title: scRNAseq, Microglia, late stage AD, untreated, CD11c negative

description:
Library name: P4_LSN_neg_7_scRNAseq
mCEL-Seq2

value: Brain


title: control_liver_4 technical rep2

status: Public on Apr 30 2025

type: SRA

city: Munich

first: Ursula

last: Ehmer

address: Ismaninger Str. 22

department: Internal Medicine II

country: Germany

institute: Klinikum rechts der Isar, TU München

description: AGGGGC

library_source: transcriptomic

data_processing:
R version 4.02
Bioconductor version 3.12
DESeq2 version 1.30.1
no trimming
gene annotation M25
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: matrix column names for each technical replicate are listed under description

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
liver samples and liver tumors were isolated using the Maxwell 16 LEV simplyRNA Kit (Promega) according to the manufacturer’s instructions
Reverse transcription was carried out for individual samples using the Maxima RT polymerase with oligo-dT primers consisting of a sample barcode, unique molecular identifiers (UMIs) and an adaptor. Ends of cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. For fragmentation of cDNA, NEB Ultra II FS kit was used, followed by end repair and A-tailing, to which a TruSeq adapter was ligated. Finally, 3’-end-fragments were amplified using primers with Illumina P5 and P7 overhangs

tag: tissue

value: liver

tag: genotype

tag: treatment


title: isolate vci_012, replicate 2

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

country: USA

institute: Harvard School of Public Health

description: Library name: vci_012_2

data_processing:
See publication for complete details. Paired end reads were demultiplexed by their inline barcodes using cutadapt and a custom demultiplexer script.
Reads were mapped with bowtie2 to H37Rv reference.
Non-unique reads were removed with picard.
Reads were mapped to H37Rv regions with a custom script, removing low mapq reads. Reported values are log2 transformed and library depth normalized.
Assembly: NC_000962.3
Supplementary files format and content: 2D csvs with gene IDs and sample names

organism: Mycobacterium tuberculosis

source_name: bacterial

growth_protocol: Mtb was grown in a 1 mL volume in 24-well plates, covered with breathe-easy film, at 37°C x 100 RPM, in 7H9 media supplemented with 0.2% glycerol, 0.05% Tween-80, and 10% OADC. Strains were grown and back diluted as necessary over a 8 day period to achieve a final OD of ~0.4.

extract_protocol:
Crosslinks were reversed by incubating at 70°C. Cells were lysed in Trizol using bead beating tubes. RNA was extracted by adding chloroform and removing the aqueous upper layer. RNA was precipitated onto carboxylate-modified magnetic beads with isopropanol-GuHCl and beads were washed with ethanol. RNA was resuspended into tris-buffered water. See publication for full details.
RNA library preps were prepared for Illumina sequencing using a custom protocol, see publication for complete details. Briefly, cDNA was barcoded using random primers with inline barcodes and an Illumina sequencing adapter. Barcoded, single-stranded cDNA was pooled and a second adapter was added using a splint ligation. Reads corresponding to rRNA were depleted using Taq polymerase's endonuclease activity, combined with a library of guides. Libraries were amplified and sequenced on either a MiSeq or NovaSeq instrument.

treatment_protocol: To halt transcriptome dynamics and sterilize cultures, PFA was added to each 1 mL culture to a final concentration of 2% and allowed to incubate for 1 hour at room temperature.

tag: cell type

value: bacterial

value: Clinical Isolate


title: scRNAseq, Microglia, early stage AD, Abx treated_ CD11c positive

city: Freiburg im Breisgau

first: Marco

last: Prinz

state: Baden-Württemberg

address: Breisacher Str. 64, C/O Institut für Neuropathologie

department: Institut für Neuropathologie

institute: Universitätsklinikum Freiburg

description:
Library name: P3_ES_Abx_pos_6_scRNAseq
mCEL-Seq2

library_source: transcriptomic single cell

data_processing:
Analysis of all datasets was performed according to the following initial pipeline: The count matrices were analyzed with R Studio (version 2022.07.1 Build 554) using the Seurat package (version 5). For quality control, duplets were excluded by selecting cells with <4000 nFeatures and ambient noise was filtered by selecting cells with >200 nFeatures. The data was normalized using the “NormalizeData” function with the “LogNormalize” method, variable features were found using “FindVariableFeatures” function with the ‘variance stabilizing transformation’ method and selecting the top 4000 features. Data was scaled using “ScaleData” function and then reduced in dimensions using principal component analysis (PCA) with the “RunPCA” function.
Reads were processed using STARsolo with the Gencode M26 reference. Barcode filtering applied standard thresholds without sample-specific optimization. Processed gene expression matrices are unique per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend  #100330, Gr1 cloneRB6-8C5, BioLegend  #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj).  Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA.
For RNA sequencing, the mCEL-Seq2 protocol was used as previously established.

tag: disease stage

value: early stage AD

value: Microglia

value: Cx3cr1-CreERT2 R26-Confetti FAD

value: Antibiotic cocktail

tag: library type

value: mRNA

tag: sample group


title: isolate vci_012, replicate 1

description: Library name: vci_012_1


title: male healthy control, baseline_replicate 11

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

description: Library name: 2794sHM0

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2, and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Raw counts from HTSeq and STAR were imported into Bioconductor/R package DESeq2, normalized, and tested for differential gene expression. This analysis was done separately for the files produced by each aligner.
Only genes with raw counts equal or more than 50 in all samples in at least one group were used for the differential gene expression analysis
For further analysis, we selected genes and exons that were differentially expressed based on one of the following two criteria: (a) either a fold change (FC) > |1.5| and false discovery rate (FDR) < 0.10 in one out of the three aligners and FC > |1.4| and FDR < 0.15 in the remaining two aligners, OR (b) a FC > |1.5| and FDR < 0.10 in two out of three aligners.
Assembly: GRCh38, release 103
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 50 in all samples in at least one group

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center) according to the manufacturer’s instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent Technologies). All RNA samples had an RNA Integrity number (RIN) above seven.
The libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit

value: peripheral blood mononuclear cells

tag: disease state

value: healthy control

tag: time point_in_exercise

value: T0 (baseline)

tag: Sex

value: male


title: scRNAseq, Microglia, early stage AD, Abx treated_ CD11c negative

description:
Library name: P3_ES_Abx_neg_5_scRNAseq
mCEL-Seq2


title: control_liver_3 technical rep2

description: CACCAA


title: isolate vci_008, replicate 2

description: Library name: vci_008_2


title: male healthy control, baseline_replicate 9

description: Library name: 2770sHM0


title: male healthy control, baseline_replicate 10

description: Library name: 2782sHM0


title: scRNAseq, Microglia_early stage AD, LPS treated, CD11c positive

description:
Library name: P2_ES_LPS_pos_4_scRNAseq
mCEL-Seq2

value: LPS


title: control_liver_2 technical rep2

description: TCATAT


title: control_liver_1 technical rep2

description: CAAATA


title: scRNAseq, Microglia, early stage AD, LPS treated_ CD11c negative

description:
Library name: P2_ES_LPS_neg_3_scRNAseq
mCEL-Seq2


title: male healthy control, baseline_replicate 8

description: Library name: 2758sHM0


title: RPK;Mek1/2_liver_4weeks_3 technical rep2

description: AATTCT

value: tamoxifen


title: scRNAseq, Microglia, early stage AD, untreated, CD11c positive

description:
Library name: P1_ESN_pos_2_scRNAseq
mCEL-Seq2

value: Untreated


title: isolate vci_007, replicate 1

description: Library name: vci_007_1


title: scRNAseq, Microglia, early stage AD, untreated, CD11c negative

description:
Library name: P1_ESN_neg_1_scRNAseq
mCEL-Seq2


title: RPK;Mek1/2_liver_4weeks_2 technical rep2

description: GGGGAC


title: isolate vci_005, replicate 2

description: Library name: vci_005_2


title: male healthy control, baseline_replicate 7

description: Library name: 2746sHM0


title: male healthy control, baseline_replicate 6

description: Library name: 2722sHM0


title: RPK;Mek1/2_liver_4weeks_1 technical rep2

description: GCACGG


title: isolate vci_005, replicate 1

description: Library name: vci_005_1


title: ATACseq, Microglia, 5xFAD positive, CD11c positive, 3

description: Library name: 5xFADpos_CD11cpositive3_ATAC

library_source: genomic

data_processing:
Reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie2 (v2.3.4.3). Adaptors and low quality read ends were trimmed using Trim Galore! (v0.4.3.1, https://github.com/FelixKrueger/TrimGalore). Mitochondrial DNA reads were removed with BAMTools (v2.5.1) and blacklisted genomic regions for mm10 defined by ENCODE were excluded using bedtools intersect (v2.3.0.0). For quality control, Transcription Start Site enrichment (TSSe) scores were calculated and samples with TSSe < 15 were removed from downstream analysis according to ENCODE standards (https://www.encodeproject.org/data-standards/atac-seq/atac-encode4/). Peaks were called with MACS2 (v2.1.1.20160309.6, –shift -100 –extsize 200 –nomodel –call-summits -q 0.05). Peaks from individual samples were combined into a consensus peak list. Differentially accessible regions (DARs) were identified using DESeq2 (v2.11.40.7, log2(fold change) ≥ 0.584 or ≤ -0.584, FDR < 0.05), followed by region annotation using ChIPSeeker (v1.18.0). DeepTools2 (Version 3.5.1) was used for visualization. Individual sample bigwig files were normalized with DESeq2 size factors before being merged with bigwigAverage. DeepTools2 (Version 3.5.1, computeMatrix, plotHeatmap) was used to visualize chromatin accessibility from merged bigwig files at defined microglia-specific primed and active enhancer regions. Motif enrichment analysis was performed using HOMER (v4.11). Pathway enrichment analysis was performed using GREAT (v4.04). The analysis workflow and visualizations were performed on the Galaxy platform.
Assembly: GRCm38/mm10
Supplementary files format and content: narrowPeak

molecule: genomic DNA

extract_protocol:
To profile chromatin accessibility, Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) protocol was performed. 50,000 microglia were sorted in 250 μl of FACS buffer (1x PBS, 2% FBS, 2mM EDTA) and pelleted by centrifugation for 5 min, 500 g at 4 °C. Cell pellets were washed with 1x PBS and pelleted by centrifugation. Cell pellets were resuspended in 50 μl of cold lysis buffer (10 mM Tris HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were pelleted by centrifugation for 10 min, 500 g at 4 °C and re-suspended in 50 μl reaction buffer containing 2.5 μl of Tn5 transposase and 25 μl of TD buffer (Nextera Sample preparation kit, Illumina). The reaction was incubated at 37 °C for 45 min with gentle mixing. Afterwards, tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen) according to manufacturer instructions. Libraries were initially amplified by a 5-cycle PCR before each sample was assessed by RT-qPCR for the optimum number of extra PCR amplification cycles (max. 9) to reduce GC and size bias. 5 μl of indexing primers and NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) were used. Library clean-up was performed twice using the NucleoMag NGS Beads (Macherey-Nagel). DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library sizes and quality were determined using Bioanalyzer (Agilent). Libraries where sequenced on Illumina HiSeq 2000 for an average of 30 million unique reads per sample
Libraries were initially amplified by a 5-cycle PCR before each sample was assessed by RT-qPCR for the optimum number of extra PCR amplification cycles (max. 9) to reduce GC and size bias. 5 μl of indexing primers as in Buenrostro et al. 2013 and NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) were used. Library clean-up was performed twice using the NucleoMag NGS Beads (Macherey-Nagel). DNA concentration was measured with a Qubit fluorometer (Life Technologies) and library sizes and quality were determined using Bioanalyzer (Agilent). Libraries where sequenced on Illumina HiSeq 2000 for an average of 30 million unique reads per sample.

