title: 293T virion 6SG PA-m6A-Seq

description:
Purified HIV virion RNA
Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

value: anti-m6A Synaptic Systems 202-003


title: LB28

status: Public on Sep 01 2021

type: SRA

city: New York

first: Michelle

middle: E

last: Ehrlich

state: NY

address: 1468 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: 4 Months old mouse striatum-Ct

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to the reference genome using STAR
FeatureCounts was used to count the read numbers mapped per gene
Readcounts were adjusted by TMM normalisation
edgeR R package was used to perform differential expression analysis.
P-values were adjusted using Benjamini Hochberg method
Mus musculus Grch38
.txt file containing a matrix of genes with readcounts against samples

molecule: total RNA

organism: Mus musculus

source_name: striatum

extract_protocol:
The striatum  from one hemisphere was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA sequencing was performed by Novogene (https://en.novogene.com) on an Illumina Novaseq 6000 S4 flow cells platform

tag: injection group

value: control miRNA

tag: strain

tag: age of injection


title: ΔTrub1 293T virion 6SG PA-Ψ-Seq

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
For hg19 alignments: tophat -N 1 --no-convert-bam --b2-N 1
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
When comparing WT to Pus KO samples, the dataset with the higher read depth down sampled to match the one with the lower read depth using "macs2 randsample"
Filtered out all reads that lack a G>A or T>C mutation (for 6SG or 4SU-pulsed samples, respectively)
Peaks called with: "macs2 callpeak --nomodel -q $q --extsize 32 --shift 0 --keep-dup 5 -g hs" where $q is 0.0005 for WT samples, $q=0.05 for KO samples
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
For WT samples, peaks further screened with "awk '{if($1!="#" && $1!="chr" && $6>=3 && $8>=5) {print $1 "\t" $2-1 "\t" $3 "\t" $10 "\t" $6 "\t."}}' macs_called_peaks.xls > significant_peaks.bed" For KO samples, the if statement in the awk script is "if($1!="#" && $1!="chr" && $6>=1 && $8>=3)"
Genome_build: NL4-3 genome: 551-9626nt of GenBank AF324493.2
Genome_build: Human hg19
Genome_build: tRNA sequences from tRNAdb (Juhling Morl 2016)
Genome_build: rRNA: GenBank #U13369 nts 7935-12969, X03205, and U13369 nts 6623-6779
Genome_build: snRNA: NC_000001.11:c16514285-16514122, NC_000017.11:c43233977-43233790, NC_000012.12:c120293237-120293094, NC_000015.10:65296051-65296167, NC_000015.10:c67840045-67839940, NC_000001.11:28648600-28648734, NC_000022.11:42615244-42615393, NC_000002.12:121530880-121531009, NC_000009.12:c134164564-134164440, all from GRCh38.p13
Supplementary_files_format_and_content: bed files, aligned to hg19, HIV-1 NL4-3 genome, or tRNA, rRNA, snRNA sequences

organism: Homo sapiens

source_name: ΔTrub1 293T

extract_protocol:
PA-Ψ-seq or PA-m6A-seq (PAR-CLIP done with a pasudouridine or m6A RNA targeting antibody)
All samples were processed with the NEB Next small RNA-seq library prep kit for Illumina

tag: virus strain

value: HIV-1 NL4-3

tag: technique

value: PA-Psi-Seq

tag: pulldown antibody

value: anti-pseudouridine (anti-Psi) (MBL #347-3)


title: CD ertugliflozin 2

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description:
Left ventricular tissue obtained from an animal fed a control diet and treated with ertugliflozin.
WC_CD-ERTU-6

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.6.0c).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 92 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Regularized logarithmic (rlog) transformation was accomplished using the rlog() function in the DESeq2 R package (version 1.22.1).
Genome_build: mm10
Supplementary_files_format_and_content: count, rlog

source_name: left ventricle of heart

growth_protocol: 8 week old C57BL/6J male mice were fed either a control low fat diet (CD) +/- Ertugliflozin or a high fat high sucrose (HFHS) diet +/- Ertugliflozin (drug formulated into diet, 0.5 mg/g) for 4 months

extract_protocol:
Snap frozen left ventricular tissue was ground with mortar & pestle into a fine powder under liquid nitrogen, and RNA was extracted with Qiagen RNeasy Universal Mini kit with on-column DNAse digest.
Libraries were prepared from 250 ng total RNA input, enriched for mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module, and the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (New England Biolabs, USA).

treatment_protocol: Mice were fed diet +/- drug ad libitum for 4 months.

tag: diet

value: control diet (CD)

tag: drug

value: ertugliflozin

tag: group

value: CD ertugliflozin


title: CD untreated 4

description:
Left ventricular tissue obtained from an animal fed a control diet and left untreated.
WC_CD-4

value: untreated

value: CD untreated


title: LT27

description: 4 Months old mouse striatum-Ct


title: After 1 day of incubation from non-inoculated roots; Bio. Rep. 3

city: Bremen

first: Barbara

last: Reinhold-Hurek

state: Bremen

address: Leobener Str. 5

department: Microbe-Plant Interactions

country: Germany

institute: University of Bremen

description: RNA isolated after one day of incubation from non-inoculated rice roots; Biological Replicate 3

data_processing:
Generated libraries were sequenced on an Illumina NextSeq 500 platform (Illumina, Inc., USA) where 150-bp paired-end reads were generated.
Raw reads were then filtered, trimmed (PHRED > 33) and mapped (minimal length fraction of 1, and minimal similarity fraction of 0.98) onto IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare genome using CLC Genomics Workbench 8.5.1 (Qiagen, Germany)
In order to perform differential gene expression analysis, raw read counts were then extracted from CLC software and analyzed using the DEseq2 package from Bioconductor in R-studio (http://www.rproject.org) based on the protocol (Anders et al., 2013). Genes were considered as differentially regulated (DEG) when the expression levels exhibited FDR < 0.05 and the fold change (FC) ³ 1.5.
Genome_build: IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

organism: Oryza sativa Japonica Group

source_name: 6 rice roots, non-inoculated (sterile)

growth_protocol: Surface sterilization of dehusked rice caryopsis was carried out as described by Hurek et al., 1994. For germination, seeds were then transferred into GA7 Magenta boxes (Sigma-Aldrich, USA) filled with 100 ml of solid plant medium (Egener et al., 1999), supplemented with 8 g per l Bacto Agar, 20 mg of neutralized DL-malic acid per l and a potassium phosphate buffer (0,439 g KH2PO4, 0,561 g K2HPO4 at pH 6.8), and incubated at 300C in the dark for three days, and in light in the phytotron (at 30°C, at 80% humidity and with a 14-h-day and 10-h-night cycle at approximately 100 μmol photons m–2 s–1) for one day. Then, one day before inoculation with bacteria, seedlings were transferred into hydroponic cultures: they were placed on top of metal mash adaptors in 200 x 30,00 x 1,1-1,2 mm glass tubes containing 50 ml of liquid plant medium (as described above but without addition of Bacto agar) and transferred back to the phytotron for an additional 24 h incubation. Certain modifications in the composition of the liquid plant medium were made according to the experimental set-up: for the boosted-colonization, liquid plant medium was supplemented with 400 mg of neutralized DL-malic acid per l instead of 20 mg, and for ammonia-containing controls 68 mg per l (NH4)2SO4 was added.

extract_protocol:
In order to extract total RNA, six rice roots were pooled together and the protocol of RNeasy Plant Mini Kit (Qiagen, Germany) was followed. Afterward, RNA quality and purity were evaluated via NanoDrop 2000 (Thermo Fisher Scientific, USA) and Agilent Bioanalyzer 2100 system (Agilent Technologies, USA), and only RNA samples with an RNA integrity number >8 were chosen for further analysis.
mRNA fraction was purified from 1 μg of the total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) and libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s recommendations. Quality of prepared libraries was assessed using Agilent Bioanalyzer 2100 system and quantity via NEBNext Library Quant Kit for Illumina (NEB, USA).

treatment_protocol: Parallel to seed preparation, bacterial cells of Azoarcus olearius BH72 or mutant strains were grown until the late exponential growth phase (optical density at 578 nm [OD578nm] = 1.0 to 1.2), washed in an N-free medium (Egener et al., 1999), and directly added to hydroponic cultures to yield an optical density of 0.067. Inoculated plants were then incubated in the phytotron for one, three or seven days depending on the experimental set-up.

tag: tissue

value: total root

tag: age

value: 6 days after planting the seeds

tag: concentration of carbon source in the medium

value: 20 mg/L of neutralized DL-malic

tag: days of incubation

value: 1 day

tag: treatment

value: non-inoculated plants


title: After 1 day of incubation from non-inoculated roots; Bio. Rep. 2

description: RNA isolated after one day of incubation from non-inoculated rice roots; Biological Replicate 2

value: Oryza sativa ssp. japonica cv. Nipponbare


title: 293T virion 6SG PA-Ψ-Seq


title: CD untreated 3

description:
Left ventricular tissue obtained from an animal fed a control diet and left untreated.
WC_CD-3


title: RB26

description: 4 Months old mouse striatum-Ct


title: ΔTrub1 293T cellular 6SG PA-Ψ-Seq

description:
Cell extract polyA+ RNA
Aligned to hg19


title: LT4

description: 4 Months old mouse striatum-Ct


title: RB8

description: 4 Months old mouse striatum-Ct

value: C/N-TAF MiRNA


title: CD untreated 1

description:
Left ventricular tissue obtained from an animal fed a control diet and left untreated.
WC_CD-1


title: TT3

description: 4 Months old mouse striatum-Ct


title: 1 day after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 2

description: RNA isolated one day after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 2

source_name: 6 rice roots, colonized with Azoarcus olearius BH72

value: plants inoculated with Azoarcus olearius BH73


title: ΔTrub1 293T cellular 4SU PA-Ψ-Seq

description:
Cell extract polyA+ RNA
Aligned to hg19


title: 1 day after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 1

description: RNA isolated one day after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 1

value: plants inoculated with Azoarcus olearius BH72


title: TT6

description: 4 Months old mouse striatum-Ct

value: control miRNA


title: Retina P16 Zfp36l1/2 DKO rep 4

city: Buffalo

first: Xiuqian

last: Mu

address: 701 Ellicott Street

department: Ophthalmology

institute: University at Buffalo

data_processing:
Illumina RTA (real-time analysis software) version 2.4.11 was used for basecalling, and Illumina bcl2fastq 2.20.0.422 was used for demultiplexeing.
The sequence reads were mapped to the mouse genome (mm10) along with the GENCODE M20 using STAR v2.6.1d with ENCODE Standard options.
Gene expression quantification was performed by using RSEM v1.3.1 with parameters --paired-end --strandedness reverse --alignments --estimate-rspd --calc-ci --seed 12345 --ci-memory 30000.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM quantification output

source_name: Retina

extract_protocol:
Neural retinas from different devlopmental stages were dissected out in cold PBS, soaked in RNAlater, and preserved at -80 degree. Total RNA was isolated/purified using the miRNeasy Mini Kit (Qiagen, 217004) along with on-column digestion of DNA with RNase-Free DNase Set (Qiagen, 79254) following the manufacturers’ instructions. RNA quality and quantity were assessed by a BioAnalyzer (Agilent, G2940CA).
The samples were then used to generate sequencing libraries with TruSeq RNA Sample Prep Kit v2 kit (Illumina, RS-122-2001) and paired-end sequenced on an Illumina HiSeq 2500 sequencer.

tag: background strain

value: retina

value: postnatal day 16

tag: genotype

value: Zfp36l1 F/F; Zfp36l1 F/F; Vsx2-Cre


title: 1 day after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 3

description: RNA isolated one day after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 3

value: plants inoculated with Azoarcus olearius BH74


title: CD untreated 2

description:
Left ventricular tissue obtained from an animal fed a control diet and left untreated.
WC_CD-2

value: control diet (CD)


title: ΔPus1 293T cellular 4SU PA-Ψ-Seq

description:
Cell extract polyA+ RNA
Aligned to hg19

source_name: ΔPus1 293T

value: HIV-1 NL4-3

value: PA-Psi-Seq

value: anti-pseudouridine (anti-Psi) (MBL #347-3)


title: Retina P16 Zfp36l1/2 DKO rep 2


title: Retina P16 Zfp36l1/2 DKO rep 3


title: XW022

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq.
fastq sequences were aligned to mm10 using Tophat.
Number of reads was calculated for each Entrez gene.
Differential expression analysis was performed using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Wei_and_Phoenix_GEO_processed.txt: Tab-delimited text file includes raw counts with genes in rows and samples in columns.

source_name: Brainstem vasculature

growth_protocol: GFP-positive regions of primary mouse tumor samples were microdissected and CD45-negative / CD31-positive vascular fragments and cells were isolated by MACS column sorting of dissociated tissue. For normal brain tissue the meninges were removed and CD45-negative / CD31-positive vascular fragments and cells were isolated by MACS column sorting of dissociated tissue.

