title: COPTG19859-treated CT26 tumors D15 rep5 [626]


title: TA4357_2|002|PanCK-

status: Public on Jul 30 2024

type: RNA

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts =  --hardtrim5 26 --dont_gzip
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts =  -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts =  --bc-pattern=NNNNNNNNNNNNNN
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts =  --end-to-end -L 4 --trim5 0 --trim3 0 --norc
Deduplication using UMI-tools, umiDedupOpts =  --edit-distance-threshold=1“
sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
4357_WTA_QC.csv: raw count data, normalised_4357_WTA_QC.csv: normalised count data

molecule: total RNA

organism: Homo sapiens

source_name: HNSCC

label_protocol: Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

extract_protocol: Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)

tag: tissue

value: head and neck cancer tumour samples from patients who received immunotherapy

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

value: SCC

value: pos

value: SD


title: COPTG19859-treated CT26 tumors D15 rep3 [952]

type: SRA

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

library_source: transcriptomic

data_processing:
The 3 first bases from read 2 were trimmed using Trimmomatic (3 extra G added by the library preparation protocol)
PCR duplicates were removed using Unique molecular identifiers (UMIs) using the program dedup from the package UMI-tools
Reads were aligned using STAR to an artificial genome containing the whole mouse genome (GRCm39) and mTG6050 viral genome.
Readcount for each murin and viral gene was quantified using HTSeq-count
Assembly: GRCm39
Supplementary files format and content: readcounts in the Htseqcount.txt.gz file

organism: Mus musculus

source_name: CT26-induced tumour

extract_protocol:
Total RNA was extracted from whole tumours using the kit Qiagen kitRNeasy Plus Mini.
Strand specific 3' mRNA sequencing libraries were prepared by Integragen, SA.

value: CT26-induced tumour

tag: strain

value: BALB/c

tag: treatment

tag: timepoint


title: TA4357_2|003|PanCK+

tag: tissue

tag: aoisurfacearea


title: SCAD2260

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

library_source: transcriptomic single cell

data_processing:
the raw data was analyzed using 10x cellranger
Assembly: HG38
Supplementary files format and content: Loupe files

source_name: Neurons

growth_protocol: the iPSC were differentiated into adult neurons using the method desribed in Flamier at al 2018

extract_protocol:
cells were trypsined and filtered using a 0.4uM filter in order to obtain a mix composed of single cells.
the single cell mixture was processed using the 10X Chromium Single Cell 3' Reagent Kits User Guide

tag: cell type

value: Neurons

value: AD


title: SIG_153 SIG-2018

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Sex was validated by gene expression for Y-specific genes and corrected if different from recorded sex.
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample

source_name: blood

extract_protocol:
Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 40 million reads per RNA sample

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes. Project SIG-2018

tag: Sex

value: f

tag: status


title: SIG_154 SIG-2018

value: m


title: TA4357_2|004|PanCK+

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

value: Residual SCC

value: PD


title: SCGB2160

value: CTL


title: SIG_152 SIG-2018


title: spleen DicerDHEL1het PKRnull LCMV 3dpi

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed in two rounds using bbduk.sh version 38.87. First, NEXTflex adapter were trimmed from right end: bbduk.sh -Xmx20G threads=6 in=${FILE}.fastq.gz out=${FILE}.atrim.fastq.gz literal=TGGAATTCTCGGGTGCCAAGG stats=${FILE}.atrim.stats overwrite=t ktrim=r k=19 rcomp=f mink=10 hdist=1 minoverlap=8 Next, 4 random bases from both sides of reads were trimmed: bbduk.sh -Xmx20G threads=6 in=${FILE}.atrim.fastq.gz out=${FILE}.trimmed.fastq.gz stats=${FILE}.ftrim.stats overwrite=t forcetrimright2=4 forcetrimleft=4 minlength=18
The genome index was created by joining mouse genome .fasta file (GCA_000001635.2, mm10) with individual viral genomes (JN048469.1, NC_001479.1, NC_004291.1, NC_004294.1, U39292.1). Trimmed reads were mapped to such genome index with STAR version 2.7.10b with the following parameters: STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 99999 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v4 from UCSC: genomeCoverageBed -ibam ${FILENAME}.bam -bg -split > ${FILENAME}.bedGraph wigToBigWig ${FILENAME}.bedGraph chrNameLength.txt ${FILENAME}.bw
Assembly: mm10
Supplementary files format and content: .bigWig
Supplementary files format and content: coverage genome browser tracks files: - bigWig format - generated in a non-stranded mode - not normalized for library size

source_name: spleen

extract_protocol:
Organs collected from sacrificed animals were either directly used for analysis or stored at -80° C for later use. Mouse organs were washed with PBS, homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method.
After isolation, RNA quality was verified by electrophoresis on 1% agarose gel and RNA concentration was determined by Qubit Broad Range Assay (Invitrogen). Small RNA libraries were prepared using NEXTFLEX® Small RNA-Seq Kit v3 for Illumina (PerkinElmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and gel purification was performed for size selection. For gel purification, libraries were separated on a 2.5% agarose gel using 1× lithium borate buffer and visualized with ethidium bromide. The 150–160 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75-nucleotide single-end reading using the Illumina NextSeq500/550 platform.

treatment_protocol: Viral infections CVB3: The in vivo viral infection was tested on the original CD1 genetic background of the DicerΔHEL1/wt mice in collaboration with the Enterovirus laboratory at the Slovak Medical University. The virus was propagated in Vero cells (origin Public Health Institute, Bratislava) and 0.5 ml of 105 TCID50/1ml virus was injected intraperitonially, per mouse. Mice were sacrificed and samples collected 3 and 5 days post infection (dpi); in two experiments organs were also collected 7 dpi, 11 dpi and 45 dpi.  EMCV: The encephalomyocarditis virus isolate BCCO_50_0517 (GenBank: PP841942.1) was passaged on VERO/E6 prior to infection. This virus was provided by the Collection of Arboviruses, Biology Centre of the Czech Academy of Sciences (https://arboviruscollection.bcco.cz). DicerΔHEL1/wt mice on the C57Bl/6 background were infected subcutaneously into the scruff of the neck with 103 PFU. Mice were euthanized by cervical dislocation and heart samples were collected 2 and 3 dpi. The samples (2-5mm3 of the organ) were placed into 600 ul Trizol and frozen (-80°C) for later RNA isolation. TBEV: The TBEV strain Hypr (GenBank MT228627.1) was passaged five times in the brains of suckling mice before it was used in this study. This strain was provided by the Collection of Arboviruses, Biology Center of the Czech Academy of Sciences (https://arboviruscollection.bcco.cz). DicerΔHEL1/wt and DicerΔHEL1/wt Pkr–/– mice on the C57Bl/6 background were infected subcutaneously into the scruff of the neck with 103 PFU. Mice were observed daily for body weight and clinical score (healthy, piloerection, hunched back, one leg paralyzed, two legs paralyzed, moribund, dead) as previously (47) until 10 dpi. Mice were euthanized by cervical dislocation and brain samples were collected and homogenized as previously (48). Brains were weighed individually and then homogenized in sterile PBS (1:1) using the TissueLyser II (Qiagen). 100 ul of the brain suspension was transferred to 600 ul Trizol and frozen (-80°C) for subsequent RNA isolation. The remainder of the homogenate was clarified by centrifugation at 14,000×g for 10 min at 4 °C and then used for virus titration using a plaque assay on A549 cells. LCMV: Viral stocks of LCMV, strains Armstrong (Arm) and Clone 13 (C13), were propagated in BHK-21 cells as described previously (49). These strains were obtained from Prof. Daniel Pinschewer (University Hospital Basel, Switzerland). The viral titer in aliquots were determined by LCMV Focus Forming Assay. Briefly, 3T3 cells were infected with different dilutions of the virus supernatant. Viral antigens were detected with rat anti-LCMV nucleoprotein antibody (Clone VL-4; BioXCell, Cat. N.: BE0106, Lot: 787521S1, diluted 1:500), and visualized by a color reaction using secondary goat anti-rat IgG HRP antibody (diluted 1:500) 48 h after infection.. For LCMV acute infection, each mouse was injected intraperitoneally 2x105 or 2.5x106 PFUs of LCMV Arm. At 3 dpi or 8 dpi, mice were euthanized by cervical dislocation and organ samples were collected for total RNA isolation. All used animals had the C57Bl/6 background. For LCMV chronic infection, each mouse was injected intraperitoneally 106 PFUs of LCMV C13. At 30 dpi, mice were euthanized by cervical dislocation and organ samples were collected for total RNA isolation.

value: spleen

tag: genotype

value: Dicer deltaHEL1/wt, Pkr-/-

value: LCMV infected

tag: age

value: adult (12 weeks)

tag: experiment year_month


title: AD2_1

description:
AD_vs_CTL.CG.DMR.bed
AD_vs_CTL.CHG.DMR.bed
AD_vs_CTL.CHH.DMR.bed

library_source: genomic

data_processing:
The original images obtained from high-throught sequencing platform are transformed into sequenced reads by CASAVA base calling. Bismark software (Krueger, 2011) is used to perform alignments of bisulfite-treated reads to a reference genome.
Assembly: HG38
Supplementary files format and content: bed files containing the DMR between AD and CTL

molecule: genomic DNA

source_name: iPSC

growth_protocol: iPSC cells

extract_protocol:
the DNA was extracted using Quiagen DNA kits according to the manufacturer instructions.
cDNA was prepared according to the manufacturer’s instructions (NEB library).

value: iPSC


title: AD1_1


title: SIG_155 SIG-2018


title: LoKe, pooled TA k.d. and ctrl

city: Heidelberg

first: Jürgen

last: Becker

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum

data_processing:
Sequenced reads were analyzed using CellRanger 7.1.0.
Assembly: hs1
Supplementary files format and content: tab-delimited text files include gene count matrix and cell meta data.

molecule: polyA RNA

source_name: LoKe

extract_protocol:
Following infection of LoKe cells a pure transduced population was selected by fluorescence activated cell sorting of GFP-positive cells. Single nuclei were stained using trypan blue for visualization, counting and viability assessment using the Countess II Automated Cell Counter and diluted as needed to a final concentration of 700-1200 nuclei/μL in 1x PBS + 0.04% BSA. A minimum of two reproducible counts (defined as standard deviation <25%) were required before droplet preparation, and <5% of input should be viable cells.
RNA library was prepared using 10X Chromium library preparation kit following the manufacturer's protocols.

