title: C. elegans scRNA-seq: VC2396 (mec-3(gk1126)) whole embryo 600 minutes

city: Seattle

first: Robert

middle: H

last: Waterston

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

description: Library name: mec3_600

data_processing:
The single-cell RNA-seq reads were mapped using the 10X genomics CellRanger pipeline (8.0.0) to a modified version of the WormBase WS290 C. elegans and C. briggsae reference genomes (available through SRA BioProject PRJNA1201888). As was previously done for the C. elegans reference genome, the C. briggsae 3’ UTR annotations were similarly extended to improve gene expression quantification. After alignment, the C. briggsae and new/mutant C. elegans datasets were filtered for cells that were likely doublets between two different cell types. Within all cells, the percentages of reads coming from the background ambient RNA profile was determined and subtracted.
To jointly project the two species data into the same reduced dimensional space, we used Reciprocal Principle Components Analysis (RPCA), implemented in Seurat V5 (5.1.0). Both species gene by cell matrix were first subsetted to the 1:1 orthologs. The cells of both species were then jointly split by collection batch and each batch was run through a standard pipeline of normalization and finding the 2,000 most variable features. Subsequently, the datasets were integrated by batch.  After integration, the data were further reduced to 2 dimensions using UMAP implemented in Seurat. Clusters were then identified inside of the integrated space using louvain clustering and matched to tissue classes using known marker genes. Cells belonging to these tissue classes were further subsetted, reintegrated using RPCA on 50 principal components, and re-projected for subsequent cell type annotation. Additional cell subsets based on the inferred embryo time were similarly reintegrated using RPCA and re-projected for subsequent progenitor annotation.  The terminal cell types were annotated using markers, trajectory relationships, and embryo time. The progenitor cell types from C. briggsae were similarly annotated using markers with known progenitor-specific expression in C. elegans. We used multiple markers per lineage branch.
To generate an aggregated quantification of each cell type's gene expression, we calculated a relative expression metric, the Transcripts Per Million (TPM) for each cell type. As 10x single-cell RNA-seq data is 3’ biased, there is no requirement for gene size correction of the TPM values. First, the background corrected gene by cell matrix was normalized for library sequencing depth and complexity by dividing by a per-cell size factor (calculated in Monocle3). Second, the matrix was subsetted to the cells corresponding to a single cell type in one species. Next, the mean expression of every gene was calculated. Finally, each cell type's expression vector was scaled to 1,000,000 using each species' full gene set. The process was repeated for every cell type from either species.
Assembly: WormBase WS290 (C. elegans and C. briggsae)
Supplementary files format and content: Supplementary_files_format_and_content: expression_matrix.mtx contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are background corrected UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, lineage, etc.) for each cell. Columns in gene_annotations.csv: elegans_gene_short_name,elegans_gene_long_name,elegans_id,briggsae_id,briggsae_gene_short_name,briggsae_gene_long_name,gene.type.  Columns in cell_annotations.csv: cell_type,lineage_broad,species,n.umi,barcode,packer_cell.type,packer_cell.subtype,packer_plot.cell.type,packer_lineage,smoothed.embryo.time,embryo.time.bin,germline_pseudotime,time.point,batch,genotype,filter,mt.frac,cel_lineage_broad,cbr_lineage_broad,cel_lineage_complete,cbr_lineage_complete,lineage_complete

organism: Caenorhabditis elegans

source_name: embryonic cells

extract_protocol: see experimental design

value: embryonic cells


title: Ex vivo cultured HBC 5-2, scRNAseq

status: Public on Mar 26 2025

type: SRA

city: Baltimore

first: Guanghui

last: Yang

state: MD

address: 3400 North Charles Street

department: Biology

country: USA

institute: Howard Hughes Medical Institute/The Johns Hopkins University

description: Library name: HBC_pair_5-2

library_source: transcriptomic single cell

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file. Trimmed paired reads were then mapped to the reference genome using STAR ver. 2.7.11a. The reference genome contains sequences of GRCm38 and ERCC spike-in.
StringTie ver. 2.2.1 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 100) as well as all ERCC spike-in genes.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM, TPM values for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Olfactory epithelium

growth_protocol: Mouse olfactory epithelium (OE) tissues were dissected from adult mice (6-8 weeks old) 2 days after the methimazole injection. The collected OE tissue was finely minced in complete HBC culture medium and subjected to multiple enzymatic digestions to collect horizontal basal cells (HBCs). HBCs were cultured in dishes pre-coated with suitable extracellular matrix based on experimental needs and complete HBC medium was used in all experiments.

extract_protocol:
Single daughter cells after division of ex vivo cultured primary HBC cells were collected individually using mouth pipette with pairing information noted. Each cell was lysed and 1 ml of pre-diluted (1:10^6) ERCC spike-in was added to the single cell lysate.
RNAs inside single cell lysate were captured by oligo-dT beads and then processed following the G&T-seq protocol to construct the single cell RNA-Seq library.

tag: tissue

value: Olfactory epithelium

tag: cell type

value: Horizontal basal cell

tag: genotype

value: Wild type


title: C. elegans scRNA-seq: VC2396 (mec-3(gk1126)) whole embryo 300 minutes

description: Library name: mec3_300

library_source: transcriptomic


title: Ex vivo cultured HBC 5-1, scRNAseq

description: Library name: HBC_pair_5-1


title: Sorghum-Root-1 h-ZnEx-2

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

description:
Library name: S51R_1
RNA-seq of Sorghum: Root-1 h-ZnEx-2

data_processing:
For mapping reads we used Sorghum bicolor v3.1BTx623 (Cooper et al., 2019). reference genome (https://phytozome-next.jgi.doe.gov/info/Sbicolor_v3_1_1). RNAseq data was analyzed with the DRAGEN Bio-IT Platform (v3.8) using default parameters (Cooper et al., 2019).
Assembly: reference genome (https://phytozome-next.jgi.doe.gov/info/Sbicolor_v3_1_1)
Supplementary files format and content: FullTPMMatrix_SampleMean_Annotations.csv

molecule: total RNA

organism: Sorghum bicolor

source_name: Root

growth_protocol: Seeds of Sorghum bicolor cv. BTx623 were germinated on filter paper in 6 cm petri dishes, then transplanted to a hydroponic growth system with a temperature setting of 21-27ºC in a greenhouse. S. bicolor cv. BTx623 seedlings were transplanted into modified Hoagland’s solution (1.25 mM KNO3, 1.25 mM Ca(NO3)2, 250 µM NH4NO3, 500 µM MgSO4, 250 µM KH2PO4, 50 µM H3BO3, 10 µM MnSO4, 0.2 µM CuSO4, 0.5 µM Na2MoO4, 1 µM ZnSO4, 50 µM NaFe(III)EDTA, pH 5.6) 7 days after germination.

extract_protocol:
Total RNA was extracted from root and leaf samples using the Spectrum Plant Total RNA kit (Sigma-Aldrich). Approximately 100 mg of ground tissues were lysed in 850 µl of preheated CTAB buffer. Proteins were removed by mixing with 600 µl of chloroform-isoamyl alcohol (24:1 v:v). After centrifugation, the supernatant was passed through the filter column provided in the Spectrum Plant Total RNA kit (Sigma-Aldrich) and total RNAs were extracted following the manufacturer's manual.
A total of 181 RNAseq libraries from sorghum samples were generated and sequenced by Texas A&M University Genomics and Bioinformatics Service (https://www.txgen.tamu.edu) using Perkin Elmer Nextflex Rapid Directional RNA-seq kit 2.0 including Nextflex Poly-A-Selection 2.0 beads for polyA enrichment. All 181 samples were sequenced using a 2X150 v1.5 bp paired end (PE) approach and four lanes on an Illumina Novaseq 6000 S4 instrument targeting 20-30 million reads per sample.

treatment_protocol: After three-week acclimation in the hydroponic system, seedlings were randomized and transplanted into modified Hoagland’s solutions with different ZnSO4 and NaFe(III)EDTA concentrations: control solution (1 µM ZnSO4, 50 µM NaFe(III)EDTA), Zn deficiency (ZnLim) solution (0 µM ZnSO4, 50 µM NaFe(III)EDTA), excess Zn (ZnEx) solution (100 µM ZnSO4, 50 µM NaFe(III)EDTA), Fe deficiency (FeLim) solution (1 µM ZnSO4, 0 µM NaFe(III)EDTA), and excess Fe (FeEx) solution (1 µM ZnSO4, 1 mM NaFe(III)EDTA). Samples for RNA extraction were collected between 10:00 AM and 12:00 PM from three individual plants to represent three biological replicates. Leaf and root samples were collected at the same time points in parallel for RNA extraction and ICP-MS measurements.

value: Root


title: C. elegans scRNA-seq: YL633 (ceh-9(tm2747)) whole embryo 600 minutes

description: Library name: ceh9_600


title: BLGSP-71-08-00025

type: genomic

city: Burnaby

first: Ryan

middle: D.

last: Morin

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to human Infinium Methylation EPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: HiScan with standard recommended settings

data_processing: minfi package (v.1.40.0) in R environment (v.4.1.3)

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumour

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Protocol

tag: cell line

value: Burkitt lymphoma biopsy


title: Ex vivo cultured HBC 4-2, scRNAseq

description: Library name: HBC_pair_4-2


title: BLGSP-71-08-00023


title: Sorghum-Root-1 h-ZnEx-1

description:
Library name: S36R_1
RNA-seq of Sorghum: Root-1 h-ZnEx-1


title: C. elegans scRNA-seq: YL633 (ceh-9(tm2747)) whole embryo 300 minutes

description: Library name: ceh9_300


title: Ex vivo cultured HBC 6-2, scRNAseq

description: Library name: HBC_pair_6-2


title: C. elegans scRNA-seq: wild-type N2 VC2010 whole embryo 600 minutes

description: Library name: wt_600


title: BLGSP-71-08-00022


title: Sorghum-Root-1 h-FeLim-3

description:
Library name: S44R_1
RNA-seq of Sorghum: Root-1 h-FeLim-3


title: Ex vivo cultured HBC 4-1, scRNAseq

description: Library name: HBC_pair_4-1


title: Sorghum-Root-1 h-FeLim-2

description:
Library name: S43R_1
RNA-seq of Sorghum: Root-1 h-FeLim-2


title: Ex vivo cultured HBC 3-2, scRNAseq

description: Library name: HBC_pair_3-2


title: Sorghum-Root-1 h-FeLim-1

description:
Library name: S12R_1
RNA-seq of Sorghum: Root-1 h-FeLim-1


title: C. elegans scRNA-seq: VC4183  (M03D4.4(gk5269)) whole embryo 300 minutes

description: Library name: M03D4.4_300


title: BLGSP-71-06-00342


title: BLGSP-71-08-00026


title: Sorghum-Root-1 h-ZnEx-3

description:
Library name: S70R_1
RNA-seq of Sorghum: Root-1 h-ZnEx-3


title: BLGSP-71-08-00021


title: C. elegans scRNA-seq: VC4183 (M03D4.4(gk5269)) whole embryo 500 minutes

description: Library name: M03D4.4_500


title: BLGSP-71-06-00340


title: Ex vivo cultured HBC 2-1, scRNAseq

description: Library name: HBC_pair_2-1


title: BLGSP-71-06-00292


title: Sorghum-Root-1 h-FeEX-3

description:
Library name: S28R_1
RNA-seq of Sorghum: Root-1 h-FeEX-3


title: Ex vivo cultured HBC 2-2, scRNAseq

description: Library name: HBC_pair_2-2


title: Sorghum-Root-1 h-FeEX-2

description:
Library name: S6R_1
RNA-seq of Sorghum: Root-1 h-FeEX-2


title: BLGSP-71-06-00289


title: Sorghum-Root-1 h-FeEX-1

description:
Library name: S35R_1
RNA-seq of Sorghum: Root-1 h-FeEX-1


title: Ex vivo cultured HBC 1-2, scRNAseq

description: Library name: HBC_pair_1-2


title: Ex vivo cultured HBC 1-1, scRNAseq

description: Library name: HBC_pair_1-1


title: Sorghum-Root-1 h-Control-3

description:
Library name: S22R_1
RNA-seq of Sorghum: Root-1 h-Control-3


title: BLGSP-71-06-00286


title: Sorghum-Root-1 h-Control-2

description:
Library name: S2R_1
RNA-seq of Sorghum: Root-1 h-Control-2


title: Umbilical cord, non-antiviral treatment,replicate 2

type: RNA

city: Nanning

first: wang

last: Cuimin

address: No. 6, Taoyuan Road, Qingxiu District

country: China

institute: Guangxi Academy of Medical Sciences

description:
U1_rep2
Umbilical cord Serum lncRNA expression of pregnant women who did not receive antiviral treatment