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel) and processed as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: WT

value: Brainstem


title: XW023


title: RT1

description: 4 Months old mouse striatum-Ct

value: 4 Months old mouse striatum-Ct


title: 293T cellular 6SG PA-Ψ-Seq_i8

description:
Cell extract polyA+ RNA
Aligned to hg19


title: ΔPus1 293T virion 6SG PA-Ψ-Seq


title: Retina P16 Zfp36l1/2 DKO rep 1


title: After 1 day of incubation from non-inoculated roots; Bio. Rep. 1

description: RNA isolated after one day of incubation from non-inoculated rice roots; Biological Replicate 1

value: total root

value: 6 days after planting the seeds

value: 20 mg/L of neutralized DL-malic

value: 1 day

value: non-inoculated plants


title: After 3 days of incubation from non-inoculated roots; Bio. Rep. 2

description: RNA isolated after three days of incubation from non-inoculated rice roots; Biological Replicate 2

value: Oryza sativa ssp. japonica cv. Nipponbare

value: 8 days after planting the seeds

value: 3 days


title: Retina P16 Zfp36l1/2 F/F rep 4

value: retina

value: postnatal day 16

value: Zfp36l1 F/F; Zfp36l1 F/F


title: Pancreatic islets cells db/db Sham sample 2

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München

description:
MUC13639_Islets_539_Hom_Sham
RNA-Seq (10X Genomics)

data_processing:
The 10X Genomics core computational software Cellranger v.3.1.0 was used for alignment and processing of next-generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Cellranger filtered UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. Tar archives contain count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.

source_name: Pancreatic islets cells

extract_protocol:
Islets were freshly isolated using collagenase and subsequent gradient centrifugation. Islets were dispersed into single-cells using TrypLE.
Single cell libraries were generated using the ChromiumTM Single cell 3' GEM, library and gel bead kit v3 (#1000075) from 10x Genomics. Libraries were sequenced on the NovaSeq6000 (Illumina) with 150bp paired-end sequencing.

treatment_protocol: Mice underwent VSG surgery, Sham surgery (Control) and Sham surgery + pair-feeding (calorie restriction control). Study end was 14 days after surgery.

tag: cell type

value: Pancreatic islets cells

value: db/db hom

value: BKS

tag: Sex

value: Male

value: 16-18 weeks

tag: treatment group

value: Sham


title: 293T cellular 4SU PA-Ψ-Seq_i4

description:
Cell extract polyA+ RNA
Aligned to hg19

value: HIV-1 NL4-3

value: PA-Psi-Seq

value: anti-pseudouridine (anti-Psi) (MBL #347-3)


title: XW020

source_name: Cerebellum vasculature

value: WT

value: Cerebellum


title: RB2

description: 4 Months old mouse striatum-Ct

tag: injection group

value: control miRNA

tag: strain

tag: age of injection


title: XW021

value: Brainstem


title: 293T virion 6SG PA-Ψ-Seq_i4

tag: virus strain

tag: technique

tag: pulldown antibody


title: ΔPus1 293T cellular 6SG PA-Ψ-Seq

description:
Cell extract polyA+ RNA
Aligned to hg19


title: XW019


title: Retina P16 Zfp36l1/2 F/F rep 3


title: Pancreatic islets cells db/db VSG sample 2

description:
MUC13640_Islets_1518_Hom_VSG
RNA-Seq (10X Genomics)

value: VSG


title: Retina P16 Zfp36l1/2 F/F rep 2

value: retina


title: XW018


title: Retina P5 Zfp36l1/2 DKO rep 4

value: postnatal day 5

value: Zfp36l1 F/F; Zfp36l1 F/F; Vsx2-Cre


title: XW015

source_name: Cortical vasculature

value: Cortical


title: 293T cellular 6SG PA-Ψ-Seq_i1

description:
Cell extract polyA+ RNA
Aligned to hg19


title: FE380_ECOLI_536_1

city: Berlin

first: Oliver

last: Nagel

address: Hindenburgdamm 30

department: Department of Gastroenterology, Rheumatology and Infectious Diseases

institute: Charité - Universitätsmedizin Berlin

data_processing:
Basecalling: Casava 1.8
Readmaping: STAR 2.7.1a, two pass mode, default parameters
count reads: Rsubread 1.37.4
differential expression analysis: DESeq2 v 1.24.0
Genome_build: GRCh38 release 97
Supplementary_files_format_and_content: csv, raw read count

source_name: Caco-2_HlyA-positive E. coli 536

growth_protocol: Confluent Caco-2 cell monolayers grown 2 weeks on PCF filters

extract_protocol:
mirVanaTM miRNA Isolation Kit
Illumina Nextera XT DNA sample preparation protocol

treatment_protocol: Infection from the apical side with HlyA-positive E. coli 536 or HlyA-deficient mutant (HDM) or uninfected control for 5 hours

tag: cell line

value: colorectal adenocarcinoma cell line

value: HlyA-positive E. coli 536


title: Pancreatic islets cells BKS WT sample 2

description:
MUC13634_Islets_937-8_WT_Chow
RNA-Seq (10X Genomics)

value: Pancreatic islets cells

value: db/db WT

value: BKS

value: Male

value: WT-Control


title: Pancreatic islets cells db/db VSG sample 1

description:
MUC13642_Islets_1137_Hom_VSG
RNA-Seq (10X Genomics)

value: db/db hom

value: 16-18 weeks


title: Retina P16 Zfp36l1/2 F/F rep 1

tag: tissue

value: postnatal day 16

value: Zfp36l1 F/F; Zfp36l1 F/F


title: Pancreatic islets cells db/db Sham sample 1

description:
MUC13641_Islets_768_Hom_Sham
RNA-Seq (10X Genomics)

tag: age

value: Sham


title: FE381_ECOLI_536_2


title: Pancreatic islets cells db/db PF sample 1

description:
MUC13632_Islets_1513_Hom_PF
RNA-Seq (10X Genomics)

value: PF


title: Retina P5 Zfp36l1/2 DKO rep 3

value: retina


title: XW012

value: WT


title: XW013


title: Pancreatic islets cells BKS WT sample 1

description:
MUC13633_Islets_942-1_WT_Chow
RNA-Seq (10X Genomics)


title: 3 days after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 1

description: RNA isolated three days after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 1

value: Oryza sativa ssp. japonica cv. Nipponbare

value: total root

value: 8 days after planting the seeds

tag: concentration of carbon source in the medium

value: 20 mg/L of neutralized DL-malic

value: 3 days

value: plants inoculated with Azoarcus olearius BH72


title: FE378_ECOLI_HDM_2

source_name: Caco-2_HlyA-deficient mutant

value: colorectal adenocarcinoma cell line

value: HlyA-deficient mutant


title: FE379_ECOLI_HDM_3


title: FE377_ECOLI_HDM_1


title: CreTW

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

institute: University of Cologne

data_processing:
Cell Ranger
pipeline Version3.1.0
Chemistry Single Cell 3'v3
Transcriptome mm10-3.0.0

source_name: isolated chondrocytes from femur head cartilage of Col2CreTW mice

extract_protocol:
Isolated PFE cartilage was chopped and incubated at 37°C under constant rotation (HBMSUV-14 Hybaid Hyberization Oven Maxi 14, Mount Holly, USA) using collagenase P solution (1.61U/ml collagenase P (Roche Diagnostics GmbH; Mannheim; Germany) in DMEM F12 (Life Techologies Europe B.V., Bleiswijk, Netherlands) containing 1% P/S (Life Techologies Europe B.V., Bleiswijk; Netherlands), 10% FCS (Biochrome GmbH, Berlin, Germany) and 0.1755mg/ml cystein (Sigma-Aldrich, St. Louis, USA). After 18 h, the cell-suspension was transferred through a 40µm cell strainer and washed with 1.5% BSA (Serva Electrophoresis GmbH, Heidelberg, Germany) in PBS (Life Technologies Limited, Paisley, UK). Cells were centrifuged at 400g for 5 min (Eppendorf Centrifuge 5415 R, Hamburg, Germany), resuspended in 200µl 1.5% BSA/PBS (200cells/µl) and cell viability (>90%) was confirmed by typan blue staining
cDNA was prepared according to the 10x Genomics Chromium Single Cell 3' Reagent Kit User Guide (v3  Chemistry) from the pool of  ~1.000 cells . At this point, all cDNA fragments carried the 16nt cellular barcode and the 12nt long Unique Molecular Identifiers (UMI) at the Poly (dT) end. 25% (10 µL) of this cDNA solution continued with the original 10x Genomics protocol to create an Illumina 3´mRNA library with P5 and P7 Illumina adapters.  Sequencing was done on Illumina NovaSeq6000 systems with a two step approach (to validate cell numbers, UMI count and saturation)
Single cell RNA Sequencing

value: Col2Cre+, Twinkle transgene+

tag: disease state

value: mitochondria dysfunction

value: chondrocytes

value: femur


title: Cre

source_name: isolated chondrocytes from femur head cartilage of Col2Cre mice

value: Col2Cre transgene+

value: control


title: XW010

source_name: DMG vasculature

value: Brainstem


title: XW009


title: FE376_CTRL_3

tag: treatment


title: Retina P5 Zfp36l1/2 DKO rep 1

tag: background strain

value: retina

value: postnatal day 5

value: Zfp36l1 F/F; Zfp36l1 F/F; Vsx2-Cre


title: FE375_CTRL_2


title: Retina P5 Zfp36l1/2 F/F rep 4

tag: genotype

value: Zfp36l1 F/F; Zfp36l1 F/F


title: Retina P5 Zfp36l1/2 F/F rep 2


title: XW006


title: FE374_CTRL_1

tag: cell type


title: Retina P5 Zfp36l1/2 DKO rep 2


title: 18465X51 14d Met+Leu 4

city: Salt Lake City

first: Micah

middle: J

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

description:
Aged male mice (22-24 mo)
18465X51

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 100.
The reference database was created using STAR version 2.7.3a with splice junctions optimized for 150 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCount output files combined into a single tab-delimited matrix

source_name: Gastrocnemius Muscle

extract_protocol:
Total RNA was isolated by homogenizing 25-30 mg gastrocnemius tissue with a handheld homogenizer in a solution containing Qiazol Lysis Reagent (Qiagen, cat# 79306). The RNA was separated and precipitated using chloroform and isopropanol. Extracted RNA was washed with ethanol then suspended in nuclease-free water. RNA concentration was determined using the EPOCH (Take3, BioTek) spectrophotometer. RNA isolated from gastrocnemius underwent DNase digestion using TURBOTM DNase (ThermoFisher, cat# AM2238) and was purified using RNA Clean and Concentrator 5 Columns (Zymo Research, cat# R1014).
Libraries were prepared with Illumina Stranded Total RNA Library Prep Ribo-Zero Gold Plus (Genome Builds mm10, M_musculus_Dec_2011, GRCm38) and RNA was sequenced using Illumina NovaSeq S4 Reagent Kit v1.5 150x150 bp Sequencing

treatment_protocol: Aged male mice were given metformin, leucine or a combination of metformin and leucine administered in their drinking water. Control mice received only drinking water.

