title: Brain, HGC, LAR, Mouse 17

description: Library name: 239_Brain_HC-LAR-17_L1_1

data_processing:
Fastq files containing raw sequencing reads were mapped against GRCm39 and miRBase (version 22.1) 65 in order to profile miRNA counts using miRmaster (version 2.0). Information about miRNA family was obtained from mirgenedb 3.0. Detection filtering was performed by keeping only miRNAs with at least 5 raw reads in at least 10% of samples in each condition-tissue group. Expression data was normalized using rpmm normalization (reads per mapped million).
Assembly: GRCm39
Supplementary files format and content: miRNA_complete_quantification_raw.tsv: Tab-separated file of raw miRNA counts per sample.
Supplementary files format and content: lncRNA_complete_quantification_raw.tsv: Tab-separated file of raw lncRNA counts per sample.
Supplementary files format and content: piRNA_complete_quantification_raw.tsv: Tab-separated file of raw piRNA counts per sample.
Supplementary files format and content: rRNA_complete_quantification_raw.tsv: Tab-separated file of raw rRNA counts per sample.
Supplementary files format and content: scaRNA_complete_quantification_raw.tsv: Tab-separated file of raw scaRNA counts per sample.
Supplementary files format and content: snoRNA_complete_quantification_raw.tsv: Tab-separated file of raw snoRNA counts per sample.
Supplementary files format and content: snRNA_complete_quantification_raw.tsv: Tab-separated file of raw snRNA counts per sample.
Supplementary files format and content: tRNA_complete_quantification_raw.tsv: Tab-separated file of raw tRNA counts per sample.

extract_protocol:
LAR mice were anesthetized with gas anesthesia and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The liver was removed, weighed, dissected into individual lobes (1- left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen. All tissues were collected and frozen within 10-16 minutes of thoracotomy procedure. All groups were treated identically. Organ samples were maintained at -80C or lower temperatures throughout the storage, and during transportation and shipment. TERM mice were anesthetized with ketamine/xylazine/acepromazine at a dose of 120/15/3 mg/kg and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The spleen was dissected fresh from each carcass and placed in a tube containing RNA Later. The carcass was then wrapped in foil and frozen in MELFI on board the ISS or in ground -80C freezers. Carcasses were maintained at -80C or lower temperatures throughout the storage on board the ISS, in ground freezers and during transportation and shipment. The mice were brought back to earth where dissection was held. It should be noted that carcasses frozen whole onboard the ISS were free-floating and thus in direct contact with air. This prevented them from snap freezing like samples collected on Earth which were placeddirectly in liquid nitrogen. Carcasses were thawed at room temperature one at a time (staggered)until the tissues were sufficiently pliable for dissection (approximately 60-90 minutes). Once thawed, multiple tissues were collected from each carcass within 30min of the first tissue collected. The liver was removed from each carcass, weighed, dissected into individual lobes (1-left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen.  The miRNeasy-96 protocol was followed for all samples with some modifications, as follows. Tissue Preparation: To avoid overloading the miRNeasy-96 columns, some frozen samples were trimmed to smaller sizes. All kidney, liver, and spleen samples were all trimmed to ~25mgs due to their high RNA content. Pancreas samples were trimmed to ~25mgs if they exceeded 45mgs. GAT, MAT, and SCAT samples >200mgs were trimmed to ~100mgs as samples of large size homogenize poorly in 96-well format, even though adipose tissues have relatively low RNA content. BAT and lung samples >100mgs were trimmed to ~50mgs, and thymi >50mgs were trimmed to ~25mgs. The diaphragm did not require trimming, and whole hemi-brains and whole hearts were homogenized by hand with the TissueRuptor in 1ml QIAzol per 50mgs tissue, since trimming samples in a reproducible way to capture the same organ subregion for each would be difficult. Bead homogenization: All samples, including those previously homogenized with the TissueRuptor, were randomized in 96-well format. Two 96-well plates were run simultaneously as follows. 96-well collection microtube plates were chilled on dry ice, and trimmed tissue samples were placed at the bottom of each well. One pre-chilled 5mm stainless steel bead was then placed on top of the tissue samples with bead dispenser. 700ul pre-chilled (4C) QIAzol was then added to each well, or 700ul QIAzol homogenate from the pre-homogenized heart and brain samples. Plates were immediately homogenized on the TissueLyser II for a total of four 5min runs at 25Hz, and plates were rotated and switched between the two arms of the TissueLyser II between each run. Plates were then left at room temperature for 5min before pelleting debris at 6000 x g for 1min at 4C. Phase Separation & RNA collection: Debris- and bead-free homogenate was then transferred to a new plate, to which 140ul chloroform was added to each well, and plates were shaken vigorously for 3min at room temperature before being spun at 6000 x g for 4min at 4C. 300ul aqueous phase was then transferred to a new S-Block, to which 525ul 100% EtOH was added and mixed by pipetting, followed by a room temperature spin at 6000 x g for 30s. The entire volume was then transferred to a miRNeasy-96 plate on top of an S-plate, sealed with AirPore tape sheet, and spun at 5600 x g for 4min at room temperature. Flow through was discarded, and columns washed with 800ul RWT and spun as above. This was repeated with 800ul RPE, and a final 800ul RPE wash was followed by a 10min spin. Finally, 50ul RNase-free water was added to each column and incubated at room temperature for 1min, then spun at 5600 x g for 4min at room temperature. The elution was repeated with a second volume of 50ul RNase-free water. RNA samples were stored at -80C.
All samples were processed using the MGIEasy Small RNA Library Prep Kit with the high-throughput MGI SP-960 sample prep system according to the manufacturer's protocol to generate sequencing libraries.

value: Brain


title: tissu DNA from high-grade colon adenoma 17

status: Public on Dec 18 2025

type: genomic

city: Besançon

first: Alexis

last: Overs

address: 16 route de Gray

country: France

institute: University of Franche-Comte

description: genomic DNA from colon high-grade adenoma

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and stadard recommended Illumina scanner setting

data_processing:
minfi package (v1.52.1) in R environnement (v4.4.2)
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: colon adenoma

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from FFPE samples using the QIAmp DNA Mini Kit according to the manufacturer’s instructions

tag: tissue

value: colon adenoma

tag: Sex

value: Male

tag: age

tag: laterality

value: Left

tag: disease state

value: high-grade colon adenoma


title: Sperm total RNA, Duroc boar 2, 10 months, mature

type: SRA

city: Hamar

first: Asmita

last: Shrestha

state: Innlandet

address: Holsetgata 22

department: Department of Biotechnology

country: Norway

institute: University of Inland Norway

description: Library name: B9_10mo_RNA

library_source: transcriptomic

data_processing:
Quality control: FastQC v0.12.1.
Adapter trimming: Trim Galore v0.6.10 with parameters --quality 20 --stringency 3 --length 35 --paired (for RNA-seq) or single-end mode (miRNA-seq), --trim-n option enabled.
Total RNA-seq alignment: HISAT2 v2.2.1 alignment to Sus scrofa genome, SAM to BAM conversion using SAMtools v1.16.1.
Gene quantification: featureCounts (Subread v2.0.4) with parameters -p (paired-end), -t exon, -g gene_id, -s 2 (reverse stranded).
miRNA-seq processing: sRNAbench from sRNAtoolbox suite v1.0 with default parameters, annotation against miRBase v21 for Sus scrofa small non-coding RNAs.
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text files with gene/miRNA identifiers in first column and sample expression counts in subsequent columns. Column headers correspond to library names from SAMPLES section. RNA-seq file contains Ensembl gene IDs and raw counts from featureCounts. miRNA-seq file contains miRNA IDs from miRBase and raw counts from sRNAbench.

molecule: total RNA

organism: Sus scrofa

source_name: spermatozoa

extract_protocol:
Fresh semen containing 200 million sperm/ml was centrifuged at 600×g for 10 min at RT. Sperm pellets were washed with PBS and subjected to somatic cell lysis using 1 mL somatic cell lysis buffer (0.1% SDS, 0.5% Triton X-100) for 30 min on ice, then washed at 200×g for 15 min at 4°C. Sperm were washed twice with PBS (600×g, 10 min, 4°C) and snap-frozen. RNA extraction: sperm lysed with 1 mL Qiazol and 120 µL TCEP, vortexed 5 min, incubated at 56°C for 60 min. RNA isolated using miRNeasy Mini Kit (Qiagen) with on-column DNase digestion, eluted in 40 µL RNase-free water.
Total RNA-seq: Using 4 µL RNA (8.8-61.2 ng), rRNA depletion performed with QiaSeq FastSelect HMR reagents following manufacturer's protocol for partially degraded RNA (RIN 2-6). Libraries prepared with NEBNext Ultra II Directional Library Prep Kit from step 4.2, adapters diluted 1:25, 16 PCR cycles amplification. miRNA-seq: Libraries prepared using QiaSeq miRNA library kit with 5.5-38.3 ng RNA input, adapters diluted per manufacturer recommendations, 18 PCR cycles amplification. All samples indexed with unique adapters.
miRNA-seq: Libraries prepared using QiaSeq miRNA library kit (Qiagen) with 5.5-38.3 ng total RNA input. Adapters diluted according to manufacturer recommendations based on RNA input amount. Libraries amplified with 18 PCR cycles. Samples indexed with unique adapters to enable multiplexing on single sequencing run.

value: spermatozoa

tag: cell type

value: sperm

tag: genotype

value: Duroc

tag: treatment

value: 10 months


title: E9.5, rep2

city: Houston

first: Ziyue

last: Yang

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

description: Library name: 5_1189G

data_processing:
The FASTQ files were downloaded from BaseSpace Sequence Hub (Illumina). The quality control, alignment, and annotation were done following COMPSRA pipeline88 with the parameters -ref mm10 -qc -ra TGGAATTCTCGGGTGCCAAGG -rb 4 -rh 20 -rt 20 -rr 20 -rlh 8,17 -aln -mt star -ann -ac 1, and then mapped reads were quantified with -fun -fm -fms 1-12 -fdclass 1,2 -fdann -pro COMPSRA_MERGE. Raw read counts for individual miRNAs with the same seed sequence89 were summed up to calculate raw counts for each miRNA family.
Assembly: GRCm39
Supplementary files format and content: txt, raw read count

organism: Mus musculus

source_name: Pancreas E9.5

extract_protocol:
Cells were sorted into Trizol LS and RNA was extracted using miRNeasy micro kit (Qiagen 217084)
Small RNA libraries were generated with the NEXTflex Small RNA-Seq kit v3(NOVA5132, Bioo Scientific). After PCR amplification, small RNA libraries were purified via TBE-PAGE (4565014, Biorad).

value: Pancreas E9.5

tag: cell line

value: Pancreas

value: Pdx1-Cre labelled cells

value: Pdx1-Cre, tdtomato+


title: E9.5, rep3

description: Library name: 6_1189I

source_name: Pancreas, E9.5

value: Pancreas, E9.5


title: Sperm total RNA, Duroc boar 6, 10 months, mature

description: Library name: B15_10mo_RNA


title: Sperm total RNA, Duroc boar 3, 10 months, mature, replicate 1

description:
Library name: B11_10mo_RNA_rep1
Technical replicate 1 - BAM files merged after alignment with B11_10mo_RNA_rep2 BAM files before downstream analysis


title: GAT, FL, VGC, LAR, Mouse 3

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

country: Germany

institute: Saarland University

description: Library name: 237_GAT_FL-LAR-3_L1_1

source_name: GAT

growth_protocol: For the Rodent Research Reference Mission 1 (RRR-1) / Rodent Research-8 (RR-8) 40 BALB/cAnNTac female mice were sent to the International Space Station (ISS) on 12/5/2018 (Flight mice).VGC mice were housed at NASA Kennedy Space Center in standard vivarium conditions at 4 mice per cage, 20-22.2 °C, 12hr light 12hr dark. HGC mice housing was matched to the conditions experienced by Flight mice (as closely as possible) by using double density housing (same Habitat Units and Transporters as Flight mice at launch), matched temperature, humidity, and carbon dioxide levels based on actual flight environmental monitoring. To dissect all mice together in matching conditions, VGC and HGC mice were transported to Scripps Institute just before the return of the Flight mice and were dissected in matching conditions (+/- 1 day).From each of the main experimental groups, half of the mice were assigned to the ISS Terminal (ISS Term) subgroup, which were sacrificed onboard the ISS (Flight) or on Earth (VGC, HGC) 22-24 days after launch. The other half were assigned to the Live Animal Return (LAR) group, which were returned alive to Earth on 1/14/2019 after 39.5 days on the ISS, and collected 2-4 days after splashdown following functional assays at Scripps Research Institute.

