normalization and subsequent data analysis were performed using the R software limma package. circRNAs with flags in 'P' or 'M' in at least 3 out of 6 samples were retained for further analysis. Differential expression analysis was performed using a t-test; circRNAs with a fold change ≥ 2.0 and a p-value ≤ 0.07 were considered significantly differentially expressed.


title: mESC , WT, UNC0638, rep1

description: Library name: Sample 4


title: AKK_1305

description:
Library name: Sample15
FPKM.AKK_1305


title: Human tissue sample C18

description: Circular RNA (circRNA) enrichment and microarray profiling: Total RNA was extracted from human tissue samples. To enrich for circular RNAs, total RNA was treated with RNase R (Epicentre, Inc.) to degrade linear RNAs. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA using a random priming method (Arraystar Super RNA Labeling Kit). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After hybridization, the arrays were washed and scanned using the Agilent Scanner G2505C.  Data processing: Raw data were extracted using Agilent Feature Extraction software (v11.0.1.1). Quantile normalization and subsequent data analysis were performed using the R software limma package. circRNAs with flags in 'P' or 'M' in at least 3 out of 6 samples were retained for further analysis. Differential expression analysis was performed using a t-test; circRNAs with a fold change ≥ 2.0 and a p-value ≤ 0.08 were considered significantly differentially expressed.


title: Human tissue sample T7

description: Circular RNA (circRNA) enrichment and microarray profiling: Total RNA was extracted from human tissue samples. To enrich for circular RNAs, total RNA was treated with RNase R (Epicentre, Inc.) to degrade linear RNAs. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA using a random priming method (Arraystar Super RNA Labeling Kit). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After hybridization, the arrays were washed and scanned using the Agilent Scanner G2505C.  Data processing: Raw data were extracted using Agilent Feature Extraction software (v11.0.1.1). Quantile normalization and subsequent data analysis were performed using the R software limma package. circRNAs with flags in 'P' or 'M' in at least 3 out of 6 samples were retained for further analysis. Differential expression analysis was performed using a t-test; circRNAs with a fold change ≥ 2.0 and a p-value ≤ 0.06 were considered significantly differentially expressed.


title: AKK_1303

description:
Library name: Sample14
FPKM.AKK_1303


title: Model_1340

description:
Library name: Sample12
FPKM.Model_1340

value: Model


title: AKK_1302

description:
Library name: Sample13
FPKM.AKK_1302


title: Model_1339

description:
Library name: Sample11
FPKM.Model_1339


title: Control_2289

description:
Library name: Sample9
FPKM.Control_2289

value: Control


title: Control_2287

description:
Library name: Sample7
FPKM.Control_2287


title: Control_2288

description:
Library name: Sample8
FPKM.Control_2288


title: Control_2286

description:
Library name: Sample6
FPKM.Control_2286


title: AKK_1309

description:
Library name: Sample17
FPKM.AKK_1309


title: Model_1341

description:
Library name: Sample3
FPKM.Model_1341


title: Model_1338

description:
Library name: Sample2
FPKM.Model_1338


title: Model_1337

description:
Library name: Sample1
FPKM.Model_1337


title: Control_2285

description:
Library name: Sample5
FPKM.Control_2285


title: scRNA-seq of B16F10 control tumor, mouse 2

city: Cleveland

first: Shuyang

last: Chen

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description:
Library name: scRNA_Ctrl_Mouse2
10x Genomics scRNA-seq of control B16F10 tumor in C57BL/6 mouse 2

data_processing:
Raw FASTQ files were processed using 10x Genomics Cell Ranger with default parameters. Reads were aligned to the mm10 (GRCm38) reference genome, and filtered gene-barcode matrices were generated. Further analysis and visualization were performed using the 10x Genomics Loupe Browser.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data includes filtered feature-barcode matrices in .h5 format (from Cell Ranger).

source_name: tumor

growth_protocol: B16F10 melanoma cells were cultured in DMEM supplemented with 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
Tumors were dissociated into single-cell suspensions. CD45+ immune cells were isolated using flow cytometry-based sorting. Total RNA was extracted following the 10x Genomics Chromium workflow.
For single-cell RNA-seq, libraries were prepared using the 10x Genomics Chromium Single Cell 3ʹ protocol (Document #CG000204), targeting 10,000 cells per sample. cDNA synthesis and barcoding were performed on the Chromium Controller. After library prep and quality control (Bioanalyzer, Q-cycler), samples were sequenced on an Illumina NovaSeq 6000 platform (28 bp Read 1, 91 bp Read 2).

treatment_protocol: Cells were transduced with lentiviral vectors encoding either ZDHHC13 or an empty vector control. In single-cell experiments, engineered B16F10 cells were inoculated subcutaneously into C57BL/6 mice.

value: tumor

value: melanoma cells and TME

value: WT

value: empty vector

tag: batch


title: Control_2668

description:
Library name: Sample4
FPKM.Control_2668


title: scRNA-seq of B16F10 ZDHHC13 tumor, mouse 2

description:
Library name: scRNA_ZDHHC13_Mouse2
10x Genomics scRNA-seq of ZDHHC13-overexpressing B16F10 tumor in C57BL/6 mouse 2

value: ZDHHC13 OE

value: lentiviral overexpression


title: scRNA-seq of B16F10 ZDHHC13 tumor, mouse 1

description:
Library name: scRNA_ZDHHC13_Mouse1
10x Genomics scRNA-seq of ZDHHC13-overexpressing B16F10 tumor in C57BL/6 mouse 1


title: scRNA-seq of B16F10 control tumor, mouse 1

description:
Library name: scRNA_Ctrl_Mouse1
10x Genomics scRNA-seq of control B16F10 tumor in C57BL/6 mouse 1


title: B16F10 control bulk RNA-seq rep2

description:
Library name: Bulk_Ctrl_Rep2
Control B16F10 cells transduced with empty vector

data_processing:
Raw FASTQ files were processed using RanaSeq, an online RNA-seq analysis platform. The pipeline included quality control (FastQC), read alignment using STAR to the mm10 reference genome, and gene-level quantification using featureCounts. All steps were performed with default settings unless otherwise noted.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed output from RanaSeq includes raw and normalized gene expression matrices in processed gene counts.xlsx.

extract_protocol:
Total RNA was extracted from cultured B16F10 cells or tumor tissues using Qiagen RNeasy Mini Kit.
For bulk RNA-seq, libraries were prepared using Illumina's Total RNA Library Prep protocol (Document #1000000124514). Ribosomal RNA was depleted, RNA was fragmented and reverse-transcribed, and cDNA was end-repaired, A-tailed, ligated to adapters, and PCR-amplified. Libraries were sequenced on the Illumina NovaSeq 6000 platform (2 × 75 bp).

treatment_protocol: Cells were transduced with lentiviral vectors encoding either ZDHHC13 or an empty vector control.

value: melanoma cells


title: CD4+ T cells, UA sample 4

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 25 South Grand Ave

department: Dermatology

institute: University of Iowa

description:
Library name: UA_4
Column name in raw_counts_all_samples.txt: UA_4

data_processing:
Reads were aligned to the reference genome using the STAR aligner (version 2.7.10a) and a genome index was generated using the GRCm39 primary assembly (FASTA) and the corresponding GENCODE vM30 annotation (GTF). Gene-level counts were quantified during alignment using the --quantMode GeneCounts option in STAR. Gene counts were imported into R (version 4.4) and consolidated into a single expression matrix for all eight samples.
Lowly expressed genes were filtered out by retaining genes with a total count greater than 30 across all samples and fewer than 6 zero-count samples. Transcript-to-gene mappings were performed using the GENCODE vM30 annotation file (tx2gene.gencode.vM30.csv), and gene-level counts were aggregated by summing counts across transcript isoforms. Differential expression analysis was performed using the DESeq2 package (version 1.46.0)
Assembly: GRCm39 primary assembly (FASTA) and the corresponding GENCODE vM30 annotation (GTF)
Supplementary files format and content: Txt file of raw gene-level counts for each sample. Rownames and column names are included.

source_name: skin draining lymph nodes

extract_protocol:
Samples were sent to MedGenome Inc for RNA extraction. 100ng of RNA was used for input.
Illumina Truseq Stranded mRNA kit (20020595) was used, following manufacturer's protocol.

treatment_protocol: AA was induced via skin graft induction. Unmanipulated, age-matched mice were used as unaffected (UA) controls.

