title: BAP1 sample11

description: Library name: BAP1 sample11 -128386


title: MapID-tRNA-seq, "-AlkB", replicate1, MDA-BA-231

status: Public on Apr 14 2025

type: SRA

city: Chestnut Hill

first: Huiqing

last: Zhou

state: Massachusetts

address: 2609 Beacon St.

department: Chemistry

country: USA

institute: Boston College

library_source: other

data_processing:
PCR dupilcates were removed by the Raw data (R2 reads of the pair-end data) were first processed with the “clumpify.sh” program in the BBMap package (BBMap-Bushnell B.-sourceforge.net/projects/bbmap/) with the option “dedupe subs=0” to remove PCR duplicates.
Adaptors were trimmed by the “cutadapt” program
Reads were aligned to the hg19 human tRNA genome, with intron removal and added CCA end, using bowtie2 aligner
Single base reads counting were performed with bam-readcount and expression are quantified by salmon
Assembly: hg19
Supplementary files format and content: .sf files containing read counts per tRNA

molecule: other

organism: Homo sapiens

source_name: MDA-MB-231 cells

extract_protocol:
RNA samples were extracted from MCF10A, MCF7 and MDA-MB-231 cells using the TRIzol reagent and standard protocol; tRNA 5s and 5.8srRNA were purified by denaturing PAGE.
Libraries were constructed using ligation-based library construction approach incoporating the evolved RT, RT-1306, in the current work.

tag: cell line

value: MDA-MB-231 cells


title: 311.Coombes.M

city: STORRS MANSFIELD

first: Grace

last: Vaziri

state: CT

address: 77 Forest Rd., Apt A

institute: University of Connecticut

library_source: transcriptomic

data_processing:
We used Trimmomatic  to trim R1 reads to 28 bp to retain the 14 bp barcode and 14 bp UMI for each sample (all genomic sequencing data were contained in the R2 read).
Following the Alithea Genomics User Guide: BRB-seq Library Preparation kit (https://25700946.fs1.hubspotusercontent-eu1.net/hubfs/25700946/MERCURIUS-BRBseq-kit-PN-10813-10814-11013-11014-User-Guide-v0.7.1.revB.pdf ) we used the “solo” mode in the STAR aligner (Dobin et al., 2013) to simultaneously align reads and produce read count matrices.
We aligned R2 reads to the wood frog genome (GenBank Accession: JAQSEC000000000.1) and used barcode and UMI data from R1 to demultiplex and deduplicate samples and read counts, respectively.
Assembly: GenBank Accession: JAQSEC000000000.1
Supplementary files format and content: matrix file with three columns, the first column denoting the identity of the transcript, the second denoting the identity of the sample, and the third denoting the counts of each transcript per sample

molecule: total RNA

organism: Lithobates sylvaticus

source_name: ventral skin

extract_protocol:
RNeasy Mini Kit (Qiagen)
Mercurius BRB-Seq (Alithea Genomics)
Tag-seq

tag: tissue

value: ventral skin


title: skMt_CTRL2_iCas9_n2

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

data_processing:
QC: FastQC ( v0.11.9 )
Filters: cutadapt ( 1.18 ), PRINSEQ-lite ( 0.20.4 )
Mapping & QC: STAR ( 2.7.6a ), samtools ( 0.1.18 )
Counting: HTSeq-count ( 0.12.4 ), DEG R (4.3) DESeq2
Assembly: EnsEMBL Human GRCh97.87
Supplementary files format and content: Differential gene expression ( RNAseq82_hipsc_DE.xlsx )

molecule: polyA RNA

source_name: hIPSC derived Myotubes

growth_protocol: Myoblasts (SkMb) were thawed on collagen I-coated plates in skeletal myoblast medium (#SKM02, AMSBIO, United Kingdom) and incubated at confluence with skeletal muscle differentiation medium (#SKM03, AMSBIO, United Kingdom) for three supplementary days to obtain myotubes (skMt).

extract_protocol:
Human skMt were lysed with RLT Plus buffer (#1030963, Qiagen, Germany). Mouse triceps biopsies were lysed with bead lysis tubes (#740814.50, Macherey-Nagel, Germany) using Qiazol (#79306, Qiagen, The Netherlands) and chloroform (#102444, Sigma-Aldrich, USA) reagents. Total RNA was isolated using an RNeasy Plus Mini extraction kit (#74134, Qiagen, Germany) according to the manufacturer’s instructions. DNase I digestion (Invitrogen, USA) was performed to degrade DNA in the sample.  RNA levels and quality were checked using the NanoDrop® spectrophotometer (ThermoFisher Scientific, United States).
For each sample, 100 ng of total RNA was used to perform the QuantSeq 3' mRNA-Seq Library Prep FWD for Illumina (Lexogene, Vienna, Austria) resulting in NGS libraries which originate from the 3' end of polyadenylated RNA. Briefly, library generation was started by oligo(dT) priming with primers. After first strand synthesis, the RNA was removed before the second strand synthesis was initiated by random primers. Libraries were PCR amplified and barcoded in 17 cycles and were quantified using Agilent High Sensitivity DNA kit (Agilent). 2nM of pooled libraries were denatured and 1.8pM was used for cluster generation before single-end sequencing on an Illumina Nextseq550 (Illumina, US).
strategy: 3’-seq

treatment_protocol: Myotubes (skMt) were then incubated with glucose-free DMEM (#11966-025, ThermoFisher Scientific, United States) supplemented with 10% Fetal Bovine Serum (#F7524, Sigma-Aldrich, United States) for 2,5 supplementary days.

tag: cell type

value: hIPSC derived Myotubes

tag: replicate

tag: genotype

value: WT


title: skMt_CTRL2_iCas9_n1


title: 66.ORI.M


title: MapID-tRNA-seq, "+AlkB", replicate2, MCF10A

source_name: MCF10A cells

value: MCF10A cells


title: BAP1 sample10

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: Library name: BAP1 sample10 -293970

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The RNA sequencing reads were aligned to the Gencode GRCh38.primary_assembly reference genome using STAR29 (v2.7.7a).
Gene-level quantification was conducted with HTSeq30 (v0.11.0) using Gencode V39 primary assembly annotations.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw values for each Sample.

source_name: FFPE

growth_protocol: Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue samples using the Maxwell RSC RNA FFPE Kit (Promega, Madison, WI, USA) on the automated Maxwell RSC 48 instrument (Promega)

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an P2-100 flow cell.

treatment_protocol: untreated

value: FFPE


title: skMt_CTRL3_i90_n3


title: BAP1 sample9

description: Library name: BAP1 sample9 -333462


title: BAP1 sample8

description: Library name: BAP1 sample8 -190152


title: 70.ORI.M


title: BAP1 sample13

description: Library name: BAP1 sample13 -293582


title: MapID-tRNA-seq, "-AlkB", replicate2, MCF10A


title: MapID-tRNA-seq, "+AlkB", replicate1, MCF10A


title: skMt_CTRL3_i90_n1


title: skMt_CTRL3_i90_n2


title: H3K27me3 loss sample1

description: Library name: H3K27me3 loss sample1 -293348

value: H3K27me3 loss


title: MapID-tRNA-seq, "+AlkB", replicate2

description:
C6
tRNA

data_processing:
PCR duplicates were removed by the Raw data (R2 reads of the pair-end data) were first processed with the “clumpify.sh” program in the BBMap package (BBMap-Bushnell B.-sourceforge.net/projects/bbmap/) with the option “dedupe subs=0” to remove PCR duplicates.
Adaptors were trimmed by the “cutadapt” program.
Reads were aligned to the hg19 human tRNA genome, with intron removal and added CCA end, using bowtie2 aligner.
Single base reads counting were performed with bam-readcount and expression are quantified by salmon.
Assembly: hg19
Supplementary files format and content: .sf files containing read counts and TPMs per tRNA.

extract_protocol:
RNA samples were extracted from HEK-293T cells using the TRIzol reagent and standard protocol; tRNA was purified by denaturing PAGE.
Libraries were constructed using ligation-based library construction approach incorporating the evolved RT, RT-1306, in the current work.

tag: treatment

value: +AlkB


title: BAP1 sample6

description: Library name: BAP1 sample6 -333472


title: 91.Barr.H


title: 295.Coombes.Pre


title: H3K27me3 loss sample4

description: Library name: H3K27me3 loss sample4 -293366


title: skMt_CTRL1_Pci1426_n2


title: MapID-tRNA-seq, "-AlkB", replicate1, MCF10A


title: BAP1 sample5

description: Library name: BAP1 sample5 -293964


title: 275.Coombes.H


title: skMt_CTRL1_Pci1426_n1


title: BAP1 sample4

description: Library name: BAP1 sample4 -87256


title: MapID-tRNA-seq, "+AlkB", replicate1

description:
C5
tRNA


title: skMt_CTRL1_Pci1426_n3


title: MapID-tRNA-seq, "-AlkB", replicate2

description:
C2
tRNA

value: -AlkB


title: 113.ORI.Pre


title: MSK-Leuk1_SKA1 rep3

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Department of Medicine I

country: Austria

institute: Medical University of Vienna

data_processing:
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long unique dual indices.
Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N’s and trim bases with a quality of less than 30 from the 3’ ends of the reads.
On average, 5 million reads were left after this procedure.
Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Raw reads per gene were counted by STAR. Differential gene expression was calculated using DESeq2 version 1.22.2.
Assembly: GRCh38 human reference genome downloaded from NCBI (2018-09-27)
Supplementary files format and content: Text file, ";"-delimited. Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (cat. No. 74104, QIAGEN)
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3’ FWD protocol version 2 with unique dual indices (Lexogen). 15 PCR cycles were used for library prep, as determined by qPCR according to the library prep manual. Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen).

tag: subline

value: SKA1 overexpression


title: BAP1 sample3

description: Library name: BAP1 sample3 -293412


title: 318.Victory.M


title: 314.Coombes.H


title: BAP1 sample7

description: Library name: BAP1 sample7 -85198


title: MSK-Leuk1_SKA1 rep2


title: MSK-Leuk1_SKA1 rep1


title: Muscle, Summer, Individual 1

city: Santiago

first: Rodrigo

last: Maldonado

address: Avenida Pedro de Valdivia 1509

country: Chile

institute: Universidad Finis Terrae

description: Library name: summer_muscle_1

data_processing:
Raw sequencing reads underwent quality control using FastQC and trimming with TrimGalore (v0.6.6; parameters: -q 30 --retain_unpaired --phred33 --illumina) to remove low-quality bases and adapter sequences. High-quality reads were aligned to the O. ascotanensis reference genome using HISAT2 (v2.2.1; parameters: --dta-cufflinks), and coordinate-sorted BAM files were generated using samtools (v1.10).
Assembly: O. ascotanensis reference genome
Supplementary files format and content: csv files include raw counts for each Sample

organism: Orestias ascotanensis

source_name: muscle

growth_protocol: Specimens were collected from the Ascotan Salt Pan (21°29'46.5"S 68°15'26.3"W) at an elevation of 3,740 meters above sea level in July 2019 (n=7) and January 2020 (n=7) using a fishing net. Euthanasia was performed by administering an overdose of tricaine methanesulphonate (MS-222, 500 mg L−1; Sigma-Aldrich). Tissue samples from gills, skin, and muscle were harvested on-site. Each tissue sample was individually preserved in RNAlater (Invitrogen) immediately after dissection to stabilize and protect RNA. The samples were transported on ice to the laboratory and subsequently stored at -80°C until RNA extraction.

