title: P1, SILP, scRNAseq, mononuclear phagocytes, GEX

city: Copenhagen

first: William

middle: Winston

last: Agace

address: Blegdamsvej 3B

department: Skin Immunology Research Center

institute: Copenhagen University

description: Library name: P1_SILP_GEX

data_processing:
scRNAseq: raw reads were processed with 10x Genomics Cell Ranger (version 2.2.0, 3.1.0, and 8.0.0). CITEseq: Sequencing data from samples stained with TotalSeq antibodies was processed with CITE-seq count.
Assembly: GRCh38
Supplementary files format and content: GEX_matrix.mtx.gz: RNA expression as sparse count matrix, cell barcodes as columns, gene features as rows
Supplementary files format and content: GEX_features.tsv.gz: gene features, consist of three columns 1) unique gene identifier from the gtf file, 2) human readable gene name 3) feature type, for GEX these are all gene expression
Supplementary files format and content: GEX_barcodes.tsv.gz: list of barcodes for the sample
Supplementary files format and content: GEX_unspliced.csv.gz: count matrix of unspliced gene information based on velocyto calculation
Supplementary files format and content: GEX_spliced.csv.gz:  count matrix of spliced gene information based on velocyto calculation
Supplementary files format and content: ADT_matrix.mtx.gz: CITEseq protein expression as sparse count matrix, cell barcodes as columns, CITEseq antibodies as rows
Supplementary files format and content: ADT_barcodes.tsv.gz: list of barcodes for the sample
Supplementary files format and content: ADT_features.tsv.gz: consist of two columns, 1) name or dentifier for each antibody or tag that was quantified, 2) feature type, for ADT this is all ADT/CITEseq data

source_name: small intestinal lamina propria

extract_protocol:
Patient samples are from resection material of patients undergoing surgery for colorectal cancer (healthy controls, samples were taken away from the cancer site) or IBD resections. The sample material underwent protocol from Jørgensen et al. (DOI: 10.1038/s41596-020-00482-1) to isolate lamina propria. Mononuclear phagocytes were sorted based on being single, live, CD45+ CD3- CD19- HLADR+ cells and using the 10x platform submitted to sc-omics analysis.
Freshly isolated sorted single cells were subjected to droplet-based massively parallel scRNA-seq using the Chromium Single Cell 3’ Reagent Kits v2, the Chromium Single Cell 3′ Reagent Kit v3.1 with Feature Cell 5’ Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein & Barcoding technology for Cell Surface Protein or the Chromium Next GEM Single Immune Receptor Mapping (10x Genomics) following the manufacturer’s instructions. For CITEseq analysis, 5 μl of the purified smaller cDNA product was used as template for antibody-derived tag (ADT) sequencing and ADT sequencing libraries were constructed and indexed following the manufacturer's instructions.

value: small intestinal lamina propria

value: mononuclear phagocytes

tag: disease state

value: healthy


title: 16S rRNA-seq,metagenome for B052 at baseline

status: Public on Dec 18 2025

type: SRA

city: Nanjing

first: xinyuan

last: ge

state: Jiangsu

address: Longmian Road 818

country: China

institute: Nanjing Medical University School of Public Health

description: Library name: B052

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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).

tag: cell type

value: feces

tag: treatment

value: exercise

tag: timepoint

value: baseline


title: P1, cLP, scRNAseq, mononuclear phagocytes, GEX

country: Denmark

description: Library name: P1_cLP_GEX

library_source: transcriptomic single cell

molecule: total RNA

source_name: colonic lamina propria

tag: tissue

value: colonic lamina propria


title: PDAC, Human Tumor, sample95

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

country: USA

institute: The University of North Carolina at Chapel Hill

description: Library name: Bulk095

library_source: transcriptomic

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

source_name: Primary PDAC

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.

value: Primary PDAC

value: Untreated


title: GAT, HGC, TERM, Mouse 11

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

country: Germany

institute: Saarland University

description: Library name: 131_GAT_HGC-_ISS_Term-_11_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.

organism: Mus musculus

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.

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: GAT

tag: experiment group

value: HGC-TERM

tag: Sex

value: female

tag: strain

value: BALB/cAnNTac

tag: mouse id

tag: age

value: 8 months


title: 16S rRNA-seq,metagenome for B040 at baseline

description: Library name: B040


title: 16S rRNA-seq,metagenome for B032 at baseline

description: Library name: B032


title: PDAC, Human Tumor, sample96

description: Library name: Bulk096


title: 16S rRNA-seq,metagenome for B031 at baseline

description: Library name: B031


title: PDAC, Human Tumor, sample93

description: Library name: Bulk093


title: Liver, HGC, LAR, Mouse 1

description: Library name: 129_Liver_HC-LAR-1_L1_1

source_name: Liver

value: Liver

value: HGC-LAR

value: 3 months


title: PDAC, Human Tumor, sample94

description: Library name: Bulk094


title: GAT, HGC, LAR, Mouse 2

description: Library name: 130_GAT_HC-LAR-2_L1_1


title: PDAC, Human Tumor, sample92

description: Library name: Bulk092


title: CONTROL_2

city: San Francisco

first: Andrea

last: Curtabbi

state: CA

address: 140 Dolores Street APT 208

institute: UCSF

description: Library name: CONTROL_2

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

molecule: polyA RNA

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.

tag: cell line

value: ostheosarcoma

tag: genotype

value: WT

value: Control


title: 16S rRNA-seq,metagenome for B017 at baseline

description: Library name: B017

value: feces


title: 16S rRNA-seq,metagenome for B009 at baseline

description: Library name: B009

value: exercise


title: Brain tissue, CA, rep3

city: London

first: Luminita

last: Ruje

address: Imperial London Hammersmith Campus, Du Cane Road

country: United Kingdom

institute: LMS MRC

description:
Library name: brain_CA3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt

data_processing:
Salmon called abundances
Differential gene expression analysis with Dream/variancePartition
Assembly: mRatBN7.2
Supplementary files format and content: Voom normalized abundances with Dream weights

organism: Rattus norvegicus

source_name: Brain

growth_protocol: The adult male Sprague Dawley rats (weight 230g-250g) were purchased from Jinan Peng Yue Laboratory Animal Breeding Co. Ltd and were kept under a 12-hour light/dark cycle in the same colony room with appropriate temperature. All animal experiments were conducted in compliance with National Institutes of Health Guidelines and were approved by the institutional animal care and use committee of Qingdao University.

extract_protocol:
Total RNA was extracted by TRIzol Reagent
RNA sequencing and quality control were provided by Beijing Novogene (Beijing, China).

treatment_protocol: The skin was cut with scissors after disinfection in the middle of the neck, and the right common carotid artery (CCA), external carotid artery (ECA), and internal carotid artery (ICA) were bluntly isolated with forceps. And all were ligated with surgical sutures. A small incision was cut at the distal end of the ECA and a filament was inserted. The filament was inserted deeper and deeper from the right CCA into the right ICA after the sutures of the ICA were undone to occlude the origin of the right middle cerebral artery (MCA), until it stops at the black mark of the filament. Rats were sacrificed after arterial occlusion for 1 hour, 2 hours and 4 hours.

value: Brain

tag: sample group/region

value: Brain tissue, CA

tag: batch


title: 16S rRNA-seq,metagenome for B008 at baseline

description: Library name: B008

value: baseline


title: Kidney, VGC, LAR, Mouse 3

description: Library name: 127_Kidney_VC-LAR-3_L1_1

source_name: Kidney

value: Kidney

value: VGC-LAR


title: PDAC, Human Tumor, sample91

description: Library name: Bulk091

value: Primary PDAC

value: Untreated


title: Brain tissue, 4z, rep1

description:
Library name: brain_4z1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt

value: Brain tissue, 4z


title: PDAC, Human Tumor, sample90

description: Library name: Bulk090

value: FOLFIRINOX


title: Lung, FL, TERM, Mouse 2

description: Library name: 126_Lung_FL-_ISS_Term-_2_L1_1

source_name: Lung

value: Lung

value: FL-TERM

value: female

value: BALB/cAnNTac


title: Kidney, HGC, TERM, Mouse 4

description: Library name: 125_Kidney_HGC-_ISS_Term-_4_L1_1

value: HGC-TERM

value: 3 months


title: Brain tissue, CA, rep1

description:
Library name: brain_CA1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


title: Brain tissue, CA, rep2

description:
Library name: brain_CA2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


title: 16S rRNA-seq,metagenome for B003 at baseline

description: Library name: B003

value: feces


title: PDAC, Human Tumor, sample89

description: Library name: Bulk089


title: PDAC, Human Tumor, sample88

description: Library name: Bulk088


title: 16S rRNA-seq,metagenome for B272m3 at 3mon

description: Library name: B272m3

value: control


title: GAT, FL, VGC, LAR, Mouse 2

description: Library name: 123_GAT_FL-LAR-2_L1_1

value: GAT


title: Brain tissue, 4p, rep3

description:
Library name: brain_4p3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt

value: Brain

value: Brain tissue, 4p


title: Brain tissue, 4z, rep3

description:
Library name: brain_4z3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