value: GAT

tag: experiment group

value: VGC-LAR

value: female

tag: strain

value: BALB/cAnNTac

tag: mouse id

value: 8 months


title: Diaphragm, VGC, TERM, Mouse 13

description: Library name: 238_Diaphragm_VGC-_ISS_Term-_13_L1_1

source_name: Diaphragm

value: Diaphragm

value: VGC-TERM


title: E11.5, rep1

description: Library name: 10_1190C

source_name: Pancreas, E11.5

value: Pancreas, E11.5


title: E8.5, rep3

description: Library name: 3_1209E

source_name: Endoderm E8.5

value: Endoderm E8.5

value: Endoderm

value: Foxa2-CreER labelled cells

value: Foxa2-CreER, tdtomato+


title: Sperm total RNA, Duroc boar 5, 7 months, pubertal

description: Library name: B14_7mo_RNA

value: spermatozoa

value: sperm

value: Duroc

value: 7 months


title: Sperm total RNA, Duroc boar 6, 7 months, pubertal

description: Library name: B15_7mo_RNA


title: hFLO, CD45- EPCAM+, day 30, line 72_3

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Samples were sequenced at a depth of 20M paired-end (40M total) reads per sample reads per sample by Medgenome Inc.
The FASTQ files from paired-end sequencing were initially processed (including trimming, filtering low-quality reads, and removing adaptors) using the command line tool fast (Chen et al. 2018, Bioinformatics)
Quantification is performed via psuedoalignment using the R package Kallisto against the human reference transcriptome hg38 (Bray et al. 2016, Nat Biotech)
Gene counts are then estimated from the resulting transcript abundances using the R package tximport (Soneson et al, 2015, F1000Res)
Samples are combined into a final counts matrix. The function mnnCorrect from the R package Batchelor was adapted to correct the counts for batch effects using a mutual nearest neighbors method60. Differentially expressed genes were then identified between populations of interest using R package DESeq2 (Love at al, 2014, Genome Biol) and visualized using volcano plots. The corrected counts matrix is log-transformed for principal component analysis, and principal components are calculated and visualized. The top and bottom 100 genes from the first four principal components are subsets from the normalized counts and used for generating the expression heatmap.
Assembly: hg38
Supplementary files format and content: comma-separated values files include CPM values for each Sample

extract_protocol:
RNA was harvested using Arcturus™ PicoPure™ RNA Isolation Kit (ThermoFisher) or Rneasy mini plus kit (Qiagen, only iPSC-derived monocytes and iPSC-derived granulocytes). Takara SMART-Seq v4 Ultra low Input RNA kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Medgenome Inc.

value: hFLO-fetal hepatocytes

value: wildtype

value: No treatment

tag: time

value: Day 30


title: tissu DNA from high-grade colon adenoma 16

value: colon adenoma

value: Male

value: Left

value: high-grade colon adenoma


title: E8.5, rep2

description: Library name: 2_1209D


title: E9.5, rep1

description: Library name: 4_1189C

value: Pancreas E9.5

value: Pancreas

value: Pdx1-Cre labelled cells

value: Pdx1-Cre, tdtomato+


title: GAT, HGC, LAR, Mouse 12

description: Library name: 236_GAT_HC-LAR-12_L1_1

value: GAT

value: HGC-LAR

value: female

value: BALB/cAnNTac

value: 8 months


title: tissu DNA from high-grade colon adenoma 13


title: Spleen, HGC, TERM, Mouse 14

description: Library name: 235_Spleen_HGC-_ISS_Term-_14_L1_1

source_name: Spleen

value: Spleen

value: HGC-TERM


title: Sperm total RNA, Duroc boar 1, 10 months, mature

description: Library name: B8_10mo_RNA

value: spermatozoa

value: sperm

value: Duroc

value: 10 months


title: Sperm total RNA, Duroc boar 4, 7 months, pubertal

description: Library name: B13_7mo_RNA

value: 7 months


title: E8.5, rep1

description: Library name: 1_1209C

value: Endoderm E8.5

value: Endoderm

value: Foxa2-CreER labelled cells

value: Foxa2-CreER, tdtomato+


title: Thymus, HGC, TERM, Mouse 14

description: Library name: 234_Thymus_HGC-_ISS_Term-_14_L1_1

source_name: Thymus

value: Thymus


title: GAT, HGC, TERM, Mouse 12

description: Library name: 240_GAT_HGC-_ISS_Term-_12_L1_1

value: GAT


title: Sperm total RNA, Duroc boar 3, 7 months, pubertal, replicate 2

description:
Library name: B11_7mo_RNA_rep2
Technical replicate 1 - BAM files merged after alignment with B11_7mo_RNA_rep1 BAM files before downstream analysis


title: tissu DNA from high-grade colon adenoma 12

value: colon adenoma

value: Male

value: Right

value: high-grade colon adenoma


title: Heart, HGC, TERM, Mouse 1

description: Library name: 233_Heart_HGC-_ISS_Term-_1_L1_1

source_name: Heart

value: Heart

value: female

value: BALB/cAnNTac

value: 3 months


title: WT_ATAC

city: Kansas City

first: Andrew

middle: Joseph

last: Price

state: MO

address: 1000 E. 50th Street

department: Computational Biology

institute: Stowers Institute for Medical Research

description:
Library name: L64391_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
Multiome data was processed with the count function from cellranger-arc-2.0.2
Assembly: Mouse mm10
Supplementary files format and content: scRNA: cellranger h5, tabl-delimited value and matrix files
Supplementary files format and content: scATAC: cellranger h5, tab-delimited fragment file

source_name: whole embryo

extract_protocol:
10X Genomics Nuclei Isolation
10X Genomics ATAC + Gene Expression

value: whole embryo

value: WT

tag: library type

value: ATAC


title: Sperm total RNA, Duroc boar 2, 7 months, pubertal

description: Library name: B9_7mo_RNA

value: spermatozoa

value: sperm

value: Duroc

value: 7 months


title: tissu DNA from high-grade colon adenoma 14


title: Mutant_ATAC

description:
Library name: L64390_ATAC
10x Genomics

value: Nr6a1 null


title: SCAT, FL, TERM, Mouse 4

description: Library name: 232_SCAT_FL-_ISS_Term-_4_L1_1

source_name: SCAT

value: SCAT

value: FL-TERM


title: tissu DNA from high-grade colon adenoma 9

value: colon adenoma

value: Male

value: Left


title: Pancreas, HGC, TERM, Mouse 2

description: Library name: 230_Pancreas_HGC-_ISS_Term-_2_L1_1

source_name: Pancreas

value: Pancreas

value: HGC-TERM


title: Sperm total RNA, Duroc boar 1, 7 months, pubertal

description: Library name: B8_7mo_RNA


title: Thymus, VGC, TERM, Mouse 2

description: Library name: 229_Thymus_VGC-_ISS_Term-_2_L1_1

value: Thymus

value: VGC-TERM

value: female

value: BALB/cAnNTac


title: Mutant_GEX

description:
Library name: L64390_RNA
10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

value: whole embryo

value: mRNA


title: tissu DNA from high-grade colon adenoma 8

value: Right

value: high-grade colon adenoma


title: WT_GEX

description:
Library name: L64391_RNA
10x Genomics

value: WT


title: BAT, HGC, LAR, Mouse 14

description: Library name: 228_BAT_HC-LAR-14_L1_1

source_name: BAT

value: BAT

value: HGC-LAR

value: 3 months


title: Tilapia gut tissue, probiotic treated group,biol rep3

city: Chengdu

first: Ying

last: JP

address: No.17, Section 3, Renmin South Road

country: China

institute: sichuan University

description:
Library name: Simple6
10x Genomics

data_processing:
Raw sequencing data from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome (Oreochromis niloticus, GCF_001858045.2) using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples. (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger, version 7.0.0). The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in <25% of cells.
Assembly: Oreochromis niloticus, GCF_001858045.2
Supplementary files format and content: Matix table with raw gene counts for every gene and every cell

organism: Oreochromis niloticus

source_name: gut

extract_protocol:
Single-cell suspension was added to the 10X Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 39,944 cells.
cDNA amplification and library construction were performed according to standard protocols with 10x Genimics

value: gut


title: Hu sheep3

city: nanjing

first: chenbo

last: yan

address: Weigang No.1

institute: Nanjing Agricultural University

description:
Library name: sample6
T3

data_processing:
Trim sequence readings of adapter/low-quality sequences using sheep genome benchmark
Assembly: GCF_016772045.1_ARS-UI_Ramb_v2.0
Supplementary files format and content: .csv

organism: Ovis aries

source_name: ovary

extract_protocol:
Collect RNA using the Rneasy mini plus kit (Qiagen). 1 μg of total RNA was used to construct a sequencing library.
According to the manufacturer's protocol, prepare an RNA seq RNA library using the SMARTER mRNA sequencing library preparation kit.

value: ovary


title: tissu DNA from high-grade colon adenoma 7

source_name: colon adenoma

value: colon adenoma

value: Female


title: Liver, VGC, LAR, Mouse 13

description: Library name: 227_Liver_VC-LAR-13_L1_1

source_name: Liver

value: Liver

value: VGC-LAR


title: Tilapia gut tissue, probiotic treated group,biol rep2

description:
Library name: Simple5
10x Genomics


title: tissu DNA from high-grade colon adenoma 15

value: Male


title: Hu sheep2

description:
Library name: sample5
T2


title: Hu sheep1

description:
Library name: sample4
T1


title: tissu DNA from high-grade colon adenoma 11

value: Left


title: Mongolian sheep3

description:
Library name: sample3
C3


title: tissu DNA from high-grade colon adenoma 5


title: tissu DNA from high-grade colon adenoma 10


title: Spleen, VGC, TERM, Mouse 11

description: Library name: 226_Spleen_VGC-_ISS_Term-_11_L1_1

value: Spleen

value: VGC-TERM

value: female

value: BALB/cAnNTac

value: 8 months


title: tissu DNA from high-grade colon adenoma 6

value: Right

value: high-grade colon adenoma


title: tissu DNA from high-grade colon adenoma 4


title: Sperm total RNA, Duroc boar 3, 7 months, pubertal, replicate 1

description:
Library name: B11_7mo_RNA_rep1
Technical replicate 1 - BAM files merged after alignment with B11_7mo_RNA_rep2 BAM files before downstream analysis

source_name: spermatozoa

value: spermatozoa

value: sperm

value: Duroc

value: 7 months


title: Liver, FL, TERM, Mouse 5

description: Library name: 225_Liver_FL-_ISS_Term-_5_L1_1

value: FL-TERM

value: 3 months


title: Mongolian sheep2

description:
Library name: sample2
C2

value: ovary


title: tissu DNA from high-grade colon adenoma 3

value: colon adenoma

value: Female


title: SCAT, HGC, TERM, Mouse 3

description: Library name: 223_SCAT_HGC-_ISS_Term-_3_L1_1

value: SCAT

value: HGC-TERM


title: WT, rep1

description: Library name: H833A

data_processing:
The FASTQ files were downloaded using the BaseSpace Sequence Hub. Raw fastq files from four lanes were concatenated. Low-quality sequences and bases were removed before downstream analysis. Sample quality and read numbers were assessed using FastQC91. The STAR package92 was used to align reads to GRCm39 using default parameters. The GenomicAlignments package93 was used to quantify read counts and the DESeq2 90 was used to determine DE mRNAs.
Assembly: GRCm39
Supplementary files format and content: csv, raw read count

extract_protocol:
Cells were sorted into Trizol LS and RNA was extracted using miRNeasy micro kit (Qiagen 217084)
For mRNA library prep, cDNA was generated via the SMART-seq v4 ultra low input RNA kit for sequencing 634889, Takara) and then 1ng of cDNA was used to make library by the Nextera XT DNA library kit (FC-131-1024, Illumina).