value: Metformin and Leucine combo

tag: intervention

value: Hindlimb Unloading + 14d reloading

tag: Sex

value: male


title: XW007


title: 18465X50 14d Met+Leu 3

description:
Aged male mice (22-24 mo)
18465X50


title: XW002

source_name: pHGG vasculature

value: Cortical


title: Retina P0 Zfp36l1/2 DKO rep 4

value: postnatal day 0


title: XW005


title: 110045033_OV

city: South San Francisco

first: Venkataraman

last: Sriram

state: California

address: 2 Tower Place

institute: Pionyr Immunotherapeutics

data_processing:
Raw Fastqs were processed using the 10x Genomics' 3.0.2 Cellranger pipeline with default parameters.
Cellranger output from individual tumor samples (both mouse and human) was processed using the Seurat package (Butler et al., 2018) in R. Data was filtered to include cells that contained not more than 8500 UMI and expressed a minimum of 200 genes.  We also required that all genes be expressed in at least 3 cells and removed any cells that contained >20% of reads associated with mitochondrial genes or >45% of reads associated with ribosomal genes.  Filtered data were then normalized using a scaling factor of 10,000, nUMI, mitochondrial and rRNA % were regressed with a negative binomial model, and data was log transformed. The highly variable genes were selected using the FindVariableFeatures. Principal component analysis was performed using the top 2000 variable genes. Clustering was performed using the FindClusters function. UMAP and TSNE were used to project cells into two dimensions using varying numbers of principal components determined by visual inspection of scree plots. For T and myeloid reclustering analyses, each human tumor was subsetted to include only CD3E/CD3D+ clusters (pan T cell) and CD14+ (pan-macrophage/monocyte).  T and myeloid cell clusters were each updated to Seurat 3.01 and then combined using parallelized versions of the functions FindIntegrationAnchors and IntegrateData using the top 2000 most variable genes per tumor and top 30 canonical variates, in accordance with the Seurat website.
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: Sorted immune cells (Live/Dead, CD45+)

extract_protocol:
Sorted cells were processed using standard protocols associated with 10X Genomics Chromium Single Cell 3' Library and Gel Bead Kit V3
Libraries were constructed using standard protocols associated with 10X Genomics Chromium Single Cell 3' Library and Gel Bead Kit V3

tag: tumor stage

value: I-A

value: Untreated

value: Immune cells from human ovarian tumor


title: 200003216_HNC

value: III

value: Immune cells from human head and neck tumor


title: 200001001_LUNG

value: III-A

value: Immune cells from human lung tumor


title: 18465X48 14d RL Leucine 5

description:
Aged male mice (22-24 mo)
18465X48

tag: strain

value: Leucine


title: Retina P0 Zfp36l1/2 DKO rep 3

value: retina


title: 18465X49 14d Met+Leu 1

description:
Aged male mice (22-24 mo)
18465X49


title: XW001


title: 18465X52 14d Met+Leu 6

description:
Aged male mice (22-24 mo)
18465X52


title: XW003


title: 18465X46 14d RL Leucine 2

description:
Aged male mice (22-24 mo)
18465X46


title: Retina P5 Zfp36l1/2 F/F rep 3

value: postnatal day 5


title: Retina P0 Zfp36l1/2 DKO rep 1

value: Zfp36l1 F/F; Zfp36l1 F/F; Vsx2-Cre


title: 18465X45 14d RL Leucine 1

description:
Aged male mice (22-24 mo)
18465X45


title: 200001077_BRCA

value: Immune cells from human breast tumor


title: 121362435_KID

value: Immune cells from human kidney tumor


title: Retina P5 Zfp36l1/2 F/F rep 1

value: Zfp36l1 F/F; Zfp36l1 F/F


title: Retina P0 Zfp36l1/2 F/F rep 4


title: 121276262_EC

value: Immune cells from human endometrial tumor


title: zip4∆_Ecm11-His6FLAG3_ChIPseq_5h

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
zip4∆_Ecm11-FLAG_scaled.bw:  data processing steps #1 to #5
zip4∆_Ecm11-FLAG_scaled_notagsubtracted.bw:  data processing steps #1 to #6

library_source: genomic

data_processing:
Step#1:  Reads were aligned to the Saccer2 version (SGD June 2008) of the S. cerevisiae S288C genome, using Bowtie, allowing for 2 mismatches. Reads that matched more than once in the genome or matching to mitochondrial or ribosomal DNA were eliminated from further analysis.
Step#2:  Reads were also aligned to current version of the S. mikatae genome, using Bowtie, and default parameters. Among the aligned reads, those that did not align to S. cerevisiae genome were kept as the spike-in reads.
Step#3:  Reads that aligned to the S. cerevisiae genome but not to the S. mikatae genome were defined as the experimental reads.
Step#4:  Aligned paired-end reads from independent replicates were merged, generating a single Bam file.
Step#5:  Bam files were converted to big wig format using Deeptools, with a step of 1bp, a smoothing window size of 200 bp and a scaling factor "2" as follows: the number of experimental reads was first divided by the number of spike-in reads, giving scaling factor “1”. Then, the factor 1 of each sample was divided by the mean untagged sample coverage (290), giving scaling factor 2.
Step#6:  For each bigwig file obtained, the scaled untagged sample was subtracted from the scaled tagged sample
Genome_build: Saccer2
Genome_build: ASM16705v1
Supplementary_files_format_and_content: bigwile format files

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: 90% S. cerevisiae+10% S. mikatae meiotic cells t=5h

growth_protocol: For synchronous meiosis, cells were grown in SPS then transferred to sporulation medium. Cells were collected after five hours in sporulation medium.

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq procedure.
Libraries were sequenced on a NovaSeq6000 apparatus generating paired-end 100 bp reads.

treatment_protocol: 1. 10^9 cells were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and chromatin immunoprecipitation was performed as described (Sanchez et al Methods Mol Biol. 2021;2153:295-306).

value: zip4delta ECM11-His6FLAG3

tag: chip antibody

value: FLAG monoclonal antibody (M2, Sigma)

tag: tag


title: zip1∆_Ecm11-His6FLAG3_ChIPseq_5h

description:
zip1∆_Ecm11-FLAG_scaled.bw:  data processing steps #1 to #5
zip1∆_Ecm11-FLAG_scaled_notagsubtracted.bw:  data processing steps #1 to #6

value: zip1delta ECM11-His6FLAG3


title: Retina P0 Zfp36l1/2 F/F rep 3

value: postnatal day 0


title: 18465X44 14d RL Metformin 6

description:
Aged male mice (22-24 mo)
18465X44

value: Metformin

value: Hindlimb Unloading + 14d reloading

value: male


title: 18465X47 14d RL Leucine 4

description:
Aged male mice (22-24 mo)
18465X47


title: 18465X42 14d RL Metformin 2

description:
Aged male mice (22-24 mo)
18465X42


title: Retina P0 Zfp36l1/2 F/F rep 2


title: 18465X41 14d RL Metformin 1

description:
Aged male mice (22-24 mo)
18465X41


title: 200005529_CRC

value: II-C

value: Untreated

value: Immune cells from human colorectal tumor


title: Ecm11-His6FLAG3_ChIPseq_5h

description:
Ecm11-FLAG_scaled.bw:  data processing steps #1 to #5
Ecm11-FLAG_scaled_notagsubtracted.bw:  data processing steps #1 to #6


title: notag_ChIPseq_5h

description: notag_scaled.bw:  data processing steps #1 to #5


title: Retina P0 Zfp36l1/2 F/F rep 1

value: retina


title: 110042463_BLCA

value: I

value: Immune cells from human bladder tumor


title: 110045042_OV

value: III-C

value: Immune cells from human ovarian tumor


title: Retina E17.5 Zfp36l1/2 DKO rep 4

value: Embryonic Day 17.5

value: Zfp36l1 F/F; Zfp36l1 F/F; Vsx2-Cre


title: Tup1(S649F)-V5_ALPHA (input)

first: David

last: Stillman

address: 15 N Medical Drive East, EEJMRB

department: Pathology

institute: University of Utah

data_processing:
Fastq files were aligned to sacCer3 genome using Novocraft Novoalign (v4.0.2) with options to trim Illumina adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) and allow for one random multi-alignment. Each of two lanes were aligned separately and merged using samtools.
Replicate ChIP and corresponding Input Bam files were processed with Multi-Replicate Macs2 ChIPSeq Pipeline (version 14.1, https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq), with options to remove optical duplicates with pixel threshold of 1000, sub-sample duplicate fragments to 6%, exclude chrM and 2-micron chromosome, exclude custom high-copy intervals (telomeres and rDNA), depth-normalize to 1 million reads and average replicates, and call peaks using Macs2 (v. 2.1.0) with q-value cutoff of 3, peak size of 250 bp, peak gap of 50 bp, and depth scaling to empirically-derived value of 9M. Normalized paired-end fragment coverage files were saved as bigWig files.
Genome_build: sacCer3
Supplementary_files_format_and_content: Paired-end fragment coverage files in bigWig format after duplicate sub-sampling, high-copy region exclusion, replicate averaging, and depth normalization to 1 million reads.

source_name: log phase yeast cells

growth_protocol: Yeast cells were grown at 30°C in YPA medium (1% yeast extract, 2% bactopeptone, 0.002% adenine) supplemented with 2% dextrose to an OD660 of 0.7 to 0.9. Cells were cross-linked in 1% formaldehyde overnight at 4°C and quenched with the addition of 2.5M glycine to a final concentration of 125mM. Cells were harvested by centrifugation and washed twice in Tris-buffered saline and stored at -80°C.

extract_protocol:
Cells were resuspended in Lysis Buffer (0.1% deoxycholic acid, 1 mM EDTA, 50 mM HEPES pH 7.5, 140 mM NaCl, 1% Triton X-100, protease inhibitors) and lysed with ten 2-min rounds of bead beating with zirconia beads. Lysed cells were collected by centrifugation, washed once with Lysis Buffer and sonicated in fresh Lysis Buffer for 9 rounds of 30 seconds each with a Misonix sonicator, power level 3.5. Sonicated material was centrifuged, and supernatants were used for chromatin immunoprecipitations. Anti-mouse magnetic Dyna beads (Invitrogen) were prepared for immunoprecipitation by blocking with 1 mg/mL BSA overnight, followed by several hours of incubation with mouse anti-V5 antibody (Abcam). Normalized chromatin amounts were added to prepared Dyna beads and incubated overnight at 4°C with rotation. Beads were washed twice with Lysis Buffer, twice with Lysis Buffer supplemented up to 500 mM NaCl, twice with LiCl Wash Buffer (0.5% deoxycholic acid, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 10 mM Tris pH 8.0) and once with TE. Protein-DNA complexes were eluted from the beads with Elution Buffer (50 mM Tris pH 8.0, 1% SDS, 10 mM EDTA) and incubated at 65°C overnight to reverse cross-links. Multiple identical ChIPs from each cell sample replicate were combined and purified using the MinElute PCR purification kit (QIAGEN), per manufacturer’s instructions.
NEB Next ChIP-Seq with dual index primers

treatment_protocol: Not applicable

value: DY19746 - MATalpha tup1(S649F)-V5::HIS3MX

tag: strain background

value: log phase yeast cells


title: Retina E17.5 Zfp36l1/2 DKO rep 3


title: 18465X39 14d RL Control 4

description:
Aged male mice (22-24 mo)
18465X39

value: Water


title: Tup1(S649F)-V5_A (input)

value: DY19743 - MATa tup1(S649F)-V5::HIS3MX


title: Retina E17.5 Zfp36l1/2 DKO rep 2


title: 18465X38 14d RL Control 3

description:
Aged male mice (22-24 mo)
18465X38


title: Retina E17.5 Zfp36l1/2 DKO rep 1


title: Tup1-V5_ALPHA (input)