value: 5xFAD positive, CD11c positive

value: ATAC


title: RPK;Pdk1_liver_4weeks_3 technical rep2

description: CCTGGC

value: liver


title: isolate vci_004, replicate 2

description: Library name: vci_004_2

value: bacterial


title: ATACseq, Microglia, 5xFAD positive, CD11c positive, 2

description: Library name: 5xFADpos_CD11cpositive2_ATAC

value: Brain


title: male healthy control, baseline_replicate 5

description: Library name: 2710sHM0


title: male healthy control, baseline_replicate 4

description: Library name: 2698sHM0


title: RPK;Pdk1_liver_4weeks_2 technical rep2

description: GTACCG


title: isolate vci_008, replicate 1

description: Library name: vci_008_1

value: Clinical Isolate


title: ATACseq, Microglia, 5xFAD positive, CD11c positive, 1

description: Library name: 5xFADpos_CD11cpositive1_ATAC

value: Microglia


title: RPK;Pdk1_liver_4weeks_1 technical rep2

description: TTTACA


title: isolate vci_007, replicate 2

description: Library name: vci_007_2


title: isolate vci_004, replicate 1

description: Library name: vci_004_1


title: ATACseq, Microglia, 5xFAD positive, CD11c negative, 3

description: Library name: 5xFADpos_CD11cnegative3_ATAC

value: 5xFAD positive, CD11c negative

value: Cx3cr1-CreERT2 R26-Confetti FAD


title: RPK_liver_4weeks_3 technical rep2

description: TAGTAA


title: ATACseq, Microglia, 5xFAD positive, CD11c negative, 2

description: Library name: 5xFADpos_CD11cnegative2_ATAC


title: male healthy control, baseline_replicate 1

description: Library name: 2662sHM0


title: ATACseq, Microglia, 5xFAD positive, CD11c negative, 1

description: Library name: 5xFADpos_CD11cnegative1_ATAC


title: RPK_liver_4weeks_2 technical rep2

description: ATTTCA


title: dgeo_0257-0281 DK mutant with H2O2

city: Seoul

first: Sung-Jae

last: Lee

address: Kyungheedae-ro 26, Dongdaemun-gu

department: Biology

country: South Korea

institute: Kyung Hee University

description: Library name: s57_81_H

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to ASM19627v1 using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: ASM19627v1
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

organism: Deinococcus geothermalis DSM 11300

growth_protocol: Experimental strains were cultivated till OD600 of 2.0 on TGY medium at 40C

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols. rRNA was removed using RIBO COP rRNA depletion kit (LEXOGEN, Inc., Austria).

treatment_protocol: Cells were normalized OD 1.0, treated with 50 mM H2O2 or not treated and continuous cultivated for 1 hour. Samples for RNA prep were prepared.

tag: strain


title: RPK_liver_4weeks_1 technical rep2

description: AATCTT


title: male GWI patient, recovery_replicate 19

description: Library name: 5272sGM2

value: GWI patient

value: T2 (recovery)


title: ATACseq, Microglia, 5xFAD negative 3

description: Library name: 5xFADneg_microglia3_ATAC

value: 5xFAD negative


title: dgeo_0257-0281 DK mutant

description: Library name: s57_81


title: male GWI patient, recovery_replicate 18

description: Library name: 2985sGM2

value: peripheral blood mononuclear cells


title: control_liver_4weeks_4 techincal rep2

description: CGAGGC


title: dgeo_0281-disrupted mutant with H2O2

description: Library name: s0281_H


title: male GWI patient, recovery_replicate 17

description: Library name: 2973sGM2

value: male


title: control_liver_4weeks_3 techincal rep2

description: ACCGGC


title: ATACseq, Microglia, 5xFAD negative 1

description: Library name: 5xFADneg_microglia1_ATAC


title: male healthy control, baseline_replicate 3

description: Library name: 2686sHM0

value: healthy control

value: T0 (baseline)


title: control_liver_4weeks_2 techincal rep2

description: TTTCTT


title: isolate vci_002, replicate 2

description: Library name: vci_002_2


title: male healthy control, baseline_replicate 2

description: Library name: 2674sHM0


title: male GWI patient, recovery_replicate 16

description: Library name: 2961sGM2


title: control_liver_4weeks_1 techincal rep2

description: TATAGA


title: dgeo_0281-disrupted mutant

description: Library name: s0281


title: male GWI patient, recovery_replicate 15

description: Library name: 2841sGM2


title: 4146 GFP sorted

city: Nice

first: Chloe

last: Feral

address: 28 avenue de valombrose

department: Ircan

country: France

institute: Inserm

description:
Library name: Sample5
GFP3 in countsTable.csv

data_processing:
The samples provided were sequenced on the NextSeq2000 of the Nice-Sophia-Antipolis Functional Genomics Platform.
The resulting sequence libraries (reads) were aligned with STAR-salmon to the GRCm39 version of the mouse genome during primary analysis
Assembly: GRCm39
Supplementary files format and content: csv file includes read count

source_name: skin

growth_protocol: Cells were isolated from backsin of d28 old mice. They were sorted based on GFP expression or the entire population was considered

extract_protocol:
Total RNA were extracted using Trizol protocol and samples were cleaned using RN easy(mini plus quiagen)
RNA libraries were constructed following France genomique protocols

value: skin

tag: cell line

value: Lrig1 positive keratinocytes sorted

value: epidermal stem cells

value: Lrig1 positive


title: dgeo_0257-disrupted mutant with H2O2

description: Library name: s0257_H


title: isolate vci_002, replicate 1

description: Library name: vci_002_1

value: bacterial


title: male GWI patient, recovery_replicate 14

description: Library name: 2829sGM2


title: dgeo_0257-disrupted mutant

description: Library name: s0257


title: 4145 GFP sorted

description:
Library name: Sample4
GFP2 in countsTable.csv


title: 4145 bulk

description:
Library name: Sample3
Bulk2 in countsTable.csv

value: basal keratinocytes

value: epidermal basal cells

value: WT


title: male GWI patient, recovery_replicate 13

description: Library name: 2805sGM2


title: D. geothermalis WT strain

description: Library name: dgeoWT


title: internal_control_3

description: GCGAGC

source_name: control

value: control


title: internal_control_2

description: GGGCAG


title: ATACseq, Microglia, 5xFAD negative 2

description: Library name: 5xFADneg_microglia2_ATAC

value: Brain

value: Microglia

value: Cx3cr1-CreERT2 R26-Confetti FAD

value: Untreated

value: ATAC


title: male GWI patient, recovery_replicate 12

description: Library name: 2793sGM2

value: peripheral blood mononuclear cells

value: GWI patient

value: T2 (recovery)

value: male


title: Tibialis anterior muscle, WT, rep6

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
RNA sequencing reads were trimmed for adapters and polyX tails, filtered by sequencing Phred quality (>=Q15) using fastp, and aligned to the mouse transcriptome (Ensembl version 107) using Kallisto. Transcript counts were converted to gene counts by using Tximport. To filter out low expressing genes, we kept genes that have more than 0.5 counts per million (CPM) in at least 5 samples. We normalized counts by weighted trimmed mean of M-values (TMM) and performed Voom transformation to transform counts into log2CPM. We applied surrogate variable analysis and adjusted the log2CPM for mouse litters and the surrogate variables.
Assembly: Mouse Ensembl version 107
Supplementary files format and content: CSV with Ensembl mouse gene ID, gene symbol, and adjusted log2CPM per sample

molecule: polyA RNA

source_name: Tibialis anterior muscle

extract_protocol:
mRNA was extracted using TRIzol (Fisher: 15 596 018)
BGI/MGI directional kit, normal total RNA oligo dT, stranded

value: Tibialis anterior muscle

value: Lrtm1 WT

tag: litter id


title: internal_control_1

description: GAGCGG


title: Gata2 KO_nutlin_5uM__rep3

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
StarAligner
Kallisto
DEseq2
R, EnhancedVolcano, GSEA
htseq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone marrow

growth_protocol: Cells were grown in IMDM medium supplemented with 15% heat inactivated FBS, 1% Penicillin/Streptomycin, 1% L-Glutamine, murine IL-3, murine IL-6 (10ng/mL), and murine SCF (20ng/mL).

extract_protocol:
Murine MA9 Gata2 f/f and Gata2 -/- (Gata2 KO) leukemias were treated with 5uM of Nutlin. After 18 hours treatment RNA was purified using Qiagen Rneasy nini or micro kits according to manufacturer's instructions
Library prep was performed using PolyA selected mRNA species (eukaryotic) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® . Samples were sequenced using Illumina HiSeq, 90bp paired-end reads, multiplexed.

value: Bone marrow

value: AML

value: MA9 leukemia

value: Gata2 -/-


title: male GWI patient, recovery_replicate 10

description: Library name: 2769sGM2


title: RPK;Pdk1;AlbCreER_tumor_6

description: TTATTG

source_name: tumor

value: tumor

value: tamoxifen


title: Tibialis anterior muscle, WT, rep4


title: Gata2 KO_nutlin_5uM__rep2


title: Gata2 KO_nutlin_5uM__rep1


title: Tibialis anterior muscle, WT, rep3


title: male GWI patient, recovery_replicate 9

description: Library name: 2757sGM2


title: male GWI patient, recovery_replicate 8

description: Library name: 2745sGM2


title: RPK;Pdk1;AlbCreER_tumor_5

description: TAATGA


title: Gata2 f/f_nutlin_5uM__rep3

value: Gata2 f/f


title: D. geothermalis WT strain with H2O2

description: Library name: dgeoWT_H


title: RPK;Pdk1;AlbCreER_tumor_4

description: ATTACT


title: 4143 GFP sorted

description:
Library name: Sample2
GFP1 in countsTable.csv

value: skin

value: Lrig1 positive keratinocytes sorted

value: epidermal stem cells

value: Lrig1 positive


title: Gata2 f/f_nutlin_5uM__rep2


title: internal_control_4

description: TCCCGC

value: control


title: Tibialis anterior muscle, KO, rep5

value: Lrtm1 KO


title: 4143 bulk

description:
Library name: Sample1
Bulk1 in countsTable.csv

value: basal keratinocytes

value: epidermal basal cells

value: WT


title: Gata2 f/f_nutlin_5uM__rep1


title: Tibialis anterior muscle, KO, rep4

value: Tibialis anterior muscle


title: male GWI patient, recovery_replicate 11

description: Library name: 2781sGM2

value: peripheral blood mononuclear cells

value: GWI patient

value: T2 (recovery)