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: umbilical cord

label_protocol: LncRNA and mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was isolated from cartilage of KOA patients and healthy volunteers using TRIzol reagent. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were labeled, purified and amplified. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

treatment_protocol: Umbilical cord serum samples and placenta tissue were obtained from six patients with high hepatitis B viral load, normal liver function, and no post-delivery antiviral treatment. Among these, three pregnant women underwent antiviral treatment, while the remaining three were observed without antiviral intervention. Blood samples were collected, centrifuged at 300g for 5 minutes, and the supernatant was aliquoted into 2 mL tubes (0.5 mL each). The samples were labeled with relevant information, including sample number, date, and time, and stored at -80℃ to maintain lncRNA integrity. Placental tissue was preserved in RNA protective solution at -80℃.

tag: treatment

value: non-antiviral treatment

tag: gender

value: female


title: Sorghum-Root-1 h-Control-1

description:
Library name: S20R_1
RNA-seq of Sorghum: Root-1 h-Control-1


title: Umbilical cord, non-antiviral treatment,replicate 3

description:
U1_rep3
Umbilical cord Serum lncRNA expression of pregnant women who did not receive antiviral treatment


title: Sorghum-Root-0 h-Control-6

description:
Library name: S90R_0
RNA-seq of Sorghum: Root-0 h-Control-6


title: Myeloid cells, 10 weeks, Gene expression

city: Minneapolis

first: Adam

last: Herman

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
10X Genomics
wk10_seurat.rds

data_processing:
Cell inference, hashtag demultiplexing, and  gene counting were perfomed with cellranger multi (v7.1.0)
Secondary hashtag demultiplexing was done with cellhashR (v.1.0.4) (https://github.com/BimberLab/cellhashR)
Integration of the wk10 and wk5 was performed in Seurat (v4.3.0) using the anchor-based method on SCT assay.
Assembly: mm10
Supplementary files format and content: .rds files containing Seurat objects of the expression and hashtag count data prior to filtering.

source_name: liver

extract_protocol:
Perfused livers were disrupted using a gentleMACS tissue dissociator and resuspended in RPMI-1640 media containing 10% FBS. This suspension was centrifuged at 60 g for 1 min and the supernatant containing hepatic immune cells was collected and centrifuged again at 480 g for 8 min. The pellet was resuspended in 10 mL of 37.5% Percoll (Sigma) in PBS and centrifuged at 850 g for 30 min. The resulting pellet was washed followed by red blood cell lysis in ammonium-chloride-potassium (ACK) lysis buffer for 2 min at room temperature.
Cells were loaded into the ports of a 10x-Genomics chip following a single-cell 3’ kit. The gene expression and CMO libraries were sequenced using a Novaseq S4 chip (2x150bp PE).

treatment_protocol: At six weeks of age, mice were fed a high-fat high-carbohydrate (HFHC, 40% kcal palm oil, 20% kcal fructose, and 2% cholesterol supplemented with 23.1 g/L d-fructose and 18.9 g/L d-glucose in the drinking water). Group-housed mice were fed the HFHC diet for an average of 14 weeks and then assigned to either a sham operation or VSG surgery. Five days before surgeries mice were single-housed and exposed to a liquid diet. Post-surgery, the mice remained single-housed and were provided a liquid diet for 2 days at which time the HFHC diet was re-introduced. Seven days post-surgery the mice were only fed the HFHC diet for the remainder of the study. To account for weight-loss-independent effects, there was a sham ad-libitum-fed group (Sham AL) and a sham group that was pair-fed (Sham PF) to the VSG group to match the weight loss post-surgery.

value: liver

value: Myeloid cells

tag: strain

value: VSG, SHAM AL, SHAM PF


title: Myeloid cells, 5 weeks, CMO

description:
10X Genomics
wk5_seurat.rds


title: Umbilical cord, antiviral treatment,replicate 3

description:
U2_rep3
Umbilical cord Serum lncRNA expression of pregnant women who receiving antiviral treatment

value: antiviral treatment


title: BLGSP-71-06-00283


title: MEFs, SRT+RSL3, 2 hours  rep2

city: Hangzhou

first: haixia

last: chen

state: Zhejiang

address: Research Building, School of Medicine, Zijingang Campus, Zhejiang University

institute: epartment of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine

description: Library name: sirt1_RSL3_r1

data_processing:
Differential gene expression was quantified using KEGG pathway enrichment analysis, identifying the metabolic and signaling pathways associated with these differentially expressed genes.
Supplementary files format and content: NCBIreadcount.xlsx

source_name: Mouse Embryo

growth_protocol: MEF were purchased from American Type Culture Collection. All cell lines were cultured in DMEM (Sigma, D5796) containing 10% fetal bovine serum (Gibco) and 1% Penicillin-Streptomycin (NCM, #C100C5) at 37°C in a 5% CO2 humidified incubator

extract_protocol:
Total RNA from HT1080 cells and lung homogenates were extracted using AG RNAex Pro Reagent (Accurate Biotechnology, #AG21102) according to the manufacturer’s instructions. RNAs were reverse-transcribed using Evo M-MLV RT Premix for qPCR (Accurate Biotechnology, #AG11706).
Libraries were constructed using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina, San Diego, CA, USA). We then sequenced these libraries on the Illumina sequencing platform ( Illumina HiSeq X Ten).

treatment_protocol: MEFs were treated with SRT 1720 0.2um 30min before， then treated with 1um RSL3 for 2 hours

value: Mouse Embryo

value: MEFs

value: Mouse Embryonic Fibroblasts

value: WT


title: Myeloid cells, 5 weeks, Gene expression

description:
10X Genomics
wk5_seurat.rds


title: Umbilical cord, antiviral treatment,replicate 2

description:
U2_rep2
Umbilical cord Serum lncRNA expression of pregnant women who receiving antiviral treatment


title: Umbilical cord, antiviral treatment,replicate 1

description:
U2_rep1
Umbilical cord Serum lncRNA expression of pregnant women who receiving antiviral treatment


title: Sorghum-Root-0 h-Control-4

description:
Library name: S88R_0
RNA-seq of Sorghum: Root-0 h-Control-4


title: Myeloid cells, 10 weeks, CMO

description:
10X Genomics
wk10_seurat.rds


title: BLGSP-71-06-00285


title: MEFs, SRT+RSL3, 2 hours  rep1

description: Library name: sirt1_RSL3


title: BLGSP-71-06-00288


title: BLGSP-71-06-00277


title: BLGSP-71-06-00281


title: Sorghum-Root-0 h-Control-5

description:
Library name: S87R_0
RNA-seq of Sorghum: Root-0 h-Control-5


title: placental tissue, non-antiviral treatment,replicate 3

description:
P1_rep3
placental tissue lncRNA expression of pregnant women who did not receive antiviral treatment

source_name: placenta


title: placental tissue, antiviral treatment,replicate 3

description:
P2_rep3
placental tissue lncRNA expression of pregnant women who receiving antiviral treatment


title: placental tissue, antiviral treatment,replicate 2

description:
P2_rep2
placental tissue lncRNA expression of pregnant women who receiving antiviral treatment


title: Sorghum-Root-0 h-Control-2

description:
Library name: S78R_0
RNA-seq of Sorghum: Root-0 h-Control-2


title: BLGSP-71-06-00280


title: MEFs, RSL3, 2 hours  rep2

description: Library name: RSL3_r1


title: BLGSP-71-06-00254


title: MEFs, RSL3, 2 hours  rep1

description: Library name: RSL3


title: BLGSP-71-06-00255


title: Sorghum-Root-0 h-Control-1

description:
Library name: S77R_0
RNA-seq of Sorghum: Root-0 h-Control-1


title: placental tissue, non-antiviral treatment,replicate 2

description:
P1_rep2
placental tissue lncRNA expression of pregnant women who did not receive antiviral treatment


title: Sorghum-Root-0 h-Control-3

description:
Library name: S79R_0
RNA-seq of Sorghum: Root-0 h-Control-3


title: BLGSP-71-06-00253


title: Sorghum-Leaf-7 d-ZnLim-2

description:
Library name: S18L_3
RNA-seq of Sorghum: Leaf-7 d-ZnLim-2

source_name: Leaf

value: Leaf


title: MEFs, CTL, 2 hours  rep2

description: Library name: control_r1

value: CTL


title: Umbilical cord, non-antiviral treatment,replicate 1

description:
U1_rep1
Umbilical cord Serum lncRNA expression of pregnant women who did not receive antiviral treatment


title: BLGSP-71-06-00252


title: MEFs, SRT, 2 hours  rep1

description: Library name: srit1


title: Sorghum-Leaf-7 d-ZnLim-3

description:
Library name: S33L_3
RNA-seq of Sorghum: Leaf-7 d-ZnLim-3


title: MEFs, CTL, 2 hours  rep1

description: Library name: control


title: OR-STH-5

city: Beijing

first: Runqing

last: Chi

address: 2 Yuanmingyuan West Rd

institute: State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences

description:
Library name: Sample 10
readcount.txt

data_processing:
paired reads containing adaptor sequences were filtered out.
paired reads with more than 0.5% N (N means base information could not be determined) were removed.
Low-quality paired reads were removed.
Assembly: The filtered reads were aligned to the reference genome using HISAT2.
Supplementary files format and content: Tab-segmented text files contain predicted chromosomal locations of small Rnas, genes of origin, etc.,.

organism: Ovis aries

source_name: longissimus dorsi

growth_protocol: muscle cells were maintained in DMEM supplemented with 10% fetalbovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
mRNA and miRNA back-transcription were performed using the HiScript® IiI All-in-one RT SuperMix kit (Vazyme, Nanjing, China) and the miRNA first-strand cDNA synthetic kit (Vazyme, Nanjing, China).
We constructed sequencing libraries using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA) following the manufacturer’s instructions.

treatment_protocol: To establish the best concentration for the experiment, estradiol was diluted in a gradient (0 nM, 1 nM, 10 nM, and 100 nM) and then added to the myoblast culture medium along with the suspended cells.

value: longissimus dorsi

value: skeletal muscle

value: Primary myoblasts


title: Sorghum-Leaf-7 d-ZnLim-1

description:
Library name: S40L_3
RNA-seq of Sorghum: Leaf-7 d-ZnLim-1


title: Sorghum-Leaf-7 d-ZnEx-5

description:
Library name: S50L_3
RNA-seq of Sorghum: Leaf-7 d-ZnEx-5


title: OR-STH-4

description:
Library name: Sample 9
readcount.txt


title: MEFs, SRT, 2 hours  rep2

description: Library name: srit1_r1


title: BLGSP-71-06-00190


title: placental tissue, antiviral treatment,replicate 1

description:
P2_rep1
placental tissue lncRNA expression of pregnant women who receiving antiviral treatment


title: placental tissue, non-antiviral treatment,replicate 1

description:
P1_rep1
placental tissue lncRNA expression of pregnant women who did not receive antiviral treatment


title: BLGSP-71-06-00180


title: Sorghum-Leaf-7 d-ZnEx-4

description:
Library name: S46L_3
RNA-seq of Sorghum: Leaf-7 d-ZnEx-4


title: Sorghum-Leaf-7 d-ZnEx-3

description:
Library name: S58L_3
RNA-seq of Sorghum: Leaf-7 d-ZnEx-3


title: OR-STH-1

description:
Library name: Sample 6
readcount.txt


title: OR-STH-3

description:
Library name: Sample 8
readcount.txt


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated six-day old_3

city: Ithaca

first: Catherine

middle: Herminia

last: Kagemann

state: NY

address: 215 Tower Rd, Ithaca, NY, Room 233

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
No reads were trimmed as FastQC scores were high and adapter content was low. Sample alignment of one seample was below 70% and was thus removed (WT three-day old infected with wMel3). DESeq2 was used for differential expression analysis
Assembly: dmel-all-chromosome-r6.39.fasta (Flybase.org)
Supplementary files format and content: WT_All_ReadCounts.txt: processed WT read count matrix, WT_All_Sample.txt: metadata file for processed WT readcount matrix, 10E7_Null_All_ReadCounts.txt: processed bam hypomorph read count matrix, 10E7_Null_All_Sample.txt: metadata for processed bam hypomorph read count matrix

organism: Drosophila melanogaster

source_name: Ovaries

extract_protocol:
We used the Zymo’s Quick-RNA 96 kit to extra total RNA from D. melanogaster ovaries
3' RNA-seq library

