title: Primary mouse hepatocytes-2, AAV-Trib3 [Trib3-6]

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
We use "FDR ≤0.001 and the absolute value of log2Ratio ≥1" as the threshold to judge the significance of gene expression difference.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized RPKM values for each Sample

source_name: primary mouse hepatocyte

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (foreukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random.  hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End  reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR  amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: 6-week-old male mice injected adeno-associated virus 8 (AAV8) expressing mouse TRIB3 (AAV-Trib3) to upregulate Trib3 expression, and isolated primary hepatocytes after four weeks.

value: primary mouse hepatocyte

tag: genotype

value: WT


title: Primary mouse hepatocytes-3, AAV-Trib3 [Trib3-8]

status: Public on May 28 2023

type: SRA

city: Shanghai

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: treatment


title: Primary mouse hepatocytes-4, AAV-GFP [GFP11]

value: AAV-GFP


title: Primary mouse hepatocytes-1, AAV-Trib3 [Trib3-1]


title: Primary mouse hepatocytes-4, AAV-Trib3 [Trib3-13]


title: HCT116 WT, 0.1 % FBS, 72 hr, rep2

city: Seoul

first: Soomin

last: Son

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Low-quality reads (phred quality <20 in 90% of nucleotides) were discarded with FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
TruSeq 3′ adapter sequence was removed, and then 4 nt-long degenerate sequences at the 3′ and 5′ ends were trimmed using cutadapt (Martin 2011). Reads shorter than 18 nt or longer than 26 nt were filtered out.
Preprocessed reads were aligned to the spike-in sequences by STAR (Dobin et al. 2013). Reads mapped to spike-in sequences with at most a single mismatch were considered reliable spike-in reads. The remaining reads were mapped to the hg38 genome using STAR (STAR --outFilterMultimapNmax 20 --outFilterMismatchNmax 0 --alignIntronMax 1).
Reads were classified into annotations from mirBase release 21 by BEDTools and used for further analysis (Kozomara and Griffiths-Jones 2014; Quinlan and Hall 2010).
Assembly: hg38
Supplementary files format and content: Tab-separated BEDTools intersect -c output

organism: Homo sapiens

extract_protocol:
Total RNAs were isolated using TRIzol (Thermo Fisher Scientific) and treated with DNase I (Takara Bio).
Sequencing libraries were generated as previously described (Kim et al. 2019). In brief, we mixed 20 µg of total RNAs with 10 nmole of 30 equimolar spike-in RNAs described in our previous study (Kim et al. 2019). Small RNAs were enriched by size fractionation by 15% urea-polyacrylamide gel electrophoresis and ligated to the randomized adaptor at the 3′ and 5′ ends. The ligated RNAs were reverse-transcribed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific), amplified using Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific), and subjected to high-throughput sequencing on the MiSeq platform (Illumina).

tag: cell line

value: human colon cancer cells

value: Cultured under serum-starvation with 0.1 % FBS


title: J01_041

type: RNA

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.

data_processing: Probe intensities were normalized with MAS5.

label: biotin

source_name: fresh frozen tumor sample obtained from radical breast cancer surgery

label_protocol: RNA (1 μg; RIN value >6) was used for generation of second-strand cDNA, and cRNA was amplified with the Oligo dT primer, then biotinated and fragmented with One-Cycle Target Labeling and control reagents (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from tumor tissues obtained at the surgery with the aid of the Qiagen RNeasy® mini kit (QIAGEN Sciences, Germantown, MD).

treatment_protocol: The patients agreed to have their research specimens cryopreserved for future use after undergoing radical breast cancer surgery, and also received endocrine therapy following the surgery.

tag: menopause

value: postmenopausal

tag: ct

tag: cn

tag: er

value: Positive

tag: pgr

value: Negative

tag: hg

value: Yes


title: CAD_S26

city: Groton

first: Seda

last: Arat

state: CT

address: 445 Eastern Point Road

country: USA

institute: Pfizer

data_processing:
Salmon quasi-mapping (indexing and quantitation)
Genome_build: Ensembl on May 9, 2019 (v.96)
Supplementary_files_format_and_content: raw counts (tab separated txt file)

source_name: Kidney

extract_protocol:
Frozen tissues of approximately 50 mg were homogenized in Qiazol Lysis Reagent (Qiagen, cat# 79306) with a cooled 5 mm stainless steel bead (Qiagen, cat# 69989) using a TissueLyser II (Qiagen, cat# 85300). Downstream RNA isolation was then performed using the Qiagen RNeasy Mini protocol on the Qiacube according to manufacturer’s instruction. After elution, 1 µL of each sample was evaluated for total RNA concentration using standard 260 nm absorbance on a NanoDrop 1000 (Thermo Scientific) UV-Vis spectrophotometer. The quality of the RNA in each sample was assessed using 2 µL of each sample via electrophoresis on the Agilent Tapestation. The remaining sample was stored at -80°C until analysis.
Total RNA from each kidney sample was prepared for sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation Kit (Illumina, cat# 20020595) according to manufacturer’s instructions on the Perkin Elmer Sciclone NGS prep system. 1,000 ng of total RNA was used to prepare the RNA libraries and fifteen cycles of library amplification PCR was performed. After library generation, 2uL of the cleaned cDNA library was used to quantify the library concentration on the ThermoFisher Scientific Qubit 4 Fluorometer (ThermoFisher Scientific, cat# Q33238). Additionally, the quality of each cDNA sample was assessed using 2 µL of each sample via electrophoresis on the Agilent Tapestation. Samples were binned according to Qubit readings to make a library pool for sequencing, which was diluted to 4 nM before denaturing and further dilution prior to loading onto the Nextseq 500. The remaining individual cDNA libraries were stored at -20°C.
Sequencing was performed at 2 x 150 bp, paired end read setting using a 300-cycle sequencing reagent kit & high output flow cell on a NextSeq 500 Sequencing System (Illumina, San Diego, CA). Condensed and quality controlled paired end fastq files were generated for data analysis.

tag: sample group

value: cadaveric


title: Primary mouse hepatocytes-3, AAV-GFP [GFP9]


title: CAD_S25


title: Control SD rats Replicate 1

type: genomic

city: Beijing

first: chongxiang

last: xue

address: No.5 BeiXianGe Street, Xicheng District, Beijing

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sci-ences

description:
C1
Biological replicate 1 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

hyb_protocol: Samples were then ready for hybridization and analysis by microarray (Hybridization System-Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Scanned on an Agilent Scanner-G2505C

data_processing: Median-centering, quantile normalization and linear smoothing were performed in this analysis process by Bioconductor packages Ringo, limma, and MEDME.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: methylated DNA immunoprecipitation (MeDIP) - DNA

label_protocol: DNA labelling was performed using the NimbleGen Dual-Color DNA Labeling Kit (Nimblegen Systems, Inc., Madison, WI, USA). And the labeled DNA was purified by isopropanol/ethanol precipitation

growth_protocol: Male Sprague-Dawley (SD) rats (8 weeks old, weighing 20–25 g) were purchased from HFK Bio-Technology.co., LTD (Beijing, China) and housed in a specific-pathogen-free (SPF) facility, with climate-controlled rooms maintained at 22±2◦C, 40-60% relative humidity, and controlled 12h light/dark cycles. All rats were allowed access to standard food and water ad libitum. Subsequently, experimental rats were injected with streptozotocin [STZ, 45 mg/kg, body weight (BW), 0.1 mol/L citric buffer, pH 0.5] intravenously, while the normal control rats were injected with the same volume of citric buffer. 72 h after STZ injection, animals were declared diabetic if their blood glucose exceeded 13.9 mmol/l (250 mg/dl) for 3 consecutive days.

