title: HA treated, replicate 2

description: Library name: HA.2


title: ET062537

status: Public on Dec 23 2025

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented  and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard   recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018.   PMID: 30085201

label: Cy3 and Cy5

molecule: genomic DNA

organism: Peromyscus maniculatus bairdii

label_protocol: Standard Illumina Protocol

extract_protocol: Quick-DNA Miniprep Plus Kit (Zymo Research, Cat#D4069) following manufacturers instructions

tag: x

tag: sid

tag: externalsampleid

tag: externalsamplename

tag: sampletype

value: DNA

tag: age

tag: Sex

value: M

tag: tissue

value: Tail

tag: species

value: BW

tag: relatedness

tag: idatsfound

value: FALSE

tag: extbasename

tag: row

tag: col

tag: project

value: male

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Bladder

tag: specieslatinname


title: scRNA-seq of Schisotosoma joponicum:18dpi Female

type: SRA

city: Shanghai

first: SHAOYUN

last: CHENG

address: Songhu Road 2005

department: Department of Microbiology and Microbial Engineering, School of Life Science

country: China

institute: Fudan University

description: Library name: Sj_18dpi_female

library_source: transcriptomic single cell

data_processing:
Raw data was processed and mapped to the Schistosoma japonicum genome (v3) using the Cell Ranger 3.0.0 (10× Genomics) pipeline.
Assembly: SjV3
Supplementary files format and content: h5 files for counts

molecule: polyA RNA

organism: Schistosoma japonicum

source_name: whole organism

growth_protocol: Twenty female C57 mice were infected percutaneously through the abdomen with 80–200 cercariae. At each time point (14, 18, 22, and 26 dpi), four mice were sacrificed for the recovery of schistosomes

extract_protocol:
Worms were collected from mice by perfusing the hepatic portal vein with 4℃ PBS (Sangon Biotech) and then rinsed in twice in DMEM (5% FBS) (Cheng et al., 2024; Luo et al., 2022; Wang et al., 2017; You et al., 2024). Freshly perfused male and female worms, except 14 dpi worms, which are difficult to distinguish gender under a light microscope, were separated by incubation in a 0.25% solution of tricaine for approximately 5 min. FACS sorting was performed as previously described with minor modifications. Worms were washed twice in 8 mL PBS, then triturated for approximately 15 min in 4 mL 0.125% Trypsin-EDTA (in PBS) until the solution became turbid and no large pieces of worms were left. The trypsin was inactivated by adding an 8 mL 10% FBS DMEM. The dissociated worms were then centrifuged at 500 g for 10 min at 4°C. Next, the worm cells were resuspended in 1 mL of PBS with 10 μL of RQ1 DNAse (Promega M6101) and incubated for 10 min at RT. The worm cells were centrifuged again at 500 g for 10 minutes at 4°C. Then the worm cells were resuspended in 1mL of PBS containing Fixable Viability Dye eFluorTM 506 (1μL/mL) (eBioscience) and incubated for 30 min at 4℃ in the dark. The worm cell suspension was centrifuged at 500 g for 10 minutes at 4°C, then washed twice in PBS, then filtered through a 40 μm cell strainer into a 12×75 mm FACS tube. Filtered cells were then sorted on a MoFlo XDP High-Speed Cell Sorter (BECKMAN COULTER) with 405/460/488/532/561/640nm lasers. Sorts were performed with a 100 μm nozzle, and cells were sorted into sorting media (0.04% BSA in PBS, pH = 7.40).
FACS-sorted cells were centrifuged at 500 g for 10 minutes at 4°C and then resuspended in 0.04% BSA in PBS. Libraries were created using a Chromium Controller (10× Genomics) according to manufacturer guidelines and sequenced using a NovaSeq6000 (Illumina) to generate 150-bp paired-end reads.

value: whole organism


title: ET062536

tag: x

tag: sid

tag: externalsampleid

value: F

value: female

value: Ear


title: untreated, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: ctr_B.3

library_source: transcriptomic

data_processing:
RNA-seq data were aligned using bowtie2 algorithm against mm10 mouse genome version and RSEM v1.2.12 software was used to estimate read counts using Ensemble transcriptome version GRCm38.89
Assembly: mm10
Supplementary files format and content: text file of counts

molecule: total RNA

organism: Mus musculus

source_name: BMDM

extract_protocol:
Total RNA was extracted from BMDMs using RNeasy Plus Mini Kit (Qiagen, 74136)
Libraries were prepared using Illumina Stranded mRNA Prep kit (500 ng DNase1 treated total RNA was used)

tag: cell type

value: BMDM

tag: ha

value: no


title: COR_nodule_rna_rep3

city: Kunming

first: Dingjie

last: Wang

state: Yunnan

address: NO. 132 Lanhei Road

institute: Kunming Institute of Botany, Chinese Academy of Sciences

description: rRNA was first depleted from total RNA using Ribo-off rRNA Depletion Kit (Vazyme, Cat. No.: N409-02). Stranded library was then prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Cat. No.:NR604-01 ) and sequenced using Illumina NovaSeq 6000

data_processing:
For transcriptomes data used in this study, reads were first cleaned using fastp v0.12.4.
Cleaned reads were then aligned to respective genomes with the same version used in SP57 using HISAT2 v2.2.1 with parameters " --mp 3,1" for normal libraries, and "--mp 3,1 --rna-strandness RF" for stranded libraries.
Abundance were esitmated using StringTie2 v2.1.4. Differential expressed genes were identified using DESeq2 v1.34.0 with at least two-fold expression change and Benjamini-Hochberg adjusted p value < 0.05 (Wald test).
Upregulated genes in treatments were retained and used in further analysis.
Assembly: Coriaria nepalensis (GWHESFM00000000); Elaeagnus umbellata (GWHESFO00000000); Alnus trabeculosa (GWHESFN00000000); Chamaecrista pumila (GWHESFQ00000000); Mimosa pudica (ASM325494v1); Populus trichocarpa (P.trichocarpa_v4.1, Populus deltoides x Populus euramericana use this)
Assembly: We have uploaded the newly assembled genomes to NGDC (https://ngdc.cncb.ac.cn/gwh/) and they will be released before March 2, 2025.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Coriaria nepalensis

source_name: nodule

extract_protocol:
Fresh roots, and nodules if available were gathered from Coriaria nepalensis, Elaeagnus umbellata, Alnus trabeculosa,  Chamaecrista pumila, and Mimosa pudica subsequently froeezed in liquid nitrogen. RNA was extracted using the Trizol (Invitrogen, USA).  For mycorrhizal inoculation of Populus deltoides × P. euramericana cv. ‘‘Nanlin895’’, three cm terminal cuttings were taken from 4-week-old Populus plants and rooted for two weeks in Lloyd & McCown's woody plant medium supplemented with 20 g L-1 sucrose and 5 µM indole-3-butyric acid (Sigma Aldrich). Rooted plants were transplanted to a mixture of vermiculite, sand, and perlite (3 : 1 : 1) containing Rhizophagus irregularis spores and cultured in phytotron with 12 h photoperiod at 25 °C constant temperature. The spores were produced by co-culturing R. irregularis with leeks and diluted to a final concentration of 400 spores per plant 11. The roots of AM-colonized and non-colonized Populus plants were harvested after 8 week post-inoculation and subsequently powdered in liquid nitrogen. Total RNA was extracted using the TRIzol reagent (Invitrogen, USA), three biological replicates were used for each sample.
For roots and nodules samples, rRNAs were first depleted from total RNA using Ribo-off rRNA Depletion Kit (Vazyme, Cat. No.: N409-02). Stranded library was then prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Cat. No.: NR604-01) and sequenced using Illumina NovaSeq 6000 by Frasergen Bioinformatics Co., Ltd. (Wuhan, China).  For mycorrhizal inoculation of Populus deltoides × P. euramericana cv. ‘‘Nanlin895’’, unstranded libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions and sequenced with Illumina NovaSeq 6000 by OE Biotech Co., Ltd. (Shanghai, China).

tag: tissue

value: nodule


title: ET062534

tag: externalsamplename

tag: sampletype

tag: age

tag: Sex

tag: species


title: scRNA-seq of Schisotosoma joponicum:14dpi Mix

description: Library name: Sj_14dpi_mix


title: mix_sensitive,s5PSeq,rep2

city: Solna

first: Honglian

last: Liu

address: Tomtebodavägen 23

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

description:
Library name: mix_sensitive_rep2
MinION flow cell

data_processing:
.pod5 files are basedcalled in SUP basecalling mode using Dorado, with minimum Q score set to 10.
basecalled fastq files are merged and demultiplexed using minibar.py (https://github.com/calacademy-research/minibar.git)
fastq files are quality/adpter trimmed using cutadapt/4.8 with parameter set to "-a AGATCGGAAGAGCAC --minimum-length 28 -e 0.2 -o 9 --nextseq-trim=20"
quality/adapter trimmed fastq files are extracted UMI using umi_tools/1.0.0 with command line set to "umi_tools extract --bc-pattern NNNNNNNN"
UMI extracted reads are mapped to reference genomes of each species or combined rRNA reference genome composed of 4 listed species using minimap2/.28-r1209 using minimap2 -ax map-ont, and sorted by coordnated by samtools/1.2.
Deduplication is processed for the output bam files using "umi_tools dedup" command
bed graph are generated using bedtools/2.31.0 using "bedtools genomecov -bg -5 -strand - -ibam" and "bedtools genomecov -bg -5 -strand + -ibam" command
Deduplicated bam files mapped to reference genomes are processed to fivepseq package/1.3.5 for context specific ribosome stalling analysis. Deduplicated bam files mapped to combined rRNA reference genomes are proceed as following. Primary alignments with MAPQ ≥ 10 were retained (samtools view -F 0x900 -q 10), and the filtered reads were quantified per rRNA reference sequence using samtools idxstats. To derive species-level abundances, the resulting table was processed using a custom python script that parsed the reference identifiers and assigned each entry to its corresponding organism via regular-expression matching (e.g., Bacillus subtilis, Staphylococcus aureus, Enterococcus faecalis, Clostridioides difficile). Mapped reads were then aggregated per sample and species.
Assembly: GCF_000009045.1(B.subtilis), GCF_018885085.1(C.difficile), GCF_000013425.1(S.aureus), GCF_000393015.1(E.faecalis)
Supplementary files format and content: tab delimited txt file contaning read count in the gene body (discarding the start and termination regions) relative to the distance from amino acid.
Supplementary files format and content: tab delimited txt file contaning summary of the processed each sample data
Supplementary files format and content: tab delimited txt file contaning rRNA-mapped read count for each species

organism:
Staphylococcus aureus
Enterococcus faecalis
Bacillus subtilis
Clostridioides difficile

source_name: 169 trpC2, ATCC 29212, ATCC 29213, erythromycin sensitive C.difficile isolates

growth_protocol: B.subtilis and S.aureus is cultured in LB media at 37°C in incubator. L.plantarum is cultured in MRS broth at 37°C in incubator. C.difficile is cultured in BHI broth at 37°C in anaerobic chamber. E.faecalis is cultured in NYCIII media at 37°C in anaerobic chamber.