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

description: Library name: 124_Diaphragm_FL-LAR-16_L1_1

source_name: Diaphragm

value: Diaphragm

value: 8 months


title: Brain tissue, 4p, rep2

description:
Library name: brain_4p2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


title: Brain tissue, 4z, rep2

description:
Library name: brain_4z2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


title: PDAC, Human Tumor, sample87

description: Library name: Bulk087

value: Primary PDAC


title: 16S rRNA-seq,metagenome for B220m3 at 3mon

description: Library name: B220m3


title: 16S rRNA-seq,metagenome for B219m3 at 3mon

description: Library name: B219m3


title: PDAC, Human Tumor, sample86

description: Library name: Bulk086

value: Untreated


title: SCAT, HGC, TERM, Mouse 13

description: Library name: 128_SCAT_HGC-_ISS_Term-_13_L1_1

source_name: SCAT

value: SCAT


title: Heart, VGC, LAR, Mouse 16

description: Library name: 121_Heart_VC-LAR-16_L1_1

source_name: Heart

value: Heart

value: VGC-LAR


title: Heart, VGC, LAR, Mouse 19

description: Library name: 122_Heart_VC-LAR-19_L1_1


title: Brain tissue, 4p, rep1

description:
Library name: brain_4p1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


title: Brain tissue, 4c, rep3

description:
Library name: brain_4c3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt

value: Brain tissue, 4c


title: PDAC, Human Tumor, sample85

description: Library name: Bulk085


title: 16S rRNA-seq,metagenome for B202m3 at 3mon

description: Library name: B202m3


title: 16S rRNA-seq,metagenome for B190m3 at 3mon

description: Library name: B190m3


title: Spleen, FL, TERM, Mouse 5

description: Library name: 120_Spleen_FL-_ISS_Term-_5_L1_1

source_name: Spleen

value: Spleen

value: FL-TERM

value: female


title: Brain tissue, 4c, rep2

description:
Library name: brain_4c2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


title: Brain tissue, 4c, rep1

description:
Library name: brain_4c1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Brain_voomWithDreamWeights-normalised.txt


title: 16S rRNA-seq,metagenome for B181m3 at 3mon

description: Library name: B181m3


title: PDAC, Human Tumor, sample84

description: Library name: Bulk084


title: PDAC, Human Tumor, sample83

description: Library name: Bulk083


title: Kidney, HGC, LAR, Mouse 16

description: Library name: 118_Kidney_HC-LAR-16_L1_1

value: Kidney

value: HGC-LAR

value: BALB/cAnNTac


title: 16S rRNA-seq,metagenome for B173m3 at 3mon

description: Library name: B173m3

value: feces

value: control


title: PDAC, Human Tumor, sample82

description: Library name: Bulk082


title: Synaptosome, 4z, rep3

description:
Library name: syn_4z3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

source_name: Brain/Synaptosome only

value: Brain/Synaptosome only

value: Synaptosome, 4z


title: 16S rRNA-seq,metagenome for B167m3 at 3mon

description: Library name: B167m3


title: Synaptosome, 4z, rep2

description:
Library name: syn_4z2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt


title: Kidney, HGC, LAR, Mouse 5

description: Library name: 117_Kidney_HC-LAR-5_L1_1

value: 3 months


title: PDAC, Human Tumor, sample81

description: Library name: Bulk081

value: Primary PDAC

value: Chemo/RT


title: BAT, HGC, TERM, Mouse 3

description: Library name: 116_BAT_HGC-_ISS_Term-_3_L1_1

source_name: BAT

value: BAT

value: HGC-TERM


title: 16S rRNA-seq,metagenome for B143m3 at 3mon

description: Library name: B143m3


title: PDAC, Human Tumor, sample80

description: Library name: Bulk080

value: Untreated


title: Diaphragm, FL, TERM, Mouse 4

description: Library name: 115_Diaphragm_FL-_ISS_Term-_4_L1_1

value: Diaphragm


title: PDAC, Human Tumor, sample79

description: Library name: Bulk079


title: PDAC, Human Tumor, sample78

description: Library name: Bulk078


title: 16S rRNA-seq,metagenome for B142m3 at 3mon

description: Library name: B142m3


title: 16S rRNA-seq,metagenome for B132m3 at 3mon

description: Library name: B132m3


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

description: Library name: 114_MAT_FL-LAR-12_L1_1

source_name: MAT

value: MAT

value: VGC-LAR

value: 8 months


title: Synaptosome, CA, rep3

description:
Library name: syn_CA3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

value: Synaptosome, CA


title: Kidney, FL, TERM, Mouse 11

description: Library name: 119_Kidney_FL-_ISS_Term-_11_L1_1

value: Kidney

value: FL-TERM

value: female


title: PDAC, Human Tumor, sample77

description: Library name: Bulk077


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

description: Library name: 113_Spleen_FL-LAR-17_L1_1

value: Spleen

value: BALB/cAnNTac


title: Synaptosome, CA, rep1

description:
Library name: syn_CA1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

value: Brain/Synaptosome only


title: Synaptosome, 4p, rep3

description:
Library name: syn_4p3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

value: Synaptosome, 4p


title: Synaptosome, 4p, rep2

description:
Library name: syn_4p2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt


title: Diaphragm, FL, TERM, Mouse 13

description: Library name: 111_Diaphragm_FL-_ISS_Term-_13_L1_1


title: PDAC, Human Tumor, sample75

description: Library name: Bulk075

value: Primary PDAC

value: FOLFIRINOX


title: 16S rRNA-seq,metagenome for B107m3 at 3mon

description: Library name: B107m3

value: feces

value: control


title: Thymus, VGC, LAR, Mouse 4

description: Library name: 110_Thymus_VC-LAR-4_L1_1

source_name: Thymus

value: Thymus


title: Synaptosome, 4p, rep1

description:
Library name: syn_4p1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt


title: Synaptosome, 4z, rep1

description:
Library name: syn_4z1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

value: Synaptosome, 4z


title: GAT, FL, TERM, Mouse 3

description: Library name: 109_GAT_FL-_ISS_Term-_3_L1_1

value: GAT

value: 3 months


title: PDAC, Human Tumor, sample73

description: Library name: Bulk073

value: Untreated


title: Synaptosome, 4c, rep3

description:
Library name: syn_4c3
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

value: Synaptosome, 4c


title: Synaptosome, CA, rep2

description:
Library name: syn_CA2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

value: Synaptosome, CA


title: PDAC, Human Tumor, sample76

description: Library name: Bulk076


title: 16S rRNA-seq,metagenome for B106m3 at 3mon

description: Library name: B106m3


title: Spleen, VGC, LAR, Mouse 19

description: Library name: 108_Spleen_VC-LAR-19_L1_1

value: VGC-LAR

value: 8 months


title: Synaptosome, 4c, rep2

description:
Library name: syn_4c2
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt


title: PDAC, Human Tumor, sample72

description: Library name: Bulk072


title: 16S rRNA-seq,metagenome for B098m3 at 3mon

description: Library name: B098m3


title: Kidney, VGC, TERM, Mouse 14

description: Library name: 107_Kidney_VGC-_ISS_Term-_14_L1_1

value: Kidney

value: VGC-TERM

value: female


title: Synaptosome, 4c, rep1

description:
Library name: syn_4c1
CA1, CA2, CA3, 4z1, 4z2, 4z3, 4c1, 4c2, 4c3, 4p1, 4p2, 4p3, gene
Syn_voomWithDreamWeights-normalised.txt

value: Brain/Synaptosome only


title: 16S rRNA-seq,metagenome for B127m3 at 3mon

description: Library name: B127m3


title: PDAC, Human Tumor, sample74

description: Library name: Bulk074

value: Primary PDAC


title: 16S rRNA-seq,metagenome for B112m3 at 3mon

description: Library name: B112m3


title: Heart, FL, TERM, Mouse 12

description: Library name: 112_Heart_FL-_ISS_Term-_12_L1_1

value: Heart

value: FL-TERM

value: BALB/cAnNTac


title: 16S rRNA-seq,metagenome for B114m3 at 3mon

description: Library name: B114m3

value: feces

value: control


title: PDAC, Human Tumor, sample71

description: Library name: Bulk071


title: 16S rRNA-seq,metagenome for B089m3 at 3mon

description: Library name: B089m3


title: Sperm miRNA, Duroc boar 6, 10 months, mature

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: B15_10mo_miRNA

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.

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

value: sperm

value: Duroc

value: 10 months


title: SCAT, HGC, LAR, Mouse 12

description: Library name: 106_SCAT_HC-LAR-12_L1_1

value: SCAT

value: HGC-LAR


title: 16S rRNA-seq,metagenome for B082m3 at 3mon

description: Library name: B082m3

source_name: feces


title: PDAC, Human Tumor, sample70

description: Library name: Bulk070

value: Untreated


title: Kidney, VGC, LAR, Mouse 14

description: Library name: 105_Kidney_VC-LAR-14_L1_1

value: Kidney

value: VGC-LAR

value: 3 months


title: 16S rRNA-seq,metagenome for B075m3 at 3mon

description: Library name: B075m3


title: Sperm miRNA, Duroc boar 5, 10 months, mature

description: Library name: B14_10mo_miRNA


title: PDAC, Human Tumor, sample69

description: Library name: Bulk069


title: 16S rRNA-seq,metagenome for B066m3 at 3mon

description: Library name: B066m3


title: Sperm miRNA, Duroc boar 4, 10 months, mature, replicate 2

description:
Library name: B13_10mo_miRNA_rep2
Technical replicate 2 - merged with B13_10mo_miRNA_rep1 before downstream analysis


title: Kidney, HGC, LAR, Mouse 14

description: Library name: 104_Kidney_HC-LAR-14_L1_1

value: female


title: PDAC, Human Tumor, sample68

description: Library name: Bulk068

value: Primary PDAC


title: Sperm miRNA, Duroc boar 4, 10 months, mature, replicate 1

description:
Library name: B13_10mo_miRNA_rep1
Technical replicate 1 - merged with B13_10mo_miRNA_rep2 before downstream analysis


title: PDAC, Human Tumor, sample67

description: Library name: Bulk067


title: 16S rRNA-seq,metagenome for B065m3 at 3mon

description: Library name: B065m3


title: PDAC, Human Tumor, sample66

description: Library name: Bulk066


title: Sperm miRNA, Duroc boar 3, 10 months, mature, replicate 2

description:
Library name: B11_10mo_miRNA_rep2
Technical replicate 2 - merged with B11_10mo_miRNA_rep1 before downstream analysis


title: 16S rRNA-seq,metagenome for B056m3 at 3mon

description: Library name: B056m3


title: PDAC, Human Tumor, sample65

description: Library name: Bulk065


title: MAT, VGC, LAR, Mouse 2

description: Library name: 102_MAT_VC-LAR-2_L1_1

value: MAT


title: SCAT, FL, TERM, Mouse 2

description: Library name: 100_SCAT_FL-_ISS_Term-_2_L1_1

value: FL-TERM


title: MAT, VGC, TERM, Mouse 11

description: Library name: 101_MAT_VGC-_ISS_Term-_11_L1_1

value: VGC-TERM

value: BALB/cAnNTac

value: 8 months


title: 16S rRNA-seq,metagenome for B047m3 at 3mon

description: Library name: B047m3

value: feces

value: control


title: 16S rRNA-seq,metagenome for B044m3 at 3mon

description: Library name: B044m3


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

description:
Library name: B11_10mo_miRNA_rep1
Technical replicate 1 - merged with B11_10mo_miRNA_rep2 before downstream analysis