extract_protocol:
Total RNA was extracted from three different tissues (gills, skin, and muscle) samples obtained from each of the 14 individuals captured during either summer (n=7) or winter (n=7), using TRIzol (Invitrogen) following the manufacturer's protocol. The concentration and quality of the extracted RNA were assessed using a Qubit fluorometer (Invitrogen) and a Bioanalyzer 2100 (Agilent), determining the integrity and purity of each sample.
Unstranded poly-A libraries were prepared from each tissue sample using the Illumina TruSeq RNA sample preparation kit (Illumina) according to the manufacturer’s instructions. The prepared RNA samples were sent to Quick Biology (Pasadena, CA, USA) for sequencing, where they were processed on the Illumina HiSeq 4000 platform to generate 150 bp paired-end reads

value: muscle

value: Summer

tag: individual number


title: Muscle, Summer, Individual 2

description: Library name: summer_muscle_2


title: 85.Barr.H


title: BAP1 sample2

description: Library name: BAP1 sample2 -293414


title: BAP1 sample1

description: Library name: BAP1 sample1 -276764


title: 248.Woodstock.M


title: skMt_GSDIII_Patient1_GM0576_n1

value: GSDIII


title: MSK-Leuk1_vec rep3

value: empty vector control


title: NF2 sample9

description: Library name: NF2 sample9 -107146


title: Muscle, Winter, Individual 4

description: Library name: winter_muscle_4


title: 17.CC.H


title: Muscle, Winter, Individual 5

description: Library name: winter_muscle_5

value: Winter


title: 272.Victory.Pre


title: NF2 sample8

description: Library name: NF2 sample8 -174028


title: Muscle, Winter, Individual 6

description: Library name: winter_muscle_6


title: NF2 sample7

description: Library name: NF2 sample7 -174006


title: MapID-tRNA-seq, "-AlkB", replicate1

description:
C1
tRNA


title: NF2 sample6

description: Library name: NF2 sample6 -174004


title: Muscle, Winter, Individual 7

description: Library name: winter_muscle_7


title: NF2 sample5

description: Library name: NF2 sample5 -410668


title: CAL-33_SKA1 rep3


title: 69.ORI.H


title: 143.Barr.Pre


title: CAL-33_SKA1 rep2


title: Gills, Summer, Individual 1

description: Library name: summer_gills_1

source_name: gills

value: gills


title: NF2 sample4

description: Library name: NF2 sample4 -410666


title: CAL-33_SKA1 rep1


title: Gills, Summer, Individual 2

description: Library name: summer_gills_2


title: NF2 sample3

description: Library name: NF2 sample3 -410664


title: 47.Burke.M


title: Gills, Summer, Individual 3

description: Library name: summer_gills_3


title: MSK-Leuk1_vec rep2


title: Gills, Summer, Individual 4

description: Library name: summer_gills_4


title: NF2 sample2

description: Library name: NF2 sample2 -410662


title: 140.Barr.Pre


title: CAL-33_vec rep3


title: MSK-Leuk1_vec rep1


title: NF2 sample1

description: Library name: NF2 sample1 -410660


title: Gills, Summer, Individual 5

description: Library name: summer_gills_5


title: 128.CC.Pre


title: CAL-33_SKA1 rep4


title: 324.Victory.M


title: 264.Woodstock.Pre


title: 202.Woodstock.H


title: CAL-33_vec rep2


title: Gills, Summer, Individual 6

description: Library name: summer_gills_6


title: DM_2

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Library name: Sample 4

library_source: transcriptomic single cell

data_processing:
Fastq files were generated using 10X Cell Ranger (version 7.0). Starting with raw Illumina BCL files from the sequencing output, the cellranger mkfastq command with default parameters was used to generate fastq files.
Fastq files were aligned using 10X Cell Ranger (version 7.0). The cellranger count command with default parameters was used to align the expression reads to the GRCh38 build of the human transcriptome (refdata-gex-GRCh38-2020-A) and generate a gene expression count matrix.
Assembly: Human reference, GRCh38 (Ensembl 98)
Supplementary files format and content: *_barcodes.tsv.gz, *_features.tsv.gz, *_matrix.mtx.gz for all samples. Filtered counts of sequencing reads

extract_protocol:
Nuclei isolation was completed using the 10x Chromium Nuclei Isolation Kit (PN-1000494, 10x Genomics)
RNA libraries were prepared using the 10x Genomics Chromium Nuclei Isolation Kit Protocol for Single Cell 3’ Gene Expression (RevA)

treatment_protocol: hCO were matured using the SF or DM protocol. At the conclusion of the experiment, media was aspirated and hCO were washed with ice cold PBS-. Intact hCO were pooled with up to 70 hCO per sample (n = 2 per maturation protocol). All PBS- was removed and hCO were snap frozen in liquid nitrogen and stored at -80oC.


title: CAL-33_vec rep1


title: 320.Victory.Pre


title: DM_1

description: Library name: Sample 3


title: BPTES, rep6

city: Boston

first: Liam

last: Kelley

state: MA

address: 260 Longwood Ave

institute: Harvard Medical School

data_processing:
Salmon v1.4.0
Sequence reads were not trimmed prior to Salmon pseudoalignment
Salmon index generated using k-mers of length 31
Salmon parameters: seqBias, useVBOpt, validateMappings
Pseudo-aligned results from Salmon were imported into R using tximport and processed with DESeq2
Imported counts were normalized using DESeq2's median of ratios method
Assembly: Ensembl 103
Supplementary files format and content: comma-separated file contains normalized transcript counts for each sample as generated by DESeq2

growth_protocol: Primary human fibroblasts were cultured in fibroblast basal media (ATCC) supplemented with fibroblast growth kit low serum (ATCC), which includes FBS, ascorbic acid, recombinant human Insulin, recombinant human FGF-b, hydrocortisone, and L-glutamine

extract_protocol:
RNA was extracted using TRIzol reagent and a Zymo RNA miniprep kit. 750 ng of RNA was used for library preparation for each sample.
RNA libraries for RNA-seq were generated using the High Throughput TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Cells were treated with relevant drug at 200x concentration in DMSO (with exception of metformin, which was at 50x concentration) for 6 hours prior to RNA extraction

value: Primary human dermal fibroblasts

value: 1 microM BPTES


title: CAL-33_vec rep4


title: Gills, Summer, Individual 7

description: Library name: summer_gills_7


title: BPTES, rep5


title: BPTES, rep4


title: 97.Barr.H

value: ventral skin


title: 321.Victory.H


title: 112.ORI.Pre


title: BPTES, rep3


title: BPTES, rep2


title: 127.CC.Pre


title: Gills, Winter, Individual 4

description: Library name: winter_gills_4


title: 73.ORI.H


title: 100.Barr.M


title: Gills, Winter, Individual 3

description: Library name: winter_gills_3


title: Gills, Winter, Individual 6

description: Library name: winter_gills_6


title: Tunicamycin, rep6

value: 1 microg/mL tunicamycin


title: Gills, Winter, Individual 5

description: Library name: winter_gills_5


title: Tunicamycin, rep5


title: 208.Woodstock.Pre


title: 263.Woodstock.H


title: Tunicamycin, rep4


title: Skin, Summer, Individual 1

description: Library name: summer_skin_1

source_name: skin

value: skin


title: Muscle, Summer, Individual 3

description: Library name: summer_muscle_3


title: Tunicamycin, rep3


title: Gills, Winter, Individual 1

description: Library name: winter_gills_1


title: tum 30

city: Puerto Montt

first: Constanza

last: Marin Marquez

address: Lago Panguipulli 1390

department: Oral Pathology

institute: Universidad San Sebastián

description: Sample 12

data_processing:
The data processing was performed with cloud-based Galaxy Europe. FASTQ files were subjected to FASTQC and Cut adapt tools, for the quality control and the trimming of the low-quality sequences, respectively
The alignment was performed using HISAT2, with the Human Genome Version GRCh38 as a reference
The feature Counts tool was used to count the number of reads per annotated gene and DESeq2 for the Differential Gene Expression analysis .
For the visualisation of the results, heatmaps of the DEGs among different phenotypes were created with heatmap2 with Euclidean distance method and complete clustering method. A significance threshold of p-value <0.05 and a fold change of 1.2 (1.2≤FC≤-1.2) were used.
The unsupervised hierarchical analysis was conducted using Cluster 3.0 for Windows between the tumour samples and visualised using Java TreeView 1.2.0 for Windows.
Assembly: Human Genome Version GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (with their library name)
Supplementary files format and content: In addition, includes the gene symbol, name, refseq, ensembl, pval, FDR and log2FC

source_name: mandibule

growth_protocol: not applicable

extract_protocol:
Thirteen tumour samples stored in RNAlaterTM solution (Invitrogen, Thermo Fisher Scientific) were provided by Dr Akinyele Adisa from the Department of Oral and Maxillofacial Surgery and Oral Pathology, College of Medicine, University of Ibadan, Nigeria. These were selected after histopathological re-evaluation by pathologists (KH and CM) and confirming that over 90% of the tissue represented tumour. Total RNA was extracted from tumours by manual macro-dissection using RNeasy Mini Kit (QIAGEN) following manufacturer’s instructions and quantified using a NanoDrop spectrophotometer. A total of  25µl of RNA from each tumour were sent to Novogene (Cambridge, UK) to perform RNA- sequencing.
The company performed a quality control of the samples firstly through an Agarose gel electrophoresis to test the RNA degradation and potential contamination; and secondly with Agilent 2100 to check the RNA integrity and quantitation.  First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. Then the quality control of the library consisted of three steps (Qubit, Agilent 2100 and qPCR). The qualified libraries were fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

treatment_protocol: not applicable

value: ameloblastoma, conventional

tag: Sex

value: Male

tag: age


title: Skin, Summer, Individual 2

description: Library name: summer_skin_2


title: Tunicamycin, rep2


title: tum 29

description: Sample 11

value: Female


title: R292C_Polg_4

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Library name: Sample6

data_processing:
Partek Flow STAR Aligner 2.7.8a to align FASTQ file data
Partek Flow Quantify to annotation model (Partek E/M) to generate raw counts file
Partek Flow Filter features - 1.0 and Normalization
Assembly: GRCm39 - mm39
Supplementary files format and content: WT_PolgR292C_lung_normalized_counts.txt

organism: Mus musculus

source_name: lung

growth_protocol: Animals were housed at The Jackson Laboratory and experimental protocols were reviewed and approved by the institutional Animal Care and Use Committees (ACUC).

extract_protocol:
Frozen lung tissue was crushed into powder in liquid nitrogen, then total RNA was extracted using a Direct-Zol RNA miniprep kit (Zymo Research, R2072).
Stranded libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq X Plus using the 10B Reagent Kit.

treatment_protocol: WT and Polg R292C/R292C mice (3 females per genotype, 3 months old) on a C57BL/6N background were challenged with 1x10^6 GFP-tagged Pseudomonas aeruginosa strain PAO1 in 25 uL volume of PBS by intratrachael instillation under anesthesia. 6 hours post instillation, mice were sacraficed and lungs were isolated and snap frozen in liquid nitrogen.