value: DY17938 - MATalpha TUP1-V5::HIS3MX


title: 18465X37 14d RL Control 1

description:
Aged male mice (22-24 mo)
18465X37

value: Hindlimb Unloading + 14d reloading


title: 18465X40 14d RL Control 5

description:
Aged male mice (22-24 mo)
18465X40

value: male


title: Retina P0 Zfp36l1/2 DKO rep 2

value: postnatal day 0


title: Retina E17.5 Zfp36l1/2 F/F rep 4

value: Zfp36l1 F/F; Zfp36l1 F/F


title: 18465X35 7d RL Met+Leu 4

description:
Aged male mice (22-24 mo)
18465X35

value: Metformin and Leucine combo

value: Hindlimb Unloading + 7d reloading


title: 18465X36 7d RL Met+Leu 6

description:
Aged male mice (22-24 mo)
18465X36


title: Retina E17.5 Zfp36l1/2 F/F rep 3

value: retina


title: Tup1(S649F)-V5_ALPHA_rep2 (ChIP-Seq)

value: anti-V5 (SV5-Pk1; Abcam)


title: Tup1(S649F)-V5_ALPHA_rep3 (ChIP-Seq)


title: 18465X34 7d RL Met+Leu 3

description:
Aged male mice (22-24 mo)
18465X34


title: Retina E17.5 Zfp36l1/2 F/F rep 1


title: Retina E14.5 Zfp36l1/2 DKO rep 4

value: Embryonic Day 14.5


title: 18465X32 7d RL Leucine 5

description:
Aged male mice (22-24 mo)
18465X32

value: Leucine


title: Tup1(S649F)-V5_ALPHA_rep1 (ChIP-Seq)


title: Retina E14.5 Zfp36l1/2 DKO rep 3


title: Tup1(S649F)-V5_A_rep3 (ChIP-Seq)


title: 18465X31 7d RL Leucine 3

description:
Aged male mice (22-24 mo)
18465X31


title: 18465X33 7d RL Met+Leu 1

description:
Aged male mice (22-24 mo)
18465X33


title: Retina E17.5 Zfp36l1/2 F/F rep 2

value: Embryonic Day 17.5


title: 18465X30 7d RL Leucine 2

description:
Aged male mice (22-24 mo)
18465X30


title: Tup1(S649F)-V5_A_rep1 (ChIP-Seq)


title: Retina E14.5 Zfp36l1/2 DKO rep 2

value: Zfp36l1 F/F; Zfp36l1 F/F; Vsx2-Cre


title: Tup1-V5_ALPHA_rep3 (ChIP-Seq)


title: 110005709_GAST

value: II-A

value: Untreated

value: Immune cells from human gastric tumor


title: Retina E14.5 Zfp36l1/2 DKO rep 1


title: Tup1-V5_ALPHA_rep2 (ChIP-Seq)

value: log phase yeast cells


title: 18465X29 7d RL Leucine 1

description:
Aged male mice (22-24 mo)
18465X29


title: Retina E14.5 Zfp36l1/2 F/F rep 4


title: 18465X28 7d RL Metformin 4

description:
Aged male mice (22-24 mo)
18465X28

value: Metformin


title: Tup1(S649F)-V5_A_rep2 (ChIP-Seq)

value: DY19743 - MATa tup1(S649F)-V5::HIS3MX


title: 18465X27 7d RL Metformin 3

description:
Aged male mice (22-24 mo)
18465X27

value: male


title: Retina E14.5 Zfp36l1/2 F/F rep 1


title: Retina E14.5 Zfp36l1/2 F/F rep 3


title: Tup1-V5_ALPHA_rep1 (ChIP-Seq)

value: DY17938 - MATalpha TUP1-V5::HIS3MX


title: Retina E14.5 Zfp36l1/2 F/F rep 2

value: Zfp36l1 F/F; Zfp36l1 F/F


title: Tup1-V5_A_rep1 (ChIP-Seq)

value: DY17937 - MATa TUP1-V5::HIS3MX


title: 18465X25 7d RL Metformin 1

description:
Aged male mice (22-24 mo)
18465X25

value: Hindlimb Unloading + 7d reloading


title: tup1(S649F)_ALPHA_rep3 (RNA-Seq)

description:
RNASeq_counts.txt
tup1-S649F_ALPHA.unique.rpm.bw

data_processing:
Optical duplicate reads were removed from the Fastq file using BBmap clumpify (version 38.34) and a pixel distance of 10000. Fastq files were then stripped of adapter sequences using Cutadapt (version 2.8) with sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, allowing for a minimum overlap of 6 bp and mimum acceptable read length of 20.
Trimmed sequences were aligned to the genome using STAR (version 2.7.3) using gene annotation as an index guide with splice junction overlap of 49 bp.
Replicate-mean, normalized-depth, unique-alignment, coverage files were generated with BioToolBox bam2wig application (version 1.69) using the options --smartcov --mean --rpm --nosecondary.
Gene counts were collected with Subread featureCounts (version 1.6.3) and a custom annotation file with UTRs defined and no dubious genes (https://github.com/tjparnell/biotoolbox-nucleosome/blob/master/yeast_positioned_nucleosomes/SacCer3_R64_all_genes_NoDubious_UTR_chromo.gff3.gz), allowing for paired alignments (option -p), reverse strand (option -s 2), and assignment to features with the largest overlap.
Genome_build: SacCer3 or R64-1-1
Supplementary_files_format_and_content: Replicate-mean, normalized-depth, unique-alignment, coverage bigWig files. Raw alignment counts for genes in a tab-delimited text file.

growth_protocol: Yeast cells were grown at 30°C in YPA medium (1% yeast extract, 2% bactopeptone, 0.002% adenine) supplemented with 2% dextrose to an OD660 of 0.6 to 0.8. Cells were harvested by centrifugation, snap frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Cells were resuspended in TES (10mM Tris, pH 7.5, 10mM EDTA, 0.5% SDS) and phenol-chloroform-isoamyl alcohol (25:24:1) and treated at 65°C for 1 hour with agitation. Samples were spun, and the aqueous layer was removed to a new tube. A second phenol-chloroform-isoamyl alcohol extraction was performed, followed by a chloroform extraction. The final aqueous layer was spun through a 5.7M CsCl, 25mM NaOAc gradient at 30,000 rpm for 18 hours (Beckman Optima Tabletop Ultracentrifuge with MLA-130 rotor), and the RNA pellet was resuspended in 10mM Tris-HCl pH 7.5, 1mM EDTA, followed by precipitation with NaCl and EtOH. Samples were then further purified using the RNeasy kit (QIAGEN), per manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA Ribo-zero Gold Library Prep

value: DY19306- MATalpha tup1(S649F)


title: Nat_M_970.1

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
isolation: phenol-chloroform extraction and TRIzol
Nat_Liv_M

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32) (Bolger, Lohse, & Usadel, 2014). Illumina TruSeq3-PE primers, leading and trailing low quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads with at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e) (Dobin et al., 2013), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score MAPQ greater than 1 for genome-wide transcript counting. FeatureCounts (version 1.5.0) (Liao, Smyth, & Shi, 2014) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Genome_build: mm10
Supplementary_files_format_and_content: Read count for each gene in each library

source_name: mouse liver

growth_protocol: At 12-weeks and 39-weeks, mice were euthanized via CO2 and cervical dislocation. All vital organs, including liver, were collected and snap frozen in liquid nitrogen. A portion of the left lobe of the liver was fixed in 10% phosphate-buffered formalin for histological analyses.

extract_protocol:
RNA were isolated from one-quarter of snap frozen liver by using phenol-chloroform extraction and TRIzol (Invitrogen, CA, USA)
Total RNA (4 µg) was used as input for poly-A selection and mRNA-sequencing library synthesis using KAPA mRNA-Seq library synthesis kit and KAPA Single-Indexed adapter kit (Kapa Biosystems, Wilmington, MA, USA). Library quality control was conducted using Agilent 2100 Bioanalyzer system, High Sensitivity dsDNA Qubit system and NEBNext Library Quantification Kit (New England Biolab, Ipswich, MA, USA). Sequencing was performed on Nextseq 500 platform (Illumina, San Diego, CA).

tag: gender

value: mouse liver

value: CF1 females mated with B6SJL males


title: 18465X23 7d RL Control 3

description:
Aged male mice (22-24 mo)
18465X23

value: Water


title: Tup1-V5_A_rep3 (ChIP-Seq)

value: anti-V5 (SV5-Pk1; Abcam)


title: Tup1-V5_A_rep2 (ChIP-Seq)


title: 18465X26 7d RL Metformin 2

description:
Aged male mice (22-24 mo)
18465X26


title: tup1(S649F)_ALPHA_rep2 (RNA-Seq)


title: Nat_F_799.6

description:
isolation: phenol-chloroform extraction and TRIzol
Nat_Liv_F

value: female


title: 18465X21 7d RL Control 1

description:
Aged male mice (22-24 mo)
18465X21


title: Nat_M_777.5


title: Nat_F_797.6


title: tup1(S649F)_ALPHA_rep1 (RNA-Seq)


title: 18465X24 7d RL Control 4

description:
Aged male mice (22-24 mo)
18465X24


title: 18465X22 7d RL Control 2

description:
Aged male mice (22-24 mo)
18465X22


title: tup1(S649F)_A_rep3 (RNA-Seq)

description:
RNASeq_counts.txt
tup1-S649F_A.unique.rpm.bw


title: tup1(S649F)_A_rep2 (RNA-Seq)


title: Nat_F_708.4


title: 18465X20 HU Met+Leu 6

description:
Aged male mice (22-24 mo)
18465X20

value: Metformin and Leucine combo

value: Hindlimb Unloading


title: 18465X19 HU Met+Leu 5

description:
Aged male mice (22-24 mo)
18465X19


title: 18465X43 14d RL Metformin 5

description:
Aged male mice (22-24 mo)
18465X43

value: Hindlimb Unloading + 14d reloading


title: tup1(S649F)_A_rep1 (RNA-Seq)

value: log phase yeast cells


title: Nat_M_794.1


title: 18465X18 HU Met+Leu 4

description:
Aged male mice (22-24 mo)
18465X18


title: IVF_M_938.2

description:
isolation: phenol-chloroform extraction and TRIzol
IVF_Liv_M

value: CF1 females mated with B6SJL males using IVF protocol by Jackson Laboratory


title: IVF_M_698.2


title: 18465X16 HU Leucine 5

description:
Aged male mice (22-24 mo)
18465X16

value: Leucine


title: IVF_F_984.1

description:
isolation: phenol-chloroform extraction and TRIzol
IVF_Liv_F


title: WT_ALPHA_rep3 (RNA-Seq)

description:
RNASeq_counts.txt
WT_ALPHA.unique.rpm.bw

value: DY3420- MATalpha


title: WT_A_rep3 (RNA-Seq)

description:
RNASeq_counts.txt
WT_A.unique.rpm.bw

value: DY150 - MATa


title: 18465X17 HU Met+Leu 1

description:
Aged male mice (22-24 mo)
18465X17

value: male


title: IVF_M_734.3


title: WT_ALPHA_rep2 (RNA-Seq)


title: 18465X14 HU Leucine 2

description:
Aged male mice (22-24 mo)
18465X14


title: WT_ALPHA_rep1 (RNA-Seq)


title: WT_A_rep1 (RNA-Seq)

description:
RNASeq_counts.txt
WT_A.unique.rpm.bw


title: 18465X15 HU Leucine 3

description:
Aged male mice (22-24 mo)
18465X15


title: 18465X12 HU Metformin 4

description:
Aged male mice (22-24 mo)
18465X12

value: Metformin


title: IVF_F_734.1


title: WT_A_rep2 (RNA-Seq)

description:
RNASeq_counts.txt
WT_A.unique.rpm.bw


title: IVF_F_906.5


title: 18465X13 HU Leucine 1

description:
Aged male mice (22-24 mo)
18465X13


title: BBS1B

first: Liheng

last: Wang

address: 1150 Saint Nicholas Avenue, Room 234

department: Department of Medicine

institute: Columbia University Medical Center

description:
single cell mRNA sequencing
LW005

data_processing:
Cell ranger (v3.1.0, 10x) was employed with default parameters to process the scRNA-seq data.
The raw counts of scRNA-seq data were filtered and normalized using the “RISC” package (v 1.0.0)
The principle components(PC=18) were used for cell clustering, based on Louvain method of “igraph” package (v1.2.5), with neighbors set to 20
The “scanpy” package (v 1.5.1) was utilized to generate the stacked violin plot for cell type markers in Python environment (v 3.8.5)
Genome_build: Hg19--GRCh38

molecule: polyA RNA

source_name: iPSC-derived hypothalamic neurons

growth_protocol: Hypothalamic neurons were generated from iPSCs using our previous published protocol (Wang L et al. Differentiation of hypothalamic-like neurons from human pluripotent stem cells. J Clin Invest. 2015;125(2):796-808.)