extract_protocol:
Total RNA is extracted using following phenol-chloroform and beads beating protocol.           1.Set up the following tubes: Tube 1 (2ml ): 500μL phenol/chloroform (acidic pH4.5) Tube 2 (2ml): 500μL chloroform Tube 3 (1.5ml): 40μL 3 M NaOAc pH 5.2 2.Add 150μL LET (25 mM Tris, pH 8.0, 100 mM LiCl, 20 mM EDTA) to frozen cell pellet. 3.Add 150μL phenol (water saturated pH 6). 4.Add equal volume (approx. 300μL) of glass beads (Sigma-AldrichG8772-500G) and vortex at RT in MultiMixer for 2 min at top speed. 5.Add 250μL nuclease free MQ H2O and 250μL phenol/chloroform (acidic pH4.5). 6.Vortex in MultiMixer for an additional 2 min followed by centrifugation at RT for 1 min at 14,000 rpm. 7.Remove aqueous phase (approx 450μL - top layer) and add to Tube #1. Vortex 30 sec and spin 1 min at 14,000 rpm. 8.Remove aqueous phase and add to Tube #2. Vortex 30 sec and spin 1 min at 14,000 rpm. 9.Remove aqueous phase and add to Tube #3; mix well. Add 1 mL 100% EtOH, mix, and place at -80 °C O/N or at -20 °C for 30min 10. Collect RNA by centrifugation at 4 °C for 20 min at 14,000 rpm. 11. Discard Sup and wash pellet with 500μL 70% EtOH Spin for 2 min at 14,000 rpm . 12. Discard Sup and centrifuge again for 1 min at 14,000 rpm 13. Discard Sup and centrifuge again for 1 min at 14,000 rpm 14. Remove residual EtOH by pipetting and air dry for 1-2 min 15. Resuspend pellet in 30-50μL autoclaved MQ H2O
Mixture of 100ng extracted RNA for each species is used for library preparation using s5PSeq library prepartion protocol. Ribosomal RNA Hybridization: rRNA was blocked using 2 μM mixture of 146 universal blocking oligonucleotides and 20 μM of two species-specific oligonucleotides targeting the 5’ ends of 16S and 23S rRNAs (Table S1). Hybridization was performed in the presence of 50 mM NaCl using the following program: 75 °C for 5 minutes, 65 °C for 5 minutes, followed by a stepwise hybridization with a temperature decrease of 3 °C every 2 minutes until 35 °C. RNA Adapter Ligation: Single-stranded RNA adapters containing unique molecular identifiers (UMIs) and barcodes were ligated using T4 RNA ligase 1, 1 mM ATP, and 1X T4 RNA ligation buffer at 25 °C for 1 hour. Ligated RNA was purified using RNA CleanXP beads (1.8X volume). Reverse Transcription and template RNA Depletion: Reverse transcription was performed using random hexamers to generate first-strand cDNA. Template RNA was degraded by incubating with 28.6 mM NaOH at 65 °C for 20 minutes. The reaction was neutralized with an equivalent concentration of Tris-HCl, and cDNA was purified using Ampure XP beads (1.8X volume). PCR Amplification and size selection: Libraries were amplified by PCR using Illumina adapters with dual barcodes (0.25 μM) and Phusion HSII master mix for 15 cycles. Libraries were size-selected using a dual size-selection strategy (0.6X–0.8X Ampure XP beads) to isolate 400–600 bp fragments. Library sequencing: Final library concentrations were quantified using Qubit DNA HS assays. Subsequenctly nanopore libraries are prepared using nanopore ligration kit v14 (SQK-LSK114) and following library preparation instruction. 4 samples (mix_resistant_rep1 and rep2, mix_sensitive_rep1 and rep2) are pooled together (200fmol) and loaded onto MinION flow cell for sequencing overnight.

treatment_protocol: For B.subtilis, E.faecalis and S.aureus, exponetially growing bacteria culture(OD600=0.6-0.8) are collected by centrification, the supernatent are removed, an the cell pellets are frozen immediately on dry ice, and stored in -20°C for RNA extraction. For C.difficile, exponetially growing bacteria culture(OD600=0.6-0.8) is treated with erythromycin for 10min. After 10min, cells are spinned, the supernatent are removed, an the cell pellets are frozen immediately on dry ice, and stored in -20°C for RNA extraction


title: ET062530

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col

value: Muscle


title: mix_sensitive,s5PSeq,rep1

description:
Library name: mix_sensitive_rep1
MinION flow cell

source_name: 168 trpC2, ATCC 29212, ATCC 29213, erythromycin sensitive C.difficile isolates


title: ALTR_nodule_rna_rep2

organism: Alnus trabeculosa


title: HA treated, replicate 1

description: Library name: HA.1

value: yes


title: untreated, replicate 1

description: Library name: ctr_B.1


title: mix_resistant,s5PSeq,rep2

description:
Library name: mix_resistant_rep2
MinION flow cell

source_name: 169 trpC2, ATCC 29212, ATCC 29213, erythromycin resistant C.difficile isolates


title: mix_resistant,s5PSeq,rep2

description: Library name: mix_resistant_rep2

data_processing:
sequencing data are transfered to fastq.gz files and demultiplexed using bcl2fastq/2.20.0
fastq.gz files are quality/adpter trimmed using cutadapt/4.8 with parameter set to "-a AGATCGGAAGAGCAC --minimum-length 28 -e 0.2 -o 9 --nextseq-trim=20"
quality/adapter trimmed fastq files are extracted UMI using umi_tools/1.0.0 with command line set to "umi_tools extract --bc-pattern NNNNNNNN"
mapping is processed with star alignent program/2.7.11a, with parameters set to "star -- readFilesCommand gunzip -c  --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outFilterMatchNminOverLread 0.9 --outFilterMultimapNmax 12 --alignIntronMax 1 --outReadsUnmapped Fastx"
Deduplication is processed for the output bam files using "umi_tools dedup" command
bed graph are generated using bedtools/2.31.0 using "bedtools genomecov -bg -5 -strand - -ibam" and "bedtools genomecov -bg -5 -strand + -ibam" command
RNA types are counted using bedtools/2.31.0 using "bedtools intersect"
Deduplicated bam files are processed to fivepseq package/1.3.5 for context specific ribosome stalling analysis.
Assembly: GCF_000009045.1(B.subtilis), GCF_018885085.1(C.difficile), GCF_000013425.1(S.aureus), GCF_000393015.1(E.faecalis)
Supplementary files format and content: tab delimited txt file contaning read count in the gene body (discarding the start and termination regions) relative to the distance from amino acid.
Supplementary files format and content: tab delimited txt file contaning summary of the processed each sample data

extract_protocol:
Total RNA is extracted using following phenol-chloroform and beads beating protocol.           1.Set up the following tubes: Tube 1 (2ml ): 500μL phenol/chloroform (acidic pH4.5) Tube 2 (2ml): 500μL chloroform Tube 3 (1.5ml): 40μL 3 M NaOAc pH 5.2 2.Add 150μL LET (25 mM Tris, pH 8.0, 100 mM LiCl, 20 mM EDTA) to frozen cell pellet. 3.Add 150μL phenol (water saturated pH 6). 4.Add equal volume (approx. 300μL) of glass beads (Sigma-AldrichG8772-500G) and vortex at RT in MultiMixer for 2 min at top speed. 5.Add 250μL nuclease free MQ H2O and 250μL phenol/chloroform (acidic pH4.5). 6.Vortex in MultiMixer for an additional 2 min followed by centrifugation at RT for 1 min at 14,000 rpm. 7.Remove aqueous phase (approx 450μL - top layer) and add to Tube #1. Vortex 30 sec and spin 1 min at 14,000 rpm. 8.Remove aqueous phase and add to Tube #2. Vortex 30 sec and spin 1 min at 14,000 rpm. 9.Remove aqueous phase and add to Tube #3; mix well. Add 1 mL 100% EtOH, mix, and place at -80 °C O/N or at -20 °C for 30min 10. Collect RNA by centrifugation at 4 °C for 20 min at 14,000 rpm. 11. Discard Sup and wash pellet with 500μL 70% EtOH Spin for 2 min at 14,000 rpm . 12. Discard Sup and centrifuge again for 1 min at 14,000 rpm 13. Discard Sup and centrifuge again for 1 min at 14,000 rpm 14. Remove residual EtOH by pipetting and air dry for 1-2 min 15. Resuspend pellet in 30-50μL autoclaved MQ H2O
Mixture of 100ng extracted RNA for each species is used for library preparation using s5PSeq library prepartion protocol. Ribosomal RNA Hybridization: rRNA was blocked using 2 μM mixture of 146 universal blocking oligonucleotides and 20 μM of two species-specific oligonucleotides targeting the 5’ ends of 16S and 23S rRNAs (Table S1). Hybridization was performed in the presence of 50 mM NaCl using the following program: 75 °C for 5 minutes, 65 °C for 5 minutes, followed by a stepwise hybridization with a temperature decrease of 3 °C every 2 minutes until 35 °C. RNA Adapter Ligation: Single-stranded RNA adapters containing unique molecular identifiers (UMIs) and barcodes were ligated using T4 RNA ligase 1, 1 mM ATP, and 1X T4 RNA ligation buffer at 25 °C for 1 hour. Ligated RNA was purified using RNA CleanXP beads (1.8X volume). Reverse Transcription and template RNA Depletion: Reverse transcription was performed using random hexamers to generate first-strand cDNA. Template RNA was degraded by incubating with 28.6 mM NaOH at 65 °C for 20 minutes. The reaction was neutralized with an equivalent concentration of Tris-HCl, and cDNA was purified using Ampure XP beads (1.8X volume). PCR Amplification and size selection: Libraries were amplified by PCR using Illumina adapters with dual barcodes (0.25 μM) and Phusion HSII master mix for 15 cycles. Libraries were size-selected using a dual size-selection strategy (0.6X–0.8X Ampure XP beads) to isolate 400–600 bp fragments. Library sequencing: Final library concentrations were quantified using Qubit DNA HS assays, and 650 pM libraries were loaded onto the Illumina NextSeq 2000 platform for sequencing.

value: 169 trpC2, ATCC 29212, ATCC 29213, erythromycin resistant C.difficile isolates


title: COR_root_rna_rep3

source_name: root

value: root


title: untreated, replicate 2

description: Library name: ctr_B.2


title: mix_sensitive,s5PSeq,rep2

description: Library name: mix_sensitive_rep2

value: 169 trpC2, ATCC 29212, ATCC 29213, erythromycin sensitive C.difficile isolates


title: KO mouse 1  replicate 3 liver immune cells  3' scRNAseq

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
Library name: liver_KO1_p3_LIC
SeqWell v3

data_processing:
The demultiplexing, gene counting and aggregation were made using an adapted version of dropSeqPipe v0.4. (https://github.com/Hoohm/dropSeqPipe)
Assembly: mm10
Supplementary files format and content: raw.tar

source_name: Liver

extract_protocol:
The liver was cut into small pieces  and incubated with 500µL of a digestion mix (80 U/mL DNase I (Sigma-Aldrich, Cat# DN25) and 1 mg/mL collagenase D (Roche, Cat# 11088858001) in FACS buffer (0.5 % BSA, 2 mmol EDTA in PBS)) for 30 min at 37 °C. All following steps were performed on ice. The suspension was further passed through a 70 µm filter, and 5 mL cold FACS buffer was added. The samples were centrifuged at 400 g for 5 min at 4°C and the supernatant was discarded. Red blood cell lysis was performed by dissolving the cells gently in 1 mL of cold RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, and 0.1 mM EDTA) and 5 min incubation. After adding 5 mL cold FACS buffer, the samples were again centrifuged (400 g, 5 min, 4 °C). the pellet were resuspended in 5 ml FACS buffer then spun down at 50g for  3 min to enrich hebatocytes. both fractions (hepatocytes and liver immune cells were used for scRNASeq. Sequencing primarily relied on the Seq-Well S3 protocol (Hughes et al., 2020), using two arrays per sample.
Sequencing primarily relied on the Seq-Well S3 protocol (Hughes et al., 2020), using two arrays per sample. Seq-Well arrays were prepared as described before (Gierahn et al., 2017). Each array was loaded with approximately 110,000 barcoded mRNA capture beads (ChemGenes, Cat: MACOSKO-2011-10) and with 30,000 cells. The procedure was executed as previously detailed (Hughes et al., 2020).

value: Liver

tag: cell line

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre

value: macrophages

tag: genotype

value: KO


title: COR_root_rna_rep2


title: ET062533

tag: x

tag: sid

value: DNA

value: Tail

value: BW

value: FALSE

tag: project

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Brain

tag: specieslatinname


title: ET062532

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: age

value: M

tag: tissue

value: male

value: Ear


title: ET06253

tag: Sex

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename


title: ET062529

tag: x

value: F

tag: row

tag: col

value: female


title: mix_resistant,s5PSeq,rep1

description:
Library name: mix_resistant_rep1
MinION flow cell

source_name: 168 trpC2, ATCC 29212, ATCC 29213, erythromycin resistant C.difficile isolates

tag: cell type


title: COR_root_rna_rep1


title: ALTR_root_rna_rep2


title: KO mouse 1  replicate 2 liver immune cells  3' scRNAseq

description:
Library name: liver_KO1_p2_LIC
SeqWell v3

tag: cell line

tag: genotype


title: mix_resistant,s5PSeq,rep1

description: Library name: mix_resistant_rep1

value: 168 trpC2, ATCC 29212, ATCC 29213, erythromycin resistant C.difficile isolates


title: ALTR_root_rna_rep1

value: root


title: ET062527

tag: sid

tag: project

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

tag: specieslatinname


title: ET062528

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: age

tag: Sex

tag: tissue

value: Adipose


title: ALTR_nodule_rna_rep1

value: nodule


title: ET062531

tag: x

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

value: Spleen


title: WT mouse 2 replicate 1 liver immune cells  3' scRNAseq

description:
Library name: WT2_p1_LIC
SeqWell v3

value: Liver

tag: cell line

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre

tag: cell type

value: macrophages

tag: genotype

value: WT


title: WT mouse 2 replicate 1 hepatocytes  3' scRNAseq

description:
Library name: WT2_p1_Hepa
SeqWell v3

value: hepatocytes


title: HCT116 PABPC1&4-AID, IAA, 4 h, bio rep 2

city: Cambridge

first: Ekaterina

last: Khalizeva

state: MA

address: 455 Main St

department: Biology

institute: Whitehead Institute

description: Library name: HCT116 PABPC1_4-AID, IAA, 4 h, bio rep 2

data_processing:
poly(A) reads were trimmed using cutadapt (v4.8) with the parameters ‘--minimum-length 1 -a A{25} -A A{25}’.
Reads were then mapped to the human genome (Gencode release 25, GRCh38.p7, downloaded from the GENCODE website) using STAR (v2.7.1a; (Dobin et al, 2013) with the parameters ‘--runThreadN 24 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate’
Exon mapping reads were quantified using htseq-count (v1.99.2; (Anders et al, 2015) with the parameters ‘-f bam -t exon -r pos -s reverse’.
A read cuttoff of ≥25 reads in each sample was applied for each gene.
Assembly: GRCh38.p7
Supplementary files format and content: All RNAseq processed data files are raw read counts as counted by htseq-count.