value: male


title: RPK;Pdk1;AlbCreER_tumor_3

description: AAGATT

value: tumor


title: male GWI patient, recovery_replicate 5

description: Library name: 2709sGM2


title: Tibialis anterior muscle, WT, rep5

value: Lrtm1 WT


title: RPK;Pdk1;AlbCreER_tumor_7

description: TCTGCA

value: tamoxifen


title: Tibialis anterior muscle, KO, rep3


title: Control: Dendritic cells without collagen matrix plus CCL19_biol rep 1

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: BSF_0106_C4GMRACXX_2_18_12_2013_sus_no_ch

data_processing:
sequencing reads were aligned to the mouse reference genome (version GRCm38.95) and  gene read counts were calculated with STAR (version 2.7.0f).
Assembly: GRCm38, Ensembl annotation version 95
Supplementary files format and content: tab delimited matrix of read count per gene

source_name: bone-marrow derived LPS stimulated dendritic cells

growth_protocol: DCs were differentiated  from bone marrow isolated from  C57Bl6/J wildtype mice (aged 8-12 weeks): cells were cultured in R10 medium (RPMI1640 + 10 % fetal calf serum (FCS), 2 mM l-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 0.1 mM 2-mercaptoethanol, all Gibco) supplemented with 10 % granulocyte–macrophage colony-stimulating factor (GM-CSF) hybridoma supernatant. On differentiation days 3 and 6, fresh medium was added. For dendritic cell maturation, DCs on differentiation day 8 were stimulated by adding 200 ng/ml lipopolysaccharide (LPS; E. coli O26:B6, MilliporeSigma). After 24 hours, the cells were loaded into the respective migration chambers with or without a collagen matrix.

extract_protocol:
Five hours after introduction of the CCL19 chemokine gradient, the gel was isolated from the chamber and immediately bathed in Trizol. Subsequently, RNA extraction was performed following the 'Total RNA extraction' protocol of the 'Immunological Genome Project' (ImmGen.org). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA).
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). Before sequencing on an Illumina HiSeq 2000 instrument following a 50 base single end protocol, samples were diluted and pooled into NGS libraries in equimolar amounts.
50 base single end protocol

treatment_protocol: Bone-marrow derived LPS-stimulated dendritic cells were incorporated into three-dimensional collagen gels of different densities. Different collagen were obtained by using different bovine collagen stock dilutions to final concentrations of 1.7 mg/ml, 2.6 mg/ml, 3.5 mg/ml, and 4.4 mg/ml. Controls were performed by placing DCs into the same migration chambers but without collagen.

value: wild-type

value: yes

tag: collagen matrix density

value: 0 mg/ml


title: male GWI patient, recovery_replicate 4

description: Library name: 2697sGM2


title: Tibialis anterior muscle, WT, rep1


title: Tibialis anterior muscle, KO, rep2


title: Dendritic cell migration in a 4.4 mg/ml collagen matrix towards a CCL19 source_biol rep 1

value: bone-marrow derived LPS stimulated dendritic cells

value: 4.4 mg/ml


title: Control: Dendritic cells without collagen matrix_biol rep 1

description: BSF_0106_C4GMRACXX_2_18_12_2013_sus_ccl_19

value: no


title: RPK;AlbCreER_tumor_8

description: CCCTGG


title: male GWI patient, recovery_replicate 2

description: Library name: 2673sGM2


title: male GWI patient, recovery_replicate 7

description: Library name: 2733sGM2


title: RPK;Pdk1;AlbCreER_tumor_1

description: CTGCGG


title: Tibialis anterior muscle, KO, rep1

value: Lrtm1 KO


title: male GWI patient, recovery_replicate 1

description: Library name: 2661sGM2


title: male GWI patient, recovery_replicate 6

description: Library name: 2721sGM2


title: Dendritic cell migration in a 3.5 mg/ml collagen matrix towards a CCL19 source_biol rep 1

value: 3.5 mg/ml


title: RPK;AlbCreER_tumor_7

description: GTTCGA


title: RPK;AlbCreER_tumor_6

description: TTAGTT


title: Dendritic cell migration in a 2.6 mg/ml collagen matrix towards a CCL19 source_biol rep 1

value: 2.6 mg/ml


title: male GWI patient, maximal exertion_replicate 17

description: Library name: 5277sGM1

value: T1 (maximal exertion)


title: RPK;Pdk1;AlbCreER_tumor_2

description: GGCCAC


title: RPK;AlbCreER_tumor_5

description: TAAGAT


title: male GWI patient, maximal exertion_replicate 16

description: Library name: 2984sGM1

value: peripheral blood mononuclear cells


title: Dendritic cell migration in a 1.7 mg/ml collagen matrix towards a CCL19 source_biol rep 1

value: 1.7 mg/ml


title: RPK;AlbCreER_tumor_4

description: ATGAAT


title: Control: Dendritic cells without collagen matrix plus CCL19_biol rep 2

description: BSF_0100_C495TACXX_3_29_01_2014_sus_no_ch


title: U87_HYP_ak_2

city: Chongqing

first: Sheng

last: Gong

address: Jinzhou Avenue, Liangjiang New District, Department of Neurosurgery, Chongqing General Hospital, Chongqing University, Chongqing 401147, China

country: China

institute: Chongqing University

description:
Library name: sample11
U87_HYP_ak_2

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36).
Clean reads were mapped to the reference genome using HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to quantify alignment results. Qualimap (version 2.2.1) was employed to check for uniform distribution and genomic structure. BEDTools (version 2.26.0) was used for statistical analysis of gene coverage.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: U-87 MG

extract_protocol:
Total RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon, China) according to the manufacturer’s protocol. A total amount of 1 μg RNA per sample was used for the construction of the sequencing library .
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: U-87 MG

value: Dual-knockout of HIF1α and HIF2α under hypoxia


title: male GWI patient, maximal exertion_replicate 15

description: Library name: 2972sGM1

value: GWI patient

value: male


title: male GWI patient, recovery_replicate 3

description: Library name: 2685sGM2

value: T2 (recovery)


title: U87_HYP_2k_3

description:
Library name: sample9
U87_HYP_2k_3

value: Knockout of HIF2α under hypoxia


title: RPK;AlbCreER_tumor_3

description: AAATTG

value: tumor

value: tamoxifen


title: U87_HYP_ak_1

description:
Library name: sample10
U87_HYP_ak_1


title: U87_HYP_ak_3

description:
Library name: sample12
U87_HYP_ak_3


title: Control: Dendritic cells without collagen matrix_biol rep 2

description: BSF_0100_C495TACXX_3_29_01_2014_sus_ccl_19_2

value: bone-marrow derived LPS stimulated dendritic cells

value: wild-type

value: 0 mg/ml


title: U87_HYP_2k_2

description:
Library name: sample8
U87_HYP_2k_2


title: RPK;AlbCreER_tumor_2

description: GGAGCC


title: male GWI patient, maximal exertion_replicate 14

description: Library name: 2960sGM1


title: U87_HYP_2k_1

description:
Library name: sample7
U87_HYP_2k_1


title: Dendritic cell migration in a 3.5 mg/ml collagen matrix towards a CCL19 source_biol rep 2

value: yes


title: Dendritic cell migration in a 4.4 mg/ml collagen matrix towards a CCL19 source_biol rep 2

value: 4.4 mg/ml


title: male GWI patient, maximal exertion_replicate 13

description: Library name: 2840sGM1


title: RPK;AlbCreER_tumor_1

description: CGTGGG


title: U87_HYP_1k_3

description:
Library name: sample6
U87_HYP_1k_3

value: Knockout of HIF1α under hypoxia


title: RPK_tumor_AAV_5

description: ATTCTA

value: AAV-Cre


title: male GWI patient, maximal exertion_replicate 12

description: Library name: 2804sGM1

value: peripheral blood mononuclear cells

value: T1 (maximal exertion)


title: U87_HYP_1k_2

description:
Library name: sample5
U87_HYP_1k_2

value: U-87 MG


title: RPK_tumor_AAV_4

description: AATACA


title: male GWI patient, maximal exertion_replicate 11

description: Library name: 2792sGM1


title: Dendritic cell migration in a 1.7 mg/ml collagen matrix towards a CCL19 source_biol rep 2

value: 1.7 mg/ml


title: Dendritic cell migration in a 2.6 mg/ml collagen matrix towards a CCL19 source_biol rep 2

value: 2.6 mg/ml


title: male GWI patient, maximal exertion_replicate 10

description: Library name: 2780sGM1

value: GWI patient

value: male


title: RPK_tumor_AAV_3

description: GGCGTC


title: U87_HYP_1k_1

description:
Library name: sample4
U87_HYP_1k_1


title: male GWI patient, maximal exertion_replicate 9

description: Library name: 2768sGM1


title: Control: Dendritic cells without collagen matrix plus CCL19_biol rep 3

description: BSF_0106_C4GMRACXX_1_05_03_2014_sus_no_ch


title: U87_HYP_Control_2

description:
Library name: sample2
U87_HYP_Control_2

value: Empty vector group under hypoxia


title: Control: Dendritic cells without collagen matrix_biol rep 3

description: BSF_0106_C4GMRACXX_1_05_03_2014_sus_ccl_19

value: no


title: male GWI patient, maximal exertion_replicate 8

description: Library name: 2756sGM1


title: RPK_tumor_AAV_1

description: CCGGAC

value: tumor


title: Dendritic cell migration in a 4.4 mg/ml collagen matrix towards a CCL19 source_biol rep 3

value: bone-marrow derived LPS stimulated dendritic cells


title: RPK_tumor_AAV_2

description: GACCGC


title: U87_HYP_Control_1

description:
Library name: sample1
U87_HYP_Control_1


title: male GWI patient, maximal exertion_replicate 7

description: Library name: 2744sGM1


title: male GWI patient, maximal exertion_replicate 6

description: Library name: 2720sGM1


title: control_liver_5

description: CCGTCG

value: liver


title: CoV-2_IFN_B3

city: Hyderabad

first: Krishnan

middle: Harnivas

last: Harshan

state: Telangana

address: Uppal Rd, IICT Colony

department: Infectious Diseases Group

country: India

institute: CSIR-CCMB

description:
Library name: Sample 18
Column name in raw_count_data_Huh7.csv: CoV-2_IFN_B3

data_processing:
Raw sequencing reads were processed with Cutadapt to remove MGI adapters and low-quality sequences. Reads with a quality score below 20 and a length of less than 36 bp were excluded.
The remaining high-quality reads were aligned to the human reference genome (GRCh38) using HISAT2 with default parameters.
Uniquely aligned reads were quantified using the featureCounts function from the Subread package, utilizing a GTF annotation file obtained from Ensembl, which provided read count data for 60,683 genes.
Genes with fewer than 10 total read counts across all samples were filtered out, yielding a final dataset of 36,743 genes for further analysis.
Assembly: GRCh38
Supplementary files format and content: raw_count_data_Huh7.csv file contains raw count data for Sample 1-18
Supplementary files format and content: raw_count_data_MEF.csv file contains raw count data for Sample 19-54

source_name: Huh7 cells

growth_protocol: Huh7 cells and MEFs were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cellular RNA samples were prepared using an MN NucleoSpin RNA kit
Library preparation was performed using the MGIEasy RNA Library Prep Set (MGI) following the manufacturer’s guidelines. Briefly, 500 ng of total RNA was used as the starting material, and rRNA was depleted using the Ribo-Zero Plus rRNA Depletion Kit (Illumina).