tag: cell line

value: LoKe

value: pooled dox-induced TA knockdown cells with uninduced control cells


title: SIG_151 SIG-2018


title: spleen PKRnull LCMV 3dpi

value: Dicerwt/wt, Pkr-/-


title: SIG_150 SIG-2018


title: COPTG19859-treated CT26 tumors D15 rep2 [556]

value: CT26-induced tumour

tag: strain


title: RELA_NT_rep2

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

country: USA

institute: Washington University in St. Louis

data_processing:
Fastq files were trimmed with Trim Galore (Cutadapt [v2.8]) and aligned with Bowtie2 [v2.3.5.1] (parameters: --local --very-sensitive- local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700) using hg38. The SAM files were converted to BAM files with samtools (1.9). BigWig files (.bw) were generated from BAM files using DeepTools (3.5.0).
Assembly: hg38
Supplementary files format and content: bigwig format files (.bw)
Library strategy: CUT&Run

source_name: priomary human PTC

growth_protocol: Human primary proximal tubular cells (human primary PTCRPTEC, Lonza; CC-2553) were cultured with renal epithelial cell growth medium kit (Lonza; CC-3190) in a humidified 5% CO2 atmosphere at 37°C. Experiments were performed on early passages.

extract_protocol:
Formaldehyde (37%, Sigma-Aldrich, 25259) was directly added to the medium of the RPTEC to achieve a final concentration of 0.5% for 1 min in room temperature. Fixation reaction was quenched by adding glycine at a final concentration of 125 mM. The cells were treated with trypsin (Gibco, 0.05%) for 2 min at 37°C, scraped from a culture dish and centrifuged at 500 × g for 5 min. The centrifugated cells were resuspended in PBS with 1% BSA and counted. manufacturer’s instructions for cross-linked samples. Library preparation was performed using the
500,000 cells in 100 ul wash buffer were mixed and incubated with Concanavalin A (ConA) conjugated paramagnetic beads. Antibodies were added to each sample (RELA antibody [Santa Cruz, sc-109, 1:25] or rabbit IgG negative control antibody [Epicypher, 13-0041, 1:50]). The remaining steps were performed according to the manufacturer’s instructions for cross-linked samples. Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645S) with the manufacturer’s instruction, including minor modifications indicated by CUTANA kit.

treatment_protocol: The human RPTEC with early passages were seeded at 800,000 cells on 10 cm culture dish at the day before the assay and treated with or without TNFα (100 ng/ml) at 3 h before the fixation.

value: priomary human PTC

value: Renal proximal tubular cells

tag: treatment

value: No Treatment (NT)


title: COPTG19289-treated CT26 tumors D15 rep10 [691]

value: BALB/c

tag: timepoint


title: TA4357_2|002|PanCK+

tag: tissue

value: head and neck cancer tumour samples from patients who received immunotherapy

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

value: SCC

value: pos

value: SD


title: TA4357_2|001|PanCK+

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

value: Recurrent SCC

value: neg


title: COPTG19289-treated CT26 tumors D15 rep8 [200]

tag: strain

tag: treatment


title: TA4357_2|001|PanCK-

tag: tissue


title: COPTG19289-treated CT26 tumors D15 rep9 [894]

tag: timepoint


title: RELA_NT_rep1

tag: cell line

tag: cell type


title: COPTG19859-treated CT26 tumors D15 rep1 [104]


title: spleen DicerDHEL1het LCMV 28Y35291

value: spleen

tag: genotype

value: Dicer deltaHEL1/wt

value: LCMV infected

tag: age

tag: experiment year_month


title: spleen DicerTG LCMV 28Y35338

value: Dicertg(O-HA)/tg(O-HA)

value: adult (12 weeks)


title: SIG_147 SIG-2018

tag: Sex

value: f

tag: status


title: RELA_TNF_rep1

value: TNF 100 ng/ml


title: COPTG19289-treated CT26 tumors D15 rep6 [685]

value: CT26-induced tumour


title: spleen DicerTG LCMV 28Y35336


title: COPTG19289-treated CT26 tumors D15 rep7 [585]


title: SIG_146 SIG-2018


title: SIG_149 SIG-2018

value: m


title: spleen DicerDHEL1het LCMV 28Y35225


title: SIG_148 SIG-2018


title: AKI4_ATAC

description: AKI

library_source: genomic single cell

data_processing:
Fastq files was processed with Cellranfer 6.0.0 (RNA) with refdata-gex-GRCh38-2020-A or CellrangerATAC 2.0.0 (ATAC) with refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Assembly: GRCh38
Supplementary files format and content: a filtered barcode-peak matrix / filtered barcode-feature matrix
Supplementary files format and content: a fragment file and an index file of a fragment file

source_name: Kidney

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitors (Promega, N2615 and Life Technologies, AM2696). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry) and scRNA-seq (3' kit v3)

value: Kidney

value: AKI


title: spleen WT LCMV 28Y35286

value: Dicerwt/wt


title: AKI3_ATAC

description: AKI


title: COPTG19289-treated CT26 tumors D15 rep4 [283]

value: BALB/c


title: COPTG19289-treated CT26 tumors D15 rep5 [423]


title: SIG_145 SIG-2018


title: COPTG19289-treated CT26 tumors D15 rep3 [297]


title: spleen WT LCMV 28Y35226


title: RELA_TNF_rep2

value: priomary human PTC

value: Renal proximal tubular cells


title: AKI1_ATAC

description: AKI


title: SIG_144 SIG-2018


title: AKI2_ATAC

description: AKI


title: spleen DicerDHEL1het CVB3 S26

value: CVB3 infected

value: juvenile (4 weeks)


title: COPTG19289-treated CT26 tumors D15 rep2 [285]


title: SIG_143 SIG-2018


title: spleen DicerDHEL1het CVB3 S25

value: spleen


title: COPTG19289-treated CT26 tumors D15 rep1 [632]


title: AKI4_RNA

description: AKI

molecule: nuclear RNA


title: AKI2_RNA

description: AKI


title: spleen WT CVB3 S33


title: untreated CT26 tumors D15 rep9 [295]

value: untreated


title: untreated CT26 tumors D15 rep10 [584]


title: SIG_139 SIG-2018


title: spleen WT CVB3 B25S


title: AKI1_RNA

description: AKI


title: heart DHEL1het EMCV 46908

source_name: heart

value: heart

value: Dicer deltaHEL1/wt

value: EMCV infected

value: young adult (6 weeks)


title: SIG_140 SIG-2018

value: f


title: untreated CT26 tumors D15 rep7 [199]

value: CT26-induced tumour


title: heart DHEL1het EMCV 46907


title: Caco2 cells, PIM1 rep3

city: Tianjin

first: Jian

middle: ming

last: Yang

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

country: China

institute: Tianjin Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp software.
Then clean reads were separately aligned to reference genome with orientation mode  using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the FPKM method.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file  includes FPKMs and counts for each sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: human colon adenocarcinoma cell lines

tag: infection


title: SIG_138 SIG-2018


title: untreated CT26 tumors D15 rep8 [165]


title: SIG_128 SIG-2018

value: infected


title: untreated CT26 tumors D15 rep6 [689]


title: heart WT EMCV 46900


title: Caco2 cells, PIM1 rep2


title: Caco2 cells, PIM1 rep1


title: heart WT EMCV 46906


title: SIG_127 SIG-2018

value: m


title: SIG_142 SIG-2018


title: SIG_141 SIG-2018


title: brain DicerDHEL1het PKRnull TBEV 10dpi

source_name: brain

value: brain

value: Dicer deltaHEL1/wt, Pkr-/-

value: TBEV infected

value: young adult (6-7 weeks)


title: untreated CT26 tumors D15 rep5 [340]

value: BALB/c


title: untreated CT26 tumors D15 rep4 [446]


title: AKI3_RNA

description: AKI

value: Kidney

value: AKI


title: SIG_126 SIG-2018


title: Caco2 cells, Vector rep3

value: Vector


title: Caco2 cells, Vector rep2


title: brain DicerDHEL1het PKRnull TBEV 3dpi


title: untreated CT26 tumors D15 rep3 [645]

value: untreated


title: SIG_125 SIG-2018


title: Caco2 cells, Vector rep1


title: untreated CT26 tumors D15 rep2 [895]


title: SIG_124 SIG-2018


title: Vector HDAC2

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp), and low-quality reads using Cutadapt v1.18 (non-default parameters: --max-n 0 --minimum-length 35) and Trimmomatic v0.38 (non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:35).
Then FastQC (with default parameters) is used to ensure high reads quality. The clean reads were mapped to the human genome (assembly GRCh38) using the Bowtie2 v2.3.4.1 (with default parameters) software.
Duplicate reads were then removed using Picard MarkDuplicates.
Peak detection was performed using the MACS v2.1.2 (non-default parameters: -f BAMPE -g hs/mm -p 0.01) peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Assembly: GRCh38
Supplementary files format and content: NarrowPeak

growth_protocol: Caco2 cells were maintained in RPMI 1640 medium supplemented with 20% fetal bovine serum.

extract_protocol:
Caco2 cells underwent crosslinking with 1% formaldehyde for 10 minutes at room temperature. The crosslinking reaction was then quenched by adding 125 mM glycine.
After reverse crosslinking, the ChIP and input DNA fragments were processed for end repair and A-tailing using the NEBNext End Repair/dA-Tailing Module (E7442, NEB). Subsequently, adaptor ligation was performed using the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified through 15 cycles of PCR and sequenced using Illumina with paired-end 2×150 sequencing mode.

tag: chip antibody


title: SIG_123 SIG-2018


title: brain PKRnull TBEV 6dpi

value: Dicerwt/wt, Pkr-/-


title: untreated CT26 tumors D15 rep1 [269]


title: COPTG19859-treated CT26 tumors D11 rep10 [102]


title: SIG_11 SIG-2018


title: Vector input


title: COPTG19859-treated CT26 tumors D11 rep9 [955]


title: PIM1 input


title: SIG_9104

data_processing:
Reads were quality checked with package FastQC (version 0.11.4, reference see link below), then trimmed using Trimgalore (version 0.4.4, reference see link below) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Sex was validated by gene expression for Y-specific genes and corrected if different from recorded sex.
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes. Project SIG-2019

value: blood


title: brain DHEL1het TBEV 3

value: Dicer deltaHEL1/wt


title: COPTG19859-treated CT26 tumors D11 rep8 [954]


title: brain DicerDHEL1het PKRnull TBEV 6dpi


title: brain DHEL1het TBEV 2


title: SIG_9100


title: PANC-1_NC_8h_rep1

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Sequenced reads were cleaned for adaptor and low-quality sequence, then CLIP-seq reads were mapped to hg19 using Bowtie2, RNA-seq reads using STAR.
Piranha was used for CLIP-seq peak calling,  RSEM was used for quantification.
Bam file were transform into bigwig format using deepTools.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: txt

source_name: PANC-1 cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
RNA libraries for miCLIP-seq and PARCLIP-seq were prepared using the NEBNext small RNA library prep kit. RNA-seq libraries were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina.
miCLIP-seq, PARCLIP-seq, RNA-seq

value: PANC-1 cells

value: pancreatic cancer cell line

value: WT

value: Actinomycin D treatment for 8h


title: brain DHEL1het TBEV 1


title: COPTG19859-treated CT26 tumors D11 rep6 [369]

value: CT26-induced tumour


title: COPTG19859-treated CT26 tumors D11 rep7 [105]


title: PANC-1_NC_8h_rep2


title: SIG_9098

value: infected

value: f


title: brain PKRnull TBEV 10dpi

value: brain

value: TBEV infected


title: SIG_9093


title: COPTG19859-treated CT26 tumors D11 rep5 [629]