extract_protocol: Then after a 12-h fasting period, all rats were sacrificed and blood samples were collected.

treatment_protocol: Thirty experimental rats were randomly assigned to three groups (n=10): (1) model (Mod.) group: administered distilled water by oral gavage; (2) calcium dobesilate (CaD.) group: administered CaD [0.25 g/kg, body weight (BW)/day)] by oral gavage and insulin (1.5 IU/time/day) by intravenous injection; and (3) LTF (LTF.) group: administered LTF [2 g/kg, herb weight/body weight (BW)/day] by oral gavage and insulin (1.5 IU/time/day) by intravenous injection. Besides, 10 normal control rats mentioned above belonged to the control (Con.) group, conventionally raised with distilled water.

tag: strain

value: Sprague Dawley

tag: age

value: 20 weeks old

tag: tissue

value: peripheral blood

value: Control SD rats

source_name: input DNA


title: HCT116 WT, 0.1 % FBS, 72 hr, rep1


title: J01_042

value: No


title: C57 strain, 6 wk room air, biological replicate 2

city: Providence

first: Sharon

last: Rounds

state: RI

address: 830 Chalkstone Avenue,, Building 35, Room 216

institute: Brown University

hyb_protocol: The biotinylated complementary RNA (cRNA) was fragmented at 94oC for 35min in fragmentation buffer and hybridized to the microarrays in 200ul of hybridization buffer. Target cRNA was hybridized to oligonucleotide microarrays containing 54,613 mouse gene probes and expressed sequence tags.

scan_protocol: The signals were further enhanced by staining for 5 min with streptavidin-phycoerythrin conjugate and scanning with the chip scanner. The hybridization intensity of the transcript was then determined using GeneChip Operating Software.

data_processing: The probe set measurements representing mouse genes were generated by Affymetrix image (.CEL) files using the Robust Multichip Average 21 involving background correction, quartile normalization, and log-2 transformation

source_name: Lung tissue

label_protocol: standard Affymetrix Protocol

tag: Sex

value: male

value: 6 wk

value: room air


title: CAD_S24


title: HCT116 WT, 9.1 % FBS, 72 hr, rep2

value: Cultured in normal condition with 9.1 % FBS


title: AKR strain, 3 wk room air, biological replicate 1

extract_protocol: The biotinylated complementary RNA (cRNA) was fragmented at 94oC for 35min in fragmentation buffer

value: AKR


title: HCT116 WT, 9.1 % FBS, 72 hr, rep1

value: human colon cancer cells


title: CAD_S22


title: CAD_S23


title: J01_039


title: 7 day post Influenza dNS1-Vector vaccinated, replicate 3, scRNAseq

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

description: Singleron Matrix GEXSCOPE

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, alignment, gene counting and aggregation were made using the Singleron Celescope software version 1.10.0 (https://github.com/singleron-RD/CeleScope)
The doublet were removed by using Doubletfinder R package and personal checking for conserved markers.
The R package Seurat version 4.1.1 was used for normalization, clustering and reduction. Cell type was annotated based on conserved markers.
Differential gene expression analysis and enrichment analysis were performed by using MAST and clusterProfiler R package.
Assembly: GRCm38
Supplementary files format and content: Compressed .tar.gz file containing genes, barcodes and matrix for each sample

source_name: Lung Tissue

extract_protocol:
Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were loaded into microfluidic devices and scRNA-seq libraries were constructed following the Singleron GEXSCOPER protocol by GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies).
Indivaidual libraries of each sample were then dilyted to 4nM, pooled and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Lung Tissue


title: 7 day post Influenza dNS1-Vector vaccinated, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: Primary mouse hepatocytes-2, AAV-GFP [GFP4]

value: primary mouse hepatocyte

value: WT

value: AAV-GFP


title: J01_038

value: postmenopausal

value: Positive

value: Negative


title: 7 day post Influenza dNS1-Vector vaccinated, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_037

value: Yes


title: C57 strain, 6 wk room air, biological replicate 1


title: HCT116 WT, 9.1 % FBS, 72 hr, rep3


title: HCT116 DROSHA KO, GFP

description: KoGFP

value: GFP expression


title: HCT116 WT, no treatment

description: Parental

value: no treatment


title: CAD_S21

value: cadaveric


title: Primary mouse hepatocytes-1, AAV-GFP [GFP3]


title: CAD_S20


title: 44 day post Influenza dNS1-Vector vaccinated, replicate 3, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_040

value: premenopausal

value: No


title: CAD_S19


title: 44 day post Influenza dNS1-Vector vaccinated, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: HEK293E DROSHA KO, DROSHA-p140, rep2

value: human embryonic kidney cells

value: DROSHA-p140 rescue


title: 44 day post Influenza dNS1-Vector vaccinated, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_036


title: HEK293E DROSHA KO, DROSHA-p140, rep1


title: 1 day post Influenza dNS1-Vector vaccinated, replicate 3, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_035


title: CAD_S17


title: CAD_S18


title: HEK293E DROSHA KO, full-length DROSHA, rep3

value: full-length DROSHA rescue


title: CAD_S16.A


title: J01_034


title: control_1,BulkRNAseq

first: Jialin

middle: C.

last: Zheng

address: Xincun Road 389

institute: Tongji Hospital Affiliated to Tongji University School of Medicine

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork.
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: prefrontal cortex

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: prefrontal cortex

value: all cells


title: 1 day post Influenza dNS1-Vector vaccinated, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE

value: Lung Tissue


title: HEK293E DROSHA KO, full-length DROSHA, rep2


title: 1 day post Influenza dNS1-Vector vaccinated, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: HEK293E DROSHA KO, full-length DROSHA, rep1


title: CAD_S15.A


title: CAD_S14.A


title: HCT116 DROSHA KO, DROSHA-p140, rep3

value: human colon cancer cells


title: J01_033


title: CAD_S13.A


title: HCT116 DROSHA KO, DROSHA-p140, rep2


title: 7 day post Influenza dNS1-RBD vaccinated, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: 7 day post Influenza dNS1-RBD vaccinated, replicate 3, scRNAseq

description: Singleron Matrix GEXSCOPE


title: 7 day post Influenza dNS1-RBD vaccinated, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: HCT116 DROSHA KO, DROSHA-p140, rep1


title: NAT_S11

value: normal adjacent tissue


title: J01_031


title: 44 day post Influenza dNS1-RBD vaccinated, replicate 3, scRNAseq

description: Singleron Matrix GEXSCOPE


title: Tumor_S10

value: kidney tumor


title: HCT116 DROSHA KO, full-length DROSHA, rep3


title: 44 day post Influenza dNS1-RBD vaccinated, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_028

value: postmenopausal

value: Positive


title: J01_029

value: Negative


title: J01_025


title: J01_023


title: J01_024


title: HCT116 DROSHA KO, full-length DROSHA, rep2


title: J01_030


title: HEK293E DROSHA KO, DROSHA-p140, rep3


title: J01_027

value: Yes


title: J01_026


title: CAD_S12


title: NAT_S9


title: Tumor_S8


title: 1 day post Influenza dNS1-RBD vaccinated, replicate 3, scRNAseq

description: Singleron Matrix GEXSCOPE


title: NAT_S7


title: 44 day post Influenza dNS1-RBD vaccinated, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: ddx-23 rep3

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

data_processing:
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, and sample contamination estimation.  Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against ws258 reference for Caenorhabditis elegans sequences using STAR/2.5.3a
Gene expression was quantified using RSEM v. 1.3.0
Genome_build: ws258
Supplementary_files_format_and_content: Text format matrix of  normalized gene expression abundance,  as measured by log2(fpkm+1). Each gene is a row, and each sample is a column.