extract_protocol:
At day 32 of differentiation, neurons were dissociated using the cell dissociation enzyme Accutase. Briefly, for each cell line, 1 ml of Accutase was added to one well of 6-well plate and incubated at 37 C for 2 min. Next, the Accutase was carefully removed, replaced with 1 ml of BrainPhys Neuronal Medium supplemented with N2 Supplement-A (StemCell Technologies) and B27 supplement minus vitamin A (N2 / B27 BrainPhys Neuronal Medium), and immediately dissociated by gently pipetting (15-20 times with P1000) using low retention and wide orifice tips (Rainin). The cell suspension was transferred into a 50 ml Falcon ® tube. The well was rinsed with an additional 6 ml of N2 / B27 BrainPhys Neuronal Medium in order to collect remaining cells and were subsequently also added to the tube. The suspension was centrifugated for 5 min at 300 g at room temperature. After centrifugation, the pellet was resuspended in 1 ml of N2 / B27 BrainPhys Neuronal Medium by gentle pipetting (10 times with P1000) using low retention and wide orifice tips, and then transferred to a low bind microcentrifuge tube (Fisher Scientific). The suspension was then spined for 5 min at 300 g at 4 C. After centrifugation, the pellet was resuspended in 100 or 200 µL of N2 / B27 BrainPhys Neuronal Medium initially by gentle pipetting with a P200 using low retention and wide orifice tips (Rainin) for 20-25 times followed by low retention and regular orifice tips (Rainin) for 10 times. Then, the suspension was diluted 1:2 with fresh medium and passed through a 40 µm cell strainer (Fisher Scientific) to obtain single cell suspension. Trypan Blue was used to determine number of viable cells. A viability between 60– 80% was obtained for all the samples. The single cell suspension for all the cell lines were kept on ice until use.
Libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kit v3 (10x Genomics Inc) and sequenced on an Illumina NovaSeq 6000.

value: BBS1M390R homo

value: Day 32 iPSC-derived hypothalamic neurons

value: Bardet-Biedl Syndrome


title: c-BBS1B

description:
single cell mRNA sequencing
LW001

value: Isogenic control--WT


title: skeletal muscle, Banded 4month #5

first: Andrew

last: Gibb

address: 3500 N. Broad St.

institute: Temple University

description: diffexp_feline_skeletal_band4mo_sham4mo.txt; diffexp_feline_skeletal_band4mo_band1mo.txt

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
High quality reads were mapped to felis_catus_9.0 whole genome using HISAT2 v2.1.0 and quantified using HTSeq v0.11.2
Differential expression was calculated using DESeq2 v1.22.2
Genome_build: felis_catus_9.0
Supplementary_files_format_and_content: tab delimited format contains log2 fold change between experimental and control groups (Differential Expression Analysis)

organism: Felis catus

source_name: feline skeletal muscle

extract_protocol:
Total RNA was harvested from cells using a Qiagen RNA Isolation kit. Illumina TruSeq stranded mRNA Library Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: skeletal muscle

value: Aortic Banding

tag: condition

value: feline model of HFpEF

tag: time

value: 4 months


title: Bcor-/-Dnmt3a-/- (886P) MEP

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description:
MEP_3A_BCOR_Cre_2
mRNA-seq
MEP_genes_fpkm.txt

data_processing:
Fastq files were aligned to mouse reference genome mm9 using STAR version 2.5.1b with the samattributes flags "NH HI NM MD nM XS".
Mapped bam files were indexed and sorted using samtools v1.9.
Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.2.1 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_genes_fpkm.txt: Tab-delimited text files of FPKM gene expression values.

source_name: MEP cells

growth_protocol: Mice were bred and housed by the “Service center of Preclinical Research” of Perugia’s animal house facility, and mouse manipulations were performed according to the protocol reviewed and approved by the Italian Health Ministry.

extract_protocol:
RNAs were extracted using RNeasy kit (Qiagen).
Libraries were prepared according to the Illumina RNA-seq library protocol.

treatment_protocol: LSK and MEP cells were isolated from BM using FACS Aria III cell sorting.

tag: genotype/variation

value: MEP-BM cells


title: NEC-Gyn-13

city: Cleveland

first: Ata

last: Abbas

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline
RNA-seq sequencing quality was checked by running FastQC and TrimGalore was used for dapter and quality trimming. RNA-seq reads were mapped against hg38 using STAR aligner.
Gene expression and other analyses were performed using DESeq2 and RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values.

source_name: Ovarian cancer

extract_protocol:
Tumor tsuues were separatted from the fixed slides/blocks after a pathologist's review and marking of the ares. Total RNA was extracted from the tumor tissues.
Strand-specific library was prepared using Illumina TruSeq stranded RNA library prep kit (Illumina, San Diego, CA) according to manufacturer’s protocols.

tag: histology

value: small cell

tag: type

value: Metastatic

tag: tissue site

value: Bladder peritoneal


title: skeletal muscle, Banded 4month #4

tag: tissue

tag: treatment


title: Bcor-/-Dnmt3a-/- (785P) MEP

description:
MEP_3A_BCOR_Cre_1
mRNA-seq
MEP_genes_fpkm.txt

tag: cell type


title: Dnmt3a-/- (8246R) MEP

description:
MEP_3A_XY_Cre_2
mRNA-seq
MEP_genes_fpkm.txt


title: 18465X10 HU Metformin 2

description:
Aged male mice (22-24 mo)
18465X10

tag: intervention

value: Hindlimb Unloading

tag: age


title: skeletal muscle, Banded 4month #2


title: NEC-Gyn-11

source_name: Cervical cancer

value: high-grade

value: Lung


title: NEC-Gyn-10

value: Primary

value: Cervix


title: skeletal muscle, Banded 4month #1


title: 18465X8 HU Control 4

description:
Aged male mice (22-24 mo)
18465X8

value: Water

tag: Sex

value: male


title: Dnmt3a-/- (244R) MEP

description:
MEP_3A_XY_Cre_1
mRNA-seq
MEP_genes_fpkm.txt

tag: strain


title: 18465X9 HU Metformin 1

description:
Aged male mice (22-24 mo)
18465X9

value: Metformin


title: 18465X7 HU Control 3

description:
Aged male mice (22-24 mo)
18465X7


title: Bcor-/- (111R_112R) MEP

description:
MEP_WT_BCOR_Cre_1
mRNA-seq
MEP_genes_fpkm.txt


title: 18465X6 HU Control 2

description:
Aged male mice (22-24 mo)
18465X6


title: 18465X11 HU Metformin 3

description:
Aged male mice (22-24 mo)
18465X11


title: skeletal muscle, Banded 1month #4

description: diffexp_feline_skeletal_band1mo_sham1mo.txt; diffexp_feline_skeletal_band4mo_band1mo.txt

value: 1 month


title: skeletal muscle, Banded 4month #3

value: skeletal muscle


title: NEC-Gyn-12


title: 18465X4 Ambulatory Control 5

description:
Aged male mice (22-24 mo)
18465X4

value: None - baseline control


title: wt (558Q)-MEP

description:
MEP_3A_XY_WT_3
mRNA-seq
MEP_genes_fpkm.txt


title: NEC-Gyn-08

value: Small cell

value: Small bowel nodule


title: skeletal muscle, Banded 1month #2

value: Aortic Banding

value: feline model of HFpEF


title: Dnmt3a-/- (898Q) MEP

description:
MEP_3A_XY_Cre_3
mRNA-seq
MEP_genes_fpkm.txt

value: MEP-BM cells


title: skeletal muscle, Banded 1month #5


title: NEC-Gyn-09

value: small cell


title: 18465X3 Ambulatory Control 4

description:
Aged male mice (22-24 mo)
18465X3


title: skeletal muscle, SHAM 4month #5

description: diffexp_feline_skeletal_band4mo_sham4mo.txt; diffexp_feline_skeletal_sham4mo_sham1mo.txt

value: SHAM

value: control

value: 4 months


title: skeletal muscle, Banded 1month #1


title: wt (245R)-MEP

description:
MEP_3A_XY_WT_1
mRNA-seq
MEP_genes_fpkm.txt


title: NEC-Gyn-04

value: Large cell

value: Primary


title: Dnmt3a-/- (8246R) LSK

description:
LSK_3A_XY_Cre_2
mRNA-seq
LSK_genes_fpkm.txt

source_name: LSK cells

value: LSK-BM cells


title: NEC-Gyn-07

value: High-grade

value: Metastatic

value: Ovary


title: Bcor-/- (113R) MEP

description:
MEP_WT_BCOR_Cre_2
mRNA-seq
MEP_genes_fpkm.txt


title: CT26_TREM2PD1

description: Treatment initiated when tumors were ~ 150 mm^3, Q5 dx2. Takedown occurred 48 hours after dose #2 of antibody.

value: BALB/c

value: anti-Trem1 + anti-PD1 mAbs

value: Immune cells from antiTrem2+antiPD1 treated CT26 tumors


title: skeletal muscle, SHAM 4month #3

value: skeletal muscle


title: Dnmt3a-/- (244R) LSK

description:
LSK_3A_XY_Cre_1
mRNA-seq
LSK_genes_fpkm.txt


title: NEC-Gyn-06

source_name: Endomaterial cancer

value: Endometrial


title: wt (251R)-MEP

description:
MEP_3A_XY_WT_2
mRNA-seq
MEP_genes_fpkm.txt


title: NEC-Gyn-01

value: Non-small cell


title: 18465X5 HU Control 1

description:
Aged male mice (22-24 mo)
18465X5

value: Water

value: Hindlimb Unloading

value: male


title: Dnmt3a-/- (898Q) LSK

description:
LSK_3A_XY_Cre_3
mRNA-seq
LSK_genes_fpkm.txt


title: Bcor-/-Dnmt3a-/- (785P) LSK

description:
LSK_3A_BCOR_Cre_1
mRNA-seq
LSK_genes_fpkm.txt


title: 18465X2 Ambulatory Control 3

description:
Aged male mice (22-24 mo)
18465X2

value: None - baseline control


title: 18465X1 Ambulatory Control 2

description:
Aged male mice (22-24 mo)
18465X1


title: Bcor-/- (113R) LSK

description:
LSK_WT_BCOR_Cre_2
mRNA-seq
LSK_genes_fpkm.txt


title: NEC-Gyn-05

value: Pelvic mass


title: Bcor-/-Dnmt3a-/- (886P) LSK

description:
LSK_3A_BCOR_Cre_2
mRNA-seq
LSK_genes_fpkm.txt


title: Tup1-V5_A (input)

value: DY17937 - MATa TUP1-V5::HIS3MX

tag: chip antibody

value: log phase yeast cells


title: skeletal muscle, SHAM 4month #2

value: SHAM

value: control

value: 4 months


title: NEC-Gyn-03

value: Small cell

value: Primary

value: Cervix


title: skeletal muscle, SHAM 4month #4


title: CT26_untreated

description: Pooled tumors (300 - 500 mm^3)