value: Ovaries

value: Tissue

value: Bam hypomorph (w1118;bamL255F/bam[3xP3dsRed]) + wMelCS2b W. pipientis

value: Mated six-day old


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated six-day old_4


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated six-day old_2


title: BLGSP-71-06-00177

value: Burkitt lymphoma biopsy


title: STH-5

description:
Library name: Sample 5
readcount.txt


title: Sorghum-Leaf-7 d-ZnEx-1

description:
Library name: S19L_3
RNA-seq of Sorghum: Leaf-7 d-ZnEx-1


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated six-day old_1


title: STH-4

description:
Library name: Sample 4
readcount.txt


title: BLGSP-71-06-00172


title: STH-3

description:
Library name: Sample 3
readcount.txt


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated three-day old_3

value: Mated three-day old


title: BLGSP-71-06-00171


title: BLGSP-71-06-00174


title: Sorghum-Leaf-7 d-ZnEx-2

description:
Library name: S67L_3
RNA-seq of Sorghum: Leaf-7 d-ZnEx-2


title: Sorghum-Leaf-7 d-FeLim-2

description:
Library name: S34L_3
RNA-seq of Sorghum: Leaf-7 d-FeLim-2


title: Sorghum-Leaf-7 d-FeLim-3

description:
Library name: S59L_3
RNA-seq of Sorghum: Leaf-7 d-FeLim-3


title: OR-STH-2

description:
Library name: Sample 7
readcount.txt


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated three-day old_4


title: STH-1

description:
Library name: Sample 1
readcount.txt


title: BLGSP-71-06-00178


title: BLGSP-71-06-00170


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated three-day old_2


title: Bam hypomorph infected with wMelCS2b W. pipientis, mated three-day old_1


title: BLGSP-71-06-00169


title: hsSKM, H2BK120ub, ChIP 0.2kpa2

city: Tianjin

first: Mingwei

last: Feng

state: Tianjin

address: Weijin road No.92

department: SPST

institute: Tianjin University

library_source: genomic

data_processing:
Sequencing was performed in paired-end reads of 2 ×150 bp using an Illumina X ten system.
raw reads were trimmed using TrimGalore (Galaxy Version 0.6.7) on Galaxy (https://usegalaxy.org) to remove extra adapters and then mapped to the reference genome (GRCh38 for human) using Bowtie2 (Galaxy Version 2.4.2) to generate BAM file.
Coverage bigWig file from the BAM was generated using bamCoverage (Galaxy Version 3.5.1.0.0).
heatmap was created using computeMatrix (Galaxy Version 3.5.1.0.0) and plotProfile (Galaxy Version 3.5.1.0.0).
enrichment analysis were perfomed on g:GOSt
Assembly: hg38
Supplementary files format and content: bigWig

source_name: hsSKM

extract_protocol:
cells were fixed with 1%FA for 10min, neutralized with 10% 1M glycine at room temperature for 5 min and washed with PBS.
ChIP–seq libraries were prepared using Hyper Prep Kit (KAPA, KK8504) according to the manufacturer’s instructions.

treatment_protocol: cells were cultured on fibronectin-coated 64kPa or 0.2kPa stiffness hydrogel for 48hours before extraction.

value: hsSKM

value: cultured on fibronectin coated 0.2kPa hydrogel


title: hsSKM, H2BK120ub, ChIP 0.2kpa1


title: Sorghum-Leaf-7 d-FeEX-3

description:
Library name: S73L_3
RNA-seq of Sorghum: Leaf-7 d-FeEX-3


title: Bam hypomorph infected with wMelCS2b W. pipientis, unmated three-day old_4

value: Unmated three-day old


title: STH-2

description:
Library name: Sample 2
readcount.txt


title: BLGSP-71-06-00166


title: Sorghum-Leaf-7 d-FeEX-2

description:
Library name: S16L_3
RNA-seq of Sorghum: Leaf-7 d-FeEX-2


title: hsSKM, H2BK120ub, ChIP 64kPa2

value: cultured on fibronectin coated 64kPa hydrogel


title: BLGSP-71-06-00167


title: Bam hypomorph infected with wMelCS2b W. pipientis, unmated three-day old_3


title: hsSKM, H2BK120ub, ChIP 64kPa1


title: Sorghum-Leaf-7 d-Control-3

description:
Library name: S10L_3
RNA-seq of Sorghum: Leaf-7 d-Control-3


title: Sorghum-Leaf-7 d-FeEX-1

description:
Library name: S4L_3
RNA-seq of Sorghum: Leaf-7 d-FeEX-1


title: Bam hypomorph infected with wMelCS2b W. pipientis, unmated three-day old_2


title: BLGSP-71-06-00164


title: Sorghum-Leaf-7 d-Control-2

description:
Library name: S29L_3
RNA-seq of Sorghum: Leaf-7 d-Control-2


title: BLGSP-71-06-00165


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated six-day old_4

value: Bam hypomorph (w1118;bamL255F/bam[3xP3dsRed]) + wMelCS2a W. pipientis


title: H460,rep1,4Cseq

city: London

first: Reuben

middle: Mangi

last: Yaa

address: Sir Michael Uren Hub, White City Campus, 86 Wood Ln, London

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Reads were trimmed to 30bps and mapped to indexed NlaIII-DnpII reduced hg38 chromosome 6 using bowtie version 1.2.2 on -m 1 mismatch condition.
Aligned reads were then transformed to reads per NlaIII fragment ends and smoothened using a 30-fragment mean running window.
fragments interacting with the viewpoint called using monotonic regression in the peakC peak caller
Assembly: hg38
Supplementary files format and content: bed  showing TBXT interacting regions
Library strategy: 4C-seq

source_name: Lung; Pleural effusion

growth_protocol: H460 and H358 cells were maintained in RPMI 1640  and A549 cells were maintained in DMEM , all supplemented with 10% (v/v) fetal bovine serum  and 100 U/mL penicillin/0.1 mg/mL streptomycin  and maintained in a humidified 37℃ incubator with 5% CO2.

extract_protocol:
Cells were cross-linked with 4% PFA in PBS pH7.4 and lysed in cold lysis buffer (50mM Tris-HCl pH 7.5, 150mM NaCl, 5mM EDTA, 0.5% Tergitol NP-40, 1% Triton® X-100 and 1X Complete protease inhibitors  First restriction enzyme digestion was done using NlaIII (NEB, R0125L) followed with ligation by T4 DNA ligase (NEB, M0202L). Reverse crosslinking was using 15 uL Proteinase K (20mg/mL) at 65℃ overnight and genomic DNA purified by ethanol precipitation method. Second restriction enzyme digest was done on the ligated products using DpnII (NEB, R0543S) and finally ligated to form 4C-templates which were purified MercK Millipore AmiconTM ultra-15 centrifugal filter units.
4C library was prepared from the 200ng template using Q5 Polymerase  and HPLC purified P7(read1) and P5(read2) illumina merged long sequencing primers (IDT) which spanned the viewpoint (TBXT promoter). (Viewpoint hg38 TBXT promoter iF 5'-GGCTTTCCCGCGGACATG-3' and iR(5'-TTATTTCCGTCCATTTCCCTC-3'). PCR done on 98℃ for 30 seconds, 30 cycles of 98℃ for 10 seconds, annealing temperature gradient of 55℃ for 30 seconds and 72℃ for 30 seconds. 4C library PCR products were purified using High Pure PCR Product Purification Kit (Roche, 11 732 668 001) and Agencourt, AMPure XP reagent. Libraries were sequenced as on Illumina platform HiseqXten

value: Lung; Pleural effusion

value: lung cancer cells

tag: disease

value: Carcinoma


title: Bam hypomorph infected with wMelCS2b W. pipientis, unmated three-day old_1


title: Sorghum-Leaf-7 d-FeLim-1

description:
Library name: S15L_3
RNA-seq of Sorghum: Leaf-7 d-FeLim-1

value: Leaf


title: BLGSP-71-06-00163


title: H358,rep2,4Cseq

source_name: Lung; Bronchiole

value: Lung; Bronchiole

value: Bronchioalveolar Carcinoma


title: BLGSP-71-06-00162


title: Sorghum-Leaf-4 d-ZnLim-3

description:
Library name: S17L_2
RNA-seq of Sorghum: Leaf-4 d-ZnLim-3


title: H358,rep1,4Cseq


title: Sorghum-Leaf-4 d-ZnLim-2

description:
Library name: S38L_2
RNA-seq of Sorghum: Leaf-4 d-ZnLim-2


title: BLGSP-71-06-00161


title: A549,rep2,4Cseq

source_name: Lung

value: Lung


title: BLGSP-71-06-00160


title: Sorghum-Leaf-4 d-ZnLim-1

description:
Library name: S76L_2
RNA-seq of Sorghum: Leaf-4 d-ZnLim-1


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated six-day old_1

value: Ovaries

value: Tissue


title: BLGSP-71-06-00159


title: H460,rep2,4Cseq


title: A549,rep1,4Cseq


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated three-day old_4


title: Sorghum-Leaf-4 d-ZnEx-3

description:
Library name: S11L_2
RNA-seq of Sorghum: Leaf-4 d-ZnEx-3


title: BLGSP-71-06-00158


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated three-day old_2


title: Sorghum-Leaf-7 d-Control-1

description:
Library name: S25L_3
RNA-seq of Sorghum: Leaf-7 d-Control-1


title: Sorghum-Leaf-4 d-ZnEx-1

description:
Library name: S57L_2
RNA-seq of Sorghum: Leaf-4 d-ZnEx-1


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated three-day old_3


title: RAC3-3

city: Xi'an

first: Dong

last: Wu

state: Shaanxi Province

address: Changle Road 169

institute: National Translational Science Center for Molecular Medicine, Fourth Military Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
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
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release111
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: Hepatocellular carcinoma

value: RAC5 overexpression


title: BLGSP-71-06-00157

value: Burkitt lymphoma biopsy


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated six-day old_3

value: Mated six-day old


title: RAC3-2

value: RAC4 overexpression


title: Ex vivo cultured HBC 3-1, scRNAseq

description: Library name: HBC_pair_3-1

value: Olfactory epithelium

value: Horizontal basal cell

value: Wild type


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated three-day old_1

value: Bam hypomorph (w1118;bamL255F/bam[3xP3dsRed]) + wMelCS2a W. pipientis

value: Mated three-day old


title: Sorghum-Leaf-4 d-FeLim-3

description:
Library name: S27L_2
RNA-seq of Sorghum: Leaf-4 d-FeLim-3


title: Sorghum-Leaf-4 d-ZnEx-2

description:
Library name: S69L_2
RNA-seq of Sorghum: Leaf-4 d-ZnEx-2


title: BLGSP-71-06-00156


title: RAC3-1

value: RAC3 overexpression


title: Sorghum-Leaf-4 d-FeLim-2

description:
Library name: S54L_2
RNA-seq of Sorghum: Leaf-4 d-FeLim-2

value: Leaf


title: Bam hypomorph infected with wMelCS2a W. pipientis, mated six-day old_2


title: Bam hypomorph infected with wMelCS2a W. pipientis, unmated three-day old_4

value: Unmated three-day old


title: NC3

value: WT


title: NC2


title: Bam hypomorph infected with wMelCS2a W. pipientis, unmated three-day old_3


title: BLGSP-71-06-00154


title: NC1


title: Sorghum-Leaf-4 d-FeLim-1

description:
Library name: S23L_2
RNA-seq of Sorghum: Leaf-4 d-FeLim-1


title: Bam hypomorph infected with wMelCS2a W. pipientis, unmated three-day old_2


title: Sorghum-Leaf-4 d-FeEX-3

description:
Library name: S55L_2
RNA-seq of Sorghum: Leaf-4 d-FeEX-3


title: Bam hypomorph infected with wMelCS2a W. pipientis, unmated three-day old_1


title: WG2_M_W3_R3

city: Greenwood

first: Bibhu

last: Simkhada

state: SC

address: 114 Gregor Mendel Cir

department: Department of Genetics and Biochemistry

institute: Clemson University

description:
RNA-seq with rRNA depletion
WG2_M3_week3_S42

data_processing:
Barcoded reads were demultiplexed using the NovaSeq Illumina BaseSpace sequencing pipeline and merged across S1 flow cell lanes
Filtering: We used the fastP pipeline (Chen et al., 2018) to filter out low quality, short, and adapter reads and quantified rRNA using the bbduk command
Read counts were generated using the feature counts pipeline from the Subread package (Liao et al. 2014).
Genes with median expression of log10 ≤ 2 or with expression of 0 in more than 25% of the samples were excluded from the analyses.
We normalized the data using the Ge-TMM method (Smid et al. 2018)
Assembly: Drosophila melanogaster reference genome (FlyBase Release 6.13)
Supplementary files format and content: text file contains raw counts for each sample

source_name: brains

extract_protocol:
Each sample contained 20 brains, flash frozen in dry ice immediately after dissection. Sample were homogenized using metal beads.
RNA libraries were prepared with a Tecan Genomics Universal PlusTM system.