value: lung

value: Polg R292C/R292C


title: Gills, Winter, Individual 2

description: Library name: winter_gills_2


title: Tunicamycin, rep1


title: R292C_Polg_1

description: Library name: Sample5


title: Muscle, Summer, Individual 4

description: Library name: summer_muscle_4


title: BPTES, rep1


title: tum 26

description: Sample 10


title: Skin, Summer, Individual 3

description: Library name: summer_skin_3


title: FK866, rep6


title: Skin, Summer, Individual 4

description: Library name: summer_skin_4


title: R292C_WT_4

description: Library name: Sample3

value: WT


title: Gills, Winter, Individual 7

description: Library name: winter_gills_7


title: Skin, Summer, Individual 5

description: Library name: summer_skin_5


title: tum 17

description: Sample 8


title: FK866, rep5


title: tum 19

description: Sample 9


title: R292C_WT_3

description: Library name: Sample2


title: Skin, Summer, Individual 6

description: Library name: summer_skin_6


title: FK866, rep4


title: 15.CC.H


title: FK866, rep3


title: Skin, Summer, Individual 7

description: Library name: summer_skin_7


title: R292C_WT_2

description: Library name: Sample1


title: FK866, rep2


title: tum 12

description: Sample 5


title: Skin, Winter, Individual 1

description: Library name: winter_skin_1


title: D257A_Polg_4

description:
Library name: Sample8
D257A_Polg_4

data_processing:
Partek Flow STAR Aligner 2.7.8a to align FASTQ file data
Partek Flow Quantify to annotation model (Partek E/M) to generate raw counts file
Partek Flow Filter features - 1.0 and Normalization
Assembly: GRCm39 - mm39
Supplementary files format and content: WT_PolgD257A_lung_normalized_counts.txt

treatment_protocol: WT and Polg D257A/D257A mice (4 females per genotype, 12 months old) on a C57BL/6J background were challenged with 1x10^5 GFP-tagged Pseudomonas aeruginosa strain PAO1 in 25 uL volume of PBS by intratrachael instillation under anesthesia. 6 hours post instillation, mice were sacraficed and lungs were isolated and snap frozen in liquid nitrogen.

value: Polg D257A/D257A


title: FK866, rep1


title: R292C_Polg_0

description: Library name: Sample4


title: tum 11

description: Sample 4


title: D257A_Polg_2

description:
Library name: Sample6
D257A_Polg_2


title: Skin, Winter, Individual 2

description: Library name: winter_skin_2


title: tum 10

description: Sample 3


title: Skin, Winter, Individual 3

description: Library name: winter_skin_3


title: Etomoxir, rep6

value: 10 microM etomoxir


title: tum 9

description: Sample 2


title: Etomoxir, rep5


title: D257A_WT_4

description:
Library name: Sample4
D257A_WT_4


title: Skin, Winter, Individual 4

description: Library name: winter_skin_4


title: D257A_Polg_1

description:
Library name: Sample5
D257A_Polg_1


title: Etomoxir, rep4


title: Skin, Winter, Individual 5

description: Library name: winter_skin_5


title: tum 8

description: Sample 1

value: ameloblastoma, unicystic

value: 18 years old (yo)


title: tum 16

description: Sample 7


title: D8_TET2TRAC_566

city: Philadelphia

first: Gregory

last: Chen

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Human_Tcell_RNA-Seq_ReadCounts.tsv
Human_Tcell_RNA-Seq_TPM.tsv

data_processing:
RNA-Seq alignment with STAR v 2.7.10a
RNA quantification with cufflinks v2.2.1
Read count quantification with Rsubread in R v4.0.2
ATAC-Seq alignment with bwa-mem
ATAC-Seq peak calling with MACS2
Assembly: mm39
Supplementary files format and content: Tab-delimited text file. First column is MGI Gene Symbol or Peak coordinate. Subsequent columns are sample names. The first row is a header. Subsequent rows represent a gene or peak

source_name: T cells

growth_protocol: Recipient mice were intravenously infected with 4 × 10^6 PFU of LCMV clone 13

extract_protocol:
RNA was isolated using the Qiagen rNeasy Micro Kit
cDNA libraries were generated following the manufacturer’s instructions with the SMART-Seq v4 Ultra Low Input RNA Kit and Nextera XT DNA library kit

treatment_protocol: WT and TET2KO P14 cells were mixed at a 1:1 ratio, and a total of 500 P14 cells (250 WT and 250 TET2KO) were adoptively transferred intravenously into recipient mice of a third congenic background.

value: T cells

value: T cells in human CAR T experiment


title: tum 13

description: Sample 6


title: D257A_WT_3

description:
Library name: Sample3
D257A_WT_3


title: Muscle, Summer, Individual 5

description: Library name: summer_muscle_5

value: muscle

value: Summer


title: Etomoxir, rep3

value: Primary human dermal fibroblasts


title: Etomoxir, rep2


title: D257A_WT_1

description:
Library name: Sample2
D257A_WT_1


title: Skin, Winter, Individual 6

description: Library name: winter_skin_6

value: Winter


title: D5_TET2TRAC_365


title: D257A_Polg_3

description:
Library name: Sample7
D257A_Polg_3


title: D257A_WT_0

description:
Library name: Sample1
D257A_WT_0


title: Skin, Winter, Individual 7

description: Library name: winter_skin_7

value: skin


title: Etomoxir, rep1


title: D4_TRAC_566

value: TRAC


title: Metformin, rep6

value: 2 mM metformin


title: Muscle, Summer, Individual 6

description: Library name: summer_muscle_6


title: Metformin, rep5


title: C2C12 Cells, untreated, Day 0, replicate 3

city: Klosterneuburg

first: Kenneth

middle: David

last: Kuhn

address: Am Campus

institute: Institute of Science and Technology Austria

description: Library name: Day0_WT_r3

data_processing:
Raw reads were mapped with RNAStar and mapped using the featureCounts tool
Assembly: mm10
Supplementary files format and content: Tab files contain counts for each sample, normalized with other samples within its timepoints (WT cells are normalized separately from other Day 0 samples)

growth_protocol: C2C12 cells were maintained in DMEM with 20% FBS and split every 48 hours, never being allowed to exceed 70% confluency. These cells were treated on two consecutive days with siRNA targeting either PSME3 or a scrambled sequence. These cells were either collected 48 hours thereafter (cycling) or plated at full confluency. The following day they were either collected (day 0) or had their media exchanged for differentiation media (DMEM + 2% horse serum) and allowed to differentiate for 48 hours before collection (day 2). Untreated (WT) cells were similarly collected after 24 hours at confluency, but were not treated with siRNA.

extract_protocol:
Cells were dissolved in TRIzol reagent. RNA was purified using the RNeasy Mini Kit from Qiagen
mRNA library preparation (polyA enrichment) and sequencing were done at Novogene (Cambridge, UK)

value: Myoblast

value: Untreated

tag: batch


title: D3_TRAC_539


title: Muscle, Summer, Individual 7

description: Library name: summer_muscle_7


title: C2C12 Cells, untreated, Day 0, replicate 2

description: Library name: Day0_WT_r2


title: D2_TRAC_502


title: Muscle, Winter, Individual 1

description: Library name: winter_muscle_1


title: C2C12 Cells, untreated, Day 0, replicate 1

description: Library name: Day0_WT_r1


title: C2C12 Cells, siScrambled, Day 2, replicate 3

description: Library name: Day2_siScr_r3

value: Scrambled siRNA


title: Metformin, rep3


title: D1_TRAC_365


title: Muscle, Winter, Individual 2

description: Library name: winter_muscle_2


title: Metformin, rep2


title: C2C12 Cells, siScrambled, Day 2, replicate 2

description: Library name: Day2_siScr_r2


title: C2C12 Cells, siScrambled, Day 2, replicate 1

description: Library name: Day2_siScr_r1


title: Muscle, Winter, Individual 3

description: Library name: winter_muscle_3


title: D6_TET2TRAC_502


title: HS449

city: San Francisco

first: Aartik

last: Sarma

state: CA

address: 513 Parnassus Ave

institute: University of California, San Francisco

data_processing:
Transcripts were aligned in Cell Ranger and filtered count matrices were imported into a Seurat object
Cells were filtered to have at least 300 counts, no more than 30,000 counts, and less than 10% mitochondrial genes
Assembly: human protein coding genes (ENSEMBL v. 99), cytosolic and mitochondrial ribosomal RNA sequences, and the sequences of ERCC RNA standards
Supplementary files format and content: a Seurat object (.Rda)

source_name: tracheal aspirate

extract_protocol:
TA cells were isolated and selected for expression of CD45
V(D)J v1.1 kit (10X genomics) aand processed on a 10x Genomics Chip A without multiplexing

value: tracheal aspirate

tag: phenotype

value: HypoARDS


title: Metformin, rep1


title: HS447


title: C2C12 Cells, siPSME3, Day 2, replicate 3

description: Library name: Day2_siE3_r3

value: PSME3 siRNA


title: HS408

value: HyperARDS


title: WT

city: ShanTou

first: juan

middle: juan

last: Luo

address: Xinling street 22

country: China

institute: ShanTou University

description: Library name: WT

data_processing:
Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters.
Assembly: GRCz11
Supplementary files format and content: Mask files, matrix files and image files.

organism: Danio rerio

source_name: Brain

extract_protocol:
Tissue sections were adhered to the Stereo-seq chip (generated by BGI, China) surface and incubated at 37℃ for 3 minutes. Then, the sections were fixed in methanol and incubated for 40 minutes at -20℃ before Stereo-seq library preparation. Where indicated, the same sections were stained with nucleic acid dye (Thermo fisher, Q10212) and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. After washed with 0.1x SSC buffer (Thermo, AM9770) supplemented with 0.05 U/ml RNase inhibitor (NEB, M0314L), tissue sections placed on the chip were permeabilized using 0.1% pepsin (Sigma, P7000) in 0.01 M HCl buffer, incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer (Thermo, AM9770) supplemented with 0.05 U/ml RNase inhibitor (NEB, M0314L). RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II (Invitrogen, 18064-014, 10 U/ml reverse transcriptase, 1 mM dNTPs, 1 M betaine solution PCR reagent, 7.5 mM MgCl2, 5 mM DTT, 2 U/ml RNase inhibitor, 2.5 mM Stereo-seq-TSO and 1x First-Strand buffer). After reverse transcription, tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer (10 mM Tris-HCl, 25 mM EDTA, 100 mM NaCl, 0.5% SDS) at 55℃ for 10 minutes. cDNA-containing chips were then subjected to Prepare cDNA Release Mix (cDNA Release Enzyme, cDNA Release buffer) treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads (0.8×).
The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit (Thermo, Q32854). A total of 20 ng of DNA were then fragmented with in-house Tn5 transposase at 55℃ for 10 minutes, after which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes after fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product, 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo-seq-Library-F primer, 0.3 mM Stereo-seq-Library-R primer in a total volume of 100 ml with the addition of nuclease-free H2O. The reaction was then run as: 1 cycle of 95℃ 5 minutes, 13 cycles of 98℃ 20 seconds, 58℃ 20 seconds and 72℃ 30 seconds, and 1 cycle of 72℃ 5 minutes. PCR products were purified using the AMPure XP Beads (0.63 and 0.153), used for DNB generation and finally sequenced on MGI DNBSEQ-Tx sequencer.

value: Brain


title: AD5

description: Library name: AD5


title: Antimycin A, rep6

value: 100 nM antimycin A


title: C2C12 Cells, siPSME3, Day 2, replicate 2

description: Library name: Day2_siE3_r2


title: HS383


title: AD4

description: Library name: AD4


title: Antimycin A, rep5


title: C2C12 Cells, siPSME3, Day 2, replicate 1

description: Library name: Day2_siE3_r1


title: HS358


title: C2C12 Cells, siScrambled, Day 0, replicate 3

description: Library name: Day0_siScr_r3


title: Metformin, rep4


title: Antimycin A, rep4


title: Antimycin A, rep3


title: Glucose 50 mM, Replicate 3

city: Gainesville

first: Alejandro

last: Riveros Walker

state: Fl

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

data_processing:
Quality control (FASTQC)
Trimming (Cutadapt)
Mapping (bwa-mem)
Gene counts (htseq-counts)
Assembly: Streptococcus mutans UA159 chromosome, complete genome, NC_004350.2
Supplementary files format and content: Text files

organism: Streptococcus mutans

growth_protocol: S. mutans strain UA159 was cultivated to early exponential phase (OD600 = 0.4) in a chemically defined medium FMC supplemented with 20 mM glucose.