value: skin draining lymph nodes

value: CD4+ T cell


title: B16F10 ZDHHC13 OE bulk RNA-seq rep2

description:
Library name: Bulk_ZDHHC13_Rep2
B16F10 cells stably overexpressing ZDHHC13


title: B16F10 ZDHHC13 OE bulk RNA-seq rep1

description:
Library name: Bulk_ZDHHC13_Rep1
B16F10 cells stably overexpressing ZDHHC13


title: CD4+ T cells, AA sample 3

description:
Library name: AA_3
Column name in raw_counts_all_samples.txt: AA_3

value: skin graft induction


title: CD4+ T cells, AA sample 2

description:
Library name: AA_2
Column name in raw_counts_all_samples.txt: AA_2


title: CD4+ T cells, AA sample 1

description:
Library name: AA_1
Column name in raw_counts_all_samples.txt: AA_1


title: CD4+ T cells, UA sample 1

description:
Library name: UA_1
Column name in raw_counts_all_samples.txt: UA_1


title: B16F10 control bulk RNA-seq rep1

description:
Library name: Bulk_Ctrl_Rep1
Control B16F10 cells transduced with empty vector


title: TNFR2_plus_rep4

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Library name: Sample 7

data_processing:
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool and was trimmed using TrimGalore software to remove adapter using the auto detection mode and the following parameters: --clip_r1 3 --three_prime_clip_r2 3.
Then reads were mapped to the mouse Ensembl GRCm38 transcriptome index using salmon (v.1.3.0).
Gene-level normalization and differential gene expression analysis were performed with Bioconductor (Gentleman et al., 2004; Huber et al., 2015) package DESeq2 v.1.28 (Love et al., 2014) using the R environment v.4.0 (R Core Team, 2015).
The Wald test was used for significance testing and the resulting false discovery rate (FDR) p-values were adjusted for multiple comparisons using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995) and genes were considered differentially expressed (DEGs) only at FDR < 0.05
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample

source_name: spleen

extract_protocol:
Total RNA was isolated with the Single Cell RNA Purification Kit (Norgen) following the manufacturer’s protocol.
RNA-Seq library for mRNA sequencing was prepared with SMARTer Stranded Total RNA-Seq kit - Pico Input Mammalian. All extracted RNA samples were quality controlled for integrity with a 2100 Bioanalyzer system (Agilent Technologies) and were sequenced on a NovaSeq 6000 System (Illumina)

value: spleen

value: Treg

value: Foxp3 YFP-cre


title: CD4+ T cells, UA sample 3

description:
Library name: UA_3
Column name in raw_counts_all_samples.txt: UA_3


title: CD4+ T cells, UA sample 2

description:
Library name: UA_2
Column name in raw_counts_all_samples.txt: UA_2


title: TNFR2_plus_rep3

description: Library name: Sample 5


title: CD4+ T cells, AA sample 4

description:
Library name: AA_4
Column name in raw_counts_all_samples.txt: AA_4


title: Model_1316

description:
Library name: Sample10
FPKM.Model_1316

value: Colon


title: TNFR2_minus_rep3

description: Library name: Sample 6


title: TNFR2_minus_rep4

description: Library name: Sample 8


title: Sample3, replicate 2, CITE-Seq

city: Santa Cruz

first: Paloma

last: Medina

state: CA

address: 1156 High St.

institute: University of California Santa Cruz

description: 10x Genomics

data_processing:
Sequencing data was initially processed via the 10X Genomics Cell Ranger Cloud pipeline, using the mouse genome (mm10) modified to allow for detection of reporter transgene RNA expression. For the downstream analysis, cells with expression of fewer than 200 genes were excluded, and genes detected in fewer than three cells were removed from subsequent analysis steps. Mitochondrial and ribosomal gene transcripts, as well as Malat1 transcripts, were removed to reduce technical bias. This resulted in a dataset of 22,790 cells and 22,870 genes. Additionally, 13 cells with absent Kit RNA were filtered out. Doublets identified by DoubletDetection 2.4.0 (p_thresh=1e-16, voter_thresh=0.5) removed 157 cells in total (Gayoso et al. 2018).  The UMI counts for each cell were normalized by the total counts across all genes (target_sum=1e4), and log-transformed with an added pseudo count of 1.
Assembly: mm10
Supplementary files format and content: comma-separated values files and matrix files

source_name: Bone Marrow

extract_protocol:
Cells were harvested and c-Kit-enriched from the long bones and hips of the hind legs of young and old mice as described above. Cc-Kit-enriched cells were then stained for lineage markers via a purified rat-anti-mouse antibody cocktail (CD3, CD4, CD5, CD8, CD11b, B220, Gr-1, and Ter119) on ice for 30 minutes. Cells were washed three times followed by incubation with goat-anti-rat Alexa Fluor 680 secondary on ice in the dark for 20 minutes. Cells were washed three times then resuspended in blocking solution (10% bovine calf serum (BCS), 10% normal mouse serum (Invitrogen), and 10% normal rat serum (Invitrogen) in 1X PBS (Cytiva). Cells were blocked for 10 minutes on ice in the dark. Following block, directly conjugated antibodies were directly added to the cells (CD117/cKit and CD150) and incubated on ice in the dark for 45 minutes, gently mixing the cells at the 30-minute mark. A small aliquot of cells was also used to perform a CD150 fluorescence minus one (FMO) control. Cells were washed three times, resuspended in 10% BCS in 1X PBS (wash buffer), with three drops of propidium iodide (diluted 1:5000 in wash buffer) added. Live, lineage-c-Kit+CD150- and live, lineage-c-Kit+CD150+ young and old cells were sorted on a BD FACSAria IIu (BD Biosciences) (Figure S6). The CD150- and CD150+ gates were touching to ensure a continuum of cells across CD150 expression were sorted. Cells were sorted into chilled 1X PBS (without Mg2+) containing 20% BCS and checked for sort purity. Following sorting, cells were washed and each of the four sorted populations (young CD150-, young CD150+, old CD150-, and old CD150+) were split into three aliquots for Cell Multiplexing Oligo (CMO) labeling (10X Genomics) following manufacturer’s instructions, with each individual group of cells receiving a single unique CMO tag. Cells were washed three times with wash buffer and manually counted via a hemocytometer. When possible, equal numbers of cells from each of the 12 CMO labeled aliquots were combined to artificially inflate the numbers of rare CD150+ cells and to equalize numbers between young and old mice. The pooled cells were then split into two replicates for further processing.
Both pooled replicates were used in parallel in the Chromium Next GEM single Cell 3’ v3.1 protocol (10X Genomics) following manufacturer’s directions. GEM generation and barcoding was performed immediately post-sorting, with resulting samples stored at -20ºC per manufacturer’s instructions. All other steps were performed simultaneously for all samples from each of the two independent experiments. Following library construction, samples were assessed via an Agilent Bioanalyzer with a High Sensitivity chip (Agilent Technologies). Final sample libraries were sequenced on a Novaseq P100 at the University of California Davis DNA Technologies and Expression Analysis Core, targeting 50,000 read pairs per cell for the gene expression libraries and 5,000 reads per cell for the CMO libraries.
scRNA-seq (10X Genomics)

value: Bone Marrow

value: HSPC

value: C57Bl/6, FlkSwitch


title: TNFR2_plus_rep1

description: Library name: Sample 1


title: TNFR2_minus_rep1

description: Library name: Sample 2


title: Sample2, replicate 2, CITE-Seq

description: 10x Genomics


title: Sample4, replicate 1, CITE-Seq

description: 10x Genomics


title: scRNAseq, neonatal liver, Kansl3 LKO, rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Counts for the old liver samples are generated using cellranger v7.0.0, using the cellranger count function with reference gex-mm10-2020-A/
Counts for the neonatal liver samples are generated using cellranger v3.0.2, using the count function with reference mm10-1.2.0
Assembly: mm10
Supplementary files format and content: Counts for the old liver samples are generated using cellranger v7.0.0, using the cellranger count function with reference gex-mm10-2020-A/
Supplementary files format and content: Counts for the neonatal liver samples are generated using cellranger v3.0.2, using the count function with reference mm10-1.2.0

source_name: liver

extract_protocol:
Neonates: The analyzed cell populations were isolated by FACS sorting. Old Livers: Cells were enriched for live cells usng LeviCell 1.0 device (Levitas Bio).
Neonatal: 10x Genomics protocol CG00052 RevB from the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237); Old liver: 10X Genomics protocol CG000204 RevD using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000121).

value: liver

value: AlbCre+/KANSL3 p/p

value: untreated


title: scRNAseq, neonatal liver, Kansl3 LKO, rep3


title: scRNAseq, old liver, Kansl3 LKO, rep1


title: scRNAseq, neonatal liver, WT, rep4

value: AlbCre+


title: scRNAseq, neonatal liver, Kansl3 LKO, rep1


title: TNFR2_plus_rep2

description: Library name: Sample 3


title: TNFR2_minus_rep2

description: Library name: Sample 4


title: Sample3, replicate 1, CITE-Seq

description: 10x Genomics


title: scRNAseq, neonatal liver, Kansl3 LKO, rep4


title: scRNAseq, old liver, Kansl3 LKO, rep2


title: scRNAseq, old liver, WT, rep1


title: scRNAseq, old liver, WT, rep2


title: scRNAseq, neonatal liver, WT, rep3


title: RNAseq, Hepa16, dTAG-NEG, pos, rep2

description:
stranded mRNA Seq
Hepa16_dTag_dTAG-NEG_EV_rep2

data_processing:
Fastq files were aligned with snakePipes version 2 against the mm10 reference genome, using the mRNA-seq command
Organoid day15 files (unstranded mRNA seq) were processed with the --libraryType 0 option in the mRNA-seq command
Assembly: mm10
Supplementary files format and content: tsv files read counts generated by featureCounts

extract_protocol:
Liver tissue and Hepa1-6 cells were lysed in TRIzol and RNA isolated with Quick-RNA Miniprep Kit (Zymo, R1055). RNA from organoid samples was extracted using the single cell RNA isolation Kit (Norgen Biotek).
For liver tissue samples libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599). For Hepa1-6 cells and organoid  day 3-8 samples, libraries were prepared using the Stranded mRNA Prep, Ligation kit (Illumina, 20040534). For day 15 samples were NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420).