value: brains

tag: Sex

value: Male

tag: age

value: Week 3

tag: replicate


title: BLGSP-71-06-00148


title: BLGSP-71-06-00146


title: Sorghum-Leaf-4 d-FeEX-1

description:
Library name: S24L_2
RNA-seq of Sorghum: Leaf-4 d-FeEX-1


title: WG2_M_W3_R2

description:
RNA-seq with rRNA depletion
WG2_M2_week3_S48


title: Bam hypomorph infected with wMel3 W. pipientis, mated six-day old_4

value: Ovaries

value: Tissue

value: Bam hypomorph (w1118;bamL255F/bam[3xP3dsRed]) + wMel3 W. pipientis


title: Sorghum-Leaf-4 d-FeEX-2

description:
Library name: S5L_2
RNA-seq of Sorghum: Leaf-4 d-FeEX-2


title: Bam hypomorph infected with wMel3 W. pipientis, mated six-day old_3

value: Mated six-day old


title: WG2_M_W3_R1

description:
RNA-seq with rRNA depletion
WG2_M1_week3_S17


title: BLGSP-71-06-00145

value: Burkitt lymphoma biopsy


title: Sorghum-Leaf-4 d-Control-3

description:
Library name: S72L_2
RNA-seq of Sorghum: Leaf-4 d-Control-3


title: Bam hypomorph infected with wMel3 W. pipientis, mated six-day old_2


title: WG2_M_W0_R3

description:
RNA-seq with rRNA depletion
WG2_M3_S2

value: Week 0


title: Sorghum-Leaf-4 d-Control-2

description:
Library name: S68L_2
RNA-seq of Sorghum: Leaf-4 d-Control-2


title: BLGSP-71-06-00155


title: Sorghum-Leaf-4 d-Control-1

description:
Library name: S14L_2
RNA-seq of Sorghum: Leaf-4 d-Control-1


title: BLGSP-71-06-00144


title: WG2_M_W0_R2

description:
RNA-seq with rRNA depletion
WG2_M2_S16


title: BLGSP-71-06-00143


title: BLGSP-71-06-00149


title: Bam hypomorph infected with wMel3 W. pipientis, mated three-day old_4


title: Bam hypomorph infected with wMel3 W. pipientis, mated six-day old_1


title: Sorghum-Leaf-21 d-ZnLim-3

description:
Library name: S32L_5
RNA-seq of Sorghum: Leaf-21 d-ZnLim-3


title: BLGSP-71-06-00142


title: WG2_F_W3_R3

description:
RNA-seq with rRNA depletion
WG2_F4_week3_S47

value: Female


title: Bam hypomorph infected with wMel3 W. pipientis, mated three-day old_3


title: BLGSP-71-06-00139


title: WG2_F_W3_R2

description:
RNA-seq with rRNA depletion
WG2_F3_week3_S39


title: Bam hypomorph infected with wMel3 W. pipientis, mated three-day old_2


title: Sorghum-Leaf-21 d-ZnLim-1

description:
Library name: S1L_5
RNA-seq of Sorghum: Leaf-21 d-ZnLim-1


title: Sorghum-Leaf-21 d-ZnLim-2

description:
Library name: S37L_5
RNA-seq of Sorghum: Leaf-21 d-ZnLim-2


title: Bam hypomorph infected with wMel3 W. pipientis, mated three-day old_1


title: WG2_F_W3_R1

description:
RNA-seq with rRNA depletion
WG2_F2_week3_S46


title: BLGSP-71-06-00098


title: BLGSP-71-06-00097


title: Sorghum-Leaf-21 d-ZnEx-2

description:
Library name: S51L_5
RNA-seq of Sorghum: Leaf-21 d-ZnEx-2


title: Bam hypomorph infected with wMel3 W. pipientis, unmated three-day old_4


title: WG2_F_W0_R3

description:
RNA-seq with rRNA depletion
WG2_F4_S29


title: Bam hypomorph infected with wMel3 W. pipientis, unmated three-day old_3


title: WG2_F_W0_R2

description:
RNA-seq with rRNA depletion
WG2_F2_S5


title: BLGSP-71-06-00095


title: Sorghum-Leaf-21 d-ZnEx-1

description:
Library name: S36L_5
RNA-seq of Sorghum: Leaf-21 d-ZnEx-1


title: WG2_F_W0_R1

description:
RNA-seq with rRNA depletion
WG2_F1_S19


title: Bam hypomorph infected with wMel3 W. pipientis, unmated three-day old_2


title: BLGSP-71-06-00094


title: Y160C_M_W3_R3

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_M4_week3_S33

value: NAGLU Y160C


title: Bam hypomorph infected with wMel3 W. pipientis, unmated three-day old_1


title: BLGSP-71-06-00093


title: Sorghum-Leaf-21 d-FeLim-2

description:
Library name: S43L_5
RNA-seq of Sorghum: Leaf-21 d-FeLim-2


title: BLGSP-71-06-00137


title: Bam hypomorph infected with wMel2a W. pipientis, mated six-day old_4

value: Bam hypomorph (w1118;bamL255F/bam[3xP3dsRed]) + wMel2a W. pipientis


title: Y160C_M_W3_R2

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_M3_week3_S30


title: Sorghum-Leaf-21 d-ZnEx-3

description:
Library name: S70L_5
RNA-seq of Sorghum: Leaf-21 d-ZnEx-3


title: BLGSP-71-06-00091


title: Sorghum-Leaf-21 d-FeLim-1

description:
Library name: S12L_5
RNA-seq of Sorghum: Leaf-21 d-FeLim-1


title: Bam hypomorph infected with wMel2a W. pipientis, mated six-day old_3


title: Sorghum-Leaf-21 d-FeEX-3

description:
Library name: S28L_5
RNA-seq of Sorghum: Leaf-21 d-FeEX-3


title: Y160C_M_W3_R1

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_M2_week3_S35


title: Sorghum-Leaf-21 d-FeLim-3

description:
Library name: S44L_5
RNA-seq of Sorghum: Leaf-21 d-FeLim-3


title: Y160C_M_W0_R3

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_M4_S15


title: BLGSP-71-06-00090


title: BLGSP-71-06-00089


title: Sorghum-Leaf-21 d-FeEX-2

description:
Library name: S6L_5
RNA-seq of Sorghum: Leaf-21 d-FeEX-2


title: Bam hypomorph infected with wMel2a W. pipientis, mated six-day old_2


title: Bam hypomorph infected with wMel2a W. pipientis, mated six-day old_1


title: Bam hypomorph infected with wMel2a W. pipientis, mated three-day old_4

value: Mated three-day old


title: BLGSP-71-06-00087


title: Sorghum-Leaf-21 d-Control-3

description:
Library name: S22L_5
RNA-seq of Sorghum: Leaf-21 d-Control-3


title: Y160C_M_W0_R2

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_M3_S9


title: BLGSP-71-06-00088


title: Sorghum-Leaf-21 d-FeEX-1

description:
Library name: S35L_5
RNA-seq of Sorghum: Leaf-21 d-FeEX-1


title: Bam hypomorph infected with wMel2a W. pipientis, mated three-day old_3


title: Sorghum-Leaf-21 d-Control-2

description:
Library name: S2L_5
RNA-seq of Sorghum: Leaf-21 d-Control-2


title: Y160C_F_W3_R3

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_F4_week3_S31


title: BLGSP-71-06-00086


title: Sorghum-Leaf-21 d-Control-1

description:
Library name: S20L_5
RNA-seq of Sorghum: Leaf-21 d-Control-1


title: Bam hypomorph infected with wMel2a W. pipientis, mated three-day old_2


title: BLGSP-71-06-00085


title: WG2_M_W0_R1

description:
RNA-seq with rRNA depletion
WG2_M1_S28


title: Y160C_M_W0_R1

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_M2_S18


title: Y160C_F_W3_R1

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_F1_week3_S38


title: Sorghum-Leaf-2 d-ZnLim-3

description:
Library name: S49L_1
RNA-seq of Sorghum: Leaf-2 d-ZnLim-3


title: Bam hypomorph infected with wMel2a W. pipientis, mated three-day old_1


title: BLGSP-71-06-00084


title: Bam hypomorph infected with wMel2a W. pipientis, unmated three-day old_3


title: BLGSP-71-06-00081


title: Bam hypomorph infected with wMel2a W. pipientis, unmated three-day old_4


title: Sorghum-Leaf-2 d-ZnLim-2

description:
Library name: S9L_1
RNA-seq of Sorghum: Leaf-2 d-ZnLim-2


title: Sorghum-Leaf-2 d-ZnLim-1

description:
Library name: S8L_1
RNA-seq of Sorghum: Leaf-2 d-ZnLim-1


title: Y160C_F_W0_R2

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_F3_S8


title: BLGSP-71-06-00080


title: BLGSP-71-06-00251


title: BLGSP-71-06-00078


title: Bam hypomorph infected with wMel2a W. pipientis, unmated three-day old_2


title: Sorghum-Leaf-2 d-ZnEx-2

description:
Library name: S46L_1
RNA-seq of Sorghum: Leaf-2 d-ZnEx-2


title: BLGSP-71-06-00076


title: W422X_M_W3_R3

description:
RNA-seq with rRNA depletion
NAGLU_W422X_M4_week3_S21

value: NAGLU W422X


title: Y160C_F_W0_R1

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_F2_S13


title: Bam hypomorph infected with wMel2a W. pipientis, unmated three-day old_1


title: Sorghum-Leaf-2 d-ZnEx-1

description:
Library name: S58L_1
RNA-seq of Sorghum: Leaf-2 d-ZnEx-1

value: Leaf


title: Bam hypomorph, mated six-day old_4


title: BLGSP-71-06-00075


title: W422X_M_W3_R2

description:
RNA-seq with rRNA depletion
NAGLU_W422X_M3_week3_S43


title: W422X_M_W3_R1

description:
RNA-seq with rRNA depletion
NAGLU_W422X_M1_week3_S25


title: Bam hypomorph, mated six-day old_3


title: BLGSP-71-06-00074


title: Sorghum-Leaf-2 d-FeLim-3

description:
Library name: S7L_1
RNA-seq of Sorghum: Leaf-2 d-FeLim-3


title: Y160C_F_W0_R3

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_F4_S7


title: W422X_M_W0_R3

description:
RNA-seq with rRNA depletion
NAGLU_W422X_M3_S4


title: BLGSP-71-06-00072


title: Sorghum-Leaf-2 d-ZnEx-3

description:
Library name: S50L_1
RNA-seq of Sorghum: Leaf-2 d-ZnEx-3


title: Bam hypomorph, mated six-day old_1


title: BLGSP-71-06-00071


title: Sorghum-Leaf-2 d-FeLim-1

description:
Library name: S3L_1
RNA-seq of Sorghum: Leaf-2 d-FeLim-1


title: BLGSP-71-06-00020


title: W422X_M_W0_R1

description:
RNA-seq with rRNA depletion
NAGLU_W422X_M1_S20


title: Bam hypomorph, mated three-day old_4


title: Sorghum-Leaf-2 d-FeEX-3

description:
Library name: S65L_1
RNA-seq of Sorghum: Leaf-2 d-FeEX-3


title: Bam hypomorph, mated three-day old_3


title: W422X_F_W3_R3

description:
RNA-seq with rRNA depletion
NAGLU_W422X_F4_week3_S44


title: BLGSP-71-06-00016


title: Sorghum-Leaf-2 d-FeEX-2

description:
Library name: S42L_1
RNA-seq of Sorghum: Leaf-2 d-FeEX-2


title: W422X_F_W3_R2

description:
RNA-seq with rRNA depletion
NAGLU_W422X_F3_week3_S11


title: Bam hypomorph, mated three-day old_2


title: Sorghum-Leaf-2 d-FeEX-1

description:
Library name: S31L_1
RNA-seq of Sorghum: Leaf-2 d-FeEX-1


title: BLGSP-71-06-00015


title: Bam hypomorph, mated three-day old_1


title: W422X_F_W3_R1

description:
RNA-seq with rRNA depletion
NAGLU_W422X_F1_week3_S41


title: Bam hypomorph, mated six-day old_2


title: Sorghum-Leaf-2 d-Control-3

description:
Library name: S45L_1
RNA-seq of Sorghum: Leaf-2 d-Control-3


title: W422X_F_W0_R3

description:
RNA-seq with rRNA depletion
NAGLU_W422X_F3_S3


title: Sorghum-Leaf-2 d-Control-2

description:
Library name: S48L_1
RNA-seq of Sorghum: Leaf-2 d-Control-2