organism: Homo sapiens

extract_protocol:
Cells were washed in PBS and resuspended in TRIzol Reagent. All RNA isolations were performed with Phasemaker™ tubes according to the manufacturer’s protocol (Invitrogen, A33248). Total RNA was resuspended in water with 4 pg spike-in RNA (equal mixture of in vitro transcribed Fluc and Nluc) per 2 ug total RNA for experiments where spike-in RNA was used for normalization. For each sample, 500 ng total RNA was used for library prep.
For NOVASEQSP sequencing runs, libraries were prepared using the KAPAHyperRiboErase kit according to manufacturer's instructions. For AVITI sequencing runs, libraries were prepared using the Watchmaker QiaSeq FastSelect Ribodepletion kit according to manufacturer’s instructions.

value: PABPC1&4 AID

tag: cell cycle_stage

tag: treatment

value: IAA


title: HeLa, STLC, actD, 3 h

description: Library name: HeLa, STLC, actD, 3 h

data_processing:
The poly(A) tail length was determined using a Hidden Markov Model trained on randomly picked 1% of the filtered read clusters (but no more than 50,000 and no less than 5000) for each library as described in (Xiang et al, 2024).
Assembly: GRCh38.p7
Supplementary files format and content: All PALseq processed data files contain 3 columns: gene id; cluster id; tail length.
Library strategy: PAL-seq

source_name: HeLa

extract_protocol:
Cells were washed in PBS and resuspended in TRIzol Reagent. All RNA isolations were performed with Phasemaker™ tubes according to the manufacturer’s protocol (Invitrogen, A33248). Total RNA was resuspended in water with 4 pg spike-in RNA (equal mixture of in vitro transcribed Fluc and Nluc) per 2 ug total RNA for experiments where spike-in RNA was used for normalization. For each sample, 500 ng total RNA was used for library prep.
Sequencing of endogenous mRNA poly(A) tail lengths in interphase and mitosis was performed with PAL-seq v4 as described in (Xiang & Bartel, 2021).

value: HeLa

value: M

value: actD


title: mix_sensitive,s5PSeq,rep1

description: Library name: mix_sensitive_rep1

value: 168 trpC2, ATCC 29212, ATCC 29213, erythromycin sensitive C.difficile isolates


title: HCT116 PABPC1&4-AID, IAA, 4 h, bio rep 1

description: Library name: HCT116 PABPC1_4-AID, IAA, 4 h, bio rep 1


title: HCT116 PABPC1&4-AID, IAA, 0 h, bio rep 2

description: Library name: HCT116 PABPC1_4-AID, IAA, 0 h, bio rep 2


title: HeLa, STLC, actD, 0 h

description: Library name: HeLa, STLC, actD, 0 h


title: WT mouse 1 replicate 2 hepatocytes  3' scRNAseq

description:
Library name: WT1_p2_Hepa
SeqWell v3


title: HeLa, RO3306, actD, 6 h

description: Library name: HeLa, RO3306, actD, 6 h


title: HeLa, STLC, actD, 6 h

description: Library name: HeLa, STLC, actD, 6 h


title: KO mouse 2  replicate 1 liver immune cells  3' scRNAseq

description:
Library name: Liver_KO2_p1_LIC
SeqWell v3

value: KO


title: HCT116 PABPC1&4-AID, IAA, 0 h, bio rep 1

description: Library name: HCT116 PABPC1_4-AID, IAA, 0 h, bio rep 1


title: HeLa, RO3306, actD, 3 h

description: Library name: HeLa, RO3306, actD, 3 h


title: WT mouse 1 replicate 2 liver immune cells  3' scRNAseq

description:
Library name: LIC_N702
SeqWell v3


title: HCT116 PABPC1&4-AID, DMSO, 4 h, bio rep 1

description: Library name: HCT116 PABPC1_4-AID, DMSO, 4 h, bio rep 1

value: DMSO


title: HeLa, RO3306, actD, 1 h

description: Library name: HeLa, RO3306, actD, 1 h


title: HeLa, STLC, actD, 1 h

description: Library name: HeLa, STLC, actD, 1 h


title: HeLa, RO3306, actD, 0 h

description: Library name: HeLa, RO3306, actD, 0 h


title: KO mouse 1  replicate 1 liver immune cells  3' scRNAseq

description:
Library name: KO1_p1_LIC
SeqWell v3


title: KO mouse 1  replicate 1 hepatocytes 3' scRNAseq

description:
Library name: KO1_p1_Hepa
SeqWell v3


title: HCT116 PABPC1&4-AID, DMSO, 0 h, bio rep 1

description: Library name: HCT116 PABPC1_4-AID, DMSO, 0 h, bio rep 1


title: HCT116 PABPC1&4-AID, DMSO, 0 h, bio rep 2

description: Library name: HCT116 PABPC1_4-AID, DMSO, 0 h, bio rep 2


title: WT mouse 1 replicate 1 hepatocytes  3' scRNAseq

description:
Library name: Hepa_N703
SeqWell v3


title: WT mouse 1 replicate 1 liver imune cells  3' scRNAseq

description:
Library name: WT1_p2_LIC
SeqWell v3


title: ET062522

tag: sid

tag: externalsampleid

value: DNA

value: Tail

value: BW

value: FALSE

tag: col

tag: project

value: male

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Muscle

tag: specieslatinname


title: WT_ISL1_OE_rep_2

city: New York City

last: Hu

state: NY

address: 430 East 67th Street

department: Developmental biology

institute: Sloan Kettering Institute

description:
Library name: Sample 21
WT-ISL1-2_IGO_17695_19

data_processing:
RNA-seq reads were aligned to the human reference genome (GRCh38, primary assembly) using STAR (v2.7.11b) with the aid of its genome indexing function and gene annotation from GENCODE (v44). Following alignment, a gene-level read count matrix was created using featureCounts (v2.1.1) using the same gene annotation.
Assembly: GRCh38, primary assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: stem cell-derived islet

growth_protocol: hPSCs were maintained using complete Essential 8 media, and differentiated into SC-islets following the differentiation receipe described in Hogrebe et al., Nature Protocols 2021 with slight modifications.

extract_protocol:
Quick-RNA Purification Kit (Zymo Research, R1055)
SMART-Seq v4 + KAPA EvoPrep Illumina NovaSeq X

treatment_protocol: On day 11 of differentiation, cells were dissociated using TrypLE, and approximately 6 × 10⁶ cells were resuspended in 5 ml S5 medium supplemented with 100 μl ISL1-BFP or BFP concentrated lentivirus, 10 μM Y-27632, and 6 μg/ml protamine sulfate. The cell suspension was transferred to a single well of an ultra–low attachment 6-well plate and incubated on an orbital shaker at 100 rpm. On day 18 of differentiation, BFP+ cells were sorted by flow cytometry.

tag: tissue

value: stem cell-derived islet

value: hPSC-derived islet differentiation

tag: time

value: day 18


title: ET062520

tag: x

tag: externalsamplename

tag: sampletype

tag: age

tag: Sex

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename

value: Brain


title: HeLa, STLC 24 h

description: Library name: HeLa, STLC 24 h

tag: cell line

tag: cell cycle_stage


title: ET062525

tag: sid

tag: externalsampleid

value: F

tag: row

tag: col

tag: project

value: female

tag: maxagecaesar

value: Bladder


title: KO5_hebatocytes

description: Library name: 8189

data_processing:
Kallisto pseudo-alignment was applied to quantify transcript abundances from bulk RNA-seq data
Assembly: mm10
Supplementary files format and content: bulkRNA-Seq_rawcounts_macrophages.csv
Supplementary files format and content: bulkRNA-Seq_rawcounts_hepatocytes.csv

extract_protocol:
The liver was cut into small pieces  and incubated with 500µL of a digestion mix (80 U/mL DNase I (Sigma-Aldrich, Cat# DN25) and 1 mg/mL collagenase D (Roche, Cat# 11088858001) in FACS buffer (0.5 % BSA, 2 mmol EDTA in PBS)) for 30 min at 37 °C. All following steps were performed on ice. The suspension was further passed through a 70 µm filter, and 5 mL cold FACS buffer was added. The samples were centrifuged at 400 g for 5 min at 4°C and the supernatant was discarded. Red blood cell lysis was performed by dissolving the cells gently in 1 mL of cold RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, and 0.1 mM EDTA) and 5 min incubation. After adding 5 mL cold FACS buffer, the samples were again centrifuged (400 g, 5 min, 4 °C). the pellet were stained with ABs mix. after staining the cell were sorted immediately stored in Trizol.
The cDNA library for sequencing was prepared following the SMART-Seq2 protocol. mRNA was isolated, primed using poly-T oligonucleotides, and then converted into cDNA via SMART reverse transcription. Pre-amplification was performed using SMART ISPCR, followed by fragmentation with the Nextera XT DNA Library Preparation kit (Illumina), amplification, and indexing. Library fragments were then selected by size (300-400 bp) and purified using SPRIBeads (Beckman-Coulter). Size distribution of the cDNA libraries was analyzed using the Agilent high-sensitivity D5000 assay on the Tapestation 4200 system (Agilent). Quantification of cDNA libraries was completed with a Qubit high-sensitivity dsDNA assay (Thermo Fisher). Sequencing employed a 75 bp single-end configuration on the NextSeq500 system (Illumina), using the NextSeq 500/550 High Output Kit v2.5.