value: Hepatocytes

value: dTAG-NEG, expressing pCHDblast MCSNard empty vector (EV)


title: RNAseq, Hepa16, dTAG-NEG, pos, rep1

description:
stranded mRNA Seq
Hepa16_dTag_dTAG-NEG_EV_rep1


title: RNAseq, Hepa16, dTAG-NEG, pos, rep3

description:
stranded mRNA Seq
Hepa16_dTag_dTAG-NEG_EV_rep3


title: Sample4, replicate 2, CITE-Seq

description: 10x Genomics


title: scRNAseq, neonatal liver, WT, rep1


title: RNAseq, Hepa16, dTAG13, rep1

description:
stranded mRNA Seq
Hepa16_dTag_dTAG13_EV_rep1

value: dTAG13, expressing pCHDblast MCSNard empty vector (EV)


title: scRNAseq, neonatal liver, WT, rep2


title: RNAseq, Hepa16, dTAG13, rep3

description:
stranded mRNA Seq
Hepa16_dTag_dTAG13_EV_rep3


title: Sample1, replicate 2, CITE-Seq

description: 10x Genomics


title: Sample2, replicate 1, CITE-Seq

description: 10x Genomics


title: Sample1, replicate 1, CITE-Seq

description: 10x Genomics


title: RNAseq, Organoid, day8, WT, rep3

description:
stranded mRNA Seq
Organoid_WT_day8_rep3

source_name: Liver

value: Liver

value: KANSL3 p/p

value: 48hr 2uM 4OHT treatment


title: RNAseq, Hepa16, dTAG13, rep2

description:
stranded mRNA Seq
Hepa16_dTag_dTAG13_EV_rep2


title: RNAseq, Organoid, day8, WT, rep1

description:
stranded mRNA Seq
Organoid_WT_day8_rep1


title: RNAseq, Organoid, day8, WT, rep2

description:
stranded mRNA Seq
Organoid_WT_day8_rep2


title: RNAseq,Organoid, day6, WT, rep3

description:
stranded mRNA Seq
Organoid_WT_day6_rep3


title: RNAseq, Organoid, day6, WT, rep2

description:
stranded mRNA Seq
Organoid_WT_day6_rep2


title: RNAseq, Organoid, day6, WT, rep1

description:
stranded mRNA Seq
Organoid_WT_day6_rep1


title: RNAseq, Organoid, day3, WT, rep1

description:
stranded mRNA Seq
Organoid_WT_day3_rep1


title: RNAseq, Organoid, day3, WT, rep2

description:
stranded mRNA Seq
Organoid_WT_day3_rep2


title: RNAseq, Organoid, day15, WT, rep3

description:
unstranded mRNA Seq
Organoid_WT_day15_rep3


title: RNAseq, Organoid, day4, WT, rep2

description:
stranded mRNA Seq
Organoid_WT_day4_rep2


title: RNAseq, Organoid, day15, WT, rep2

description:
unstranded mRNA Seq
Organoid_WT_day15_rep2


title: RNAseq, Organoid, day15, WT, rep1

description:
unstranded mRNA Seq
Organoid_WT_day15_rep1


title: RNAseq, Organoid, day8, KO, rep2

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day8_rep2

value: Cag-CreERT2T/+;KANSL3 p/p


title: RNAseq, Organoid, day8, KO, rep4

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day8_rep4


title: RNAseq, Organoid, day8, KO, rep3

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day8_rep3


title: RNAseq, Organoid, day6, KO, rep2

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day6_rep2


title: RNAseq, Organoid, day6, KO, rep4

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day6_rep4


title: RNAseq, Organoid, day8, KO, rep1

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day8_rep1


title: RNAseq,Organoid, day4, KO, rep1

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day4_rep1


title: RNAseq, Organoid, day4, KO, rep2

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day4_rep2


title: RNAseq, Organoid, day3, KO, rep4

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day3_rep4


title: RNAseq, Organoid, day3, KO, rep3

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day3_rep3


title: RNAseq, Organoid, day3, KO, rep1

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day3_rep1


title: RNAseq, Organoid, day4, KO, rep4

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day4_rep4


title: RNAseq, Organoid, day3, KO, rep2

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day3_rep2


title: RNAseq, Organoid, day4, KO, rep3

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day4_rep3


title: RNAseq, Organoid, day6, KO, rep3

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day6_rep3


title: RNAseq, Organoid, day15, KO, rep3

description:
unstranded mRNA Seq
Organoid_Kansl3iKO_day15_rep3


title: RNAseq, Organoid, day15, KO, rep2

description:
unstranded mRNA Seq
Organoid_Kansl3iKO_day15_rep2


title: RNAseq, Organoid, day6, KO, rep1

description:
stranded mRNA Seq
Organoid_Kansl3iKO_day6_rep1


title: RNAseq, Organoid, day4, WT, rep3

description:
stranded mRNA Seq
Organoid_WT_day4_rep3


title: RNAseq, Organoid, day3, WT, rep3

description:
stranded mRNA Seq
Organoid_WT_day3_rep3


title: RNAseq, Organoid, day15, KO, rep1

description:
unstranded mRNA Seq
Organoid_Kansl3iKO_day15_rep1


title: RNAseq, Organoid, day4, WT, rep1

description:
stranded mRNA Seq
Organoid_WT_day4_rep1


title: RNAseq, Liver, P21, KO, rep5

description:
stranded mRNA Seq
Liver_P21_Kansl3LKO_rep5


title: RNAseq, Liver, P21, KO, rep6

description:
stranded mRNA Seq
Liver_P21_Kansl3LKO_rep6


title: RNAseq, Liver, P21, KO, rep3

description:
stranded mRNA Seq
Liver_P21_Kansl3LKO_rep3


title: RNAseq, Liver, P21, KO, rep1

description:
stranded mRNA Seq
Liver_P21_Kansl3LKO_rep1


title: RNAseq, Liver, P21, KO, rep4

description:
stranded mRNA Seq
Liver_P21_Kansl3LKO_rep4


title: mESC, dTAG, input, rep1

description: Library name: Sample 4

library_source: genomic

data_processing:
Biological and technical replicates were merged using zcat
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
PCR duplicates were removed from mapped reads using picard v2.26.0 with parameters: VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true ASSUME_SORTED=true
After duplicate removal, reads that overlapped ranges annotated as "High Signal Region" from the ENCODE Blacklist (mm10 v2) were removed using samtools v1.14
Bam files were converted to bedpe files using bedtools v2.30.0 with parameters: -bedpe and then reformatting using: sort -k 1,1 -k 2,2n | cut -f 1,2,6,7
Peaks were called on bed files using MACS2 v2.2.6 using parameters: -f BEDPE --nomodel --seed 123 --keep-dup all -p 0.05
After peak calling with MACS2, peak files were filtered to only include peaks with q-value < 0.05 using a custom python script.
Bigwigs were made from bed files using deeptools v3.5.1 using parameters: --binSize 10 --ignoreForNormalization chrX chrM --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads 200 --ignoreDuplicates --blackListFileName mm10-blacklist.v2_highSignalRegions.bed
Bigwigs were z-normalized per chromsome arm using a custom R script (v4.1.2 "Bird Hippie").
Assembly: mm10
Supplementary files format and content: z-normalized bigwigs of ChIP and Input
Supplementary files format and content: narrowpeak files of called peaks from ChIP and Input

molecule: genomic DNA

growth_protocol: ESCs were cultured  in KO-DMEM (Invitrogen) supplemented with L-Glutamine, penicillin-streptomycin, nonessential amino acids, β-mercaptoethanol, LIF and heat-inactivated fetal bovine serum (FBS).

extract_protocol:
For HA CHIP 30M treated cells were first fixed with DSG for 50 followed by  1% formaldehyde fixation at room temperature (RT) for 10 minutes and quenched with 125mM glycine 5 mins at RT.Cell pellets were washed twice in PBS and resuspended in 400ul lysis buffer per 20 million cells (10mM Tris pH8, 1mM EDTA, 0.5% SDS). Cells were sonicated in a bioruptor device and spin down 10 minutes at 4 degrees at maximum speed. Supernatants were diluted 5 times with dilution buffer (0.01%SDS, 1.1% triton,1.2mM EDTA,16.7mM Tris pH8, 167mM NaCl) and incubated with ab9110 (4ug/30M cells) O/N with rotation at 4oC. Next day, protein G Dynabeads (ThermoScientific) preblocked with BSA protein (100ng per 10ul Dynabeads) were added (10ul blocked Dynabeads per 10 million cells) and incubated for 2-3 hours at 4oC. Beads were immobilized on magnet and washed twice in low salt buffer (0.1% SDS,1% triton, 2mM EDTA, 150mM NaCl, 20mM Tris pH8), twice in high salt buffer (0.1% SDS,1% triton, 2mM EDTA, 500mM NaCl, 20mM Tris pH8), twice in LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris pH8) and once in TE. DNA was then eluted from the beads by incubating with 150ul elution buffer (1% SDS, 100mM NaHCO3) for 20 minutes at 65 degrees (vortex every 10min). Supernatants were collected and reverse-crosslinked by incubation at 65 degrees O/N in presence of proteinase K. After Rnase A treatment for 1hr at 37oC, DNA was purified using the Qiagen minElute kit. 6-10ng of immunoprecipitated material was used for ChIP-seq.
ChIP-seq library preparation using the KAPA Hyper prep kit from KAPA Biosystems. Libraries were sequenced on NextSeq 2000

treatment_protocol: Cells were treated with DMSO or dTAG for 24 hours.