title: Sorghum-Leaf-2 d-FeLim-2

description:
Library name: S13L_1
RNA-seq of Sorghum: Leaf-2 d-FeLim-2


title: BLGSP-71-06-00013


title: W422X_F_W0_R2

description:
RNA-seq with rRNA depletion
NAGLU_W422X_F2_S22


title: W422X_M_W0_R2

description:
RNA-seq with rRNA depletion
NAGLU_W422X_M2_S14


title: Bam hypomorph, unmated three-day old_3

value: Unmated three-day old


title: Sorghum-Leaf-2 d-Control-1

description:
Library name: S30L_1
RNA-seq of Sorghum: Leaf-2 d-Control-1


title: BLGSP-71-06-00012


title: BLGSP-71-06-00019


title: Bam hypomorph, unmated three-day old_4


title: W422X_F_W0_R1

description:
RNA-seq with rRNA depletion
NAGLU_W422X_F1_S40


title: BLGSP-71-06-00011


title: Bam hypomorph, unmated three-day old_2


title: Bam hypomorph, unmated three-day old_1


title: Sorghum-Leaf-14 d-ZnLim-2

description:
Library name: s39L_4
RNA-seq of Sorghum: Leaf-14 d-ZnLim-2


title: Sorghum-Leaf-14 d-ZnLim-3

description:
Library name: s21L_4
RNA-seq of Sorghum: Leaf-14 d-ZnLim-3


title: WT bam infected with wMelCS2b W. pipientis,, Mated six -day old_4

value: WT bam w1118 + wMelCS2b W. pipientis


title: Sorghum-Leaf-14 d-ZnLim-1

description:
Library name: S61L_4
RNA-seq of Sorghum: Leaf-14 d-ZnLim-1


title: KO_M_W3_R1

description:
RNA-seq with rRNA depletion
NAGLU_KO_M1_week3_S26

value: brains

value: NAGLU KO


title: BLGSP-71-06-00008


title: BLGSP-71-06-00005


title: WT bam infected with wMelCS2b W. pipientis,, Mated six -day old_3


title: Sorghum-Leaf-14 d-ZnEx-3

description:
Library name: S63L_4
RNA-seq of Sorghum: Leaf-14 d-ZnEx-3


title: BLGSP-71-06-00007


title: KO_M_W0_R3

description:
RNA-seq with rRNA depletion
NAGLU_KO_M4_S10

value: Male


title: BLGSP-71-06-00004


title: Sorghum-Leaf-14 d-ZnEx-2

description:
Library name: S52L_4
RNA-seq of Sorghum: Leaf-14 d-ZnEx-2


title: WT bam infected with wMelCS2b W. pipientis,, Mated six -day old_2

value: Ovaries


title: KO_M_W0_R2

description:
RNA-seq with rRNA depletion
NAGLU_KO_M2_S45


title: WT bam infected with wMelCS2b W. pipientis,, Mated six -day old_1

value: Tissue


title: BLGSP-71-06-00002


title: KO_M_W0_R1

description:
RNA-seq with rRNA depletion
NAGLU_KO_M1_S23


title: WT bam infected with wMelCS2b W. pipientis,, Mated three-day old_4


title: Sorghum-Leaf-14 d-FeLim-3

description:
Library name: s26L_4
RNA-seq of Sorghum: Leaf-14 d-FeLim-3


title: BLGSP-71-06-00001


title: WT bam infected with wMelCS2b W. pipientis,, Mated three-day old_3


title: KO_M_W3_R3

description:
RNA-seq with rRNA depletion
NAGLU_KO_M4_week3_S36

value: Week 3


title: KO_F_W3_R3

description:
RNA-seq with rRNA depletion
NAGLU_KO_F3_Week3_S12


title: T group, Donor #11

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Allele calling was performed with GenomeStudio 2.0 Genotyping module using default parameters and human reference GRCh38. Data points with GenCall score < 0.15 were deemed unreliable and noted as "No call". Call rates for 16 samples were all > 0.997. For a specific donor, the cytokine-treated sample was designated as subject, and the control sample as reference. We performed paired sample analysis using GenomeStudio and obtained the Paired Sample Table. SNP-based Log2 (Rsub/Rref) values representing the total copy number estimates for treated CD33+ cells relate to the control cells.

label: Cy3, Cy5

source_name: Flow sorted CD33+ cells

label_protocol: not provided

extract_protocol: Cells were harvested from dishes. Accutase 37C incubation for 10 min was used to harvest adherent cells. CD33+ cells from each group were isolated by flow cytometry. Genomic DNA was extracted from cell pellets using Qiamp DNA Micro kit and processed with CytoSNP array.

treatment_protocol: MDSCs were generated by treating PBMCs with GM-CSF (10ng/mL) + IL-6 (10ng/mL) at 5x10^5 cell/mL in full media at 37C with 5%CO2. Cytokines were added daily for 3 days.

tag: tag

value: IL-6 treated

value: Flow sorted CD33+ cells


title: Y160C_F_W3_R2

description:
RNA-seq with rRNA depletion
NAGLU_Y160C_F2_week3_S27


title: KO_M_W3_R2

description:
RNA-seq with rRNA depletion
NAGLU_KO_M3_week3_S34


title: KO_F_W3_R2

description:
RNA-seq with rRNA depletion
NAGLU_KO_F2_Week3_S24


title: Sorghum-Leaf-14 d-FeLim-1

description:
Library name: S66L_4
RNA-seq of Sorghum: Leaf-14 d-FeLim-1


title: C group, Donor #11

value: Control


title: WT bam infected with wMelCS2b W. pipientis,, Mated three-day old_2


title: KO_F_W3_R1

description:
RNA-seq with rRNA depletion
NAGLU_KO_F1_week3_S32

value: Female


title: T group, Donor #9


title: WT bam infected with wMelCS2b W. pipientis, unmated three-day old_3


title: Sorghum-Leaf-14 d-FeEX-3

description:
Library name: S60L_4
RNA-seq of Sorghum: Leaf-14 d-FeEX-3


title: C group, Donor #9


title: KO_F_W0_R3

description:
RNA-seq with rRNA depletion
NAGLU_KO_F3_S37

value: Week 0


title: Sorghum-Leaf-14 d-ZnEx-1

description:
Library name: S47L_4
RNA-seq of Sorghum: Leaf-14 d-ZnEx-1


title: T group, Donor #8


title: KO_F_W0_R2

description:
RNA-seq with rRNA depletion
NAGLU_KO_F2_S1


title: Sorghum-Leaf-14 d-FeEX-2

description:
Library name: s75L_4
RNA-seq of Sorghum: Leaf-14 d-FeEX-2


title: WT bam infected with wMelCS2b W. pipientis, unmated three-day old_1


title: Sorghum-Leaf-14 d-FeEX-1

description:
Library name: S56L_4
RNA-seq of Sorghum: Leaf-14 d-FeEX-1


title: KO_F_W0_R1

description:
RNA-seq with rRNA depletion
NAGLU_KO_F1_S6


title: Sorghum-Leaf-14 d-FeLim-2

description:
Library name: s53L_4
RNA-seq of Sorghum: Leaf-14 d-FeLim-2


title: C group, Donor #8


title: WT bam infected with wMelCS2a W. pipientis, Mated six -day old_4

value: WT bam w1118 + wMelCS2a W. pipientis

value: Mated six-day old


title: T group, Donor #7


title: Sorghum-Leaf-14 d-Control-2

description:
Library name: S41L_4
RNA-seq of Sorghum: Leaf-14 d-Control-2


title: WT bam infected with wMelCS2a W. pipientis, Mated six -day old_3


title: C group, Donor #7


title: Sorghum-Leaf-14 d-Control-1

description:
Library name: S71L_4
RNA-seq of Sorghum: Leaf-14 d-Control-1


title: WT bam infected with wMelCS2a W. pipientis, Mated six -day old_2


title: multiplexed sample set 4, WAT, HTO

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description:
Library name: MUX HTOs 25-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise

library_source: other

data_processing:
Raw sequencing reads were processed into count matrices using Cell Ranger (10x Genomics; version 6.1.2) and using GENCODE vM24 of the GRCm38 mouse assembly.
HTO sequencing reads were processed into corresponding cout matrices using the Cumulus Tool on Feature Barcoding (https://github.com/lilab-bcb/cumulus_feature_barcoding)
DemuxEM (version 0.1.6) was used to sort cells into individual samples based on their antibody hashtags.
Ambient RNA was removed from the processed DGEs using CellBender (version 0.2.0)
Assembly: GRCm38
Supplementary files format and content: Cell Ranger output files: *.counts.h5 (same as raw_feature_bc_matrix.h5)
Supplementary files format and content: CellBender output files *.cellbender.tsv.gz
Supplementary files format and content: Cumulus Tool on Feature Barcoding output: *.htos.csv

molecule: protein

source_name: white adipose tissue

growth_protocol: C57BL/6J DIO male mice, 12-13 weeks of age, were purchased from Jackson Labs and maintained on 60% HFD for an additional 2-4 weeks prior to surgery.

extract_protocol:
Adipose sNuc-seq was performed as previously described (PMID: 38416649). Briefly, for each 10x run, 8-12 adipose samples were separately homogenized in TST buffer using a gentleMACS Dissociator (Miltenyi Biotec). Lysate was filtered through 40 µm and 20 µm nylon filters (CellTreat), centrifuging and resuspending in fresh buffer each time. After the second wash, each sample was incubated with NucBlue (Thermofisher scientific) as well as an individual hashtag antibody (BioLegend) for 45 minutes. After incubation, nuclei were washed and flow sorted together into RT Reagent B (10x Genomics) using a Beckman Coulter MoFlo Astrios EQ with a 70 μm nozzle to remove poor quality nuclei and count the same number of nuclei per sample.
Sorted nuclei were immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol. Single Cell 3’ v3.1 chemistry was used to process all samples and cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). Gene expression libraries were multiplexed and sequenced on the Nextseq 500 (Illumina).

treatment_protocol: Mice were fasted overnight prior to surgery. Animals were anesthetized using isoflurane, and a small laparotomy incision was made in the abdominal wall. The lateral 80% of the stomach along the greater curvature was excised in VSG animals by using an ETS 35-mm staple gun. Sham surgery was performed by the application of gentle pressure on the stomach with blunt forceps for 15 seconds. All mice received one dose of Buprinex (0.1 mg/kg) and Carprofen (5 mg/kg) immediately after surgery. All mice received Carprofen (5 mg/kg) for 3 days after surgery. Animals were placed on DietGel Boost for 3 days after surgery. They were placed back on the pre-operative solid diet (60% HFD) on day 4 post-surgery. Body weight and food intake as well as overall health were monitored daily for the first 7 days after surgery and once weekly until the end of the studies. Semaglutide (0.04 mg/kg) was administered to some sham-operated mice subcutaneously once daily starting at day 1 post-surgery. Animals were sacrificed at two timepoints post-surgery, at 10 days for all groups (timepoint 1), and at 25 days for semaglutide treated animals and at 35 days for sham and VSG animals (timepoint 2). All mice were fasted for 4 hours prior to tissue collection.