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the Ribo-Zero Plus Kit
https://www.seqcenter.com/service/illumina-rna-sequencing/
SeqCenter relies on Illumina’s stranded technology to translate strand-specificity through library preparation and sequencing. Briefly, stranded information is captured through the use of dUTPs (instead of dTTPs) in the second strand synthesis step of cDNA synthesis. After adaptor ligation, second strand amplification will be suppressed in the final library amplification due to polymerase stalling at the location of the incorporated dUTPs. Due to directionality of sequencing adaptors, Read 1 (R1) will always map to the antisense strand and Read 2 (R2) will always map to the sense strand.

treatment_protocol: Bacteria were harvested by centrifugation and resuspended in fresh FMC containing 50 mM fructose, 50 mM glucose, or 5 mM methylglyoxal. An equal portion of the culture was kept in the original FMC-glucose medium as control. All samples were returned to incubation for 30 min before being harvested for RNA extraction.


title: C2C12 Cells, siScrambled, Day 0, replicate 2

description: Library name: Day0_siScr_r2


title: A02596F2-E20

city: Cincinnati

first: Guolun

last: Wang

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The raw sequencing reads were mapped to chicken reference genomeGRC7b using Stereo-seq Analysis Workflow (SAW_7.1)
The .cellbin.gef output file from SAW pipeline was further normalized, using Stereopy pipeline with default parameters
Assembly: GRC7b
Supplementary files format and content: A02596F2.adjusted.cellbin.gef: direct alignment cellbin output
Supplementary files format and content: A02596F2.adjusted.cell.cluster.h5ad: processed cellbin data
Supplementary files format and content: A02596F2.barcodeToPos.h5: mask file
Supplementary files format and content: A02596F2_SC_20240124_152343_3.0.2.ipr: image processing data
Supplementary files format and content: A02596F2_SC_20240124_152343_3.0.2.tar.gz: compressed image data
Library strategy: Spatial transcriptomics

organism: Gallus gallus

source_name: E20 lung

extract_protocol:
E20 chicken lungs stored at -80°C until used for a Stereo-seq experiment. Cryo-sections were cut at the thickness of 10 μm and mounted on Stereo-seq permeabilization chips (210CP118) or transcriptomics chips (210CT114).
Spatial transcriptome sequencing library was prepared using the library preparation kit (111KL114, STOmics) according to manufacture’s instruction.

value: E20 lung

value: Leghorn


title: C2C12 Cells, siScrambled, Day 0, replicate 1

description: Library name: Day0_siScr_r1


title: Antimycin A, rep2


title: HS21


title: Antimycin A, rep1


title: Rotenone, rep6

value: 100 nM rotenone


title: C2C12 Cells, siPSME3, Day 0, replicate 3

description: Library name: Day0_siE3_r3


title: TA575

data_processing:
Sequencing reads were pseudo-aligned with kallisto (v. 0.46.1; including bias correction)
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport, with the scaledTPM method
Assembly: human protein coding genes (ENSEMBL v. 99), cytosolic and mitochondrial ribosomal RNA sequences, and the sequences of ERCC RNA standards
Supplementary files format and content: cohort1.rnaseq.csv

extract_protocol:
RNA was extracted using Zymo Pathogen Magbead Kit followed by DNase treatment. human cytosolic and mitochondrial ribosomal RNA was then depleted using Qiagen FastSelect
RNA was then fragmented and underwent library preparation using the NEBNext Ultra II RNASeq Kit (New England Biolabs)


title: Glucose 50 mM, Replicate 1


title: TA565


title: Glucose 50 mM, Replicate 2


title: C2C12 Cells, siPSME3, Day 0, replicate 2

description: Library name: Day0_siE3_r2


title: Rotenone, rep4

value: Primary human dermal fibroblasts


title: TA563

value: Control


title: C2C12 Cells, siPSME3, Day 0, replicate 1

description: Library name: Day0_siE3_r1


title: Rotenone, rep3


title: AD3

description: Library name: AD3


title: C2C12 Cells, siScrambled, Cycling, replicate 3

description: Library name: Cycling_siScr_r3


title: Rotenone, rep2


title: C2C12 Cells, siScrambled, Cycling, replicate 2

description: Library name: Cycling_siScr_r2


title: HS347


title: TA551


title: Fructose 50 mM, Replicate 1


title: TA555


title: Fructose 50 mM, Replicate 3


title: TA543


title: C2C12 Cells, siScrambled, Cycling, replicate 1

description: Library name: Cycling_siScr_r1


title: Methylglyoxal 5 mM, Replicate 3


title: HS16


title: C2C12 Cells, siPSME3, Cycling, replicate 3

description: Library name: Cycling_siE3_r3


title: Methylglyoxal 5 mM, Replicate 2


title: DNP, rep6

value: 100 microM DNP


title: Rotenone, rep1


title: Rotenone, rep5


title: C2C12 Cells, siPSME3, Cycling, replicate 2

description: Library name: Cycling_siE3_r2


title: Methylglyoxal 5 mM, Replicate 1


title: TA540


title: DNP, rep5


title: Fructose 50 mM, Replicate 2


title: Control, Glucose 20 mM, Replicate 3


title: TA539


title: Control, Glucose 20 mM, Replicate 2


title: DNP, rep4


title: C2C12 Cells, siPSME3, Cycling, replicate 1

description: Library name: Cycling_siE3_r1


title: TA530


title: DNP, rep3


title: Control, Glucose 20 mM, Replicate 1


title: 4T1-BOTOX-replicate4

city: Mobile, AL

first: Simon

last: Grelet

state: Alabama

address: 1660 Spring Hill Ave - USA Drive North,

institute: University of South Alabama - Mitchell Cancer Institute

description: Library name: Botox4

data_processing:
Reads were trimmed for quality control to remove low-quality bases and adapter sequences. Samples failing QA/QC thresholds (based on read quality, length, or count) were excluded.
Quality-trimmed reads were aligned to the Mus musculus mm39 genome using Bowtie2 (2.2.5) with seed length 22, mismatch penalty N 0, and gapped alignment penalty rdg 3,2, in paired-end mode with a 500 bp fragment length.
SAM and BAM files were processed with SAMtools and Sambamba, and alignment quality was assessed using SAMtools idxstats, retaining only reads aligning to mm39.
Read counts were normalized with DESeq2's median-of-ratios method, and genes with expression below 1.0 (geometric mean) were filtered out.
Gene Set ANOVA was performed on gene sets after excluding low expression (geometric mean < 1.0) on sets containing between 2 and 50 genes. ANOVA with a log-normal model and AICc criterion was applied, with FDR correction for multiple comparisons. KEGG pathways were analyzed to identify differentially regulated gene sets.
Assembly: mm39
Supplementary files format and content: .txt file of the aligned reads in TPM for each condition
Supplementary files format and content: .txt file of the KEGG analysis output

source_name: 4T1 in MFP

growth_protocol: The mammary fat pads of syngeneic BALB/c mice were pre-treated with either saline (control) or botox to achieve chemical denervation. Seven days after the respective injections, the mammary fat pads were injected with mCherry-expressing 4T1 triple-negative breast cancer cells. Following tumor onset, the mCherry-positive cells were sorted using fluorescence-activated cell sorting (FACS), and RNA was extracted to compare the impact of denervation (botox treatment) versus the control condition (saline treatment) on the cancer cell transcriptome signature.

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's instructions
Samples were ribodepleted and prepared using the NEBNext Stranded mRNA Library Prep Kit (NEB). Sequencing was performed on all samples in a multiplexed format at Paired-End 150 bp on the Illumina NovaSeq XP platform.

treatment_protocol: 100 μL phosphate-buffered saline versus 0.3 units of Botox in 100 μL of phosphate-buffered saline

value: 4T1 in MFP

value: TNBC

value: mCherry expression

value: Not treated

value: BOTOX mouse 4


title: TA524

value: tracheal aspirate


title: 4T1-BOTOX-replicate3

description: Library name: Botox3

value: BOTOX mouse 3


title: reduced resilient replicate 3

city: Rehovot

first: Avia

last: Mizrachi

address: 234 Herzl St.

department: Plant and Environmental Sciences

country: Israel

institute: Weizmann Institute of Science

description:
reduced chl-roGFP
reduced3_20k

data_processing:
Data was proccessed and analyzed using the UTAP pipeline (https://doi.org/10.1186/s12859-019-2728-2).
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to P. tricornutum genome using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
Counting was done using htseq-count (DOI: 10.1093/bioinformatics/btu638) (union mode).
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8).
Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. The p-adjusted values were corrected by fdrtool (R package, DOI: 10.1186/1471-2105-9-303).
Assembly: P. tricornutum genome annotation version 3 (Phatr3) on EnsemblProtist, assembly ASM15095v2
Supplementary files format and content: A csv file that includes the raw counts, normalized counts, log2 fold changes, p values and adjusted p values.
Library strategy: MARS-seq

organism: Phaeodactylum tricornutum

source_name: accession Pt1 8.6 (CCMP2561)

growth_protocol: Cultures were grown in filtered sea water (FSW) supplemented with F/2 media (trace metals, Fe citrate, vitamins, NaH2PO4·2H2O and NaNO3 (Guillard and Ryther, 1962)) at 18°C with 16: 8 hours light:dark cycle and light intensity of 170 μmol photons m-2 sec-1 supplied by cool-white LED lights (Edison, New Taipei, Taiwan).

extract_protocol:
20,000 cells were sorted per sample. Samples were sorted directly into cold lysis buffer, in Eppendorf™ LoBind tubes that were kept on ice prior to sorting and during sorting at 4°C, and immediately after sorting underwent vortex, spin down, and flash frozen using liquid N2. Samples were kept at -80°C until further processing. RNA extraction was conducted using the NucleoSpin® RNA XS kit (Machery-Nagel, Düren, Germany).
cDNA library preparation was done using the MARS-seq protocol as described in Keren-Shaul et al., 2019 (https://doi.org/10.1038/s41596-019-0164-4), adapted for small amount bulk RNA samples. Following RNA extraction, reverse transcription (RT) was done to generate barcoded cDNA containing the unique molecular identifier (UMI) sequences (unique to each mRNA molecule) and the sample ID barcodes. Unused primers were then degraded with Exonuclease I (NEB). The cDNA from different samples was then combined into pools, and underwent second-strand synthesis and in vitro transcription to amplify the sequences linearly. RNA products were fragmented and ligated with single-stranded DNA adapters containing pool-specific barcodes. A second round of RT was carried out, followed by polymerase chain reaction with primers containing Illumina adapters to construct DNA libraries for paired-end sequencing on a NextSeq machine (Illumina).

treatment_protocol: P. tricornutum cells expressing chl-roGFP were treated with 80 µM H2O2 and sensitive oxidized cells and resilient more reduced cells were then FACS sorted 2.7 h later using BD FACS AriaII based on chl-roGFP oxidation. Untreated control cells were sorted immediately after H2O2 treated samples based on positive roGFP signal regardless of their oxidation state (the parent gate of “oxidized” and “reduced” subpopulations).