value: BALB/c

value: Untreated

value: Immune cells from untreated CT26 tumors


title: NEC-Gyn-02

value: Combined

value: Metastatic

value: Portal tumor


title: skeletal muscle, SHAM 1month #1

description: diffexp_feline_skeletal_band1mo_sham1mo.txt; diffexp_feline_skeletal_sham4mo_sham1mo.txt

value: skeletal muscle

value: 1 month


title: left ventricle, Banded 4month #5

description: diffexp_full_band4mo-sham4mo.txt; diffexp_heart_band4mo-band1mo.txt

source_name: feline left ventricle

value: left ventricle

value: Aortic Banding

value: feline model of HFpEF


title: skeletal muscle, SHAM 1month #3

value: SHAM


title: skeletal muscle, Banded 1month #3


title: wt (558Q)-LSK

description:
LSK_3A_XY_WT_3
mRNA-seq
LSK_genes_fpkm.txt

value: LSK-BM cells


title: CT26_PD1

value: anti-PD1 mAb

value: Immune cells from antiPD1 treated CT26 tumors


title: left ventricle, Banded 4month #4

value: 4 months


title: left ventricle, Banded 4month #3


title: B6: HSC, Osmr-/-

city: Brisbane

first: Jean-Pierre

last: Levesque

state: Queensland

address: 37 Kent St

department: Mater Research Institute

country: Australia

institute: Mater Research Institute-University of Queensland

data_processing:
Illumina NextSeq500 (NextSeq control software v2.2.0 / Real Time Analysis v2.4.11)
Analysis was performed using Galaxy Australia platform (usegalaxy.org.au )
Trimmomatic (Galaxy Version 0.36.6) : trim adaptor sequences
FastQC (Galaxy Version 0.72+galaxy1): quality control performed using FastQC. B4 was removed from differential expression analysis due to high GC content
HISAT2 (Galaxy Version 2.1.0+galaxy5): sequencing reads were then aligned to mouse reference genome, mm10
htseq-count (Galaxy Version 0.9.1): read counts
DESeq2 (Galaxy Version 2.11.40.6) : differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of tabular format including normalised counts, rlog and VST of each sample (except for B4) exported from DESeq2

source_name: hematopoietic stem cells

extract_protocol:
Femur, tibias and ilium were collected from naïve C57BL/6 or Osmr-/- mice and crushed and KIT+ cell-enriched. KIT+-enriched BM cells were then stained in suspension on ice for 40 minutes in mouse CD16/CD32 hybridoma 2.4G2 supernatant containing Lin-FITC antibody cocktail (CD3ε, CD5, B220, CD11b, Gr-1, Ter119), anti-SCA-1-PECY7, anti-KIT-APC, anti-FLT3-PECF594, CD48-PacBlue and CD150-PE. Dead cell were excluded using FVS-700. On thousand Lin- KIT+ SCA-1+ FLT3- CD48- cells were sorted per mouse using BD FACS Aria IIu cell sorter equipped with 405nm, 488nm, and 633nm lasers. Cells (contained in a9.5µL sheath fluid) were directly sorted into 1µL 10X lysis buffer containing RNAase inhibitors (SMART-Seq v4 kit) and frozen at -80ºC until further processing.
RNA from the thawed, lysed cells was reverse transcribed into cDNA and amplified using the SMART-Seq v4 Ultra Low Input RNA Kit. Between 13 and 18 cycles of PCR were used to amplify the cDNA, generating between 1 and 24 ng of cDNA for each sample.The purified cDNA was quantified on the Qubit fluorometer using the Qubit dsDNA HS assay kit (Invitrogen, Q32854) to assess concentration, and the Agilent Bioanalyzer 2100 using the High Sensitivity DNA kit (Agilent Technologies, 5067-4626). 0.15 ng of cDNA from each sample was used to prepare a library using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096), with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were purified with 30 µL (0.6x ratio) of AxyPrep Mag PCR Clean-up beads (Axygen, MAG-PCR-CL-250). Libraries were not normalized as described in the manufacturer’s protocol, instead the final libraries were quantified on the Perkin Elmer LabChip GX Touch with the DNA High Sensitivity Reagent kit (Perkin Elmer, CLS760672). Libraries were pooled in equimolar ratios.

value: hematopoietic stem cells

tag: source of bm

value: Femur, tibias and ilium

tag: genotype

value: Osmr-/-

tag: cell sorting markers

value: LKS+ FLT3- CD48-


title: B2: HSC, Osmr-/-


title: CT26_Isotype

value: BALB/c

value: Isotype mAb

value: Immune cells from Isotype treated CT26 tumors


title: Bcor-/- (111R_112R) LSK

description:
LSK_WT_BCOR_Cre_1
mRNA-seq
LSK_genes_fpkm.txt


title: skeletal muscle, SHAM 4month #1

value: skeletal muscle

tag: condition

value: control


title: left ventricle, Banded 4month #1

value: left ventricle

tag: time


title: wt (251R)-LSK

description:
LSK_3A_XY_WT_2
mRNA-seq
LSK_genes_fpkm.txt

tag: genotype/variation


title: Kupffer Cells + IL2 - rep3

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description:
Total sorted Kupffer Cells
kcPBS_kcIL2.counts.txt
kcPBS_kcIL2.tpm.txt

data_processing:
Reads were trimmed using the JAVA tool trimmomatic (V 0.32)
Raw reads were alignmed using STAR aligner V 2.5.3a
Read counts per gene calculated using the featureCounts function from the Rsubread package (V 1.32.4), based on GENCODE gene annotation M16
TPM values where calculated using an in-house script
Genome_build: GRCm38 (GENCODE)
Supplementary_files_format_and_content: Read counts per gene
Supplementary_files_format_and_content: TPM normalized gene expression levels

source_name: Kupffer Cells IL2

extract_protocol:
Cells were lysed in ReliaPrep™ RNA Cell Miniprep System (Promega #Z6011) and total RNA was isolated following manual extraction. DNA digestion was performed with TURBO DNA-free™ Kit (Invitrogen #AM1907).
SMART-seq Ultra Low Input 48 library protocol
NovaSeq 6000 SP Reagent Kit 100xSE (100 cycles)

treatment_protocol: Where indicated, mice were treated in-vivo with IL2 complexes. IL-2/anti-IL-2 complexes (IL-2c) were prepared by incubating 1.5 μg of rIL-2(402 ML/CF, R&D Systems #402 ML/CF) with 50 μg anti-IL-2 mAb (clone S4B6-1, BioXcell) per mouse, as previously described.

value: Kupffer Cells


title: A6: HSC, WT

value: WT


title: left ventricle, Banded 1month #3

description: diffexp_full_band1mo-sham1mo.txt; diffexp_heart_band4mo-band1mo.txt

value: Aortic Banding

value: feline model of HFpEF

value: 1 month


title: skeletal muscle, SHAM 1month #2

value: SHAM


title: Kupffer Cells + PBS - rep3

source_name: Kupffer Cells PBS

value: PBS


title: A4: HSC, WT

value: hematopoietic stem cells


title: Kupffer Cells + PBS - rep2


title: left ventricle, Banded 4month #2

value: 4 months


title: B4: HSC, Osmr-/-

value: Femur, tibias and ilium

value: Osmr-/-


title: CT26_TREM2

value: BALB/c

value: anti-Trem1 mAb

value: Immune cells from antiTrem2 treated CT26 tumors


title: left ventricle, SHAM 4month #5

description: diffexp_full_band4mo-sham4mo.txt; diffexp_full_sham4mo-sham1mo.txt


title: Kupffer Cells + PBS - rep1


title: A3: HSC, WT

value: LKS+ FLT3- CD48-


title: left ventricle, SHAM 4month #3

value: control


title: B3: HSC, Osmr-/-


title: B1: HSC, Osmr-/-


title: left ventricle, Banded 1month #5

value: left ventricle


title: left ventricle, Banded 1month #2


title: left ventricle, Banded 1month #1


title: wt (245R)-LSK

description:
LSK_3A_XY_WT_1
mRNA-seq
LSK_genes_fpkm.txt

value: LSK-BM cells


title: left ventricle, SHAM 4month #2


title: 2 MPI cells treated with 60 µg/cm^2 tremolite cleavage fragments

city: Morgantown

first: Timur

middle: Oskarovich

last: Khaliullin

state: WV

address: 1000 Frederick Lane

department: HELD

institute: NIOSH

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.TremoliteCF2

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software.
The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited txt file with the expression level (FPKM value) of known genes and transcripts for all samples

source_name: cell culture

growth_protocol: Cells were cultured in Roswell Park Memorial Institute (RPMI) medium with 10% fetal Bovine Serum (FBS), 1% L-glutamine (HyClone), 1% penicillin-streptomycin mixture (HyClone), and 30 ng/ml of mouse recombinant GM-CSF (R&D Systems). Humidified incubator (Fisher Scientific) at 37 °C and an atmosphere of 5% v/v CO2 was used.

extract_protocol:
Cells were washed with PBS, lysed with the TRIzol™ reagent and stored at -80˚ C in RNAse/DNAse-free tubes. RNA was purified using RNeasy MiniKits (Qiagen, Mississauga, ON, Canada), quantified using Thermo Scientific™ Nanodrop™ ND-1000 and qualified by agarose gel electrophoresis. The mRNA was enriched by oligo(dT) magnetic beads.
Illumina kits were used for the RNA-seq library preparation, which included procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification.

treatment_protocol: MPI cells in 6-well plates at the density of 1 x 10^6 cells per well, were washed with PBS and treated with the fibers surface area-equivalent (9 and 40 µg/cm^2 for riebeckite asbestos and CF, 5 and 60 µg/cm^2 for tremolite asbestos and CF) doses of asbestiform/non-asbestiform riebeckite or tremolite EMPs for 24 hours.

value: female

value: fetal liver

tag: agent

value: 60 µg/cm^2 tremolite cleavage fragments


title: 1 MPI cells treated with 60 µg/cm^2 tremolite cleavage fragments

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.TremoliteCF1


title: left ventricle, Banded 1month #4

value: Aortic Banding

value: feline model of HFpEF

value: 1 month


title: A5: HSC, WT

value: hematopoietic stem cells

value: WT


title: left ventricle, SHAM 4month #4

value: SHAM

value: 4 months


title: 3 MPI cells treated with 5 µg/cm^2 tremolite asbestos

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Tremolite3

value: 5 µg/cm^2 tremolite asbestos


title: B5: HSC, Osmr-/-

value: Femur, tibias and ilium

value: Osmr-/-


title: A2: HSC, WT

value: LKS+ FLT3- CD48-


title: left ventricle, SHAM 1month #3

description: diffexp_full_band1mo-sham1mo.txt; diffexp_full_sham4mo-sham1mo.txt

value: control


title: 3 MPI cells treated with 60 µg/cm^2 tremolite cleavage fragments

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.TremoliteCF3


title: Kuffer Cells + IL2 - rep1

value: Kupffer Cells


title: 3 MPI cells treated with 40 µg/cm^2 riebeckite cleavage fragments

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.RiebeckiteCF3


title: A1: HSC, WT


title: 24h 3

city: Punta Arenas

first: Alejandro

last: Font

state: Punta Arenas

address: Plaza Muñoz Gamero 1055

country: Chile

institute: Instituto Antartico Chileno

data_processing:
Galaxy platform
Trimmomatic
Trinity
Salmon
Supplementary_files_format_and_content: gene recount

organism: Glyptonotus antarcticus

source_name: full organism

extract_protocol:
EZNA total RNA extraction kit
Library preparation TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: RNAlater preservation