value: Mouse embryonic stem cell

value: ESC

value: dTAG

tag: antibody


title: RNAseq, Liver, P21, KO, rep2

description:
stranded mRNA Seq
Liver_P21_Kansl3LKO_rep2


title: mESC, DMSO, Input, rep1

description: Library name: Sample 3

value: DMSO


title: RNAseq, Liver, P21, WT, rep5

description:
stranded mRNA Seq
Liver_P21_AlbCre_rep5


title: RNAseq, Liver, P21, WT, rep6

description:
stranded mRNA Seq
Liver_P21_AlbCre_rep6


title: RNAseq, Organoid, day15, KO, rep4

description:
unstranded mRNA Seq
Organoid_Kansl3iKO_day15_rep4


title: RNAseq, Liver, P21, WT, rep3

description:
stranded mRNA Seq
Liver_P21_AlbCre_rep3


title: mESC, dTAG, ChIP, rep1

description: Library name: Sample 2


title: ChIPseq, Liver, H4K16ac, P6

description: RELACS pellet 6

data_processing:
Fastq files were aligned with snakePipes version 2 against the mm10 reference genome, using the DNA-mapping mode and the ChIP-seq mode.
Assembly: mm10
Supplementary files format and content: deepTools bamCompare (v3) was used to generate the log2 and subtract bigwig files.

extract_protocol:
Cells and liver tissue cell suspensions were fixed with 1% PFA for 15 minutes at RT , Nuclei extraction, quantification and ChIP was performed using the published RELACS protocol (Arrigoni et al, 2018) Antibodies: KANSL3 ( Sigma HPA035018), H3K27ac (Diagenode C15410196), H3K4me3 (Diagenode C15410003), H3K9ac (Cell Signaling 9649), H4K16ac (abcam ab109463, Hepa1-6), H4K16ac (Milipore 07-329, liver tissue).
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645)


title: Heart_Ex1_L35P_2

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: Library name: XMC_Ex1_L35P_2

data_processing:
Basecalls performed using CASAVA version 1.8.2
For RNA-seq analysis,reads were aligned to the mouse reference genome  GRCm38 (mm10) using the Hisat (version 2.0.0) aligner using default settings. Aligned reads were counted using featureCounts (version 1.4.6) per gene ID.
Assembly: GRCh38/mm10
Supplementary files format and content: TXT file for RNAseq RawCount

source_name: Heart

extract_protocol:
Flash-frozen cardiac samples were homogenized in 1 ml of TRIzol (Thermo Fisher Scientific, 15596026) using Precellys Evolution. RNA was isolated using RNeasy Micro Kit (Qiagen, 74004) as per the provider’s instructions.
RNA-seq libraries (n=3 mice per group) were prepared using KAPA mRNA HyperPrep (Kapa Biosystems, kk8580) kit following manufacturer’s specifications.Paired-end sequencing (50 cycles) was performed on a NextSeq 2000 Sequencer (Illumina)

value: Heart


title: RNAseq, Liver, P21, WT, rep2

description:
stranded mRNA Seq
Liver_P21_AlbCre_rep2


title: Heart_Ex1_corrected_3

description: Library name: XMC_Ex1_corrected_3


title: Heart_Ex1_corrected_2

description: Library name: XMC_Ex1_corrected_2


title: RNAseq, Liver, P21, WT, rep1

description:
stranded mRNA Seq
Liver_P21_AlbCre_rep1


title: Heart_Ex1_WT_2

description: Library name: XMC_Ex1_WT_2

value: WT


title: ChIPseq, Liver, H3K9ac, P5

description: RELACS pellet 5


title: Heart_Ex1_corrected_1

description: Library name: XMC_Ex1_corrected_1


title: ChIPseq, Liver, Input, P6

description: RELACS pellet 6


title: ChIPseq, Liver, H3K4me3, P5

description: RELACS pellet 5


title: Heart_Ex1_L35P_3

description: Library name: XMC_Ex1_L35P_3


title: ChIPseq, Liver, H3K9ac, P6

description: RELACS pellet 6


title: Heart_Ex1_L35P_1

description: Library name: XMC_Ex1_L35P_1


title: Heart_Ex1_WT_3

description: Library name: XMC_Ex1_WT_3


title: ChIPseq, Liver, H3K4me3, P6

description: RELACS pellet 6


title: Heart_Ex4_R249Q_2

description: Library name: XMC_R249_2


title: ChIPseq, Liver, H3K27ac, P6

description: RELACS pellet 6


title: ChIPseq, Liver, H4K16ac, P5

description: RELACS pellet 5


title: ChIPseq, Liver, Input, P4

description: RELACS pellet 4


title: ChIPseq, Liver, Input, P5

description: RELACS pellet 5


title: Heart_Ex1_WT_1

description: Library name: XMC_Ex1_WT_1


title: RNAseq, Liver, P21, WT, rep4

description:
stranded mRNA Seq
Liver_P21_AlbCre_rep4


title: ChIPseq, Liver, H3K9ac, P4

description: RELACS pellet 4


title: Heart_Ex4_WT_2

description: Library name: XMC_WT_2


title: mESC, DMSO, ChIP, rep1

description: Library name: Sample 1


title: Heart_Ex4_corrected_2

description: Library name: XMC_corrected_2


title: ChIPseq, Liver, H3K27ac, P4

description: RELACS pellet 4


title: Heart_Ex4_corrected_1

description: Library name: XMC_corrected_1


title: ChIPseq, Liver, H3K27ac, P5

description: RELACS pellet 5


title: Heart_Ex4_R249Q_3

description: Library name: XMC_R249_3


title: ChIPseq, Liver, H4K16ac, P4

description: RELACS pellet 4


title: ChIPseq, Liver, H3K4me3, P4

description: RELACS pellet 4


title: ChIPseq, Liver, H3K9ac, P3

description: RELACS pellet 3


title: Heart_Ex4_WT_3

description: Library name: XMC_WT_3


title: M6_CD27+ CD69+

city: Seattle

first: Kevin

last: Barry

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Library name: lib90561_S23
Column Name in RawGeneCounts_AllSamples.csv: 23_M6 - lib90561

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the mouse reference genome and gene counts were generated using htseq-count. QC and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCm38.91
Supplementary files format and content: csv file containing read counts for all samples

source_name: Tumor

extract_protocol:
100 cells were sorted directly into SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) lysis buffer and reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

value: Tumor

value: Melanoma

value: Female WT (B6)


title: M6_CD11b+ CD69-

description:
Library name: lib90559_S21
Column Name in RawGeneCounts_AllSamples.csv: 21_M6 - lib90559


title: M6_CD11b+ CD69+

description:
Library name: lib90560_S22
Column Name in RawGeneCounts_AllSamples.csv: 22_M6 - lib90560


title: Heart_Ex4_R249Q_1

description: Library name: XMC_R249_1


title: Heart_Ex4_WT_1

description: Library name: XMC_WT_1


title: M5_CD27+ CD69+

description:
Library name: lib90557_S19
Column Name in RawGeneCounts_AllSamples.csv: 19_M5 - lib90557


title: ChIPseq, Liver, Input, P3

description: RELACS pellet 3

value: AlbCre+


title: Heart_Ex4_corrected_3

description: Library name: XMC_corrected_3


title: ChIPseq, Liver, H3K9ac, P2

description: RELACS pellet 2


title: ChIPseq, Liver, H3K4me3, P2

description: RELACS pellet 2


title: M5_CD11b+ CD69-

description:
Library name: lib90555_S17
Column Name in RawGeneCounts_AllSamples.csv: 17_M5 - lib90555


title: M5_CD11b+ CD69+

description:
Library name: lib90556_S18
Column Name in RawGeneCounts_AllSamples.csv: 18_M5 - lib90556


title: M6_CD27+ CD69-

description:
Library name: lib90562_S24
Column Name in RawGeneCounts_AllSamples.csv: 24_M6 - lib90562


title: M4_CD27+ CD69-

description:
Library name: lib90554_S16
Column Name in RawGeneCounts_AllSamples.csv: 16_M4 - lib90554


title: ChIPseq, Liver, H3K4me3, P3

description: RELACS pellet 3


title: ChIPseq, Liver, H3K27ac, P3

description: RELACS pellet 3


title: M4_CD11b+ CD69+

description:
Library name: lib90552_S14
Column Name in RawGeneCounts_AllSamples.csv: 14_M4 - lib90552


title: ChIPseq, Liver, H4K16ac, P1

description: RELACS pellet 1


title: ChIPseq, Liver, H4K16ac, P3

description: RELACS pellet 3


title: M5_CD27+ CD69-

description:
Library name: lib90558_S20
Column Name in RawGeneCounts_AllSamples.csv: 20_M5 - lib90558


title: ChIPseq, Liver, H4K16ac, P2

description: RELACS pellet 2


title: ChIPseq, Liver, H3K27ac, P2

description: RELACS pellet 2


title: ChIPseq, Liver, Input, P1

description: RELACS pellet 1


title: ChIPseq, Liver, H3K9ac, P1

description: RELACS pellet 1


title: M3_CD27+ CD69-

description:
Library name: lib90550_S12
Column Name in RawGeneCounts_AllSamples.csv: 12_M3 - lib90550


title: M4_CD11b+ CD69-

description:
Library name: lib90551_S13
Column Name in RawGeneCounts_AllSamples.csv: 13_M4 - lib90551


title: M3_CD11b+ CD69+

description:
Library name: lib90548_S10
Column Name in RawGeneCounts_AllSamples.csv: 10_M3 - lib90548


title: ChIPseq, Liver, H3K27ac, P1

description: RELACS pellet 1


title: ChIPseq, Liver, Input, P2

description: RELACS pellet 2


title: M3_CD27+ CD69+

description:
Library name: lib90549_S11
Column Name in RawGeneCounts_AllSamples.csv: 11_M3 - lib90549