tag: strain

value: accession Pt1 8.6 (CCMP2561)

value: chl-roGFP

value: 80 microM H2O2


title: DNP, rep2


title: DNP, rep1


title: TA503

value: HyperARDS


title: 4T1-BOTOX-replicate2

description: Library name: Botox2

value: BOTOX mouse 2


title: reduced resilient replicate 2

description:
reduced chl-roGFP
reduced2_20k


title: TA488

value: HypoARDS


title: 4T1-BOTOX-replicate1

description: Library name: Botox1

value: BOTOX mouse 1


title: Chloramphenicol, rep6

value: Primary human dermal fibroblasts

value: 100 microg/mL chloramphenicol


title: TA541


title: reduced resilient replicate 1

description:
reduced chl-roGFP
reduced1_20k


title: Chloramphenicol, rep5


title: 4T1-PBS-replicate3

description: Library name: Control3

value: PBS mouse 3


title: TA479


title: TA477

value: Control


title: 4T1-PBS-replicate2

description: Library name: Control2

value: 4T1 in MFP

value: TNBC

value: PBS mouse 2


title: Chloramphenicol, rep4


title: oxidized sensitive replicate 3

description:
oxidized chl-roGFP
oxidized3_20k


title: oxidized sensitive replicate 2

description:
oxidized chl-roGFP
oxidized2_20k


title: 4T1-PBS-replicate1

description: Library name: Control1

value: mCherry expression

value: Not treated

value: PBS mouse 1


title: TA463

value: tracheal aspirate


title: Chloramphenicol, rep3


title: High Se3

city: China

first: Meiling

last: Xiang

state: Henan

address: 100 Science Avenue

institute: Zhengzhou university

data_processing:
Using the Illumina paired-end RNA-seq approach
We used Bowtie2 and Hisat2 to map reads to the genome of the alfalfa genome(https://figshare.com/articles/dataset/genome_fasta_sequence_and_annotation_files/12327602)
StringTie and edgeR were used to estimate the expression level of mRNA and LncRNAs.
The differentially expressed lncRNAs were selected with log2 (fold change) > 1 or log2 (fold change) < -1 and with statistical significance (P-value < 0.05) by R package – edgeR (Robinson et al., 2010).
Assembly: https://figshare.com/articles/dataset/genome_fasta_sequence_and_annotation_files/12327602
Supplementary files format and content: xls include FPKM values for each Sample

organism: Medicago sativa

source_name: plant cell

growth_protocol: We used Medicago sativa L.cv.Kangsai grown in a field at Henan Agricultural University field experimental station in Xinxiang (113°N, 35°E), Henan, China

extract_protocol:
Complete RNA was collected using TRK-1001. A Bioanalyzer 2100 and the RNA 6000 Nano LabChip Kit (Agilent Technologies, Santa Clara, CA, United States) with RIN number > 7.0. The NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA) was used to test the volume and purity of RNA.
Approximately 5 μg of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under high temperatures.  Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which was next used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H, and dUTP.

treatment_protocol: The alfalfa was divided into three groups (n=3), CK, 100 mg L-1 and 500 mg L-1 Se treat when it reached a height of 20 cm.Three groups were both sprayed once every 7 days for three consecutive sprays.

value: leaf

value: 500 mg L-1 Se


title: Chloramphenicol, rep2


title: TA458


title: control untreated replicate 3

value: accession Pt1 8.6 (CCMP2561)

value: chl-roGFP

value: control


title: High Se2


title: Chloramphenicol, rep1


title: TA414

value: HypoARDS


title: High Se1


title: Doxycycline, rep6

value: Primary human dermal fibroblasts

value: 20 microg/mL doxycycline


title: control untreated replicate 2


title: control untreated replicate 1


title: Low Se3


title: Doxycycline, rep4


title: TA413


title: 12_6_D257A_Polg_C

description: Library name: Sample12

data_processing:
Illumina BaseSpace FASTQ Generation | Version: 1.0.0
Illumina BaseSpace RNA-Seq Alignment | Version: 2.0.0; Incroporates STAR Aligner (Version: 2.6.1a) and Salmon Quantification (Version 0.11.2)
Assembly: Mus_musculus (UCSC mm10)
Supplementary files format and content: WT_PolgD257A_BMDM_normalized_counts.txt

source_name: bone marrow

growth_protocol: Primary bone marrow-derived macrophages (BMDMs) were isolated from femurs of 6-12 month old WT and Polg D257A mice. Briefly, whole femurs were crushed in media and passed through a 70 µm filter. Red blood cells were lysed through osmosis by resuspending in ACK lysis buffer (Quality Biological, 118-156-101) for 2 minutes. Remaining cells were passed through a 40 µm filter, counted, and plated on non-tissue culture treated dishes. Macrophages were differentiated over for 7 days using 30% L929 conditioned medium.

extract_protocol:
Total cellular RNA was prepared using the Quick-RNA microprep kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GFP-expressing PAO1 was provided by Dr. Carolyn Cannon and was grown on Soy agar plates (BD, 211043) with 100 μg/mL carbenicillin (Dot Scientific, 46000-5) overnight from a glycerol stock. A single colony was incubated in 5 mL Mueller Hinton broth (BD, 275730) with carbenicillin at 37 ᵒC spinning overnight. Overnight culture was back diluted 1:5 and grown for 2 hours until bacteria reached log-phase. Bacteria were washed with sterile phosphate-buffered saline (PBS) and opsonized for 20 minutes in mouse serum (Fisher, PI31880). After two more washed with PBS macrophages were infected at a multiplicty of infection of 5 and spun at 250 g for 5 minutes to synchronize infection. One hour after infection, wells were washed and treated with 300 μg/mL gentamicin (VWR, 0304) for 30 minutes to inactivate extracellular bacteria. The remainder of the experiment was completed with media supplemented with 50 μg/mL gentamicin.

value: bone marrow

value: Bone marrow derived macrophage

value: Polg D257A/D257A

value: 6hr PAO1, MOI=5


title: TA411


title: Low Se2


title: 11_6_D257A_Polg_B

description: Library name: Sample11


title: TA409


title: Low Se1


title: Doxycycline, rep3


title: TA402


title: oxidized sensitive replicate 1

description:
oxidized chl-roGFP
oxidized1_20k

value: 80 microM H2O2


title: 10_6_D257A_Polg_A

description: Library name: Sample10


title: Doxycycline, rep2


title: 09_6_D257A_WT_C

description: Library name: Sample9

value: WT


title: TA462

value: Control


title: CK2

value: CK


title: TA392

value: tracheal aspirate


title: Doxycycline, rep5


title: CK1

value: leaf


title: Doxycycline, rep1


title: 07_6_D257A_WT_A

description: Library name: Sample7


title: TA358


title: UK-5099, rep5

value: 20 microM UK-5099


title: 08_6_D257A_WT_B

description: Library name: Sample8


title: TA353

value: HyperARDS


title: UK-5099, rep4


title: 06_UN_D257A_Polg_C

description: Library name: Sample6

value: Unchallenged


title: 2211

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

description: Library name: S000005_38110_002

data_processing:
Fastqc was used to exclude poor quality samples.
STAR was used to align reads to transcriptome using a GRCm38.p4 genome build with Ensembl v86 gene annotation.
Salmon quantification in alignment-based mode was used to obtain transcript-level abundance.
Transcript-level abundance was imported into gene-level abundance with the R package tximport.
Genes with low expression were identified and filtered out from further analysis if total read counts for a given gene across all samples was less than ten.
Regularized log transformation (rlog) was performed using the DESeq2 R package.
Differential gene expression analysis was also conducted using DESeq2.
Gene Set Enrichment Analysis (GSEA) software version 4.3.3 were used for pathway analysis.
RLOG normalized and transformed expression values were used for heirarchical clustering and plotting of heatmaps.
Assembly: GRCm38.p4
Assembly: genome annotation: Ensembl v86
Supplementary files format and content: Salmon quant.sf files contain transcirpt level abundances.

source_name: Mouse TNBC Tumor

growth_protocol: The UTHSC Animal Care and Use Committee (IACUC) approved all protocols and methods following protocol #24.0504. All animals in the study were kept on a 12 hr light/dark cycle and fed a low fat diet (10% kcal from fat, Research Diets Inc D12450Ji). E0771 cells were harvested in serum-free RPMI media and suspended into equal volumes of Matrigel (Product No. 354234, Corning®, Tewksbury, MA) for orthotopic mammary injection in N = 19 female C57BL/6J mice (8 weeks of age). 250,000 cells were injected in 100 µL into the 4th right mammary gland at a final Matrigel concentration of 4.5 mg/mL. The injected mice were palpated three times weekly until endpoint at Day 17.

extract_protocol:
Total RNA was isolated from tumors using the RNeasy Mini Kit (#74104, Qiagen) according to the manufacturer’s instructions for all (N = 19) fresh-frozen samples. The integrity of the RNA was assessed using Agilent TapeStation, and samples with RIN > 6.0 were used.
Library prep was conducted at Azenta.
mRNA-seq libraries for the Illumina platform were generated and sequenced at Azenta using the Illumina HiSeq 2 × 150 bp configuration following the manufacturer’s protocol. ~350M raw paired-end reads per lane.

treatment_protocol: Mice were treated with antibiotic cocktail (vancomycin, 0.5 g/L, neomycin, 1 g/L, ampicillin, 1 g/L, and cefoperazone, 1 g/L) in autoclaved water or plain autoclaved water in water bottles for 8 days to ablate the commensal gut microbiome. Mice were gavaged with 50 µL fecal slurry every three days for two weeks for a total of 4 FMT gavages. Three days following E0771 cell injection, immune checkpoint blockade anti-PD-1 antibody or rat IgG2a isotype control were administered at 200 µg per mouse in 50 µL PBS by intraperitoneal injection (Obese FMT + IgG N = 6, Obese FMT + aPD1 N = 4, VSG FMT + IgG N = 5, VSG FMT + aPD1 N = 4). Immune checkpoint blockade was administered thrice a week until the endpoint. Tumor size was calculated using the formula (width2 × length/2). Body weights were recorded weekly. Mice were sacrificed at endpoint. Tumors were excised for ex vivo measurement of tumor weight and snap-frozen in liquid nitrogen.

value: Mouse TNBC Tumor

value: Triple negative breast cancer cells

value: VSG FMT + IgG

value: treated with 4x FMT from VSG donor via oral gavage and 200 ug IgG i.p. every three days


title: 05_UN_D257A_Polg_B

description: Library name: Sample5

value: bone marrow


title: 2219

description: Library name: S000005_38114_002


title: UK-5099, rep3

value: Primary human dermal fibroblasts


title: 2216

description: Library name: S000005_38126_002


title: TA341

value: HypoARDS


title: 04_UN_D257A_Polg_A

description: Library name: Sample4

value: Bone marrow derived macrophage

value: Polg D257A/D257A


title: TA337


title: UK-5099, rep2


title: 2221

description: Library name: S000005_38115_002


title: CK3


title: 03_UN_D257A_WT_C

description: Library name: Sample3

value: WT


title: TA400


title: UK-5099, rep1


title: 2218

description: Library name: S000005_38113_002


title: 02_UN_D257A_WT_B

description: Library name: Sample2


title: UK-5099, rep6


title: TA334


title: DMSO, rep6

value: 0.5percent DMSO


title: TA335


title: 01_UN_D257A_WT_A

description: Library name: Sample1


title: TA320


title: DMSO, rep5


title: 8_D

city: Durham

first: Benjamin

last: Devlin

state: North Carolina

address: 210 Research Drive

department: Psychology and Neuroscience

institute: Duke University

description: Library name: X8_D

data_processing:
Raw fastQ files were aligned to Mus Musculus GRCm38 using STAR (v2.7.5c) and featurecounts (v1.6.3)
Genes were filtered and only included in analysis if they were present at 10 counts in at least 4 samples.
Differentially expressed genes were calculated using DESeq268 in R 4.4.0.
All analysis scripts are available on GitHub. https://github.com/bendevlin18/IL34blocking_seq_analysis_2024.git.
Assembly: Mus Musculus GRCm38
Supplementary files format and content: combined_counts_protein_coding.csv contains raw counts with each sample combined in one table
Supplementary files format and content: tpm.csv contains calculated TPM values for all samples
Supplementary files format and content: il34_seq_full_sample_metadata.csv contains sample metadata for reference