tag: tissue

value: Liver

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre

tag: cell type

value: hepatocytes

tag: genotype


title: ET062519

tag: x

tag: externalsamplename

tag: sampletype

tag: age

value: M

tag: gestationtimeinyears

tag: highmaxagecaesar

tag: specieslatinname


title: ET062518

value: DNA

tag: Sex

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename


title: WT_ISL1_OE_rep_1

description:
Library name: Sample 20
WT-ISL1-1_IGO_17695_11

tag: cell line

value: WT

tag: treatment

tag: time


title: ET062524

tag: sid

tag: externalsampleid

tag: tissue

value: Tail

value: BW

tag: row

tag: col

tag: project

tag: maxagecaesar


title: ET062521

tag: x

tag: externalsamplename

tag: sampletype

tag: age

value: FALSE

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Fibroblast


title: ET062523

tag: Sex

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename

value: Skin

tag: specieslatinname


title: HeLa, STLC 0 h

description: Library name: HeLa, STLC 0 h

tag: cell line

value: HeLa

tag: cell cycle_stage


title: KO5_macrophages

description: Library name: 8188

tag: tissue

tag: cell type

value: macrophages

tag: genotype

value: KO


title: KO4_hebatocytes

description: Library name: 8187


title: Chicken primary myoblasts (CPMs), pcDNA3.1, repeat 3

city: Zhengzhou

first: Li

last: Yuanfang

address: No. 26 Longyuan East 7th Street, Zhengdong New District

institute: Harbin Institute of Technology Zhengzhou Research Institute

description:
Library name: Sample 6
pcDNA3_1_3

data_processing:
Sequence reads generated by the high-throughput sequencer were base-called from image data using CASAVA, converting them into sequence data. The output files are in FASTQ format, which primarily contains the sequence information of the reads along with their corresponding sequencing quality scores.
Assembly: Gallus_gallus.GRCg6a (galGal6)
Supplementary files format and content: txt files include FPKM values for each Sample

organism: Gallus gallus

source_name: leg muscle

extract_protocol:
Total RNA was purified using the RNeasy Mini Kit (Qiagen). Libraries were constructed using more than 1 µg of total RNA.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: leg muscle

value: Chicken primary myoblasts (CPMs)

value: myoblasts


title: Chicken primary myoblasts (CPMs), pcDNA3.1, repeat 2

description:
Library name: Sample 5
pcDNA3_1_2


title: WT_control_rep_1

description:
Library name: Sample 18
WT-BFP-1_IGO_17695_10

value: stem cell-derived islet

tag: treatment

value: hPSC-derived islet differentiation

tag: time

value: day 18


title: KO4_macrophages

description: Library name: 8186

value: Liver

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre


title: PDX1_KO_ISL1_OE_rep_2

description:
Library name: Sample 17
PDX1-ISL1-4_IGO_17695_9


title: ET06252

tag: x

tag: sid

tag: externalsampleid

tag: externalsamplename

tag: sampletype

value: DNA

value: M

tag: row

tag: col

tag: project

value: male

tag: maxagecaesar


title: ET062515

tag: age

tag: Sex

value: F

value: Tail

tag: species

value: BW

tag: relatedness

tag: idatsfound

value: FALSE

tag: extbasename

value: female

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Brain

tag: specieslatinname


title: ET062517

tag: x

tag: sid

tag: tissue


title: Chicken primary myoblasts (CPMs), pcDNA3.1, repeat 1

description:
Library name: Sample 4
pcDNA3_1_1

value: leg muscle

tag: cell line

tag: cell type


title: KO3_hebatocytes

description: Library name: 8185

value: hepatocytes

tag: genotype

value: KO


title: Chicken primary myoblasts (CPMs), ANKRD9 overexpression, repeat 3

description:
Library name: Sample 3
ANKRD9_3

value: Chicken primary myoblasts (CPMs)

value: myoblasts


title: ET062513

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: row

tag: col

tag: project

value: Adipose


title: PDX1_KO_ISL1_OE_rep_1

description:
Library name: Sample 16
PDX1-ISL1-2_IGO_17695_21

value: stem cell-derived islet

tag: treatment

value: hPSC-derived islet differentiation

tag: time

value: day 18


title: WT_control_rep_2

description:
Library name: Sample 19
WT-BFP-3_IGO_17695_1

value: WT


title: KO3_macrophages

description: Library name: 8184

value: Liver

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre

value: macrophages

tag: age


title: ET062516

value: DNA

tag: Sex

value: M

value: Tail

tag: species

value: BW

tag: relatedness

tag: idatsfound

tag: extbasename

value: male

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Lung


title: HeLa, STLC 6 h

description: Library name: HeLa, STLC 6 h

tag: cell line

value: HeLa

tag: cell cycle_stage


title: ET062512

tag: x

tag: sid

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: tissue

value: FALSE

value: Ear

tag: specieslatinname


title: PDX1_KO_control_rep_2

description:
Library name: Sample 14
PDX1-BFP-2_IGO_17695_20

tag: cell type

tag: genotype

tag: treatment

tag: time


title: HCT116 PABPC1&4-AID, DMSO, 4 h, bio rep 2

description: Library name: HCT116 PABPC1_4-AID, DMSO, 4 h, bio rep 2

value: PABPC1&4 AID

value: DMSO


title: KO2_hebatocytes

description: Library name: 8183

value: hepatocytes

value: KO

tag: age


title: KO2_macrophages

description: Library name: 8182


title: PDX1_KO_control_rep_1

description:
Library name: Sample 13
PDX1-BFP-1_IGO_17695_12

value: stem cell-derived islet

value: hPSC-derived islet differentiation

value: day 18


title: Chicken primary myoblasts (CPMs), ANKRD9 overexpression, repeat 2

description:
Library name: Sample 2
ANKRD9_2

value: leg muscle

value: Chicken primary myoblasts (CPMs)

value: myoblasts


title: ET062510

value: DNA

tag: Sex

value: F

value: Tail

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col

tag: project

value: female

tag: maxagecaesar


title: WT5_hepatocytes

description: Library name: 8181

value: Liver

tag: cell line

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre

value: WT


title: ET062511

tag: x

tag: sid

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: tissue

value: BW

value: FALSE

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Muscle


title: ET062526

tag: age

tag: Sex

value: M

tag: species

value: male

value: Brain

tag: specieslatinname


title: PAX6_KO_ISL1_OE_rep_3

description:
Library name: Sample 12
PAX6-ISL1-3_IGO_17695_6

value: stem cell-derived islet

tag: cell type

tag: genotype

tag: treatment

value: hPSC-derived islet differentiation

tag: time

value: day 18


title: WT5_macrophages

description: Library name: 8180

tag: cell line

value: macrophages


title: PAX6_KO_ISL1_OE_rep_2

description:
Library name: Sample 11
PAX6-ISL1-2_IGO_17695_23


title: ET06251

tag: x

value: DNA

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col

tag: project

tag: maxagecaesar


title: WT_Isw2-MNase R2

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Library name: WT_Isw2-MNase R2

library_source: genomic

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Sequences were trimmed to remove adapters using TRIMMOMATIC with options “TRAILING:30”. Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
For RNA-seq, the number of reads mapping on each of the genes was calculated by featurecount version 2.0.1. Differential gene expression was calculated with DESeq2 version 1.26.0.
For the CheC-seq and MNase-seq experiment, reads were mapped to the C. albicans genome (Candida_albicans_SC5314 assembly 22) using Bowtie2 with “-q --phred33 --no-unal” options. Peaks were determined using MACS2 algorithm with options “-BAM -nomodel-extsize 200-keep-dup all.”.
Assembly: Reference genome of the C. albicans SC5314 strain assembly 22 were used (http://www.candidagenome.org).
Supplementary files format and content: RNA-seq processed data files contain the raw counts for each sequencing experiment.
Library strategy: ChEC-seq

organism: Candida albicans

source_name: Yeast cells

growth_protocol: For RNA-seq, MNase-seq and ChEC-seq experiments, overnight cultures were diluted to an OD600 of 0.1 in 100 ml of fresh SC medium, grown at 30˚C to logarithmic phase (OD600 of 0.6) under normoxia. Cells were then harvested by centrifugation, washed once with PBS, and resuspended in 400 μl of SC medium.

extract_protocol:
Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater. For ChEC-seq, DNA was purified using the MasterPure Yeast DNA Purification Kit (Epicentre) following the manufacturer’s instructions and resuspended in 50µl of 10 mM Tris-HCl buffer (pH 8.0). For MNase-seq, DNA was extracted using phenol-chloroform-isoamyl alcohol and precipited with sodium acetate and ethanol.
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library. For the ChEC-seq and Mnase-seq, sequencing libraries were prepared using the KAPA HyperPrep Kits.

treatment_protocol: For RNA-seq, MNase-seq and ChEC-seq experiments, cultures were incubated at 30 °C with shaking at 220 rpm for 15 min in 6-well plates under normoxic (21% O2) or hypoxic (5% O2) conditions using the Cytation 5 plate reader equipped with O2 and CO2 gas controllers. Cells were then centrifuged for 2 min at 3,500 rpm and pellets were rapidly frozen and stored at -80°C.

tag: tissue

value: Yeast cells

value: SN148- ISW2/ISW2::Mnase

value: Grown exponentially in the synthetic complete (SC) medium


title: Pti5_NahG_mock_plant1

city: Ljubljana

first: Maja

last: Križnik

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: Library name: KM16

data_processing:
Read alignment was performed using STAR 2.7.8a  (Dobin et al., 2013) with following parameters: (--outFilterMultimapNmax 10 --outFilterMismatchNoverReadLmax 0.05, --quantTranscriptomeBan Singleend, --outFilterType BySJout, --alignSJoverhangMin 10, --alignSJDBoverhangMin 1, --alignIntronMin 20, --alignIntronMax 10000, --alignMatesGapMax 10000
Assembly: Solanum tuberosum Phureja clone DM 1-3 genome assembly version 4.04,using the merged genome annotations (Petek et al., 2020)
Supplementary files format and content: Genome_mapped_reads.txt

organism: Solanum tuberosum

source_name: leaf

growth_protocol: Plants were grown under  environmental conditions 21 ± 2 °C in the light and 18 ± 1 °C in the dark, at a relative humidity of 75% ± 2%, with a90 µmol m-2 s-1 radiation (L36W/77 lamp, Osram, Germany) and a 16-h photoperiod (Baebler et al., 2009).

extract_protocol:
RNA was extracted with TRIzol (Invitrogen) and Direct-zol RNA MicroPrep Kit, DNAse treated and purified with RNA Clean & Concentrator kit (both Zymo Research) according to the manufacturer’s instructions with prior homogenization using Tissue Lyser.
Libraries were prepared using SMART-Seq_v4 Ultra Low Input RNA Kit (TaKaRa) and Nextera XT kit (Illumina) (Illumina) at LC Sciences, and sequenced on the HiSeq platform (Illumina) using 150-bp paired-end reads

treatment_protocol: Pti5-silenced NahG (Coll et al. 2014) and NahG-Rywal plants were inoculated with PVYN-Wilga (PVYN–Wi; accession no. EF558545) or mock-inoculated, as described in Baebler et al. (2009).

value: leaf

value: mock

tag: batch


title: Pti5_NahG_mock_plant3

description: Library name: KM18


title: Pti5_NahG_mock_plant2

description: Library name: KM17


title: PDX1_KO_control_rep_3

description:
Library name: Sample 15
PDX1-BFP-3_IGO_17695_3


title: PAX6_KO_ISL1_OE_rep_1

description:
Library name: Sample 10
PAX6-ISL1-1_IGO_17695_15


title: WT Mnase-free R2

description: Library name: WT_Mnase-free R2


title: WT4_hepatocytes

description: Library name: 8179

value: Liver

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre

value: hepatocytes

value: WT

tag: age


title: ET062514

tag: sid

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: Sex

value: M

value: Tail

tag: species

value: BW

value: FALSE

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Muscle

tag: specieslatinname


title: PAX6_KO_control_rep_3

description:
Library name: Sample 9
PAX6-BFP-3_IGO_17695_5

value: stem cell-derived islet

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: hPSC-derived islet differentiation

tag: time

value: day 18


title: Pti5_NahG_PVY-N-Wilga_plant3

description: Library name: KM14

tag: tissue

value: PVY-N-Wilga


title: WT Mnase-free R1

description: Library name: WT_Mnase-free R1

value: Yeast cells


title: PAX6_KO_control_rep_2

description:
Library name: Sample 8
PAX6-BFP-2_IGO_17695_22


title: Chicken primary myoblasts (CPMs), ANKRD9 overexpression, repeat 1

description:
Library name: Sample 1
ANKRD9_1

value: leg muscle

value: Chicken primary myoblasts (CPMs)

value: myoblasts


title: Pti5_NahG_PVY-N-Wilga_plant2

description: Library name: KM12

value: leaf

tag: batch


title: WT_Isw2-MNase R1

description: Library name: WT_Isw2-MNase R1

value: SN148- ISW2/ISW2::Mnase

value: Grown exponentially in the synthetic complete (SC) medium


title: WT3_hepatocytes

description: Library name: 8177

value: Liver

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre

value: hepatocytes

value: WT

tag: age


title: ISW2_AMB_1h_R2

description: Library name: ISW2_AMB_1h_R2

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Sequences were trimmed to remove adapters using TRIMMOMATIC with options “TRAILING:30”. Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
For RNA-seq, the number of reads mapping on each of the genes was calculated by featurecount version 2.0.1. Differential gene expression was calculated with DESeq2 version 1.26.0.
For the CheC-seq and MNase-seq experiment, reads were mapped to the C. albicans genome (Candida_albicans_SC5314 assembly 22) using Bowtie2 with “-q --phred33 --no-unal” options. Peaks were determined using MACS2 algorithm with options “-BAM -nomodel-extsize 200-keep-dup all.”.
Assembly: Reference genome of the C. albicans SC5314 strain assembly 22 were used (http://www.candidagenome.org).
Supplementary files format and content: RNA-seq processed data files contain the raw counts for each sequencing experiment.