title: ChIPseq, Liver, H3K4me3, P1

description: RELACS pellet 1


title: ChIPseq, Liver, Input, rep4


title: M2_CD11b+ CD69+

description:
Library name: lib90544_S6
Column Name in RawGeneCounts_AllSamples.csv: 6_M2 - lib90544


title: M2_CD11b+ CD69-

description:
Library name: lib90543_S5
Column Name in RawGeneCounts_AllSamples.csv: 5_M2 - lib90543


title: ChIPseq, Liver, Input, rep3


title: M3_CD11b+ CD69-

description:
Library name: lib90547_S9
Column Name in RawGeneCounts_AllSamples.csv: 9_M3 - lib90547


title: M4_CD27+ CD69+

description:
Library name: lib90553_S15
Column Name in RawGeneCounts_AllSamples.csv: 15_M4 - lib90553


title: M2_CD27+ CD69+

description:
Library name: lib90545_S7
Column Name in RawGeneCounts_AllSamples.csv: 7_M2 - lib90545


title: M2_CD27+ CD69-

description:
Library name: lib90546_S8
Column Name in RawGeneCounts_AllSamples.csv: 8_M2 - lib90546


title: M1_CD11b+ CD69+

description:
Library name: lib90540_S2
Column Name in RawGeneCounts_AllSamples.csv: 2_M1 - lib90540


title: ChIPseq, Liver, Input, rep1


title: ChIPseq, Liver, Input, rep2


title: M1_CD27+ CD69-

description:
Library name: lib90542_S4
Column Name in RawGeneCounts_AllSamples.csv: 4_M1 - lib90542


title: M1_CD11b+ CD69-

description:
Library name: lib90539_S1
Column Name in RawGeneCounts_AllSamples.csv: 1_M1 - lib90539


title: RNA-seq, acla2, young panicle, rep2

city: Wuhan

first: Xiaoyuan

last: Guo

state: Hubei

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description: Library name: LTSZ180

data_processing:
RNA-seq: Raw RNA-seq reads were quality-filtered using FastP (v 0.23.4) to remove adapter sequences and low-quality reads. Clean reads were aligned to the rice reference genome (MSU v7.0) using HISAT2 (v2.2.0). Differential gene expression analysis was performed with Cufflinks (v2.2.1). Genes with p value< 0.05 and fold change >2 (1.5 for acla2) in mutants relative to wild type were considered as differentially expressed genes.The root tip specifically expressed genes were identified by generating cuffnorm data by comparing root tips with other tissues. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value of gene expression in root tips must be more than five times the average FPKM value of the same gene in other tissues. Additionally, the FPKM value in root tips must be at least 2 units higher than the maximum FPKM value observed in any of the other tissues. The enrichment of root specifically expressed genes compared to the genomic background was calculated by Fisher’s exactly test. CUT&Tag: Raw reads were filtered using FastP (v0.23.4) to eliminate adapter sequences and low-quality reads. Clean reads were aligned to the rice reference genome (MSU v7.0) using Bowtie2 (v2.5.2). Then, duplicated reads were discarded using samtools (v1.9). SICER2 software (version 1.0.2) was used to call histone modification peaks with “-w 200 -g 600 -f 150 -egf 0.74 -fdr 0.01” parameters. BigWig files generated by deepTools software with RPKM normalization were used for data visualization by IGV (version 2.3.88).
Assembly: RGAP version 7.0
Supplementary files format and content: RNA-seq:The diff file containing information of differential expression analysis between transcriptomes; CUT&Tag:The bigwig file incorporating data on chromosomal regions, signal intensity, and coverage.

organism: Oryza sativa Japonica Group

source_name: young panicle

growth_protocol: In this study, the rice variety Zhonghua11 (Oryza sativa ssp. Japonica) was used to produce the transgenic plants. For in vitro cultures, seeds were surface-sterilized and germinated in media containing 0.3% phytagel supplemented with 2% (w/v) sucrose at 28 °C (in light) and 24 °C (in dark) with a 14 h light/10 h dark cycle.

extract_protocol:
RNA-seq: Total RNA was isolated from either 1 cm rice root tips of 7-day-old post-germination seedlings and 0.1 cm inflorescence meristems using the RNeasy Plus Micro Kit (Qiagen, 74034). First-strand cDNA was synthesized from 100 ng of total RNA using a reverse transcription kit (Vazyme, N712). Sequencing libraries were then prepared with the Vazyme TD502 kit and sequenced on an Illumina HiSeq 3000 system. CUT&Tag: Root tips from 7-day-old germinated rice seedlings were harvested to isolate nuclei. The nuclei were washed with wash buffer (Vazyme, TD903), followed by incubation with ConA Beads (Vazyme, TD903) at room temperature for 10 minutes.CUT&Tag experiment and DNA libraries were performed according to the instruction of Hyperactive Universal CUT&Tag Assay Kit (Vazyme, TD903).The PCR-amplified library was purified using VAHTS DNA Clean Beads (Vazyme, N411-01) and sequenced on the Illumina NovaSeq X Plus  platform.
RNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's protocols. DNA libraries for CUT&Tag were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina following manufacturer's protocols.

value: young panicle


title: ChIPseq, Hepa16, dTAG-NEG, Input, rep3

value: Hepatocyte

value: dTAG-NEG


title: M1_CD27+ CD69+

description:
Library name: lib90541_S3
Column Name in RawGeneCounts_AllSamples.csv: 3_M1 - lib90541


title: RNA-seq, acla2, young panicle, rep1

description: Library name: LTSZ179


title: RNA-seq, GCN5 RNAi, young panicle, rep2

description: Library name: LTSZ178

value: GCN5 RNAi


title: ChIPseq, Hepa16, dTAG-NEG, H4K16ac, rep3


title: RNA-seq, GCN5 RNAi, young panicle, rep1

description: Library name: LTSZ177


title: RNA-seq, ada2, young panicle, rep2

description: Library name: LTSZ176


city: Bethesda

first: Gordon

middle: Yiu Chong

last: Cheung

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

description: Gene expression data from Staphylococcus haemolyticus agr mutant time 8hr rep 3

hyb_protocol: The biotinylated S. haemolyticus cDNA was hybridized to Custom Affymetrix GeneChips (RMLChip 3:GPL4692) overnight at 45 degrees.

scan_protocol: Scans were performed according to standard GeneChip protocols (Affymetrix)

data_processing: Analysis of the custom chips at the probe-set level was performed using Affymetrix GeneChip Operating Software (GCOS v1.4, http://www.affymetrix.com)

label: biotin

organism: Staphylococcus haemolyticus

source_name: agr mutant 8hrs

label_protocol: RNA was then converted into biotinylated cDNA using the Ovation® Pico WTA System V2 (Nugen) according to the manufacturer's instructions.

growth_protocol: Bacteria were grown in tryptic soy broth (TSB, Oxoid) at 37 °C with shaking at 180 revolutions per minute (rpm)

extract_protocol: RNA, from ~109 CFU collected at selected timepoints, was isolated using the protocol previously described (72). Briefly, washed bacteria were disrupted in Lysing Matrix B tubes (MP Biomedical) by homogenization in a FastPrep-96™ (MP Biomedical) homogenizer. Total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen) with RNase-free DNase I (Amersham Biosciences) treatments for removal of contaminant DNA.

treatment_protocol: total RNA was harvested and purified from bacterial cultures grown for 4 and 8 hours.

tag: group

value: Staphylococcus haemolyticus_agr mutant 8hrs


title: RNA-seq, ada2, young panicle, rep1

description: Library name: LTSZ175


description: Gene expression data from Staphylococcus haemolyticus agr mutant time 8hr rep 2


title: ChIPseq, Hepa16, dTAG-NEG, Input, rep2


title: RNA-seq, WT, young panicle, rep2

description: Library name: LTSZ174


title: RNA-seq, WT, young panicle, rep1

description: Library name: LTSZ173


title: ChIPseq, Hepa16, dTAG-NEG, H4K16ac, rep2


title: RNA-seq, acla2, root tips, rep3

description: Library name: LTSZ135

source_name: root

value: root


description: Gene expression data from Staphylococcus haemolyticus wild type time 8hr rep 3

source_name: wild type 8hrs

value: Staphylococcus haemolyticus_wild type 8hrs


description: Gene expression data from Staphylococcus haemolyticus wild type time 8hr rep 2


description: Gene expression data from Staphylococcus haemolyticus agr mutant time 8hr rep 1


description: Gene expression data from Staphylococcus haemolyticus wild type time 8hr rep 1


title: RNA-seq, acla2, root tips, rep2

description: Library name: LTSZ134


title: ChIPseq, Hepa16, dTAG-NEG, Input, rep1


description: Gene expression data from Staphylococcus haemolyticus agr mutant time 4hr rep 3

source_name: agr mutant 4hrs

value: Staphylococcus haemolyticus_agr mutant 4hrs


description: Gene expression data from Staphylococcus haemolyticus agr mutant time 4hr rep 2


title: RNA-seq, acla2, root tips, rep1

description: Library name: LTSZ133


title: ChIPseq, Hepa16, dTAG-NEG, H4K16ac, rep1


title: RNA-seq, GCN5 RNAi, root tips, rep3

description: Library name: LTSZ132


description: Gene expression data from Staphylococcus haemolyticus agr mutant time 4hr rep 1


title: RNA-seq, GCN5 RNAi, root tips, rep2

description: Library name: LTSZ131


description: Gene expression data from Staphylococcus haemolyticus wild type time 4hr rep 2

source_name: wild type 4hrs

value: Staphylococcus haemolyticus_wild type 4hrs


description: Gene expression data from Staphylococcus haemolyticus wild type time 4hr rep 3