source_name: Microglia

extract_protocol:
Mice were saline-perfused, and their brains dissected and split at the midline using a razor blade. Whole forebrain was collected, and microglia were isolated from one half using a CD11b antibody based procedure, according to published methods. RNA was extracted from whole forebrain and CD11b+ isolated microglia using the TRIzol based chloroform extraction.
Takara SMART-Seq v4 Ultra low Input RNA kit

value: Microglia

value: Female

tag: experiment

value: ab


title: DMSO, rep4

data_processing:
Salmon v1.4.0
Sequence reads were not trimmed prior to Salmon pseudoalignment
Salmon index generated using k-mers of length 31
Salmon parameters: seqBias, useVBOpt, validateMappings
Pseudo-aligned results from Salmon were imported into R using tximport and processed with DESeq2
Imported counts were normalized using DESeq2's median of ratios method
Assembly: Ensembl 103
Supplementary files format and content: comma-separated file contains normalized transcript counts for each sample as generated by DESeq2


title: 2509

description: Library name: S000005_40618_002

value: Obese FMT + IgG

value: treated with 4x FMT from obese donor via oral gavage and 200 ug IgG i.p. every three days


title: TA319

value: tracheal aspirate

value: Control


title: TA315


title: 8_B

description: Library name: X8_B

value: Brain


title: DMSO, rep3


title: 2505

description: Library name: S000005_40617_002

value: Mouse TNBC Tumor

value: Triple negative breast cancer cells


title: 7_D

description: Library name: X7_D

value: Male


title: 2504

description: Library name: S000005_40616_002


title: TA314

value: HyperARDS


title: 7_B

description: Library name: X7_B


title: 2203

description: Library name: S000005_40612_002


title: 2502

description: Library name: S000005_42376_002


title: 6_A

description: Library name: X6_A

value: IL34 KO

value: KO


title: TA288

value: HypoARDS


title: 2522

description: Library name: S000005_38119_002

value: VSG FMT + aPD1

value: treated with 4x FMT from VSG donor via oral gavage and 200 ug aPD1 i.p. every three days


title: TA251


title: TA257


title: TA311


title: KO6

city: Vancouver

first: Francis

middle: C

last: Lynn

state: BC

address: 950 28th Ave W

department: Surgery

country: Canada

institute: University of British Columbia

description:
Library name: Sample 13
10x genomics

data_processing:
Illumina bcl files from the NextSeq 500 sequencer  were used as input to demultiplex each sample in each sequencing run and generate fastq files using 10x Genomics Cell Ranger software version 7.0.0. in a linux environment (cellranger mkfastq).
Cell Ranger (cellranger count) was used to take the generated fastq files and align them to the GRCm38 genome, count barcodes, count Unique Molecular Identifiers (UMI), and filter out suspected empty droplets/background noise.
The output matrices of Cell Ranger were used as input into the R package Seurat (version 4.0.4). Seurat was used to transform matrices into seurat objects, and filter out genes not expressed in at least 3 cells, and cells that expressed more than 7500 genes.
Seurat was used to filter each donor dataset's cells one more time, keeping cells that had greater than 3000 genes (nFeature >3000) and less than 40% mitochondrial genes expressed in a cell.
Seurat was used to normalize each dataset and prep for SCTransform method and integration.
All 13 samples' worth of datasets were integrated using Seurat, generating a final integrated Seurat Object  that was used for downstream dimensional reduction, clustering, visualization, and identification of differentially expressed genes across conditions and genotypes.
Assembly: GRCm38
Supplementary files format and content: Integrated Seurat Object (.rds) of all samples (CT1-7, KO1-6)

source_name: mediobasal hypothalamus

growth_protocol: Male mice were weaned at 3 weeks of age, gavaged with tamoxifen 3 times over a week (8mg/dose/day) regardless of genotype at 6 weeks of age, and fed 60% high fat diet ad libitum for 6 more weeks until harvesting brains when mice were 13 weeks of age.

extract_protocol:
All mice were weighed, anesthetized with isoflurane, and euthanized by CO2 asphyxiation. The head was decapitated and whole brains were harvested and immediately put on ice in cold Hibernate AB complete media. Thick 1mm coronal sections were made through the area encompassing the mediobasal hypothalamus, identified morphologically under a dissecting microscope. The mediobasal hypothalamus and trace amounts of surrounding regions in the hypothalamus were manually microdissected and dissociated following the protocol in PMID: 17545985, with adjustments as in PMID: 28355573. All tissues and cell solutions were kept on ice whenever possible.
The 10x Genomics Chromium Controller was used to capture single cells, with each treatment condition from each donor islet preparation as 1 sample. cDNA libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3’ version 3.1 reagents.

treatment_protocol: All mice were fasted overnight (10-12 hours) with access to water. 4 CT and 3 KO mice were refed for 1 hour following the fast in the morning, resulting in 4 groups: 4 Refed CT, 3 Fasted CT, 3 Refed KO, and 3 Refed KO.

value: mediobasal hypothalamus

value: POMC-NPAS4 knockout (KO)

value: Overnight fasted


title: 2212

description: Library name: S000005_38109_002


title: 6_C

description: Library name: X6_C

value: Microglia

value: Female


title: 2533

description: Library name: S000005_38124_002


title: KO2

description:
Library name: Sample 9
10x genomics

value: Overnight fasted + 1 hour Refed


title: KO5

description:
Library name: Sample 12
10x genomics


title: 2210

description: Library name: S000005_42372_002

value: Obese FMT + aPD1

value: treated with 4x FMT from obese donor via oral gavage and 200 ug aPD1 i.p. every three days


title: 24_C

description: Library name: X24_C


title: 3_A

description: Library name: X3_A

value: Brain


title: 3_C

description: Library name: X3_C


title: 2501

description: Library name: S000005_42375_002

value: Mouse TNBC Tumor

value: Triple negative breast cancer cells

value: Obese FMT + IgG

value: treated with 4x FMT from obese donor via oral gavage and 200 ug IgG i.p. every three days


title: KO3

description:
Library name: Sample 10
10x genomics


title: 2521

description: Library name: S000005_38118_002


title: KO1

description:
Library name: Sample 8
10x genomics


title: DMSO, rep2

extract_protocol:
RNA was extracted using TRIzol reagent and a Zymo RNA miniprep kit. 750 ng of RNA was used for library preparation for each sample.
RNA libraries for RNA-seq were generated using the High Throughput TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: Primary human dermal fibroblasts

value: 0.5percent DMSO


title: DMSO, rep1


title: TA229

value: tracheal aspirate

value: HyperARDS


title: 2208

description: Library name: S000005_42371_002


title: TA235

value: HypoARDS


title: 24_B

description: Library name: X24_B

value: Male

value: ab


title: TA234


title: KO4

description:
Library name: Sample 11
10x genomics

value: mediobasal hypothalamus

value: POMC-NPAS4 knockout (KO)

value: Overnight fasted


title: 24_D

description: Library name: X24_D

value: Microglia


title: CT7

description:
Library name: Sample 7
10x genomics

value: POMC-CreER control (CT)


title: 2209

description: Library name: S000005_40615_002

value: Obese FMT + aPD1

value: treated with 4x FMT from obese donor via oral gavage and 200 ug aPD1 i.p. every three days


title: 24_A

description: Library name: X24_A

value: Brain

value: Female

value: IL34 KO

value: KO


title: TA225


title: CT6

description:
Library name: Sample 6
10x genomics


title: 2205

description: Library name: S000005_40613_002

value: Mouse TNBC Tumor

value: Triple negative breast cancer cells


title: NT7_rep3

city: PARMA

first: Barbara

last: Montanini

state: PR

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description:
Library name: FDL
Column name in D7_raw_count_matrix.tsv: NT7_rep3

data_processing:
Read quality analysis was performed with the FastQC.
Adapters’ sequences were trimmed with BBduk from the suite BBtools (http://jgi.doe.gov/data-and-tools/bb-tools/).
RNA-seq reads were aligned on the rabbit genome (Oryctolagus cuniculus, OryCun2.0) with STAR v. 2.7.10a.
Gene counts were obtained with STAR v. 2.7.10a, using the latest Ensembl available annotation on rabbit. A custom GTF was employed to account for reads mapping to unannotated 3’ UTRs of protein coding genes. Gene coordinates are present in the D7_raw_count_matrix.tsv file.
Assembly: OryCun2.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Oryctolagus cuniculus

source_name: Lung

growth_protocol: Preterm pups were delivered through C-section on the 28th day of gestation, maintained in custom-made incubators and were fed twice daily via a milk replacer, at 21% or 95% oxygen for 3, 5, or 7 days

extract_protocol:
After collection, lungs were immediately placed in RNA Later (Sigma Aldrich, USA) and stored at -20°C. Samples were homogenized in QIAzol® Lysis Reagent. Total RNA was extracted with the miRNeasy Mini Kit protocol (QIAGEN, Germany), using an automated method (QIAcube: QIAGEN, Germany), adapted to include DNase I treatment.
Libraries for massive parallel RNA sequencing (RNA-seq) were prepared with the Truseq Stranded mRNA Library kit (Illumina) and sequenced with an Illumina NovaSeq 6000 platform, which generated at least 20 million reads/sample (100x2 pb PE)

treatment_protocol: Preterm animals were maintained in custom-made incubators at 21% or 95% of Oxygen for 7 days and fed twice daily via an orogastric tube with a milk replacer

value: Lung

value: Total Right Lung Homogenate

value: New Zealand White

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 7 days


title: TA213

value: tracheal aspirate

value: HypoARDS


title: 21_C

description: Library name: X21_C

value: Male

value: IL34 Het


title: CT4

description:
Library name: Sample 4
10x genomics

value: mediobasal hypothalamus

value: POMC-CreER control (CT)

value: Overnight fasted + 1 hour Refed


title: 20_C

description: Library name: X20_C

value: Microglia


title: Fungus cells, Deletion_MtFKH1, Avicel medium, rep3

city: Auckland

first: Yapeng

last: Lai

address: 55 Wellesley Street East,  Auckland Central

department: School of Science

country: New Zealand

institute: Auckland University of Technology

description:
Myceliophthora thermophila ATCC 42464
Deletion_MtFKH1_3

data_processing:
Raw reads containing adapters or low quality bases were further filtered by fastp (version 0.18.0). An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
RNAs differential expression analysis was performed by DESeq2 software between two different groups.
Assembly: The Reference genome is ASM22609v1
Supplementary files format and content: Excel (.xlsx) file includes FPKM values for each sample.