treatment_protocol: Experiment 1: Huh7 cells were either transfected with an Empty Vector control or a plasmid containing Full lengh MAVS. Huh7 cells were also treated with IFN-α or vehicle control at a concentration of 1000 Units/mL before subjecting the cells to Mock-infection or SARS-CoV-2 infection for 24 hours.                                                                                Experiment 2: WT and MAVS KO Mouse Embrynoic Fibroblasts (MEFs) were subjected to either mock-infection or SARS-COV-2 infection for different time points (12, 24 and 48 hours)

value: Huh7 cells

value: hepatocarcinoma

value: IFN

tag: batch

value: Batch 3


title: Dendritic cell migration in a 2.6 mg/ml collagen matrix towards a CCL19 source_biol rep 3

value: wild-type

value: yes


title: male GWI patient, maximal exertion_replicate 5

description: Library name: 2708sGM1

value: peripheral blood mononuclear cells

value: T1 (maximal exertion)


title: control_liver_3

description: TTGAAA


title: CoV-2_IFN_B1

description:
Library name: Sample 16
Column name in raw_count_data_Huh7.csv: CoV-2_IFN_B1

value: Batch 1


title: control_liver_4

description: CCAACC


title: CoV-2_IFN_B2

description:
Library name: Sample 17
Column name in raw_count_data_Huh7.csv: CoV-2_IFN_B2

value: Batch 2


title: Dendritic cell migration in a 1.7 mg/ml collagen matrix towards a CCL19 source_biol rep 3

value: 1.7 mg/ml


title: male GWI patient, maximal exertion_replicate 4

description: Library name: 2696sGM1

value: GWI patient

value: male


title: THC/SIV_6

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Library name: THCSIV6

data_processing:
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina based-calling software and then analyzed using Zymo Research proprietary analysis pipeline, which is written in Python along with Bismark (www.bioinfomatics.babraham.ac.uk/projects/bismark/) to perform the alignment. Index files were constructed using the bismark_genome_preparation) command and the entire reference genome.
The non-directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off while doing methylation calling. The methylation level of each sampled cystosine (C) was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or thymine.
Fisher’s exact test or t test was performed for each CpG site which has at least five reads coverage, and promoter, gene body, and CpG island annotations were added for each CpG included in the comparison.
genome build/assembly: rheMac8
processed data files format and content: Excel file showing delta-beta values and methylation status (hyper or hypo) at the chromosomal locations with p value

organism: Macaca mulatta

source_name: Colon

extract_protocol:
Colon epithelial total DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen Inc, CA). ~1 ug of DNA was used for reduced restriction bisulfite sequencing.
Methyl-MiniSeq Library preparation was performed by Zymo Research. Libraries were prepared from 200-500ng of genomic DNA digested with 60 units of Taql and 30 units of MspI (NEB) sequentially and then extracted with DNA Clean & ConcentratorTM-5 (Zymo Research). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine according to Illumina’s specified guidelines (www.illumina.com). Adapter-ligated fragments of 150-250bp and 250-300bp were recovered from a 2/5% NuSieve 1:1 agarose gel (Zymoclean Gel DNA Recovery Kit, Zymo Research). The fragments were then bisulfite treated using EX DNA Methylation-Lightning Kit (Zymo Research). Preparative-scale PCR was performed, and the resulting products purified for sequencing on an Illumina HiSeq.

treatment_protocol: Eighteen age and weight-matched male Indian RMs were randomly distributed into three groups. Group 1 [controls (n = 5)] served as uninfected controls. Groups 2 and 3 (n = 13) were infected intravenously with 100 times the 50% tissue culture infective dose (100TCID50) of SIVmac251. Since nonhuman-primates are “an acutely scarce resource and due to the current shortage of Indian rhesus macaques, females are being used for breeding purposes to expand the colonies. Group 2 [VEH/SIV] (n=7) received twice daily injections of vehicle (VEH) (1:1:18 of emulphor:ethanol:saline), intramuscularly. Groups 3 [THC/SIV] (n=6) received twice daily injection of THC intramuscularly four weeks before SIV infection at 0.18mg/kg. This dose of THC was increased to 0.32mg/kg over a period of 2 weeks and maintained for the duration of the study.

value: Colon

value: Colon Epithelium

value: SIV Infected with THC treatment


title: U87_HYP_Control_3

description:
Library name: sample3
U87_HYP_Control_3

value: U-87 MG

value: Empty vector group under hypoxia


title: control_liver_1

description: ATCAAA

value: liver


title: CoV-2_MAVS_B3

description:
Library name: Sample 15
Column name in raw_count_data_Huh7.csv: CoV-2_MAVS_B3

value: Huh7 cells

value: hepatocarcinoma

value: MAVS


title: CoV-2_MAVS_B2

description:
Library name: Sample 14
Column name in raw_count_data_Huh7.csv: CoV-2_MAVS_B2


title: male GWI patient, maximal exertion_replicate 3

description: Library name: 2684sGM1


title: control_liver_2

description: TACTAT


title: THC/SIV_5

description: Library name: THCSIV5


title: male GWI patient, maximal exertion_replicate 2

description: Library name: 2672sGM1


title: RPK;Mek1/2_liver_4weeks_3

description: AAAGTT

value: tamoxifen


title: THC/SIV_4

description: Library name: THCSIV4


title: RPK;Mek1/2_liver_4weeks_2

description: GCTCGC


title: Dendritic cell migration in a 3.5 mg/ml collagen matrix towards a CCL19 source_biol rep 3

value: bone-marrow derived LPS stimulated dendritic cells

value: wild-type

value: yes

value: 3.5 mg/ml


title: male GWI patient, maximal exertion_replicate 1

description: Library name: 2660sGM1

value: peripheral blood mononuclear cells

value: T1 (maximal exertion)


title: CoV-2_Huh7_B3

description:
Library name: Sample 12
Column name in raw_count_data_Huh7.csv: CoV-2_Huh7_B3

value: Empty Vector

value: Batch 3


title: THC/SIV_3

description: Library name: THCSIV3

value: Colon

value: Colon Epithelium


title: RPK;Mek1/2_liver_4weeks_1

description: CGGTGG


title: male GWI patient, baseline_replicate 19

description: Library name: 5278sGM0

value: GWI patient

value: T0 (baseline)

value: male


title: THC/SIV_2

description: Library name: THCSIV2

value: SIV Infected with THC treatment


title: THC/SIV_1

description: Library name: THCSIV1


title: CoV-2_Huh7_B2

description:
Library name: Sample 11
Column name in raw_count_data_Huh7.csv: CoV-2_Huh7_B2

value: Huh7 cells

value: hepatocarcinoma

value: Batch 2


title: CoV-2_Huh7_B1

description:
Library name: Sample 10
Column name in raw_count_data_Huh7.csv: CoV-2_Huh7_B1

value: Batch 1


title: male GWI patient, baseline_replicate 17

description: Library name: 2983sGM0


title: RPK;Pdk1_liver_4weeks_3

description: CCCACG

value: liver

value: tamoxifen


title: male GWI patient, baseline_replicate 18

description: Library name: 5265sGM0


title: RPK;Pdk1_liver_4weeks_2

description: GCTAGA


title: Mock_IFN_B3

description:
Library name: Sample 9
Column name in raw_count_data_Huh7.csv: Mock_IFN_B3

value: Mock-infected

value: IFN


title: RPK;Pdk1_liver_4weeks_1

description: TGTTTA


title: male GWI patient, baseline_replicate 16

description: Library name: 2971sGM0

value: peripheral blood mononuclear cells


title: male GWI patient, baseline_replicate 15

description: Library name: 2928sGM0


title: VEH/SIV_6

description: Library name: VEHSIV6

value: SIV Infected with Vehicle treatment


title: RPK_liver_4weeks_3

description: GTTTAT


title: VEH/SIV_5

description: Library name: VEHSIV5


title: male GWI patient, baseline_replicate 14

description: Library name: 2839sGM0


title: Mock_IFN_B1

description:
Library name: Sample 7
Column name in raw_count_data_Huh7.csv: Mock_IFN_B1


title: CoV-2_MAVS_B1

description:
Library name: Sample 13
Column name in raw_count_data_Huh7.csv: CoV-2_MAVS_B1

value: MAVS


title: RPK_liver_4weeks_2

description: ATATAG


title: VEH/SIV_4

description: Library name: VEHSIV4

value: Colon


title: Mock_MAVS_B3

description:
Library name: Sample 6
Column name in raw_count_data_Huh7.csv: Mock_MAVS_B3

value: Batch 3


title: VEH/SIV_3

description: Library name: VEHSIV3

value: Colon Epithelium


title: RPK_liver_4weeks_1

description: AAAACT


title: male GWI patient, baseline_replicate 12

description: Library name: 2803sGM0

value: GWI patient

value: T0 (baseline)


title: control_liver_4weeks_4

description: CCCCGT


title: Mock_MAVS_B1

description:
Library name: Sample 4
Column name in raw_count_data_Huh7.csv: Mock_MAVS_B1


title: VEH/SIV_7

description: Library name: VEHSIV7


title: VEH/SIV_1

description: Library name: VEHSIV1


title: control_liver_4weeks_3

description: GGGATT


title: Mock_Huh7_B3

description:
Library name: Sample 3
Column name in raw_count_data_Huh7.csv: Mock_Huh7_B3

value: Empty Vector


title: male GWI patient, baseline_replicate 11

description: Library name: 2791sGM0

value: male


title: male GWI patient, baseline_replicate 10

description: Library name: 2779sGM0


title: Mock_IFN_B2

description:
Library name: Sample 8
Column name in raw_count_data_Huh7.csv: Mock_IFN_B2

value: Huh7 cells

value: hepatocarcinoma


title: Mock_Huh7_B2

description:
Library name: Sample 2
Column name in raw_count_data_Huh7.csv: Mock_Huh7_B2

value: Batch 2


title: Uninfected Controls_5

description: Library name: CONT5

value: Untreated


title: control_liver_4weeks_2

description: TTAATC

value: liver


title: male GWI patient, baseline_replicate 9

description: Library name: 2767sGM0


title: Uninfected Controls_4

description: Library name: CONT4


title: control_liver_4weeks_1

description: TAAAGT


title: male GWI patient, baseline_replicate 8

description: Library name: 2755sGM0


title: male GWI patient, baseline_replicate 7

description: Library name: 2743sGM0


title: male GWI patient, baseline_replicate 13

description: Library name: 2827sGM0


title: Mock_Huh7_B1

description:
Library name: Sample 1
Column name in raw_count_data_Huh7.csv: Mock_Huh7_B1

value: Mock-infected

value: Batch 1


title: Mock_MAVS_B2

description:
Library name: Sample 5
Column name in raw_count_data_Huh7.csv: Mock_MAVS_B2


title: RPK;Mek1/2_7

description: TTTACA

data_processing:
R version 4.02
Bioconductor version 3.12
DESeq2 version 1.30.1
no trimming
gene annotation M25
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: matrix column names are listed under decription

source_name: liver tumor

value: liver tumor

value: tamoxifen


title: Uninfected Controls_3

description: Library name: CONT3


title: RPK;Mek1/2_6

description: TAGTAA


title: male GWI patient, baseline_replicate 6

description: Library name: 2719sGM0

value: peripheral blood mononuclear cells


title: Uninfected Controls_1

description: Library name: CONT1

value: Colon


title: Uninfected Controls_2

description: Library name: CONT2


title: RPK;Mek1/2_5

description: ATTTCA


title: VEH/SIV_2

description: Library name: VEHSIV2

value: SIV Infected with Vehicle treatment


title: RPK;Mek1/2_4

description: AATCTT


title: PBMCs from FIP diseased cat 3

city: Jeongeup-Si

first: Ju Young

address: 30 Baekhak 1 Gil,

institute: Korea institute of toxicology

description: Library name: 138210

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Felis_catus_9.0(NCBI) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: Felis_catus_9.0
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Felis catus

source_name: peripheral blood mononuclear cells (PBMCs)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.