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Age-synchronized young adult hermaphrodites (200 in total, picked manually) from wild-type, lin-29(n836), mab-10(tm2497), and ddx-23(n5705)

extract_protocol:
total RNA from three biological replicates for each genotype were prepared using a BeadBug microtube homogenizer (Sigma) and 0.5 mm zirconium beads (Sigma). RNA was extracted using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (using the NeoPrep system).

value: young adult

value: whole animal

value: ddx-23 mutant


title: ddx-23 rep2


title: 1 day post Influenza dNS1-RBD vaccinated, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: Tumor_S6


title: 1 day post Influenza dNS1-RBD vaccinated, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_032

value: premenopausal

value: No


title: ddx-23 rep1


title: Control sample

description: Singleron Matrix GEXSCOPE


title: mab-10 rep3

value: mab-10 mutant


title: 7 day post Influenza CA04 infected, replicate 3, scRNAseq

description: Singleron Matrix GEXSCOPE


title: Tumor_S4


title: mab-10 rep2


title: HCT116 DROSHA KO, full-length DROSHA, rep1

value: full-length DROSHA rescue


title: NAT_S3


title: J01_022


title: OD_S2

value: organ donor


title: J01_021


title: lin-29 rep3

value: lin-29 mutant


title: OD_S1


title: 44 day post Influenza CA04 infected, replicate 3, scRNAseq

description: Singleron Matrix GEXSCOPE

value: Lung Tissue


title: NAT_S5


title: lin-29 rep2


title: 44 day post Influenza CA04 infected, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_019


title: lin-29 rep1


title: 44 day post Influenza CA04 infected, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: 7 day post Influenza CA04 infected, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: vaccine_day28_1

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to GRcm39 Hisat2
Raw count were calculated by using featurecounts
Assembly: GRcm39
Supplementary files format and content: tab-delimited txt files include raw count values for each Sample

source_name: C57BL/6 Lung, 28th day post vaccinated with dNS1-RBD vaccine

extract_protocol:
The mouse lung lobe was removed, shredded into small pieces and stored in RNA Later Solution (Thermo Fisher Scientific) for a maximum of 24 h at 4 °C. Lung tissue was homogenized using TissueLyser II (Qiagen, Hilden, Germany) and RNA extraction was performed according to the manufacturer’s instructions (QIAamp Viral RNA Mini Kit (Qiagen)).
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Lung

value: Vaccinated with dNS1-RBD Vaccine

tag: time

value: Day 28


title: J01_016


title: vaccine_day28_2


title: WT rep3

value: wild-type


title: mab-10 rep1


title: J01_017

value: Positive


title: J01_014

value: postmenopausal

value: Negative


title: 7 day post Influenza CA04 infected, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: J01_015


title: J01_012


title: WT rep2

value: young adult


title: vaccine_day14_3

source_name: C57BL/6 Lung, 14th day post vaccinated with dNS1-RBD vaccine

value: Day 14


title: 1 day post Influenza CA04 infected, replicate 1, scRNAseq

description: Singleron Matrix GEXSCOPE


title: vaccine_day28_3


title: J01_020


title: J01_013


title: vaccine_day14_2


title: Mouse Alveolar Macrophage, 2 months post vaccinated with PBS 2

library_source: genomic

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to mm10 mouse genome by using bowtie2
The duplicated and low-quality fragments were removed by using picard and samtools
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were extended to 150 bp to represent sequenced fragments, renormalized and reformatted in the bigWig file format.
Peaks were called uing MACS2 with the significance cut-off q-value <=0.01, narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Alveolar Macrophage

extract_protocol:
Cells were lysed with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.1% IGEPAL CA-630). Libraries were prepared using the TruePrep DNA library prep kit V2 for Illumina (Vazyme) according to the manufacturer’s instructions.
Libraries were cleaned up with AMPure XP beads (Beckman coulter) at a ratio of 0.7 and the quality was assessed using the 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced with 150 paired ends using a NovaSeq 6000 instrument (Illumina) for an average of 20 million reads per sample.

treatment_protocol: C57BL/6v mice lungs were collected 2 months post-vaccination and sorted for bronchoalveolar lavage AMs using a BD FACS Aria Fusion machine. One hundred thousand sorted cells were centrifuged at 500 × g for 10 min at 4 °C per replicate.

value: Alveolar Macrophage

value: Vaccinated with PBS


title: vaccine_day14_1


title: J01_018

value: premenopausal

value: No


title: Mouse Alveolar Macrophage, 2 months post vaccinated with PBS 1


title: J01_010


title: Mouse Alveolar Macrophage, 2 months post vaccinated with dNS1-Vector 2

value: Vaccinated with dNS1-Vector


title: Mouse Alveolar Macrophage, 2 months post vaccinated with dNS1-Vector 1


title: vaccine_day7_2

source_name: C57BL/6 Lung, 7th day post vaccinated with dNS1-RBD vaccine

value: Day 7


title: 1 day post Influenza CA04 infected, replicate 2, scRNAseq

description: Singleron Matrix GEXSCOPE


title: vaccine_day7_3


title: Mouse Alveolar Macrophage, 2 months post vaccinated with dNS1-RBD 2


title: vaccine_day7_1


title: Mouse Alveolar Macrophage, 2 months post vaccinated with dNS1-RBD 1


title: vaccine_day1_3

source_name: C57BL/6 Lung, 1st day post vaccinated with dNS1-RBD vaccine

value: Day 1


title: WT rep1

value: whole animal


title: J01_011


title: vaccine_day1_2

value: Lung


title: Homo_NC_1_1

city: shenzhen

first: Donge

last: Tang

state: Guangdong

address: NO.1017 Dongmen North, Shenzhen People’s Hospital, Shenzhen, Guangdong

institute: shenzhen people's hospital

description: The normal control that was extracted RNA by the same methods.

data_processing:
Clean reads were obtained by removing adapter dimers,, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats in the NCBI GenBank, Repbase, and Rfam databases.
Clean reads then were gathered and mapped to miRbase database (Release 22) by BLAST.
The identified miRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2 × 2 test, Chi-squared nXn test, Student’s t-test, and ANOVA based on the experiments design.
Genome_build: GRCH38
Supplementary_files_format_and_content: Excel files include normalized expression values for each Sample.