title: PBMC, cohort 2,  Orai1 Mother

first: Maxwell

last: McDermott

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

description:
Library name: ORAI1_Mother
10x genomics

data_processing:
The demulitplexing, barcode processing, gene counting, and aggregration were made using cell ranger software v 7.0.0
The CITE-seq-Count pipeline was used to count the unique molecular identifier (UMI) of Cell Hashing Oligo Tags (HTOs) in the raw sequencing reads of the Cell Hashing library FASTQ files and to build cell-hashtag count matrices using a whitelist of only the cell barcodes called as cells by the Cell Ranger software from the gene expression analysis.
Assembly: hg38
Supplementary files format and content: Tab delimited values and matrix files

source_name: PBMC

extract_protocol:
Collected cells were also quantified using a Bio-Rad TC20 automated cell counter. Stained cells were encapsulated into emulsion droplets using Chromium Controller (10x Genomics) for library prep. scRNA-seq and antibody multiplexing libraries were constructed using Chromium Single Cell 3′ v3.1 Reagent Kit and 3’ Feature Barcode Kit (PN-1000268 & 1000262 respectively) according to the manufacturer’s protocol.
Individual libraries were diluted to 2nM and pooled for sequencing. Pooled batches were sequenced with 100 cycle run kits (28bp Read1, 8bp Index1 and 91bp Read2) on the NovaSeq6000 Sequencing System (Illumina).  Amplified cDNA was evaluated with an Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies). Final libraries were evaluated with an Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).

treatment_protocol: Frozen PBMCs were thawed and stained with Annexin-V (Biolegend, Cat. 640912) in Annexin-V binding buffer (Biolegend, Cat. 422201). Live PBMC were defined as Annexin-V- Live/Dead- on Aria II (BD Biosciences). Cells were collected in RPMI1640 medium (Corning, Cat. 10040CV) with 10% fetal bovine serum. Collected cells were then stained using Type A hashing antibodies (BioLegend), ffor patient demultiplexing and quantified using a Bio-Rad TC20 automated cell counter, according to manufacturer’s protocol.

value: PBMC

value: paired-end

value: Illumina NovaSeq 6000

value: 10x genomics


title: RNA-seq, ada2, root tips, rep2

description: Library name: LTSZ128


title: Epidermis, wild-type, untreated, replicate 3

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

data_processing:
Gene-level counts were quantified from single-end reads aligned to the GRCh38.d1.vd1 genome using STAR v2.7.5a
Assembly: GRCh38.d1.vd§
Supplementary files format and content: tab-delimited file; First column is ENSEMBL gene name, Second column is raw count output from STAR alignment

source_name: skin equivalent

growth_protocol: Briefly, 2.5 x 105 HPKs, wild-type or CRISPR/Cas9-modified, were seeded per dermal equivalent in FAD medium containing 10% FBS and 1% antibiotics/antimycotics, supplemented with 2-phospho-l-ascorbic acid-trisodium salt (200 μg/mL), hydrocortisone ( 0.4 μg/mL - Sigma), and cholera toxin ( 1×10−10 M - Sigma). After 3 days of submersed growth, the epithelial cocultures were air-lifted and the medium changed every other day, throughout 2 weeks.

extract_protocol:
Epidermis and dermis were separated with dispase II digestion and RNA isolated with RNeasy Plus Universal Mini Kit (QIAGEN), upon homogenization with the TissueLyser II (QIAGEN).
Library preparation was achieved with approximately 0.1 – 1 μg total RNA, using the Illumina Truseq Stranded mRNA kit, according to the manufacturers’ instructions

treatment_protocol: Skin equivalents were stimulated with Opti-MEM containing talabostat (0.3 or 10 μM), anakinra (10 μg/mL - Swedish orphan biovitrum, Sweden) or rh IL-1β or rh IL-1α (1 ng/mL - Peprotech).

value: skin equivalent

value: untreated


title: RNA-seq, GCN5 RNAi, root tips, rep1

description: Library name: LTSZ130


title: ChIPseq, Hepa16, dTAG13, Input, rep2


title: RNA-seq, ada2, root tips, rep3

description: Library name: LTSZ129


title: PBMC, cohort 2, Orai1 Patient

description:
Library name: ORAI1_Patient
10x genomics


title: ChIPseq, Hepa16, dTAG13, H4K16ac, rep3


title: ChIPseq, Hepa16, dTAG13, Input, rep3


description: Gene expression data from Staphylococcus haemolyticus wild type time 4hr rep 1


title: RNA-seq, WT, root tips, rep3

description: Library name: LTSZ126

value: WT


title: RNA-seq, WT, root tips, rep2

description: Library name: LTSZ125


title: RNA-seq, WT, root tips, rep1

description: Library name: LTSZ124


title: Epidermis, wild-type, untreated, replicate 1


title: HFF KO HCMV GFP4, rep3

city: Rehovot

first: Noa

last: Aharon-Hefetz

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample 18
GFP2_GFP4_geneSummary_MAGeCK.txt
GFP1_GFP4_geneSummary_MAGeCK.txt
GFP3_GFP4_geneSummary_MAGeCK.txt

data_processing:
MAGeCK software quantifies and tests for sgRNA enrichment (DOI: 10.1186/s13059-014-0554-4). The abundance of sgRNAs was first determined using the MAGeCK "count" module for the raw fastq files. To test for robust sgRNA and gene-level enrichment, the MAGeCK "test" module was used with default parameters and with the method “alphamedian” to calculate gene log fold change.
Assembly: sgRNA sequences were used as reference sequences
Supplementary files format and content: tab-delimited text file includes MAGeCK gene summary data for signficant gene knockouts between ancestor and competing (no HCMV infection) cell populations, in three biological repeats
Supplementary files format and content: tab-delimited text file includes MAGeCK sgRNA summary data for signficant sgRNA enrichment between ancestor and competing (no HCMV infection) cell populations, in three biological repeats
Supplementary files format and content: tab-delimited text file includes MAGeCK gene summary data for signficant gene knockouts between GFP2-sorted and GFP4- sorted cell populations (HCMV-infected cells), in three biological repeats
Supplementary files format and content: tab-delimited text file includes MAGeCK gene summary data for signficant gene knockouts between GFP1-sorted and GFP4- sorted cell populations (HCMV-infected cells), in three biological repeats
Supplementary files format and content: tab-delimited text file includes MAGeCK gene summary data for signficant gene knockouts between GFP3-sorted and GFP4- sorted cell populations (HCMV-infected cells), in three biological repeats

source_name: HFF

growth_protocol: Human Foreskin Fibroblasts (ATCC) were grown in DMEM high glucose medium (Biological Industries) supplemented with 10% heat-inactivated FBS (Life Technologies), 1% penicillin/ streptomycin (P/S), and 1% L-Glutamine.

extract_protocol:
Genomic DNA was extracted from each sorted population, ancestor samples, and samples without HCMV infection using the NK lysis protocol (DOI: 10.1016/j.cell.2015.02.038).
Genomic DNA was used as a template for PCR to amplify the sgRNAs, as described in (DOI: 10.7554/eLife.58461). Here, we used 1ug of genomic DNA for the first PCR reaction and ran the PCR program for 16 cycles. Shifted primers were used to increase library complexity.

treatment_protocol: HFF (passage 25) were transduced with lentivirus containing the tRNA-CRISPR library at a low MOI (0.3) to ensure that most cells receive only one viral construct with a high probability. Media containing lentiviruses was supplemented with 8ug/ml of Hexadimethrine Bromide (Sigma Aldrich). 48 hours after transduction, 1.75ug/ml puromycin (Thermo Fisher) was added to select for infected cells. Then, the media was refreshed (without antibiotics), and cells were recovered for 48 hours. Six days after lentiviral transduction, the cells were divided into three populations. The first was harvested immediately (i.e., ancestor samples). The second population continued to grow for 72 hours in a competition mode and was harvested. This population was used to determine the effects of tRNA knockouts on cell growth. To determine the tRNA effect on HCMV infection, the third population was infected with the HCMV Merlin strain with a GFP tag fused to the IE2 protein (Stanton et al., 2010), with a high MOI of 5, as follows: cells were incubated with the virus for 1 h, washed, and supplemented with fresh DMEM medium. 72 hours post-HCMV infection, cells were harvested in a medium enriched with 2% FCS, and FACS sorted into 4 cell populations based on GFP intensity (GFP1 to 4).

value: HFF

value: tRNA-CRISPR library

value: after 3 days of HCMV infection, GFP4 sorted sample


title: ChIPseq, Hepa16, dTAG13, H4K16ac, rep2

value: Hepatocyte


title: Epidermis, wild-type, untreated, replicate 2


title: ChIPseq, Hepa16, dTAG13, Input, rep1


title: HFF KO HCMV GFP3, rep3

description:
Library name: Sample 15
GFP3_GFP4_geneSummary_MAGeCK.txt

value: after 3 days of HCMV infection, GFP3 sorted sample


title: HFF KO HCMV GFP4, rep1

description:
Library name: Sample 16
GFP2_GFP4_geneSummary_MAGeCK.txt
GFP1_GFP4_geneSummary_MAGeCK.txt
GFP3_GFP4_geneSummary_MAGeCK.txt


title: Whole mouse pyloric tumour

city: Singapore

first: Grace

last: Lim

address: 61 Biopolis Drive, Proteos

department: IMCB

country: Singapore

institute: A*STAR

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed using the software CellRanger (version 7.1.0).
Downstream analyses were performed on the filtered count matrix using Seurat version 4.3, R version 4.2.1. Cells with less than 200 genes detected were excluded, as were genes expressed in less than 3 cells. Cells with more than 20% of reads coming from mitochondrial genes were also excluded. Expression data was normalized using the "LogNormalize" method in Seurat with an scaling factor of 10,000. Principal components analysis was performed using the 2000 most variable genes across cells. Dimension reduction was performed using  UMAP, with 19 principal components being used as input. The "FindNeighbors" Seurat method was applied using the 2000 most variable genes. Clustering was performed using the "FindClusters" method, with a resolution of 0.3.
Assembly: mm10
Supplementary files format and content: The following filtered matrix outputfiles  from CellRanger are provided: "barcodes.tsv.gz", "features.tsv.gz" and "matrix.mtx.gz".  In addition, the file "cell_metadata.csv" contains the cluster assignment and UMAP co-ordinates for each cell.