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Mycelia

growth_protocol: For analysis of MtFKH1-specific transcriptomes, conidia from the wild type (WT) and ΔMtfkh1 strains of M. thermophila were pre-grown in liquid glucose medium, and then transferred the washed mycelia into liquid medium containing 2% (w/v) Avicel as the carbon source for 48 h.

extract_protocol:
Total fungal RNAs were extracted from fresh mycelia harvested from 2% (w/v) Avicel media through vacuum filtration. Total RNAs were isolated using an RNA extraction kit TransZol Up (TransGen Biotech, Beijing, China) following the manufacturer’s protocols, and RNA extracts were assessed by electrophoresis and quantified using the NanoDrop 2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).
After total RNA was obtained, the mRNA for each sample was enriched by Oligo (dT) beads and reversely transcribed into cDNA via the aid of NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).

value: Mycelia

value: MtFKH1 deletion

tag: growth medium

value: Avicel


title: 23_C

description: Library name: X23_C

value: Female

value: KO


title: NT5_rep2

description:
Library name: FDH
Column name in D7_raw_count_matrix.tsv: NT5_rep2

value: Lung

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 5 days


title: CT5

description:
Library name: Sample 5
10x genomics

value: Overnight fasted


title: 23_A

description: Library name: X23_A

value: Brain


title: 21_A

description: Library name: X21_A


title: TA203

value: tracheal aspirate


title: NT7_rep2

description:
Library name: FDK
Column name in D7_raw_count_matrix.tsv: NT7_rep2

value: Total Right Lung Homogenate

value: New Zealand White

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 7 days


title: NT7_rep1

description:
Library name: FDJ
Column name in D7_raw_count_matrix.tsv: NT7_rep1


title: CT1

description:
Library name: Sample 1
10x genomics

value: mediobasal hypothalamus


title: NT5_rep3

description:
Library name: FDI
Column name in D7_raw_count_matrix.tsv: NT5_rep3


title: CT3

description:
Library name: Sample 3
10x genomics

value: POMC-CreER control (CT)


title: Fungus cells, Deletion_MtFKH1, Avicel medium, rep2

description:
Myceliophthora thermophila ATCC 42464
Deletion_MtFKH1_2


title: CT2

description:
Library name: Sample 2
10x genomics

value: Overnight fasted + 1 hour Refed


title: 20_A

description: Library name: X20_A

value: IL34 Het


title: NT5_rep1

description:
Library name: FDG
Column name in D7_raw_count_matrix.tsv: NT5_rep1


title: TA227

value: HyperARDS


title: 24h_blood, scRNA-seq

city: Guangzhou

first: Jingjing

last: Ji

address: Liuhua Road

institute: General Hospital of Southern Theater Command of PLA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
BALF and blood were collected from mice treated with LPS for 0, 6, and 24 h. CD45-positive cells in the BALF and blood were sorted for further scRNA-seq. The scRNA-seq libraries were generated by using Chromium Single Cell 3’ Library (10x Genomics) according to the manufacturer’s protocol.
The scRNA-seq libraries were generated by using Chromium Single Cell 3’ Library (10x Genomics) according to the manufacturer’s protocol.

value: blood

tag: time point

tag: agent

value: LPS


title: Fungus cells, WT, Avicel medium, rep3

description:
Myceliophthora thermophila ATCC 42464
WT_3

value: Mycelia

value: WT

value: Avicel


title: 2_D

description: Library name: X2_D

value: Microglia

value: Male

value: ab


title: NT3_rep3

description:
Library name: FDF
Column name in D7_raw_count_matrix.tsv: NT3_rep3

value: Lung

tag: cell line

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 3 days


title: 24h_balf, scRNA-seq

source_name: bronchoalveolar lavage fluid

tag: tissue

value: bronchoalveolar lavage fluid


title: NT3_rep2

description:
Library name: FDE
Column name in D7_raw_count_matrix.tsv: NT3_rep2

value: Total Right Lung Homogenate

value: New Zealand White


title: 6h_blood, scRNA-seq


title: 2_B

description: Library name: X2_B

value: Brain


title: 6h_balf, scRNA-seq


title: Fungus cells, Deletion_MtFKH1, Avicel medium, rep1

description:
Myceliophthora thermophila ATCC 42464
Deletion_MtFKH1_1

tag: cell type

value: MtFKH1 deletion


title: 15_B

description: Library name: X15_B

value: Female


title: 11_B

description: Library name: X11_B


title: HT7_rep3

description:
Library name: FCW
Column name in D7_raw_count_matrix.tsv: HT7_rep3

value: Delivered on 28th day of gestation (preterm birth) and kept at 95% O2 for 7 days


title: 10_D

description: Library name: X10_D


title: spnE_ZF_mutant_ovaries_sRNA_rep2

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

institute: The Australian National University

description:
Library name: spnE_ZF_mutant_ovaries_sRNA_rep2
Small RNA sequencing from spnE ZF mutant ovaries replicate 2

data_processing:
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting. The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses. Trimmed reads were mapped with bowtie v1.2.3 to the Drosophila melanogaster dm6 genome (allowing up to one mismatch) or to the transposon reference sequences (allowing up to three mismatches). The sam file was further processed to the bam file, then to the bed file using samtools/1.19 and bedtools/2.28.0.
Assembly: dmel r6.31
Supplementary files format and content: *_TE_3MM_mappers.bed: bed file of small RNA reads that are mapping to the transposon consensus sequences (allowing up to three mismatches, --all --best --strata option in bowtie)

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were kept at standard conditions at room temperature.

extract_protocol:
Small RNA sequencing was performed on Drosophila ovaries. About 10 pairs of ovaries from 2 to 7 days old females have been dissected per genotype, and total RNA was extracted by TRIZOL (Thermo Fisher) and the genomic DNA was removed by DNase I (Thermo Fisher).
Small RNAs were first size-selected from the total RNA by 12% w/v UREA-PAGE using radio-labelled 19mer (5′-CGUACGCGGGUUUAAACGA) and 35mer (5'-CUCAUCUUGGUCGUACGCGGAAUAGUUUAAACUGU) spikes, and oxidised using sodium periodate. The oxidised small RNAs were further size-selected by PAGE. The size-selected oxidised small RNAs were ligated to the 3' adapter 5rApp/NNNNAGATCGGAAGAGCACACGTCT/3ddC, and then to the 5' adapter ACACUCUUUCCCUACACGACGCUCUUCCGAUCUNNNN where Ns are randomised. The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the RT primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT. The library was amplified using KAPA LongRange DNA polymerase (Sigma) with a universal TruSeq forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcode-containing TruSeq reverse primer (e.g. CAAGCAGAAGACGGCATACGAGATxxxxxxGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where xxxxxx were the barcode).

value: ovaries

value: female

value: Oregon R

value: spnE[P8] x spnE[P64]

value: oxidised

value: 2 -7 days old


title: spnE_null_mutant_ovaries_sRNA_rep2

description:
Library name: spnE_null_mutant_ovaries_sRNA_rep2
Small RNA sequencing from spnE null mutant ovaries replicate 2

value: spnE[P8] x spnE[P53]


title: 0h_blood, scRNA-seq

value: blood

value: LPS


title: 11_D

description: Library name: X11_D

value: Microglia

value: ab


title: spnE_null_mutant_ovaries_sRNA_rep1

description:
Library name: spnE_null_mutant_ovaries_sRNA_rep1
Small RNA sequencing from spnE null mutant ovaries replicate 1


title: 0h_balf, scRNA-seq

value: bronchoalveolar lavage fluid


title: HT7_rep1

description:
Library name: FCU
Column name in D7_raw_count_matrix.tsv: HT7_rep1

value: Lung

value: Total Right Lung Homogenate

value: New Zealand White


title: spnE_ZF_mutant_ovaries_sRNA_rep1

description:
Library name: spnE_ZF_mutant_ovaries_sRNA_rep1
Small RNA sequencing from spnE ZF mutant ovaries replicate 1


title: TU_pos3

city: Birmingham

first: Mingyong

last: Liu

state: AL

address: SHEL 531, 1825 University Blvd

department: Clinical Immunology and Rheumatology

institute: University of Alabama at Birmingham

description: ST2+ Tregs from tumor-bearing omentum of mouse #6

data_processing:
FASTQ reads were first processed by Trim Galore! to trim adapter and low-quality reads
Trimmed FASTQ reads were mapped to the mm10 mouse genome using TopHat2 with the default parameters.
Samtools was used to sort the resulting BAM files and generate SAM files, which were then processed by htseq-count of HTSeq to create gene counts.
Assembly: mm10
Supplementary files format and content: HTSeq-count files that include raw counts of sequencing reads for each sample

source_name: tumor-bearing omentum

growth_protocol: EG7.1.15 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum, 50 μM 2-Mercaptoethanol, 0.024 mM NaHCO3, 600 μg/mL G418, 10 μg/mL kanamycin, 200 μg/mL penicillin and streptomycin.

extract_protocol:
Tumor-free omenta or omental tumors were excised, and ST2+ and ST2- Tregs were collected directly into Qiagen RLT buffer plus 2-mercaptoethanol (Sigma). Total RNA was purified using the Quick-RNA MicroPrep kit.
Total RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). The resulting cDNA was then used as input for the NexteraXT kit (Illumina) for tagmentation, PCR amplification and indexing. Final libraries were quantitated by Qubit, pooled at equimolar ratio.

treatment_protocol: Mice were either injected with 3x10^6 EG7.1.15 cells intraperitoneally or left tumor-free.

value: B6 Foxp3-DTR/GFP

value: tumor-bearing omentum

tag: sorting markers


title: HT7_rep2

description:
Library name: FCV
Column name in D7_raw_count_matrix.tsv: HT7_rep2

tag: genotype

value: Delivered on 28th day of gestation (preterm birth) and kept at 95% O2 for 7 days


title: TU_pos2

description: ST2+ Tregs from tumor-bearing omentum of mouse #5


title: HT5_rep2

description:
Library name: FCT
Column name in D7_raw_count_matrix.tsv: HT5_rep2

tag: treatment

value: Delivered on 28th day of gestation (preterm birth) and kept at 95% O2 for 5 days


title: w1118_ovaries_sRNA_rep2

description:
Library name: w1118_ovaries_sRNA_rep2
Small RNA sequencing from w1118 ovaries replicate 2

value: ovaries

value: female

value: Oregon R


title: HT5_rep1

description:
Library name: FCR
Column name in D7_raw_count_matrix.tsv: HT5_rep1


title: 10_B

description: Library name: X10_B

value: Brain

value: Male


title: Fungus cells, WT, Avicel medium, rep1

description:
Myceliophthora thermophila ATCC 42464
WT_1

value: Mycelia

value: WT

value: Avicel


title: Fungus cells, WT, Avicel medium, rep2

description:
Myceliophthora thermophila ATCC 42464
WT_2


title: 15_D

description: Library name: X15_D

value: Microglia

value: Female

value: ab


title: NT3_rep1

description:
Library name: FDD
Column name in D7_raw_count_matrix.tsv: NT3_rep1

value: Lung

value: Total Right Lung Homogenate

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 3 days


title: 1_D

description: Library name: X1_D


title: HT3_rep3

description:
Library name: FCQ
Column name in D7_raw_count_matrix.tsv: HT3_rep3

value: New Zealand White

value: Delivered on 28th day of gestation (preterm birth) and kept at 95% O2 for 3 days


title: 1_C

description: Library name: X1_C

value: IL34 Het

value: KO


title: TU_neg2

description: ST2- Tregs from tumor-bearing omentum of mouse #5

value: B6 Foxp3-DTR/GFP

value: tumor-bearing omentum


title: HT3_rep2

description:
Library name: FCP
Column name in D7_raw_count_matrix.tsv: HT3_rep2


title: spnE_null_mutant_ovaries_pA_rep3

description:
Library name: spnE_null_mutant_ovaries_pA_rep3
polyA selected RNA sequencing from spnE null mutant ovaries replicate 3

data_processing:
We used both R1 and R2 reads from the 150bp Novaseq paired-end sequencing runs. Reads were trimmed of the adapters 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' and 'AGATCGGAAGAGCGTCGTGTAGGGAAAGA' at the 3' ends of R1 and R2 reads, respectively, using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting. Trimmed reads were mapped against the dm6 r6.31 transcriptome combined by a collection of D.melanogaster transposon consensus sequences (Senti et al., 2015 EMBO J, PMID: 26302790) using salmon/1.10.0 using options of --validateMappings --incompatPrior 0.0 --seqBias --gcBias. The output files of salmon (quant.sf) were used for the differential expression analysis of transposon and the host mRNAs. The processed quant.sf files contain the counts of r6.31 transcriptome and transposons (marked by TE:<transposon name>.
Assembly: dmel r6.31
Supplementary files format and content: *_quant.sf: mRNA counts produced after the mapping by salmon; <transcript Name> <transcript Length> <Effective Length of the transcript> <transcript counts per one million transcripts (TPM)> <Number of mapped Reads>

extract_protocol:
RNA sequencing was performed on Drosophila ovaries. About 10 pairs of ovaries from 2 to 7 days old females have been dissected per genotype, and total RNA was extracted by TRIZOL (Thermo Fisher) and the genomic DNA was removed by DNase I (Thermo Fisher).
The RNA-seq library was made from polyA+ RNA using NEB Ultra II Directional RNA library prep kit (NEB). We used the Kapa LongRange DNA polymerase (Sigma) with TruSeq compatible primers to amplify the libraries.