source_name: Cord blood

extract_protocol:
Total RNA was extracted from the PS and NC using TRIzol reagent (Epicentre, USA) according to the manufacturer’s methods.
The blood-derived RNA were used for small RNA sequencing  library preparation according to the manufacturer's instruction.

tag: disease state

value: normal control

value: Cord blood


title: Homo_PS_2_1

source_name: Peripheral blood

value: Patau syndrom

value: Peripheral blood


title: Homo_PS_1_1

description: The cord blood and peripheral blood of pregnant woman with patau syndrom were used to extract RNA and  build the RNA library.


title: pbs_3

source_name: C57BL/6 Lung, Vaccinated with PBS

value: Day 0


title: J01_008

value: Positive

value: Negative


title: Differentiated 3T3-L1 cells, lysine free 3

city: Hong Kong

first: Man Yuen

last: LEE

address: Hunghom

department: Department of Applied Biology and Chemical Technology

country: Hong Kong

institute: The Hong Kong Polytechnic University

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Perform alignments with HISAT2 (v2.0.5) to the reference.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And   then FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample (gene_count.txt)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample (gene_fpkm.txt)

growth_protocol: 3T3-L1 cell was obtained from ATCC. It was maintained in high glucose DMEM with 10 % BCS at confluent for 3 days, after which the cell was stimulated with a dif-ferentiation medium consisting of 1 μM dexamethasone (Sigma), 0.5 mM 3-isobutyl-1-methylxanthine (Sigma), 1 μM rosiglitazone (Sigma) and 10 μg/mL insulin (Sigma) to induce adipocyte differentiation.

extract_protocol:
RNA was harvested using Total RNA extraction kit (Favorgen).
RNA libraries for RNA-seq were prepared using poly A enrichment preparation by the sequencing service provider Novogene

treatment_protocol: For lysine-free treatment, confluent pre-adipocytes were treated with a differentiation medium without lysine during the differentiation

value: fibroblast

value: Adipogenic differentiation+lysine free medium


title: Differentiated 3T3-L1 cells, lysine free 1


title: J01_009


title: Differentiated 3T3-L1 cells, lysine free 2


title: J01_007

value: postmenopausal


title: Differentiated 3T3-L1 cells 3

value: Adipogenic differentiation


title: pbs_2

value: Vaccinated with PBS


title: pbs_1


title: Golden Hamster Alveolar Macrophage, 2 weeks post vaccinated with dNS1-RBD, rep2

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to BCM_Maur_2.0 genome by using bowtie2
The duplicated and low-quality fragments were removed by using picard and samtools
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were extended to 150 bp to represent sequenced fragments, renormalized and reformatted in the bigWig file format.
Peaks were called uing MACS2 with the significance cut-off q-value <=0.01, narrowPeak files were generated using MACS v2 with default settings.
Assembly: BCM_Maur_2.0
Supplementary files format and content: bigWig, narrowPeak

organism: Mesocricetus auratus

treatment_protocol: Golden Hamster lungs were collected 2 weks post-vaccination and sorted for bronchoalveolar lavage AMs using a BD FACS Aria Fusion machine. One hundred thousand sorted cells were centrifuged at 500 × g for 10 min at 4 °C per replicate.

value: Alveolar Macrophage

value: Vaccinated with dNS1-RBD Vaccine


title: CB_pb3

city: Changchun

first: zhang

last: yue

address: xincheng street num 2888

institute: Jilin Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample

organism: Cyprinus carpio

source_name: brain

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

tag: agent

value: lead

value: brain


title: Differentiated 3T3-L1 cells 2

tag: cell type


title: Homo_NC_2_1


title: CB_pb2


title: Golden Hamster Alveolar Macrophage, 2 weeks post vaccinated with dNS1-RBD, rep1

tag: treatment


title: Differentiated 3T3-L1 cells 1

tag: cell line


title: CB_pb1


title: THP-1 shPIWIL4_2 (exp. rep2)

city: Ulm

first: Shiva

last: Bamezai

address: Albert Einstein Allee 11

country: Germany

institute: Institute for Experimental Cancer Research

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR (Dobin et al. 2013)
Read counts for each transcript were measured using featureCounts (Liao et al. 2014)
The differentially expressed genes were determined using DESeq2 and cut off parameters of read count >10, p<0.05 and p-adjusted (FDR, corrected for multiple hypotheses testing) < 0.01
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files containing a matrix table of normalized counts for each gene in every sample

source_name: AML cell line

growth_protocol: THP-1 cells were cultured in RPMI supplemented with 10% FBS and 1% penicillin streptomycin

extract_protocol:
1x106 THP-1 cells transduced with either scrambled or shRNA against PIWIL4 were sacrificed, washed with PBS and resuspended in 1mL TRIZOL reagent.  RNA was harvested and Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 x 106 cells were lentivirally transduced with PGP-Scrambled and PGP-shPIWIL4 and FACS sorted 48h post-transduction

value: Transduced with lentivirus containing scrambled  shRNA against PIWIL4


title: vaccine_day1_1

value: Lung

value: Day 1


title: THP-1 shPIWIL4_1 (exp. rep1)

value: Transduced with lentivirus containing scrambled shRNA against PIWIL4


title: Golden Hamster Alveolar Macrophage, 2 weeks post vaccinated with dNS1-Vector, rep2

value: Vaccinated with dNS1-Vector


title: J01_005

source_name: fresh frozen tumor sample obtained from radical breast cancer surgery

tag: menopause

value: No


title: Undifferentiated 3T3-L1 cells 3

value: Undifferentiation control


title: CB_bk3


title: J01_006

tag: ct

value: Positive

value: Negative


title: Golden Hamster Alveolar Macrophage, 2 weeks post vaccinated with dNS1-Vector, rep1


title: THP-1 Scrambled_2 (exp. rep2)

value: Transduced with lentivirus containing scrambled shRNA


title: Undifferentiated 3T3-L1 cells 1

value: fibroblast


title: Undifferentiated 3T3-L1 cells 2


title: CB_bk2


title: Golden Hamster Alveolar Macrophage, 2 weeks post vaccinated with PBS, rep2


title: THP-1 Scrambled_1 (exp. rep1)


title: CB_bk1


title: Golden Hamster Alveolar Macrophage, 2 weeks post vaccinated with PBS, rep1


title: J01_002

value: premenopausal

tag: cn


title: J01_001

value: postmenopausal

tag: er


title: J01_004

tag: pgr


title: J01_003

tag: hg


title: Subject 743, Cohort D, visit 3

status: Public on May 27 2023

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: Hybridization was performed on HG-133plus2.0PM chips per manufacturer's protocol

scan_protocol: Plates were scanned per manufacturer's protocol

data_processing: RMA

label: Biotin

source_name: blood

label_protocol: Fragmented RNA was lalebeld with biotin

extract_protocol: RNA was extracted using RNAeasy kit (Qiagen)