title: RPK;Mek1/2_3

description: GGGCAG


title: male GWI patient, baseline_replicate 4

description: Library name: 2695sGM0


title: PBMCs from FIP recovered cat 2

description: Library name: FR_cat1

value: peripheral blood mononuclear cells (PBMCs)


title: RPK;Mek1/2_2

description: GAGCGG


title: male GWI patient, baseline_replicate 3

description: Library name: 2683sGM0

value: GWI patient


title: PBMCs from FIP recovered cat 3

description: Library name: FR_cat2


title: GOX_DOX_2

city: Hsinchu City

first: YenNhi

middle: Ngoc

last: Ta

address: No. 101, Sec. 2, Guangfu Rd., East District

department: Institute of Biomedical Engineering

country: Taiwan

institute: National Tsing Hua University

description: Library name: GOX_DOX_2

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: mm_GRChm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

growth_protocol: Murine HCC HCA-1 cells were orthotopically implanted in the liver of 6–8-week-old male C3H mice. 1 × 10^6 HCA-1 cells were injected in the subcapsular region through a 28-gauge needle.

extract_protocol:
The integrity of RNA extracted from the treatment and control groups using the RNeasy Kit (Qiagen) was evaluated with the RNA Nano6000 assay kit (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: The experimental design involved orthotopically implanting murine HCC (HCA-1) cells in C3H mice, followed by IV administration of nanoparticle loaded with  GOX and DOX on days 18, 19, and 20. Subsequent transcriptome analysis of the tumors was performed after 3-hour circulation on day 17.

value: tumor

value: HCC

value: nanoparticles loaded with GOX and DOX


title: GOX_DOX_1

description: Library name: GOX_DOX_1


title: Control_5

description: Library name: Control_5

value: untreat


title: Control_6

description: Library name: Control_6


title: Control_7

description: Library name: Control_7


title: male GWI patient, baseline_replicate 2

description: Library name: 2671sGM0

value: T0 (baseline)

value: male


title: PBMCs from FIP recovered cat 1

description: Library name: FIPTrP_1


title: GOX_DOX_5

description: Library name: GOX_DOX_5


title: RPK;Mek1/2_1

description: CCGTCG


title: male GWI patient, baseline_replicate 1

description: Library name: 2659sGM0


title: PBMCs from FIP diseased cat 2

description: Library name: M1


title: Treated 8 Male

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E. 3rd St. Bloomington, IN 47405

institute: Indiana University

description:
Library name: Mouse_977
10X FLEX scRNAseq

data_processing:
Demultiplexing, alignment, and barcode processing , gene counting, and aggregation were made using Cellranger Multi Pipeline. (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi)
Assembly: Mouse mm10 Human GRC38
Supplementary files format and content: Tab seperated values files and matrix files

source_name: colon tumor

extract_protocol:
For sample preparation, 20-25 mg of fresh TP KO tumors (7 vehicle and 8 BRAFi+EGFRi) or 817 (3 vehicle and 3 BRAFi+EGFRi) were processed using the Tissue Fixation and Dissociation for Chromium Fixed RNA Profiling protocol (CG000553, 10X Genomics) and the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (1000414, 10X Genomics).
Gene expression libraries were prepared at the Indiana University School of Medicine (IUSM) Center for Medical Genomics using the Chromium Fixed RNA Kit, Mouse Transcriptome (1000497, 10x Genomics), in accordance with the user guide (Chromium Fixed RNA Profiling, CG000527- RevD). Briefly, 8,000 cells per sample were targeted for Gel-Beads-in-Emulsion (GEMs) formation after hybridization and pooling equally. The final library was generated and then sequenced using an Illumina NovaSeq X plus with approximately 2500 million reads.

value: colon tumor

value: TP KO organoids

value: Tumor Epithelial Cells

value: Encorafenib + Gefitinib


title: RPK_8

description: TTGAAA

value: liver tumor

value: RPK;AlbCreER


title: PBMCs from FIP diseased cat 1

description: Library name: F_2


title: male GWI patient, baseline_replicate 5

description: Library name: 2707sGM0

value: peripheral blood mononuclear cells


title: female healthy control, recovery_replicate 17

description: Library name: 2982sHF2

value: healthy control

value: T2 (recovery)

value: female


title: Treated 7 Male

description:
Library name: Mouse_967
10X FLEX scRNAseq


title: RPK_9

description: CCAACC

value: tamoxifen


title: Treated 6 Male

description:
Library name: Mouse_965
10X FLEX scRNAseq


title: RPK_7

description: TACTAT


title: PBMCs from normal cat 3

description: Library name: Cat_M3_0

value: peripheral blood mononuclear cells (PBMCs)


title: RPK_6

description: ATTCTA


title: Treated 5 Male

description:
Library name: Mouse_959
10X FLEX scRNAseq


title: female healthy control, recovery_replicate 16

description: Library name: 2926sHF2


title: Treated 4 Male

description:
Library name: Mouse_0
10X FLEX scRNAseq


title: PBMCs from normal cat 2

description: Library name: F6_0


title: PBMCs from normal cat 1

description: Library name: F5_0


title: female healthy control, recovery_replicate 15

description: Library name: 2838sHF2


title: RPK_5

description: AATACA


title: Treated 3 Female

description:
Library name: Mouse_964
10X FLEX scRNAseq


title: Treated 2 Female

description:
Library name: Mouse_975
10X FLEX scRNAseq


title: female healthy control, recovery_replicate 18

description: Library name: 5264sHF2


title: female healthy control, recovery_replicate 13

description: Library name: 2814sHF2


title: RPK_3

description: GACCGC


title: Treated 1 Female

description:
Library name: Mouse_963
10X FLEX scRNAseq


title: female healthy control, recovery_replicate 14

description: Library name: 2826sHF2


title: Control 7 Male

description:
Library name: Mouse_983
10X FLEX scRNAseq

value: Vehicle


title: RPK_1

description: TCTGCA


title: RPK_2

description: CCGGAC


title: female healthy control, recovery_replicate 12

description: Library name: 2802sHF2


title: Control 6 Male

description:
Library name: Mouse_969
10X FLEX scRNAseq


title: female healthy control, recovery_replicate 10

description: Library name: 2778sHF2


title: RPK;Pdk1_8

description: TTATTG


title: female healthy control, recovery_replicate 11

description: Library name: 2790sHF2


title: Control 5 Male

description:
Library name: Mouse_978
10X FLEX scRNAseq


title: female healthy control, recovery_replicate 9

description: Library name: 2766sHF2


title: RPK;Pdk1_7

description: TAATGA


title: female healthy control, recovery_replicate 8

description: Library name: 2754sHF2


title: RPK;Pdk1_6

description: ATTACT


title: Control 4 Male

description:
Library name: Mouse_960
10X FLEX scRNAseq


title: RPK_4

description: GGCGTC


title: female healthy control, recovery_replicate 7

description: Library name: 2742sHF2


title: Control 3 Female

description:
Library name: Mouse_979
10X FLEX scRNAseq


title: RPK;Pdk1_5

description: AAGATT


title: female healthy control, recovery_replicate 6

description: Library name: 2730sHF2


title: Control 2 Female

description:
Library name: Mouse_966
10X FLEX scRNAseq


title: RPK;Pdk1_4

description: GGCCAC


title: 882_mg_l_control

type: RNA

city: Ann Arbor

first: Erin

last: Giles

state: MI

address: 830 N University Ave

department: School of Kinesiology

institute: University of Michigan

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix). Hybridization of the Clariom S peg plate was carried out using the GeneTitan MC instrument (Affymetrix).

scan_protocol: Scanning of the Clariom S peg plate was carried out using the GeneTitan MC instrument (Affymetrix).

data_processing:
Transcriptome Analysis Console Software v 4.0 (TAC, Thermo Fisher Scientific) was used for basic data analysis and quality control.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Rat
program-name = Expression Console
program-version = 1.4.1.46

label: TdT

organism: Rattus norvegicus

source_name: Mammary gland, lean+control

label_protocol: Total RNA was used to synthesize fragmented and labeled sense-strand cDNA and hybridized onto the Clariom S peg plate. Samples were prepared using the GeneChip WT PLUS Reagent Kit (Affymetrix), following the manufacturer's instructions.

growth_protocol: Female Wistar rats were given ad libitum access to a purified high-fat diet to induce obesity. At 7 weeks of age, rats received a single intraperitoneal injection of MNU. Animals were ranked by their percent body fat at 28 weeks of age to classify adiposity.

extract_protocol: Total RNA was isolated from flash-frozen mammary tissue using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s protocol. Total RNA integrity was assessed via RNA ScreenTape analysis (Agilent Technologies).

treatment_protocol: At 37 weeks of age, lean and obese rats were randomized to receive either a daily oral does of 3mg BZA + 0.07mg CE/kg body weight), for 8 weeks, or vehicle control. Rats were euthanized following 8 weeks of treatment and fat pads collected and processed.