value: Pancreas

value: Pdx1-Cre labelled cells

value: pancreatic progenitors

value: Pdx1-Cre+, Tdtomato+, miR-302WT


title: tissu DNA from high-grade colon adenoma 2

value: Right


title: Tilapia gut tissue, probiotic untreated group,biol rep3

description:
Library name: Simple3
10x Genomics

value: gut


title: tissu DNA from high-grade colon adenoma 1

value: high-grade colon adenoma


title: Diaphragm, FL, VGC, LAR, Mouse 12

description: Library name: 221_Diaphragm_FL-LAR-12_L1_1

value: Diaphragm

value: VGC-LAR

value: female

value: BALB/cAnNTac

value: 8 months


title: TFEB_DOX_05

city: Columbus

first: Wa

last: Du

address: 460 West 12th Avenue, Biomedical Research Tower, Rm 360A

department: Department of Surgery, Division of Vascular Diseases and Surgery

institute: The Ohio State University

description: Library name: Sample 20

data_processing:
Isas (3.19.5.13)
SAMtools (0.1.20)
STAR (Aligner, STAR_2.6.1a)
Salmon Quantification (0.11.2)
Illumina Annotation Engine (2.0.10.0)
Assembly: Homo_sapiens (NCBI Grch38Decoy)
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: HUVEC

growth_protocol: HUVEC expressing empty vector or TFEB were maintained in endothelial cell growth medium 2 supplemented with Supplement Pack and antibiotics in humidified atmosphere with 5% CO2 at 37 degree

extract_protocol:
RNA was harvested using RNAeasy mini plus kit (Qiagen). 1mg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep following manufacturer's protocols

treatment_protocol: ECs were treated with vehicle (DMSO) or DOX (1µM) for 24 hours

value: HUVEC

value: endothelial cell

value: sfTFEB

value: doxorubicin (1µM)

tag: batch


title: Mongolian sheep1

description:
Library name: sample1
C1

value: ovary


title: WT, rep2

description: Library name: H841D

value: Pancreas


title: Tilapia gut tissue, probiotic treated group,biol rep1

description:
Library name: Simple4
10x Genomics


title: Tilapia gut tissue, probiotic untreated group,biol rep2

description:
Library name: Simple2
10x Genomics


title: TFEB_DOX_04

description: Library name: Sample 19


title: Tilapia gut tissue, probiotic untreated group,biol rep1

description:
Library name: Simple1
10x Genomics


title: KO, rep1

description: Library name: H841C

value: Pdx1-Cre labelled cells

value: Pdx1-Cre+, Tdtomato+, miR-302KO


title: Diaphragm, VGC, TERM, Mouse 3

description: Library name: 224_Diaphragm_VGC-_ISS_Term-_3_L1_1

value: VGC-TERM

value: 3 months


title: TFEB_DOX_03

description: Library name: Sample 18


title: Diaphragm, HGC, LAR, Mouse 16

description: Library name: 222_Diaphragm_HC-LAR-16_L1_1

value: HGC-LAR


title: SCAT, HGC, TERM, Mouse 14

description: Library name: 220_SCAT_HGC-_ISS_Term-_14_L1_1

value: SCAT

value: HGC-TERM


title: tissu DNA from low-grade colon adenoma 13

description: genomic DNA from colon low-grade adenoma

value: colon adenoma

value: Male

value: Right

value: low-grade colon adenoma


title: KO, rep2

description: Library name: H937E

value: pancreatic progenitors


title: tissu DNA from low-grade colon adenoma 12

value: Left


title: TFEB_DOX_02

description: Library name: Sample 17

value: HUVEC

value: endothelial cell

value: sfTFEB


title: tissu DNA from low-grade colon adenoma 11


title: KO, rep3

description: Library name: H940E

value: Pancreas


title: Kidney, VGC, LAR, Mouse 2

description: Library name: 218_Kidney_VC-LAR-2_L1_1

source_name: Kidney

value: Kidney

value: VGC-LAR

value: female

value: BALB/cAnNTac


title: WT, rep3

description: Library name: H941A

value: Pdx1-Cre labelled cells

value: Pdx1-Cre+, Tdtomato+, miR-302WT


title: TFEB_DOX_01

description: Library name: Sample 16

value: doxorubicin (1µM)


title: MAT, FL, TERM, Mouse 2

description: Library name: 219_MAT_FL-_ISS_Term-_2_L1_1

source_name: MAT

value: MAT

value: FL-TERM

value: 3 months


title: tissu DNA from low-grade colon adenoma 10

value: colon adenoma

value: Male

value: Right

value: low-grade colon adenoma


title: GAT, HGC, TERM, Mouse 1

description: Library name: 217_GAT_HGC-_ISS_Term-_1_L1_1

source_name: GAT

value: GAT

value: HGC-TERM


title: tissu DNA from low-grade colon adenoma 9

value: Left


title: Empty_vector_DOX_04

description: Library name: Sample 14

value: HUVEC

value: endothelial cell

value: Empty vector


title: Pancreas, FL, TERM, Mouse 1

description: Library name: 216_Pancreas_FL-_ISS_Term-_1_L1_1

value: Pancreas

value: female

value: BALB/cAnNTac


title: tissu DNA from low-grade colon adenoma 8


title: tissu DNA from low-grade colon adenoma 7


title: Thymus, VGC, LAR, Mouse 1

description: Library name: 214_Thymus_VC-LAR-1_L1_1

value: Thymus

value: VGC-LAR


title: sir3dot1_MNASE_T3_Rep2

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 24 Waverly Place

department: Department of Biology

institute: New York University

description: Library name: sir3dot1_MNASE_T3_Rep2

library_source: genomic

data_processing:
MNAse-seq Data Processing: To improve read alignment in repetitive subtelomeric regions, Bowtie 2 was configured to report multiple alignments using the “best match” mode as described for ChIP-seq. For signal quantification, paired-end fragments ≥200 bp were isolated using samtools and awk, then processed with MACS2 (--nomodel --keep-dup all --SPMR) to generate normalized coverage tracks. To map MNase cleavage sites at nucleotide resolution, the 5’ end of each properly paired fragment was extracted from BAM files. This yielded single-base BED files representing MNase cut frequency, which were used for downstream metaplot analysis of nucleosome positioning.
Assembly: SK1 (Yue et al., 2017)
Supplementary files format and content: MACS2 normalized coverage tracks

organism: Saccharomyces cerevisiae

source_name: Nucleus

growth_protocol: Cells were grown in YPD for 24 hours at room temperature and then were transferred to BYTA (1% yeast extract, 2% bactotryptone, 1% potassium acetate, 50mM potassium phtalate) media at OD600 = 0.3. After growing at 30C for ~16.5 hours, cells were washed twice with water and resuspended in SPO (0.3% potassium acetate) media at OD600 = 1.9. Then the cultures were incubated at 30C. Further details are described in (Blitzblau et al., 2012).

extract_protocol:
For MNase-seq, 50 ml of synchronized meiotic cultures was harvested at the 3-hour time point and crosslinked with 1% formaldehyde for 30 minutes at room temperature. Crosslinking was quenched with 125 mM glycine, and cells were spheroplasted in Buffer Z (0.5 M sorbitol, 50 mM Tris-HCl pH 7.4, 10 mM β-mercaptoethanol) containing zymolyase. Spheroplasts were pelleted and resuspended in NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl₂, 1 mM CaCl₂, 0.5 mM spermidine, 1 mM β-mercaptoethanol, 0.075% NP-40) and digested with 5–80 units of micrococcal nuclease (MNase; Thermo Fisher Scientific, EN0181). MNase was diluted from a 300 U/µl stock to 20 U/µl, and mononucleosome-sized fragments were consistently obtained using 2 µl of a 1:4 dilution of this intermediate stock (10 units). Digestions were stopped with SDS and EDTA, followed by proteinase K treatment and overnight incubation at 65°C.
Library Protocol:_x000B_ MNAse samples were processed as described in Blitzblau et al., 2012. The quality of the libraries was assessed using the 2100 Bioanalyzer or 2200 Tapestation. Library concentrations were quantified using qPCR prior to pooling. Sequencing was performed on Illumina NextSeq 500 instruments at the NYU Biology Genomics Core.

value: Nucleus

value: Meiosis Hour 3

value: sir3 dot1

value: MNASE


title: sir3dot1_MNASE_T3_Rep1

description: Library name: sir3dot1_MNASE_T3_Rep1


title: Empty_vector_DOX_03

description: Library name: Sample 13

value: doxorubicin (1µM)


title: Empty_vector_DOX_02

description: Library name: Sample 12


title: sir3_MNASE_T3_Rep2

description: Library name: sir3_MNASE_T3_Rep2


title: tissu DNA from low-grade colon adenoma 6

value: colon adenoma

value: Male

value: low-grade colon adenoma


title: Empty_vector_DOX_01

description: Library name: Sample 11


title: Liver, FL, TERM, Mouse 14

description: Library name: 213_Liver_FL-_ISS_Term-_14_L1_1

value: Liver

value: FL-TERM

value: 8 months


title: sir3_MNASE_T3_Rep1

description: Library name: sir3_MNASE_T3_Rep1


title: tissu DNA from low-grade colon adenoma 5

value: Female

value: Right


title: TFEB_vehicle_05

description: Library name: Sample 10

value: HUVEC

value: endothelial cell

value: sfTFEB

value: vehicle


title: dot1_MNASE_T3_Rep2

description: Library name: dot1_MNASE_T3_Rep2

value: Nucleus


title: tissu DNA from low-grade colon adenoma 3


title: Heart, FL, TERM, Mouse 2

description: Library name: 212_Heart_FL-_ISS_Term-_2_L1_1

value: Heart

value: female

value: BALB/cAnNTac

value: 3 months


title: Empty_vector_DOX_05

description: Library name: Sample 15

value: Empty vector

value: doxorubicin (1µM)


title: dot1_MNASE_T3_Rep1

description: Library name: dot1_MNASE_T3_Rep1

value: Meiosis Hour 3

value: MNASE


title: TFEB_vehicle_03

description: Library name: Sample 8


title: Diaphragm, FL, VGC, LAR, Mouse 11

description: Library name: 211_Diaphragm_FL-LAR-11_L1_1

source_name: Diaphragm

value: Diaphragm

value: VGC-LAR


title: TFEB_vehicle_04

description: Library name: Sample 9


title: tissu DNA from low-grade colon adenoma 2

value: colon adenoma

value: Female

value: Left

value: low-grade colon adenoma


title: Liver, HGC, LAR, Mouse 11

description: Library name: 210_Liver_HC-LAR-11_L1_1

value: Liver

value: HGC-LAR

value: 8 months


title: TFEB_vehicle_02

description: Library name: Sample 7

value: HUVEC

value: endothelial cell

value: sfTFEB

value: vehicle


title: Kidney, FL, TERM, Mouse 5

description: Library name: 215_Kidney_FL-_ISS_Term-_5_L1_1

value: Kidney

value: FL-TERM

value: female

value: BALB/cAnNTac

value: 3 months


title: WT_MNASE_T3_Rep1

description: Library name: WT_MNASE_T3_Rep1

value: Nucleus

value: Meiosis Hour 3

value: WT

value: MNASE


title: WT_MNASE_T3_Rep2

description: Library name: WT_MNASE_T3_Rep2


title: ndt80Δ_T3_Rep2

description: Library name: ndt80Δ_T3_Rep2

data_processing:
RNA-seq Data Processing: Fastq files were processed using the Nextflow nf-core RNA-seq pipeline (doi: 10.5281/zenodo.1400710) with the --save_reference, --trim_nextseq, and --remove_ribo_rna options. The pipeline utilized Trim Galore! for trimming and quality control, STAR for read alignment, and Salmon for read quantification.
Assembly: SK1 (Yue et al., 2017)
Supplementary files format and content: Output of salmon quantification, R object

extract_protocol:
RNA-seq Extract Protocol:_x000B_1.5 ml of meiotic culture was collected per sample, and total RNA was extracted using the RNeasy Mini Kit (Qiagen), following the manufacturer’s protocol for mechanical extraction. RNA quality was evaluated using the Tapestation 2200.
RNA-seq Library Protocol:_x000B_Library preparation began with 1.2 µg of total RNA. PolyA enrichment was performed using Sera-Mag oligo(dT) Magnetic particles (Sigma-Aldrich), and cDNA synthesis followed the method described in Parkhomchuk et al., 2009. Libraries were prepared using Illumina TruSeq adapters, quantified by qPCR, and sequenced on Illumina NextSeq 500 instruments at the NYU Genome Center.