tag: subject

tag: cohort

value: D

tag: visit

tag: time point


title: Subject 217, Cohort D, visit 3


title: Subject 718, Cohort D, visit 3


title: Subject 455, Cohort D, visit 3


title: Subject 194, Cohort D, visit 3


title: Subject 734, Cohort D, visit 3


title: Subject 445, Cohort D, visit 3


title: Subject 43, Cohort D, visit 3


title: Subject 810, Cohort D, visit 3


title: Subject 553, Cohort D, visit 3


title: Subject 785, Cohort D, visit 3


title: Subject 64, Cohort D, visit 3


title: Subject 986, Cohort D, visit 3


title: Subject 181, Cohort D, visit 3


title: Subject 52, Cohort D, visit 3


title: Subject 521, Cohort D, visit 3


title: Subject 738, Cohort D, visit 3


title: Subject 615, Cohort D, visit 3


title: Subject 640, Cohort D, visit 3


title: Subject 724, Cohort D, visit 3


title: Subject 578, Cohort D, visit 3


title: Subject 32, Cohort D, visit 3


title: Subject 935, Cohort D, visit 3


title: Subject 881, Cohort D, visit 3


title: Subject 222, Cohort D, visit 3


title: Subject 933, Cohort D, visit 3


title: Subject 334, Cohort D, visit 3


title: Subject 743, Cohort D, visit 2


title: Subject 217, Cohort D, visit 2


title: Subject 64, Cohort D, visit 2


title: Subject 521, Cohort D, visit 2


title: Subject 516, Cohort D, visit 3


title: Subject 785, Cohort D, visit 2


title: Subject 640, Cohort D, visit 2


title: Subject 734, Cohort D, visit 2


title: Subject 810, Cohort D, visit 2


title: Subject 32, Cohort D, visit 2


title: Subject 43, Cohort D, visit 2


title: Subject 718, Cohort D, visit 2


title: Subject 282, Cohort D, visit 2


title: Subject 935, Cohort D, visit 2


title: Subject 445, Cohort D, visit 2


title: Subject 986, Cohort D, visit 2


title: Subject 553, Cohort D, visit 2


title: Subject 455, Cohort D, visit 2


title: Subject 52, Cohort D, visit 2


title: Subject 194, Cohort D, visit 2


title: Subject 578, Cohort D, visit 2


title: Subject 490, Cohort D, visit 2


title: Subject 222, Cohort D, visit 2


title: Subject 181, Cohort D, visit 2


title: Subject 615, Cohort D, visit 2


title: Subject 881, Cohort D, visit 2


title: Subject 724, Cohort D, visit 2


title: Subject 738, Cohort D, visit 2


title: Subject 516, Cohort D, visit 2


title: Subject 933, Cohort D, visit 2


title: Subject 334, Cohort D, visit 2


title: Subject 718, Cohort D, visit 0

value: Baseline


title: Subject 785, Cohort D, visit 0


title: Subject 282, Cohort D, visit 0


title: Subject 734, Cohort D, visit 0


title: Subject 521, Cohort D, visit 0


title: Subject 217, Cohort D, visit 0


title: Subject 194, Cohort D, visit 0


title: Subject 181, Cohort D, visit 0


title: Subject 43, Cohort D, visit 0


title: Subject 445, Cohort D, visit 0


title: Subject 986, Cohort D, visit 0


title: Subject 640, Cohort D, visit 0


title: Subject 810, Cohort D, visit 0


title: Subject 578, Cohort D, visit 0


title: Subject 743, Cohort D, visit 0


title: Subject 52, Cohort D, visit 0


title: Subject 933, Cohort D, visit 0


title: Subject 32, Cohort D, visit 0


title: Subject 553, Cohort D, visit 0


title: Subject 64, Cohort D, visit 0


title: Subject 724, Cohort D, visit 0


title: Subject 490, Cohort D, visit 0


title: Subject 541, Cohort C, visit 6

value: C

value: D3 post boost


title: Subject 334, Cohort D, visit 0


title: Subject 738, Cohort D, visit 0


title: Subject 615, Cohort D, visit 0


title: Subject 881, Cohort D, visit 0


title: Subject 355, Cohort C, visit 6


title: Subject 455, Cohort D, visit 0


title: Subject 821, Cohort C, visit 6


title: Subject 516, Cohort D, visit 0


title: Subject 935, Cohort D, visit 0


title: Subject 222, Cohort D, visit 0


title: Subject 307, Cohort C, visit 6


title: Subject 733, Cohort C, visit 6


title: Subject 891, Cohort C, visit 6


title: Subject 900, Cohort C, visit 6


title: Subject 651, Cohort C, visit 6


title: Subject 943, Cohort C, visit 6


title: Subject 932, Cohort C, visit 6


title: Subject 484, Cohort C, visit 6


title: Subject 362, Cohort C, visit 6


title: Subject 324, Cohort C, visit 6


title: Subject 963, Cohort C, visit 6


title: Subject 454, Cohort C, visit 6


title: Subject 157, Cohort C, visit 6


title: Subject 494, Cohort C, visit 6


title: Subject 664, Cohort C, visit 6


title: Subject 101, Cohort C, visit 4

value: Baseline 2


title: Subject 84, Cohort C, visit 6


title: Subject 176, Cohort C, visit 6


title: Subject 94, Cohort C, visit 6


title: Subject 547, Cohort C, visit 4


title: Subject 664, Cohort C, visit 4


title: Subject 412, Cohort C, visit 6


title: Subject 350, Cohort C, visit 6


title: Subject 547, Cohort C, visit 6


title: Subject 443, Cohort C, visit 6


title: Subject 454, Cohort C, visit 4


title: Subject 350, Cohort C, visit 4


title: Subject 821, Cohort C, visit 4


title: Subject 84, Cohort C, visit 4


title: Subject 651, Cohort C, visit 4


title: Subject 412, Cohort C, visit 4


title: Subject 932, Cohort C, visit 4


title: Subject 943, Cohort C, visit 4


title: Subject 733, Cohort C, visit 4


title: Subject 900, Cohort C, visit 4


title: Subject 484, Cohort C, visit 4


title: Subject 891, Cohort C, visit 4


title: Subject 355, Cohort C, visit 4


title: Subject 176, Cohort C, visit 4


title: Subject 470, Cohort C, visit 6


title: Subject 963, Cohort C, visit 4


title: Subject 494, Cohort C, visit 4


title: Subject 157, Cohort C, visit 4


title: Subject 443, Cohort C, visit 4


title: Subject 574, Cohort C, visit 4


title: Subject 307, Cohort C, visit 4


title: Subject 669, Cohort B, visit 5

value: B

value: D1 post boost


title: Subject 470, Cohort C, visit 4


title: Subject 513, Cohort B, visit 5


title: Subject 362, Cohort C, visit 4


title: Subject 156, Cohort B, visit 5


title: Subject 948, Cohort B, visit 5


title: Subject 324, Cohort C, visit 4


title: Subject 284, Cohort C, visit 4


title: Subject 690, Cohort B, visit 5


title: Subject 296, Cohort B, visit 5


title: Subject 807, Cohort B, visit 5


title: Subject 797, Cohort B, visit 5


title: Subject 592, Cohort B, visit 5


title: Subject 414, Cohort B, visit 5


title: Subject 936, Cohort B, visit 5


title: Subject 537, Cohort B, visit 5


title: Subject 94, Cohort C, visit 4


title: Subject 665, Cohort B, visit 5


title: Subject 531, Cohort B, visit 5