value: BALB/c


title: PANC-1_NC_6h_rep2

value: Actinomycin D treatment for 6h


title: PIM1 HDAC2

value: human colon adenocarcinoma cell lines


title: SIG_122 SIG-2018

value: m


title: PANC-1_NC_6h_rep1


title: brain WT TBEV 6

value: Dicerwt/wt

value: young adult (6-7 weeks)


title: SIG_9090

value: blood


title: brain WT TBEV 5


title: brain PKRnull TBEV 3dpi

value: Dicerwt/wt, Pkr-/-


title: COPTG19859-treated CT26 tumors D11 rep4 [972]


title: PANC-1_NC_4h_rep2

value: PANC-1 cells

value: Actinomycin D treatment for 4h


title: COPTG19859-treated CT26 tumors D11 rep3 [742]


title: brain WT TBEV 4


title: COPTG19859-treated CT26 tumors D11 rep2 [365]


title: PANC-1_NC_4h_rep1

value: pancreatic cancer cell line

value: WT


title: SIG_9083


title: mESC Dicer03 MosIR TrapR S7

source_name: ESC

growth_protocol: Mouse ESCs were cultured in 2i-LIF media: KO-DMEM (Gibco) supplemented with 15% fetal calf serum (Sigma), 1x L-Glutamine (Thermo Fisher Scientific), 1x non-essential amino acids (Thermo Fisher Scientific), 50 µM β-Mercaptoethanol (Gibco), 1000 U/mL LIF (Isokine), 1 µM PD0325901, 3 µM CHIR99021(Selleck Chemicals), penicillin (100 U/mL), and streptomycin (100 µg/mL) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
ESCs infected with LCMV at a MOI of 0.1 or transfected with a plasmid expressing a MosIR dsRNA hairpin were used for isolation of RISC complexes by Trans-kingdom, rapid, affordable Purification of RISCs (TrapR, Lexogen, Austria) according to manufacturer’s instructions 24 hpi and 48 hpi, respectively. RISC-associated small RNAs were extracted by a mixture of acidic phenol, chloroform and isoamylalcohol and precipitated by cold isopropanol. RISC-associated small RNAs were immediately used for small RNA library preparation.
After isolation, RNA quality was verified by electrophoresis on 1% agarose gel and RNA concentration was determined by Qubit Broad Range Assay (Invitrogen). Small RNA libraries were prepared using NEXTFLEX® Small RNA-Seq Kit v3 for Illumina (PerkinElmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and gel purification was performed for size selection. For gel purification, libraries were separated on a 2.5% agarose gel using 1× lithium borate buffer and visualized with ethidium bromide. The 150–160 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75-nucleotide single-end reading using the Illumina NextSeq500/550 platform.

treatment_protocol: Viral infections LCMV: Viral stocks of LCMV, strains Armstrong (Arm) and Clone 13 (C13), were propagated in BHK-21 cells as described previously (49). These strains were obtained from Prof. Daniel Pinschewer (University Hospital Basel, Switzerland). The viral titer in aliquots were determined by LCMV Focus Forming Assay. Briefly, 3T3 cells were infected with different dilutions of the virus supernatant. Viral antigens were detected with rat anti-LCMV nucleoprotein antibody (Clone VL-4; BioXCell, Cat. N.: BE0106, Lot: 787521S1, diluted 1:500), and visualized by a color reaction using secondary goat anti-rat IgG HRP antibody (diluted 1:500) 48 h after infection. Mouse ESCs were infected with Arm at an MOI of 0.01 or 1 and collected 24 or 48 hours post infection (hpi). Transfection For transfection, cells were plated on a 24-well plate, grown to 50 % density and transfected using Lipofectamine 3000 (Thermo Fisher Scientific) according to the manufacturer’s protocol.

value: ESC

value: MosIR transfected, 48 hpi


title: SIG_9087

value: infected


title: COPTG19859-treated CT26 tumors D11 rep1 [973]

value: CT26-induced tumour


title: SIG_9080


title: PANC-1_NC_2h_rep2

value: Actinomycin D treatment for 2h


title: mESC DicerS4 MosIR TrapR S6


title: PANC-1_NC_2h_rep1


title: SIG_9070

value: f


title: COPTG19289-treated CT26 tumors D11 rep10 [583]

value: BALB/c


title: COPTG19289-treated CT26 tumors D11 rep9 [734]


title: PANC-1_NC_0h_rep1

value: Actinomycin D treatment for 0h


title: mESC DicerDHEL1 MosIR TrapR S4

value: Dicer deltaHEL1/ deltaHEL1


title: COPTG19289-treated CT26 tumors D11 rep8 [450]


title: mESC DicerDHEL1 MosIR TrapR S3


title: SIG_9068

value: m


title: PANC-1_KHSRPKO_8h_rep2

value: KHSRP knockout

value: Actinomycin D treatment for 8h


title: COPTG19289-treated CT26 tumors D11 rep7 [339]


title: PANC-1_KHSRPKO_8h_rep1


title: mESC WT MosIR TrapR S2

value: Dicerwt/wt


title: SIG_9066

value: blood


title: mESC Dicer03 MosIR TrapR S8


title: COPTG19289-treated CT26 tumors D11 rep6 [635]


title: mESC WT MosIR TrapR S1


title: COPTG19289-treated CT26 tumors D11 rep5 [690]


title: PANC-1_KHSRPKO_6h_rep2

value: PANC-1 cells

value: Actinomycin D treatment for 6h


title: mESC Dicer03 LCMV MOI 0.01 TrapR S16

value: LCMV infected, MOI 0.01


title: mESC DicerS4 MosIR TrapR S5

value: ESC


title: PANC-1_KHSRPKO_6h_rep1

value: pancreatic cancer cell line


title: PANC-1_NC_0h_rep2

value: WT


title: SIG_9078

value: infected


title: mESC Dicer03 LCMV MOI 0.01 TrapR S15


title: SIG_9060


title: PANC-1_KHSRPKO_4h_rep2

value: Actinomycin D treatment for 4h


title: SIG_9058

value: f


title: mESC DicerS4 LCMV MOI 0.01 TrapR S14


title: COPTG19289-treated CT26 tumors D11 rep2 [162]

value: CT26-induced tumour

value: BALB/c


title: SIG_9062


title: PANC-1_KHSRPKO_4h_rep1


title: COPTG19289-treated CT26 tumors D11 rep3 [448]


title: SIG_9055


title: mESC DicerS4 LCMV MOI 0.01 TrapR S13


title: SIG_9053


title: COPTG19289-treated CT26 tumors D11 rep1 [282]


title: SIG_9064


title: mESC DicerDHEL1 LCMV MOI 0.01 TrapR S12

value: Dicer deltaHEL1/ deltaHEL1


title: SIG_9046


title: mESC DicerDHEL1 LCMV MOI 0.01 TrapR S11


title: untreated CT26 tumors D11 rep9 [342]

value: untreated


title: PANC-1_KHSRPKO_0h_rep1

value: KHSRP knockout

value: Actinomycin D treatment for 0h


title: SIG_9034


title: COPTG19289-treated CT26 tumors D11 rep4 [373]


title: untreated CT26 tumors D11 rep8 [272]


title: PANC-1_KHSRPKO_2h_rep2

value: Actinomycin D treatment for 2h


title: mESC WT LCMV MOI 0.01 TrapR S10

value: Dicerwt/wt


title: PANC-1_NC_RNA-seq_rep3

value: PANC-1 cells


title: mESC WT LCMV MOI 0.01 TrapR S9


title: untreated CT26 tumors D11 rep7 [735]


title: mESC Dicer03 MosIR S8

extract_protocol:
Infected and non-infected cells were washed with PBS, homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method.
After isolation, RNA quality was verified by electrophoresis on 1% agarose gel and RNA concentration was determined by Qubit Broad Range Assay (Invitrogen). Small RNA libraries were prepared using NEXTFLEX® Small RNA-Seq Kit v3 for Illumina (PerkinElmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and gel purification was performed for size selection. For gel purification, libraries were separated on a 2.5% agarose gel using 1× lithium borate buffer and visualized with ethidium bromide. The 150–160 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75-nucleotide single-end reading using the Illumina NextSeq500/550 platform.

value: MosIR transfected, 48 hpi


title: untreated CT26 tumors D11 rep5 [688]


title: mESC Dicer03 MosIR S7


title: PANC-1_NC_RNA-seq_rep2


title: PANC-1_KHSRPKO_RNA-seq_rep3


title: untreated CT26 tumors D11 rep10 [164]


title: SIG_9030

value: blood


title: PANC-1_NC_RNA-seq_rep1


title: untreated CT26 tumors D11 rep6 [270]


title: SIG_9024


title: mESC DicerS4 MosIR S5

value: ESC


title: SIG_9017


title: mESC DicerS4 MosIR S6


title: SIG_9010


title: untreated CT26 tumors D11 rep4 [163]


title: PANC-1_KHSRPKO_2h_rep1

value: pancreatic cancer cell line


title: SIG_9013

value: m


title: SIG_9043

value: infected


title: PANC-1_KHSRPKO_RNA-seq_rep2


title: PANC-1_KHSRPKO_0h_rep2


title: untreated CT26 tumors D11 rep3 [413]


title: mESC DicerDHEL1 MosIR S4


title: PANC-1_KHSRPKO_RNA-seq_rep1


title: SIG_9008


title: untreated CT26 tumors D11 rep2 [449]


title: mESC DicerDHEL1 MosIR S3


title: SIG 9171

data_processing:
Reads were quality checked with package FastQC (version 0.11.9), then trimmed using Trimgalore (version 0.6.7) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.7.9a) with default settings.
Mapped reads were counted using RsubRead (version 2.8.1). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.26.0).
Assembly: ENSMBL hg38 release 91
Supplementary files format and content: txt matrix with log2 normalized values per sample.

extract_protocol:
Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on NovaSeq S4 6000 SBS Kit (300 cycles) with an average of 80M PE reads (40M in each direction).