tag: developmental stage

value: juvenile

value: whole individuals

value: temperature at 5C

tag: samples

value: Pool of 3 individuals


title: 1 MPI cells treated with 40 µg/cm^2 riebeckite cleavage fragments

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.RiebeckiteCF1

value: female

tag: tissue

value: fetal liver


title: 3 MPI cells treated with 9 µg/cm^2 riebeckite asbestos

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Riebeckite3

value: 9 µg/cm^2 riebeckite asbestos


title: NSG_Non-Treatment_326_RNAseq

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

data_processing:
RNAseq:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
TCRseq:
Illumina MiSeq for TCRseq base calling
TCRseq reads were mapped and quantified using MiXCR
raw MiXCR outputs for all samples were analysis by tcR
Supplementary_files_format_and_content:
RNA-seq: Normalized count values for each sample
TCRseq: TRQ morisita index for all samples
Genome_build: mm10

source_name: NSG_bladder tumor_Vehicle

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
TCR libraries were prepared using SMARTer Mouse TCR a/b Profiling Kit (TaKaRa)

tag: host strain

value: NSG

tag: cell line source

value: bladder tumor

tag: treatment

value: Vehicle


title: NSG_Non-Treatment_323_RNAseq


title: 12h 3


title: left ventricle, SHAM 4month #1

value: left ventricle

value: SHAM

value: 4 months


title: NSG_Non-Treatment_308_RNAseq


title: NSG_Non-Treatment_311_RNAseq


title: 2 MPI cells treated with 9 µg/cm^2 riebeckite asbestos

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Riebeckite2


title: 12h 2


title: Kupffer Cells + IL2 - rep2

tag: cell type


title: NSG_Entinostat_306_RNAseq

source_name: NSG_bladder tumor_Entinostat

value: Entinostat


title: 12h 1


title: NSG_Non-Treatment_302_RNAseq


title: 1 MPI cells treated with 5 µg/cm^2 tremolite asbestos

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Tremolite1

tag: Sex

value: 5 µg/cm^2 tremolite asbestos


title: NSG_Baseline_320_RNAseq

source_name: NSG_bladder tumor_Baseline

value: Baseline


title: NSG_Entinostat_327_RNAseq


title: left ventricle, SHAM 1month #1

value: control

value: 1 month


title: 2 MPI cells treated with 5 µg/cm^2 tremolite asbestos

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Tremolite2

tag: strain


title: NSG_Baseline_316_RNAseq


title: left ventricle, SHAM 1month #2


title: 24h 2

value: juvenile

value: whole individuals


title: NSG_Baseline_305_RNAseq


title: 2 MPI cells treated with 40 µg/cm^2 riebeckite cleavage fragments

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.RiebeckiteCF2


title: NSG_Entinostat_319_RNAseq


title: NSG_Entinostat_315_RNAseq


title: NSG_Entinostat_312_RNAseq


title: 1h 3

value: temperature at 5C

value: Pool of 3 individuals


title: 426_Baseline_RNAseq

source_name: C57BL/6_bladder tumor_Baseline


title: scRNA-seq KO Tumor cells

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

description: scRNA-seq

data_processing:
Cellranger count was run to generate single cell feature counts from FASTQ files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text file, feature counts and indexes

source_name: Liver metastasized cancer cells after splenic injection of Dkk2 knockout colon tumor organoids carrying mutations in Apc, Kras and Tp53 genes.

growth_protocol: Organoid fragments were prepared as single cells following 10-30 min of digestion in TrypLE solution (Thermo, 12605010) at 37 °C, followed by centrifugation with advanced DMEM-F12 (Thermo, 12634010). The isolated single cells were re-suspended with PBS as 300,000 cells per 100 μl of PBS. Surgical instruments were sterilized by steam autoclave (250 degrees F., 15 p.s.i. for 30 minutes). 8-12 weeks old C57BL/6 mice were anesthetized with Ketamine (100 mg/kg) plus Xylazine (10 mg/kg) via intraperitoneal injection. Puralube Vet ointment was applied to the eyes to prevent drying while surgery. Spleen was divided by two Horizon medium size ligating clips (Teleflex, 002200) in the center of the spleen and one hemi-spleen was returned into the peritoneum. Using a 26-½ Gauge needle, 100-200 μl volume of cells was injected underneath of the splenic capsule over the course of 30s. A small Horizon clip (Teleflex, 001200) was applied to ligate the pancreas and splenic vessels and the injected hemi-spleen was removed. The incision was closed with a 5-0 running stitch using Vicryl (Ethicon, J493G) and 2-3 skin clips. Meloxicam (0.3 mg/kg) was injected subcutaneously to alleviate postsurgical pain at 24-72 h post-surgery.

extract_protocol:
Liver metastasized tumors were collected and dissociated in the digestion buffer containing 200 U/ml of type IV collagenase (Worthington, LS004188), 125 μg/ml of type II dispase (Sigma, D4693), 2.5 % fetal bovine serum, 1x Penicillin/Streptomycin in DMEM at 37 °C for 30-60 min with agitation. Isolated cells were centrifuged at 400 g and 4 °C for 5 min, then re-suspended in chilled PBS and filtered through the 40 μm pore size strainer. Epithelial marker gene (EpCAM) and transplanted organoid reporter gene (tdTomato) double positive tumor cells were sorted by flow cytometry for single cell RNA sequencing.
single cell RNA-seq library was generated using Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) following the manufacturer’s protocol.

value: Liver

value: Primary cancer cells


title: 1h 1


title: 24h 1


title: 6h 3


title: 1 MPI cells treated with 9 µg/cm^2 riebeckite asbestos

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Riebeckite1

value: female

value: fetal liver

value: 9 µg/cm^2 riebeckite asbestos


title: Control 24h, 3

value: Control


title: 6h 1


title: 421_Treated_RNAseq

source_name: C57BL/6_bladder tumor_Entinostat

value: bladder tumor


title: NSG_Baseline_303_RNAseq

value: NSG


title: Control 24h, 2


title: 6h 2


title: NSG_Baseline_304_RNAseq


title: Control 24h, 1


title: Control treated GEX

city: Durham

first: Erika

last: Crosby

address: 203 Research Dr. MSRBI Room 407

institute: DUKE UNIVERSITY MEDICAL CENTER

description: Gene expression library

data_processing:
Fastq files for paired-end reads and the index file for each samples was processed using 10X cellranger v 2.1.0 count program to generate an expression count matrix for TCR library for each sample.
Fastq files for paired-end reads and the index file for each samples was processed using Partek® Genomics Suite® software (version 9.0.20, Copyright ©; 2018 Partek Inc)
GEX files had tags trimmed and sequences were aligned to the mm10 reference genome (STAR aligner 2.6.1) and UMI counts were deduplicated and filtered to include only barcodes that corresponded to a cell.
Transcripts were quantified and single cell counts were filtered to include cells with total reads between 655-20,000; expressed genes 60-3,500; and a maximum of 10% mitochondrial reads.
Counts were normalized to counts per million and log(2) transformed. TCR genes were removed prior to performing PCA and graph-based clusters were assigned using the top 15 principle components.
Genome_build: mm10
Supplementary_files_format_and_content: 4T1_GroupA_S1.txt or 4T1_GroupC_S8.txt contains the following in columns: cellular barcode, gene expression, graph based cluster ID, cell classification ID, corresponding TCR (if applicable), treatment group
Supplementary_files_format_and_content: Meta-data-onlyTCR+_CD3_cells.txt contains the following in columns: cellular barcode, graph based cluster ID, cell classification ID, corresponding TCR, cel cycle info, treatment group, clonal expansion, exhaustion, activation, and CXCR3 signature scores

source_name: Tumor

growth_protocol: HER2 expression was induced in mammary tissues of one month old mice, spontaneous breast tumor growth were monitored weekly

extract_protocol:
Breast tumors were removed and processed into single cell suspensions as described in manuscript, and live single CD45+ cells were sorted.
10X Genomics gene expression and TCR libraries were generated using Chromium Single Cell 5’ Library Construction Kit (V1.1). A targeted cell recovery of 10,000 cells were used for each sample.
scRNA seq (10X Genomics), Single Cell 5' Gene Expression and TCR Libraries, 26x8x98 single i7 index. GEX sequenced on NovaSeq 6000 (500M PE-reads/sample) and TCR sequenced on MiSeq (1.5M PE-reads/sample)

treatment_protocol: Control or IL12 plasmid injected intratumorally followed by electroporation

value: Control plasmid


title: 1h 2


title: Vehicle_3_bulkRNAseq

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

country: China

institute: Sichuan University

data_processing:
Illumina sequencing workflow
Sequenced reads were mapped to GRCm38 whole genome using STAR v2.6.0 .
Transcripts Per Kilobase Million of library size (TPM) were calculated .
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files include TPM values for each Sample ...

source_name: bladder tumor organoids

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder tumor organoids

value: Vehicle treated


title: scRNA-seq Control Tumor cells

description: scRNA-seq

source_name: Liver metastasized cancer cells after splenic injection of colon tumor organoids carrying mutations in Apc, Kras and Tp53 genes.


title: 424_NonTreated_RNAseq

source_name: C57BL/6_bladder tumor_Vehicle

value: Vehicle


title: 3 Untreated MPI cells

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Control3


title: 2 Untreated MPI cells

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Control2


title: Vehicle_2_bulkRNAseq


title: 416_Baseline_RNAseq

value: Baseline


title: IL12 treated GEX

description: Gene expression library

value: IL-12 plasmid


title: 415_Baseline_RNAseq


title: 423_Treated_RNAseq

value: Entinostat


title: Vehicle_1_bulkRNAseq


title: 1 Untreated MPI cells

description:
mrna expression in the MPI cells 24 hours after treatment with various elongated mineral particles or vehicle control
MPI.Control1


title: EpiLC_Untreated_Rep3

city: Los Angeles

first: Steen

middle: Kian Thye

last: Ooi

state: CA

address: 621 Charles E. Young Drive S.

department: Institute for Society and Genetics

institute: UCLA

description:
2-24-EpiLC-Water-Rep2_S48_L004
2-24-EpiLC-Water-Rep2_S6_L001
2-24-EpiLC-Water-Rep2_S6_L002

data_processing:
Data quality check was performed using Illumina Sequencing Analysis Viewer (SAV) software
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.19.1.403 program
Fastq reads were checked for overall quality by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 using STAR (Dobin, 2013) with parameters --runThreadN 20 --readFilesCommand zcat --runMode alignReads --outFilterMultimapNmax 1 --outSAMtype BAM Unsorted --quantMode GeneCounts --twopassMode Basic
Read counts were obtained using HTSeq (https://htseq.readthedocs.io/en/master/) using the following commands: htseq-count --mode=union --stranded=no --idattr=gene_id -r pos -f sam
Output files were filtered to remove genes with 9 or fewer read counts, Gene counts were normalized using the trimmed mean of M-values normalization (TMM) method (Robinson, 2010) before determining counts per million (cpm) values
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: BVSC_H18_d5_cpm_FC_FDR.xlsx: Analysis of RNA-seq data from day 5 BVSC-H18 PGC like cells (PGCLCs) derived from either untreated or 100nM Bisphenol A exposed epiblast like cells (EpiLCs). Table shows trimmed mean of M-values (TMM)-normalised counts per million (cpm) of genes indicated. Note, data set pre-filtered to remove genes with a low number of reads (< 10 reads). In addition, columns show log10 fold-change, p-value and Benjamini-Hochberg adjusted p-value (FDR).

growth_protocol: BVSC ESCs were grown in 2i + LIF for 2-3 days, before harvesting and culturing in EpiLC Media. After 48 hours of culture, EpiLCs were harvested, counted and cultured in in U-bottom well plates in PGCLC media

extract_protocol:
For EpiLCs, cells were harvested using TrypLETM Select (ThermoFisher Scientific), before counting, pelleting and snap-freezing. For PGCLCs, Blimp1+Stella+ were FACS purified from TrypLETM Select dissociated aggregates.
Strand-specific RNA-seq libraries were prepared with Universal Plus mRNA-Seq kit (Nugen), according to the manufacturer’s protocol

treatment_protocol: For EpiLC exposure, 100nM BPA containing media was added 24 hours after seeding and cells were cultured for 24 hours.