value: mammary gland (mammary adipose)

tag: adiposity

value: lean

tag: ovarian status

value: ovary intact

value: control

tag: group

value: lean+control


title: 876_mg_l_BZA/CE

source_name: Mammary gland, lean+BZA/CE

tag: tissue

value: BZA/CE

value: lean+BZA/CE


title: Control 1 Female

description:
Library name: Mouse_968
10X FLEX scRNAseq

value: colon tumor

value: TP KO organoids

value: Tumor Epithelial Cells

tag: treatment


title: female healthy control, recovery_replicate 5

description: Library name: 2718sHF2

value: peripheral blood mononuclear cells


title: RPK;Pdk1_3

description: CTGCGG

extract_protocol:
liver samples and liver tumors were isolated using the Maxwell 16 LEV simplyRNA Kit (Promega) according to the manufacturer’s instructions
Reverse transcription was carried out for individual samples using the Maxima RT polymerase with oligo-dT primers consisting of a sample barcode, unique molecular identifiers (UMIs) and an adaptor. Ends of cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. For fragmentation of cDNA, NEB Ultra II FS kit was used, followed by end repair and A-tailing, to which a TruSeq adapter was ligated. Finally, 3’-end-fragments were amplified using primers with Illumina P5 and P7 overhangs

value: liver tumor

tag: genotype


title: 890_mg_ob_control

source_name: Mammary gland, obese+control

value: obese

value: obese+control


title: 873_mg_l_BZA/CE

value: female


title: female healthy control, recovery_replicate 4

description: Library name: 2706sHF2

value: healthy control

value: T2 (recovery)


title: ATG9A, HER2, rep2, scRNAseq

city: San Francisco

first: Meng

last: Zhang

address: 1450 3rd Street

institute: University of California, San Francisco

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v8.0.0.
Assembly: mm39
Supplementary files format and content: output files from cell ranger, including the h5 file, count matrix, barcodes and features

source_name: xenograft tumor

growth_protocol: SKOV3 cells were cultured in RPMI supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂. Cells were infected with lentiviral vectors expressing either sgGAL4 or sgATG9A. Following infection, cells were selected with puromycin (5 µg/mL) for 72 hours to ensure stable integration of the lentiviral constructs.

extract_protocol:
Harvested tumor tissue was minced into small pieces (≤ 2 mm), transferred to tubes containing digestion medium, and incubated at 37°C for 20-30 minutes on a shaking platform (500 rpm) with intermittent pipetting. The digested tissue was filtered through 70 μm and 40 μm nylon mesh strainers, centrifuged at 300 x g for 10 minutes, and the pellet was resuspended in 1-2 mL PBS. Cells were stained for 1 hour with LIVE/DEAD™ Fixable Green Dead Cell Stain (L23101, Invitrogen) and a mouse CD45 antibody (Biolegend, 157212) before being run on a Fusion 1 cell sorter to isolate CD45+ dead cell stain- cells, which were then prepared for single-cell RNA sequencing following the standard 10x Genomics protocol.
We followed Chromium Next GEM Single Cell 3' Gene Expression v3.1 Dual Index (Rev E) Protocol. Briefly, single cells were isolated from harvested tumor tissue, counted, and loaded into the Chromium Next GEM Chip G with reagents. Gel Bead-In-EMulsions (GEMs) were generated using the Chromium Controller, incorporating unique molecular identifiers and cell-specific barcodes during reverse transcription. The barcoded cDNA was cleaned, amplified via PCR, fragmented, end-repaired, and ligated with sequencing adapters. Libraries were indexed, quantified, and quality-checked before sequencing on an Illumina platform.

treatment_protocol: Mice received intraperitoneal (IP) injections of Trastuzumab (Bio X cell, SIM0005) or human IgG isotype control (Bio X cell, BE0297) at a dose of 10 mg/kg every 2-3 weeks. Concurrently, mice were fed a diet containing the CSF1R inhibitor PLX5622 (MedChemExpress, HY-114153) at a concentration of 1200 ppm, which corresponds to an estimated mean plasma concentration of 9090 ng/mL. The diet was provided by Research Diets, USA.

tag: cell type

value: mouse immune cells

value: xenograft tumor

value: NSG

tag: age

value: 6-8 weeks


title: RPK;Pdk1_2

first: Ursula

address: Ismaninger Str. 22

institute: Klinikum rechts der Isar, TU München

description: CCCTGG

value: tamoxifen


title: female healthy control, recovery_replicate 3

description: Library name: 2682sHF2

source_name: peripheral blood mononuclear cells


title: 897_mg_l_BZA/CE

value: mammary gland (mammary adipose)

value: lean

value: ovary intact

value: BZA/CE


title: 864_mg_l_BZA/CE

value: lean+BZA/CE


title: 894_mg_l_control

value: control

value: lean+control


title: 844_mg_ob_control

value: obese


title: 899_mg_ob_control

value: obese+control


title: RPK;Pdk1_1

description: GTTCGA

value: liver tumor


title: 834_mg_ob_control

value: female


title: ATG9A, HER2, rep1, scRNAseq

description: 10X genomics


title: female healthy control, recovery_replicate 2

description: Library name: 2658sHF2

value: peripheral blood mononuclear cells

value: healthy control

value: T2 (recovery)


title: control liver_4

description: TTAGTT

source_name: liver

value: liver


title: 824_mg_l_control


title: female healthy control, maximal exertion_replicate 18

description: Library name: 5271sHF1

value: T1 (maximal exertion)


title: 833_mg_l_control


title: control liver_3

description: TAAGAT


title: female healthy control, maximal exertion_replicate 17

description: Library name: 2981sHF1


title: RRBS of Deer Mouse Left Ventricle:Lowland_normoxia7

city: Princeton

first: Dhriti

last: Tandon

state: New Jersey

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

data_processing:
We prepared the reference Peromyscus genome (Pman_2.0) with bowtie2 in BS-Seeker2 for BS-converted reads that were bounded from 50-500bp.
We demultiplexed sequence pools by retaining reads that had a perfect sequence match to the expected barcode sequence tags with an in-house python script. We then trimmed FASTQ files to remove low quality reads (Q<20) and adapter sequences clipped using cutadapt 1.8.1, discarding reads that are <20bp in length.
Trimmed reads were mapped to the reference using the bs-seeker_2-align.py script in BS-Seeker2, which uses bowtie2 to align reads in reduced representation mode by using the -r flag. The lower (-L) and upper (-U) bounds of fragment length were set to 50 and 500, respectively.
To call methylation we used the bs_seeker2-call-methylation.py script in BS-Seeker2, with default settings and the -x flag that removes reads not fully converted by the bisulfite treatment.
Assembly: Pman_2.0
Supplementary files format and content: .CGmap files contain chromosome number in column 1, nucleotide on Watson (+) strand in column 2, position (in bp) in column 3, CpG context (CG/CHG/CHH) in column 4, dinucleotide-context (CA/CC/CG/CT) in column 5, methylation-level = #_of_C / (#_of_C + #_of_T) in column 6, number of C (methylated C, the count of reads showing C here) in column 7, and number of C + number of T (all Cytosines, the count of reads showing C or T here) in column 8. Description taken from https://github.com/BSSeeker/BSseeker2.

organism: Peromyscus maniculatus

source_name: Left Ventricle

growth_protocol: Lowland mice were derived from wild-caught individuals collected in eastern Nebraska (9 mile prairie; Lancaster County, Nebraska, USA; 40°52′ 12′′ N, 96°48′ 20.3′′ W; 430 m above sea level; standard pO2=20.2 kPa). We collected highland mice from the summit of Mt. Evans in the Rocky Mountains (Clear Creek County, Colorado, USA; 39°35′ 18′′ N, 105°38′ 38′′ W; 4,350 m above sea level; standard PO2=12.8 kPa) under permits from Colorado Parks and Wildlife (CO CWP 17TR2168a) and the United States Forest Service (Authorization ID: CLC772).

extract_protocol:
We extracted genomic DNA from left ventricle tissue following Qiagen DNeasy’s protocol (Qiagen). For RRBS, we digested high molecular weight genomic DNA with the Msp1 restriction enzyme. We prepared libraries following the NEBNext sample preparation kit protocol (New England Biolabs), with a spike-in of 1ng of enterobacteria phage DNA to each genomic library as a non-methylated internal control for estimating the efficiency of bisulfite (BS) conversion downstream.
We used AMPure beads for DNA purification and to retain fragments between 100-400bp in size. The resulting fragments were treated with BS to convert unmethylated cytosines following the low DNA input (1ng-2μg) protocol in the Qiagen EpiTect Fast Bisulfite Conversion kit (Qiagen). We then conducted low amplification of the converted DNA with 12 cycles of PCR to enrich for adapter-ligated fragments with MyTaq Mix (Bioline Inc.), during which each sample was also barcoded with unique sequence tags that permitted the pooling of final genomic libraries. We collected single-end (1x100nt) SP sequencing on an Illumina Novaseq6000 in Princeton University’s Lewis Sigler Genomics Core Facility.

treatment_protocol: We exposed 28 laboratory-born and reared highland and lowland deer mice to experimental hypobaric hypoxia to assess population specific methylation responses to hypoxia exposure. We collected data from 11 additional mice captured in lowland and highland habitats.

value: Left Ventricle

tag: population

value: Lowland

tag: condition

value: Normoxia


title: GAL4, HER2, rep1, scRNAseq

description: 10X genomics

value: mouse immune cells

value: xenograft tumor

value: NSG

value: 6-8 weeks


title: RRBS of Deer Mouse Left Ventricle:Lowland_normoxia6


title: female healthy control, maximal exertion_replicate 16

description: Library name: 2957sHF1

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2, and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Raw counts from HTSeq and STAR were imported into Bioconductor/R package DESeq2, normalized, and tested for differential gene expression. This analysis was done separately for the files produced by each aligner.
Only genes with raw counts equal or more than 50 in all samples in at least one group were used for the differential gene expression analysis
For further analysis, we selected genes and exons that were differentially expressed based on one of the following two criteria: (a) either a fold change (FC) > |1.5| and false discovery rate (FDR) < 0.10 in one out of the three aligners and FC > |1.4| and FDR < 0.15 in the remaining two aligners, OR (b) a FC > |1.5| and FDR < 0.10 in two out of three aligners.
Assembly: GRCh38, release 103
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 50 in all samples in at least one group

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center) according to the manufacturer’s instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent Technologies). All RNA samples had an RNA Integrity number (RIN) above seven.
The libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: disease state

tag: time point_in_exercise


title: RRBS of Deer Mouse Left Ventricle:Lowland_normoxia5


title: female healthy control, maximal exertion_replicate 15

description: Library name: 2945sHF1

tag: Sex


title: control liver_1

city: Munich

last: Ehmer

description: AAATTG


title: Wildtype replicate 3

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Statistical tests for differential expression were performed using sleuth.
Assembly: mm10
Supplementary files format and content: Comma-separated file includes tpm levels of individual primary transcripts for each sample as well as statistical results for differential gene abundance between genotypes.

source_name: colonic organoids

growth_protocol: Colonic epithelial crypts were isolated from colons of wildtype or Tnfr1-/- mice, embedded within Matrigel, and grown with a layer of Intesticult media. The resulting organoids were passaged 5 times before filtration through a 70-µm nylon mesh filter and subsequent seeding for the experiment. Organoids of both wildtype and knockout genotypes were isolated at 7 days post-passage.

extract_protocol:
Organoids were placed in Trizol and homogenized. The Direct-zol kit (Zymo) was used to isolate total RNA.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on a NextSeq High Output Run.