value: ovaries

value: female

value: Oregon R

value: spnE[P8] x spnE[P53]

tag: ages

value: 2 -7 days old


title: HT3_rep1

description:
Library name: FCO
Column name in D7_raw_count_matrix.tsv: HT3_rep1


title: spnE_ZF_mutant_ovaries_pA_rep3

description:
Library name: spnE_ZF_mutant_ovaries_pA_rep3
polyA selected RNA sequencing from spnE ZF mutant ovaries replicate 3

value: spnE[P8] x spnE[P64]


title: 1_A

description: Library name: X1_A

value: Brain

value: Male


title: spnE_null_mutant_ovaries_pA_rep2

description:
Library name: spnE_null_mutant_ovaries_pA_rep2
polyA selected RNA sequencing from spnE null mutant ovaries replicate 2


title: Naive_pos3

description: ST2+ Tregs from tumor-free omentum of mouse #3

source_name: tumor-free omentum

value: tumor-free omentum


title: spnE_null_mutant_ovaries_pA_rep1

description:
Library name: spnE_null_mutant_ovaries_pA_rep1
polyA selected RNA sequencing from spnE null mutant ovaries replicate 1


title: 1_B

description: Library name: X1_B

value: ab


title: KO3

city: Tianjin

first: Shuo

last: He

address: 22 Weather Station Road

institute: Tianjin Medical University

description: Library name: Sample 11

data_processing:
SOAPnuke was used to get the "clean reads".
Assembly: mm8
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample ...
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: MEFs

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

value: MEFs


title: KO2

description: Library name: Sample 9


title: TU_neg1

description: ST2- Tregs from tumor-bearing omentum of mouse #4


title: Naive_pos2

description: ST2+ Tregs from tumor-free omentum of mouse #2


title: spnE_ZF_mutant_ovaries_pA_rep2

description:
Library name: spnE_ZF_mutant_ovaries_pA_rep2
polyA selected RNA sequencing from spnE ZF mutant ovaries replicate 2


title: E20 scrnaseq

city: Houston

first: Kamryn

last: Gerner-Mauro

state: Texas

address: 1 Baylor Plz

institute: Baylor College of Medicine

data_processing:
Raw fastq files were demultiplexed with 10X Genomics Cell Ranger
Further analysis can be done with 10X Genomics Loupe Cell Browser using the .cloupe files
Assembly: galgal6
Supplementary files format and content: .tsv, matrix, barcodes, and features files can be opened and analyzed wtih Seurat and Signac (R packages). Cloupe files can be opened with Loupe Cell Browser, a software from 10X Genomics.
Supplementary files format and content: .h5 file can be opened with Seruat (R package).

molecule: nuclear RNA

extract_protocol:
Lungs were extracted from embryos and subsequently dissociated. They were stained for the major cell populations of the lungs and FACs sorted. Roughly equal proportions of collected cell populations were mixed for scMultiome. Only epithelial cells or samples depleted of immune cells were taken for scRNA. Sorted cells were then sequenced.
50 cycles read1, 49 cycles read2, 8 cycles index1, 24 cycles index2
28 cycles read1, 90 cycles read2, 10 cycles index1, 10 cycle index2

value: Lung

value: epithelial cells

value: wild-type


title: spnE_ZF_mutant_ovaries_pA_rep1

description:
Library name: spnE_ZF_mutant_ovaries_pA_rep1
polyA selected RNA sequencing from spnE ZF mutant ovaries replicate 1


title: E13 scmultiome ATAC

library_source: genomic single cell

molecule: genomic DNA

value: all lung cells


title: TU_pos1

description: ST2+ Tregs from tumor-bearing omentum of mouse #4

value: B6 Foxp3-DTR/GFP


title: w1118_ovaries_sRNA_rep1

description:
Library name: w1118_ovaries_sRNA_rep1
Small RNA sequencing from w1118 ovaries replicate 1

value: oxidised


title: Naive_neg3

description: ST2- Tregs from tumor-free omentum of mouse #3


title: Naive_pos1

description: ST2+ Tregs from tumor-free omentum of mouse #1


title: KO1

description: Library name: Sample 7


title: w1118_ovaries_pA_rep3

description:
Library name: w1118_ovaries_pA_rep3
polyA selected RNA sequencing from w1118 ovaries replicate 3

value: ovaries


title: E13 scmultiome GE


title: WT3

description: Library name: Sample 5


title: TU_neg3

description: ST2- Tregs from tumor-bearing omentum of mouse #6

value: tumor-bearing omentum


title: MaAgo-associated siDNA, with MaACE1

city: Wageningen

first: Daan

middle: C.

last: Swarts

address: Stippeneng 4

department: Laboratory of Biochemistry

country: Netherlands

institute: Wageningen University

description: Protein-nucleic acid complexes purified from E. coli, nucleic acids extracted, DNA library generated as described by Olovnikov et al. (https://pubmed.ncbi.nlm.nih.gov/24034694/)

data_processing:
Paired-end small DNA reads were merged and adapter sequences were trimmed using BBmap (Bbtools; https://pubmed.ncbi.nlm.nih.gov/29073143/). Max length was set at 50 bp.
Reads were aligned against the genome of E. coli BL21(DE3) (CP053602.1) and protein expression plasmids (pPB001 or pPB001+pPB041) using HISAT2 (https://pubmed.ncbi.nlm.nih.gov/25751142/)
Mapped reads were filtered using Samtools and analyzed using fastQC to determine read length and to investigate nucleotide bias
Aligned reads were analyzed using FeatureCounts to determine mapping frequence on genomic and plasmid features.
Assembly: Reads were aligned against the genome of E. coli BL21(DE3) (CP053602.1) and protein expression plasmids (pPB001 or pPB001+pPB041)
Supplementary files format and content: Analysis to which genome/plasmid they map and fastqc read length and nucleotide bias analyses for each of the two datasets (siDNA_analyses.xlsx)
Supplementary files format and content: FeatureCounts analyses for each genome/plasmid present for each of the two datasets  (FeatureCounts_results.xlsx)

organism: Escherichia coli

growth_protocol: Expression cultures were inoculated in LB supplemented with 50 mg/ml kanamycin. Expression cultures were shaken at 120 rpm in an incubator at 37 °C until an optical density at 600 nm (OD600 nm) of 0.4 was reached. The incubation temperature was then decreased to 18 °C. When the OD600 nm reached 0.6, expression of the proteins was induced by adding isopropyl b-D-thiogalactoside (IPTG) to a final concentration of 0.2 mM. Expression of pAgo and ACE proteins took place at 18 °C for 20 h. Cells were harvested by centrifugation at 4,000 x g at 4 °C for 30 min.

extract_protocol:
To extract nucleic acids co-puriﬁed with MaAgo, 40 µl of purified protein was mixed with 310 µl of amylose buffer supplemented with EDTA (10 mM ﬁnal concentration) and 40 µl proteinase K (20 mg/ml, New England Biolabs). The sample mix was incubated for two hours at room temperature. After incubation, 400 µl Roti phenol/chloroform/isoamyl alcohol was added, the sample was vortexed, and centrifuged for 15 min. The upper aqueous phase was isolated and 0.1 volumes of 1M sodium acetate, 3 volumes 100% ethanol, and 10 µl of linear polyacrylamide (Alfa Aesar) were added. This mix was briefly vortexed and incubated at -20 °C for 16 h. The samples were centrifuged for 30 min, after which the supernatant was removed without disturbing the pellet. The pellet was washed with 500 µl 70% ethanol (pre-cooled to -20 °C) and centrifuged for 15 min. Without disturbing the pellet, the ethanol was removed. The pellets containing the copuriﬁed nucleic acids were further dried for 10 min at 50 °C, and were resuspended in 50 µl of RNase free water.
The DNA extracted from purified MaAgo was treated with RNase A (Thermo Scientific) according to the protocol of the manufacturer. The remaining DNA was puriﬁed using PCI extraction, and treated with T4 PNK (Thermo Fisher, EK0031) according to the protocol of the manufacturer. Subsequently, the DNA was again purified using PCI extraction and used as input for library preparation using the protocol described in Olovnikov, et al. (https://pubmed.ncbi.nlm.nih.gov/24034694/)

treatment_protocol: Cells were lysed by sonication (QSONICA Q700A-220 sonicator with ½” tip, amplitude 35%, 1s on/2 s off, 4 min total on-time) in Lysis Buffer (125 mM NaCl, 5 mM Imidazole, 20 mM Tris-HCl pH 8, and 5 mM MnCl2) supplemented with protease inhibitors (100 μg/ml 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF) and 1 μg/ml Pepstatin A). After centrifugation at 40,000 x g at 4 °C for 45 min, the cell-free extract was loaded on a 5 ml HisTrap HP column (Cytiva Life Sciences), which was subsequently washed with 25 ml of Washing Buffer I (125 mM NaCl, 20 mM Imidazole, 20 mM Tris-HCl pH 8, and 5 mM MnCl2). Bound protein was eluted with Elution Buffer I (125 mM NaCl, 250 mM Imidazole, 20 mM Tris-HCl pH 8, and 5 mM MnCl2). The eluted protein was loaded on a custom 20 ml amylose resin column and was washed with Washing Buffer II (125 mM NaCl, 20 mM Tris-HCl pH 8, 1 mM DTT, and 5 mM MnCl2). The protein was eluted with Elution Buffer II (125 mM NaCl, 20 mM Tris-HCl pH8, 10 mM Maltose, 1 mM DTT, and 5 mM MnCl2).

value: BL21 Star (DE3)

value: MaACE1 co-expressed


title: E20 CD45 negative scrnaseq

data_processing:
Raw fastq files were demultiplexed with 10X Genomics Cell Ranger
Assembly: galgal6
Supplementary files format and content: .tsv, matrix, barcodes, and features files can be opened and analyzed wtih Seurat and Signac (R packages). Cloupe files can be opened with Loupe Cell Browser, a software from 10X Genomics.
Supplementary files format and content: .h5 file can be opened with Seruat (R package).

extract_protocol:
Lungs were extracted from embryos and subsequently dissociated. They were stained for the major cell populations of the lungs and FACs sorted. Roughly equal proportions of collected cell populations were mixed for scMultiome. Only epithelial cells or samples depleted of immune cells were taken for scRNA. Sorted cells were then sequenced.
50 cycles for read 1, 49 cycles for read2, 8 cycles for index1, and 24 cycles for index2
28 cycles read1, 90 cycles read2, 10 cycles Index1, and 10 cycles Index2

value: all lung cells, except immune cells


title: MaAgo-associated siDNA, no MaACE1

value: No treatment


title: Naive_neg2

description: ST2- Tregs from tumor-free omentum of mouse #2


title: WT2

description: Library name: Sample 3


title: Naive_neg1

description: ST2- Tregs from tumor-free omentum of mouse #1


title: w1118_ovaries_pA_rep1

description:
Library name: w1118_ovaries_pA_rep1
polyA selected RNA sequencing from w1118 ovaries replicate 1

value: female

value: Oregon R

value: 2 -7 days old


title: WT1

description: Library name: Sample 1