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes.

tag: gender


title: SIG_9003


title: untreated CT26 tumors D11 rep1 [198]


title: mESC WT MosIR S2


title: SIG 9136


title: SIG_9000


title: SIG 9115


title: SIG_8016


title: SIG 2161


title: Whole testis, synchronized, 763.2hr, EP4

city: Pullman

first: Michael

middle: D

last: Griswold

state: WA

address: Biotechnilogy Life Sciences

department: School of Molecular Biosciences; Center for Reproductive Biology

institute: Washington State University

data_processing:
After raw data processing, the resulting gene-cell matrix was analyzed further in R software using the Seurat package (v4.3.0.1). Transcriptomes were excluded if the percent of reads mapping to the mitochondrial genome was greater than 25%. Doublets were identified and excluded from analysis using the package DoubletFinder (v2.0.3). Gene expression data were then normalized, scaled, and variable genes identified using the default parameters in Seurat. Dimensional reduction was then performed via principal component (PC) analysis and the number of PCs was selected by identifying the point at which the percent change in variation between the consecutive PCs was less than 0.1%, and then corroborated by determining statistical significance (P > 0.05) using the “JackStraw” procedure. Individual cells were projected onto UMAP two-dimensional representations using the selected PCs. Graph-based clustering was performed via Louvain algorithm with the “FindClusters” function (resolution = 0.8).
Assembly: mm10
Supplementary files format and content: paired-end FASTQ and index files

source_name: Whole testis

extract_protocol:
To create a single cell suspension, testes were detunicated and placed in 10 mL of collagenase solution (1mg/mL, X7H9763A, Worthington Biochemical, Lakewood, NJ, USA) and 1mL DNase solution (7mg/mL, 9003-98-9, Sigma, St. Louis, MO, USA) diluted in 1x HBSS (Thermo Fisher, Waltham, MA, USA) in a 50mL conical. Tubules were dissociated by pipetting up and down once with a 10mL serological pipet, then swirling the tube several times before incubating the tubules in a 37°C water bath for three minutes. After incubation, testes were swirled again vigorously and incubated for three additional three-minute periods. Tubules were then placed on ice for 1 minute to allow the tubules to settle to the bottom of the conical, and the collagenase/DNase solution was removed. Tubules were then rinsed with 10mL 1x HBSS, swirled, again set on ice for one minute to allow the tubules to settle, and the supernatant was removed. This process was repeated three additional times and then a 9mL 0.25% trypsin and 1mL DNase solution was added and the resulting mixture was then pipetted up and down 10 times with a p1000 micropipette to dissociate the tubules further before being placed in a 37°C water bath for five minutes. This step was repeated, with another 1mL of the DNase solution being added when necessary to support tubule degeneration, another five times. 10% of the total volume of fetal bovine serum (FBS) was then added and cells were put through at 40μM cell strainer that was prerinsed with 1mL 1x HBSS. The 50mL conical that had previously contained the cells was then rinsed three times with 1x HBSS to collect any lingering cells, and this solution was also sent through the 40μM cell strainer. Cell counts were estimated using a hemocytometer, spun down at 600 × g for 7 min at 4°C, and resuspended at 4 million cells/mL in 10% DNase in 1x DPBS (ThermoFisher, Waltham, MA, USA). To determine cell viability, 20µL of the cell suspension was diluted 1:1 with 0.4% trypan blue (Invitrogen, Waltham, MA, USA), and on average the cell suspensions used for scRNA-seq library had a live cell percentage of at least 96.95% (+/- 1.13%).
Cells from triplicate males were pooled at equal proportions and loaded into a Chromium Controller (10× Genomics, Inc., Pleasanton, CA, USA). Single-cell cDNA libraries were generated using v3.1 chemistry according to the manufacturers protocol (10× Genomics, Inc.) and sequenced via NovaSeq PE150 (Novagene, Sacramento, California). Raw data were processed, demultiplexed, and aligned to the 10-mm mouse transcriptome using the 10× Genomics Cell Ranger pipeline (v3.0.2)

value: Whole testis

tag: time


title: SIG_8015

value: f


title: Whole testis, synchronized, 350.4hr, EP2


title: mESC WT MosIR S1


title: Whole testis, synchronized, 556.8hr, EP3


title: mESC DicerO3 LCMV MOI 0.01 S15

value: LCMV infected, MOI 0.01


title: mESC DicerO3 LCMV MOI 0.01 S16


title: SIG_8014


title: SIG 2149


title: Whole testis, synchronized, 144hr, EP1


title: SIG 9027


title: mESC DicerO3 LCMV MOI 0.01 2


title: Whole testis, synchronized, 0hr, Control


title: mESC DicerO3 LCMV MOI 0.01 1


title: SIG_8013


title: SIG 2146


title: BMDM, PPARg T166A, Input

city: Nanjing

first: Yuxin

last: Wang

address: 163 Xianlin Road

institute: Nanjing University

data_processing:
Reads were aligned to reference mouse genome (mm10 assembly, UCSC) using Bowtie2 (v2.5.1), and clonal reads were removed from further analysis.
We used the MACS2 (v2.1.0) peak calling software to identify regions of IP enrichment over background.
ChIPseeker (v1.36.0) R package was used to retrieve the nearest genes around the peak and annotate genomic region of the peak.
Assembly: mm10 (UCSC)
Supplementary files format and content: bigWIg

source_name: Bone marrow

growth_protocol: BMDMs were maintained in RPMI-1640 medium containing 10% FBS and 50 ng/ml M-CSF at 37°C in a 5% CO2 incubator.

extract_protocol:
BMDMs were fixed with 1% formaldehyde in culture medium at room temperature for 10 min. Subsequently, the crosslinked cells were collected, lysed and digested with MNase. The sheared chromatin was subjected to immunoprecipitation with a rabbit anti-PPARγ antibody (#81B8, Cell Signaling Technology) or rabbit IgG control overnight at 4 °C with constant rotation. The isolated complexes were collected with Protein G magnetic beads and eluted by incubating at 65 °C in a buffer with high salt concentration.
ChIP-seq library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: BMDMs were isolated from the femurs and tibiase of C57BL/6J or PPARg T166A mice. Bone marrow cells were differentiated for 7 days in the presence of M-CSF (50 ng/ml). On day 7, macrophage purity of the culture was routinely tested by the expression of F4/80 and CD11b by flow cytometry. Around 95-99% of the cells expressed high levels of F4/80 and CD11b after differentiation.

value: Bone marrow

value: IgG

value: Bone marrow-derived macrophages

value: PPARg T166A


title: SIG_8012


title: mESC DicerS4 LCMV MOI 0.01 S14


title: SIG 2143


title: BMDM, PPARg T166A, ChIP

value: PPARg (#81B8, Cell Signaling Technology)


title: mESC DicerS4 LCMV MOI 0.01 S13


title: SIG 2077


title: SIG_8011


title: SIG_8010


title: SIG 2068


title: SIG_8009


title: BMDM, PPARg WT, ChIP

value: WT


title: SIG 2038


title: SIG 2028


title: BMDMs, TA, RNA-seq rep1

data_processing:
Read quality was assessed with FastQC (v0.12.1) and adapters trimmed using Cutadapt (v4.4)
Reads were then aligned to the mm10 genome (UCSC) using HISAT2 (v2.2.1), and counted using featureCounts
Assembly: mm10 (UCSC)
Supplementary files format and content: tab-delimited text files include read counts for each sample

extract_protocol:
Total RNA was extracted from differentiated adipocytes in vitro, using the TRIzol reagent (Invitrogen).
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

tag: batch


title: mESC DicerKO LCMV MOI 0.01 1

value: Dicer-/-


title: SIG_8007


title: BMDMs, TA, RNA-seq rep2


title: mESC DicerKO LCMV MOI 0.01 2


title: SIG 1720


title: SIG_8008


title: BMDMs, WT, RNA-seq rep3


title: SIG 1719


title: mESC DicerDHEL1 PKRnull LCMV MOI 1 24

value: Dicer deltaHEL1/ deltaHEL1, Pkr-/-

value: LCMV infected, MOI 1


title: SIG_8004

value: blood


title: mESC DicerDHEL1 PKRnull LCMV MOI 1 23

value: ESC


title: SIG_8005


title: SIG 1718


title: BMDMs, WT, RNA-seq rep2


title: mESC DicerDHEL1 PKRnull LCMV MOI 0.01 12


title: mESC DicerS4 LCMV MOI 0.01 2


title: BMDMs, WT, RNA-seq rep1


title: SIG 1717


title: BMDM, PPARg WT, Input


title: mESC DicerS4 LCMV MOI 0.01 1


title: BMDMs, TA, RNA-seq rep3


title: mESC DicerDHEL1 PKRnull LCMV MOI 0.01 11


title: SIG 1716


title: SIG_8006


title: 42day-3

data_processing:
Fastq files was processed with CellrangerATAC 2.0.0 with refdata-cellranger-arc-mm10-2020-A-2.0.0
Assembly: mm10
Supplementary files format and content: a filtered barcode-peak matrix
Supplementary files format and content: a fragment file and an index file of a fragment file

source_name: post IRI (42day)

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)
snATAC-seq

value: Kidney

value: IRI


title: mESC DicerDHEL1 LCMV MOI 1 20

value: Dicer deltaHEL1/ deltaHEL1


title: SIG 1715


title: SIG_8002

value: infected


title: SIG_8001

value: m


title: mESC DicerDHEL1 LCMV MOI 0.01 S12

value: LCMV infected, MOI 0.01


title: sham-3

source_name: sham

value: sham


title: SIG 1714


title: SIG_2095


title: SIG 1713


title: SIG_2092

value: f


title: SIG_2089


title: SIG_8003


title: mESC DicerDHEL1 LCMV MOI 0.01 S11


title: SIG 1712


title: 4hr-3

source_name: post IRI (4hr)


title: 4hr-4


title: SIG 1711


title: 12hr-3

source_name: post IRI (12hr)


title: SIG_2086


title: SIG_2083


title: 12hr-2


title: mESC DicerDHEL1 LCMV MOI 0.01 10


title: SIG_2080


title: SIG 1709


title: mESC WT LCMV MOI 1 15

value: Dicerwt/wt


title: SIG 1708


title: 12hr-1


title: SIG 1707


title: 2day-3

source_name: post IRI (2day)


title: mESC DicerDHEL1 LCMV MOI 1 19


title: mESC WT LCMV MOI 1 16


title: SIG 1706

source_name: blood


title: 42day-2


title: 42day-1


title: SIG_2077


title: mESC WT LCMV MOI 0.01 S10


title: mESC DicerDHEL1 LCMV MOI 0.01 9


title: SIG 1704


title: SIG_2068


title: SIG_2065


title: 4hr-2


title: mESC WT LCMV MOI 0.01 8


title: SIG_2059


title: 4hr-1


title: SIG 1703


title: mESC WT LCMV MOI 0.01 7


title: SIG_2056


title: SIG 1702


title: SIG 1701


title: sham-2


title: 14day-3

source_name: post IRI (14day)


title: mESC WT LCMV MOI 0.01 S9


title: SIG 1700


title: SIG_2053


title: SIG_2050


title: H3K27ac ChIP-DKO_1.1_H3K27ac

city: Rockville

first: Kun-Lin

last: Ho

state: MD

address: 10322 Strathmore Hall St Apt 405

institute: HJF

data_processing:
BWA (version 0.6.1) was used to align the ChIP-seq datasets to build version NCB37/MM9 of the mouse genome. Alignments were performed using default parameters that preserved reads mapping uniquely to the genome without mismatches. Bam files were concatenated to sum the biological replicates of each state and bigwiggle files were calculated for comparing the different states.
Assembly: mm9
Supplementary files format and content: BW, narrowpeak

source_name: prostate

extract_protocol:
Fresh-frozen prostatic tumor tissue was pulverized (Cryoprep Pulvrizer, Covaris), resuspended in PBS + 1% formaldehyde, and incubated at room temperature for 20 minutes. Fixation was stopped by addition of 0.125 M glycine (final concentration) for 15 minutes at room temperature, then washing in ice cold PBS + EDTA-free protease inhibitor cocktail. Chromatin was isolated from biological triplicates by the addition of lysis buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl (pH 7.4), 1 mM EDTA (pH 8.0), 0.1% NaDOC, 0.13 M NaCl, 1X PIC) + sonication buffer (0.25% sarkosyl, 1 mM DTT) to the samples, which were maintained on ice for 30 minutes. Lysates were sonicated (E210 Focused-ultrasonicator, Covaris) and the DNA was sheared to an average length of ~200-500 bp.
ChIPseq libraries were prepared using the KAPA HTP Library Preparation Kit according to the manufacturers’ protocols; ChIP-seq libraries were uniquely indexed in equimolar ratios.