value: white adipose tissue

value: male

tag: condition

value: 5x VSG, 1x sham, 1x sham+SEMA

tag: timepoint

value: 3x timepoint 1 (0d), 2x timepoint 2 (35d)

tag: hto

value: see feature_README.txt for mapping


title: multiplexed sample set 2+, WAT, HTO

description:
Library name: MUX HTOs 21-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise

value: 2x VSG, 2x sham, 3x sham+SEMA (2 iWAT, 1 eWAT)

value: 4x timepoint 1 (0d; 1 eWAT, 3 iWAT), 3x timepoint 2 (25/35d)


title: WT bam infected with wMelCS2b W. pipientis,, Mated three-day old_1

value: Ovaries

value: WT bam w1118 + wMelCS2b W. pipientis

value: Mated three-day old


title: T group, Donor #5

value: IL-6 treated


title: multiplexed sample set 1, iWAT, HTO

description:
Library name: MUX HTOs 18-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise

source_name: inguinal white adipose tissue

value: inguinal white adipose tissue

value: 2x VSG, 2x sham, 2x sham+SEMA

value: 3x timepoint 1 (0d), 3x timepoint 2 (25/35d)


title: WT bam infected with wMelCS2a W. pipientis, Mated six -day old_1

value: Tissue


title: C group, Donor #5

value: Control

value: Flow sorted CD33+ cells


title: multiplexed sample set 3, eWAT, HTO

description:
Library name: MUX HTOs 11-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue


title: WT bam infected with wMelCS2b W. pipientis, unmated three-day old_2

value: Unmated three-day old


title: WT bam infected with wMelCS2a W. pipientis, Mated three-day old_4

value: WT bam w1118 + wMelCS2a W. pipientis


title: Sorghum-Leaf-0 h-Control-5

description:
Library name: S87L_0
RNA-seq of Sorghum: Leaf-0 h-Control-5

value: Leaf


title: Sorghum-Leaf-14 d-Control-3

description:
Library name: S62L_4
RNA-seq of Sorghum: Leaf-14 d-Control-3


title: multiplexed sample set 2, eWAT, HTO

description:
Library name: MUX HTOs 08-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise

value: male

value: see feature_README.txt for mapping


title: WT bam infected with wMelCS2a W. pipientis, Mated three-day old_3


title: Sorghum-Leaf-0 h-Control-4

description:
Library name: S88L_0
RNA-seq of Sorghum: Leaf-0 h-Control-4


title: T group, Donor #4


title: Sorghum-Leaf-0 h-Control-3

description:
Library name: S79L_0
RNA-seq of Sorghum: Leaf-0 h-Control-3


title: C group, Donor #4


title: T group, Donor #3


title: multiplexed sample set 3, iWAT, HTO

description:
Library name: MUX HTOs 20-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise


title: multiplexed sample set 1, eWAT, HTO

description:
Library name: MUX HTOs 06-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise


title: WT bam infected with wMelCS2a W. pipientis, Mated three-day old_2


title: Sorghum-Leaf-0 h-Control-1

description:
Library name: S77L_0
RNA-seq of Sorghum: Leaf-0 h-Control-1


title: C group, Donor #3


title: WT bam infected with wMelCS2a W. pipientis, Mated three-day old_1


title: Sorghum-Leaf-0 h-Control-2

description:
Library name: S78L_0
RNA-seq of Sorghum: Leaf-0 h-Control-2


title: WT bam infected with wMelCS2a W. pipientis, unmated three-day old_4


title: T group, Donor #1


title: Sorghum-Leaf-0 h-Control-6

description:
Library name: S90L_0
RNA-seq of Sorghum: Leaf-0 h-Control-6


title: multiplexed sample set 3, iWAT, GEX

description:
Library name: MUX 20-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript


title: multiplexed sample set 2+, WAT, GEX

description:
Library name: MUX 21-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript

value: white adipose tissue

value: 2x VSG, 2x sham, 3x sham+SEMA (2 iWAT, 1 eWAT)

value: 4x timepoint 1 (0d; 1 eWAT, 3 iWAT), 3x timepoint 2 (25/35d)


title: WT bam infected with wMelCS2a W. pipientis, unmated three-day old_3

value: Ovaries


title: C group, Donor #1


title: multiplexed sample set 4, WAT, GEX

description:
Library name: MUX 25-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript

value: 5x VSG, 1x sham, 1x sham+SEMA

value: 3x timepoint 1 (0d), 2x timepoint 2 (35d)


title: multiplexed sample set 1, iWAT, GEX

description:
Library name: MUX 18-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript

value: inguinal white adipose tissue

value: 2x VSG, 2x sham, 2x sham+SEMA


title: WT bam infected with wMelCS2a W. pipientis, unmated three-day old_2

value: Tissue


title: sfRNA2, 1m7 noMod control , Rep4

city: Aurora

first: Matthew

last: Szucs

state: CO

institute: University of Colorado Denver Anschutz Medical Campus

description:
sfRNA2_minus1m7_Rep4
In vitro transcribed RNA
sfRNA2_1m7_Rep4_normalized_reactivities.txt

data_processing:
Raw reads were processed using shapemapper2 v2.1.5. args:  --overwrite --verbose --name --out  --temp  --target --min-depth 5000 --modified --folder plus --untreated --folder minus
Assembly: HM440560.1
Supplementary files format and content: Textfile output of normalized reactivity and counts from Shapemapper2

molecule: other

organism: Powassan virus

source_name: in vitro transcribed RNA

extract_protocol:
Modified RNAs were cleaned up with the RNEasy Micro Kit
Reverse transcription, second strand synthesis, and library prep of modified RNA. The following protocol was applied to the full length 3′UTR, sfRNA1 and sfRNA2 RNA species. Approximately 400 ng of modified or control RNA was incubated with of 200 ng/μL random nonamer primer (NEB; S1254S) and 1.0 μL of POWV_SHAPEMAP_RT_Primer (Supplemental Table S2) at 65°C for 5 minutes and then cooled on ice. To each of the reactions 8.0 μL of MAP buffer (125mM Tris pH 8.0, 187.5mM KCl, 15mM MnCl2, 25mM DTT, 1.25mM equimolar dNTP mix, and 200U Superscript III) was added to the reaction and incubated at 25°C for 2 minutes. The reaction was then incubated at 25°C for 10 minutes, 42°C for 3 hours, 70°C for 15 minutes, and cooled to 4°C. The RNA/cDNA hybrids were then purified on the G25 (Cyteva) spin column following the manufacturers protocol. Second strand synthesis of the cDNA was carried out using the NEBNext second strand synthesis kit (NEB) following the manufacturer’s instructions. The resultant cDNA was purified using the DNA Clean & Concentrator-5 kit (Zymo) eluting in 10 μL of DEPC-treated H2O and quantified fluorometrically with the Qubit (Thermo) using the dsDNA HS Assay Kit (Thermo). Next generation sequencing library prep was performed with the Nextera XT DNA library preparation kit (Illumina) using the Nextera XT Index Kit v2 Set B (Illumina). Samples were normalized and pooled together using a combination of the Qubit (Thermo) and the 4200 TapeStation System (Agilent Technologies) with the High Sensitivity D1000 Screen Tape (Agilent Technologies). Final libraries were sequenced on the NovaSeq 6000 platform (Illumina).

treatment_protocol: 1m7 and DMS probing of the POWV 3’UTR: 1.0 μg of in vitro transcribed full length POWV 3′UTR was heat denatured in 12 μLDEPC treated H2O at 95°C for two minutes and then immediately cooled on ice. To this 8.0 μLof concentrated RNA folding buffer was added to a final concentration of 100 mM NaCl, 50 mM Tris pH 7.5, 4 mM MgCl2, and folded for 20 minutes at 55°C. The folded RNA was slow cooled to room temperature. After cooling the reaction was split into two, and 0.5 μg of the RNA was labeled with 10mM 1m7 (Sigma) or DMSO (Sigma) at 37°C for 75 seconds (five 1m7 hydrolysishalf-lives). In parallel, 0.5 μg of folded RNA was modified with 0.5% DMS (Sigma) or an equal mount of EtOH as a negative control for 5 minutes at 37°C, and then quenched with 2-Mercaptoethanol (Sigma). All conditions were purified and concentrated using the Qiagen RNeasy micro kit.1m7 and DMS probing of the POWV sfRNA1 and sfRNA2: 2 μg of folded in vitro transcribed POWV 3′UTR was treated with Xrn1 for two hours. After incubation, DMS, 1m7, or their appropriate controls was added to the reaction at the same final concentrations as the 3’UTR probing outlined above. The reactions were cleaned up using the RNeasy Micro Kit (Qiagen) and separated on a 6% denaturing PAGE gel. The sfRNA1 and sfRNA2 bands were visualized by UV shadowing and cut from the gel. The RNA was eluted from the gel using the crush soak method at 4°C overnight in ~ 5 mL 50 mM Sodium cacodylate pH 6.5, 0.1 mM EDTA, and 50mM NaCl. The RNA was concentrated with a 30K molecular weight cut off Amicon Ultra spin Concentrators (Millipore-Sigma) and buffer exchanged into DEPC water.

value: in vitro transcribed RNA

value: no Mod (EtOH)


title: N1 SubPlacenta Pup1, Control, Sham

city: Gainesville

first: Rebecca

last: Wilson

address: 1345 Center Dr

institute: University of Florida

data_processing:
Short reads were trimmed using trimmomatic (v 0.36), and QC on the original and trimmed reads was performed using FastQC (v 0.11.4) and MultiQC.
The reads were aligned to the transcriptome using STAR version 2.7.9a
Transcript abundance was quantified using RSEM (RSEM v1.3.1)
Assembly: Cavpor3.0
Supplementary files format and content: comma-separated values containing fastq counts in all samples
Supplementary files format and content: comma-separated values containing raw FPKM values for all genes in all samples

organism: Cavia porcellus

source_name: Subplacenta/Decidua

extract_protocol:
Total RNA was extracted from frozen sub-placenta/decidua using Qiagen RNeasy Midi extraction kit
RNA libraries were prepared using Illumina Stranded mRNA Prep Kit following manufacturers instructions

value: Subplacenta/Decidua

tag: breed

value: Dunkin-Hartley

tag: diet

value: Control

value: Sham


title: GR2 SubPlacenta Pup3, Control, Sham

tag: tissue


title: WT bam infected with wMelCS2a W. pipientis, unmated three-day old_1

tag: cell type

value: WT bam w1118 + wMelCS2a W. pipientis

value: Unmated three-day old


title: WT bam infected with wMel3 W. pipientis, Mated six -day old_4

tag: genotype

value: WT bam w1118 + wMel3 W. pipientis

value: Mated six-day old


title: multiplexed sample set 3, eWAT, GEX

description:
Library name: MUX 11-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript

value: epididymal white adipose tissue

value: male

value: 3x timepoint 1 (0d), 3x timepoint 2 (25/35d)


title: F43 SubPlacenta Pup3, Control, Sham


title: multiplexed sample set 2, eWAT, GEX

description:
Library name: MUX 08-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript


title: multiplexed sample set 1, eWAT, GEX

description:
Library name: MUX 06-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript


title: sfRNA2, 1m7 noMod control , Rep3

description:
sfRNA2_minus1m7_Rep3
In vitro transcribed RNA
sfRNA2_1m7_Rep3_normalized_reactivities.txt


title: sfRNA2 , 1m7 treated, Rep4

description:
sfRNA2_plus1m7_Rep4
In vitro transcribed RNA
sfRNA2_1m7_Rep4_normalized_reactivities.txt


title: WT bam infected with wMel3 W. pipientis, Mated six -day old_2

value: Ovaries


title: WT bam infected with wMel3 W. pipientis, Mated six -day old_3


title: L5

city: Melbourne

first: Andrew

middle: Ian

last: Jobling

state: Victoria

address: Medical Building, Cnr Grattan St and Royal Pde

department: Anatomy & Physiology

country: Australia

institute: University of Melbourne

description:
Library name: Sample 11
column name in LASER.VS.CONTROL-all_genes.txt: L5

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.18.0.12 pipeline was used to generate the sequence data.
Reads were trimmed using trim_galore v(0.4.4)1 package using the following parameters: quality=10, length=30. The trimmed reads were then aligned to the MM10 genome using STAR (v2.5.3a)2 using the following parameters: outSamType=’BAM Sorted ByCoordinate’, outFilterMultimapNmax 2
featureCounts (v1.5.3) from the subread3 package was using to assign alignments to known features of the MM10 genome with the following parameters: t exon, g gene_id, s 0 (for unstranded sequencing).
Sufficiently low-levels of rRNA were found in sequencing using the sortmeRNA4 package. High levels of alignments were seen across all samples along with high levels of mapping to unique features.
The transcripts were assembled with Stringtie (v1.3.3).
Assembly: The Gencode annotation containing both coding and non-coding annotation for mouse genome version GRcm38 (Ensemble release81) were used as a guide.
Supplementary files format and content: edgeR (v 3.22.3)6 to perform differential expression analysis.
Supplementary files format and content: tab-delimited text files with gene counts and transcript assemblies. Differential expression analysis table

source_name: RPE/choroid

growth_protocol: C57BL/6J mice were initailly used at 9 months of age and taken out to 12 months of age

extract_protocol:
RPE / choroidal tissue from control and laser-treated C57BL/6J mice (n = 6 control, n = 5 laser treated) were isolated using the RNeasy Micro total RNA kit (Qiagen, Hilden, Germany) and purity analysed (Agilent Technologies, Santa Clara, CA, USA). A SmartSeq v4 kit (Clontech Laboratories, Mountain View, CA, USA) was used for a preamplification step.
RNA libraries were prepared for sequencing using standard Illumina protocols - NexteraXT

treatment_protocol: 9 month old C57BL/6J mice were treated with the 2RT nanosecond laser at 9 months and then allowed to recover before tissue was isolated at 12 months of age. Age-mathced untreated control aniamls were also taken at 12 months of age.