title: Liver, HGC, LAR, Mouse 2

description: Library name: 208_Liver_HC-LAR-2_L1_1


title: RPA_ChIP

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

description: Library name: sample1

data_processing:
A customized genome that an rDNA copy (GenBank accession: BK000964.3) was added to mouse reference mm10 as a separate chromosome named 'rDNA'. Reads were aligned to this reference using bowtie(v1.1.2) with parameters -n 2 -l 50 -m 1. Functions 'view' and 'sort' of samtools (v.1.11) were used to convert and sort the aligned SAM files to sorted BAM files. BAM files were further converted to Bed files using the bedtools (v.2.29.2) bamToBed command. BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig for visualization at rDNA by JBrowse.
Assembly: mm10 + rDNA
Supplementary files format and content: bigwig

source_name: Activated primary B cells

extract_protocol:
Twenty million cells were harvested for chromatin immunoprecipitation (ChIP) using an anti-RAD51 (10ug/sample) or anti-RPA antibody (10ug/sample). ssDNA that spontaneously forms hairpins after heat renaturation was then enriched and sequenced as described (Brick et al., 2018)
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads). libraries were prepared and sequenced following standard Illumina protocols

value: Activated primary B cells

tag: chip antibody

value: RPA Abcam #10359


title: Liver, VGC, TERM, Mouse 5

description: Library name: 207_Liver_VGC-_ISS_Term-_5_L1_1

value: Liver

value: VGC-TERM


title: Kidney, FL, VGC, LAR, Mouse 1

description: Library name: 209_Kidney_FL-LAR-1_L1_1

value: VGC-LAR


title: TFEB_vehicle_01

description: Library name: Sample 6

value: HUVEC

value: endothelial cell


title: Huh7 cells, controls - rep3

city: Rome

first: Niccolò

last: Liorni

address: Via Enea 57

department: Computational Biology and Bioinformatics

country: Italy

institute: Policlinico Universitario Agostino Gemelli

description:
Library name: GC-MV-11753-18-Huh7-L3_S24
count_matrix_Huh7.tsv

data_processing:
Trimming - Trimmomatic v0.36 (CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35, adapter = AGATCGGAAG)
Alignment - Reads were then aligned to the human reference genome (GRCh38/hg38) using STAR (v2.7.10a) as a splice-aware short-read aligner with Gencode v43 gene annotation. STAR was used to generate a gene-level raw count matrix.
Differential gene expression analysis was conducted using the DESeq2 package in R. Genes were considered differentially expressed (DEGs) if they met the significance thresholds of an adjusted p-value ≤ 0.05 and an absolute log₂(fold change) > 0.5
Assembly: GRCh38/hg38
Supplementary files format and content: csv

growth_protocol: HepG2 and Huh-7 liver cancer cells were obtained from CLS-GmbH (Eppelheim, Germany) and were authenticated using STR profiling. They were cultured in high glucose (4.5 g/l) DMEM (1 ×) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, UK), 15 mM Hepes buffer (Biowest, France), glutamine, 1% penicillin/streptomycin solution, and 100 μg/ml Normocin (InvivoGen, CA, USA) at 37 °C and 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Indexed RNA-seq libraries were prepared from 250 ng of polyA-selected mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: For AAV2/8 viral transduction, cultured cells at 70-80% confluency were serum-deprived cells for 2 hours before adding virus. AAV2/8 stocks were thawed on ice and diluted with serum-free medium to the target multiplicity of infection (MOI) (104 to 106 viral genomes). The old medium was replaced with the virus-containing medium, and cells were incubated for different times until downstream analyses.

value: Luc


title: tissu DNA from low-grade colon adenoma 1

value: colon adenoma

value: Female

value: Left

value: low-grade colon adenoma


title: Empty_vector_vehicle_05

description: Library name: Sample 5

value: Empty vector

value: vehicle


title: sir3ndt80Δ_T3_Rep2

description: Library name: sir3ndt80Δ_T3_Rep2

value: Nucleus

value: Meiosis Hour 3


title: Huh7 cells, controls - rep2

description:
Library name: GC-MV-11753-17-Huh7-L2_S23
count_matrix_Huh7.tsv


title: tissu DNA from low-grade colon adenoma 4


title: Thymus, FL, TERM, Mouse 11

description: Library name: 206_Thymus_FL-_ISS_Term-_11_L1_1

source_name: Thymus

value: Thymus

value: FL-TERM

value: female

value: BALB/cAnNTac

value: 8 months


title: sir3dot1Δdmc1Δ_T3_Rep2_TrAEL-seq

description: Library name: sir3dot1Δdmc1Δ_T3_Rep2_TrAEL-seq

data_processing:
TrAEL-seq Data Processing: Reads were aligned to the SK1 genome (Yue et al., 2017) using Bowtie2 (Langmead et al., 2012) with a reporting mode that allowed multiple read alignments while reporting the best alignment. Data processing followed the procedures described in Kara et al., 2021.
Assembly: SK1 (Yue et al., 2017)

extract_protocol:
TrAEL-seq Extract Protocol:_x000B_Meiotic cultures (20 ml per strain) were harvested 5 hours into meiosis, pelleted, and washed twice with CHEF TE buffer (10 mM Tris-HCl, pH 7.5, 50 mM EDTA, pH 8.0). The cell pellet was resuspended in 300 µl CHEF TE, treated with 4 µl zymolyase (10 mg/ml), briefly vortexed, and incubated at 42°C for ~30 seconds. Low-melting-point agarose (1% SeaPlaque GTG in 125 mM EDTA, pH 8.0) was added, and the mixture was transferred into plug molds. After solidification on ice, plugs were transferred to LET buffer (10 mM Tris-HCl, pH 7.5, 0.5 M EDTA, pH 8.0) and incubated overnight at 37°C. Proteinase K treatment was performed in NDS buffer (10 mM Tris-HCl, pH 7.5, 0.5 M EDTA, 1% N-lauroylsarcosine) at 50°C overnight, followed by sequential washes with CHEF TE (1 hour), CHEF TE containing PMSF (two washes, 1 hour each), RNase T1 in CHEF TE (37°C for 1 hour), and a final wash with CHEF TE (1 hour). Plugs were stored at 4°C in CHEF TE until library preparation.
TrAEL-seq Library Protocol:_x000B_Library preparation and sequencing were conducted as described in Kara et al., 2021.

value: Meiosis Hour 5

value: WT


title: Empty_vector_vehicle_04

description: Library name: Sample 4

value: HUVEC

value: endothelial cell


title: GAT, VGC, LAR, Mouse 12

description: Library name: 205_GAT_VC-LAR-12_L1_1

value: GAT

value: VGC-LAR


title: Empty_vector_vehicle_03

description: Library name: Sample 3


title: Huh7 cells, controls - rep1

description:
Library name: GC-MV-11753-16-Huh7-L1_S22
count_matrix_Huh7.tsv

value: Liver

value: Luc


title: Huh7 cells, expressing wild-type SIRT6 - rep3

description:
Library name: GC-MV-11753-15-Huh7-W3_S21
count_matrix_Huh7.tsv


title: Empty_vector_vehicle_02

description: Library name: Sample 2

value: Empty vector


title: SCAT, HGC, LAR, Mouse 13

description: Library name: 204_SCAT_HC-LAR-13_L1_1

value: SCAT

value: HGC-LAR

value: 3 months


title: dot1Δdmc1Δ_T3_Rep2_TrAEL-seq

description: Library name: dot1Δdmc1Δ_T3_Rep2_TrAEL-seq

value: Nucleus


title: sir3dot1Δdmc1Δ_T3_Rep1_TrAEL-seq

description: Library name: sir3dot1Δdmc1Δ_T3_Rep1_TrAEL-seq


title: Huh7 cells, expressing wild-type SIRT6 - rep2

description:
Library name: GC-MV-11753-14-Huh7-W2_S20
count_matrix_Huh7.tsv


title: Empty_vector_vehicle_01

description: Library name: Sample 1

value: vehicle


title: dot1Δdmc1Δ_T3_Rep1_TrAEL-seq

description: Library name: dot1Δdmc1Δ_T3_Rep1_TrAEL-seq


title: Lung, HGC, LAR, Mouse 4

description: Library name: 203_Lung_HC-LAR-4_L1_1

source_name: Lung

value: Lung

value: female


title: Huh7 cells, expressing wild-type SIRT6 - rep1

description:
Library name: GC-MV-11753-13-Huh7-W1_S19
count_matrix_Huh7.tsv


title: Spleen, FL, TERM, Mouse 14

description: Library name: 202_Spleen_FL-_ISS_Term-_14_L1_1

source_name: Spleen

value: Spleen

value: FL-TERM

value: BALB/cAnNTac

value: 8 months


title: sir3dmc1Δ_T3_Rep2_TrAEL-seq

description: Library name: sir3dmc1Δ_T3_Rep2_TrAEL-seq

value: Meiosis Hour 5

value: WT


title: MAT, VGC, TERM, Mouse 3

description: Library name: 201_MAT_VGC-_ISS_Term-_3_L1_1

value: MAT

value: VGC-TERM


title: Huh7 cells, expressing centenarian-associated SIRT6 - rep2

description:
Library name: GC-MV-11753-11-Huh7-C2_S17
count_matrix_Huh7.tsv

value: Liver

value: Cent


title: Huh7 cells, expressing centenarian-associated SIRT6 - rep3

description:
Library name: GC-MV-11753-12-Huh7-C3_S18
count_matrix_Huh7.tsv


title: GAT, VGC, TERM, Mouse 2

description: Library name: 200_GAT_VGC-_ISS_Term-_2_L1_1

value: GAT


title: dmc1Δ_T3_Rep2_TrAEL-seq

description: Library name: dmc1Δ_T3_Rep2_TrAEL-seq


title: sir3dmc1Δ_T3_Rep1_TrAEL-seq

description: Library name: sir3dmc1Δ_T3_Rep1_TrAEL-seq


title: Huh7 cells, expressing centenarian-associated SIRT6 - rep1

description:
Library name: GC-MV-11753-10-Huh7-C1_S16
count_matrix_Huh7.tsv


title: HepG2 cells, controls - rep3

description:
Library name: GC-MV-11753-9-HepG2-L3_S15
count_matrix_HepG2.tsv

value: Luc


title: Thymus, FL, TERM, Mouse 5

description: Library name: 198_Thymus_FL-_ISS_Term-_5_L1_1

value: Thymus

value: 3 months


title: sir3_Input_SpikeIn_T3_Rep2

description: Library name: sir3_Input_SpikeIn_T3_Rep2

data_processing:
ChIP-seq Data Processing: Illumina output reads were processed as described in Paul et al., 2017. The reads were mapped to the SK1 genome (Yue et al., 2017) using Bowtie2 (Langmead et al., 2012) with a reporting mode that allowed multiple read alignments while reporting the best alignment. The 3' ends of the reads were extended to a final length of 200 bp using MACS2 2.1.1 (https://github.com/taoliu/MACS). Input and ChIP pileups were SPMR-normalized (signal per million reads), and the fold-enrichment of ChIP over input data was used for further analyses. Bedgraph files were created from pooled replicates.
Assembly: SK1 (Yue et al., 2017)
Supplementary files format and content: bedGraph files, and spike-in text files for spike-in samples

extract_protocol:
ChIP-seq Extract Protocol:_x000B_25 ml of meiotic cell cultures were collected at various time points and fixed for 30 minutes in 1% formaldehyde, which was quenched with 125 mM glycine. ChIP samples were processed as described in Blitzblau et al., 2012.
ChIP-seq Library Protocol:_x000B_ChIP samples were processed as described in Blitzblau et al., 2012. The quality of the libraries was assessed using the 2100 Bioanalyzer or 2200 Tapestation. Library concentrations were quantified using qPCR prior to pooling. Sequencing was performed on Illumina NextSeq 500 instruments at the NYU Biology Genomics Core.

value: Nucleus

value: Meiosis Hour 3


title: Heart, VGC, TERM, Mouse 3

description: Library name: 197_Heart_VGC-_ISS_Term-_3_L1_1

source_name: Heart

value: Heart

value: female


title: Kidney, FL, VGC, LAR, Mouse 16

description: Library name: 196_Kidney_FL-LAR-16_L1_1

value: Kidney

value: VGC-LAR


title: sir3_Input_SpikeIn_T3_Rep1

description: Library name: sir3_Input_SpikeIn_T3_Rep1


title: HepG2 cells, controls - rep2

description:
Library name: GC-MV-11753-8-HepG2-L2_S14
count_matrix_HepG2.tsv


title: HepG2 cells, controls - rep1

description:
Library name: GC-MV-11753-7-HepG2-L1_S13
count_matrix_HepG2.tsv


title: Lung, HGC, LAR, Mouse 3

description: Library name: 199_Lung_HC-LAR-3_L1_1

value: Lung

value: HGC-LAR

value: BALB/cAnNTac

value: 8 months


title: sir3_ChIP_SpikeIn_T3_antiRed1_Rep2

description: Library name: sir3_ChIP_SpikeIn_T3_antiRed1_Rep2

value: WT


title: Liver, VGC, LAR, Mouse 2

description: Library name: 195_Liver_VC-LAR-2_L1_1

value: Liver


title: HepG2 cells, expressing wild-type SIRT6 - rep3

description:
Library name: GC-MV-11753-6-HepG2-W3_S12
count_matrix_HepG2.tsv


title: sapanisertib [CAlv-Ext-12_MPFR_3_F-C-M]

type: RNA

city: Odense M

first: Carla

last: Alves

address: Fioniavej 36, 2. sal

country: Denmark

institute: SDU

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on human transcriptome array 2.0 (HTA). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data analysis was conducted in Transcriptome Analysis Console (Thermo Fisher Scientific). A fold change ≤ -3 or ≥3, p-value < 0.05, and false discovery rate (FDR) < 0.05 cutoffs were set to select differentially expressed genes between MCF-7 and MPiF-R cells

label: biotin

source_name: MPFR cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MPFR cells were cultured in phenol red-free Dulbecco’s modified Eagle medium (D-MEM)/F-12 (Gibco) supplemented with 1% heat-inactivated fetal bovine serum (FBS, Gibco), 2 mM glutamine (Gibco) and 6 ng/ml insulin (Sigma-Aldrich) supplemented with 200 nM CDK4/6i and 100 nM fulvestrant.