value: Treated with 0.45 µg/ml Amphotericin B for one hour


title: Pti5_NahG_PVY-N-Wilga_plant1

description: Library name: KM10


title: WT3_macrophages

description: Library name: 8176

value: macrophages


title: WT4_macrophages

description: Library name: 8178


title: PAX6_KO_control_rep_1

description:
Library name: Sample 7
PAX6-BFP-1_IGO_17695_14

value: stem cell-derived islet


title: KO1hebatocytes

description: Library name: 8175

value: KO


title: NahG_mock_plant3

description: Library name: KM09

value: NahG-Rywal

value: mock


title: ISW2_AMB_1h_R1

description: Library name: ISW2_AMB_1h_R1

value: Yeast cells


title: NahG_mock_plant2

description: Library name: KM08


title: ISL1_KO_ISL1_OE_rep_2

description:
Library name: Sample 5
ISL1-ISL1-2_IGO_17695_25

value: hPSC-derived islet differentiation

value: day 18


title: WT2_hebatocytes

description: Library name: 8173


title: WT2_macrophages

description: Library name: 8172


title: NahG_mock_plant1

description: Library name: KM07


title: ISL1_KO_control_rep_3

description:
Library name: Sample 3
ISL1-BFP-3_IGO_17695_7


title: ISL1_KO_ISL1_OE_rep_1

description:
Library name: Sample 4
ISL1-ISL1-1_IGO_17695_17


title: NahG_PVY-N-Wilga_plant3

description: Library name: KM05

value: PVY-N-Wilga


title: ISW2_SC_5min_R2

description: Library name: ISW2_SC_5min_R2


title: NahG_PVY-N-Wilga_plant1

description: Library name: KM01

value: leaf


title: SN250_SC_5min_R2

description: Library name: SN250_SC_5min_R2


title: WT1_hepatocytes

description: Library name: 8171


title: NahG_PVY-N-Wilga_plant2

description: Library name: KM03


title: ISL1_KO_control_rep_1

description:
Library name: Sample 1
ISL1-BFP-1_IGO_17695_16


title: WT1_macrophages

description: Library name: 8170


title: ISL1_KO_control_rep_2

description:
Library name: Sample 2
ISL1-BFP-2_IGO_17695_24


title: wt_rep2

status: Public on Dec 22 2025

city: Shenzhen

first: Yu

last: Ma

address: 1088 Xueyuan Bivd, Nanshan District

institute: Southern University of Science and Technology

description:
Library name: wt_rep2
BS-seq of wide-type leaf in 35 days

data_processing:
clean reads were mapped to tomato SL4.0 genome using bismark version 0.22.3 with parameters set to “-N 1 -I 0 -X 1000”
Assembly: SL4.0
Supplementary files format and content: bigwig

organism: Solanum lycopersicum

source_name: leave

extract_protocol:
Dneasy®  Plant  Maxi Kit (Qiagen)
Leaf genomic DNA of tomato mbd5 mutants and WT were extracted using a DNeasy plant Mini kit (Qiagen), and then DNA library was treated with Illmina’s standard DNA methylation analysis protocol and NEB Ultran II dna Library Prep kit. The samples were sequenced at the Genomics Core Facility of the Shanghai Centre for Plant Stress Biology, Chinese Academy of Sciences using Illumina nova6000.

value: leave

value: Alisa Craig


title: slmdb5_2_rep1

description:
Library name: slmdb5_2_rep1
BS-seq of slmbd5-2 leaf in 35 days


title: slmbd5_1_rep2

description:
Library name: slmbd5_1_rep2
BS-seq of slmbd5-1 leaf in 35 days


title: slmbd5_2-endosperm-rep3

description:
Library name: slmbd5_2-endosperm-rep3
RNA-seq of slmbd5-2 endosperm

data_processing:
clean reads were mapped to tomato SL4.0 genome using STAR
Assembly: SL4.0
Supplementary files format and content: bigwig

source_name: endosperm

extract_protocol:
Dneasy®  Plant  Maxi Kit (Qiagen)
Seed RNA of tomato mbd5 mutants and WT were extracted using a RNeasy plant Mini kit (Qiagen), and then the library prepared and sequenced as mRNA sequencing.

value: endosperm


title: slmbd5_2_rep2

description:
Library name: slmbd5_2_rep2
BS-seq of slmbd5-2 leaf in 35 days


title: wt_rep1

description:
Library name: wt_rep1
BS-seq of wide-type leaf in 35 days


title: ISL1_KO_ISL1_OE_rep_3

description:
Library name: Sample 6
ISL1-ISL1-3_IGO_17695_8


title: SN250_AMB_1h_R2

description: Library name: SN250_AMB_1h_R2


title: KO1macrophages

description: Library name: 8174

value: Liver

value: C57BL/6 Spiflox Tnfrsf11aeGFPCre


title: slmdb5_1_rep1

description:
Library name: slmdb5_1_rep1
BS-seq of slmbd5-1 leaf in 35 days


title: slmbd5_2-endosperm-rep2

description:
Library name: slmbd5_2-endosperm-rep2
RNA-seq of slmbd5-2 endosperm


title: SN250_AMB_1h_R1

description: Library name: SN250_AMB_1h_R1

value: WT


title: slmbd5_1-endosperm-rep3

description:
Library name: slmbd5_1-endosperm-rep3
RNA-seq of slmbd5-1 endosperm


title: slmbd5_2-endosperm-rep1

description:
Library name: slmbd5_2-endosperm-rep1
RNA-seq of slmbd5-2 endosperm


title: ISW2_SC_5min_R1

description: Library name: ISW2_SC_5min_R1

value: Grown exponentially in the synthetic complete (SC) medium


title: slmbd5_1-endosperm-rep2

description:
Library name: slmbd5_1-endosperm-rep2
RNA-seq of slmbd5-1 endosperm


title: slmbd5_2-embryo-rep2

description:
Library name: slmbd5_2-embryo-rep2
RNA-seq of slmbd5-2 embryo

source_name: embryo

value: embryo


title: WT-endosperm-rep2

description:
Library name: WT-endosperm-rep2
RNA-seq of wide-type endosperm


title: WT-endosperm-rep1

description:
Library name: WT-endosperm-rep1
RNA-seq of wide-type endosperm


title: WT-endosperm-rep3

description:
Library name: WT-endosperm-rep3
RNA-seq of wide-type endosperm


title: SN250_SC_5min_R1

description: Library name: SN250_SC_5min_R1


title: slmbd5_2-embryo-rep3

description:
Library name: slmbd5_2-embryo-rep3
RNA-seq of slmbd5-2 embryo


title: slmbd5_2-embryo-rep1

description:
Library name: slmbd5_2-embryo-rep1
RNA-seq of slmbd5-2 embryo


title: slmbd5_1-embryo-rep2

description:
Library name: slmbd5_1-embryo-rep2
RNA-seq of slmbd5-1 embryo


title: slmbd5_1-embryo-rep3

description:
Library name: slmbd5_1-embryo-rep3
RNA-seq of slmbd5-1 embryo


title: WT-embryo-rep3

description:
Library name: WT-embryo-rep3
RNA-seq of wide-type embryo


title: WT-embryo-rep2

description:
Library name: WT-embryo-rep2
RNA-seq of wide-type embryo


title: slmbd5_2-allseed-rep2

description:
Library name: slmbd5_2-allseed-rep2
RNA-seq of slmbd5-2 seed

source_name: seed

value: seed


title: WT-embryo-rep1

description:
Library name: WT-embryo-rep1
RNA-seq of wide-type embryo


title: slmbd5_1-allseed-rep3

description:
Library name: slmbd5_1-allseed-rep3
RNA-seq of slmbd5-1 seed


title: slmbd5_2-allseed-rep3

description:
Library name: slmbd5_2-allseed-rep3
RNA-seq of slmbd5-2 seed


title: slmbd5_1-allseed-rep1

description:
Library name: slmbd5_1-allseed-rep1
RNA-seq of slmbd5-1 seed


title: WT-allseed-rep3

description:
Library name: WT-allseed-rep3
RNA-seq of wide-type seed


title: slmbd5_1-allseed-rep2

description:
Library name: slmbd5_1-allseed-rep2
RNA-seq of slmbd5-1 seed


title: WT-allseed-rep2

description:
Library name: WT-allseed-rep2
RNA-seq of wide-type seed


title: ampDAP_input_rep1

description:
Library name: ampDAP_input_rep1
ampDAP-seq of HALO-tag incubated with leaf genomic DNA in 35 days

data_processing:
clean reads were mapped to tomato SL4.0 genome using bowtie2
Assembly: SL4.0
Supplementary files format and content: bigwig
Library strategy: DAP-Seq

extract_protocol:
Dneasy®  Plant  Maxi Kit (Qiagen)
The experiment was carried out as described by Bartlett et al (2017). Briefly, leaf genomic DNA (gDNA) was extracted from tomato AC leaf , then the gDNA was fragmented into around 200bp fragments by Covaris S2 ultrasonicator; End-repair and A-tailing was performed sequentially, after that the truncated Illumina TruSeq adaptor was ligated and gDNA library was prepared; Meanwhile, full-length CDS of MBD5 was cloned into pIX-HALO tagged vector, and the fusion protein was expressed in vitro via TNT Coupled Wheat Germ Extract Systems; then the fusion protein was purified byMagne HaloTag Beads; Finally, beads coupled with protein were incubated with the gDNA library, then clean unbound gDNA fragments, MBD5 specific bound gDNA was purified and amplified for sequencing.


title: ampDAP_MBD5_rep2

description:
Library name: ampDAP_MBD5_rep2
ampDAP-seq of HALO-MBD5 incubated with leaf genomic DNA in 35 days


title: ampDAP_input_rep3

description:
Library name: ampDAP_input_rep3
ampDAPP-seq of HALO-tag incubated with leaf genomic DNA in 35 days


title: ampDAP_MBD5_rep1

description:
Library name: ampDAP_MBD5_rep1
ampDAP-seq of HALO-MBD5 incubated with leaf genomic DNA in 35 days


title: slmbd5_1-endosperm-rep1

description:
Library name: slmbd5_1-endosperm-rep1
RNA-seq of slmbd5-1 endosperm


title: ampDAP_MBD5_rep3

description:
Library name: ampDAP_MBD5_rep3
ampDAP-seq of HALO-MBD5 incubated with leaf genomic DNA in 35 days


title: slmbd5_1-embryo-rep1

description:
Library name: slmbd5_1-embryo-rep1
RNA-seq of slmbd5-1 embryo


title: DAP_input_rep2

description:
Library name: DAP_input_rep2
DAP-seq of HALO-tag incubated with leaf genomic DNA in 35 days


title: DAP_input_rep1

description:
Library name: DAP_input_rep1
DAP-seq of HALO-tag incubated with leaf genomic DNA in 35 days


title: DAP_MBD5

description:
Library name: DAP_MBD5
DAP-seq of GST-MBD5 incubated with leaf genomic DNA in 35 days


title: AC_ChIP_rep1

description:
Library name: AC_ChIP_rep1
AC_ChIP_rep1

data_processing:
clean reads were mapped to tomato SL4.0 genome using bowtie2
Assembly: SL4.0
Supplementary files format and content: bigwig

extract_protocol:
Dneasy®  Plant  Maxi Kit (Qiagen)
The ChIP-seq experiment was performed as described in Zhao et al (2020). Young leaves were crossed with 1% formaldehyde in phosphate-buffered saline (PBS) to fixed DNA and protein. Then 0.2M glycine was used to stop the fixation, then washed with ddH2O for 3 times and freeze in liquid nitrogen. About 0.4g samples were ground in liquid nitrogen and resuspend in EB1 buffer in 2.4ml. The mixture was mixed in 4°C for 15mins. Samples were sonicated for 20 cycles firstly and then centrifuged at 10000xg for 10min at 4°C, and the supernatant was collected for the following 45 cycles to fragmented into 200-600bp. The chromatin samples was then took out and saved 50ul supernatant as input for subsequent analysis. 50 μl of Dynabeads® protein G beads (Invitrogen, 10003D) per sample were washed with 300 μl of PBST buffer (PBS with 0.1% Tween 20) twice and resuspended in 200 μl of PBST buffer. Then antibody (anti-flag, 5-10 μl) was added to the beads and incubated for about 4-6 h on a rotator at 4 °C to form antibody coated beads . Next step, The following samples was incubate with pre-cleared beads for 1-3h at 4 °C , and then washed with PBST twice. IP products was incubated with antibody coated with protein G for overnight at 4 °C on a rotator at 4 °C to immunoprecipitated the target chromatin. In the next day, beads were collected and washed with ice cold low-salt ChIP buffer (50mM HEPES-KOH, 150Mm Nacl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and 0.1% SDS) twice, high Salt buffer (NaCl in low salt ChIP wash buffer was replaced with 350mM NaCl) twice; ChIP wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 1 mM EDTA, 0.1% sodium deoxycholate) once, and TE buffer (10 mM Tris-HCl, pH 8.0, and 1 mM EDTA) twice. Then protein -DNA was eluted twice with 100ul and 200ul ChIP Elution buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS) ;After that, 5 μl of proteinase K and 6μl of 5M NaCl was added to the elute and incubated for 6 h or overnight at 55 °C to reverse crosslinking the protein-DNA complexes. Then, ChIP DNA was purified with DNA clean Kit＆concentrator kit from ZYMO Research. ChIP DNA library was built with NEB Next Ultra II DNA library prep kit for Illumina sequencing.