tag: cell line

value: In vitro derived EpiLC

value: Blimp1-mVenus; Stella-ECFP (BVSC)

value: none (untreated)


title: SRT1720_3_bulkRNAseq

value: SRT1720 treated


title: 414_NonTreated_RNAseq


title: GF3_bi_2

city: Norwich

first: Wenbo

last: Ma

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

description:
3_3_S139_L005
Biological replicate 3, technical replicate 2

data_processing:
The quality of the raw sequencing data was checked with FastQC v0.11.9
Read adapters were trimmed from reads using Trimmomatic v 0.36
reads were aligned with the indexed CLas-Psy62 isolate genome assembly (NC_012985.3) and parsed to it using HISAT2 v2.1.0
The number of reads mapped to each gene was counted using the feature counts function of the Rsubread package
Read counts were normalized for each sample for differential expression analysis using DESeq2 v1.30.1
Genome_build: NC_012985.3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized read counts for every genes and every sample

organism: Citrus x paradisi

source_name: midrib

extract_protocol:
Freeze-dried HLB-infected midribs (from 15–25 leaves) were ground to a fine powder in liquid nitrogen. 1ml of TLE extraction buffer was added to 100 mg citrus powder or the pellet obtained after the above bacterial isolation. Then, 60 µL of 500 mM CaCl2 was added, mixed thoroughly, and placed on ice for 10 min. Centrifugation at 12,000 x g for 10 min at 4 °C was performed, followed by two rounds of separation with 500 µl of phenol:Chloroform:isoamyl alcohol (25:25:1) and centrifugation at 15,000 x g for 10 min at 4 °C. The supernatant was mixed with 2 M LiCl and incubated overnight at -20 °C. RNA was precipitated by centrifugation at 15,000 x g for 30 min, washed twice with ice-cold 75% ethanol, centrifuged at 15,000 x g for 15 min and re-suspended in 20 µl of RNAse-free water. 10–15 adult psyllids were ground in liquid nitrogen, immediately suspended in 50 μl TRIzol® (Invitrogen) and ground until complete homogenization. An additional 950 μl of TRIzol® was added to the homogenate, followed by separation with 200 µl of chloroform, precipitation with 500 µl of isopropanol, and two washes with 75% ethanol as indicated by the manufacturer. The pellet was resuspended in 20-30 µl of RNAse-free water.
RNA was converted into sequencing-ready libraries for Illumina sequencing using TruSeq Stranded Total RNA reagents. Poly(A) Polymerase (NEB) treatment (polyA) and Poly(dT)-depleted library construction was tested in parallel. cDNA libraries were subjected to RNASeq, using an Illumina HiSeq-4000 system with 150-bp strand-specific single-end reads with technical duplicates.

treatment_protocol: pre-enrichment (bacterial isolation) performed according to Nobori et al. 2018, 1-step post enrichment using MICROBEnrich, 2-step enrichment using MICROBEnrich followed byRiboMinus Eukaryote Kit. All samples underwent ribodepletion using Illumina Ribo-Zero Plus except a subset of 2-step enrichmed RNA samples that underwent poly(A) polymerase treatment (polyA)

tag: cultivar

value: C. paradisi Macfadyen (Ri Red grapefruit)

value: midrib

value: bacterial isolation pre-enrichment


title: 413_Treated_RNAseq


title: Control 1h, 3

value: juvenile

value: whole individuals

value: Control

value: Pool of 3 individuals


title: Control 1h, 2


title: GF3_bi_1

description:
3_3_S389_L006
Biological replicate 3, technical replicate 1


title: 408_NonTreated_RNAseq

value: bladder tumor


title: 419_Baseline_RNAseq


title: Kupffer Cells 2 - rep3

description:
Sorted Kupffer Cells were further divided based on low ESAM and CD206 surface markers (KC1) or high ESAM and CD206 (KC2)
kc1_kc2.counts.txt
kc1_kc2.tpm.txt

source_name: Kupffer Cells 2

treatment_protocol: Where indicated, mice were treated in-vivo with IL2 complexes. IL-2/anti-IL-2 complexes (IL-2c) were prepared by incubating 1.5 ug of rIL-2(402 ML/CF, R&D Systems #402 ML/CF) with 50 ?g anti-IL-2 mAb (clone S4B6-1, BioXcell) per mouse, as previously described.

value: Kupffer Cells with high ESAM and CD206 cell surface markers

value: untreated


title: Kupffer Cells 2 - rep2


title: 405_NonTreated_RNAseq

value: Vehicle


title: GF4_bi_2

description:
t1_3_S138_L005
Biological replicate 4, technical replicate 2


title: 418_Treated_RNAseq


title: 402_NonTreated_RNAseq


title: EpiLC_Untreated_Rep2

description:
2-EpiLC-Water-Rep2_S47_L004
2-EpiLC-Water-Rep2_S5_L001
2-EpiLC-Water-Rep2_S5_L002

tag: genotype


title: EpiLC_Untreated_Rep1

description:
1-EpiLC-Water-Rep1_S46_L004
1-EpiLC-Water-Rep1_S4_L001
1-EpiLC-Water-Rep1_S4_L002


title: SRT1720_2_bulkRNAseq

value: bladder tumor organoids


title: SRT1720_1_bulkRNAseq


title: Control 1h, 1


title: NF24 Suv4-20H1/2 rep3 (dataset4)

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
50 bp paired-end reads were mapped to the reference genome (X. tropicalis v9.0 available from Xenbase) using STAR (version 2.4.2a).
Genome_build: Xenopus tropicalis v9.0, http://ftp.xenbase.org/pub/Genomics/JGI/Xentr9.0/Xtropicalisv9.0.Named.primaryTrs.gff3.gz
Supplementary_files_format_and_content: Tab-separated text file: read counts per gene

organism: Xenopus tropicalis

extract_protocol:
RNA extraction was performed usingTRIzol (Ambion) and phenol/chloroform extraction. RNA clean-up and DNA digestion were performed with RNeasy Mini-Kit (Qiagen).  RNA quality was checked with an Agilent Bioanalyzer 2100 using Agilent RNA 6000 Pico Kit. rRNA was depleted using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina). rRNA depleted RNa was cleaned up using RNA Clean & ConcentratorTM-5 (Zymo Research).
Library preparation was performed using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (New England Biolabs) with NEBNext Multiplex Oligos for Illumina primer sets 1 and 2. DNA purification and size selection was performed using Agencourt AMPure XP (Beckman Coulter). Quality and size of the libraries were verified on the Agilent Bioanalyzer using Agilent DNA 1000 Kit.

tag: morpholino treatment

value: Suv4-20H1/2 morpholino

value: Suv4-20H1/2 knockdown

value: animal caps


title: GF4_bi_1

description:
t1_3_S388_L006
Biological replicate 4, technical replicate 1


title: GF2_bi_1

description:
2_2_S387_L006
Biological replicate 2, technical replicate 1


title: Kupffer Cells 1 - rep3

source_name: Kupffer Cells 1

value: Kupffer Cells with low ESAM and CD206 cell surface markers


title: 403_Treated_RNAseq

value: Entinostat


title: GF1_e2r

description:
G7T2_3_S118_L006
Biological replicate 1

value: C. paradisi Macfadyen (Ri Red grapefruit)

value: 2-step enrichment ribodepletion


title: Kupffer Cells 2 - rep1


title: NF24 CoMo rep3 (dataset4)

value: control morpholino (CoMo)

value: control


title: NF24 Suv4-20H1/2 rep1 (dataset4)


title: 410_NonTreated_RNAseq


title: Kupffer Cells 1 - rep2


title: GF2_bi_2

description:
2_2_S137_L005
Biological replicate 2, technical replicate 2

value: midrib

value: bacterial isolation pre-enrichment


title: nevus tissue 4 (1201244)

type: RNA

city: Xuzhou

first: Suwei

last: Dong

address: NO.32 Meijian RD

institute: The Second Affiliated Hospital of Xuzhou Medical University

description:
253816610054-2_3
Gene expression

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to AgilentHuman miRNA 8×60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B scanner (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: nevus tissue 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The miRNeasy FFPE Kit (Qiagen, Germany) was used to extract RNA from paraffin-embedded specimens.

value: nevus

tag: gender

value: male

tag: age


title: nevus tissue 3 (1202575)

description:
253816610054-2_2
Gene expression

source_name: nevus tissue 3


title: 411_Treated_RNAseq

value: bladder tumor


title: NF16 Suv4-20H1/2 rep2 (dataset4)


title: melanoma tissue 5 (11-2176)

description:
253816610054-1_4
Gene expression

source_name: melanoma tissue 5

value: melanoma

value: female


title: nevus tissue 1 (1202425)

description:
253816610053-2_4
Gene expression

source_name: nevus tissue 1


title: GF1_e1

description:
QM4_S286_L006
Biological replicate 1

value: 1-step enrichment


title: melanoma tissue 4 (11-1877)

description:
253816610054-1_3
Gene expression

source_name: melanoma tissue 4


title: Kupffer Cells 1 - rep1

value: untreated


title: nevus tissue 5 (1201179)

description:
253816610054-2_4
Gene expression

source_name: nevus tissue 5


title: GF1_e2a

description:
CL100125429_L2_HK500CITdpmRAAARAAPEI-505
Biological replicate 1

value: 2-step enrichment polyA


title: NF16 Suv4-20H1/2 rep1 (dataset4)

value: Suv4-20H1/2 morpholino

value: Suv4-20H1/2 knockdown

value: animal caps


title: NF24 CoMo rep2 (dataset4)


title: NF24 CoMo rep1 (dataset4)


title: NF24 Suv4-20H1/2 rep2 (dataset4)


title: T cells, J30_WT6

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

country: Canada

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 using STAR version 2.5.1b.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include rawcount values for each sample and normalized values determined by DESeq2 version 1.16.1 on R plateform.

source_name: CD8+CD44+Tet-gp33+ T cells

extract_protocol:
Mouse spleens were harvested and mechanically dissociated. CD8+CD44+Tet-gp33+ T cells were FACS-sorted and RNA was isolated using Trizol reagent.
Library preparation was done with the KAPA mRNAseq stranded library preparation kit (Roche).

treatment_protocol: Mice were infected i.v. with 2x10^6 PFU of LCMV clone 13 and spleens were harvested at day 8 or 30 post-infection.

tag: infection

value: LCMV clone 13

value: gp33-specific T cells

tag: time

value: 30 days


title: GF1_n

description:
QM3_S285_L006
Biological replicate 1

value: C. paradisi Macfadyen (Ri Red grapefruit)


title: T cells, J30_WT3


title: melanoma tissue 3 (12-0003)

description:
253816610054-1_2
Gene expression

source_name: melanoma tissue 3


title: NF10 Suv4-20H1/2 rep3 (dataset4)

tag: developmental stage


title: nevus tissue 2 (1202723)

description:
253816610054-2_1
Gene expression

source_name: nevus tissue 2


title: T cells, J30_WT5


title: T cells, J30_WT2


title: NF10 Suv4-20H1/2 rep2 (dataset4)


title: T cells, J30_WT1


title: NF16 CoMo rep2 (dataset4)

value: control morpholino (CoMo)

value: control


title: melanoma tissue 1 (1110914)

description:
253816610053-1_4
Gene expression

source_name: melanoma tissue 1


title: T cells, J8_WT6

value: 8 days


title: melanoma tissue 2 (1109223)

description:
253816610054-1_1
Gene expression

source_name: melanoma tissue 2

value: male


title: T cells, J30_WT4


title: T cells, J8_WT4


title: NF10 CoMo rep2 (dataset4)


title: T cells, J8_WT5


title: NF16 CoMo rep1 (dataset4)


title: T cells, J8_WT1


title: NF10 CoMo rep3 (dataset4)


title: T cells, J8_WT3


title: T cells, J8_WT2


title: NF10 Suv4-20H1/2 rep1 (dataset4)


title: NF10 CoMo rep1 (dataset4)