title: Subject 30, Cohort B, visit 5


title: Subject 732, Cohort B, visit 5


title: Subject 346, Cohort B, visit 5


title: Subject 904, Cohort B, visit 5


title: Subject 688, Cohort B, visit 5


title: Subject 609, Cohort B, visit 5


title: Subject 714, Cohort B, visit 5


title: Subject 168, Cohort B, visit 3


title: Subject 323, Cohort B, visit 3


title: Subject 168, Cohort B, visit 5


title: Subject 537, Cohort B, visit 3


title: Subject 797, Cohort B, visit 3


title: Subject 62, Cohort B, visit 5


title: Subject 904, Cohort B, visit 3


title: Subject 714, Cohort B, visit 3


title: Subject 510, Cohort B, visit 3


title: Subject 450, Cohort B, visit 5


title: Subject 974, Cohort B, visit 5


title: Subject 688, Cohort B, visit 3


title: Subject 665, Cohort B, visit 3


title: Subject 296, Cohort B, visit 3


title: Subject 669, Cohort B, visit 3


title: Subject 609, Cohort B, visit 3


title: Subject 948, Cohort B, visit 3


title: Subject 317, Cohort B, visit 3


title: Subject 690, Cohort B, visit 3


title: Subject 513, Cohort B, visit 3


title: Subject 156, Cohort B, visit 3


title: Subject 335, Cohort B, visit 3


title: Subject 807, Cohort B, visit 3


title: Subject 414, Cohort B, visit 3


title: Subject 936, Cohort B, visit 3


title: Subject 974, Cohort B, visit 3


title: Subject 592, Cohort B, visit 3


title: Subject 62, Cohort B, visit 3


title: Subject 450, Cohort B, visit 3


title: Subject 732, Cohort B, visit 3


title: Subject 30, Cohort B, visit 3


title: Subject 692, Cohort A, visit 2

value: A

value: D1 post prime


title: Subject 126, Cohort A, visit 2


title: Subject 616, Cohort A, visit 2


title: Subject 58, Cohort A, visit 2


title: Subject 457, Cohort A, visit 2


title: Subject 808, Cohort A, visit 2


title: Subject 725, Cohort A, visit 2


title: Subject 456, Cohort A, visit 2


title: Subject 938, Cohort A, visit 2


title: Subject 839, Cohort A, visit 2


title: Subject 99, Cohort A, visit 2


title: Subject 584, Cohort A, visit 2


title: Subject 816, Cohort A, visit 2


title: Subject 588, Cohort A, visit 2


title: Subject 849, Cohort A, visit 2


title: Subject 232, Cohort A, visit 2


title: Subject 681, Cohort A, visit 2


title: Subject 331, Cohort A, visit 2


title: Subject 555, Cohort A, visit 2


title: Subject 275, Cohort A, visit 2


title: Subject 848, Cohort A, visit 2


title: Subject 125, Cohort A, visit 2


title: Subject 946, Cohort A, visit 2


title: Subject 661, Cohort A, visit 2


title: Subject 373, Cohort A, visit 2


title: Subject 417, Cohort A, visit 2


title: Subject 99, Cohort A, visit 0

value: Baseline 1


title: Subject 584, Cohort A, visit 0


title: Subject 616, Cohort A, visit 0


title: Subject 839, Cohort A, visit 0


title: Subject 53, Cohort A, visit 2


title: Subject 849, Cohort A, visit 0


title: Subject 607, Cohort A, visit 2


title: Subject 58, Cohort A, visit 0


title: Subject 126, Cohort A, visit 0


title: Subject 227, Cohort A, visit 0


title: Subject 275, Cohort A, visit 0


title: Subject 588, Cohort A, visit 0


title: Subject 232, Cohort A, visit 0


title: Subject 125, Cohort A, visit 0


title: Subject 681, Cohort A, visit 0


title: IL3A: ATDC5 cells with IL-1β

city: Guangzhou

first: Kai

last: Li

address: 183 Zhongshan Avenue West

institute: The Third Affiliated Hospital of Southern Medical University

data_processing:
The Fastq format file contains the sequence of reads and the sequencing quality of base.
Basecalls performed using  Solexa pipeline v1.8.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0)software.
The transcript abundances for each sample was estimated with StringTie.
Assembly: mm10
Supplementary files format and content: The tab-delimited text files include RPKM values for each Sample.

growth_protocol: ATDC5 cells were maintained in DMEM with 4.5 g glucose supplemented with 6% FBS and 1% antibiotics at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: ATDC5 cells were stimulated with 10 ng/mL IL-1β, or 10 ng/mL IL-1β plus 10 μM NP-G2-044.

value: chondrogenic cell line


title: Subject 613, Cohort A, visit 0


title: Subject 331, Cohort A, visit 0


title: Subject 373, Cohort A, visit 0


title: Subject 938, Cohort A, visit 0


title: Subject 456, Cohort A, visit 0


title: Subject 725, Cohort A, visit 0


title: Subject 808, Cohort A, visit 0


title: Subject 848, Cohort A, visit 0


title: Subject 457, Cohort A, visit 0


title: Subject 692, Cohort A, visit 0


title: Subject 417, Cohort A, visit 0


title: ILN1a: ATDC5 cells with IL-1β plus NP-G2-044

value: IL-1b plus Fascin1 inhibitor NP-G2-047


title: ILN2a: ATDC5 cells with IL-1β plus NP-G2-044


title: C148 B cell, elderly, replicate 2, VDJ (BCR)

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: VDJ library: read1 file contains cell barcode and UMI; read2 file contains the constant region of the antibody chains

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation, and the BCR clonotype assembly were performed using the 10x Genomics Cell Ranger software v7.1.0 via the pipeline `multi`
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Venous blood samples were collected into Heparin and Serum-gel monovette tubes by standard phlebotomy at The Rockefeller University. Peripheral Blood Mononuclear Cells (PBMCs) obtained from samples collected were further purified as previously reported by gradient centrifugation and stored in liquid nitrogen in the presence of Fetal Calf Serum (FCS) and Dimethylsulfoxide (DMSO). Peripheral blood mononuclear cells (PBMC) were enriched for B cells by negative selection using a pan-B-cell isolation kit according to the manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, B cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences were added.
V(D)J libraries were generated with 350 the Chromium Single Cell 5′ Library & Gel Bead Kit and 351 Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (10x Genomics protocol)

tag: tissue

value: B cell

tag: condition

value: elderly

tag: library type

value: VDJ

tag: antibodies/tags


title: ILN3a: ATDC5 cells with IL-1β plus NP-G2-044

tag: cell type


title: Subject 555, Cohort A, visit 0


title: C146 B cell, elderly, replicate 2, VDJ (BCR)

source_name: Peripheral Blood Mononuclear Cells (PBMCs)


title: C148 B cell, elderly, replicate 1, VDJ (BCR)