title: ampDAP_input_rep2

description:
Library name: ampDAP_input_rep2
ampDAP-seq of HALO-tag incubated with leaf genomic DNA in 35 days


title: AC_ChIP_rep2

description:
Library name: AC_ChIP_rep2
AC_ChIP_rep2


title: AC_input_rep1

description:
Library name: AC_input_rep1
AC_input_rep1


title: AC_input_rep2

description:
Library name: AC_input_rep2
AC_input_rep2


title: WT-allseed-rep1

description:
Library name: WT-allseed-rep1
RNA-seq of wide-type seed


title: MBD5_ChIP_rep2

description:
Library name: MBD5_ChIP_rep2
MBD5_ChIP_rep2


title: MBD5_input_rep1

description:
Library name: MBD5_input_rep1
MBD5_input_rep1


title: slmbd5_2-allseed-rep1

description:
Library name: slmbd5_2-allseed-rep1
RNA-seq of slmbd5-2 seed


title: DAP_input_rep3

description:
Library name: DAP_input_rep3
DAP-seq of HALO-tag incubated with leaf genomic DNA in 35 days


title: MBD5_ChIP_rep1

description:
Library name: MBD5_ChIP_rep1
MBD5_ChIP_rep1


title: MBD5_input_rep2

description:
Library name: MBD5_input_rep2
MBD5_input_rep2


title: Influenza A infected

city: New York

first: Filip

middle: K

last: Swirski

address: 1470 Madison Avenue, 7th Floor

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: HeartINF_0
10X Genomics

data_processing:
The barcoded processing, counting and aggregation were made using the Cell Ranger software v5.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse mm10
Assembly: Influenza A virus (A/Puerto Rico/8/34/Mount Sinai(H1N1))
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism:
Mus musculus
Influenza A virus (A/Puerto Rico/8/34/Mount Sinai(H1N1))

source_name: Heart tissue

extract_protocol:
Heart tissue nuclei were isolated using the nucleus isolation kit according to the manufacturer’s instructions (10x).
After nucleus counting and viability control, the library was constructed on the Chromium 10x instrument using Chromium single cell 3 ’reagent v3.0 kits, followed by sequencing on Illumina HiSeq 2500 instruments, which resulted in approximately 205-209 million reads per sample from approximately 14 000 sequenced nuclei.

value: Heart tissue

value: Mice heart cell types


title: R. parkeri, time course, 24hpi, rep 4

first: Allison

middle: T

last: Scott

address: 31 Ames St

institute: Massachusetts Institute of Technology

description: Library name: Sample83

data_processing:
Read alignment was performed using STAR (Default parameters, except --alignIntronMax 1  to signal no introns within the bacterial genome). Reads were assigned to features using featureCounts from the subreads module (using the following flags: -t CDS -s 2 -O -f -p -B)
Assembly: NCBI Reference Sequence: NC_017044.1
Supplementary files format and content: comma separated tables with raw counts for each sample. Fig1Counts.csv has raw reads for samples 1-32 and TimeCourseCounts.csv has raw reads for samples 33-86.

organism: Rickettsia parkeri str. Portsmouth

source_name: Tissue Culture

growth_protocol: For all assays, A549s were grown in 6-well plates and infected with R. parkeri at an MOI of 1. For temporal profiling, the 6–8 biological replicates were collected on the same day to minimize batch effects. R. parkeri were added to media and spun at 200 x g for 5 minutes to settle bacteria onto the host cell monolayer, then incubated at 33°C until the time point of interest. A549s were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was collected by aspirating cell culture medium and adding 500 µL of Trizol Reagent (Thermo Fisher Scientific 15596026) to each well. Each replicate used material from 1–2 wells. 0 hpi samples were collected by adding purified R. parkeri directly to Trizol Reagent. RNA was extracted using PureLink RNA mini kit (Thermo Fisher Scientific 12183018A) following manufacturer’s Trizol extraction protocol.
Total RNA from infected host cells was used to create stranded, barcoded cDNA libraries using Twist RNA Library Prep Kit (Twist Biosciences 107061) according to manufacturer’s protocol. cDNA libraries from replicates of the same biological condition were pooled together. R. parkeri cDNA was enriched from these pooled libraries using the Twist standard hyb and wash kit v2 (Twist Biosciences 105561), our custom R. parkeri probe panel (Twist Biosciences), and Twist’s target enrichment standard hybridization v2 protocol.

value: Tissue Culture

value: R. parkeri/A549

value: 24 hpi post-capture


title: R. parkeri, time course, 24hpi, rep 1

description: Library name: Sample81


title: R. parkeri, time course, 24hpi, rep 5

description: Library name: Sample84


title: R. parkeri, time course, 24hpi, rep 6

description: Library name: Sample85


title: R. parkeri, time course, 16hpi, rep 8

description: Library name: Sample80

value: 16 hpi post-capture


title: R. parkeri, time course, 16hpi, rep 7

description: Library name: Sample79


title: R. parkeri, time course, 16hpi, rep 6

description: Library name: Sample78


title: R. parkeri, time course, 16hpi, rep 5

description: Library name: Sample77


title: R. parkeri, time course, 24hpi, rep 7

description: Library name: Sample86


title: R. parkeri, time course, 16hpi, rep 4

description: Library name: Sample76


title: R. parkeri, time course, 16hpi, rep 3

description: Library name: Sample75


title: R. parkeri, time course, 16hpi, rep 2

description: Library name: Sample74


title: R. parkeri, time course, 12hpi, rep 8

description: Library name: Sample72

value: 12 hpi post-capture


title: R. parkeri, time course, 12hpi, rep 5

description: Library name: Sample69


title: R. parkeri, time course, 16hpi, rep 1

description: Library name: Sample73


title: R. parkeri, time course, 12hpi, rep 4

description: Library name: Sample68


title: R. parkeri, time course, 12hpi, rep 6

description: Library name: Sample70


title: R. parkeri, time course, 12hpi, rep 1

description: Library name: Sample65


title: R. parkeri, time course, 12hpi, rep 2

description: Library name: Sample66


title: R. parkeri, time course, 8hpi, rep 8

description: Library name: Sample64

value: 8 hpi post-capture


title: R. parkeri, time course, 12hpi, rep 3

description: Library name: Sample67


title: R. parkeri, time course, 8hpi, rep 6

description: Library name: Sample62


title: R. parkeri, time course, 12hpi, rep 7

description: Library name: Sample71


title: R. parkeri, time course, 8hpi, rep 5

description: Library name: Sample61


title: R. parkeri, time course, 24hpi, rep 2

description: Library name: Sample82


title: R. parkeri, time course, 8hpi, rep 4

description: Library name: Sample60


title: R. parkeri, time course, 8hpi, rep 3

description: Library name: Sample59


title: R. parkeri, time course, 8hpi, rep 7

description: Library name: Sample63


title: uninfected

description:
Library name: HeartnonINF_0
10X Genomics


title: R. parkeri, time course, 8hpi, rep 2

description: Library name: Sample58


title: R. parkeri, time course, 8hpi, rep 1

description: Library name: Sample57


title: R. parkeri, time course, 4hpi, rep 4

description: Library name: Sample52

value: 4 hpi post-capture


title: R. parkeri, time course, 4hpi, rep 8

description: Library name: Sample56


title: R. parkeri, time course, 4hpi, rep 6

description: Library name: Sample54


title: R. parkeri, time course, 4hpi, rep 7

description: Library name: Sample55


title: R. parkeri, time course, 4hpi, rep 5

description: Library name: Sample53


title: R. parkeri, time course, 4hpi, rep 2

description: Library name: Sample50


title: R. parkeri, time course, 1hpi, rep 7

description: Library name: Sample47

value: 1 hpi post-capture


title: R. parkeri, time course, 4hpi, rep 3

description: Library name: Sample51


title: R. parkeri, time course, 1hpi, rep 6

description: Library name: Sample46


title: R. parkeri, time course, 1hpi, rep 4

description: Library name: Sample44


title: R. parkeri, time course, 1hpi, rep 2

description: Library name: Sample42


title: R. parkeri, time course, 4hpi, rep 1

description: Library name: Sample49


title: R. parkeri, time course, 1hpi, rep 3

description: Library name: Sample43


title: R. parkeri, time course, 0hpi, rep 4

description: Library name: Sample36

value: 0 hpi post-capture


title: R. parkeri, time course, 0hpi, rep 1

description: Library name: Sample33


title: R. parkeri, time course, 0hpi, rep 5

description: Library name: Sample37


title: R. parkeri, time course, 1hpi, rep 5

description: Library name: Sample45


title: R. parkeri, 48hpi, rep 6

description: Library name: Sample30

value: 48 hpi post-capture


title: R. parkeri, time course, 0hpi, rep 3

description: Library name: Sample35


title: R. parkeri, time course, 0hpi, rep 8

description: Library name: Sample40


title: R. parkeri, 48hpi, rep 8

description: Library name: Sample32


title: R. parkeri, time course, 1hpi, rep 1

description: Library name: Sample41


title: R. parkeri, 48hpi, rep 4

description: Library name: Sample28


title: R. parkeri, 48hpi, rep 7

description: Library name: Sample31


title: R. parkeri, time course, 0hpi, rep 6

description: Library name: Sample38


title: R. parkeri, time course, 0hpi, rep 7

description: Library name: Sample39


title: R. parkeri, 24hpi, rep 3, pre-capture

description: Library name: Sample23

value: 24 hpi pre-capture


title: R. parkeri, 24hpi, rep 2, pre-capture

description: Library name: Sample22


title: R. parkeri, 24hpi, rep 4, pre-capture

description: Library name: Sample24


title: R. parkeri, 48hpi, rep 5

description: Library name: Sample29


title: R. parkeri, time course, 0hpi, rep 2

description: Library name: Sample34


title: R. parkeri, 48hpi, rep 1

description: Library name: Sample25


title: R. parkeri, time course, 1hpi, rep 8

description: Library name: Sample48


title: R. parkeri, 48hpi, rep 3

description: Library name: Sample27


title: R. parkeri, 24hpi, rep 1, pre-capture

description: Library name: Sample21


title: R. parkeri, 24hpi, rep 8

description: Library name: Sample20


title: R. parkeri, 24hpi, rep 7

description: Library name: Sample19


title: R. parkeri, 24hpi, rep 5

description: Library name: Sample17


title: R. parkeri, 24hpi, rep 6

description: Library name: Sample18


title: R. parkeri, 24hpi, rep 4

description: Library name: Sample16


title: R. parkeri, 0hpi, rep 3, pre-capture

description: Library name: Sample11

value: 0 hpi pre-capture


title: R. parkeri, 48hpi, rep 2

description: Library name: Sample26


title: R. parkeri, 24hpi, rep 2

description: Library name: Sample14


title: R. parkeri, 0hpi, rep 1, pre-capture

description: Library name: Sample9


title: R. parkeri, 24hpi, rep 1

description: Library name: Sample13


title: R. parkeri, 24hpi, rep 3

description: Library name: Sample15


title: R. parkeri, 0hpi, rep 6

description: Library name: Sample6


title: R. parkeri, 0hpi, rep 4, pre-capture

description: Library name: Sample12


title: R. parkeri, 0hpi, rep 4

description: Library name: Sample4


title: R. parkeri, 0hpi, rep 8

description: Library name: Sample8


title: R. parkeri, 0hpi, rep 7

description: Library name: Sample7


title: R. parkeri, 0hpi, rep 5

description: Library name: Sample5


title: R. parkeri, 0hpi, rep 1

description: Library name: Sample1


title: R. parkeri, 0hpi, rep 2

description: Library name: Sample2


title: Lung adventitial fibroblasts from young B6 mouse Y5

city: San Francisco

first: Nancy

last: Allen

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

description:
Library name: Young B6 Y5
E235_Feature_counts_all_samples.csv

data_processing:
QC was performed with FastQC (Babraham Bioinformatics) and adaptor contamination was trimmed with Trim Galore! Trimmed reads were aligned to the reference genome Mus musculus UCSC version mm10 with STAR (Spliced Transcripts Alignment to a Reference). Gene counts were generated with featureCounts using the built-in mm10 gene annotations.
Assembly: mm10
Supplementary files format and content: .csv file containing raw gene counts for all samples