value: prostate

value: prostate cancer

value: Pten:Rb1 KO


title: H3K27ac ChIP-SKO_2.1_H3K27ac

value: Pten KO


title: 14day-2


title: SIG 1699


title: ATACseq-DKO_1_ATAC

data_processing:
BWA (version 0.6.1) was used to align the ATAC-seq datasets to build version NCB37/MM9 of the mouse genome. Alignments were performed using default parameters that preserved reads mapping uniquely to the genome without mismatches. Bam files were concatenated to sum the biological replicates of each state and bigwiggle files were calculated for comparing the different states.
Assembly: mm9
Supplementary files format and content: BW, narrowpeak

extract_protocol:
Cells were collected by incubating in trypsin for 5 min at room temperature and subsequent centrifugation at 592g for 5 min at 4 °C. Fifty-thousand cells were used for tagmentation by incubating in 50 μl of 1× THS-seq buffer (25 μl 2× THS buffer (66 mM Tris acetate, pH 7.8, 132 mM potassium acetate, 20 mM magnesium acetate and 32% dimethylformamide), 5 μl 10× Digitonin, 2 μl Illumina-TDE1) for 20 minutes at 37 °C. To stop the tagmentation reaction, an equal volume of 2× Tagmentation Stop Buffer (10 mM Tris-HCl (pH 8.0), 20 mM EDTA (pH 8.0)) was added to the reaction and incubated for 10 min on ice. For cell lysis, an equal volume of 2× lysis buffer (100 mM Tris-HCl (pH 8.0), 100 mM NaCl, 40 μg ml−1 proteinase K, 0.4% SDS) was added to the tagmentation mix and incubated at 65 °C for 15 min.
Library construction was performed using standard Illumina protocols using a Nextera Library Prep Kit.


title: SIG 1698


title: H3K27ac ChIP-SKO_1.1_H3K27ac


title: sham-1


title: ATACseq-SKO_2_ATAC


title: 2day-2


title: SIG_2044

extract_protocol:
Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 40 million reads per RNA sample


title: SIG 136


title: SIG_2041


title: 2day-1


title: SIG 135


title: ATACseq-SKO_1_ATAC


title: 14day-1


title: SIG 134


title: SIG_2038


title: MUV101

city: Boston

first: Ilon

last: Liu

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: DFCI

data_processing:
Illumina bcl2fastq 1.5 is used for demultiplexing
RNA-seq sequenced reads were mapped to hg19  using hisat2(2.1.0) with parameters --met 5 -k 10 --mp 1,1 --np 1 --score-min L,0,-0.1 --secondary --no-mixed --no-softclip --no-discordant --rdg 99999999,99999999 --rfg 99999999,99999999 --no-spliced-alignment --seed 12345
RNA-seq TPM were calculated using RSEM (v1.3.0) with parameters --estimate-rspd --paired-end -sam
Assembly: hg19
Supplementary files format and content: a single tab-delimited text files including TPM values for all Samples

source_name: Human patient DHG-H3G34

extract_protocol:
Smart-seq2 protocol
Illumina, Nextera XT Library Prep kit,

value: Human patient DHG-H3G34

tag: age at diagnosis

value: Male

tag: sample type

value: Fresh whole-cell sample


title: Female cortex 4

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim_Galore v0.6.7, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.110  whole genome using star2.7.1a.  Counts were generated with the subread v2.0.1 and the featureCounts -p -t expm -g gene_id -a -o
Count matrixes were then analyzed using DESeq2 v1.28.1 to caculate differentialy expressed genes and normalized counts
DeSeq2 Normalized counts were calcuated by counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene
Assembly: Homo_sapiens.GRCh38.110
Supplementary files format and content: excel file with normalized counts for each gene

extract_protocol:
completed by Origene
Libraries were prepared for sequencing using standard Illumina protocols, and poly A selection

value: Female

tag: treatment

value: 100% cortex


title: SIG_2047

tag: tissue

value: blood


title: SIG 133


title: Colon cancer organoids, Norepinephrine treatment, rep4

city: New York

first: Hiroki

last: Kobayashi

state: NY

address: Irving Cancer Research Center, Room 901, 1130 St. Nicholas Avenue

department: Division of Digestive & Liver Diseases

institute: Columbia University

description:
TH008
est_counts_genes_kallisto.txt

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We performed a pseudoalignment to a kallisto index created from transcriptomes (Mouse:GRCm38.p6) using kallisto (0.44.0).
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text file includes estimated counts for each gene (computed from tximport R package) for each sample.

source_name: Colon cancer cells

growth_protocol: ApcΔ/Δ, KrasG12D/Δ, Trp53Δ/Δ mouse colon tumor organoids were maintained within Cultrex type II BME in humidified atmosphere with 5% CO2 at 37C using the following growth medium. Advanced Dulbecco’s modified Eagle medium/F12 supplemented with 1x antimycotic/antibiotic, 10 mM HEPES, 2 mM GlutaMAX, 1 x B27, 1 x N2, and 100 ng/ml mouse recombinant Noggin.

extract_protocol:
Total RNA were exacted with Trizol reagent and further purified by NucleoSpin RNA purification kit.
We used poly-A pull-down to enrich mRNAs from total RNA samples, then proceeded with library construction using Illumina TruSeq chemistry. Libraries were then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplexed samples in each lane, which yielded targeted number of paired-end 100bp reads for each sample.

treatment_protocol: ApcΔ/Δ, KrasG12D/Δ, Trp53Δ/Δ mouse colon tumor organoids were grown within Cultrex type II BME and treated with norepinephrine (10 uM) or vehicle in advanced Dulbecco's Modified Eagle Medium/F12 containing 0.5% fetal bovine serum for 48 hours.

value: Colon cancer cells

value: Norepinephrine


title: SIG_2028

value: infected

value: m


title: SIG_2025


title: Colon cancer organoids, Norepinephrine treatment, rep3

description:
TH007
est_counts_genes_kallisto.txt


title: SIG_2022


title: male medulla 3

source_name: Kidney

value: Kidney

value: 45% cortex, 55% medulla


title: SIG 132


title: Colon cancer organoids, Norepinephrine treatment, rep2

description:
TH006
est_counts_genes_kallisto.txt


title: SIG 131


title: SIG_2019

value: f


title: male cortex 2


title: male cortex 3

value: 100% Cortex, 0% Medulla


title: Colon cancer organoids, Norepinephrine treatment, rep1

description:
TH005
est_counts_genes_kallisto.txt


title: Colon cancer organoids, Vehicle treatment, rep4

description:
TH004
est_counts_genes_kallisto.txt

value: Vehicle


title: SIG 129


title: SIG 130


title: Colon cancer organoids, Vehicle treatment, rep3

description:
TH003
est_counts_genes_kallisto.txt


title: SIG_2013


title: Colon cancer organoids, Vehicle treatment, rep2

description:
TH002
est_counts_genes_kallisto.txt


title: male medulla 1

value: 30% cortex, 70% medulla


title: male cortex 1

value: 100% cortex, 0% medulla


title: SIG_2010


title: SIG_2004


title: SIG_2007


title: Female medulla 4

value: 40% cortex, 60% medulla


title: SIG_2001


title: SIG_167


title: IECs, PIM1+/- rep4

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default  parameters.
Then clean reads were separately aligned to reference genome with orientation mode  using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances.R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.

source_name: Colon

value: Intestinal epithelial cells

value: Colon

tag: strain


title: Female cortex 3

value: Female


title: Female cortex 2

value: 100% medulla


title: IECs, PIM1+/- rep3


title: SIG_1573

value: blood


title: SIG_1571


title: male medulla 2

value: Male

value: 20% cortex, 80% medulla


title: IECs, PIM1+/- rep2


title: IECs, PIM1+/- rep1


title: Female cortex 1

value: 100% cortex


title: SIG_1570

value: infected


title: Female medulla 2

value: Kidney


title: IECs, WT rep4

value: wild type


title: Female medulla 1


title: SIG_1567

value: f


title: IECs, WT rep3


title: SIG_1569

value: m


title: Prolif,HBECS,Donor2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: No HTO

data_processing:
CellRanger v6.0.0. count
No CITE-seq-Count
Assembly: GRCh38/hg38
Supplementary files format and content: CellRanger output files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CITE-seq Count output files :  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: bronchial airways

growth_protocol: Proliferation in PneumaExPlus medium

extract_protocol:
Cells were incubated in trypsin 0.05%-EDTA for 5 min at 37°C. Then, cells were gently detached by pipetting and transferred into a 50mL tube and An excess of HBSS containing 2% BSA was added. Cells were centrifuged at 150 g for 5 min and resuspended in 500 µL of supplemented HBSS containing 2% BSA, centrifuged again at 150 g for 5 min and resuspended in 500 µL HBSS with 10% FBS and dissociated mechanically 4 times through a 26G syringe. Finally, cell suspensions were filtered through a 40 µm porosity FlowmiTM Cell Strainer (Bel-Art), centrifuged at 150 for 5 min and resuspended in 500 µL of HBSS. Cell concentration and viability were measured with a CountessTM automated cell counter (Thermo Fisher Scientific), after incubation with NucGreen to detect dead cells (Thermo Fisher scientific). All steps, except trypsin incubation were performed on ice.  Cell concentration of each cell suspension (4 conditions per time point) was determined, and 500 000 cells of each were centrifuged and resuspended in 100 µL of HBSS containing 2% BSA. Each cell suspension was then incubated with 0.5 µg of a distinct hashtag antibody (TotalSeqTM-A0251, A0252, A0253 and A0254, BioLegend). Each cell suspension was washed twice with HBSS, and cell concentration was measured again. Cells from each of the 4 conditions were pooled in order to obtain a final cell suspension containing identical cell concentration of each condition. We aimed at reaching a total concentration of 300 cells/mL in HBSS for the cell capture by 10X genomics Chromium.
The manufacturer’s protocol (Chromium™ Single Cell 3’ Reagent Kits, v2) was followed to obtain single cell 3’ libraries for Illumina sequencing.