extract_protocol: Total RNA was extracted and purified with RNeasy Mini kit (Qiagen) according to the manufacturer´s instructions.

treatment_protocol: The combined resistant cell line was established through long-term treatment with 100 nM fulvestrant and 200 nM CDK4/6i over a period of 3 months.

value: Combined CDK4/6i and fulvestrant resistant cells

value: sapanisertib


title: HepG2 cells, expressing wild-type SIRT6 - rep2

description:
Library name: GC-MV-11753-5-HepG2-W2_S11
count_matrix_HepG2.tsv


title: sapanisertib [CAlv-Ext-10_MPFR_1_F-C-M]


title: gedatolisib [CAlv-Ext-14_MPFR_2_F-C-MP]

value: gedatolisib


title: HepG2 cells, expressing wild-type SIRT6 - rep1

description:
Library name: GC-MV-11753-4-HepG2-W1_S10
count_matrix_HepG2.tsv


title: SCAT, VGC, LAR, Mouse 3

description: Library name: 194_SCAT_VC-LAR-3_L1_1

data_processing:
Fastq files containing raw sequencing reads were mapped against GRCm39 and miRBase (version 22.1) 65 in order to profile miRNA counts using miRmaster (version 2.0). Information about miRNA family was obtained from mirgenedb 3.0. Detection filtering was performed by keeping only miRNAs with at least 5 raw reads in at least 10% of samples in each condition-tissue group. Expression data was normalized using rpmm normalization (reads per mapped million).
Assembly: GRCm39
Supplementary files format and content: miRNA_complete_quantification_raw.tsv: Tab-separated file of raw miRNA counts per sample.
Supplementary files format and content: lncRNA_complete_quantification_raw.tsv: Tab-separated file of raw lncRNA counts per sample.
Supplementary files format and content: piRNA_complete_quantification_raw.tsv: Tab-separated file of raw piRNA counts per sample.
Supplementary files format and content: rRNA_complete_quantification_raw.tsv: Tab-separated file of raw rRNA counts per sample.
Supplementary files format and content: scaRNA_complete_quantification_raw.tsv: Tab-separated file of raw scaRNA counts per sample.
Supplementary files format and content: snoRNA_complete_quantification_raw.tsv: Tab-separated file of raw snoRNA counts per sample.
Supplementary files format and content: snRNA_complete_quantification_raw.tsv: Tab-separated file of raw snRNA counts per sample.
Supplementary files format and content: tRNA_complete_quantification_raw.tsv: Tab-separated file of raw tRNA counts per sample.

source_name: SCAT

extract_protocol:
LAR mice were anesthetized with gas anesthesia and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The liver was removed, weighed, dissected into individual lobes (1- left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen. All tissues were collected and frozen within 10-16 minutes of thoracotomy procedure. All groups were treated identically. Organ samples were maintained at -80C or lower temperatures throughout the storage, and during transportation and shipment. TERM mice were anesthetized with ketamine/xylazine/acepromazine at a dose of 120/15/3 mg/kg and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The spleen was dissected fresh from each carcass and placed in a tube containing RNA Later. The carcass was then wrapped in foil and frozen in MELFI on board the ISS or in ground -80C freezers. Carcasses were maintained at -80C or lower temperatures throughout the storage on board the ISS, in ground freezers and during transportation and shipment. The mice were brought back to earth where dissection was held. It should be noted that carcasses frozen whole onboard the ISS were free-floating and thus in direct contact with air. This prevented them from snap freezing like samples collected on Earth which were placeddirectly in liquid nitrogen. Carcasses were thawed at room temperature one at a time (staggered)until the tissues were sufficiently pliable for dissection (approximately 60-90 minutes). Once thawed, multiple tissues were collected from each carcass within 30min of the first tissue collected. The liver was removed from each carcass, weighed, dissected into individual lobes (1-left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen.  The miRNeasy-96 protocol was followed for all samples with some modifications, as follows. Tissue Preparation: To avoid overloading the miRNeasy-96 columns, some frozen samples were trimmed to smaller sizes. All kidney, liver, and spleen samples were all trimmed to ~25mgs due to their high RNA content. Pancreas samples were trimmed to ~25mgs if they exceeded 45mgs. GAT, MAT, and SCAT samples >200mgs were trimmed to ~100mgs as samples of large size homogenize poorly in 96-well format, even though adipose tissues have relatively low RNA content. BAT and lung samples >100mgs were trimmed to ~50mgs, and thymi >50mgs were trimmed to ~25mgs. The diaphragm did not require trimming, and whole hemi-brains and whole hearts were homogenized by hand with the TissueRuptor in 1ml QIAzol per 50mgs tissue, since trimming samples in a reproducible way to capture the same organ subregion for each would be difficult. Bead homogenization: All samples, including those previously homogenized with the TissueRuptor, were randomized in 96-well format. Two 96-well plates were run simultaneously as follows. 96-well collection microtube plates were chilled on dry ice, and trimmed tissue samples were placed at the bottom of each well. One pre-chilled 5mm stainless steel bead was then placed on top of the tissue samples with bead dispenser. 700ul pre-chilled (4C) QIAzol was then added to each well, or 700ul QIAzol homogenate from the pre-homogenized heart and brain samples. Plates were immediately homogenized on the TissueLyser II for a total of four 5min runs at 25Hz, and plates were rotated and switched between the two arms of the TissueLyser II between each run. Plates were then left at room temperature for 5min before pelleting debris at 6000 x g for 1min at 4C. Phase Separation & RNA collection: Debris- and bead-free homogenate was then transferred to a new plate, to which 140ul chloroform was added to each well, and plates were shaken vigorously for 3min at room temperature before being spun at 6000 x g for 4min at 4C. 300ul aqueous phase was then transferred to a new S-Block, to which 525ul 100% EtOH was added and mixed by pipetting, followed by a room temperature spin at 6000 x g for 30s. The entire volume was then transferred to a miRNeasy-96 plate on top of an S-plate, sealed with AirPore tape sheet, and spun at 5600 x g for 4min at room temperature. Flow through was discarded, and columns washed with 800ul RWT and spun as above. This was repeated with 800ul RPE, and a final 800ul RPE wash was followed by a 10min spin. Finally, 50ul RNase-free water was added to each column and incubated at room temperature for 1min, then spun at 5600 x g for 4min at room temperature. The elution was repeated with a second volume of 50ul RNase-free water. RNA samples were stored at -80C.
All samples were processed using the MGIEasy Small RNA Library Prep Kit with the high-throughput MGI SP-960 sample prep system according to the manufacturer's protocol to generate sequencing libraries.

value: SCAT


title: SCAT, HGC, TERM, Mouse 5

description: Library name: 193_SCAT_HGC-_ISS_Term-_5_L1_1

value: HGC-TERM

value: 3 months


title: sapanisertib [CAlv-Ext-11_MPFR_2_F-C-M]


title: dmc1Δ_T3_Rep1_TrAEL-seq

description: Library name: dmc1Δ_T3_Rep1_TrAEL-seq

value: Nucleus

value: Meiosis Hour 5


title: alpelisib [CAlv-Ext-09_MPFR_3_F-P-C]

value: alpelisib


title: alpelisib [CAlv-Ext-08_MPFR_2_F-P-C]


title: WT_ChIP_SpikeIn_T3_antiRed1_Rep1

description: Library name: WT_ChIP_SpikeIn_T3_antiRed1

value: Meiosis Hour 3


title: gedatolisib [CAlv-Ext-13_MPFR_1_F-C-MP]


title: Thymus, VGC, TERM, Mouse 1

description: Library name: 192_Thymus_VGC-_ISS_Term-_1_L1_1

value: Thymus

value: VGC-TERM

value: female


title: control [CAlv-Ext-06-MPF_R_B3]

value: control


title: gedatolisib [CAlv-Ext-15_MPFR_3_F-C-MP]


title: alpelisib [CAlv-Ext-07_MPFR_1_F-P-C]


title: sir3_ChIP_T3_antiRed1_Rep2

description: Library name: sir3_ChIP_T3_antiRed1_Rep2


title: HepG2 cells, expressing centenarian-associated SIRT6 - rep1

description:
Library name: GC-MV-11753-1-HepG2-C1_S7
count_matrix_HepG2.tsv

value: Cent


title: Spleen, VGC, LAR, Mouse 8

description: Library name: 191_Spleen_VC-LAR-8_L1_1

value: Spleen

value: VGC-LAR

value: BALB/cAnNTac

value: 8 months


title: sir3_ChIP_SpikeIn_T3_antiRed1_Rep1

description: Library name: sir3_ChIP_SpikeIn_T3_antiRed1_Rep1

value: WT


title: HepG2 cells, expressing centenarian-associated SIRT6 - rep2

description:
Library name: GC-MV-11753-2-HepG2-C2_S8
count_matrix_HepG2.tsv

value: Liver


title: sir3_Input_T3

description: Library name: sir3_Input_T3


title: HepG2 cells, expressing centenarian-associated SIRT6 - rep3

description:
Library name: GC-MV-11753-3-HepG2-C3_S9
count_matrix_HepG2.tsv


title: EX2

first: Jiaquan

last: Lin

address: Hankou road

institute: nanjing university

description: Library name: EX2

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCm39
Supplementary files format and content: excel,expression profiles

source_name: Skeletal muscle-derived EVs

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Skeletal muscle-derived EVs

value: Skeletal muscle under exercise training pulsed electrical stimulation


title: 16S rRNA-seq,metagenome for B277m3 at 3mon

city: Nanjing

first: xinyuan

last: ge

state: Jiangsu

address: Longmian Road 818

institute: Nanjing Medical University School of Public Health

description: Library name: B277m3

data_processing:
Raw sequencing reads were quality controlled and processed using QIIME 2 (version 2023.13). Denoising was performed using the Deblur plugin, and taxonomic classification was conducted based on the SILVA reference database (release 138). After taxonomic assignment, ASV tables were collapsed to the genus level, and genera detected in more than 20% of samples were retained for downstream analyses.
Supplementary files format and content: Processed data files include genus-level relative abundance tables derived from 16S rRNA gene sequencing. Only taxa detected in more than 20% of samples were retained for downstream analyses and data deposition. Taxonomic annotation was performed using the SILVA database (release 138). Files are provided in tab-delimited text format, with rows representing genera and columns representing samples.
Library strategy: 16S rRNA-seq

source_name: feces

growth_protocol: Not applicable. Fecal samples were collected directly from human participants without microbial culture.

extract_protocol:
Microbial DNA was extracted from fecal samples using a standardized bead-beating and column-based extraction protocol.
For taxonomic profiling, the V3–V4 hypervariable region of the bacterial 16S rRNA gene was amplified by PCR and sequenced on the Illumina MiSeq platform according to standard protocols.

treatment_protocol: Participants were randomized to a 3-month aerobic exercise intervention or usual care. Fecal samples were collected at baseline and after the 3-month intervention from participants who provided samples at both timepoints (30 control and 33 intervention).