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: IL2A: ATDC5 cells with IL-1β

tag: treatment


title: IL1A: ATDC5 cells with IL-1β

tag: cell line


title: C145 B cell, elderly, VDJ (BCR)


title: C144 B cell, elderly, VDJ (BCR)


title: Subject 661, Cohort A, visit 0


title: C094 B cell, young, VDJ (BCR)

value: young


title: C146 B cell, elderly, replicate 1, VDJ (BCR)


title: C004 B cell, young, VDJ (BCR)


title: C005 B cell, young, replicate 1, VDJ (BCR)


title: Subject 946, Cohort A, visit 0


title: C031 B cell, young, VDJ (BCR)


title: C005 B cell, young, replicate 2, VDJ (BCR)


title: FLC Primary tumor RNA-seq sample #9

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC24_DJZW

data_processing:
Sequencing was aligned and quantified using STAR/Salmon (RNA-seq).
RNA-seq data was normalized using DESeq2.
Assembly: Paired end RNA sequencing results were aligned to the human genome (hg38) using STAR (v2.4.2a) and quantified using Salmon (v0.8).
Supplementary files format and content: Normalized counts

source_name: FLC tumor samples

extract_protocol:
Libraries were prepared using the NEBNext Ultra II Directional Library Prep Kit following PolyA enrichment at the Cornell Transcriptional Regulation and Expression Facility (Cornell University, Ithaca, NY).
RNA was isolated from the new cohort using the Total RNA Purification Kit (Norgen Biotek).

value: FLC tumor samples

tag: Stage

value: tumor stage


title: FLC NML tumor RNA-seq sample #4

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
NML_FLC89_N


title: FLC Primary tumor RNA-seq sample #7

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC88_T


title: FLC Metastatic tumor RNA-seq sample #2

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC90_T


title: FLC Primary tumor RNA-seq sample #8

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC89_T


title: FLC NML tumor RNA-seq sample #3

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
NML_FLC87_N


title: FLC Primary tumor RNA-seq sample #6

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC84_T


title: FLC Metastatic tumor RNA-seq sample #1

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC85_T


title: FLC Primary tumor RNA-seq sample #3

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC58L_T


title: FLC Primary tumor RNA-seq sample #4

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC82_T


title: FLC Primary tumor RNA-seq sample #2

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC57_T


title: FLC Recurrent tumor RNA-seq sample

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC55_T


title: FLC NML tumor RNA-seq sample #1

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
NML_FLC56_N


title: FLC NML tumor RNA-seq sample #2

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
NML_FLC83_N


title: Subject 607, Cohort A, visit 0


title: FLC NML tumor RNA-seq sample #5

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
NML_FLC90_N


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#4, replicate #2

city: Munich

first: Felix

middle: Archibald

last: Bayerl

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Molecular Immunology

institute: Technical Univerity of Munich

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#4, technical replicate #2

data_processing:
Raw non-demultiplexed fastq files were processed using zUMIs (version 2.4.1 or newer) with STAR (v2.5.4b) to generate expression profiles.
Mouse cDC1 cells were mapped against GrCm38 (mm10) genome build.
Assembly: Ensembl GRCm38.91
Supplementary files format and content: tab delimited text file include sequence read counts of each sample

source_name: CD103+ cDC1

growth_protocol: Endogeneous cDC1 were sorted from tumors six days after subcutaneous injection of 2x10E6 BRAFV600E Control or Ptgs1/Ptgs2 KO melanoma cells in either C57BL6/J Wt mice or Clec9A-Cre Ptger2 KO Ptger4 fl/fl mice (which lack the EP2 and EP4 receptor on cDC1). For each group, four biological replicates, containing three technical replicates of 10 cDC1 each, were sequenced using SMART-Seq3.

extract_protocol:
RNA extraction was performed by the VBCF.NGS core facility using the Smart-seq3 protocol by Illumina. (Hagemann-Jenssen et al., Nat.Biotechnol. 2020; https://pubmed.ncbi.nlm.nih.gov/32518404/)
Library prep was performed according to the manufacturer’s instructions using the Nextera kit after direct sorting into RNA lysis buffer.

treatment_protocol: After resection, tumors were cut into small pieces and digested with 200 U/ml Collagenase IV and 100 µg/ml DNAse I. The filtered single cell suspension was enriched for myeloid cells by density centrifugation. LiveDead-CD45+MHC-II+CD11c+CD103+CD11b- cells were directly sorted into RNA-lysis buffer.

tag: strain

value: subcutaneously injected melanoma

tag: biological replicate

tag: technical replicate


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#3, replicate #3

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#3, technical replicate #3


title: normal skin rep3

city: Shanghai

first: Jing

last: Zhang

address: No. 83, Fenyang Road,

institute: Eye, Ear, Nose and Throat Hospital, Fudan University

data_processing:
HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument used for basecalling.
Libraries were then denatures to yield single-stranded DNA that was captured and amplified in situ based on provided protocols. Sequencing was carried out using a 2x150 paired-end (PE) configuration.
Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. According to the alignment file(*.sam), circRNA is identified by software CIRI (v2.0). The junction reads at the back-splicing loci of circRNA is used to calculate its expression. SRPBM(spliced reads per billion mapping) is used to normalize the reads.
Genome_build: GRCh37/hg19

source_name: normal skin

extract_protocol:
Keloids were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®). Libraries were then denatures to yield single-stranded DNA that was captured and amplified in situ based on provided protocols.

value: skin


title: normal skin rep2


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#3, replicate #2

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#3, technical replicate #2


title: FLC Primary tumor RNA-seq sample #5

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC83_T


title: FLC Primary tumor RNA-seq sample #1

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
FLC_FLC56_T


title: normal skin rep1


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#3, replicate #1

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#3, technical replicate #1


title: keloid rep3

source_name: keloid


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#4, replicate #1

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#4, technical replicate #1


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#2, replicate #2

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#2, technical replicate #2


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#2, replicate #3

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#2, technical replicate #3


title: keloid rep2


title: keloid rep1


title: MV4-11-5_RNA seq

city: Tokyo

first: Kotoko

last: Yamatani

address: Building A 6F, Hongo Bunkyo-ku 2-1-1

institute: Juntendo University

data_processing:
The sequenced data were mapped to the hg38 genome using STAR RNA-seq aligner.
Genome_build: hg38
Supplementary_files_format_and_content: txt file, featureCounts

source_name: Human acute myelocytic leukemia cell

growth_protocol: Cells were cultured in IMDM  medium supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted from cells with the RNeasy Mini Kit
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). The library fragments were purified with QIAQuick PCR kits (QIAGEN).The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina). After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: myelomonocytic

value: Blood (leukemia)

tag: genotype


title: GEX1A-3.total-RNA-seq

city: Hangzhou

first: Fengli

last: Zhao

state: Zhejiang

address: No. 28 of Shuidaosuo Road

department: State Key Laboratory of Rice Biology and Breeding

institute: China National Rice Research Institute

description:
total-RNA-seq data
total RNA

data_processing:
The adapters, Ns, and low-quality bases were removed from raw data using the Trimmomatic package (version 0.39)
The clean reads were mapped to the TAIR10 genome using HISAT2 (version 2.2.0) with default parameters.
RNA-seq: The uniquely mapped reads were retained for further processing using SAMtools [3] (version 1.3.1)
pNET-seq: Reads mapping to the reference genome and non-uniquely mapped read filtering were conducted as described above. And PCR duplications were filtered by gencore [7] (version 0.16.0) according to unique molecular identifiers (UMIs).
Assembly: TAIR10 genome
Supplementary files format and content: BigWig, or tab-separated text