value: bronchial airways

value: Human Bronchial Epithelial Cells (HBECS)

tag: differentiation day

value: Prolif

tag: hto

value: No HTO


title: IECs, WT rep2

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: Intestinal epithelial cells

tag: genotype


title: Neuron, un, biol rep 3

city: San Francisco

first: Gokul

middle: Nathan

last: Ramadoss

state: California

address: 1200 Mariposa St

institute: UCSF

description: harvested 3 d post transduction

data_processing:
Sequencing reads were trimmed using CutAdapt (DOI:10.14806/ej.17.1.200) and aligned using HISAT2 (DOI:10.1038/s41587-019-0201-4), and then a read count matrix was generated using featureCounts (DOI: 10.1093/bioinformatics/btt656).
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: induced pluripotent stem cells

extract_protocol:
RNA was extracted using the Quick-RNA™ Microprep Kit (cat. #R1050).
Using 500 ng of total RNA, we prepared the mRNA libraries using the QuantSeq 3’ mRNA-Sequencing Library FWD V1 Prep Kit (cat. #015.96). After cDNA synthesis, we used 17 PCR cycles to amplify the libraries. Following bead purification, mRNA concentrations were determined by Qubit and fragment lengths were quantified using High Sensitivity d5000 Reagents (cat. #5067-5593) on the Agilent TapeStation 4200. We normalized our libraries to 8.25 nM for pooling and sequenced through single-end sequencing on the Illumina NovaSeqX 10B flow cell with read lengths 101x12x24 (Read 1, Index 1, Index 2).

value: induced pluripotent stem cells

tag: cell line

value: neuron

value: WT

value: No VLP


title: Colon cancer organoids, Vehicle treatment, rep1

description:
TH001
est_counts_genes_kallisto.txt

value: Colon cancer cells

value: Vehicle


title: Prolif,HBECS,Donor1

description: No HTO


title: SIG_1565

tag: Sex

value: blood


title: Neuron, un, biol rep 2

description: harvested 3 d post transduction


title: SIG_128

tag: status

value: infected


title: IECs, WT rep1

value: Colon


title: ALI28,HBECS,Donor2

description: HTO

data_processing:
CellRanger v6.0.0. count
Cell barcodes from CellRanger output were used as whitelist to quantify HTOs using CITE-seq-Count (v1.4.2)
Assembly: GRCh38/hg38
Supplementary files format and content: CellRanger output files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CITE-seq Count output files :  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

growth_protocol: Differention in specific medium

extract_protocol:
Cells were incubated with 0.1% protease type XIV Streptomyces griseus in HBSS for 4-6 hours at 4°C for the ALI28 time point until dissociation was clearly visible. Then, cells were gently detached from the culture insert by pipetting and transferred into a microtube. An excess of HBSS containing 2% BSA was added. Cells were centrifuged at 150 g for 5 min and resuspended in 500 µL of supplemented HBSS containing 2% BSA, centrifuged again at 150 g for 5 min and resuspended in 500 µL HBSS with 10% FBS and dissociated mechanically 4 times through a 26G syringe. Finally, cell suspensions were filtered through a 40 µm porosity FlowmiTM Cell Strainer (Bel-Art), centrifuged at 150 for 5 min and resuspended in 500 µL of HBSS. Cell concentration and viability were measured with a CountessTM automated cell counter (Thermo Fisher Scientific), after incubation with NucGreen to detect dead cells (Thermo Fisher scientific). All steps were performed on ice. Each cell suspension was then incubated with 0.5 µg of a distinct hashtag antibody (TotalSeqTM-A0251, A0252, A0253 and A0254, BioLegend). Each cell suspension was washed twice with HBSS, and cell concentration was measured again. Cells from each of the 4 conditions were pooled in order to obtain a final cell suspension containing identical cell concentration of each condition. We aimed at reaching a total concentration of 700 cells/mL in HBSS for the cell capture by 10X genomics Chromium, in order to capture 10 000 cells i.e. 2500 cells per condition.
The manufacturer’s protocol (Chromium™ Single Cell 3’ Reagent Kits, v2) was followed to obtain single cell 3’ libraries for Illumina sequencing.

value: TotalSeq-A0251 medium Clancy, TotalSeq-A0252 medium Half, TotalSeq-A0253 medium BEGMALI, TotalSeq-A0254 medium PneumaALI


title: ALI28,HBECS,Donor1

description: HTO

value: TotalSeq-A0251 medium BEGMALI, TotalSeq-A0252 medium Clancy, TotalSeq-A0253 medium Half, TotalSeq-A0254 medium PneumaALI


title: Neuron, un, biol rep 1

description: harvested 3 d post transduction


title: Female medulla 3

value: Kidney

value: Female

value: 100% medulla


title: Neuron, NTg1, biol rep 3

description: harvested 3 d post transduction

value: Cas9-NTg1 VLP


title: Arfloxed CD4-Cre+, Rep 3

city: Chicago

first: Alexander

last: Chervonsky

state: IL

address: 924 E 57th St

institute: University of Chicago

data_processing:
Single cell reads were processed with Cellranger version 6.1.2 using the mm10 version 3.0.0 reference genome.
Assembly: mm10
Supplementary files format and content: 10x sparse matrix format

source_name: Pancreatic Lymph Node

extract_protocol:
Pancreatic lymph nodes from three mice per group were harvested and single cell suspensions were prepared.
Cells were loaded onto a 10x platform with a target recovery of 104 cells per sample for construction of single cell RNA sequence (scRNAseq) library as detailed in 10x Genomics manual. Sequencing was performed on scRNAseq libraries using the Illumina NovaseqX platform at the University of Chicago Genomics Core.

value: Pancreatic Lymph Node

tag: group

value: Arfloxed CD4-Cre+


title: ALI0,HBECS,Donor1

description: HTO

extract_protocol:
Cells were incubated in trypsin 0.05%-EDTA for 15 min at 37°C. Then, cells were gently detached from the culture insert by pipetting and transferred into a microtube. An excess of HBSS containing 2% BSA was added. Cells were centrifuged at 150 g for 5 min and resuspended in 500 µL of supplemented HBSS containing 2% BSA, centrifuged again at 150 g for 5 min and resuspended in 500 µL HBSS with 10% FBS and dissociated mechanically 4 times through a 26G syringe. Finally, cell suspensions were filtered through a 40 µm porosity FlowmiTM Cell Strainer (Bel-Art), centrifuged at 150 for 5 min and resuspended in 500 µL of HBSS. Cell concentration and viability were measured with a CountessTM automated cell counter (Thermo Fisher Scientific), after incubation with NucGreen to detect dead cells (Thermo Fisher scientific). All steps, except trypsin incubation were performed on ice.  Cell concentration of each cell suspension (4 conditions per time point) was determined, and 500 000 cells of each were centrifuged and resuspended in 100 µL of HBSS containing 2% BSA. Each cell suspension was then incubated with 0.5 µg of a distinct hashtag antibody (TotalSeqTM-A0251, A0252, A0253 and A0254, BioLegend). Each cell suspension was washed twice with HBSS, and cell concentration was measured again. Cells from each of the 4 conditions were pooled in order to obtain a final cell suspension containing identical cell concentration of each condition. We aimed at reaching a total concentration of 700 cells/mL in HBSS for the cell capture by 10X genomics Chromium, in order to capture 10 000 cells i.e. 2500 cells per condition.
The manufacturer’s protocol (Chromium™ Single Cell 3’ Reagent Kits, v2) was followed to obtain single cell 3’ libraries for Illumina sequencing.

value: bronchial airways

value: Human Bronchial Epithelial Cells (HBECS)

value: TotalSeq-A0251 medium BEGM, TotalSeq-A0252 medium Clancy, TotalSeq-A0253 medium PneumaExPlus, TotalSeq-A0254 medium Wu


title: Arfloxed CD4-Cre+, Rep 2


title: Neuron, NTg1, biol rep 2

description: harvested 3 d post transduction

value: induced pluripotent stem cells

value: neuron

value: WT


title: Neuron, NTg1, biol rep 1

description: harvested 3 d post transduction


title: FAPs_DEN-28dpi

city: Seoul

first: Kyusang

last: Yoo

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences Department

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.5.7.0 was used for the data acquisition on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7., and Fastqc v.0.11.7 was used for QC by Phred scoring.
BCL to fastq file conversion was performed with bcl2fastq v2.20.0 by running mkfastq on CellRanger 3.1.0 with the default settings as parameters.
CellRanger(3.1.0) count was run to generate barcode.tsv files and aligned, demultiplexed BAM files using mouse genome build mm10, and velocyto(0.17.17) was run to generate loom files using BAM files and barcode.tsv files that contain raw count data of both spliced and unspliced mRNAs.
Loom files were loaded onto R 4.0.5 using ReadVelocity in R package SeuratWrappers 0.3.1,  and were transformed into Seurat objects using as.Seurat in R package Seurat 4.3.0. The same R package was used for clearing of the data by dead cell removal and doublet cell gating out. After quality control, all nine samples were merged into a single Seurat object for further processes including normalization, filtering-out non-FAPs by gene expression, variable gene selection, cell cycle regression, PCA, UMAP clustering, DEG analyses and RNA velocity analysis(velocyto.R v0.6).
Assembly: mm10-2020-A (10x Genomics)
Supplementary files format and content: csv files with genes as rows, columns as individual cells (barcodes) and values in raw counts of either spliced mRNA or unspliced mRNA

source_name: Limb muscle (below knee)

extract_protocol:
Limb muscles below knee were dissected from mice at indicated time points post either sciatic nerve crush injury or denervation at indicated time points. After removal of nerves and tendons, muscles were finely chopped with surgical scissors and mechanically dissociated in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% horse serum (Hyclone, Logan, UT, USA), collagenase II (800 units/mL; Worthington, Lakewood, NJ, USA), and dispase (1.1 units/mL; ThermoFisher Scientific, Waltham, MA, USA) at 37°C for 40 min with mild agitation. Digested suspensions were subsequently triturated by sterilized syringe with 20G1/2 needle (BD Biosciences, Franklin Lakes, NJ, USA) and washed with DMEM to harvest mononuclear cells. Mononuclear cells were stained with anti-CD45-APC, anti-CD31-APC, anti-Ter119-PE, anti-Sca1-FITC, anti-Vcam1-biotin and streptavidin-PE/Cy7. To exclude dead cells, 7AAD (Sigma aldrich; St. Louis, MO, USA) was used prior to FACS sorting. 7AAD–Lin–Vcam–Sca1+ FAPs were isolated using a FACS Aria III cell sorter (BD Biosciences) with 4-way-purity precision. Isotype control density plots were used as a reference for positive gating.
Libraries for each sample of FAPs were generated with the 10X Genomics Chromium Next GEM Single Cell 3p RNA library v3.1 kit, following the manufacturer’s instructions, and a total of 5,000 cells were targeted for recovery from each sample of FAPs. Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: Mice were deeply anesthesized via intraperitoneal injection of Avertin (32 mg/ml, ~800 mg/kg), and the incision site on the posterior side of the right hindlimb was shaved and depilated using surgical clippers and hair removal cream. After cleansing the incision site with 70% ethanol, incision was made on the skin with surgical scissors and the biceps femoris muscle was punctured open with fine-tip forceps to expose the sciatic nerve. For sciatic nerve crush injury, the exposed nerve was crushed with fine forceps for 30 seconds at the site just proximal to where the tibial, peroneal and sural nerves branched out from the sciatic nerve. For denervation, ~5 mm of the sciatic nerve proximal from the crush injury site was cut and removed. The punctured biceps femoris muscle and skin were then sutured, and the incision site was sterilized with povidion-iodine. Samples were then collected at indicated time points post injury.