source_name: Lung

extract_protocol:
After euthanasia with isoflurane the chest cavity was opened and the lungs were perfused with PBS via the right ventricle. The lungs were then tracheally insufflated with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was incubated in digestion cocktail for 45 minutes at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM) and passed through a 70 μm cell strainer. Cells were pelleted at 550xg for 5 minutes and then resuspended in red blood cell (RBC) lysis buffer for 2 minutes. After RBC lysis cells were passed through a 40 μm cell strainer. Cells were FcR blocked for 15 minutes and then incubated for 30 minutes with the following biotinylated antibodies to deplete lineage+ cells: Ter119-biotin, CD146-biotin, CD45-biotin, CD31-biotin, Epcam-biotin. Lineage+ cells were then removed via magnetic bead using the EasySep Mouse Streptavidine RapidSpheres Isolation Kit (StemCell Technologies #19860). Remaining cells were then incubated with the following fluorescently-conjugated antibodies in sorting buffer for 30 min at 4C: anti-CD45 BV421, anti-CD31-eFluor450, anti-Epcam-BV421, anti-Sca1 BUV395, anti-CD9-PE, and anti-PDGFRA APC. After washing with FACS buffer cells were sorted. Doublets and dead cells were excluded based on forward and side scatter and DAPI, respectively. Adventitial fibroblasts were identified as Live, Lin- (Dump channel = DAPI, anti-CD45, anti-CD31, anti-EPCAM) and Sca1+. FACS was performed on a BD FACS Aria using FACSDiva Software.
ribosomal RNA depletion

value: Lung

value: Adventitial fibroblast

value: Homeostasis


title: Lung adventitial fibroblasts from aged B6 mouse A4

description:
Library name: Aged B6 A4
E235_Feature_counts_all_samples.csv


title: Lung adventitial fibroblasts from aged B6 mouse A2

description:
Library name: Aged B6 A2
E235_Feature_counts_all_samples.csv


title: Lung adventitial fibroblasts from aged B6 mouse A3

description:
Library name: Aged B6 A3
E235_Feature_counts_all_samples.csv


title: Lung resident CD8+ T cell TCR analysis

description:
Library name: Lung_resident_CD8_TCR
feature_reference.csv

data_processing:
Raw Fastq files were aligned with Cellranger. Demultiplexing was performed in Seurat using HTODemux
Assembly: mm10
Supplementary files format and content: Gene expression data are provided as a sparse gene-by-cell UMI count matrix (matrix.mtx.gz) with corresponding gene annotations (features.tsv.gz) and cell barcodes (barcodes.tsv.gz). TCR sequencing data include annotated V(D)J contigs (all_contig_annotations.csv). Sample multiplexing results from hashtag oligo demultiplexing are provided as per-cell tag assignments (tag_calls_per_cell.csv), assignment confidence metrics (assignment_confidence_table.csv), summary statistics (tag_calls_summary.csv), and per-tag cell counts (cells_per_tag.json).

extract_protocol:
Prior to sacrifice animals were anesthetized and administerd 3ug of fluorescently labeled anti-mouse CD45 BV421 (clone 30-F11) in 150 uL PBS. After 3 minutes of antibody circulation mice were euthanized with isofluorane. After cardiac perfusion with PBS, lungs were removed from the chest and chopped for approximately 1 minute with a razor blade to dissociate the tissue. Chopped lungs were then incubated in a digestion cocktail of Collagenase IV (125 units/mL), DNase (50U/mL) and 1x Penicillin-streptomycin in HBSS (with Ca2+Mg2+) and incuated for 1 hour at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM) and passed through a 70 μm cell strainer. Cells were pelleted at 550xg for 5 minutes and then resuspended in red blood cell (RBC) lysis buffer for 2 minutes. After RBC lysis cells were passed through a 40 μm cell strainer. Cell suspensions were blocked with mouse FcR blocking reagent (Miltenyl Biotec 130-092-575) for 15 minutes and then incubated with the appropriate fluorescently-conjugated antibodies and Biolegend barcode antibodies in sorting buffer for 30 min at 4C. After washing with FACS buffer cells were sorted. Doublets and dead cells were excluded based on forward and side scatter and Sytox Red, respectively. The following antibodies were used for staining: anti-CD45 UVC (BD 564279),  anti-CD3 FITC, anti-CD4 BV711, anti-CD8 BV786. Endogenous tdTomato was used to identify Gzmk+ cells within the CD8+ population. FACS was performed on a BD FACS Aria using FACSDiva Software.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument with 5' v3 GEM-X technology with feature barcode and TCR.

value: CD8+ T

value: C57BL/6 (Aged WT), Dermo1-cre/+;Tnfaip3f/f;GATOR/+ (Young Tnfaip3 CKO), and GATOR/+ (Young LCMV)

value: Homeostasis or LCMV clone 13 infected


title: Lung adventitial fibroblasts from aged B6 mouse A1

description:
Library name: Aged B6 A1
E235_Feature_counts_all_samples.csv


title: Lung resident CD8+ T cell gene expression

description:
Library name: Lung_resident_CD8_GEX
feature_reference.csv


title: Lung resident CD8+ T cell hastag oligos (HTO) for multiplexing

description:
Library name: Lung_resident_CD8_HTO
feature_reference.csv

library_source: other

molecule: protein


title: Lung adventitial fibroblasts from young B6 mouse Y4

description:
Library name: Young B6 Y4
E235_Feature_counts_all_samples.csv


title: Lung adventitial fibroblasts from young B6 mouse Y2

description:
Library name: Young B6 Y2
E235_Feature_counts_all_samples.csv


title: Lung adventitial fibroblasts from young B6 mouse Y1

description:
Library name: Young B6 Y1
E235_Feature_counts_all_samples.csv


title: R. parkeri, 0hpi, rep 2, pre-capture

description: Library name: Sample10

value: Tissue Culture

value: R. parkeri/A549


title: Lung adventitial fibroblasts from young Dermo1cre/+;Tnfaip3f/f (Tnfaip3 CKO) mouse D4

description:
Library name: Tnfaip3 CKO D4
E235_Feature_counts_all_samples.csv

value: Dermo1-cre/+;Tnfaip3 f/f


title: Lung adventitial fibroblasts from young Dermo1cre/+;Tnfaip3f/f (Tnfaip3 CKO) mouse D3

description:
Library name: Tnfaip3 CKO D3
E235_Feature_counts_all_samples.csv


title: Lung adventitial fibroblasts from young Dermo1cre/+;Tnfaip3f/f (Tnfaip3 CKO) mouse D1

description:
Library name: Tnfaip3 CKO D1
E235_Feature_counts_all_samples.csv


title: Lung adventitial fibroblasts from young Tnfaip3f/f mouse C5

description:
Library name: Tnfaip3 Control C5
E235_Feature_counts_all_samples.csv

value: Tnfaip3 f/f


title: Lung adventitial fibroblasts from young Tnfaip3f/f mouse C2

description:
Library name: Tnfaip3 Control C2
E235_Feature_counts_all_samples.csv


title: Lung adventitial fibroblasts from young Tnfaip3f/f mouse C4

description:
Library name: Tnfaip3 Control C4
E235_Feature_counts_all_samples.csv


city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

description:
Library name: CD45+ choroid plexus cells from C57BL6 mice after ICV injection of CD45-Hashtag (ADT TotalSeq B Mouse CD45)
10x Genomics

data_processing:
CellRanger 9.0.0
Assembly: GRCm39
Supplementary files format and content: .h5ad

source_name: Brain

extract_protocol:
Eight 3-month-old C57BL6 female mice were deeply anesthetized with Ketamine/Xylazine before receiving bilateral intra-cerebro-ventricular (ICV) injections of 0.5μg CD45-Hashtag (Biolegend TotalSeq-B0096) at 0.5μl/min and using the following Bregma coordinates: AP: -0.5mm; ML: +/- 1mm; Z: 2mm. Mice were euthanized 30 min after injection. Upon perfusion, brains were harvested and placed into a 10 cm Petri dish with ice-cold PBS, and the choroid plexus (ChP) from the fourth and lateral ventricles were dissected using surgical magnifier glasses. Briefly, the hindbrain was resected using a scalpel, and the fourth ventricle was exposed by gently separating the cerebellum and midbrain with forceps. The ChP from the fourth ventricle was then carefully removed using curved dissection forceps. Next, the brain was bisected sagittally along the midline with a scalpel. The lateral ventricles were exposed by separating the cortex from the midbrain and unfolding the hippocampus. The ChP from the lateral ventricles was dissected from both hemispheres using curved dissection forceps. The ChP was then transferred into a 5 ml Eppendorf tube with ice-cold Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 0.5% Bovine Serum Albumin (BSA, Rockland) and 2.5 mM EDTA (Corning). The dissected ChP was mechanically homogenized with a 3 ml syringe, using 20- and 23-gauge needles in sequence. The ChP cell suspension was filtered through a 30 μm strainer, collected into 5 ml FACS tubes, and spun down at 450g for 5 min. Cell pellets were stained with Fc block and CD45.2-PE (1:100, Biolegend) for 30 minutes. For live/dead discrimination, a 1 mg/ml of DAPI (Sigma) at 1:5000 final dilution was added to the sample immediately prior to sorting. The DAPI negative, CD45+ population was sorted on FACS Aria-III (BD Bioscience) using a 85µm nozzle. Cells were collected into a 1.5ml Eppendorf tube containing PBS + 0.4% UltraPure BSA (Thermo Fisher) + 1U/µl of Recombinant RNasin Ribonuclease Inhibitor (Promega). Sorted cells were washed in PBS and resuspended into PBS + 0.04% UltraPure BSA buffer at a final volume of 35µl.
Single-cell libraries were prepared using the Chromium GEM-X Single Cell 3' v4 protocol, targeting 20,000 cells/sample. Briefly, cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads, and cDNA concentration was determined on the Bioanalyzer. GEX libraries were prepared as recommended by the Chromium GEM-X Single Cell 3' Reagent Kits v4 with Feature Barcode technology for Cell Surface Protein (CG000732) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium GEM-X Single Cell 3' Kit v4 - 16 rxns (PN-1000691), Chromium GEM-X Single Cell 3' Chip Kit v4 - 4 chips (PN-1000690), Chromium GEM-X Single Cell 3' Feature Barcode Kit v4 16 rxns (PN-1000702), Dual Index Kit TT Set A, 96 rxns (PN-1000215) and Dual Index Kit NT Set A 96 rxns (PN-1000242) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq X Plus instrument. Normalized libraries were sequenced on a NovaSeq X Plus Flow Cell using the 151x10x10x151 sequencing recipe according to manufacturer protocol. Read 1 was trimmed to the 10x Genomics recommendation of 28bp. A median sequencing depth of 50,000 reads/cell was targeted for each gene expression library and 10,000 reads/cell was targeted for each Feature library.