value: feces

value: exercise

tag: timepoint


title: WT_Input_SpikeIn_T3

description: Library name: WT_Input_SpikeIn_T3

tag: tissue

value: Nucleus


title: MAT, HGC, TERM, Mouse 16

description: Library name: 190_MAT_HGC-_ISS_Term-_16_L1_1

value: MAT

value: HGC-TERM

tag: Sex


title: EX1

description: Library name: EX1


title: BAT, VGC, LAR, Mouse 16

description: Library name: 189_BAT_VC-LAR-16_L1_1

source_name: BAT

value: BAT

tag: age


title: sir3_ChIP_T3_antiRed1_Rep1

description: Library name: sir3_ChIP_T3_antiRed1_Rep1

value: Meiosis Hour 3


title: ST2

description: Library name: ST2

value: Skeletal muscle under sedentary pulsed electrical stimulation


title: Lung, HGC, LAR, Mouse 14

description: Library name: 188_Lung_HC-LAR-14_L1_1

value: Lung

value: HGC-LAR

value: female

value: 3 months


title: 16S rRNA-seq,metagenome for B273m3 at 3mon

description: Library name: B273m3


title: control [CAlv-Ext-05-MPF_R_B2]

value: Combined CDK4/6i and fulvestrant resistant cells

value: control


title: WT_Input_T3_Input_Rep2

description: Library name: WT_Input_T3_Input_Rep2

value: WT


title: 16S rRNA-seq,metagenome for B264m3 at 3mon

description: Library name: B264m3


title: WT_Input_T3_Input_Rep1

description: Library name: WT_Input_T3_Input_Rep1


title: ST1

description: Library name: ST1

value: Skeletal muscle-derived EVs


title: Brain, FL, VGC, LAR, Mouse 17

description: Library name: 187_Brain_FL-LAR-17_L1_1

source_name: Brain

value: Brain

value: VGC-LAR

value: BALB/cAnNTac


title: control [CAlv-Ext-04-MPF_R_B1]


title: WT_ChIP_T3_antiSir3_Rep2

description: Library name: WT_ChIP_T3_antiSir3_Rep2

value: Nucleus


title: 16S rRNA-seq,metagenome for B263m3 at 3mon

description: Library name: B263m3

value: feces

value: exercise


title: 16S rRNA-seq,metagenome for B258m3 at 3mon

description: Library name: B258m3


title: 16S rRNA-seq,metagenome for B253m3 at 3mon

description: Library name: B253m3


title: IgG

city: Austin

first: Muyoung

last: Lee

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: IgG

data_processing:
ChIP-seq samples were adapter-trimmed by TrimGalore v0.6.10 (https://github.com/FelixKrueger/TrimGalore), aligned by Bowtie v2.5.1 (Langmead & Salzberg, 2012), then processed with Samtools v1.20 (Danecek et al, 2021) and Picard MarkDuplicates v3.0.0 (http://broadinstitute.github.io/picard).
Peak calling was performed using Macs3 v3.0.1 (Zhang et al, 2008), and the heatmap was generated using DeepTools v3.5.5 (Ramírez et al, 2016).
Assembly: mm10
Supplementary files format and content: bigWig (except for input samples)

source_name: embryonic stem cells

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Fisher Bioreagents, BP531-500) for 7 minutes at room temperature, and the reaction was quenched by adding glycine (Fisher Scientific, BP381-1) to a final concentration of 0.125 M. The bioChIP protocol was conducted as previously described (Kim et al, 2009). Genomic DNA was sheared to an average fragment size of ~200 bp using a Bioruptor sonicator (Diagenode). Cross-linked chromatin was pre-cleared with Protein A agarose beads (Thermofisher, 10008D) and subsequently subjected to immunoprecipitation using Dynabeads MyOne Streptavidin T1 (Invitrogen, 65602).
Library preparation was performed using the NEBNext® Ultra™ DNA Library Prep Kit (NEB, 7103L)

treatment_protocol: bioChIP-seq was performed on PREB- and PREBΔTM-OE ES cells treated with 0.5 µg/mL doxycycline for 24 hours.

value: embryonic stem cells


title: Sorted Macrophages from Synovial Tissue, RA, Patient 66

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

description:
Library name: HS66
RA_206pos_HS66

data_processing:
RNA-seq data were de-multiplexed using bcl2fastq, and RNA-seq reads were aligned to the human reference genome (NCBI, hg19) using TopHat2 (version 2.17.1.14) aligners (51). Gene coverage of samples was calculated using the RseQC package (52). Normalized gene counts were calculated using HTSeq.
Assembly: hg19
Supplementary files format and content: table of raw gene expression count
Supplementary files format and content: table of normalized expression by Fragments Per Kilobase per Million reads (FPKM)

source_name: Joint Synovium

extract_protocol:
RA tissue was obtained by minimally invasive ultrasound guided synovial biopsy of the wrist.  OA tissue was obtained from the discards after whole joint replacement.  Single-cell suspension was generated through chemical and mechanical digestion and run over a 40-micron filter. Red blood cells were lysed and sample was washed twice with HBSS.  CD45+CD11B+HLA-DR+CD15-CD1c-CD206+ macrophages were isolated by fluorescence-activated cell sorting (FACS). RNA was extracted from sorted macrophages using a PicoPure RNA isolation kit according to manufacturer’s instructions (Arcturus Bioscience, Inc.).
RNA-seq libraries from sorted macrophage populations were prepared using a SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc.) followed by NexteraXT protocol (Illumina). RNA-seq libraries were sequenced on an NextSeq 500 instrument (Illumina Inc.) with ~5-10x106 aligned reads per sample.

value: Joint Synovium

tag: sample group

value: RA

value: CD206+ Macrohages


title: WT_Input_T0_Input_Rep2

description: Library name: WT_Input_T0_Input_Rep2

value: Meiotic Induction


title: BirA strep-pulldown

description: Library name: BirA strep-pulldown


title: Brain, HGC, TERM, Mouse 7

description: Library name: 185_Brain_HGC-_ISS_Term-_7_L1_1

value: HGC-TERM

value: female


title: Thymus, VGC, TERM, Mouse 13

description: Library name: 186_Thymus_VGC-_ISS_Term-_13_L1_1

value: Thymus

value: VGC-TERM

value: 8 months


title: WT_ChIP_T3_antiSir3_Rep1

description: Library name: WT_ChIP_T3_antiSir3_Rep1

value: Meiosis Hour 3

value: WT


title: Sorted Macrophages from Synovial Tissue, RA, Patient 65

description:
Library name: HS65
RA_206pos_HS65


title: 16S rRNA-seq,metagenome for B237m3 at 3mon

description: Library name: B237m3


title: WT_Input_T0_Input_Rep1

description: Library name: WT_Input_T0_Input_Rep1


title: Sorted Macrophages from Synovial Tissue, RA, Patient 62

description:
Library name: HS62
RA_206pos_HS62


title: WT_ChIP_T0_antiSir3_Rep2

description: Library name: WT_ChIP_T0_antiSir3_Rep2


title: Liver, VGC, LAR, Mouse 4

description: Library name: 183_Liver_VC-LAR-4_L1_1

source_name: Liver

value: Liver

value: VGC-LAR


title: 16S rRNA-seq,metagenome for B235m3 at 3mon

description: Library name: B235m3


title: 16S rRNA-seq,metagenome for B250m3 at 3mon

description: Library name: B250m3


title: WT_ChIP_T0_antiSir3_Rep1

description: Library name: WT_ChIP_T0_antiSir3_Rep1

value: Nucleus


title: MAT, HGC, LAR, Mouse 2

description: Library name: 181_MAT_HC-LAR-2_L1_1

source_name: MAT

value: MAT

value: HGC-LAR

value: BALB/cAnNTac

value: 3 months


title: 16S rRNA-seq,metagenome for B211m3 at 3mon

description: Library name: B211m3

value: feces

value: exercise


title: Sorted Macrophages from Synovial Tissue, RA, Patient 60

description:
Library name: HS60
RA_206pos_HS60

value: Joint Synovium

value: RA

value: CD206+ Macrohages


title: Sorted Macrophages from Synovial Tissue, RA, Patient 59

description:
Library name: HS59
RA_206pos_HS59


title: WT_Input_midLog_Input

description: Library name: WT_Input_midLog

source_name: Nucleus

value: Mid-Log Phase


title: 16S rRNA-seq,metagenome for B209m3 at 3mon

description: Library name: B209m3


title: BAT, VGC, TERM, Mouse 4

description: Library name: 180_BAT_VGC-_ISS_Term-_4_L1_1

value: BAT

value: VGC-TERM

value: female


title: Sorted Macrophages from Synovial Tissue, RA, Patient 57

description:
Library name: HS57
RA_206pos_HS57


title: WT_ChIP_midLog_antiSir3_Rep2

description: Library name: WT_ChIP_midLog_antiSir3_Rep2

value: WT


title: GAT, VGC, LAR, Mouse 3

description: Library name: 184_GAT_VC-LAR-3_L1_1

source_name: GAT

value: GAT

value: 8 months


title: Diaphragm, HGC, TERM, Mouse 4

description: Library name: 179_Diaphragm_HGC-_ISS_Term-_4_L1_1

source_name: Diaphragm

value: Diaphragm

value: HGC-TERM


title: 16S rRNA-seq,metagenome for B205m3 at 3mon

description: Library name: B205m3


title: Sorted Macrophages from Synovial Tissue, RA, Patient 55

description:
Library name: HS55
RA_206pos_HS55


title: WT_ChIP_midLog_antiSir3_Rep1

description: Library name: WT_ChIP_midLog_antiSir3_Rep1

value: Nucleus


title: 16S rRNA-seq,metagenome for B197m3 at 3mon

description: Library name: B197m3


title: WT_ChIP_3hr_anti-H3_Rep2

description: Library name: WT_ChIP_3hr_anti-H3_Rep2

value: Meiosis Hour 3


title: GAT, VGC, LAR, Mouse 13

description: Library name: 178_GAT_VC-LAR-13_L1_1

value: VGC-LAR

value: BALB/cAnNTac

value: 3 months


title: 16S rRNA-seq,metagenome for B166m3 at 3mon

description: Library name: B166m3

value: feces

value: exercise


title: Spleen, VGC, LAR, Mouse 12

description: Library name: 182_Spleen_VC-LAR-12_L1_1

value: Spleen


title: WT_ChIP_3hr_anti-H3K79me3_Rep2

description: Library name: WT_ChIP_3hr_anti-H3K79me3_Rep2


title: Sorted Macrophages from Synovial Tissue, OA, Patient 52

description:
Library name: HS52
OA_206pos_HS52

value: Joint Synovium

value: OA

value: CD206+ Macrohages


title: Sorted Macrophages from Synovial Tissue, OA, Patient 53

description:
Library name: HS53
OA_206pos_HS53


title: Spleen, VGC, LAR, Mouse 20

description: Library name: 176_Spleen_VC-LAR-20_L1_1

value: female


title: 16S rRNA-seq,metagenome for B164m3 at 3mon

description: Library name: B164m3


title: Brain, VGC, LAR, Mouse 17

description: Library name: 175_Brain_VC-LAR-17_L1_1

value: Brain


title: WT_ChIP_3hr_anti-H3K79me3_Rep1

description: Library name: WT_ChIP_3hr_anti-H3K79me3_Rep1

value: WT


title: WT_ChIP_3hr_anti-H3_Rep1

description: Library name: WT_ChIP_3hr_anti-H3_Rep1


title: Sorted Macrophages from Synovial Tissue, RA, Patient 51

description:
Library name: HS51
RA_206pos_HS51

value: RA


title: 16S rRNA-seq,metagenome for B158m3 at 3mon

description: Library name: B158m3


title: 16S rRNA-seq,metagenome for B161m3 at 3mon

description: Library name: B161m3


title: sir3ndt80Δ_T3_Rep1

description: Library name: sir3ndt80Δ_T3_Rep1


title: Sorted Macrophages from Synovial Tissue, OA, Patient 48

description:
Library name: HS48
OA_206pos_HS48


title: Thymus, FL, VGC, LAR, Mouse 16

description: Library name: 173_Thymus_FL-LAR-16_L1_1

source_name: Thymus

value: Thymus

value: 8 months


title: Brain, HGC, LAR, Mouse 13

description: Library name: 174_Brain_HC-LAR-13_L1_1

value: HGC-LAR


title: Sorted Macrophages from Synovial Tissue, OA, Patient 46

description:
Library name: HS46
OA_206pos_HS46


title: 16S rRNA-seq,metagenome for B155m3 at 3mon

description: Library name: B155m3


title: ndt80Δ_T3_Rep1

description: Library name: ndt80Δ_T3_Rep1

value: Nucleus

value: Meiosis Hour 3


title: Sorted Macrophages from Synovial Tissue, RA, Patient 56

description:
Library name: HS56
RA_206pos_HS56


title: Kidney, HGC, TERM, Mouse 11

description: Library name: 177_Kidney_HGC-_ISS_Term-_11_L1_1

source_name: Kidney

value: Kidney

value: HGC-TERM

value: BALB/cAnNTac


title: Pancreas, VGC, LAR, Mouse 12

description: Library name: 172_Pancreas_VC-LAR-12_L1_1

source_name: Pancreas

value: Pancreas

value: VGC-LAR


title: 16S rRNA-seq,metagenome for B154m3 at 3mon

description: Library name: B154m3

value: feces

value: exercise


title: E. coli WT infected with lambda, 30 min, RIL-seq rep2

city: Jerusalem

first: Reut

last: Bruner

address: Hadassah Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

description: RNA after application of RIL-seq

data_processing:
For RNAseq and RILseq: adapters removal (cutadapt version 3.5, parameters: -m 25 -q 15 -a AGATCGGAAGAGC -n 5 -e 0.15 -j 0),  mapping (bwa Version 0.7.17-r1188 with parameters aln -n 3 -t 8 -R 200 and then with sampe  -a 1500 -P  parameters) and BigWig files generation
For RILseq: finding chimeras, filtering the significant chimeras, reproducibility analysis, and unifying libraries (RIL-seq pipeline version 0.82)
Assembly: Escherichia coli str. K-12 substr. MG1655 (NC_000913-3) and Escherichia phage Lambda (J02459.1)
Supplementary files format and content: BigWig files
Library strategy: RIL-seq

growth_protocol: Bacterial strains were grown at 37˚C in LB medium with 10 mM MgSO4 , shaking at 250 rpm, separated into two flasks, and one flask was infected by phage lambda (MOI = 5). Samples were collected from these cultures 30 and 60 minutes following the infection.