value: spermatozoa

value: sperm

value: Duroc


title: 16S rRNA-seq,metagenome for B037m3 at 3mon

description: Library name: B037m3


title: Lung, HGC, LAR, Mouse 2

description: Library name: 99_Lung_HC-LAR-2_L1_1

value: Lung

value: HGC-LAR


title: Sperm miRNA, Duroc boar 1, 10 months, mature

description: Library name: B8_10mo_miRNA

value: 10 months


title: Brain, VGC, LAR, Mouse 1

description: Library name: 98_Brain_VC-LAR-1_L1_1

value: Brain

value: VGC-LAR


title: PDAC, Human Tumor, sample64

description: Library name: Bulk064

value: Untreated


title: Sperm miRNA, Duroc boar 6, 7 months, pubertal

description: Library name: B15_7mo_miRNA

value: 7 months


title: 16S rRNA-seq,metagenome for B028m3 at 3mon

description: Library name: B028m3


title: PDAC, Human Tumor, sample62

description: Library name: Bulk062

value: Primary PDAC


title: Heart, HGC, TERM, Mouse 4

description: Library name: 97_Heart_HGC-_ISS_Term-_4_L1_1

value: Heart

value: HGC-TERM

value: female

value: 3 months


title: Sperm miRNA, Duroc boar 5, 7 months, pubertal

description: Library name: B14_7mo_miRNA


title: GAT, VGC, LAR, Mouse 11

description: Library name: 103_GAT_VC-LAR-11_L1_1

value: GAT

value: BALB/cAnNTac

value: 8 months


title: PDAC, Human Tumor, sample61

description: Library name: Bulk061


title: 16S rRNA-seq,metagenome for B024m3 at 3mon

description: Library name: B024m3

value: feces

value: control


title: Sperm miRNA, Duroc boar 4, 7 months, pubertal

description: Library name: B13_7mo_miRNA

value: spermatozoa

value: sperm

value: Duroc


title: 16S rRNA-seq,metagenome for B013m3 at 3mon

description: Library name: B013m3


title: PDAC, Human Tumor, sample60

description: Library name: Bulk060

value: Gemcitabine


title: Lung, HGC, TERM, Mouse 3

description: Library name: 79_Lung_HGC-_ISS_Term-_3_L1_1

value: Lung


title: Sperm miRNA, Duroc boar 2, 10 months, mature

description: Library name: B9_10mo_miRNA

value: 10 months


title: 16S rRNA-seq,metagenome for B002m3 at 3mon

description: Library name: B002m3


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

description:
Library name: B11_7mo_miRNA_rep2
Technical replicate 2 - merged with B11_7mo_miRNA_rep1 before downstream analysis

value: 7 months


title: PDAC, Human Tumor, sample59

description: Library name: Bulk059

value: Primary PDAC

value: Untreated


title: Kidney, VGC, LAR, Mouse 4

description: Library name: 78_Kidney_VC-LAR-4_L1_1

value: Kidney

value: VGC-LAR


title: PDAC, Human Tumor, sample58

description: Library name: Bulk058


title: 16S rRNA-seq,metagenome for B272 at baseline

description: Library name: B272

value: baseline


title: 16S rRNA-seq,metagenome for B220 at baseline

description: Library name: B220


title: Diaphragm, HGC, LAR, Mouse 2

description: Library name: 77_Diaphragm_HC-LAR-2_L1_1

value: Diaphragm

value: HGC-LAR

value: female

value: 3 months


title: PDAC, Human Tumor, sample63

description: Library name: Bulk063


title: Sperm miRNA, Duroc boar 2, 7 months, pubertal

description: Library name: B9_7mo_miRNA


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

description:
Library name: B11_7mo_miRNA_rep1
Technical replicate 1 - merged with B11_7mo_miRNA_rep2 before downstream analysis


title: Sperm miRNA, Duroc boar 1, 7 months, pubertal

description: Library name: B8_7mo_miRNA


title: PDAC, Human Tumor, sample56

description: Library name: Bulk056


title: PDAC, Human Tumor, sample57

description: Library name: Bulk057


title: 16S rRNA-seq,metagenome for B219 at baseline

description: Library name: B219

value: feces

value: control


title: BAT, FL, TERM, Mouse 3

description: Library name: 76_BAT_FL-_ISS_Term-_3_L1_1

value: BAT

value: FL-TERM

value: BALB/cAnNTac


title: 16S rRNA-seq,metagenome for B202 at baseline

description: Library name: B202


title: PDAC, Human Tumor, sample55

description: Library name: Bulk055


title: Liver, FL, VGC, LAR, Mouse 2

description: Library name: 80_Liver_FL-LAR-2_L1_1

value: Liver


title: Kidney, HGC, TERM, Mouse 5

description: Library name: 74_Kidney_HGC-_ISS_Term-_5_L1_1

value: HGC-TERM


title: Mice liver,Vande_L2

city: Hangzhou

first: Wu

middle: Wen

last: Tong

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Library name: SAMPLES_4

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

growth_protocol: C57BL/6J mice were housed under controlled conditions with a 12-hour light/dark cycle, temperatures maintained between 21°C and 23°C, and humidity levels of 40% to 70%.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were given 0.5% carboxymethyl cellulose sodium or 100 mg/kg vandetanib daily for 4 weeks.

value: liver

value: WT

value: 100 mg/kg/day vandetanib


title: 16S rRNA-seq,metagenome for B190 at baseline

description: Library name: B190


title: Mice liver,Vande_L1

description: Library name: SAMPLES_3


title: BAT, VGC, TERM, Mouse 12

description: Library name: 73_BAT_VGC-_ISS_Term-_12_L1_1

value: VGC-TERM

value: 8 months


title: PDAC, Human Tumor, sample54

description: Library name: Bulk054

source_name: Primary PDAC

value: Primary PDAC

value: Untreated


title: Mice liver,Control_L2

description: Library name: SAMPLES_2

value: CMC-Na


title: 16S rRNA-seq,metagenome for B181 at baseline

description: Library name: B181

value: baseline


title: PDAC, Human Tumor, sample52

description: Library name: Bulk052

value: FOLFIRINOX


title: Pancreas, HGC, LAR, Mouse 2

description: Library name: 70_Pancreas_HC-LAR-2_L1_1

source_name: Pancreas

value: Pancreas

value: HGC-LAR

value: female

value: 3 months


title: Mice liver,Control_L1

description: Library name: SAMPLES_1


title: Heart, VGC, TERM, Mouse 12

description: Library name: 71_Heart_VGC-_ISS_Term-_12_L1_1

value: Heart

value: BALB/cAnNTac


title: 16S rRNA-seq,metagenome for B173 at baseline

description: Library name: B173

value: feces

value: control


title: 16S rRNA-seq,metagenome for B167 at baseline

description: Library name: B167


title: MAT, FL, TERM, Mouse 4

description: Library name: 69_MAT_FL-_ISS_Term-_4_L1_1

value: MAT

value: FL-TERM


title: PDAC, Human Tumor, sample50

description: Library name: Bulk050

value: FOLFIRINOX with XRT


title: Mock-infected E. coli, 60min, rep2

city: Urbana

first: Ido

last: Golding

state: IL

address: 1110 W Green St.

department: Physics

institute: University of Illinois Urbana-Champaign

description: Library name: FB7

data_processing:
FASTQ files for each sample were mapped to the genome using BWA (v0.7.17)
BEDTools (v2.28.0) was used to calculate per-base read depth across the phage genome and per-gene read counts across the E. coli genome.
Assembly: E. coli MG1655 reference genome (NCBI accession: U00096.3) and the phage lambda genome (NCBI accession: NC_001416)
Supplementary files format and content: Raw read counts for E. coli genes are provided in a .txt file (first column: gene name; second column: read count).
Supplementary files format and content: Raw read depth for the phage genome is provided in a .txt file (first column: 1-based genomic position; second column: read depth).

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

source_name: E. coli

growth_protocol: Bacterial cells were grown at 30°C in LB medium supplemented with 10 mM MgSO₄, 0.2% maltose, and 10 μM IPTG, with shaking at 220 rpm. When cultures reached OD₆₀₀ ≈ 0.4, cells were harvested by centrifugation and concentrated to 100× the original density. Infection was initiated by mixing the concentrated host cells with phage lysate (MOI ≈ 4 or ≈ 0.3) or with SM buffer for mock infection. The infection mixture was incubated on ice for 30 minutes, followed by a 5-minute incubation in a 35°C water bath. The culture was then diluted 1:1000 into fresh medium and incubated at 30°C with shaking. Samples were collected at 0+, 2.5, 5, 10, 20, 45, and 60 minutes post-infection.

extract_protocol:
Cell lysis was performed by resuspending the cell pellets in TE buffer containing 1 mg/mL lysozyme and incubating for 5 minutes at room temperature. Subsequent steps—including removal of cell debris, ethanol precipitation of RNA, DNase I treatment, washing, and RNA elution—were carried out using the Quick-RNA Fungal/Bacterial Microprep Kit (Zymo Research) according to the manufacturer's protocol.
The total RNAs were converted into individually barcoded RNA-seq libraries without rRNA depletion with the RNA Library Prep kit from Watchmaker Genomics. Sequencing was performed on a single 10B lane of a NovaSeq X Plus, generating 100-nt single-end reads.

treatment_protocol: Cell cultures were collected and resuspended in 2× volume of RNAprotect Bacteria Reagent (Qiagen), vortexed briefly to mix, and incubated at room temperature for at least 5 minutes. Cells were then pelleted by centrifugation, and the supernatant was discarded.