value: colonic organoids

tag: days post passage

value: Wildtype


title: 817_mg_ob_BZA/CE

value: mammary gland (mammary adipose)

value: obese

value: ovary intact

value: BZA/CE

value: obese+BZA/CE


title: female healthy control, maximal exertion_replicate 14

first: Lubov

address: 3321 College Ave.

institute: Nova Southeastern University

description: Library name: 2930sHF1

value: peripheral blood mononuclear cells

value: healthy control

value: female


title: RRBS of Deer Mouse Left Ventricle:Lowland_normoxia4

value: Left Ventricle


title: RRBS of Deer Mouse Left Ventricle:Lowland_normoxia3

value: Lowland


title: Knockout replicate 3


title: Wildtype replicate 2


title: female healthy control, maximal exertion_replicate 13

description: Library name: 2929sHF1

value: T1 (maximal exertion)


title: 816_mg_ob_BZA/CE


title: control liver_2

description: ATGAAT

value: liver


title: Knockout replicate 2


title: RRBS of Deer Mouse Left Ventricle:Lowland_normoxia1

value: Normoxia


title: female healthy control, maximal exertion_replicate 11

description: Library name: 2777sHF1


title: 807_mg_l_BZA/CE

value: lean

value: lean+BZA/CE


title: RRBS of Deer Mouse Left Ventricle:Lowland_hypoxia4

value: Hypoxia


title: female healthy control, maximal exertion_replicate 12

description: Library name: 2825sHF1


title: Wildtype replicate 1

value: colonic organoids

value: Wildtype


title: nPaf_KPCY2

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

country: Japan

institute: Hirosaki University Graduate School of Medicine

hyb_protocol: Fragmented and biotin-labeled single-strand cDNA (5.5 μg each) hybridized on Clariom™D array, mouse (Themofisher Scientific, #902511) for 16 h at 45°C with rotation at 60 rpm using GeneChip® Hybridization Oven 645.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (ThermoFisher Scientific).

data_processing:
The data were analyzed with Transcriptome Analysis Console version 4.0.2 (ThermoFisher Scientific) using default settings for backgroud correction, normalization and summarization.
algorithm-name-0 = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
algorithm-name-1 = gc-correction,pm-only,dabg
Q_probeset_summarize-Version = V957
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program_name = q_probeset_summarize.exe

label: biotin

source_name: subcutaneous tumor, nPaf+KPCY

label_protocol: Fragmented single-strand cDNA were subjected to 3' terminal labeling with biotin using GeneChip® WT PLUS Reagent Kit in accordance with manufacturer's protocol.

growth_protocol: Mice were housed in plastic cages containing wood chips and covered with a wire lid. The cages were kept at 23±2 °C under a 12 h light/dark cycle (lights on at 8:00). The diet were standard laboratory food and water ad libitum. The mixture of fibroblasts and cancer cell lines was injected into the right flank of 10-week-old female mice, which were sacrificed four weeks later.

extract_protocol: For gene expression analysis, subcutaneous tumors were dissected at day 14, lysed in 1 mL TRI reagent (Molecular Research Center, Inc.) and total RNA was isolated using RNeasy kits (QIAGEN Sciences, Germantown RD, MD, USA) following manufacturers recommendations.100 ng of total RNA was subsequently carried out to First-strand cDNA synthesis using GeneChip® WT PLUS Reagent Kit (ThermoFisher Scientific, #902281).

treatment_protocol: One the day of injection, dissociated cells were washed twice with ice-cold PBS and counted in duplicate using TC20 Automated Cell Counter on bright-field mode. Ice-cold growth factor reduced Matrigel were added using pre-cooled pipette tips to obtain a final concentration of each cell type of 5000 cells/uL and gently mixed on ice. BD Lo-Dose™ U-100 Insulin Syringes (Becton Dickinson™, Franklin Lakes, NJ, USA) were used to accurately measure 20 uL of cell/ Matrigel mix with no dead-volume, which was injected subcutaneously into the right flank of the mouse.

tag: strain

value: 14-week old

value: subcutaneous tumor, nPaf+KPCY


title: Knockout replicate 1


title: RRBS of Deer Mouse Left Ventricle:Lowland_hypoxia3


title: female healthy control, maximal exertion_replicate 10

city: Fort Lauderdale

last: Nathanson

description: Library name: 2765sHF1


title: 815_mg_ob_BZA/CE

value: mammary gland (mammary adipose)

value: obese

value: ovary intact

value: BZA/CE


title: 802_mg_ob_BZA/CE

source_name: Mammary gland, obese+BZA/CE

value: female

value: obese+BZA/CE


title: MHCC97H cells,shPTBP1-3

city: Guangzhou

first: wenying

last: zheng

state: --- Select One ---

address: No.78 Hengzhigang Road, Yuexiu District, Guangzhou City, Guangdong Province, Chi

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Cutadapt(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
HISAT2(https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package was used to align reads of all samples to the reference genome
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: hg38
Supplementary files format and content: FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencinglibrary. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)(Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module(NEB, cat.e6150, USA) under 94℃ 5-7min).
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used tosynthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR.

value: Liver

tag: cell line

value: Hepatocellular carcinoma cell

value: PTBP1 Knockdown


title: 813_mg_ob_BZA/CE


title: 806_mg_l_control

value: control

value: lean+control


title: nPaf_KPCY1


title: RRBS of Deer Mouse Left Ventricle:Lowland_hypoxia1

value: Left Ventricle

value: Lowland


title: female healthy control, maximal exertion_replicate 8

description: Library name: 2741sHF1

value: peripheral blood mononuclear cells

value: healthy control

value: T1 (maximal exertion)


title: MHCC97H cells,shPTBP1-1


title: female healthy control, maximal exertion_replicate 7

description: Library name: 2729sHF1


title: female healthy control, maximal exertion_replicate 9

description: Library name: 2753sHF1


title: RRBS of Deer Mouse Left Ventricle:Lowland_normoxia2

value: Normoxia


title: nPaf_KPCY3

value: 14-week old

value: subcutaneous tumor, nPaf+KPCY


title: RRBS of Deer Mouse Left Ventricle:Lowland_hypoxia2

value: Hypoxia


title: myPaf_KPCY2

source_name: subcutaneous tumor, myPaf+KPCY

value: subcutaneous tumor, myPaf+KPCY


title: MHCC97H cells,shPTBP1-2


title: myPaf_KPCY3

value: female


title: myPaf_KPCY1


title: MHCC97H cells,shControl-3

value: WT


title: female healthy control, maximal exertion_replicate 6

description: Library name: 2717sHF1


title: 803_mg_ob_control

value: mammary gland (mammary adipose)

value: obese

value: ovary intact

value: obese+control


title: female healthy control, maximal exertion_replicate 5

description: Library name: 2705sHF1


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia9

value: Highland


title: MHCC97H cells,shControl-2

value: Liver

value: Hepatocellular carcinoma cell


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia8

value: Left Ventricle


title: Rat Cd43+ cells M2 +rat MCSF 50 ng +IL4 (106 cells) 3

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

data_processing:
nf-core/rnaseq
Assembly: rn6
Supplementary files format and content: comma delimeted text files include raw gene count values for each Sample

source_name: Cd43+ cells

extract_protocol:
Total RNA was extracted with the Extract RNA reagent (Evrogen, Russia) according to the manufacturer’s protocol.
Libraries were constracted with TruSeq RNA Sample Prep Kit v2 using standart Illumina protocol

value: Cd43+ cells

value: Rat Cd43+ cells M2


title: MHCC97H cells,shControl-1


title: Rat Cd43+ cells M2 +rat MCSF 50 ng +IL4 (106 cells) 2


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia7

value: Normoxia


title: ESC~MNs_Replicate 3

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

institute: Academia Sinica

description:
Library name: ESC~MNs_Replicate 3
NP271_pass

data_processing:
Base-calling using Guppy (22.10.7) in MinKNOW, reads that passed the quality threshold were subjected to post-run base-calling with the latest version of Guppy (6.3.9) under default parameters. A reference transcriptome file was generated from the mouse genome reference and corresponding annotation. The Nanopore data provided in FASTQ format were initially aligned to the mouse genome reference from GenCode M20 using the minimap2 aligner. The resulting SAM format output was then converted to a sorted BAM format using samtools.
Assembly: mm10
Supplementary files format and content: xlsx file revealed the m6A modifications sites from Epinano and m6Anet prediction

source_name: mouse ESC

growth_protocol: Mouse embryonic stem cells were differentiated into motor neurons following published protocols. Specifically, in this condition, we cultured the 3D embryoid bodies for five days, then attached the culture of the embryoid bodies to poly-ornithine and laminin-coated plates with an enrichment of neurotrophic factors (30 ng/mL GDNF, Peprotech) and cultured them for an extra 5 days (Day12). Change the medium every two days.

extract_protocol:
Trizol RNA were extracted by Trizo follow by mRNA enrichment by Dynabeads™ mRNA Purification Kit.
Direct RNA sequencing (SQK-RNA002) were adapted for the library construction.

value: mouse ESC

value: ESC~MNs (mature)


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia6


title: ESC~MNs_Replicate 2

description:
Library name: ESC~MNs_Replicate 2
NP270_pass


title: female healthy control, maximal exertion_replicate 2

description: Library name: 2657sHF1

value: peripheral blood mononuclear cells

value: healthy control

value: T1 (maximal exertion)


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia5


title: ESC~MNs_Replicate 1

description:
Library name: ESC~MNs_Replicate 1
NP185_pass

value: WT


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia10


title: Rat Cd43+ cells M1 +rat MCSF 50 ng +LPS 50 ng (106 cells) 2

value: Rat Cd43+ cells M1


title: Rat Cd43+ cells M1 +rat MCSF 50 ng +LPS 50 ng (106 cells) 1


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia4


title: female healthy control, baseline_replicate 17

description: Library name: 2956sHF0

value: T0 (baseline)

value: female


title: RNAseq_Caf40KD_testes_rep2

city: Stanford

first: Neuza

last: Reis Matias

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

description: Library name: RNAseq_Caf40KD_testes_rep2

data_processing:
Adapters and low-quality bases were trimmed with trimGalore: trim_galore –quality 20 –stringency 1 –length 30 –paired_end –clip_R1 3 $Input1 $Input2 –output_dir trim_PE/
Reads were mapped to the Drosophila melanogaster genome build dm6 using STAR. Reads that fell within gene regions were counted with STAR using Ensembl annotation BDGP6.84. star_pass1: STAR –runThreadN 4 –runMode alignReads –genomeDir $star_index –alignSJoverhangMin 10 –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –readFilesIn $Input1_trimmed $Input2_trimmed –outFileNamePrefix $pass1_prefix –outSAMtype None. star_pass2: STAR –runThreadN 4 –runMode alignReads –quantMode GeneCounts –genomeDir $star_index –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –sjdbFileChr- StartEnd $junction –readFilesIn $Input1_trimmed $Input2_trimmed –out- SAMtype BAM SortedByCoordinate –limitBAMsortRAM 10000000000 –outFileNamePrefix $pass2_prefix.
DEseq2 was used for gene expression analysis
Assembly: Ensembl annotation BDGP6.84
Supplementary files format and content: STAR output: ReadsPerGene
Supplementary files format and content: DEseq2 output: normalized counts and fold change (txt)

organism: Drosophila melanogaster

source_name: Testes

extract_protocol:
total RNA was extracted using the kit: RNeasy Plus Mini Kit from QIAGEN
Library was constructed using the kit: NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760S) using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490S).