value: RPE/choroid

value: laser treated


title: sfRNA2 , 1m7 treated, Rep3

description:
sfRNA2_plus1m7_Rep3
In vitro transcribed RNA
sfRNA2_1m7_Rep3_normalized_reactivities.txt


title: Whole mouse heart after PBS inhalation treatment (control) (hearts from multiple mice)

city: New York

first: Ke

last: Cheng

address: 3960 Broadway

institute: Columbia University

description:
Library name: Sample 2
10x Genomics

data_processing:
Data split First, according to the sample Index, the FASTQ sequence of each sample was obtained, and then 10x Barcode, UMI sequence, and insert part (cDNA insert/RNA reads) were obtained according to the library structure, and then we performed Barcode Filter. Barcode should meet any of the following conditions: (1) The Identified Barcode exists in the known Barcode list.; (2) The identified Barcode has only one Hamming distance from the sequence in the known Barcode library, and the posterior probability is calculated according to the sequencing error rate, the detected base quality of the Barcode, and the prior probability of the candidate Barcode (frequency distribution).  If The Posterior Probability of the candidate Barcode is greater than 0.975, then the Barcode sequence is correct and then entered the downstream analysis.  Read alignment The RNA reads section was compared to the previously constructed reference genome database using STAR alignment software. Based on the alignment of STAR61, combined with the information in the reference dataset (gtf/gff file), statistical coverage of the coverage of the various regions of the genome can be compared to the exon, intron, and intergenic region ratio information, as a reference for data quality control. STAR is an RNA-Seq data analysis commonly used as the segmentation comparison tool, which can be used to discover the connection and fusion phenomenon of exons. The basic working principle is mainly divided into two steps: the search for seed sequences, and the clustering/joining/scoring.  Quantitative statistics of gene expression 10x scRNA-Seq gene expression quantification is mainly based on UMI counts. If some pairs of reads have the same Barcode sequence, UMI tags, and alignment to the same position, they will be defined as PCR repeats; only non- PCR Repeated, and checked barcodes and UMI will be used for downstream gene quantification analysis. UMI needs to meet the following conditions: (1) Sequencing quality value is greater than 10 (90% sequencing accuracy); (2) UMI is not continuous polybase; (3) If a UMI in the same cell Barcode has only one Hamming distance from other UMIs (with more reads), then the UMI will be corrected to the UMI with more readers.  Preprocessing and data integration We adopted multiple quality control criteria to filter out low-quality single-cell transcriptomes. First, we only retained single cells that had more than 2,000 and fewer than 5,000 expressed genes, and genes that were detected in more than three cells. Totals of 19, 568 single cells and 23, 038 genes were retained for downstream analyses. scRNA-seq integration of the MI control group and the MI treatment group was conducted using the methods developed by Stuart et al62. The methods were chosen because they were well-accepted as effective approaches to correcting technical differences and removing potential batch effects. These methods first identify “anchors’, cross-dataset pairs of cells that are recognized as cells in a similar biological stage. After that, conserved cell markers were identified. Finally, datasets integration was performed, and normalized with SCTransform.  Identification of variable genes and dimensional reduction analysis All scRNA-seq analyses followed the procedures of the Seurat R package v463,64. We first identified the set of genes that were most variable in single-cell data. We employed a global-scaling normalization method “LogNormalize” that normalizes the feature expression measurements for each cell to the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result. We next calculated a subset of features that exhibited high cell-to-cell variation in the dataset. We computed 2000 highly variable features for the downstream analysis.  Single-cell clustering and differential gene expression Clustering of single cells was performed using the weighted shared nearest-neighbor graph-based clustering method30. To find markers differentially expressed among clusters, we used the same approach30. We used the binary classifier with the receiver operating characteristic curve that was incorporated in Seurat’s ‘find.markers’ function with parameters test.use = ‘wilcox’, avg_log2FC>1,  and min.pct = 0.25, which selects genes that are expressed in more than 25% of single cells in the given cluster and with average expression larger than log2(FPKM) for differential expression analysis. The selected genes were ranked based on fold changes. The higher the area under the curve or power value the more differentially expressed the gene is for the given cluster. In addition, Differential expression analyses were performed using the Seurat v4 R package to find marker genes.  Pathway enrichment analysis Pathway enrichment analysis of previously identified differentially expressed genes was performed using enrichR (https://maayanlab.cloud/Enrichr/) with GO Biological Process 202165. The differentially expressed genes had a fold change higher than 2 and adjusted p-value smaller than 0.1. To assess the statistical significance of gene overlaps we computed p-values using the hypergeometric test. Only the top significant pathways for upregulated genes and downregulated genes were plotted in Figure 4.  Partitioned approximate graph abstraction A recent approach has proposed organizing single-cell transcriptome data into a partitioned approximate graph abstraction (PAGA) that relates clusters of cells that might be developmentally related to one another30. In brief, this algorithm constructs a k-nearest neighbor graph of cells and then identifies ‘communities’ of cells via the Louvain method, similar to previous methods for analyzing CyTOF or single-cell RNA-seq data30. PAGA then constructs a graph in which the vertices are Louvain communities. Two vertices are linked with an edge in the PAGA graph when the cells in the respective communities are neighbors in the k-nearest neighbor graph more frequently than would be expected under a simple binomial model30.
Assembly: Mouse mm10

source_name: Heart

extract_protocol:
The sample was first prepared as a single cell suspension by using gentleMACS and associated tissue kit, followed by cell counting and cell viability assay. If the cell viability was 80%, the cell concentration was adjusted to 1000/µL.
The prepared cell suspensions were captured as a cell and a bead with a cell Barcode in a droplet using a microfluidic chip, and a droplet containing the cell was collected. In the droplet, the cells were lysed so that the mRNA in the cells was connected to the cell Barcode on the bead to form Single Cell GEMs (Gel Bead-in-Emulsions), and an RT reaction was carried out in the droplets, followed by demulsification to construct a cDNA library. The cell Barcode on the library sequence distinguished which cell the target sequences were from, and the sample Index on the sequence distinguished which sample the target sequences were from.  The raw data obtained by sequencing is called raw reads. We split the Barcode, UMI and insert parts of reads according to the unique library structure of 10x scRNA-Seq, and then inserted the fragments for comparison to the reference genome. Then, the ratios of the comparisons to the respective regions were statistically analyzed, and the expression amount statistics were performed; based on the results of the expression amount, the cell cluster analysis and the screening and identification of the marker genes were performed.

value: Heart

tag: cell line

value: Mixture of cells in whole heart

value: Inhalation of PBS (control)


title: L4

description:
Library name: Sample 10
column name in LASER.VS.CONTROL-all_genes.txt: L4

tag: treatment


title: WT bam infected with wMel3 W. pipientis, Mated six -day old_1

value: Tissue


title: F17 SubPlacenta Pup3, Control, Sham

value: Subplacenta/Decidua

value: Dunkin-Hartley


title: sfRNA2, 1m7 noMod control , Rep2

description:
sfRNA2_minus1m7_Rep2
In vitro transcribed RNA
sfRNA2_1m7_Rep2_normalized_reactivities.txt

value: in vitro transcribed RNA

value: no Mod (EtOH)


title: Whole mouse heart after exosome inhalation treatment (hearts from multiple mice)

description:
Library name: Sample 1
10x Genomics

value: Inhalation of exosome


title: L3

description:
Library name: Sample 9
column name in LASER.VS.CONTROL-all_genes.txt: L3


title: sfRNA2 , 1m7 treated, Rep2

description:
sfRNA2_plus1m7_Rep2
In vitro transcribed RNA
sfRNA2_1m7_Rep2_normalized_reactivities.txt


title: WT bam infected with wMel3 W. pipientis, Mated three-day old_4

value: WT bam w1118 + wMel3 W. pipientis

value: Mated three-day old


title: sfRNA2, 1m7 noMod control , Rep1

description:
sfRNA2_minus1m7_Rep1
In vitro transcribed RNA
sfRNA2_1m7_Rep1_normalized_reactivities.txt


title: F43 SubPlacenta Pup2, Control, Sham

value: Control

value: Sham


title: WT bam infected with wMel3 W. pipientis, Mated three-day old_3


title: L1

description:
Library name: Sample 7
column name in LASER.VS.CONTROL-all_genes.txt: L1


title: sfRNA2 , 1m7 treated, Rep1

description:
sfRNA2_plus1m7_Rep1
In vitro transcribed RNA
sfRNA2_1m7_Rep1_normalized_reactivities.txt


title: F43 SubPlacenta Pup1, Control, Sham


title: WT bam infected with wMel3 W. pipientis, Mated three-day old_2


title: F42 SubPlacenta Pup2, MNR, Nanoparticle

value: Maternal Nutrient Restriction

value: Nanoparticle


title: F42 SubPlacenta Pup3, MNR, Nanoparticle


title: WT bam infected with wMel3 W. pipientis, Mated three-day old_1

value: Ovaries


title: C6

description:
Library name: Sample 6
column name in LASER.VS.CONTROL-all_genes.txt: C6

value: RPE/choroid

value: age matched control


title: C5

description:
Library name: Sample 5
column name in LASER.VS.CONTROL-all_genes.txt: C5


title: F41 SubPlacenta Pup3, MNR, Nanoparticle


title: sfRNA2 , DMS treated, Rep4

description:
sfRNA2_plusDMS_Rep4
In vitro transcribed RNA
sfRNA2_DMS_Rep4_normalized_reactivities.txt

value: DMS


title: WT bam infected with wMel3 W. pipientis, unmated three-day old_4

value: Unmated three-day old


title: F41 SubPlacenta Pup2, MNR, Nanoparticle


title: WT bam infected with wMel3 W. pipientis, unmated three-day old_3

value: Tissue


title: F40 SubPlacenta Pup3, MNR, Nanoparticle

value: Subplacenta/Decidua


title: C4

description:
Library name: Sample 4
column name in LASER.VS.CONTROL-all_genes.txt: C4


title: WT bam infected with wMel3 W. pipientis, unmated three-day old_2


title: sfRNA2 , DMS treated, Rep3

description:
sfRNA2_plusDMS_Rep3
In vitro transcribed RNA
sfRNA2_DMS_Rep3_normalized_reactivities.txt


title: L2

description:
Library name: Sample 8
column name in LASER.VS.CONTROL-all_genes.txt: L2

value: laser treated


title: C3

description:
Library name: Sample 3
column name in LASER.VS.CONTROL-all_genes.txt: C3


title: F40 SubPlacenta Pup2, MNR, Nanoparticle

value: Dunkin-Hartley


title: sfRNA2, DMS noMod control , Rep2

description:
sfRNA2_minusDMS_Rep2
In vitro transcribed RNA
sfRNA2_DMS_Rep2_normalized_reactivities.txt

value: in vitro transcribed RNA

value: no Mod (DMSO)


title: C2

description:
Library name: Sample 2
column name in LASER.VS.CONTROL-all_genes.txt: C2


title: WT bam infected with wMel3 W. pipientis, unmated three-day old_1

value: WT bam w1118 + wMel3 W. pipientis


title: F39 SubPlacenta Pup3, MNR, Sham


title: sfRNA2, DMS noMod control , Rep4

description:
sfRNA2_minusDMS_Rep4
In vitro transcribed RNA
sfRNA2_DMS_Rep4_normalized_reactivities.txt


title: C1

description:
Library name: Sample 1
column name in LASER.VS.CONTROL-all_genes.txt: C1


title: sfRNA2 , DMS treated, Rep2

description:
sfRNA2_plusDMS_Rep2
In vitro transcribed RNA
sfRNA2_DMS_Rep2_normalized_reactivities.txt


title: F39 SubPlacenta Pup2, MNR, Sham


title: Replicate 3 Day 2 Control

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

description: Library name: GL72_12_13_S12

data_processing:
Adapter trimming and QC were performed using Trim Galore. Then, clean sequencing reads were mapped to the mouse mm9 transcriptome using STAR aligner and quantified using RSEM.
Assembly: mm9
Supplementary files format and content: RSEM raw counts and TPM tables

source_name: MEFs

growth_protocol: MEFs were cultured in haematopoietic media (1× Iscove’s modified Dulbecco’s medium, 10% FBS (Gibco) 10% protein-free hybridoma medium [PFM; GIBCO], 1% L-glutamine, 1% penicillin-streptomycin, 25 ug/ml ascorbic acid, 4.5 X 10−4 M MTG, 180 mg/ml transferrin (R&D systems), 50ng SCF (PeproTech), 25ng IL-3 (PeproTech), 25ng IL-6 (PeproTech), 1% granulocyte-macrophage colony-stimulating factor, 1% thrombopoietin conditioned media, 2000 U erythropoietin, 10 ng macrophage colony-stimulating factor and 100 ng Flt3 ligand (PeproTech))

extract_protocol:
RNA was isolated using the RNeasy Micro or Mini kit (QIAGEN), according to manufacturer’s instructions.
Library preparation was performed using a SureSelect polyA kit (Agilent).

treatment_protocol: To initiate reprogramming 1 ug/ml of doxycycline was added to the haematopoietic medium.