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: PDAC, Human Tumor, sample49

description: Library name: Bulk049

value: Primary PDAC


title: PDAC, Human Tumor, sample51

description: Library name: Bulk051

value: Combination


title: Lung, HGC, TERM, Mouse 12

description: Library name: 68_Lung_HGC-_ISS_Term-_12_L1_1

value: Lung

value: HGC-TERM

value: 8 months


title: Mock-infected E. coli, 45min, rep2

description: Library name: FB6


title: PDAC, Human Tumor, sample48

description: Library name: Bulk048

value: FOLFIRINOX


title: 16S rRNA-seq,metagenome for B143 at baseline

description: Library name: B143

value: baseline


title: Mock-infected E. coli, 20min, rep2

description: Library name: FB5


title: Kidney, FL, TERM, Mouse 14

description: Library name: 66_Kidney_FL-_ISS_Term-_14_L1_1

value: Kidney

value: female


title: Mock-infected E. coli, 10min, rep2

description: Library name: FB4


title: PDAC, Human Tumor, sample47

description: Library name: Bulk047


title: 16S rRNA-seq,metagenome for B127 at baseline

description: Library name: B127


title: PDAC, Human Tumor, sample46

description: Library name: Bulk046

value: FOLFOX


title: Spleen, VGC, TERM, Mouse 4

description: Library name: 64_Spleen_VGC-_ISS_Term-_4_L1_1

value: Spleen

value: VGC-TERM

value: BALB/cAnNTac

value: 3 months


title: Mock-infected E. coli, 5min, rep2

description: Library name: FB3


title: Lung, VGC, TERM, Mouse 4

description: Library name: 63_Lung_VGC-_ISS_Term-_4_L1_1


title: Mock-infected E. coli, 2.5min, rep2

description: Library name: FB2


title: 16S rRNA-seq,metagenome for B114 at baseline

description: Library name: B114

value: feces

value: control


title: Lung, FL, TERM, Mouse 14

description: Library name: 62_Lung_FL-_ISS_Term-_14_L1_1

value: FL-TERM


title: Mock-infected E. coli, 0+min, rep2

description: Library name: FB1

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: 16S rRNA-seq,metagenome for B112 at baseline

description: Library name: B112


title: PDAC, Human Tumor, sample44

description: Library name: Bulk044

value: Primary PDAC

value: FOLFIRINOX with XRT


title: Mock-infected E. coli, 60min, rep1

description: Library name: FA7


title: 16S rRNA-seq,metagenome for B107 at baseline

description: Library name: B107


title: Lung, HGC, TERM, Mouse 16

description: Library name: 61_Lung_HGC-_ISS_Term-_16_L1_1

value: Lung

value: HGC-TERM

value: 8 months


title: 16S rRNA-seq,metagenome for B142 at baseline

description: Library name: B142

value: baseline


title: PDAC, Human Tumor, sample42

description: Library name: Bulk042

value: FOLFIRINOX


title: Heart, HGC, TERM, Mouse 12

description: Library name: 67_Heart_HGC-_ISS_Term-_12_L1_1

value: Heart

value: female


title: Lung, VGC, TERM, Mouse 14

description: Library name: 59_Lung_VGC-_ISS_Term-_14_L1_1

value: VGC-TERM


title: 16S rRNA-seq,metagenome for B098 at baseline

description: Library name: B098


title: Mock-infected E. coli, 20min, rep1

description: Library name: FA5


title: PDAC, Human Tumor, sample41

description: Library name: Bulk041


title: 16S rRNA-seq,metagenome for B132 at baseline

description: Library name: B132


title: 16S rRNA-seq,metagenome for B106 at baseline

description: Library name: B106


title: Mock-infected E. coli, 45min, rep1

description: Library name: FA6


title: Thymus, VGC, TERM, Mouse 11

description: Library name: 57_Thymus_VGC-_ISS_Term-_11_L1_1

value: Thymus

value: BALB/cAnNTac


title: 16S rRNA-seq,metagenome for B089 at baseline

description: Library name: B089

value: feces


title: PDAC, Human Tumor, sample39

description: Library name: Bulk039

value: Untreated


title: Mock-infected E. coli, 5min, rep1

description: Library name: FA3


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

description: Library name: 56_MAT_FL-LAR-3_L1_1

value: MAT

value: VGC-LAR


title: PDAC, Human Tumor, sample45

description: Library name: Bulk045


title: Pancreas, FL, VGC, LAR, Mouse 13

description: Library name: 55_Pancreas_FL-LAR-13_L1_1

value: Pancreas

value: 3 months


title: Mock-infected E. coli, 2.5min, rep1

description: Library name: FA2

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: 16S rRNA-seq,metagenome for B075 at baseline

description: Library name: B075

value: control


title: PDAC, Human Tumor, sample38

description: Library name: Bulk038

value: Primary PDAC


title: PDAC, Human Tumor, sample43

description: Library name: Bulk043


title: BAT, HGC, TERM, Mouse 16

description: Library name: 60_BAT_HGC-_ISS_Term-_16_L1_1

value: BAT

value: HGC-TERM

value: 8 months


title: Spleen, FL, TERM, Mouse 11

description: Library name: 54_Spleen_FL-_ISS_Term-_11_L1_1

value: Spleen

value: FL-TERM

value: female


title: Mock-infected E. coli, 0+min, rep1

description: Library name: FA1


title: 16S rRNA-seq,metagenome for B065 at baseline

description: Library name: B065

value: baseline


title: Liver, HGC, TERM, Mouse 11

description: Library name: 53_Liver_HGC-_ISS_Term-_11_L1_1

source_name: Liver

value: Liver

value: BALB/cAnNTac


title: E. coli infected by P+ phage at low MOI, 60min, rep2

description: Library name: SB7


title: PDAC, Human Tumor, sample35

description: Library name: Bulk035

value: Gemcitabine


title: Kidney, VGC, TERM, Mouse 1

description: Library name: 52_Kidney_VGC-_ISS_Term-_1_L1_1

source_name: Kidney

value: Kidney

value: VGC-TERM


title: PDAC, Human Tumor, sample36

description: Library name: Bulk036

value: Untreated


title: E. coli infected by P+ phage at low MOI, 45min, rep2

description: Library name: SB6

value: E. coli


title: 16S rRNA-seq,metagenome for B047 at baseline

description: Library name: B047

value: feces


title: Spleen, HGC, TERM, Mouse 13

description: Library name: 51_Spleen_HGC-_ISS_Term-_13_L1_1


title: PDAC, Human Tumor, sample40

description: Library name: Bulk040

value: FOLFIRINOX


title: 16S rRNA-seq,metagenome for B056 at baseline

description: Library name: B056

value: control


title: Mock-infected E. coli, 10min, rep1

description: Library name: FA4

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: 16S rRNA-seq,metagenome for B082 at baseline

description: Library name: B082


title: PDAC, Human Tumor, sample34

description: Library name: Bulk034

value: Primary PDAC


title: E. coli infected by P+ phage at low MOI, 20min, rep2

description: Library name: SB5


title: Thymus, HGC, LAR, Mouse 13

description: Library name: 50_Thymus_HC-LAR-13_L1_1

value: Thymus

value: HGC-LAR

value: 3 months


title: PDAC, Human Tumor, sample33

description: Library name: Bulk033


title: 16S rRNA-seq,metagenome for B044 at baseline

description: Library name: B044


title: Spleen, VGC, TERM, Mouse 13

description: Library name: 49_Spleen_VGC-_ISS_Term-_13_L1_1

value: Spleen

value: female

value: 8 months


title: E. coli infected by P+ phage at low MOI, 5min, rep2

description: Library name: SB3


title: PDAC, Human Tumor, sample32

description: Library name: Bulk032


title: 16S rRNA-seq,metagenome for B066 at baseline

description: Library name: B066

value: baseline


title: PDAC, Human Tumor, sample37

description: Library name: Bulk037


title: Lung, VGC, TERM, Mouse 3

description: Library name: 48_Lung_VGC-_ISS_Term-_3_L1_1

source_name: Lung

value: Lung

value: BALB/cAnNTac


title: E. coli infected by P+ phage at low MOI, 2.5min, rep2

description: Library name: SB2


title: 16S rRNA-seq,metagenome for B028 at baseline

description: Library name: B028


title: E. coli infected by P+ phage at low MOI, 0+min, rep2

description: Library name: SB1


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

description: Library name: 47_Diaphragm_FL-LAR-5_L1_1

source_name: Diaphragm

value: Diaphragm

value: VGC-LAR


title: PDAC, Human Tumor, sample30

description: Library name: Bulk030

value: Untreated


title: 16S rRNA-seq,metagenome for B013 at baseline

description: Library name: B013

value: feces


title: Kidney, VGC, TERM, Mouse 11

description: Library name: 46_Kidney_VGC-_ISS_Term-_11_L1_1

value: Kidney

value: VGC-TERM


title: Diaphragm, FL, VGC, LAR, Mouse 13

description: Library name: 45_Diaphragm_FL-LAR-13_L1_1


title: PDAC, Human Tumor, sample28

description: Library name: Bulk028


title: 16S rRNA-seq,metagenome for B002 at baseline

description: Library name: B002

value: control


title: E. coli infected by P+ phage at high MOI, 60min, rep2

description: Library name: RB7

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: PDAC, Human Tumor, sample27

description: Library name: Bulk027

value: Primary PDAC

value: FOLFIRINOX


title: PDAC, Human Tumor, sample29

description: Library name: Bulk029


title: E. coli infected by P+ phage at high MOI, 20min, rep2

description: Library name: RB5


title: E. coli infected by P+ phage at low MOI, 10min, rep2

description: Library name: SB4


city: New York

first: Andreas

last: Hochwagen

state: NY

address: 24 Waverly Place

department: Department of Biology

institute: New York University

description: Library name: hht1/2-K79R_Input_SpikeIn_T3_antiRed1_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

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:
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: E. coli infected by P+ phage at high MOI, 10min, rep2

description: Library name: RB4


title: E. coli infected by P+ phage at high MOI, 45min, rep2

description: Library name: RB6


title: Liver, FL, VGC, LAR, Mouse 4

description: Library name: 44_Liver_FL-LAR-4_L1_1

value: Liver

value: female

value: 8 months


title: PDAC, Human Tumor, sample26

description: Library name: Bulk026

value: Gemcitabine with XRT


title: 16S rRNA-seq,metagenome for B037 at baseline

description: Library name: B037

value: baseline


title: Kidney, VGC, TERM, Mouse 16

description: Library name: 43_Kidney_VGC-_ISS_Term-_16_L1_1

value: BALB/cAnNTac


title: MAT, VGC, TERM, Mouse 5

description: Library name: 42_MAT_VGC-_ISS_Term-_5_L1_1

value: MAT

value: 3 months


title: PDAC, Human Tumor, sample25

description: Library name: Bulk025

value: Untreated


title: PDAC, Human Tumor, sample31

description: Library name: Bulk031

value: FOLFIRINOX with XRT


description: Library name: hht1/2-K79R_ChIP_SpikeIn_T3_antiRed1_Rep2


title: Heart, VGC, LAR, Mouse 9

description: Library name: 41_Heart_VC-LAR-9_L1_1

source_name: Heart

value: Heart

value: VGC-LAR


title: E. coli infected by P+ phage at high MOI, 5min, rep2

description: Library name: RB3

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: 16S rRNA-seq,metagenome for B024 at baseline