extract_protocol:
Standard TRI Reagent protocol was used for total RNA extraction and standard TRI Reagent LS protocol was used for RNA extraction in the RIL-seq protocol
Library construction was carried out based on the RNAtag-Seq methodology (Shishkin et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018)

treatment_protocol: Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen by liquid nitrogen.

value: E. coli with untagged Hfq

value: infected with lambda


title: MAT, HGC, TERM, Mouse 13

description: Library name: 171_MAT_HGC-_ISS_Term-_13_L1_1

value: MAT

value: female


title: Sorted Macrophages from Synovial Tissue, RA, Patient 43

description:
Library name: HS43
RA_206pos_HS43

value: Joint Synovium

value: RA

value: CD206+ Macrohages


title: E. coli WT infected with lambda, 30 min, RIL-seq rep1

description: RNA after application of RIL-seq

organism: Escherichia coli str. K-12 substr. MG1655


title: 16S rRNA-seq,metagenome for B085m3 at 3mon

description: Library name: B085m3


title: 16S rRNA-seq,metagenome for B131m3 at 3mon

description: Library name: B131m3


title: E. coli WT, 30 min, RIL-seq rep2

description: RNA after application of RIL-seq

value: uninfected


title: Sorted Macrophages from Synovial Tissue, RA, Patient 42

description:
Library name: HS42
RA_206pos_HS42


title: 16S rRNA-seq,metagenome for B084m3 at 3mon

description: Library name: B084m3


title: Sorted Macrophages from Synovial Tissue, RA, Patient 27

description:
Library name: HS27
1479


title: 16S rRNA-seq,metagenome for B068m3 at 3mon

description: Library name: B068m3


title: E. coli WT, 30 min, RIL-seq rep1

description: RNA after application of RIL-seq


title: Diaphragm, HGC, TERM, Mouse 13

description: Library name: 169_Diaphragm_HGC-_ISS_Term-_13_L1_1

value: Diaphragm

value: 8 months


title: Sorted Macrophages from Synovial Tissue, OA, Patient 22

description:
Library name: HS22
1132

value: OA


title: E. coli with FLAG-tagged Hfq infected with lambda, 60 min, RIL-seq rep1

description: RNA after application of RIL-seq

value: E. coli with FLAG-tagged Hfq


title: E. coli with FLAG-tagged Hfq infected with lambda, 60 min, RIL-seq rep2

description: RNA after application of RIL-seq


title: Sorted Macrophages from Synovial Tissue, OA, Patient 24

description:
Library name: HS24
1469


title: Sorted Macrophages from Synovial Tissue, OA, Patient 21

description:
Library name: HS21
1130


title: Heart, HGC, LAR, Mouse 13

description: Library name: 167_Heart_HC-LAR-13_L1_1

source_name: Heart

value: Heart

value: HGC-LAR

value: BALB/cAnNTac

value: 3 months


title: Liver, FL, VGC, LAR, Mouse 12

description: Library name: 166_Liver_FL-LAR-12_L1_1

value: Liver

value: VGC-LAR


title: 16S rRNA-seq,metagenome for B062m3 at 3mon

description: Library name: B062m3

value: feces

value: exercise


title: E. coli with FLAG-tagged Hfq, 60 min, RIL-seq rep2

description: RNA after application of RIL-seq


title: 16S rRNA-seq,metagenome for B063m3 at 3mon

description: Library name: B063m3


title: Pancreas, HGC, LAR, Mouse 13

description: Library name: 165_Pancreas_HC-LAR-13_L1_1

value: Pancreas

value: female


title: 16S rRNA-seq,metagenome for B052m3 at 3mon

description: Library name: B052m3


title: Sorted Macrophages from Synovial Tissue, RA, Patient 19

description:
Library name: HS19
1023

value: Joint Synovium

value: RA


title: E. coli with FLAG-tagged Hfq, 60 min, RIL-seq rep1

description: RNA after application of RIL-seq

value: uninfected


title: Heart, HGC, LAR, Mouse 17

description: Library name: 164_Heart_HC-LAR-17_L1_1


title: Sorted Macrophages from Synovial Tissue, OA, Patient 16

description:
Library name: HS16
798

value: CD206+ Macrohages


title: Diaphragm, HGC, TERM, Mouse 11

description: Library name: 170_Diaphragm_HGC-_ISS_Term-_11_L1_1

value: Diaphragm

value: HGC-TERM

value: 8 months


title: E. coli with FLAG-tagged Hfq infected with lambda, 30 min, RIL-seq rep1

description: RNA after application of RIL-seq

value: E. coli with FLAG-tagged Hfq

value: infected with lambda


title: Sorted Macrophages from Synovial Tissue, RA, Patient 14

description:
Library name: HS14
P012


title: GAT, FL, TERM, Mouse 2

description: Library name: 163_GAT_FL-_ISS_Term-_2_L1_1

value: GAT

value: FL-TERM

value: BALB/cAnNTac


title: 16S rRNA-seq,metagenome for B040m3 at 3mon

description: Library name: B040m3


title: 16S rRNA-seq,metagenome for B031m3 at 3mon

description: Library name: B031m3


title: 16S rRNA-seq,metagenome for B032m3 at 3mon

description: Library name: B032m3


title: GAT, HGC, LAR, Mouse 4

description: Library name: 161_GAT_HC-LAR-4_L1_1

value: HGC-LAR


title: E. coli with FLAG-tagged Hfq, 30 min, RIL-seq rep2

description: RNA after application of RIL-seq


title: Heart, VGC, LAR, Mouse 10

description: Library name: 168_Heart_VC-LAR-10_L1_1

value: Heart

value: VGC-LAR

value: 3 months


title: Lung, HGC, LAR, Mouse 1

description: Library name: 162_Lung_HC-LAR-1_L1_1

source_name: Lung

value: Lung

value: female


title: Sorted Macrophages from Synovial Tissue, RA, Patient 20

description:
Library name: HS20
1024

value: Joint Synovium

value: RA


title: E. coli with FLAG-tagged Hfq, 30 min, RIL-seq rep1

description: RNA after application of RIL-seq

value: uninfected


title: 16S rRNA-seq,metagenome for B017m3 at 3mon

description: Library name: B017m3

value: feces

value: exercise


title: E. coli WT infected with lambda, 30 min, RNA-seq rep2

data_processing:
For RNAseq and RILseq: adapters removal (cutadapt version 3.5, parameters: -m 25 -q 15 -a AGATCGGAAGAGC -n 5 -e 0.15 -j 0),  mapping (bwa Version 0.7.17-r1188 with parameters aln -n 3 -t 8 -R 200 and then with sampe  -a 1500 -P  parameters) and BigWig files generation
For RILseq: finding chimeras, filtering the significant chimeras, reproducibility analysis, and unifying libraries (RIL-seq pipeline version 0.82)
Assembly: Escherichia coli str. K-12 substr. MG1655 (NC_000913-3) and Escherichia phage Lambda (J02459.1)
Supplementary files format and content: BigWig files

value: E. coli with untagged Hfq


title: Thymus, HGC, TERM, Mouse 13

description: Library name: 159_Thymus_HGC-_ISS_Term-_13_L1_1

value: Thymus

value: HGC-TERM

value: 8 months


title: 16S rRNA-seq,metagenome for B008m3 at 3mon

description: Library name: B008m3


title: PDAC, Human Tumor, scRNA-Seq sample129

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

description:
Library name: SC05
10x Genomics

data_processing:
Cell Ranger 6.1.2 was used. BCL files was converted into fastq files using “cellranger mkfastq” based on bcl2fastq2 (v2.20.0).
Fastq files for each sample was then processed by “cellranger count” to derive unique molecular identifier (UMI) count for each gene, using the human GRCh38 genome.
Samples were then aggregated by cellranger aggr.
Assembly: GENCODE Release 38 (GrCh38.p14)
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: Primary PDAC

extract_protocol:
Fresh tissue was dissociated into single cells using Miltenyi human dissociation kits (Miltenyi, 130-095-929) and red blood cells were removed using red blood cell lysis solution (Miltenyi, 130-094-183). Cell counts were performed using an automated cell counter and live cell counts were determined using trypan blue staining. Up to 10,000 cells were encapsulated into droplets for droplet-based 3’ end single-cell RNAseq using Chromium 3’ v3 reagents (10X Genomics).
cDNA libraries were quantified using the Qubit dsDNA Assay Kit (Thermo, Q32851) and library quality was assessed with the 4150 Tapestation System (Agilent) and D5000 screen tapes (Agilent, 5067-5588).
cDNA libraries were sequenced on a NextSeq500 (Illumina) using NextSeq 500/550 High Output Kit v2.5 (150 Cycles) (Illumina, 20024907) at 200M reads per sample.

value: Primary PDAC

value: Gemcitabine


title: PDAC, Human Tumor, scRNA-Seq sample50

description:
Library name: SC04
10x Genomics

value: FOLFIRINOX with XRT


title: Diaphragm, VGC, TERM, Mouse 16

description: Library name: 158_Diaphragm_VGC-_ISS_Term-_16_L1_1

value: Diaphragm

value: VGC-TERM

value: BALB/cAnNTac


title: 16S rRNA-seq,metagenome for B003m3 at 3mon

description: Library name: B003m3


title: E. coli with FLAG-tagged Hfq infected with lambda, 30 min, RIL-seq rep2

description: RNA after application of RIL-seq

value: E. coli with FLAG-tagged Hfq

value: infected with lambda


title: E. coli WT, 30 min, RNA-seq rep2


title: PDAC, Human Tumor, scRNA-Seq sample125

description:
Library name: SC03
10x Genomics

value: FOLFIRINOX


title: E. coli WT, 30 min, RNA-seq rep1


title: 16S rRNA-seq,metagenome for B277 at baseline

description: Library name: B277

value: baseline


title: Pancreas, VGC, LAR, Mouse 1

description: Library name: 157_Pancreas_VC-LAR-1_L1_1

value: Pancreas

value: VGC-LAR

value: female

value: 3 months


title: Sorted Macrophages from Synovial Tissue, OA, Patient 6

description:
Library name: HS06
P010

value: Joint Synovium

value: OA

value: CD206+ Macrohages


title: Thymus, HGC, LAR, Mouse 1

description: Library name: 156_Thymus_HC-LAR-1_L1_1

value: Thymus

value: HGC-LAR


title: E. coli with FLAG-tagged Hfq infected with lambda, 60 min, RNA-seq rep2


title: PDAC, Human Tumor, scRNA-Seq sample44

description:
Library name: SC01
10x Genomics

value: Primary PDAC

value: FOLFIRINOX with XRT


title: MAT, VGC, TERM, Mouse 12

description: Library name: 155_MAT_VGC-_ISS_Term-_12_L1_1

value: MAT

value: VGC-TERM

value: 8 months


title: PDAC, Human Tumor, sample125

description: Library name: Bulk125

data_processing:
Raw base call (BCL) files were converted to fastq files using bcl2fastq2 (v2.19.0).
RefSeq assembly (GCF_000001405.40) of the human reference genome GRCh38.p14 was used as the reference for gene quantification by Salmon 1.9.064 ("-- gcBias -- seqBias").
The total expected read counts per gene were normalized to transcripts per million (TPM).
Assembly: GENCODE Release 38 (GrCh38.p14)
Supplementary files format and content: comma-separated file containing Bulk RNAseq gene expression normalized TPM for all samples

extract_protocol:
Total RNA was extracted from tissues using the AllPrep DNA/RNA Kit (Qiagen, 80204). RNA was quantified using the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and quality assessed with the 4150 TapeStation System (Agilent) and RNA ScreenTape Analysis Kit (Agilent, 5067-5576).
RNA expression libraries were generated for flash frozen samples or FFPE samples, with TruSeq Stranded mRNA kits or with KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer’s instructions.