value: Limb muscle (below knee)

value: Lin-Vcam1-Sca1+ Fibro/adipogenic progenitors (FAPs)

value: wildtype

tag: age

value: Sciatic nerve denervation, 28 days post injury


title: FAPs_DEN-14dpi

description: 10x Genomics

value: Sciatic nerve denervation, 14 days post injury


title: Arfloxed CD4-Cre+, Rep 1


title: Arfloxed CD4-Cre-, Rep 2

value: Arfloxed CD4-Cre-


title: Neuron, NEFLg1, biol rep 2

description: harvested 3 d post transduction

value: Cas9-NEFLg1 VLP


title: MSCs derived from Chorionic fluid RNA-seq 1

city: Swansea

first: David

last: James

address: Swansea University, Singleton Park

department: Medical School

country: United Kingdom

institute: Swansea University

data_processing:
Read quality assessed using FASTQC software
Adaptor contamination removed using Scythe software
Low quality read ends removed using Sickle software
Reads were aligned to the genome using HISAT2 software
Differential analysis performed using DESeq2 R package
Assembly: hg38

source_name: Chorionic Villi

extract_protocol:
Total RNA was extracted from AF- and CV-MSCs at passage 2 (P2) using total RNA Purification Plus Kit (Norgen) and processed by the Functional Genomic Center (University of Verona, Italy)
NA-seq library preparation was performed using the TruSeq stranded mRNA kit (Illumina) from 1μg of RNA per sample. Library size was assessed by capillary electrophoretic analysis with the Agilent 4200 Tape station.
RNA libraries were analysed on an Illumina NextSeq 500 sequencer using 75nt single reads.

value: Chorionic Villi

value: Mesenchymal Stem cell


title: FAPs_DEN-7dpi

description: 10x Genomics

value: Sciatic nerve denervation, 7 days post injury


title: Arfloxed CD4-Cre-, Rep 1

value: Pancreatic Lymph Node


title: FAPs_DEN-3dpi

description: 10x Genomics

value: Sciatic nerve denervation, 3 days post injury


title: MSCs derived from Amniotic fluid RNA-seq 2

source_name: Amniotic fluid

value: Amniotic fluid


title: Neuron, NEFLg1, biol rep 1

description: harvested 3 d post transduction


title: FAPs_SNC-14dpi

description: 10x Genomics

value: Sciatic nerve crush injury, 14 days post injury


title: Neuron, B2Mg1, biol rep 3

description: harvested 3 d post transduction

value: induced pluripotent stem cells

value: Cas9-B2Mg1 VLP


title: MSCs derived from Amniotic fluid RNA-seq 3


title: Ac, N , RIP-seq-N3

city: Shenzhen

first: Hao

last: Chen

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

data_processing:
Pre-processed reads of RNA-seq, Ribo-seq and MeRIP-seq were then subjected to alignment against Acart.genome.v1 using software STAR (version 2.7.10a), allowing for no more than 2 mismatches.
The sorted mapping files of Ribo-seq and RNA-seq were used for quantification with StringTie (v2.1.7) (Pertea, Pertea et al., 2015). Note that Ribo-Seq reads were mapped with additional parameters: --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33. Next, the obtained read counts were converted to TPM (transcripts per million).
Genes with cutoff values of TPM > 5 for RNA-Seq were used for downstream analysis. The R package DESeq2 was used to perform differential gene expression of RNA-seq datasets. Next, translational efficiency (TE) analysis was calculated by dividing the ribosome footprint density by the Ribo-seq TPM value when it's larger than 0 with mRNA abundance (RNAseq TPM).
The differential translation efficiency gene (DTEG) was analyzed by RiboDiff (v0.2.2). After alignment, m1A peaks enriched via IP over input control were detected based on a combination of corresponding biological replicates using MACS2 (v2.2.7.1) algorithm with -q 0.05. Minimum free energy (MFE) calculation of m1A methylated genes was performed by using the ViennaRNA package.
Assembly: Acart.genome.v1.fa.gz
Supplementary files format and content: Differential_peaks_by_edgeR.txt
Supplementary files format and content: RNA-Seq_gene_count_matrix.csv
Supplementary files format and content: Ribo-Seq-Differential_translation efficiency.txt
Supplementary files format and content: Ribo-Seq-gene_count_matrix.csv

organism: Amphidinium carterae

source_name: exponentially grown cells

growth_protocol: Dinoflagellate Amphidinium carterae was cultured in f/2 medium at a constant temperature of 23°C. The lighting conditions were maintained under a 12:12 hour light-dark cycle with a photon flux density of 50µmol·m-2·s-1.

extract_protocol:
Total RNA was extracted from A. carterae using RNAzol®RT (MRC) according to the manufacturer’s protocol.  Polyadenylated RNA (polyA+ RNA) was enriched from the total RNA samples by using two successive rounds of purification with VAHTS mRNA Capture Beads (Vazyme Biotech, Nanjing, China).
m1A-RIP RNA library was prepared by VAHTS Universal V8 RNA-seq Library Prep Kit. For RNA-seq, the isolated total RNA from A. carterae cells (three biological replicates for all treatments) was sent to the Beijing Genomics Institute (BGI, Shenzhen, China) for strand specific mRNA library construction. For Ribo-seq, library was prepared using VAHTSTM Small RNA Library Prep Kit for Illumina.

treatment_protocol: For nitrogen depletion experiment in A. carterae, the exponentially grown cells were washed once with sterile sea water and then cultured in normal and nitrogen-depletion f/2 medium respectively at an initial concentration of 2.5 × 10^4 cells/ml. For Ribo-seq, A. carterae cells (~40 million cells, two biological samples for each treatment) collected in the morning were treated with 100 µg/ml Cycloheximide (CHX) for 8 minutes.

value: exponentially grown cells

tag: antibody

value: nitrogen-depletion f/2 medium


title: FAPs_SNC-28dpi

description: 10x Genomics

value: Limb muscle (below knee)

value: Lin-Vcam1-Sca1+ Fibro/adipogenic progenitors (FAPs)

value: Sciatic nerve crush injury, 28 days post injury


title: MSCs derived from Chorionic fluid RNA-seq 3


title: MUV343Nuc

description:
cm_tpm_frozen_prefilter.csv
cm_tpm_frozen_postfilter.csv
metadata_frozen_postfilter.csv

data_processing:
Illumina bcl2fastq 1.5 is used for demultiplexing
RNA-seq sequenced reads were mapped to hg19  using hisat2(2.1.0) with parameters --met 5 -k 10 --mp 1,1 --np 1 --score-min L,0,-0.1 --secondary --no-mixed --no-softclip --no-discordant --rdg 99999999,99999999 --rfg 99999999,99999999 --no-spliced-alignment --seed 12345
RNA-seq TPM were calculated using RSEM (v1.3.0) with parameters --estimate-rspd --paired-end -sam
Assembly: hg19
Supplementary files format and content: a single tab-delimited text files include TPM values for all Samples

tag: tissue type

value: Human patient DHG-H3G34

tag: gender

value: Male

value: Frozen single-nuclei sample


title: Arfloxed CD4-Cre-, Rep 3

value: Arfloxed CD4-Cre-


title: Neuron, B2Mg1, biol rep 2

description: harvested 3 d post transduction

value: neuron

value: WT


title: Neuron, NEFLg1, biol rep 3

description: harvested 3 d post transduction

value: Cas9-NEFLg1 VLP


title: FAPs_SNC-3dpi

description: 10x Genomics

value: wildtype

value: Sciatic nerve crush injury, 3 days post injury


title: Ac, N, input-seq-N2


title: Ac, N , RIP-seq-N2


title: MUV342Nuc

tag: age at diagnosis


title: MSCs derived from Chorionic fluid RNA-seq 2

value: Chorionic Villi

value: Mesenchymal Stem cell


title: iPSC, un, biol rep 3

description: harvested 1 d post transduction

value: induced pluripotent stem cells

value: iPSC

value: No VLP


title: Neuron, B2Mg1, biol rep 1

description: harvested 3 d post transduction

value: Cas9-B2Mg1 VLP


title: iPSC, un, biol rep 2

description: harvested 1 d post transduction


title: MSCs derived from Amniotic fluid RNA-seq 1

value: Amniotic fluid


title: FAPs_SNC-7dpi

description: 10x Genomics

value: Limb muscle (below knee)

value: Lin-Vcam1-Sca1+ Fibro/adipogenic progenitors (FAPs)

value: Sciatic nerve crush injury, 7 days post injury


title: Ac, N, input-seq-N3

value: exponentially grown cells

value: nitrogen-depletion f/2 medium


title: ICR-CXJ-058Nuc

value: Human patient DHG-H3G34

value: Female

tag: sample type

value: Frozen single-nuclei sample


title: Ac, N, input-seq-N1

tag: treatment


title: ICR-CXJ-041Nuc

value: Male


title: Ac, N , RIP-seq-N1

tag: tissue


title: FAPs_Uninjured

description: 10x Genomics

tag: strain

value: wildtype


title: iPSC, NTg1, biol rep 3

description: harvested 1 d post transduction

value: WT

value: Cas9-NTg1 VLP


title: RP19_cells, infected, 72hrs, rep1

city: Provo

first: Abraham

last: Quaye

state: UT

address: 4007 Life Sciences Building

department: Microbiology & Molecular Biology

institute: Brigham Young University

data_processing:
Reads were trimmed with the Trim-galore (v0.6.6) program to achieve an overall Mean Sequence Quality of 36
Trimmed reads were mapped simultaneously to the complete genomic sequence of avirulent turkey hemorrhagic enteritis virus (THEV) and Meleagris gallopavo using Hisat2  (v 2.2.1), and reads mapping to THEV filtered as new BAM files with Samtools (v1.16.1)
StringTie (v 2.2.1) was used to assemble the transcriptome using a GTF file derived from a gff3 file obtained from NCBI,  which contains the predicted ORFs of THEV as a guide. GFFCOMPARE (v0.12.6) was used to merge all transcripts from all time points without redundancy.
StringTie set to expression estimation mode was used to calculate FPKM scores for all transcripts after which Ballgown (ve2.33.0)  in R was used to perform the statistical analysis on the transcript expression levels.
Regtools (1.0.0) was used to count all junctions, the reads supporting them, and extract all other information related to the junction.
Assembly: melGal5 and AY849321.1
Supplementary files format and content: tab-delimted text file containing the FPKM values for each sample
Supplementary files format and content: tab-delimted text file containing combined unique junctions from all replicates and time points