description: Library name: B024

value: feces

value: control


title: E. coli infected by P+ phage at high MOI, 2.5min, rep2

description: Library name: RB2


description: Library name: hht1/2-K79R_ChIP_SpikeIn_T3_antiRed1_Rep1

value: Nucleus

value: Meiosis Hour 3


title: PDAC, Human Tumor, sample24

description: Library name: Bulk024

value: Primary PDAC

value: FOLFIRINOX


title: BAT, VGC, TERM, Mouse 13

description: Library name: 40_BAT_VGC-_ISS_Term-_13_L1_1

value: BAT

value: VGC-TERM

value: female

value: 8 months


title: E. coli infected by P+ phage at high MOI, 0+min, rep2

description: Library name: RB1


title: PDAC, Human Tumor, sample23

description: Library name: Bulk023

value: Gemcitabine


title: WT_Input_SpikeIn_T3_antiRed1_Rep2

description: Library name: WT_Input_SpikeIn_T3_antiRed1_Rep2

value: WT


title: PDAC, Human Tumor, sample22

description: Library name: Bulk022


title: Liver, VGC, LAR, Mouse 12

description: Library name: 39_Liver_VC-LAR-12_L1_1

value: Liver

value: BALB/cAnNTac


title: WT_ChIP_SpikeIn_T3_antiRed1_Rep1

description: Library name: WT_ChIP_SpikeIn_T3_antiRed1_Rep1


description: Library name: hht1/2-K79R_Input_SpikeIn_T3_antiRed1_Rep1


title: PDAC, Human Tumor, sample21

description: Library name: Bulk021

value: Untreated


title: Kidney, VGC, LAR, Mouse 11

description: Library name: 38_Kidney_VC-LAR-11_L1_1

value: Kidney

value: VGC-LAR


title: hht1/2-K79R_Input_T3_antiRed1_Rep2

description: Library name: hht1/2-K79R_Input_T3_antiRed1_Rep2


title: PDAC, Human Tumor, sample20

description: Library name: Bulk020


title: E. coli infected by P+ phage at low MOI, 20min, rep1

description: Library name: SA5

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: hht1/2-K79R_Input_T3_antiRed1_Rep1

description: Library name: hht1/2-K79R_Input_T3_antiRed1_Rep1

value: Nucleus


title: MAT, FL, TERM, Mouse 16

description: Library name: 37_MAT_FL-_ISS_Term-_16_L1_1

value: MAT

value: FL-TERM


title: Thymus, FL, VGC, LAR, Mouse 2

description: Library name: 36_Thymus_FL-LAR-2_L1_1

value: Thymus

value: 3 months


title: hht1/2-K79R_ChIP_T3_antiRed1_Rep2

description: Library name: hht1/2-K79R_ChIP_T3_antiRed1_Rep2

value: Meiosis Hour 3


title: PDAC, Human Tumor, sample19

description: Library name: Bulk019

value: Primary PDAC


title: GAT, VGC, LAR, Mouse 4

description: Library name: 35_GAT_VC-LAR-4_L1_1

source_name: GAT

value: GAT

value: female

value: 8 months


title: PDAC, Human Tumor, sample18

description: Library name: Bulk018


title: hht1/2-K79R_ChIP_T3_antiRed1_Rep1

description: Library name: hht1/2-K79R_ChIP_T3_antiRed1_Rep1


title: E. coli infected by P+ phage at low MOI, 5min, rep1

description: Library name: SA3


title: GAT, FL, VGC, LAR, Mouse 4

description: Library name: 34_GAT_FL-LAR-4_L1_1


title: PDAC, Human Tumor, sample17

description: Library name: Bulk017


title: sir3dot1_Input_SpikeIn_T3_Rep2

description: Library name: sir3dot1_Input_SpikeIn_T3_Rep2


title: E. coli infected by P+ phage at low MOI, 2.5min, rep1

description: Library name: SA2


title: E. coli infected by P+ phage at low MOI, 0+min, rep1

description: Library name: SA1


title: E. coli infected by P+ phage at low MOI, 60min, rep1

description: Library name: SA7


title: sir3dot1_Input_SpikeIn_T3_Rep1

description: Library name: sir3dot1_Input_SpikeIn_T3_Rep1


title: PDAC, Human Tumor, sample16

description: Library name: Bulk016

value: Gemcitabine with XRT


title: sir3dot1_ChIP_SpikeIn_T3_antiRed1_Rep2

description: Library name: sir3dot1_ChIP_SpikeIn_T3_antiRed1_Rep2


title: Diaphragm, VGC, LAR, Mouse 4

description: Library name: 32_Diaphragm_VC-LAR-4_L1_1

value: Diaphragm

value: BALB/cAnNTac


title: E. coli infected by P+ phage at high MOI, 60min, rep1

description: Library name: RA7


title: MAT, HGC, TERM, Mouse 5

description: Library name: 31_MAT_HGC-_ISS_Term-_5_L1_1

value: HGC-TERM


title: PDAC, Human Tumor, sample15

description: Library name: Bulk015

value: Untreated


title: E. coli infected by P+ phage at low MOI, 45min, rep1

description: Library name: SA6

value: E. coli


title: PDAC, Human Tumor, sample13

description: Library name: Bulk013

value: Combination


title: Diaphragm, FL, TERM, Mouse 5

description: Library name: 30_Diaphragm_FL-_ISS_Term-_5_L1_1


title: E. coli infected by P+ phage at high MOI, 20min, rep1

description: Library name: RA5

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: sir3dot1_ChIP_SpikeIn_T3_antiRed1_Rep1

description: Library name: sir3dot1_ChIP_SpikeIn_T3_antiRed1_Rep1

value: Nucleus


title: PDAC, Human Tumor, sample14

description: Library name: Bulk014


title: E. coli infected by P+ phage at high MOI, 45min, rep1

description: Library name: RA6


title: Thymus, VGC, LAR, Mouse 13

description: Library name: 29_Thymus_VC-LAR-13_L1_1

value: VGC-LAR


title: sir3dot1_Input_T3_Rep2

description: Library name: sir3dot1_Input_T3_Rep2


title: PDAC, Human Tumor, sample12

description: Library name: Bulk012


title: sir3dot1_Input_T3_Rep1

description: Library name: sir3dot1_Input_T3_Rep1


title: E. coli infected by P+ phage at high MOI, 5min, rep1

description: Library name: RA3


title: Spleen, VGC, LAR, Mouse 13

description: Library name: 28_Spleen_VC-LAR-13_L1_1

source_name: Spleen

value: Spleen


title: PDAC, Human Tumor, sample10

description: Library name: Bulk010


title: E. coli infected by P+ phage at high MOI, 10min, rep1

description: Library name: RA4


title: sir3dot1_ChIP_T3_antiRed1_Rep2

description: Library name: sir3dot1_ChIP_T3_antiRed1_Rep2


title: Diaphragm, HGC, TERM, Mouse 16

description: Library name: 33_Diaphragm_HGC-_ISS_Term-_16_L1_1


title: Kidney, HGC, LAR, Mouse 1

description: Library name: 27_Kidney_HC-LAR-1_L1_1

value: Kidney

value: HGC-LAR

value: 3 months


title: sir3dot1_ChIP_T3_antiRed1_Rep1

description: Library name: sir3dot1_ChIP_T3_antiRed1_Rep1

value: Meiosis Hour 3


title: E. coli infected by P+ phage at high MOI, 2.5min, rep1

description: Library name: RA2


title: BAT, FL, TERM, Mouse 13

description: Library name: 26_BAT_FL-_ISS_Term-_13_L1_1

source_name: BAT

value: BAT

value: FL-TERM

value: female


title: E. coli infected by P+ phage at high MOI, 0+min, rep1

description: Library name: RA1


title: PDAC, Human Tumor, sample6

description: Library name: Bulk006

value: Primary PDAC


title: SCAT, VGC, TERM, Mouse 2

description: Library name: 25_SCAT_VGC-_ISS_Term-_2_L1_1

source_name: SCAT

value: SCAT

value: VGC-TERM

value: BALB/cAnNTac


title: Liver, HGC, LAR, Mouse 12

description: Library name: 24_Liver_HC-LAR-12_L1_1

value: Liver

value: 8 months


title: Lambda lysogen, rep2

description: Library name: LD

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB) and prophage lambda cI857 parS


title: PDAC, Human Tumor, sample5

description: Library name: Bulk005

value: FOLFIRI


title: SCAT, VGC, LAR, Mouse 13

description: Library name: 21_SCAT_VC-LAR-13_L1_1

value: VGC-LAR


title: Lambda lysogen, rep1

description: Library name: LC


title: Mixed cells from medial preoptic area, from dam, biol rep 1

city: Princeton

first: Forrest

middle: Dylan

last: Rogers

state: NJ

address: 40 Woodlands Way

department: Princeton Neuroscience Institute

institute: Princeton University

description:
Library name: rd1
10x Genomics Chromium

data_processing:
Data was demultiplexed by barcode and processed with 10x Genomics Cell Ranger
Demultiplexed and processed data was filtered with CellBender to remove background and the R package scDblFinder to filter and remove doublets and nuclei with high mitochondrial reads or ambient RNA and random barcode swapping.
Assembly: PU_Rpum_1.0
Supplementary files format and content: R Data Serialization file (RDS)

molecule: nuclear RNA

organism: Rhabdomys pumilio

source_name: Mixed brain cells from MPOA

extract_protocol:
Nuclei were isolated from frozen tissue punches in batches of 4 samples, counterbalanced by phenotype. The protocol for nuclei preparation was modified from 10X protocol GC000393. For more details, refer to Supplementary Methods. Samples were removed from storage (-80ºC) and immediately submerged in 500µL of ice-cold homogenization buffer containing RNasin Plus RNase Inhibitor (Promega N2611) and Complete, EDTA-free Protease Inhibitor Cocktail (Sigma, Roche 11873580001). Samples were Dounce homogenized 10 times in the homogenization buffer with a 2ml Kimble Kontes Dounce tissue grinder on ice. 5% IGEPAL CA-630 was added to the Dounce and each sample was further homogenized 5 times before filtering through a 40µm cell strainer (BD Falcon 352340). The filtrate was then diluted 1:1 with a 50% Iodixanol solution (OptiPrep Density Gradient Medium (Sigma D1556) diluted to 50%) and added to a 1.5mL microcentrifuge tube containing 100µl layers (from bottom to top) of 40% and 30% Iodixanol. Samples were then centrifuged at 4500rcf in a swinging bucket centrifuge at 4ºC for 45-minutes with a moderated ramp-up speed and the lowest break setting. Nuclei were then extracted in a 60µL volume from the resulting interstitial layer between the 40% and 30% Iodixanol layers. Nuclei concentrations were then determined via hemocytometer.
Isolated nuclei were transferred to the Genomics Core Facility in the Lewis-Sigler Institute for Integrative Genomics at Princeton for library preparation with the 10X Genomics Chromium system and sequencing. Libraries were prepared based on an estimated input of 20,000 and recovery of ~12,535 nuclei per sample. All subsequent sequencing was carried out on an Illumina NovaSeq 6000 and samples were sequenced to a mean depth of 42,426 reads per nucleus (SD=8894) and a mean saturation of 71.64 (SD=10.01).