source_name: Pylorus tumour tissue

extract_protocol:
The isolated tumour was incubated in a dissociation buffer containing collagenase I. Thereafter, the cells were mechanically dissociated by vigorous pipetting before treatment with TrypLE and DNase I to obtain a single cell suspension.
Library construction was performed with the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit (v3.1), following manufacturer's instructions.

value: Pylorus tumour tissue


title: Dermis, wild-type, untreated, replicate 2


title: HFF KO HCMV GFP3, rep2

description:
Library name: Sample 14
GFP3_GFP4_geneSummary_MAGeCK.txt


title: RNA-seq, ada2, root tips, rep1

description: Library name: LTSZ127

value: root


title: HFF KO HCMV GFP2, rep2

description:
Library name: Sample 11
GFP2_GFP4_geneSummary_MAGeCK.txt

value: after 3 days of HCMV infection, GFP2 sorted sample


title: Pyloric tumour from mouse KO413, Aqp5 knockout, GFP+

data_processing:
Reads were trimmed using TrimGalore (version 0.6.7). Trimmed reads were aligned using STAR (version 2.7.10a) using default setttings. Alignment was performed against the mouse genome GRCm39, and a GTF file for gencode annotation vM30 was used to augment the alignment.
Quantification was performed using featureCounts (from the Subread suite, version 2.0.3) using default settings to obtain the counts matrix.
Assembly: GRCm39
Supplementary files format and content: The tab-delimited text file "featurecounts_output_matrix.txt"  contains the quantification output from featureCounts, which is essentially the raw count of reads mapped to each gene. The tab-delimited text file "MD5_checksums.txt" contains the MD5 checksums of the raw read files and the file "featurecounts_output_matrix.txt".

source_name: Mouse gastric pylorus tumour

extract_protocol:
RNA was extracted using Qiagen RNeasy Micro Kit following manufacturer's instructions.
Library construction was performed using polyA enrichment method following manufacturer's instructions.

value: Mouse gastric pylorus tumour

value: Pyloric tumour stem cells

value: Aqp5 knockout, GFP+

value: Aqp5 knockout


title: HFF KO HCMV GFP2, rep1

description:
Library name: Sample 10
GFP2_GFP4_geneSummary_MAGeCK.txt


title: HFF KO HCMV GFP1, rep3

description:
Library name: Sample 9
GFP1_GFP4_geneSummary_MAGeCK.txt

value: after 3 days of HCMV infection, GFP1 sorted sample


title: Epidermis, wild-type, Talabostat, replicate 2

value: 0.3 uM talabostat


title: Pyloric tumour from mouse KO413, Aqp5 knockout, GFP-

value: Rest of pyloric tumour cells

value: Aqp5 knockout, GFP-


title: HFF KO HCMV GFP1, rep2

description:
Library name: Sample 8
GFP1_GFP4_geneSummary_MAGeCK.txt


title: HFF KO HCMV GFP1, rep1

description:
Library name: Sample 7
GFP1_GFP4_geneSummary_MAGeCK.txt


title: Pyloric tumour from mouse KO411, Aqp5 knockout, GFP+


title: HFF KO competiting, rep2

description:
Library name: Sample 5
noIE2_Anc_geneSummary_MAGeCK.txt
noIE2_Anc_sgRNAsummary_MAGeCK.txt

value: after 3 days of cell competition


title: Epidermis, wild-type, Talabostat, replicate 1

value: skin equivalent


title: HFF KO competiting, rep3

description:
Library name: Sample 6
noIE2_Anc_geneSummary_MAGeCK.txt
noIE2_Anc_sgRNAsummary_MAGeCK.txt

value: HFF

value: tRNA-CRISPR library


title: Dermis, wild-type, Talabostat, replicate 3


title: HFF KO HCMV GFP4, rep2

description:
Library name: Sample 17
GFP2_GFP4_geneSummary_MAGeCK.txt
GFP1_GFP4_geneSummary_MAGeCK.txt
GFP3_GFP4_geneSummary_MAGeCK.txt

value: after 3 days of HCMV infection, GFP4 sorted sample


title: HFF KO ancestor, rep3

description:
Library name: Sample 3
noIE2_Anc_geneSummary_MAGeCK.txt
noIE2_Anc_sgRNAsummary_MAGeCK.txt


title: Pyloric tumour from mouse KO411, Aqp5 knockout, GFP-


title: Dermis, wild-type, untreated, replicate 1

value: untreated


title: HFF KO ancestor, rep1

description:
Library name: Sample 1
noIE2_Anc_geneSummary_MAGeCK.txt
noIE2_Anc_sgRNAsummary_MAGeCK.txt


title: Dermis, wild-type, untreated, replicate 3


title: Pyloric tumour from mouse KO407, Aqp5 knockout, GFP-


title: HFF KO competiting, rep1

description:
Library name: Sample 4
noIE2_Anc_geneSummary_MAGeCK.txt
noIE2_Anc_sgRNAsummary_MAGeCK.txt


title: ChIPseq, Hepa16, dTAG13, H4K16ac, rep1

value: Hepatocyte


title: HFF KO HCMV GFP3, rep1

description:
Library name: Sample 13
GFP3_GFP4_geneSummary_MAGeCK.txt

value: after 3 days of HCMV infection, GFP3 sorted sample


title: HFF KO HCMV GFP2, rep3

description:
Library name: Sample 12
GFP2_GFP4_geneSummary_MAGeCK.txt

value: after 3 days of HCMV infection, GFP2 sorted sample


title: HFF KO ancestor, rep2

description:
Library name: Sample 2
noIE2_Anc_geneSummary_MAGeCK.txt
noIE2_Anc_sgRNAsummary_MAGeCK.txt


title: Dermis, wild-type, Talabostat, replicate 2


title: HFF HCMV 72hpi, rep2

description:
Library name: Sample 20
HFF_72hpi_Rep2_S13

data_processing:
tRNA-seq analysis is described in (DOI: 10.1073/pnas.2106556118)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes read counts of mature tRNA genes for all samples
Supplementary files format and content: tab-delimited text file includes modification fraction per tRNA gene and modified residue for all samples

extract_protocol:
Samples were harvested with Tri-Reagent (Sigma-Aldrich). Total RNA was extracted according to the manufacturer’s protocol.
tRNA-seq libraries were constructed based on DM-TGIRT-seq protocol (DOI: 10.1038/nmeth.3478) with some modifications, as described in (DOI: 10.1073/pnas.2106556118)

treatment_protocol: HFF cells (passage 27) were grown to full confluence in 10 cm plates and then infected with the HCMV merlin UL32-GFP strain (Stanton et al., 2010) at a Multiplicity of infection (MOI) of 5. Cells were incubated with the virus for 1 hour, washed, and supplemented with fresh medium. Cells were harvested at 4 time points following infection- 5, 16, 24, and 72 hours post-infection. HFF treated with IFN were incubated with 550U/ml IFNα (PBL) and 700U/mL IFNβ (Peprotech) and harvested after 5 hours. Infected cells treated with ruxolitinib were supplemented with a medium containing 4uM ruxolitinib (InvivoGen) after 1-hour incubation with HCMV and harvested 24 hours post-infection.

value: WT

value: HCMV-infection, 72hpi


title: HFF HCMV 24hpi-ruxo, rep3

description:
Library name: Sample 18
HFF_24hpi_ruxo3_S22

value: HCMV-infection with ruxolitinib, 24hpi


title: Pyloric tumour from mouse KO407, Aqp5 knockout, GFP+

value: Mouse gastric pylorus tumour

value: Pyloric tumour stem cells

value: Aqp5 knockout, GFP+

value: Aqp5 knockout


title: Pyloric tumour from mouse AQP1550, Aqp5 wild-type, GFP-

value: Rest of pyloric tumour cells

value: Aqp5 wild-type, GFP-

value: Aqp5 wild-type (no treatment)


title: Epidermis, wild-type, Talabostat, replicate 3

value: skin equivalent

value: 0.3 uM talabostat


title: Dermis, wild-type, Talabostat, replicate 1


title: HFF HCMV 24hpi-ruxo, rep2

description:
Library name: Sample 17
HFF_24hpi_ruxo2_S14

value: HFF


title: Calu3 SARS-CoV-2 6hpi, rep2

description: Library name: Sample 4

growth_protocol: Calu3 cells (ATCC) were cultured in 6-well or 10-cm plates with RPMI (Thermo Fisher) supplemented with 10% fetal bovine serum (FBS, Life Technologies), MEM non-essential amino acids, 2 mM L-glutamine, 100 units per ml penicillin, and 1% Na-pyruvate

treatment_protocol: Calu3 cells were infected with the SARS-CoV-2 virus at an MOI of 0.2 using RPMI medium without FBS for 1 hour.