value: Brain

value: Immune cells

value: Mice euthanized 30 min after receiving ICV injection of CD45-Hashtag


title: R. parkeri, 0hpi, rep 3

description: Library name: Sample3

value: 0 hpi post-capture


description:
Library name: CD45+ choroid plexus cells from C57BL6 mice after ICV injection of CD45-Hashtag (RNA)
10x Genomics


title: CD45+ choroid plexus cells from Tgfbr2-flox: Lyz2-Cre mice

description:
Library name: KO
10x Genomics

extract_protocol:
Each sequenced sample contains a pool of 10 mice, 5 males and 5 females, 8-12 weeks old. Upon transcardial perfusion, the brain was harvested and placed into a 10 cm Petri dish with ice-cold PBS, and the choroid plexus (ChP) from the fourth and lateral ventricles were dissected using surgical magnifier glasses. Briefly, the hindbrain was resected using a scalpel, and the fourth ventricle was exposed by gently separating the cerebellum and midbrain with forceps. The ChP from the fourth ventricle was then carefully removed using curved dissection forceps. Next, the brain was bisected sagittally along the midline with a scalpel. The lateral ventricles were exposed by separating the cortex from the midbrain and unfolding the hippocampus. The ChP from the lateral ventricles was dissected from both hemispheres using curved dissection forceps. The ChP was then transferred into a 5 ml Eppendorf tube with ice-cold Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 0.5% Bovine Serum Albumin (BSA, Rockland) and 2.5 mM EDTA (Corning). The dissected ChP was mechanically homogenized with a 3 ml syringe, using 20- and 23-gauge needles in sequence. The choroid plexus cell suspension was filtered through a 30 μm strainer, collected into 5 ml FACS tubes, and spun down at 450g for 5 min. Cell pellets were stained with Fc block and CD45-PE (1:200, Biolegend) for 30 minutes. For live/dead discrimination, a 1 mg/ml of DAPI (Sigma) at 1:5000 final dilution was added to the sample immediately prior to sorting. The DAPI negative, CD45+ population was sorted on FACS Aria-III (BD Bioscience) using a 85µm nozzle. Cells were collected into a 1.5ml Eppendorf tube containing PBS + 0.4% UltraPure BSA (Thermo Fisher) + 1U/µl of Recombinant RNasin Ribonuclease Inhibitor (Promega). Sorted cells were washed in PBS and resuspended into PBS + 0.04% UltraPure BSA buffer at a final volume of 35µl.
Single-cell libraries were prepared using the Chromium GEM-X Single Cell 3' v4 protocol, targeting 20,000 cells/sample. Briefly, cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads, and cDNA concentration was determined on the Bioanalyzer. GEX libraries were prepared as recommended by the Chromium GEM-X - Single Cell 3' Reagent Kits v4 (CG000731) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium GEM-X Single Cell 3' Kit v4 - 16 rxns (PN-1000691), Chromium GEM-X Single Cell 3' Chip Kit v4 - 4 chips (PN-1000690) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq X Plus instrument. Normalized libraries were sequenced on a NovaSeq X Plus Flow Cell using the 151x10x10x151 sequencing recipe according to manufacturer protocol. Read 1 was trimmed to the 10x Genomics recommendation of 28bp. A median sequencing depth of 50,000 reads/cell was targeted for each gene expression library.

value: Tgfbr2-flox :Lyz2-Cre


title: CD45+ choroid plexus cells from Tgfbr2-flox mice

description:
Library name: WT
10x Genomics


title: PPCM LV rep1

city: Torrance

first: Michelle

middle: L

last: Matter

address: 1124 West Carson Street

department: Genomics

institute: The lundquist Institute

description:
Library name: PPCM Sample 1
PPCM_180107

data_processing:
DNBSEQ-T7 Platform (Human) and Illumina NextSeq 500 sequence platform (mouse)
For Human samples: Raw data contained reads of low quality, reads with adaptor sequence and reads with high level of N base. Those reads were filtered and cleaned by cutadapt (version 1.9) and paired end were produced. Bowtie2 was used to align clean reads to reference genes and HISAT was used to align clean reads to reference genome. For mouse: Data Files were uploaded to Partek flow, contaminants were removed using Bowtie2 (version 2.2.5) and unaligned reads were aligned to STAR (version 2.7.8a) using mouse genome as reference.
Assembly: Human:GCF_000001405.39_GRCh38.p13; Mouse: Mus_musculus.GRCm38.dna
Supplementary files format and content: csv files include FPKMs for all human data and csv files include TPMs for all mouse data

source_name: Human LV heart

extract_protocol:
Total RNA (human and mouse) was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
Human: RNA libraries for RNAseq were prepared with MGIEasy RNA library Prep Set (Proprietary for DNBSEQ platforms). Mouse: RNA libraries for RNAseq were prepared with  Illumina Stranded Total RNA prep with Ribo-Zero Plus according to manufacturer’s instructions.

value: Human LV heart

value: Knockout


title: Donor LV rep2

description:
Library name: NORMAL Sample 2
NORMAL_4163

value: wildtype


title: PPCM LV rep2

description:
Library name: PPCM Sample 2
PPCM_200507


title: Donor LV rep3

description:
Library name: NORMAL Sample 3
NORMAL_42G


title: PPCM LV rep3

description:
Library name: PPCM Sample 3
PPCM_210324


title: Donor LV rep1

description:
Library name: NORMAL Sample 1
NORMAL_412m


title: A375_IBET726_Oxa_1

first: Xiaohan

last: Chen

address: Tongji University

institute: Tongji University/ major in Bioinformatics

description:
Library name: Sample 7
S1_A375_726_Oxa

data_processing:
RNA-Seq raw reads were filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). Clean reads were aligned using STAR (version 2.7.9a) to human reference sequence (Homo_sapiens.GRCh38.dna.primary_assembly). Gene expression values TPM (Transcripts Per Kilobase Million) were quantitated with RSEM (version 1.3.1).
Assembly: GRCh38
Supplementary files format and content: xlsx files include TPM values for each Sample

source_name: Skin

growth_protocol: A375 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), and 1% penicillin-streptomycin was added to all media. Cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
High-quality genomic DNA and total RNA were simultaneously extracted from the same sample using the AllPrep DNA/RNA kit. Tissue (~30 mg) or up to 1 × 10⁷ snap-frozen cells were lysed in Buffer RLT Plus and homogenized, followed by centrifugation to separate the lysate. The supernatant was applied to an AllPrep DNA spin column for DNA purification, and the flow-through was used for RNA purification. RNA was purified on RNeasy spin columns with ethanol precipitation and sequential washes using buffers RW1 and RPE, and finally eluted in RNase-free water. DNA was washed with buffers AW1 and AW2 and eluted in Buffer EB. Purity and quality of both RNA and DNA were assessed following elution, ensuring suitability for downstream RNA-seq library preparation.
RNA sequencing (RNA-seq) was performed using high-throughput next-generation sequencing technology to profile gene expression comprehensively. Total RNA was first assessed for quality, and mRNA was enriched using oligo(dT)-attached magnetic beads. The enriched mRNA was fragmented, and first- and second-strand cDNA were synthesized. Double-stranded cDNA fragments underwent end repair, addition of a single ‘A’ nucleotide at 3’ ends, and adaptor ligation. The resulting cDNA library was PCR-amplified and quality-checked according to standard protocols. For sequencing, single-stranded PCR products were circularized, and DNA nanoballs (DNBs) were generated via rolling circle amplification. DNBs were loaded onto patterned nanoarrays and sequenced using combinatorial Probe-Anchor Synthesis (cPAS) technology, generating high-quality digital transcriptomic profiles suitable for downstream analyses.

treatment_protocol: For drug treatments, cells were exposed to the following conditions:A375 cells: untreated control (DMSO),single drug treatment (2 µM I-BET726 for 72 h), seqeuntial treatment (2 µM I-BET726 for 72 h followed by 10 µM Oxaliplatin for 72 h) and withdrawal treatment (2 µM I-BET726 for 72 h followed by 72 h without drug). After treatment, cells were harvested for RNA extraction following standard protocols for RNA-seq analysis.

value: Skin

value: Human malignant melanoma cell


title: A375_IBET726_w3d_1

description:
Library name: Sample 5
S1_A375_IBET726W


title: A375_IBET726_2

description:
Library name: Sample 4
S2_A375_IBET726


title: A375_IBET726_Oxa_2

description:
Library name: Sample 8
S2_A375_726_Oxa


title: A375_DMSO_2

description:
Library name: Sample 2
S2_A375_NC


title: A375_DMSO_1

description:
Library name: Sample 1
S1_A375_NC


title: RNAseq_D4_IFNy_rux_LPS3H

first: Aleksandr

last: Gorin

address: 611 Charles E Young Dr E 570C Boyer Hall

institute: UCLA

description: Library name: RNAseq_D4_IFNy_rux_LPS3H

data_processing:
Low quality reads were trimmed (cutoff q=20) and adapter sequences were removed with cutadapt. Reads were aligned to the hg38 human genome using STAR with the following options: --outSAMunmapped Within, --outSAMtype BAM SortedByCoordinate, --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterMismatchNoverLmax 0.04, --seedSearchStartLmax 30. Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. Counts for each gene were generated using featureCounts. Counts were normalized by CPM. Analysis of gene expression was limited to protein coding gene. Pseudocount was set a 1.
Assembly: hg38
Supplementary files format and content: csv file of CPM of reads for each gene

source_name: MCSF differentiated monocyte-derived macrophages

growth_protocol: Human blood from deidentified donors was obtained from the UCLA CFAR Centralized Laboratory Support Core in accordance with UCLA IRB 11-000443. PBMC were isolated from blood by Ficoll (Cytiva 17-1440-03) density centrifugation and cryopreserved in 10%DMSO (Sigma-Aldrich, D2438) in Embryonic Stem cell FBS (Gibco, 11875-093). Monocytes were purified from PBMC using pan-monocyte isolation magnetic beads (Miltenyi 130-096-537). Monocytes were plated on 6-well tissue culture plates at a density of 1.2 x106 cells/well for 6 days in 3mL of RPMI (Gibco, 11875-093) supplemented with 10% ES fetal bovine serum (Gibco, 10439-024), penicillin-streptomycin (Corning, 30-002-CI), L-glutamine (2mM; Corning, 25-005-CI) and human M-CSF (20 ng/ml; R&D systems 216-MC-100). M-CSF was replenished to a concentration of 20ng/mL by adding 60ng M-CSF to each well (assuming that all M-CSF was depleted).

extract_protocol:
Qiagen RNEase miniprep kit
Libraries were constructed by BGI.

treatment_protocol: Macrophages were treated with human IFNy or PBS control for 8 hours. Cells were washed and subsequently cultured in either regular media or media with 1µM ruxolitinib for an additional 88 hours at which time they were restimulated with 100ng/mL LPS. Cells were collected for RNAseq on Day 0 after the 8 hour stimulation or on day 4 during (or immediately prior to) LPS restimulation.


title: Lung adventitial fibroblasts from young Dermo1cre/+;Tnfaip3f/f (Tnfaip3 CKO) mouse D2

description:
Library name: Tnfaip3 CKO D2
E235_Feature_counts_all_samples.csv

value: Lung

value: Adventitial fibroblast

value: Homeostasis


title: RNAseq_D4_IFNy_rux_LPS1H

description: Library name: RNAseq_D4_IFNy_rux_LPS1H

value: MCSF differentiated monocyte-derived macrophages


title: RNAseq_D4_IFNy_rux_LPS6H

description: Library name: RNAseq_D4_IFNy_rux_LPS6H


title: RNAseq_D4_IFNy_rux_LPS0H

description: Library name: RNAseq_D4_IFNy_rux_LPS0H


title: RNAseq_D4_PBS_rux_LPS6H

description: Library name: RNAseq_D4_PBS_rux_LPS6H


title: RNAseq_D4_IFNy_LPS12H

description: Library name: RNAseq_D4_IFNy_LPS12H


title: RNAseq_D4_PBS_rux_LPS0H

description: Library name: RNAseq_D4_PBS_rux_LPS0H


title: RNAseq_D4_PBS_rux_LPS3H

description: Library name: RNAseq_D4_PBS_rux_LPS3H


title: Lung adventitial fibroblasts from young Tnfaip3f/f mouse C3

description:
Library name: Tnfaip3 Control C3
E235_Feature_counts_all_samples.csv


title: RNAseq_D4_PBS_rux_LPS1H

description: Library name: RNAseq_D4_PBS_rux_LPS1H


title: RNAseq_D4_IFNy_LPS1H

description: Library name: RNAseq_D4_IFNy_LPS1H


title: RNAseq_D4_IFNy_LPS0H

description: Library name: RNAseq_D4_IFNy_LPS0H


title: RNAseq_D4_IFNy_LPS3H

description: Library name: RNAseq_D4_IFNy_LPS3H


title: RNAseq_D4_PBS_LPS12H

description: Library name: RNAseq_D4_PBS_LPS12H


title: A375_IBET726_w3d_2

description:
Library name: Sample 6
S2_A375_IBET726W


title: A375_IBET726_1

description:
Library name: Sample 3
S1_A375_IBET726


title: RNAseq_D4_PBS_LPS6H

description: Library name: RNAseq_D4_PBS_LPS6H


title: RNAseq_D4_PBS_LPS0H

description: Library name: RNAseq_D4_PBS_LPS0H


title: RNAseq_D0_IFNy_8H

description: Library name: RNAseq_D0_IFNy_8H


title: RNAseq_D4_PBS_LPS3H

description: Library name: RNAseq_D4_PBS_LPS3H


title: RNAseq_D4_PBS_LPS1H

description: Library name: RNAseq_D4_PBS_LPS1H


title: RNAseq_D0_unstim

description: Library name: RNAseq_D0_unstim