value: Mixed brain cells from MPOA

value: Neurons and glia

value: WT

value: adult

tag: sexual experience

value: experienced


title: Uninfected E. coli host, rep2

description: Library name: UD

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: Uninfected E. coli host, rep1

description: Library name: UC


title: Mixed cells from medial preoptic area, from dam, biol rep 3

description:
Library name: rd3
10x Genomics Chromium

value: female


title: Mixed cells from medial preoptic area, from dam, biol rep 4

description:
Library name: rd4
10x Genomics Chromium


title: PDAC, Human Tumor, sample3

description: Library name: Bulk003

value: Primary PDAC

value: Untreated


title: Mixed cells from medial preoptic area, from dam, biol rep 2

description:
Library name: rd2
10x Genomics Chromium


title: PDAC, Human Tumor, sample2

description: Library name: Bulk002


title: Diaphragm, VGC, TERM, Mouse 4

description: Library name: 20_Diaphragm_VGC-_ISS_Term-_4_L1_1

value: Diaphragm

value: VGC-TERM

value: 3 months


title: PDAC, Human Tumor, sample4

description: Library name: Bulk004


title: Mixed cells from medial preoptic area, from sire, biol rep 3

description:
Library name: rs3
10x Genomics Chromium

value: male


title: Mixed cells from medial preoptic area, from sire, biol rep 4

description:
Library name: rs4
10x Genomics Chromium


title: PDAC, Human Tumor, sample9

description: Library name: Bulk009


title: PDAC, Human Tumor, sample1

description: Library name: Bulk001

value: FOLFIRINOX


title: WBO2 (iN 1), Control, Biol Rep 4

city: Notre Dame

first: Christopher

last: Patzke

state: IN

address: 109A Galvin Life Sciences Building

department: Department of Biological Sciences

institute: University of Notre Dame

description:
Library name: Wbo2_control_05-20_Seq_07-25_S23
P4 XLEAP 100 cycle

data_processing:
To deconvolve neuronal and glial transcripts, sequencing reads were binned by mapping to human (GRCh38.p14) and mouse (GRCm39) reference genomes using BBMap (v. 39.08). Reads that mapped to both references were discarded. Binned reads were aligned to respective reference genomes and counted using STAR (v. 2.7.2).
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

organism:
Homo sapiens
Mus musculus

extract_protocol:
Zymo Research, Direct-zol RNA Miniprep Kit (R2051)
NEBNext Ultra II Directional RNA Library Prep kit

value: control


title: Pancreas, FL, TERM, Mouse 3

description: Library name: 19_Pancreas_FL-_ISS_Term-_3_L1_1

value: Pancreas

value: FL-TERM

value: BALB/cAnNTac


title: WBO2 (iN 1), Compressed, Biol Rep 4

description:
Library name: Wbo2_compress_05-20_Seq_07-25_S24
P4 XLEAP 100 cycle

value: compressed


title: Spleen, FL, TERM, Mouse 12

description: Library name: 18_Spleen_FL-_ISS_Term-_12_L1_1

value: Spleen

value: 8 months


title: Mixed cells from medial preoptic area, from sire, biol rep 2

description:
Library name: rs2
10x Genomics Chromium

value: Mixed brain cells from MPOA

value: Neurons and glia

value: WT

value: adult

value: experienced


title: PDAC, Human Tumor, sample8

description: Library name: Bulk008

value: Primary PDAC

value: Gemcitabine with XRT


title: Mixed cells from medial preoptic area, from sire, biol rep 1

description:
Library name: rs1
10x Genomics Chromium


title: I27 (iN 2), Compressed, Biol Rep 4

description:
Library name: I27_compress_05-20_Seq_07-25_S22
P4 XLEAP 100 cycle


title: P2, SILP, scRNAseq, mononuclear phagocytes, GEX

description: Library name: P2_SILP_GEX

source_name: small intestinal lamina propria

value: small intestinal lamina propria

value: mononuclear phagocytes

value: healthy


title: I27 (iN 2), Control, Biol Rep 4

description:
Library name: I27_control_05-20_Seq_07-25_S21
P4 XLEAP 100 cycle

value: control


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

description: Library name: 17_Thymus_FL-LAR-11_L1_1

source_name: Thymus

value: Thymus

value: VGC-LAR

value: female


title: Diaphragm, HGC, LAR, Mouse 11

description: Library name: 23_Diaphragm_HC-LAR-11_L1_1

value: Diaphragm

value: HGC-LAR

value: BALB/cAnNTac


title: Mixed cells from medial preoptic area, from infanticidal sexually-naïve male, biol rep 3

description:
Library name: ri3
10x Genomics Chromium

value: Mixed brain cells from MPOA

value: male

value: naïve


title: 1019 (iN 3), Compressed, Biol Rep 4

description:
Library name: 1019_compress_05-20_Seq_07-25_S20
P4 XLEAP 100 cycle

value: compressed


title: P2, cLP, scRNAseq, mononuclear phagocytes, GEX

description: Library name: P2_cLP_GEX

source_name: colonic lamina propria

value: colonic lamina propria


title: Mixed cells from medial preoptic area, from infanticidal sexually-naïve male, biol rep 2

description:
Library name: ri2
10x Genomics Chromium

value: Neurons and glia

value: WT

value: adult


title: 1019 (iN 3), Control, Biol Rep 4

description:
Library name: 1019_control_05-20_Seq_07-25_S19
P4 XLEAP 100 cycle


title: Sample 6_T=4 hours at 23˚C_Rep Z

city: Northampton

first: Christine

middle: Ann

last: White-Ziegler

state: MA

address: Clark Science Center

department: Biological Sciences

institute: Smith College

data_processing:
Residual rRNA reads were removed from FASTQ files.Rockhopper 2.0.3 was used to align reads in FASTQ files to the published genome of CFT073 and to determine read counts usig the default parameters.
Read counts from Rockhopper were utilized in DESeq2 to determine differentially expressed genes.
Sample quality/outlier analysis was completed using arrayQualityMetrics 3.14
Gene identification and function (locus_tag, cNum, upec_gene, gene_function) was matched and updated using RefSeq assembly accession: GCF_000007445.1
Genome_build: GCF_000007445.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log2 fold change ratios for every gene (DESeq)

organism: Escherichia coli

source_name: T=4 hours at 23˚C, exponential growth phase

growth_protocol: For each biological replicate, an initial 200 ml culture was grown to mid-exponential phase (A600= 0.2-0.6) with shaking at 225 rpm at 23˚C in M9 minimal medium containing glycerol as a carbon source.  Four paired biological replicates (Y,Z,DY,Fab 3_7) were included in the experiment. An additional 23˚C sample (Fab_2) was also included in the analysis.

extract_protocol:
Bacterial cultures were immediately iced.  Aliquots of cells were centrifuged, the supernatant removed, and pellets containing 5 x 10e8 cells were frozen at -80˚C.  Total RNA was isolated using phenol-chloroform extraction, followed by cleanup and concentration using QIAGEN RNEasy Mini columns.  DNAse digestion was completed twice in solution. rRNA was depleted using Ribo-Zero.
The libraries were constructed using New England Biolabs NEBNext® Ultra RNA Library Prep Kit. Libraries were sequenced on the Illumina HiSeq (Samples 1,2,5,6) or on an Illumina MiSeq (Samples 3,4,7,8,9) following the manufacturer's protocols.

treatment_protocol: Aliquots (20 ml) from the 200 ml culture were shifted to 37˚C to allow harvest of cells at T=4 hours after a shift to 37˚C; a culture retained at 23˚C harvested at T=4 hours was used as the control.   The aliquots were differentially diluted with M9 minimal glycerol medium at the time of the temperature upshift to ensure collection of cells within the exponential phase.

tag: culture condition


title: WBO2 (iN 1), Compressed, Biol Rep 3

description:
Library name: Wbo2_compress_05-18_Seq_07-23_S18
P4 XLEAP 100 cycle


title: Mixed cells from medial preoptic area, from control sexually-naïve male, biol rep 3

description:
Library name: rc3
10x Genomics Chromium


title: SCAT, HGC, LAR, Mouse 5

description: Library name: 15_SCAT_HC-LAR-5_L1_1

value: SCAT

value: 3 months


title: Mixed cells from medial preoptic area, from infanticidal sexually-naïve male, biol rep 1

description:
Library name: ri1
10x Genomics Chromium


title: Sample 5_T=4 hours at 23˚C_Rep Y

value: T=4 hours at 23˚C, exponential growth phase


title: Sample 2_T=4 hours at 37˚C_Rep Z

source_name: T=4 hours at 37˚C, exponential growth phase


title: WBO2 (iN 1), Control, Biol Rep 3

description:
Library name: Wbo2_control_05-18_Seq_07-23_S17
P4 XLEAP 100 cycle

value: control


title: GAT, FL, TERM, Mouse 1

description: Library name: 14_GAT_FL-_ISS_Term-_1_L1_1

value: GAT

value: FL-TERM


title: Mixed cells from medial preoptic area, from control sexually-naïve male, biol rep 2

description:
Library name: rc2
10x Genomics Chromium


title: Spleen, HGC, TERM, Mouse 3

description: Library name: 12_Spleen_HGC-_ISS_Term-_3_L1_1

value: Spleen

value: HGC-TERM

value: female


title: Sample 1_T=4 hours at 37˚C_Rep Y

value: T=4 hours at 37˚C, exponential growth phase


title: Sample 9_T=4 hours at 23˚C_Rep_Fab 2


title: Pancreas, HGC, TERM, Mouse 4

description: Library name: 11_Pancreas_HGC-_ISS_Term-_4_L1_1

source_name: Pancreas

value: Pancreas

value: BALB/cAnNTac


title: Mixed cells from medial preoptic area, from control sexually-naïve male, biol rep 1