treatment_protocol: 150 pairs of testes per sample were dissected in PBS in a glass cyclops dish in batches of 50 pairs. Testes were transferred to a 1.7 ml tube with PBS using forceps. PBS was removed and the sample snap-frozen in liquid nitrogen. Samples were kept at −80°C until the next step.

value: Testes

value: Flies were raised at 25˚C for 3 days, then shifted to 29˚C after discarding adults. Males were dissected 0-2 days after eclosion.


title: female healthy control, maximal exertion_replicate 4

description: Library name: 2693sHF1


title: Rat Cd43+ cells M0+rat MCSF 50 ng (106 cells) 3

value: Rat Cd43+ cells M0


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia2

value: Highland


title: female healthy control, maximal exertion_replicate 3

description: Library name: 2681sHF1


title: Rat Cd43+ cells M2 +rat MCSF 50 ng +IL4 (106 cells) 1


title: RNAseq_bam_testes_rep2

description: Library name: RNAseq_bam_testes_rep2

value: Flies were raised at 22˚C until there were mid- and late-stage pupa. Then bottles were placed in a 37˚C water bath for 30 minutes to induce heat shock (although no heat shock promoter present) and returned to 25˚C. Flies were dissected after 48hrs post-heat shock


title: Rat Cd43+ cells M0+rat MCSF 50 ng (106 cells) 2

value: Cd43+ cells


title: RRBS of Deer Mouse Left Ventricle:Highland_hypoxia7

value: Left Ventricle

value: Hypoxia


title: female healthy control, baseline_replicate 14

description: Library name: 2836sHF0


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia1

value: Normoxia


title: female healthy control, baseline_replicate 18

description: Library name: 2980sHF0


title: Rat Cd43+ cells M1 +rat MCSF 50 ng +LPS 50 ng (106 cells) 3


title: female healthy control, baseline_replicate 13

description: Library name: 2812sHF0


title: G73_25_Piwi-sKD

city: Montpellier

first: severine

last: chambeyron

address: 141 rue de la cardonille

institute: CNRS-Montpellier University

description: Library name: G73_25_Piwi-sKD

library_source: other

data_processing:
Raw reads were trimmed from their 3′ linkers and loaded on a homemade pipeline available at (https://bitbucket.org/blaiseli/pirna-pipeline ) previously used.
Trimmed reads (18–30nts in size) were mapped with Bowtie2 using mismatch-tolerant settings to the Drosophila melanogaster genome (release 5; dm3) complemented with canonical TEs (Drosophila consensus TE sequences taken from https:// github.com/cbergman/transposons).
Reads were annotated based on their mapping coordinates. Small RNAs mapping on piRNA clusters, ovary siRNA clusters, TEs or 3′UTR of coding genes (ftp://ftp.flybase.net/), and not to rRNAs or miRNAs were defined.
Candidate piRNAs were a subset of the above defined reads with a size between 23 and 30 nucleotides. Candidate piRNAs were mapped again on canonical TE sequences. Data were normalized using the total of piRNA reads.Biqwig were computed using bamCoverage package from deepTools (default parameters).
Assembly: Release 5 ; dm 3
Supplementary files format and content: bam

molecule: other

source_name: ovaries

extract_protocol: Small RNAs from ovaries collected at permissive (25°C) and non-permissive (20°C) temperature, for Piwi-sKD, were isolated using TraPR ion exchange spin columns (Lexogen, Catalog Nr.128.08). The libraries were performed by MGX-Biocampus Montpellier platform using the NEBNext® Small RNA Library Prep Set for Illumina® from NEB. 150 nt paired-end read (28 bp for R1 and 90 bp for R2) sequencing on NOVASEQ 6000 apparatus was performed by MGX. Only the R2 file contains information.

treatment_protocol: Purified PGC cells and somatic cells by flow cytometry

value: ovaries

value: Flies at 25 degrees


title: RRBS of Deer Mouse Left Ventricle:Highland_hypoxia6


title: female healthy control, baseline_replicate 12

description: Library name: 2788sHF0

value: peripheral blood mononuclear cells

value: healthy control


title: G73_20_ctrl

description: Library name: G73_20_ctrl

value: Flies at 20 degrees


title: female healthy control, baseline_replicate 16

description: Library name: 2927sHF0


title: RNAseq_Caf40KD_testes_rep1

description: Library name: RNAseq_Caf40KD_testes_rep1


title: RRBS of Deer Mouse Left Ventricle:Highland_normoxia3


title: female healthy control, baseline_replicate 11

description: Library name: 2776sHF0


title: RRBS of Deer Mouse Left Ventricle:Highland_hypoxia5


title: RRBS of Deer Mouse Left Ventricle:Highland_hypoxia4


title: female healthy control, baseline_replicate 15

description: Library name: 2925sHF0


title: female healthy control, baseline_replicate 10

description: Library name: 2764sHF0


title: G0-F100_25_Piwi-sKD

description: Library name: G0-F100_25_Piwi-sKD


title: G0-F100_20_ctrl

description: Library name: G0-F100_20_ctrl


title: RRBS of Deer Mouse Left Ventricle:Highland_hypoxia3


title: Rat Cd43+ cells M0 +rat MCSF 50 ng (106 cells) 1


title: female healthy control, baseline_replicate 9

description: Library name: 2752sHF0


title: ATAC-seq,somatic cells,late Drosophila embryos rep2

data_processing:
Using cutadapt (v4.2) the ATAC-seq read were trimmed in 3’ and 5’ (-a CTGTCTCTTATACACATCTNNNNNNNN -A AGATGTGTATAAGAGACAGNNNNNNNN)
Trimmed reads were aligned to he Drosophila genome using bowtie2 (v2.5.1)
Duplicates were removed using the fixmate and mardup packages of samtools (v1.17)
The read coverage normalized by RPKM (--normalizeUsing) were computed using bamCoverage package from deepTools (v3.5.4.post1) with default parameters, excluding regions (-bl) identified as blacklisted in dm6.
Assembly: Dmel_R6.32
Supplementary files format and content: bigWig

source_name: Purified somatic cells from late embryos

growth_protocol: The flies were kept at 25°C

extract_protocol:
ATAC-Seq experiments were performed using the ATAC-Seq kit from Diagenode (catalogue no. C01080002). Input material was between 100,000 to 130,000 cryopreserved PGCs (GFP positive) cells or somatic (GFP negative) cells isolated from whole embryos.
Tagmentated DNA was amplified by PCR using 13 cycles and the purified DNA libraries were sequenced (paired-end sequencing 150 bp, roughly 2 Gb per sample) by Novogene (https://en.novogene.com/). ATAC-Seq were performed in duplicates, following Encode’s standards (https://www.encodeproject.org/atac-seq/#standards).


title: RNAseq_bam_testes_rep1

description: Library name: RNAseq_bam_testes_rep1


title: Heart_3days_Sham_rep3

city: Zhanjiang

first: Fanji

last: Meng

address: 12# Minyou Road, Xiashan District

department: Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University

institute: Guangdong Medical University

description: tsRNA expression after 3days in myocardium of sham mouse

hyb_protocol: 22.5 uL 2X Hybridization buffer (Agilent) was mixed with the completed labeling reaction to a final volume of 45 uL. The mixture was heated at 100°C for 5 min and chilled immediately to 0°C. 45 uL labeled sample mix was hybridized onto a microarray at 55°C for 20 hrs. The slides were washed at room temperature in 6X SSC with 0.005% Triton X-102 for 10 min, then in 0.1X SSC with 0.005% Triton X-102 for 5 min. The slides were scanned on an Agilent G2505C microarray scanner.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies).After normalization, the probe signals having Present (P) or Marginal (M) QC flags in a certain proportion were retained. Multiple probes from the same small RNA (miRNA/TsRNA (tRF&tiRNA)/pre-miRNA/tRNA/snoRNA) were combined into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds. Hierarchical Clustering heatmaps, scatter plots and volcano plots were plotted to display small RNAs expression pattern among samples by R software.

label_protocol: For Small RNA Microarray profiling, 100 ng total RNA was firstly dephosphorylated with 3 units T4 polynucleotide kinase (T4 PNK) at 37°C for 40 min to remove both (P) and (cP) chemical groups from the 3' end of RNAs to form a 3-OH end. The reaction was terminated at 70°C for 5 min and cooled immediately to 0°C. 7 uL of DMSO was added and heated to 100°C for 3 min to denature the RNAs and chilled immediately to 0°C. RNA end labeling was performed by adding ligase buffer, BSA, final 50 mM pCp-Cy3, and 15 units T4 RNA ligase in a 28 uL reaction at 16°C overnight.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis.

treatment_protocol: Mice were randomly divided into the sham group and the myocardial infraction (MI) group. Ligation of left anterior descending coronary artery was conducted in the MI group and myocardial ischemia was confirmed withe elevated ST-segment in electrocardiogram. However, string went through the corresponding myocardial region without ligation in the sham group. Finally, heart samples were collected from the infarction area in the MI group and the corresponding region in the sham group. Heart samples were refrigerated at −80°C for further detection.

value: heart

tag: gender

value: male

value: 6-8 weeks

tag: weight


title: RRBS of Deer Mouse Left Ventricle:Highland_hypoxia2


title: Heart_3days_Sham_rep1


title: ATAC-seq,somatic cells,late Drosophila embryos rep1

value: Purified somatic cells from late embryos


title: female healthy control, baseline_replicate 8

description: Library name: 2740sHF0

value: T0 (baseline)

value: female


title: GAL4, HER2, rep2, scRNAseq

description: 10X genomics

value: mouse immune cells

value: xenograft tumor

value: NSG


title: ATAC-seq,PGC,late Drosophila embryos rep2

source_name: Purified PGC cells from late embryos

value: Purified PGC cells from late embryos


title: 8 Control

description:
Library name: Sample_8
Illumina NovaSeq X

source_name: colon tumor

value: colon tumor

value: 817 Organoids

value: Tumor Epithelial Cells

value: Vehicle


title: RRBS of Deer Mouse Left Ventricle_wild11

value: Left Ventricle

value: Wild (Highland habitat)

value: Female


title: female healthy control, baseline_replicate 6

description: Library name: 2716sHF0

value: peripheral blood mononuclear cells

value: healthy control


title: Heart_3days_Coronary artery ligation_rep3

description: tsRNA expression after 3days in coronary artery ligation-induced myocardial infarction in mouse

value: heart

value: male

value: 6-8 weeks


title: ATAC-seq,PGC,late Drosophila embryos rep1


title: Heart_3days_Coronary artery ligation_rep2


title: RRBS of Deer Mouse Left Ventricle_wild10

value: Wild (Lowland habitat)


title: 7 Control

description:
Library name: Sample_7
Illumina NovaSeq X