value: MEFs

value: Indicible SCL and LMO2

value: Untreated


title: sfRNA2, DMS noMod control , Rep1

description:
sfRNA2_minusDMS_Rep1
In vitro transcribed RNA
sfRNA2_DMS_Rep1_normalized_reactivities.txt


title: F36 SubPlacenta Pup3, MNR, Nanoparticle

value: Maternal Nutrient Restriction


title: WT bam infected with wMel2a W. pipientis, Mated six -day old_3

value: WT bam w1118 + wMel2a W. pipientis

value: Mated six-day old


title: Replicate 1 Day 14 Dox c-KIT

description: Library name: GL72_11_10_S11

value: Doxycylcine


title: sfRNA2, DMS noMod control , Rep3

description:
sfRNA2_minusDMS_Rep3
In vitro transcribed RNA
sfRNA2_DMS_Rep3_normalized_reactivities.txt


title: sfRNA2 , DMS treated, Rep1

description:
sfRNA2_plusDMS_Rep1
In vitro transcribed RNA
sfRNA2_DMS_Rep1_normalized_reactivities.txt


title: Replicate 2 Day 2 Control

description: Library name: GL72_10_3_S10


title: sfRNA1 ,1m7 treated, Rep3

description:
sfRNA1_plus1m7_Rep3
In vitro transcribed RNA
sfRNA1_1m7_Rep3_normalized_reactivities.txt


title: Replicate 2 Day 4 Dox

description: Library name: GL72_09_9_S9


title: WT bam infected with wMel2a W. pipientis, Mated six -day old_1

value: Ovaries


title: F33 SubPlacenta Pup4, MNR, Sham

value: Sham


title: F33 SubPlacenta Pup3, MNR, Sham


title: sfRNA1, 1m7 noMod control , Rep2

description:
sfRNA1_minus1m7_Rep2
In vitro transcribed RNA
sfRNA1_1m7_Rep2_normalized_reactivities.txt

value: no Mod (EtOH)


title: sfRNA1 ,1m7 treated, Rep2

description:
sfRNA1_plus1m7_Rep2
In vitro transcribed RNA
sfRNA1_1m7_Rep2_normalized_reactivities.txt


title: WT bam infected with wMel2a W. pipientis, Mated three-day old_3

value: Tissue

value: Mated three-day old


title: WT bam infected with wMel2a W. pipientis, Mated six -day old_4


title: F22 SubPlacenta Pup2, Control, Nanoparticle

value: Subplacenta/Decidua

value: Control

value: Nanoparticle


title: WT bam infected with wMel2a W. pipientis, Mated three-day old_2


title: F22 SubPlacenta Pup1, Control, Nanoparticle

value: Dunkin-Hartley


title: sfRNA1, 1m7 noMod control , Rep1

description:
sfRNA1_minus1m7_Rep1
In vitro transcribed RNA
sfRNA1_1m7_Rep1_normalized_reactivities.txt

value: in vitro transcribed RNA


title: Replicate 3 Day 2 Dox

description: Library name: GL72_06_14_S6

value: MEFs


title: F36 SubPlacenta Pup1, MNR, Nanoparticle


title: N1 Placenta Pup2, Control, Sham

source_name: Placenta

extract_protocol:
Total RNA was extracted from frozen placenta using Qiagen RNeasy Midi extraction kit
RNA libraries were prepared from 1.5 ug RNA using Illumina Stranded mRNA Prep Kit following manufacturers instructions

value: Placenta


title: WT bam infected with wMel2a W. pipientis, Mated three-day old_1


title: Replicate 1 Day 4 Dox

description: Library name: GL72_05_7_S5

value: Indicible SCL and LMO2


title: WT bam infected with wMel2a W. pipientis, unmated three-day old_4

value: Unmated three-day old


title: WT bam infected with wMel2a W. pipientis, Mated six -day old_2

value: WT bam w1118 + wMel2a W. pipientis


title: sfRNA1, DMS noMod control , Rep3

description:
sfRNA1_minusDMS_Rep3
In vitro transcribed RNA
sfRNA1_DMS_Rep3_normalized_reactivities.txt

value: no Mod (DMSO)


title: sfRNA1, 1m7 noMod control , Rep3

description:
sfRNA1_minus1m7_Rep3
In vitro transcribed RNA
sfRNA1_1m7_Rep3_normalized_reactivities.txt


title: WT bam infected with wMel2a W. pipientis, Mated three-day old_4


title: WT bam infected with wMel2a W. pipientis, unmated three-day old_3


title: Replicate 1 Day 2 Dox

description: Library name: GL72_04_4_S4

value: Doxycylcine


title: Replicate 3 Day 4 Dox

description: Library name: GL72_03_15_S3


title: Replicate 2 Day 14 Dox c-KIT

description: Library name: GL72_07_12_S7


title: GR2 Placenta Pup1, Control Sham


title: sfRNA1 , DMS treated, Rep3

description:
sfRNA1_plusDMS_Rep3
In vitro transcribed RNA
sfRNA1_DMS_Rep3_normalized_reactivities.txt

value: DMS


title: GR2 Placenta Pup3, Control, Sham

value: Sham


title: N1 Placenta Pup1, Control, Sham


title: sfRNA1, DMS noMod control , Rep2

description:
sfRNA1_minusDMS_Rep2
In vitro transcribed RNA
sfRNA1_DMS_Rep2_normalized_reactivities.txt


title: sfRNA1 , DMS treated, Rep2

description:
sfRNA1_plusDMS_Rep2
In vitro transcribed RNA
sfRNA1_DMS_Rep2_normalized_reactivities.txt


title: WT bam, Mated six -day old_4

value: Ovaries

value: WT bam w1118

value: Mated six-day old


title: Replicate 2 Day 2 Dox

description: Library name: GL72_02_6_S2


title: Replicate 3 Day 14 Dox c-KIT

description: Library name: GL72_01_16_S1


title: sfRNA1, DMS noMod control , Rep1

description:
sfRNA1_minusDMS_Rep1
In vitro transcribed RNA
sfRNA1_DMS_Rep1_normalized_reactivities.txt


title: F43 Placenta Pup3, Control, Sham


title: sfRNA1 ,1m7 treated, Rep1

description:
sfRNA1_plus1m7_Rep1
In vitro transcribed RNA
sfRNA1_1m7_Rep1_normalized_reactivities.txt


title: Mouse visual cortex cell mRNA, Psi-Light treatment, Sample 9vc

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

description: Library name: 9vc

data_processing:
Quality and adaptor trimming with cutadapt
Read mapping with STAR
Read counting with HTSeq
Assembly: mm10
Supplementary files format and content: TSV matrix raw counts

source_name: Brain

extract_protocol:
Qiagen RNAeasy minikit according to the manufacturer's protocol
RNA-seq using illumina kit and protocol for library construction

value: Brain

value: visual cortex

value: Psi-Light


title: F40 Placenta Pup2, MNR, Nanoparticle

value: Dunkin-Hartley

value: Maternal Nutrient Restriction

value: Nanoparticle


title: F40 Placenta Pup3, MNR, Nanoparticle

value: Placenta


title: Mouse visual cortex cell mRNA, Psi-Light treatment, Sample 8vc

description: Library name: 8vc


title: F33 Placenta Pup2, MNR, Sham


title: Full 3'UTR, 1m7 noMod control , Rep3

description:
3UTR_minus1m7_Rep3
In vitro transcribed RNA
3UTR_1m7_Rep3_normalized_reactivities.txt

value: in vitro transcribed RNA

value: no Mod (EtOH)


title: Mouse visual cortex cell mRNA, Psi-Light treatment, Sample 7vc

description: Library name: 7vc


title: WT bam, Mated six -day old_2

source_name: Ovaries

value: Tissue


title: WT bam, Mated six -day old_3


title: WT bam, Mated six -day old_1


title: F33 Placenta Pup1, MNR, Sham


title: Full 3'UTR, 1m7 treated, Rep3

description:
3UTR_plus1m7_Rep3
In vitro transcribed RNA
3UTR_1m7_Rep3_normalized_reactivities.txt


title: F30 Placenta Pup1, MNR, Sham


title: WT bam, Mated three-day old_3

value: Mated three-day old


title: Mouse visual cortex cell mRNA, PBS-Light treatment, Sample 6vc

description: Library name: 6vc

value: PBS-Light


title: F30 Placenta Pup2, MNR, Sham


title: WT bam, Mated three-day old_4


title: sfRNA1 , DMS treated, Rep1

description:
sfRNA1_plusDMS_Rep1
In vitro transcribed RNA
sfRNA1_DMS_Rep1_normalized_reactivities.txt

value: DMS


title: Mouse visual cortex cell mRNA, PBS-Light treatment, Sample 5vc

description: Library name: 5vc


title: Mouse visual cortex cell mRNA, PBS-Light treatment, Sample 4vc

description: Library name: 4vc


title: GR2 Placenta Pup2, Control, Sham

value: Control

value: Sham


title: Full 3'UTR, 1m7 noMod control , Rep1

description:
3UTR_minus1m7_Rep1
In vitro transcribed RNA
3UTR_1m7_Rep1_normalized_reactivities.txt


title: F43 Placenta Pup2, Control, Sham


title: Full 3'UTR, 1m7 treated, Rep1

description:
3UTR_plus1m7_Rep1
In vitro transcribed RNA
3UTR_1m7_Rep1_normalized_reactivities.txt


title: Mouse visual cortex cell mRNA, PBS-Light treatment, Sample 2vc

description: Library name: 2vc


title: F43 Placenta Pup1, Control, Sham


title: Full 3'UTR, 1m7 treated, Rep2

description:
3UTR_plus1m7_Rep2
In vitro transcribed RNA
3UTR_1m7_Rep2_normalized_reactivities.txt


title: WT bam, Mated three-day old_2

value: Ovaries

value: WT bam w1118


title: Replicate 1 Day 2 Control

description: Library name: GL72_08_1_S8

value: MEFs

value: Indicible SCL and LMO2

value: Untreated


title: Full 3'UTR, DMS noMod control , Rep4

description:
3UTR_minusDMS_Rep4
In vitro transcribed RNA
3UTR_DMS_Rep4_normalized_reactivities.txt

value: no Mod (DMSO)


title: WT bam, Mated three-day old_1


title: WT bam, unmated three-day old_3

value: Unmated three-day old


title: Mouse visual cortex cell mRNA, PBS-Light treatment, Sample 3vc

description: Library name: 3vc

value: Brain

value: visual cortex


title: WT bam, unmated three-day old_4


title: Mouse visual cortex cell mRNA, Psi-Dark treatment, Sample 24vc

description: Library name: 24vc

value: Psi-Dark


title: Full 3'UTR, 1m7 noMod control , Rep2

description:
3UTR_minus1m7_Rep2
In vitro transcribed RNA
3UTR_1m7_Rep2_normalized_reactivities.txt

value: in vitro transcribed RNA

value: no Mod (EtOH)


title: WT bam infected with wMel2a W. pipientis, unmated three-day old_2

value: Tissue

value: WT bam w1118 + wMel2a W. pipientis


title: WT bam, unmated three-day old_2


title: Mouse visual cortex cell mRNA, Psi-Dark treatment, Sample 22vc

description: Library name: 22vc


title: F42 Placenta Pup3, MNR, Nanoparticle

value: Placenta

value: Dunkin-Hartley

value: Maternal Nutrient Restriction

value: Nanoparticle


title: Full 3'UTR, DMS treated, Rep4

description:
3UTR_plusDMS_Rep4
In vitro transcribed RNA
3UTR_DMS_Rep4_normalized_reactivities.txt

value: DMS


title: Mouse visual cortex cell mRNA, Psi-Dark treatment, Sample 23vc

description: Library name: 23vc


title: F41 Placenta Pup3, MNR, Nanoparticle


title: Mouse visual cortex cell mRNA, Psi-Dark treatment, Sample 21vc

description: Library name: 21vc


title: F42 Placenta Pup2, MNR, Nanoparticle


title: Full 3'UTR, DMS noMod control , Rep3

description:
3UTR_minusDMS_Rep3
In vitro transcribed RNA
3UTR_DMS_Rep3_normalized_reactivities.txt


title: F39 Placenta Pup3, MNR, Sham

value: Sham


title: Full 3'UTR, DMS treated, Rep2

description:
3UTR_plusDMS_Rep2
In vitro transcribed RNA
3UTR_DMS_Rep2_normalized_reactivities.txt


title: F20 SubPlacenta Pup4, Control, Nanoparticle

value: Subplacenta/Decidua

value: Control


title: F39 Placenta Pup2, MNR, Sham


title: Full 3'UTR, DMS noMod control , Rep2

description:
3UTR_minusDMS_Rep2
In vitro transcribed RNA
3UTR_DMS_Rep2_normalized_reactivities.txt

value: no Mod (DMSO)


title: F41 Placenta Pup2, MNR, Nanoparticle


title: Mouse visual cortex cell mRNA, Psi-Dark treatment, Sample 19vc

description: Library name: 19vc