description:
Library name: rc1
10x Genomics Chromium

value: Mixed brain cells from MPOA

value: male

value: naïve


title: I27 (iN 2), Control, Biol Rep 3

description:
Library name: I27_control_05-18_Seq_07-23_S15
P4 XLEAP 100 cycle


title: Sample 8_T=4 hours at 23˚C_Rep_ Fab 3_7


title: Mixed cells from medial preoptic area, from allopaternal sexually-naïve male, biol rep 3

description:
Library name: ra3
10x Genomics Chromium

value: Neurons and glia

value: WT


title: 1019 (iN 3), Compressed, Biol Rep 3

description:
Library name: 1019_compress_05-18_Seq_07-23_S14
P4 XLEAP 100 cycle

value: compressed


title: Heart, HGC, TERM, Mouse 5

description: Library name: 10_Heart_HGC-_ISS_Term-_5_L1_1

value: Heart

value: 3 months


title: Mixed cells from medial preoptic area, from allopaternal sexually-naïve male, biol rep 2

description:
Library name: ra2
10x Genomics Chromium

value: adult


title: Sample 7_T=4 hours at 23˚C_Rep_DY

value: T=4 hours at 23˚C, exponential growth phase


title: Kidney, FL, TERM, Mouse 12

description: Library name: 16_Kidney_FL-_ISS_Term-_12_L1_1

value: Kidney

value: FL-TERM

value: 8 months


title: Liver, HGC, LAR, Mouse 5

description: Library name: 9_Liver_HC-LAR-5_L1_1

source_name: Liver

value: Liver

value: HGC-LAR

value: female


title: Mixed cells from medial preoptic area, from allopaternal sexually-naïve male, biol rep 1

description:
Library name: ra1
10x Genomics Chromium


title: 1019 (iN 3), Control, Biol Rep 3

description:
Library name: 1019_control_05-18_Seq_07-23_S13
P4 XLEAP 100 cycle

value: control


title: MAT, FL, TERM, Mouse 5

description: Library name: 13_MAT_FL-_ISS_Term-_5_L1_1

source_name: MAT

value: MAT

value: BALB/cAnNTac


title: WBO2 (iN 1), Compressed, Biol Rep 2

description:
Library name: Wbo2_compress_04-25_Seq_06-27_S12
P4 XLEAP 100 cycle


title: Thymus, HGC, LAR, Mouse 4

description: Library name: 8_Thymus_HC-LAR-4_L1_1

value: Thymus


title: I27 (iN 2), Compressed, Biol Rep 3

description:
Library name: I27_compress_05-18_Seq_07-23_S16
P4 XLEAP 100 cycle


title: Sample 3_T=4 hours at 37˚C_Rep_DY

value: T=4 hours at 37˚C, exponential growth phase


title: Leuven4

type: other

city: Leuven

first: Olivier

last: Govaere

address: ON6 Herestraat 49

country: Belgium

institute: KU Leuven

description: (Left to right): F3, F3, MASL

hyb_protocol: Following hybridization of ISH probes or antibody incubation, slides were washed and a coverslip with a spacer of predefined height (50–100 μm) was applied. The slide plus coverslip constitutes the flow cell, which was placed within a fluidic manifold on the SMI instrument for analyte readout and morphological imaging.

scan_protocol: The in situ chemistry and imaging analyses were performed on a prototype instrument with a custom large FOV, high numerical aperture (NA) and low aberration objective and associated optics that permit >6,000 cells to be imaged per FOV from a flow cell assembled onto a standard glass slide. The prototype system can run up to four flow cells simultaneously and can interleave fluidics and optical imaging operations to maximize throughput.    The optical system has an epifluorescent configuration based on a custom water objective ( ×13/0.82 NA). FOV size was customized to 0.7 × 0.9 mm2. Illumination is widefield, with a mix of lasers and light-emitting diodes (130 W cm–2 at 488 nm, 69 W cm–2 at 530 nm, 26 W cm–2 at 590 nm, 81 W cm–2 at 647 nm) that allow imaging of Alexa Fluor-488, Atto 532, Dyomics Dy-605 and Alexa Fluor-647, as well as cleaving of photolabile dye components. The camera used was a FLIR BFS-U3_200S6M-C based on the IMX183 Sony industrial CMOS sensor, and sampling at the image plane was 180 nm per pixel. An xy stage moves the flow cell above the objective lens while a z-axis motor moves the objective lens.

data_processing: Cloud-based AtoMx™ Spatial Informatics Platform (Bruker Spatial Biology) was used to export data and images for Seurat (v5.1.0). (https://pubmed.ncbi.nlm.nih.gov/37231261/).

label: CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) supplemented with 14 custom genes of interest

molecule: other

source_name: n=3 Biopsies

label_protocol: Samples were prepared as follows: 5 µm-thick FFPE sections were mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked for 4h at 37°C and stored at 4°C, then processed 7 days later using the Leica Bond RXm system (Leica) for staining and probe incubation according to CosMx guidelines. RNA target readout was performed on the CosMx SMI instrument as described previously (https://pubmed.ncbi.nlm.nih.gov/36203011/).

extract_protocol: Material was extracted from patients either using core-needle biopsies or during transplantation of patients with end-stage MASLD in the routine clinical practices of the University Hopsitals Leuven

tag: tag

value: liver


title: WBO2 (iN 1), Control, Biol Rep 2

description:
Library name: Wbo2_control_04-25_Seq_06-27_S11
P4 XLEAP 100 cycle


title: Leuven3

description: (Left to right): F1, F4

source_name: n=2 Biopsies


title: CIA mouse, HTO

city: New Haven

first: Edward

last: Doherty

state: CT

address: 300 Cedar street

department: Internal Medicine

institute: Yale School of Medicine

description:
Library name: CIA_Mouse_03072023_citeseq
10x Genomics Chromium

library_source: other

data_processing:
The raw scRNA-seq data were aligned to the mouse reference genome, mm10, using Cell Ranger (v7.1.0, 10x Genomics). The filtered gene-cell barcode count matrices were analyzed using the R (v4.1.3) package Seurat (v4.2.1) following the standardized analysis pipelines 3 outlined by the Satija lab (https://satijalab.org/seurat/). The cells were de-multiplexed based on enrichment of hashtag oligos (HTO). Doublets and negatives were removed.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: Spleen, lymph node, paw

extract_protocol:
Spleens were ground through a 70um mesh filter before being spun down 500g. Followed by a 5-minute incubation on ice in ACK buffer to lyse red blood cells.  Cells were spun down 500g, counted and pooled together before being washed in PBS and resuspended at 1x106 cells/100ul prior to barcoding
This enriched cell suspension was processed using the Chromium 5′ Single-Cell Gene Expression system (10X Genomics) to generate scRNA seq libraries following the manufacturer’s protocol. Briefly, single-cell suspensions with ≥85% viability were incubated with a pool of oligonucleotide-conjugated antibodies (BioLegend TotalSeq™) for sample indexing. Labeled cells were loaded into a Chromium Next GEM Chip G to generate Gel Bead-In-Emulsions (GEMs), enabling barcoding of individual cells and transcripts. Reverse transcription, cDNA amplification, and separate library construction for gene expression and feature barcodes were performed as described in the 10x Genomics protocol. Libraries were quantified, pooled, and sequenced on an Illumina NovaSeq platform with recommended read configurations.

value: Spleen, lymph node, paw

value: splenocytes, immune cells

value: WT C57BL/6J

value: mixed sample(HTO:Control_SPL, CIA_SPL, CIA_LN, CIA_Paw)


title: Brain, VGC, TERM, Mouse 18

description: Library name: 6_Brain_VGC-_ISS_Term-_18_L1_1

source_name: Brain

value: Brain

value: VGC-TERM


title: WBO2 (iN 1), Compressed, Biol Rep 1

description:
Library name: Wbo2_compress_04-25_Seq_06-26_S10
P4 XLEAP 100 cycle

value: compressed


title: BAT, FL, TERM, Mouse 12

description: Library name: 7_BAT_FL-_ISS_Term-_12_L1_1

value: BAT

value: FL-TERM

value: 8 months


title: Liver, FL, VGC, LAR, Mouse 13

description: Library name: 5_Liver_FL-LAR-13_L1_1

value: Liver

value: VGC-LAR

value: female

value: 3 months


title: CIA mouse, GEX

description:
Library name: CIA_Mouse_03072023_MMT
10x Genomics Chromium

data_processing:
The raw scRNA-seq data were aligned to the mouse reference genome, mm10, using Cell Ranger (v7.1.0, 10x Genomics). The filtered gene-cell barcode count matrices were analyzed using the R (v4.1.3) package Seurat (v4.2.1) following the standardized analysis pipelines 3 outlined by the Satija lab (https://satijalab.org/seurat/). The cells were de-multiplexed based on enrichment of hashtag oligos (HTO). Doublets and negatives were removed.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: WBO2 (iN 1), Control, Biol Rep 1

description:
Library name: Wbo2_control_04-25_Seq_06-26_S9
P4 XLEAP 100 cycle

value: control


title: Leuven2

description: (Left to right): F3, MASL, Normal, F3

source_name: n=4 Biopsies


title: 2.0 MAC_rep3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

description: Library name: Sample 9

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 23.0.5. (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 23.0.5. (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Hypothalamus

growth_protocol: To examine the effects of sevoflurane on gene expression and neural nuclei in the brain using immunohistochemistry, 0.7 MAC sevoflurane was used as a model for normal breathing (eupnoea) for comparison. After 0.7 MAC sevoflurane-induced anaesthesia under hyperoxic conditions (100% O2), the animals were subjected to the following three distinct experimental stress conditions: (1) 30 min of 2.0 MAC sevoflurane to induce gasping respiration, followed by 90 min of 0.7 MAC sevoflurane, (2) continuous 0.7 MAC sevoflurane for a total of 120 min (eupnoea group), and (3) control conditions maintained without sevoflurane and allowed free movement for 120 min (CTRL). All mice were euthanised under anaesthesia and brain samples were prepared. Mice were intracardially perfused with ice-cold diethylpyrocarbonate-treated phosphate buffered saline (PBS) to remove blood cells from the brain.