value: SARS-CoV-2-infection, 6hpi


title: Calu3 SARS-CoV-2 6hpi, rep1

description: Library name: Sample 3


title: HFF HCMV 24hpi-ruxo, rep1

description:
Library name: Sample 16
HFF_24hpi_ruxo1_S6


title: Pyloric tumour from mouse AQP1523, Aqp5 wild-type, GFP+

value: Aqp5 wild-type, GFP+


title: Dermis, ASC knockout, untreated, replicate 2

value: untreated


title: HFF HCMV 24hpi, rep3

description:
Library name: Sample 15
HFF_24hpi_Rep3_S20

value: HCMV-infection, 24hpi


title: Pyloric tumour from mouse AQP1587, Aqp5 wild-type, GFP+


title: Calu3 uninfected, rep2

description: Library name: Sample 2

value: WT


title: Calu3 uninfected, rep1

description: Library name: Sample 1


title: Dermis, ASC knockout, untreated, replicate 1


title: HFF HCMV 16hpi, rep3

description:
Library name: Sample 12
HFF_16hpi_Rep3_S19

value: HCMV-infection, 16hpi


title: Epidermis, ASC knockout, untreated, replicate 1


title: Pyloric tumour from mouse AQP1587, Aqp5 wild-type, GFP-


title: HFF HCMV 5hpi, rep3

description:
Library name: Sample 9
HFF_5hpi_Rep3_S18

value: HCMV-infection, 5hpi


title: Epidermis, ASC knockout, Talabostat, replicate 1


title: DE_LINC01612_KO3

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

description:
Library name: Sample 11
Column name in featureCounts.txt: LINC01612_KO3

data_processing:
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to human genome (hg38) using HISAT2 (v2.1.0)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw gene counts for each Sample

source_name: Human embryonic stem cells

extract_protocol:
The cells were washed by DPBS and harvested by buffer RL. The HiPure Total RNA Mini Kit (Magen, Cat# R4111-03) was used to extract total RNA following the manufacturer’s instructions and the RNA was quantitated with nanodrop 2000 (ThermoFisher).
RNA libraries were prepared using standard protocols, including mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

value: Human embryonic stem cells

value: differentiated hESCs

value: LINC01612 knockout

value: Definitive endoderm differentiation


title: HFF IFN, rep2

description:
Library name: Sample 5
HFF_IFN_Rep2_S16

value: IFNα+β


title: Epidermis, ASC knockout, untreated, replicate 2


title: HFF HCMV 72hpi, rep3

description:
Library name: Sample 21
HFF_72hpi_Rep3_S21

value: HCMV-infection, 72hpi


title: DE_LINC01612_KO2

description:
Library name: Sample 10
Column name in featureCounts.txt: LINC01612_KO2


title: HFF HCMV 72hpi, rep1

description:
Library name: Sample 19
HFF_72hpi_Rep1_S5


title: HFF uninfected, rep3

description:
Library name: Sample 3
HFF_uninf_Rep3_S17


title: Pyloric tumour from mouse AQP1550, Aqp5 wild-type, GFP+

value: Mouse gastric pylorus tumour

value: Pyloric tumour stem cells

value: Aqp5 wild-type (no treatment)


title: Epidermis, ASC knockout, untreated, replicate 3

value: skin equivalent


title: Dermis, ASC knockout, Talabostat, replicate 2

value: 0.3 uM talabostat


title: Pyloric tumour from mouse AQP1523, Aqp5 wild-type, GFP-

value: Rest of pyloric tumour cells

value: Aqp5 wild-type, GFP-


title: DE_shC_3

description:
Library name: Sample 9
Column name in featureCounts.txt: H8_C_rep3

value: WT of LINC01612_ko


title: HFF uninfected, rep1

description:
Library name: Sample 1
HFF_uninf_Rep1_S1

value: HFF

value: WT


title: HFF HCMV 24hpi, rep1

description:
Library name: Sample 13
HFF_24hpi_Rep1_S4

value: HCMV-infection, 24hpi


title: HFF HCMV 16hpi, rep2

description:
Library name: Sample 11
HFF_16hpi_Rep2_S11

value: HCMV-infection, 16hpi


title: E12.5 Placenta

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

data_processing:
Raw Illumina BCL files were processed using the spaceranger mkfastq pipeline to generate demultiplexed fastq files
spaceranger count was run to capture spatial feature counts for each sample
Data was imported using Seurat and performed clustering and marker identification
CellChat R package was used to get the crosstalk of cells in our placenta samples of each developmental stages.
SCENIC R package was used based for gene regulatory network analysis
Assembly: mm10 (refdata-gex-mm10-2020-A_ downloaded from https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build
Supplementary files format and content: zipped tab-delimited text files having raw counts, barcodes and metadata for each sample

source_name: Placenta

growth_protocol: Wild type mice (6-8wk) were mated and embryos were isolated on day 10.5 and 12.5 post-conception. The whole conceptus was snap frozen and then sectioned using a cryostat.

extract_protocol:
For RNA extraction we used Qiagen RNeasy Kit (Catalog#74104) following manufacturer's protocol. For each experimental conditions, 1 million cells were used to isolate total RNA.
For sequencing, libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) designed for transcriptome analysis from samples as small as a single cell.  For library preparation, the mRNA fraction was enriched, fragmented, sized, reverse transcribed into cDNA and ligated with the appropriate adaptors. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

value: Placenta

tag: developmental stage


title: Dermis, ASC knockout, Talabostat, replicate 1


title: Epidermis, ASC knockout, Talabostat, replicate 3


title: Dermis, ASC knockout, untreated, replicate 3

value: untreated


title: HFF HCMV 16hpi, rep1

description:
Library name: Sample 10
HFF_16hpi_Rep1_S3


title: Epidermis, ASC knockout, Talabostat, replicate 2


title: E10.5 Placenta


title: DE_shC_1

description:
Library name: Sample 7
Column name in featureCounts.txt: H8_C_rep1

value: Human embryonic stem cells

value: differentiated hESCs

value: Definitive endoderm differentiation


title: DE_WT_3

description:
Library name: Sample 6
Column name in featureCounts.txt: H8_rep3

value: WT of DVL2_kd


title: DE_LINC01612_KO1

description:
Library name: Sample 12
Column name in featureCounts.txt: LINC01612_KO1

value: LINC01612 knockout


title: HFF HCMV 5hpi, rep2

description:
Library name: Sample 8
HFF_5hpi_Rep2_S10

value: HCMV-infection, 5hpi


title: Control, organoids, 5 days, mouse 2

city: Groningen

first: Davide

last: Cinat

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

description:
Library name: Control 5 days 2
Lexogen

data_processing:
For the alignment of the fastq files the mouse genome GRCm39 was used. The gene counts per sample were detected with the QuantSeq 3' mRNA-seq Integrated Data Analysis Pipeline on the BlueBee Genomics Platform provided by Lexogen with default settings. Rstudion v4.1.3 was used for downstream analysis and for the generation of CPM files. The R package edgeR was used for normalization and identification of differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files including the raw counts from all replicates and conditions are provided.

source_name: Submandibular salivary gland

growth_protocol: Organoids from all animals and conditions were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
For the cDNA library preparation, total RNA was extracted from organoids using Rneasy Mini Kit according to the manufacturer`s instructions and its quality was determined using High Sensitivity RNA ScreenTapes on an Agilent 2100 Bioanalyzer. 100 ng of RNA was used as an input for all samples.
100 ng of highly intact RNA (RIN values > 9) was processed for the cDNA library preparation using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following the manufacturers protocol.

treatment_protocol: Organoids are untreated

value: Submandibular salivary gland

value: Salivary gland cells derived from organoids

value: 8-12 weeks old mice, C57BL/6

value: Non-irradiated


title: Dermis, ASC knockout, Talabostat, replicate 3

value: skin equivalent

value: 0.3 uM talabostat


title: HFF HCMV 5hpi, rep1

description:
Library name: Sample 7
HFF_5hpi_Rep1_S2

value: HFF

value: WT


title: HFF IFN, rep1

description:
Library name: Sample 4
HFF_IFN_Rep1_S8

value: IFNα+β


title: Control, organoids, 5 days, mouse 1

description:
Library name: Control 5 days 1
Lexogen


title: CrePos_3_24h

data_processing:
Reads were aligned using STAR (version 2.7.10a) using default setttings. Alignment was performed against the human genome version GRCh38, and a GTF file for Gencode annotation v41 was used to augment the alignment.
Quantification was performed using featureCounts (from the Subread suite, version 2.0.3) using default settings to obtain the counts matrix.
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text file "featurecounts_output_matrix.txt"  contains the quantification output from featureCounts, which is essentially the raw count of reads mapped to each gene. The tab-delimited text file "MD5_checksums.txt" contains the MD5 checksums of the raw read files and the file "featurecounts_output_matrix.txt".

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 24 hour timepoint, replicate 3

value: Human organoid

value: AQP5 knockout

value: Treated to induce knockout of AQP5


title: HFF IFN, rep3

description:
Library name: Sample 6
HFF_IFN_Rep3_S24


title: HFF HCMV 24hpi, rep2

description:
Library name: Sample 14
HFF_24hpi_Rep2_S12

value: HCMV-infection, 24hpi


title: DE_WT_2

description:
Library name: Sample 5
Column name in featureCounts.txt: H8_rep2

value: Human embryonic stem cells

value: differentiated hESCs

value: Definitive endoderm differentiation