organism: Meleagris gallopavo

growth_protocol: Mock and infected MDTC-RP19 cells were grown as suspension cultures in 1:1 complete Leibovitz's L-15/McCoy's 5A medium with  10% fetal bovine serum (FBS), 20% chicken serum (ChS), 5% tryptose phosphate broth (TPB), and 1% antibiotics  solution (100 U/mL Penicillin and 100ug/mL Streptomycin), at 41C in a humidified atmosphere with 5% CO2. When infected or mock infected, cells were maintained in 1:1 serum-reduced Leibovitz's L15/McCoy's 5A media (SRLM) with 2.5% FBS, 5% ChS, 1.2% TPB, and 1% antibiotics solution (100 U/mL Penicillin and 100ug/mL Streptomycin)

extract_protocol:
Total RNA was extracted from infected cells using Thermofishers' RNAqueous™-4PCR Total RNA Isolation Kit (#AM1914)  per manufacturer's instructions.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. 1ug of total RNA was used for this library construction

treatment_protocol: A commercially available THEV live vaccine was purchased from Hygieia Biological Labs. The stock virus was titrated using an  in-house qPCR assay with titer expressed as genome copy number(GCN)/mL, similar to Mahshoub et al (https://doi.org/10.1016/j.jviromet.2016.11.002) with modifications. Cells were infected in triplicates at a multiplicity of infection (MOI)  of 100 GCN/cell, incubate at 41C for 1 hour, and washed three times to get rid of free virion particles. Samples in triplicates were  harvested at 4-, 12-, 24-, and 72-h.p.i for total RNA extraction and RNA-sequencing

value: B lymphocytes

value: Infected

tag: time point


title: RP19_cells, infected, 72hrs, rep3


title: iPSC, NEFLg1, biol rep 3

description: harvested 1 d post transduction

value: induced pluripotent stem cells

value: iPSC

value: Cas9-NEFLg1 VLP


title: RP19_cells, infected, 24hrs, rep1


title: RP19_cells, infected, 72hrs, rep2


title: Ac, F2, input-seq-F2

value: normal


title: Ac, F2, RIP-seq-F3


title: iPSC, NTg1, biol rep 1

description: harvested 1 d post transduction


title: Ac, F2, input-seq-F1


title: Ac, F2, input-seq-F3


title: iPSC, NEFLg1, biol rep 2

description: harvested 1 d post transduction


title: RP19_cells, infected, 12hrs, rep2


title: ICR-CXJ-046Nuc


title: iPSC, B2Mg1, biol rep 3

description: harvested 1 d post transduction

value: Cas9-B2Mg1 VLP


title: Myotubes, Zfp697 adenovirus infected, rep1

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterMultimapNmax 50   --outFilterMultimapScoreRange 3   --outFilterScoreMinOverLread 0.7   --outFilterMatchNminOverLread 0.7   --outFilterMismatchNmax 10   --alignIntronMax 500000   --alignMatesGapMax 1000000   --sjdbScore 2
Reads aligning to gene exons (Mus_musculus.GRCm38.102.gtf) were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level with extra parameters -s 0
Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package, genes with total raw counts less then 1 across all samples were excluded from analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text file includes differetial gene expression analysis output from DESeq2

source_name: mouse primary satellite cells

growth_protocol: Primary mouse myoblasts were seeded on a 6-well plate and differentiated in DMEM supplemented by 5% horse serum

extract_protocol:
Cells were lysed and RNA was extracted using Trizol reagent
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq RNA

treatment_protocol: Fully differentiated myotubes were transduced overnight with an adenovirus at an MOI of 100

value: mouse primary satellite cells

value: myotubes

value: wild-type

value: Adenovirus infection

tag: condition


title: Rome8Nuc

value: Human patient DHG-H3G34

value: Female


title: iPSC, NTg1, biol rep 2

description: harvested 1 d post transduction

tag: cell type


title: Ac, F2, RIP-seq-F2

value: exponentially grown cells


title: RP19_cells, infected, 24hrs, rep3

tag: genotype


title: RP19_cells, infected, 24hrs, rep2

tag: cell line


title: iPSC, B2Mg1, biol rep 2

description: harvested 1 d post transduction


title: Myotubes, GFP adenovirus infected, rep3


title: MUV94

value: Fresh whole-cell sample


title: RP19_cells, infected, 12hrs, rep1

value: WT


title: RP19_cells, infected, 4hrs, rep2


title: RP19_cells, infected, 4hrs, rep1


title: Negative human nasopharyngeal swab group 3

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

institute: Lunenfeld-Tanenbaum Research Institute

data_processing:
Samples sequenced using Illumina NextSeq, MiSeq, and MiniSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were developed to track and quantify key mutations within samples and to aggregate data.
Final anaylsis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1)
Supplementary files format and content: positive sample text file [sparseq_sample_data_GEOver.txt] has 63036 patient samples with bowtie alignment counts and variant analysis pipeline results
Supplementary files format and content: negative control text file [sparseq_negative_data_GEOver.txt] has 1928 negative human samples with bowtie alignment counts
Supplementary files format and content: non-patient control text file [sparseq_control_data_GEOver.txt] has 2886 total synthetic control samples with bowtie alignment counts
Library strategy: RNAseq with limited amplicons.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: human nasopharyngeal swab

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample)  and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library)  (A66514, Beckman Coulter)

value: human nasopharyngeal swab

value: negative sample


title: Ac, F2, RIP-seq-F1


title: iPSC, un, biol rep 1

description: harvested 1 d post transduction

value: No VLP


title: iPSC, B2Mg1, biol rep 1

description: harvested 1 d post transduction

value: induced pluripotent stem cells


title: Myotubes, Zfp697 adenovirus infected, rep3


title: iPSC, NEFLg1, biol rep 1

description: harvested 1 d post transduction

value: iPSC


title: Myotubes, Zfp697 adenovirus infected, rep2


title: Positive human nasopharyngeal swab group 5

value: positive sample


title: RP19_cells, infected, 4hrs, rep3

value: B lymphocytes

value: Infected


title: MUV341Nuc

value: Male

value: Frozen single-nuclei sample


title: Negative human nasopharyngeal swab group 5


title: Myotubes, GFP adenovirus infected, rep2

value: mouse primary satellite cells

value: myotubes

value: wild-type


title: Myotubes, GFP adenovirus infected, rep1

value: Adenovirus infection


title: Control 1

status: Public on Jul 29 2024

city: Madrid

first: Ana Belen

last: Sanz

address: Avda. Reyes Catolicos 2

country: Spain

institute: IIS-Fundacion Jimenez Diaz

description: Kidney

hyb_protocol: RNA was hybridized to GeneChip Mouse Gene 1.0 ST Arrays following manufacturers instructions (Affymetrix, Santa Clara, CA) in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Genechip Expression Console Software

label: biotin

source_name: MCTs control

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit (Affymetrix, High Wycombe, UK).

growth_protocol: MCT cells are a proximal tubular cell line harvested originally from the renal cortex of SJL mice and have been extensively characterized. They were cultured in RPMI 1640 (GIBCO, Grand Island, NY), 10 % decomplemented fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin, in 5 % CO2 at 37 ºC.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Subconfluent cells were rested in serum-free medium overnight and then stimulated with 100 ng/mL TWEAK (Ref, GF102, Millipore-Merck, Darmstadt, Germany) for 6 hours.

value: MCT

value: kidney

value: proxima tubular epithelial cells

value: control

tag: time


title: Control 2

description: Kidney


title: AKI 3

description: 12 weeks

source_name: AKI kidney 24h

growth_protocol: Three mice were housed per cage at 25 ± 1°C on a 12-h light/dark cycle and given free access to food and water

treatment_protocol: C57BL/6 female mice received a single intraperitoneal injection of folic acid (Sigma-Aldrich, Merck Darmstadt, Germany) 250 mg/kg in 0.3 mol/L sodium bicarbonate or vehicle (n=3 per group). Mice were euthanized at 24h

value: 12 weeks

tag: Sex

value: female

value: AKI


title: Positive human nasopharyngeal swab group 4

value: human nasopharyngeal swab


title: CONT3

description: 12 weeks

source_name: Control kidney

tag: group


title: TWEAK 3

description: Kidney

source_name: MCTs+TWEAK

value: TWEAK


title: AKI 1

description: 12 weeks

tag: age


title: CONT2

description: 12 weeks


title: p22rv1-Replicate 2 hypoxia (0%O2)

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0. Non-normalized data are listed in SampleProbe_NonNormalized.txt.

source_name: Prostate cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: The cells were kept in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin–streptomycin and 1% L-glutamine.

extract_protocol: RNA was extracted using miRNeasy MiniKit (Quiagen), according to the manufacturers’ instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Hypoxia treatment (0%, 0.2%, 0.5%, 1%, 2% or 5% O2) of exponentially growing cells was carried out at 60-70% cell confluence in an In Vivo2 200 chamber for 24 hours at 37°C.

value: Primary, from xenograft CWR22R subline

value: Hypoxia


title: TWEAK 1

description: Kidney


title: Control 3

description: Kidney


title: p22rv1-Replicate 2 hypoxia (0.2%O2)


title: TWEAK 2

description: Kidney


title: p22rv1-Replicate 2 normoxia (control for 0%O2)

value: Normoxia


title: p22rv1-Replicate 2 hypoxia (0.5%O2)


title: p22rv1-Replicate 2 normoxia (control for 5%O2)


title: p22rv1-Replicate 2 hypoxia (5%O2)


title: p22rv1-Replicate 1 hypoxia (0%O2)


title: AKI 2

description: 12 weeks


title: p22rv1-Replicate 2 normoxia (control for 2%O2)


title: p22rv1-Replicate 1 normoxia (control for 0.2%O2)


title: p22rv1-Replicate 2 hypoxia (1%O2)


title: p22rv1-Replicate 2 normoxia (control for 0.2%O2)


title: p22rv1-Replicate 1 normoxia (control for 5%O2)


title: CONT1

description: 12 weeks


title: p22rv1-Replicate 1 hypoxia (2%O2)


title: p22rv1-Replicate 2 normoxia (control for 0.5%O2)


title: p22rv1-Replicate 2 normoxia (control for 1%O2)


title: p22rv1-Replicate 2 hypoxia (2%O2)


title: p22rv1-Replicate 1 normoxia (control for 0.5%O2)


title: p22rv1-Replicate 1 hypoxia (0.2%O2)


title: PC3-Replicate 2 normoxia (control for 0%O2)

value: Bone metastasis


title: PC3-Replicate 2 hypoxia (0.2%O2)


title: PC3-Replicate 2 normoxia (control for 1%O2)


title: p22rv1-Replicate 1 hypoxia (0.5%O2)


title: p22rv1-Replicate 1 normoxia (control for 1%O2)


title: PC3-Replicate 2 normoxia (control for 2%O2)


title: p22rv1-Replicate 1 normoxia (control for 2%O2)


title: p22rv1-Replicate 1 hypoxia (1%O2)


title: PC3-Replicate 2 hypoxia (0.5%O2)


title: p22rv1-Replicate 1 hypoxia (5%O2)


title: PC3-Replicate 2 normoxia (control for 5%O2)