title: 16S rRNA-seq,metagenome for B009m3 at 3mon

description: Library name: B009m3

value: feces

value: exercise


title: GAT, VGC, LAR, Mouse 5

description: Library name: 160_GAT_VC-LAR-5_L1_1

value: GAT

value: BALB/cAnNTac


title: PDAC, Human Tumor, scRNA-Seq sample130

description:
Library name: SC06
10x Genomics

value: FOLFIRINOX


title: 16S rRNA-seq,metagenome for B264 at baseline

description: Library name: B264

value: baseline


title: Thymus, VGC, LAR, Mouse 12

description: Library name: 154_Thymus_VC-LAR-12_L1_1

value: VGC-LAR

value: female


title: E. coli with FLAG-tagged Hfq, 60 min, RNA-seq rep2

value: E. coli with FLAG-tagged Hfq

value: uninfected


title: PDAC, Human Tumor, sample118

description: Library name: Bulk118


title: E. coli with FLAG-tagged Hfq infected with lambda, 60 min, RNA-seq rep1

value: infected with lambda


title: Kidney, FL, TERM, Mouse 1

description: Library name: 153_Kidney_FL-_ISS_Term-_1_L1_1

value: Kidney

value: FL-TERM

value: 3 months


title: E. coli WT infected with lambda, 30 min, RNA-seq rep1

value: E. coli with untagged Hfq


title: 16S rRNA-seq,metagenome for B263 at baseline

description: Library name: B263


title: 16S rRNA-seq,metagenome for B258 at baseline

description: Library name: B258


title: E. coli with FLAG-tagged Hfq, 60 min, RNA-seq rep1


title: PDAC, Human Tumor, sample117

description: Library name: Bulk117

value: Primary PDAC


title: 16S rRNA-seq,metagenome for B253 at baseline

description: Library name: B253


title: Spleen, HGC, LAR, Mouse 8

description: Library name: 152_Spleen_HC-LAR-8_L1_1

source_name: Spleen

value: Spleen

value: HGC-LAR

value: 8 months


title: E. coli with FLAG-tagged Hfq infected with lambda, 30 min, RNA-seq rep2


title: PDAC, Human Tumor, sample116

description: Library name: Bulk116

value: Combination


title: PDAC, Human Tumor, scRNA-Seq sample46

description:
Library name: SC02
10x Genomics

value: FOLFOX


title: 16S rRNA-seq,metagenome for B273 at baseline

description: Library name: B273

source_name: feces

value: feces

value: exercise


title: E. coli with FLAG-tagged Hfq infected with lambda, 30 min, RNA-seq rep1


title: Thymus, FL, VGC, LAR, Mouse 12

description: Library name: 150_Thymus_FL-LAR-12_L1_1

value: Thymus

value: VGC-LAR

value: BALB/cAnNTac


title: Liver, VGC, TERM, Mouse 2

description: Library name: 151_Liver_VGC-_ISS_Term-_2_L1_1

value: Liver

value: VGC-TERM

value: female


title: E. coli with FLAG-tagged Hfq, 30 min, RNA-seq rep2

value: E. coli with FLAG-tagged Hfq

value: uninfected


title: 16S rRNA-seq,metagenome for B237 at baseline

description: Library name: B237

value: baseline


title: PDAC, Human Tumor, sample114

description: Library name: Bulk114

value: Primary PDAC

value: FOLFIRINOX


title: E. coli with FLAG-tagged Hfq, 30 min, RNA-seq rep1


title: 16S rRNA-seq,metagenome for B235 at baseline

description: Library name: B235


title: 16S rRNA-seq,metagenome for B211 at baseline

description: Library name: B211


title: PDAC, Human Tumor, sample112

description: Library name: Bulk112


title: Thymus, FL, VGC, LAR, Mouse 14

description: Library name: 148_Thymus_FL-LAR-14_L1_1

value: 3 months


title: SCURINH_4

city: San Francisco

first: Andrea

last: Curtabbi

state: CA

address: 140 Dolores Street APT 208

institute: UCSF

description: Library name: SCURINH_4

data_processing:
Downstream analysis was performed using nf-core/rnaseq analysis pipeline using Nextflow version 24.10.5
adapter sequences were removed using Trim Galore!
reads were then aligned to the Homo sapiens reference genome (GRCh38, Ensembl release 104) using the STAR aligner.
Transcript-level abundances were quantified with Salmon, and gene-level read counts were generated using featureCounts.
Raw counts were normalized using the Variance Stabilizing Transformation (VST) function and differential gene expression analysis was performed within the DESeq2 package.
Assembly: GRCh38, Ensembl relase 104
Supplementary files format and content: .csv file include Normalized counts (output of DEseq2)
Supplementary files format and content: salmon.merged.gene_counts.tsv contains output of the aligner

growth_protocol: Cells were grown in complete DMEM medium (D5796, containing 4500 mg/L glucose, 2 mM l-glutamine) supplemented with dialyzed 10 % fetal bovine serum (FBS, Sigma F7524), 1 % penicillin-streptomycin (PenStrep, Lonza), at 37 °C in an atmosphere of 5 % CO2/95 % air.

extract_protocol:
RNA was extracted using RNAeasy mini plus kit
RNA libraries were produced using TrueSeq RNASeq kit from Illumina

treatment_protocol: Antimycin A/myxothiazol (20 μM each) or vehicle (EtOH) were added for 3 days.

value: ostheosarcoma

value: ScURA

value: Antimycin/myxothiazol


title: PDAC, Human Tumor, sample113

description: Library name: Bulk113


title: PDAC, Human Tumor, sample111

description: Library name: Bulk111


title: SCURINH_3

description: Library name: SCURINH_3


title: 16S rRNA-seq,metagenome for B205 at baseline

description: Library name: B205

value: feces


title: PDAC, Human Tumor, sample110

description: Library name: Bulk110

value: Untreated


title: SCURINH_2

description: Library name: SCURINH_2


title: Liver, HGC, TERM, Mouse 1

first: Friederike

last: Grandke

address: Saarbrücken Campus

institute: Saarland University

description: Library name: 145_Liver_HGC-_ISS_Term-_1_L1_1

value: HGC-TERM


title: 16S rRNA-seq,metagenome for B197 at baseline

description: Library name: B197

value: exercise


title: PDAC, Human Tumor, sample109

description: Library name: Bulk109


title: SCURINH_1

description: Library name: SCURINH_1


title: PDAC, Human Tumor, sample115

description: Library name: Bulk115


title: 16S rRNA-seq,metagenome for B250 at baseline

description: Library name: B250


title: Heart, FL, VGC, LAR, Mouse 12

description: Library name: 144_Heart_FL-LAR-12_L1_1

value: Heart

value: VGC-LAR

value: BALB/cAnNTac

value: 8 months


title: 16S rRNA-seq,metagenome for B166 at baseline

description: Library name: B166


title: SCURA_4

description: Library name: SCURA_4

value: Control


title: PDAC, Human Tumor, sample108

description: Library name: Bulk108


title: Lung, VGC, LAR, Mouse 5

description: Library name: 143_Lung_VC-LAR-5_L1_1

value: Lung

value: female


title: SCURA_3

description: Library name: SCURA_3


title: 16S rRNA-seq,metagenome for B164 at baseline

description: Library name: B164

value: baseline


title: Diaphragm, HGC, LAR, Mouse 1

description: Library name: 149_Diaphragm_HC-LAR-1_L1_1

value: Diaphragm

value: HGC-LAR


title: PDAC, Human Tumor, sample107

description: Library name: Bulk107

value: Primary PDAC

value: Gemcitabine


title: PDAC, Human Tumor, sample106

description: Library name: Bulk106


title: 16S rRNA-seq,metagenome for B161 at baseline

description: Library name: B161


title: 16S rRNA-seq,metagenome for B209 at baseline

description: Library name: B209


title: Lung, VGC, LAR, Mouse 13

description: Library name: 147_Lung_VC-LAR-13_L1_1

value: 3 months


title: SCURA_2

description: Library name: SCURA_2

value: ostheosarcoma

value: ScURA


title: SCAT, FL, VGC, LAR, Mouse 11

description: Library name: 141_SCAT_FL-LAR-11_L1_1

source_name: SCAT

value: SCAT


title: Liver, VGC, TERM, Mouse 3

description: Library name: 142_Liver_VGC-_ISS_Term-_3_L1_1

value: Liver

value: VGC-TERM


title: SCURA_1

description: Library name: SCURA_1


title: 16S rRNA-seq,metagenome for B158 at baseline

description: Library name: B158

value: feces

value: exercise


title: Lung, FL, VGC, LAR, Mouse 12

description: Library name: 146_Lung_FL-LAR-12_L1_1

value: VGC-LAR

value: BALB/cAnNTac

value: 8 months


title: Heart, FL, VGC, LAR, Mouse 5

description: Library name: 140_Heart_FL-LAR-5_L1_1

value: Heart

value: female


title: 16S rRNA-seq,metagenome for B155 at baseline

description: Library name: B155

value: baseline


title: PDAC, Human Tumor, sample104

description: Library name: Bulk104

value: Untreated


title: Kidney, FL, TERM, Mouse 13

description: Library name: 139_Kidney_FL-_ISS_Term-_13_L1_1

value: Kidney

value: FL-TERM


title: INHIBITOR_3

description: Library name: INHIBITOR_3

value: WT

value: Antimycin/myxothiazol


title: PDAC, Human Tumor, sample103

description: Library name: Bulk103

value: Primary PDAC


title: 16S rRNA-seq,metagenome for B154 at baseline

description: Library name: B154


title: 16S rRNA-seq,metagenome for B131 at baseline

description: Library name: B131


title: INHIBITOR_2

description: Library name: INHIBITOR_2

value: ostheosarcoma


title: Lung, VGC, TERM, Mouse 1

description: Library name: 137_Lung_VGC-_ISS_Term-_1_L1_1

value: Lung

value: 3 months


title: PDAC, Human Tumor, sample105

description: Library name: Bulk105


title: PDAC, Human Tumor, sample102

description: Library name: Bulk102


title: 16S rRNA-seq,metagenome for B085 at baseline

description: Library name: B085

value: feces


title: MAT, HGC, LAR, Mouse 3

description: Library name: 138_MAT_HC-LAR-3_L1_1

value: MAT

value: HGC-LAR


title: INHIBITOR_1

description: Library name: INHIBITOR_1


title: PDAC, Human Tumor, sample101

description: Library name: Bulk101


title: BAT, HGC, LAR, Mouse 13

description: Library name: 136_BAT_HC-LAR-13_L1_1

source_name: BAT

value: BAT

value: BALB/cAnNTac


title: CONTROL_4

description: Library name: CONTROL_4

value: Control


title: 16S rRNA-seq,metagenome for B084 at baseline

description: Library name: B084

value: exercise


title: PDAC, Human Tumor, sample100

description: Library name: Bulk100


title: Heart, VGC, TERM, Mouse 5

description: Library name: 135_Heart_VGC-_ISS_Term-_5_L1_1

value: Heart

value: VGC-TERM

value: female


title: PDAC, Human Tumor, sample99

description: Library name: Bulk099

value: Gemcitabine


title: CONTROL_3

description: Library name: CONTROL_3

value: WT


title: 16S rRNA-seq,metagenome for B068 at baseline

description: Library name: B068

value: baseline


title: 16S rRNA-seq,metagenome for B063 at baseline

description: Library name: B063


title: INHIBITOR_4

description: Library name: INHIBITOR_4

value: Antimycin/myxothiazol


title: PDAC, Human Tumor, sample98

description: Library name: Bulk098

value: Primary PDAC

value: Untreated


title: Liver, HGC, TERM, Mouse 4

description: Library name: 133_Liver_HGC-_ISS_Term-_4_L1_1

value: Liver

value: HGC-TERM

value: 3 months


title: Thymus, FL, TERM, Mouse 12

description: Library name: 134_Thymus_FL-_ISS_Term-_12_L1_1

value: Thymus

value: FL-TERM

value: 8 months


title: 16S rRNA-seq,metagenome for B062 at baseline

description: Library name: B062

value: feces


title: PDAC, Human Tumor, sample97

description: Library name: Bulk097

value: XRT Alone


title: CONTROL_1

description: Library name: CONTROL_1

value: ostheosarcoma

value: Control


title: GAT, VGC, TERM, Mouse 14

description: Library name: 132_GAT_VGC-_ISS_Term-_14_L1_1

value: GAT

value: VGC-TERM

value: female

value: BALB/cAnNTac