extract_protocol:
Total RNA was extracted from whole brain and primary neurospheres using ISOGEN reagent (Fujifilm, Japa). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Hypothalamus

value: 8- to 15-weeks-old

value: male

value: Wildtype

tag: treatment group

value: 2.0 MAC


title: SCAT, VGC, TERM, Mouse 3

description: Library name: 4_SCAT_VGC-_ISS_Term-_3_L1_1

value: SCAT

value: BALB/cAnNTac


title: 2.0 MAC_rep2

description: Library name: Sample 8


title: I27 (iN 2), Compressed, Biol Rep 2

description:
Library name: I27_compress_04-25_Seq_06-27_S8
P4 XLEAP 100 cycle


title: Top2 cdc5 cdc14 IP

city: Edinburgh

first: Lucia

middle: F

last: Massari

address: 6.22 Michael Swann Building, Max Born Crescent

department: Discovery Research Platform for the Hidden Cell Biology, Institute of Cell Biology

institute: University of Edinburgh

description: Library name: IP_Top2_cdc5_cdc14

data_processing:
Reads were trimmed with cutadapt v3.0 (MAPQ 10, min. length 65)
To obtain reads mapping only to S.cerevisiae sacCer3; ChIP-Seq reads were first mapped with MiniMap2 v2.10-r763-dirty (-ax sr) to S. pombe ASM294v2.22. Unmapped pombe reads were filtered using samtools v1.9. Unmapped pombe reads were then mapped to sacCer3. Unmapped reads were filtered using samtools. rDNA regions were removed from chrXII (saturated with reads) using bedtools v2.27.0. chrMito was excluded with samtools
To obtain reads mapping only to Pombe ASM294v2.22; Reads were also mapped to S. cerevisiae sacCer3. Unmapped sacCer3 reads were filtered using samtools. Unmapped sacCer3 reads were then mapped to ASM294v2.22. Unmapped reads were filtered using samtools. chrMito was excluded using bedtools
bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs; samtools flagstat was used to count reads mapping to sacCer3 and ASM294v2.22 only for each sample the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (ASM294v2.22);x=experimental genome (sacCer3)), calibrated sacCer3 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig
Assembly: sacCer3 (experimental genome) + ASM294v2.22 (calibrating genome)
Supplementary files format and content: BigWIg

source_name: haploid

growth_protocol: Cells were grown overnight in YPAD media at 23°, then diluted to OD(600)=1.8 and treated with alphaFactor to arrest them in G1. Cells were then released from the G1 arrest into YPDA containing auxin and DMSO (Top2 IP cdc20 and Top2 IP cdc20 notag) or auxin and nocodazole (Top2 IP cdc20+noco) or CMK (Top2 IP cdc5 cdc14) at 37C and harvested after 2.30 hours (Top2 cdc20, Top2 cdc20+noco, Top2 cdc20 notag) or 3 hours (Top2 cdc5 cdc14).

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 30 seconds 3 times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/1x PI/1mM PMSF/0.1% SDS before sonicating in a Bioruptor (Diagenode) for 2 times 20 cycles at 30sec on/off intervals at "High" setting. The supernatant was collected, a INPUT fraction was taken and the rest was subjected to IP with mouse monoclonal SV5-Pk1 antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure XP bead purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

treatment_protocol: Cells were fixed in 1% formaldehyde for 80min before washing twice in TBS and once in FA lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate) with 0.1% SDS.

tag: cell type

value: haploid

value: MATa TOP2-PK9 cdc14-1 cdc5L158G

value: CMK

tag: cell cycle_stage

value: mini-anaphase

tag: chip antibody

value: SV5-Pk1 (Biorad, MCA1360)


title: Leuven1

description: Left and right: explant livers

source_name: n=2 Explant livers

value: liver


title: Sample 4_T=4 hours at 37˚C_Rep_Fab 3_7

value: T=4 hours at 37˚C, exponential growth phase


title: Brain, HGC, LAR, Mouse 5

description: Library name: 3_Brain_HC-LAR-5_L1_1

tag: tissue

value: Brain

value: HGC-LAR

value: female


title: 2.0 MAC_rep1

description: Library name: Sample 7

value: Hypothalamus


title: Top2 cdc20 no tag IP

description: Library name: IP_Top2_cdc20_notag

value: MATa pADH1-OsTIR1-9MYC CDC20-AID

tag: treatment

value: Auxin, DMSO

value: metaphase


title: Top2 cdc20+noco IP

description: Library name: IP_Top2_cdc20_noco

value: MATa TOP2-PK9 pADH1-OsTIR1-9MYC CDC20-AID

value: Auxin, Nocodazole


title: I27 (iN 2), Compressed, Biol Rep 1

description:
Library name: I27_compress_04-25_Seq_06-26_S6
P4 XLEAP 100 cycle

value: compressed


title: Spleen, FL, TERM, Mouse 1

description: Library name: 2_Spleen_FL-_ISS_Term-_1_L1_1

source_name: Spleen

value: Spleen

tag: experiment group

value: FL-TERM

tag: Sex

value: BALB/cAnNTac

value: 3 months


title: Liver, VGC, LAR, Mouse 11

description: Library name: 1_Liver_VC-LAR-11_L1_1

value: Liver

value: VGC-LAR

tag: strain

tag: mouse id

value: 8 months


title: I27 (iN 2), Control, Biol Rep 1

description:
Library name: I27_control_04-25_Seq_06-26_S5
P4 XLEAP 100 cycle

tag: cell line

value: control


title: Top2 cdc20 IP

description: Library name: IP_Top2_cdc20

value: haploid

tag: genotype

value: Auxin, DMSO,

value: SV5-Pk1 (Biorad, MCA1360)


title: WT Muscle EV Rep2

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

institute: Cardiff University

data_processing:
Quality control was performed using fastqc
Reads were aligned to the UCSC mm10 genome using version bwa
miRNA expression was quantified using featureCounts
Assembly: mm10
Supplementary files format and content: bwa_counts.txt includes counts for each miRNA across all samples

source_name: muscle

growth_protocol: C2C12 were cultured in DMEM media with 10% FBS and 1x pen/strep under 37C at 5% CO2.

extract_protocol:
EVs were purified using standard differential centrifugation protocol and sent for miRNA-seq
miRNA-seq

value: muscle

value: myoblast

value: WT


title: 0.7 MAC_rep2

description: Library name: Sample 5

value: Hypothalamus

tag: age

value: 8- to 15-weeks-old

value: male

value: Wildtype

value: 0.7 MAC


title: Top2 cdc5 cdc14  input

description: Library name: INPUT_Top2_cdc5_cdc14

value: MATa TOP2-PK9 cdc14-1 cdc5L158G

value: CMK

value: mini-anaphase


title: WT Muscle EV Rep1


title: 0.7 MAC_rep1

description: Library name: Sample 4


title: 1019 (iN 3), Control, Biol Rep 2

description:
Library name: 1019_control_04-25_Seq_06-27_S3
P4 XLEAP 100 cycle

tag: batch


title: 1019 (iN 3), Compressed, Biol Rep 2

description:
Library name: 1019_compress_04-25_Seq_06-27_S4
P4 XLEAP 100 cycle

value: compressed


title: CTRL_rep3

description: Library name: Sample 3

value: CTRL


title: Damaged Muscle EV Rep 2

value: hydrogen peroxide


title: 1019 (iN 3), Compressed, Biol Rep 1

description:
Library name: 1019_compress_04-25_Seq_06-26_S2
P4 XLEAP 100 cycle


title: Top2 cdc20 no tag  input

description: Library name: INPUT_Top2_cdc20_notag

value: haploid

value: MATa pADH1-OsTIR1-9MYC CDC20-AID

value: Auxin, DMSO

value: metaphase


title: I27 (iN 2), Control, Biol Rep 2

description:
Library name: I27_control_04-25_Seq_06-27_S7
P4 XLEAP 100 cycle

value: control


title: Top2 cdc20+noco  input

description: Library name: INPUT_Top2_cdc20_noco

value: MATa TOP2-PK9 pADH1-OsTIR1-9MYC CDC20-AID

value: Auxin, Nocodazole


title: CTRL_rep2

description: Library name: Sample 2

value: Hypothalamus

value: 8- to 15-weeks-old


title: Top2 cdc20 input

description: Library name: INPUT_Top2_cdc20

value: Auxin, DMSO,


title: 1019 (iN 3), Control, Biol Rep 1

description:
Library name: 1019_control_04-25_Seq_06-26_S1
P4 XLEAP 100 cycle


title: CTRL_rep1

description: Library name: Sample 1

value: male

value: Wildtype


title: V24GW Middle Part Of The Midbrain

status: Public on Dec 17 2025

city: Jinan

first: ChengXin

last: Liu

state: Shandong

address: No. 16766, Jingshi Road

department: Cheeloo College of Medicine

institute: Shandong University

description:
Library name: V8
V24GW Middle Part Of The Midbrain

data_processing:
SOAPnuke was used to remove adapter-containing reads, low-quality reads, and reads with high N content.
Clean reads were aligned to the reference genome using HISAT2.
Ericscript and rMATS were used for fusion genes and differential splicing analysis.
Bowtie2 was used to align reads to the gene set.
RSEM was used for gene expression quantification.
Assembly: GRCh38.p13
Supplementary files format and content: csv file include FPKM values for each Sample

source_name: brainstem

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen) according to the manual instruction.Tissue was ground under liquid nitrogen, mixed with TRIzol, centrifuged, and treated with chloroform/isoamyl alcohol. RNA was precipitated with isopropanol, washed with ethanol, and dissolved in DEPC-treated water. RNA quality was assessed using Fragment Analyzer, Agilent 2100 Bioanalyzer, or Qseq-400.
Library preparation was performed using the Optimal Dual-mode mRNA Library Prep Kit (BGI) following manufacturer's protocols.

value: brainstem


description:
Library name: V10
V24GW Lower Part Of The Basal Region Of The Left Pons


title: V24GW Right Pons

description:
Library name: V12
V24GW Right Pons


title: 0.7 MAC_rep3

description: Library name: Sample 6

value: 0.7 MAC


title: V24GW Right Upper Midbrain

description:
Library name: V7
V24GW Right Upper Midbrain


description:
Library name: V11
V24GW Lower Part Of The Tegmental Region Of The Left Pons


description:
Library name: V3
V24GW Middle Part Of The right Medulla Oblongata


description:
Library name: V4
V24GW Upper Part Of The Left Medulla Oblongata


description:
Library name: V9
V24GW Anterior-superior Part Of The Basal Region Of The Left Pons