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
Total RNA was extracted using E.Z.N.A. Plant RNA Kit (Omega)
The resulting total RNA and mRNA were used to construct the strand-specific sequencing library with NEBNext Ultra II Directional RNA Library Prep Kit (NEB)
pNET-seq; CB-RNA-seq; total-RNA-seq

value: seedling

value: Herboxidiene

tag: age


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#1, replicate #2

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#1, technical replicate #2


title: cDC1 from BRAFV600E melanoma#4, replicate #3

description: cDC1 from BRAFV600E melanoma in a wt mouse#4, technical replicate #3


title: cDC1 from BRAFV600E melanoma#3, replicate #1

description: cDC1 from BRAFV600E melanoma in a wt mouse#3, technical replicate #1


title: cDC1 from BRAFV600E melanoma#2, replicate #2

description: cDC1 from BRAFV600E melanoma in a wt mouse#2, technical replicate #2


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#1, replicate #3

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#1, technical replicate #3


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#1, replicate #1

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#1, technical replicate #1


title: cDC1 from BRAFV600E melanoma#3, replicate #2

description: cDC1 from BRAFV600E melanoma in a wt mouse#3, technical replicate #2


title: cDC1 from BRAFV600E melanoma#4, replicate #2

description: cDC1 from BRAFV600E melanoma in a wt mouse#4, technical replicate #2


title: cDC1 from BRAFV600E melanoma#2, replicate #3

description: cDC1 from BRAFV600E melanoma in a wt mouse#2, technical replicate #3


title: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma#4, replicate #3

description: cDC1 from BRAFV600E Ptgs1/Ptgs2 KO melanoma in a wt mouse#4, technical replicate #3


title: cDC1 from BRAFV600E melanoma#1, replicate #2

description: cDC1 from BRAFV600E melanoma in a wt mouse#1, technical replicate #2


title: DMSO-3.total-RNA-seq

description:
total-RNA-seq data
total RNA

value: DMSO


title: cDC1 from BRAFV600E melanoma#3, replicate #3

description: cDC1 from BRAFV600E melanoma in a wt mouse#3, technical replicate #3


title: cDC1 from BRAFV600E melanoma#4, replicate #1

description: cDC1 from BRAFV600E melanoma in a wt mouse#4, technical replicate #1


title: m20wp52w_3

city: shanghai

first: li

last: zihao

address: dongchuan road 800

institute: shanghai jiao tong university

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.

source_name: Antrum epithelium

extract_protocol:
Antrum epithelium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Atrophic gastritis mice model was induced by MNNG and Ranitine treatment for 20w, while PEEPA-P5 was given via gavage administration for 2w

value: Antrum epithelium

value: MNNG and Ranitine treatment for 20w and PEEPA-P5 treatment for 2w


title: cDC1 from BRAFV600E melanoma#2, replicate #1

description: cDC1 from BRAFV600E melanoma in a wt mouse#2, technical replicate #1


title: cDC1 from BRAFV600E melanoma#1, replicate #3

description: cDC1 from BRAFV600E melanoma in a wt mouse#1, technical replicate #3


title: MV4-11-11_RNA seq


title: cDC1 from BRAFV600E melanoma#1, replicate #1

description: cDC1 from BRAFV600E melanoma in a wt mouse#1, technical replicate #1


title: m20wp52w_1


title: DMSO-2.total-RNA-seq

description:
total-RNA-seq data
total RNA


title: m20wV2w_2

value: MNNG and Ranitine treatment for 20w and vehicle treatment for 2w


title: GEX1A-1.total-RNA-seq

description:
total-RNA-seq data
total RNA


title: GEX1A-2.total-RNA-seq

description:
total-RNA-seq data
total RNA


title: m20wV2w_3


title: m20wp52w_2


title: DMSO-1.total-RNA-seq

description:
total-RNA-seq data
total RNA


title: xrn3-2.cb-RNA-seq

description:
CB-RNA-seq data
nuclear RNA

molecule: nuclear RNA


title: Col-0-2.cb-RNA-seq

description:
CB-RNA-seq data
nuclear RNA


title: GEX1A-2.Ser2.NET

description:
pNET-seq data
nuclear RNA

value: Herboxidiene; Pol II Ser 2P antibody (3E10, AB_2687450, ACTIVE MOTIF)


title: xrn3-1.cb-RNA-seq

description:
CB-RNA-seq data
nuclear RNA


title: C146 B cell, elderly, replicate 2, scRNAseq

description: 5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: B cell

value: elderly

value: mRNA


title: Col-0-1.cb-RNA-seq

description:
CB-RNA-seq data
nuclear RNA


title: C148 B cell, elderly, replicate 1, scRNAseq

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: GEX1A-1.Ser2.NET

description:
pNET-seq data
nuclear RNA


title: DMSO-2.Ser2.NET

description:
pNET-seq data
nuclear RNA

value: DMSO; Pol II Ser 2P antibody (3E10, AB_2687450, ACTIVE MOTIF)


title: C144 B cell, elderly, scRNAseq


title: C145 B cell, elderly, scRNAseq


title: C146 B cell, elderly, replicate 1, scRNAseq


title: C031 B cell, young, scRNAseq

value: young


title: C148 B cell, elderly, replicate 2, scRNAseq


title: xrn3-2.Ser2.NET

description:
pNET-seq data
nuclear RNA

value: Pol II Ser 2P antibody (3E10, AB_2687450, ACTIVE MOTIF)


title: C094 B cell, young, scRNAseq


title: m20wV2w_1


title: Infected

city: Manchester

first: Matthew

middle: Christopher

last: Sinton

state: Greater Manchester

address: Core Technology Facility

department: Division of Immunology, Immunity to Infection and Respiratory Medicine

country: United Kingdom

institute: University of Manchester

description: single cell RNA

data_processing:
For FASTQ generation and alignments, illumina basecall files (*.bcl) were converted to FASTQs using bcl2fastq
Gene counts were generated using CellRanger for single cell RNAseq (v.6.0.0)
Mapping strategy was conducted on CellRanger against a combined Mus musculus (mm10) and Trypanosoma brucei (TREU927) transcriptome reference
After alignment, reads were grouped based on barcode sequences and demultiplexed using the Unique Molecular Identifiers (UMIs)
Assembly: mm10 + TREU927
Supplementary files format and content: .h5 files were generated as outputs from CellRanger

source_name: White adipose tissue

extract_protocol:
Single cell suspensions were obtained from murine adipose tissue using enzymatic dissociation, followed by library preparation using the 10X Chromium platform.
Illumina compatible, RNA libraries were prepared with the 10X Chromium technolgy

value: White adipose tissue

value: Infected


title: Naïve

description: single cell RNA

value: Naive


title: IL-17A_4

data_processing:
Raw reads in fastq format were processed through proprietary Perl scripts developed by Novogene (Cambridge, UK). Clean reads were obtained by removing reads containing adapters, poly-N, or low-quality reads from raw data. Concurrently, the Q20, Q30 and GC content of the clean data was calculated.
Genome and genome annotation files (Genome Reference Consortium Mouse Build; GRCm39) were downloaded. An index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The featureCounts (v. 1.5.0-p3) package was used to count read numbers mapped to each gene, before calculating the Fragments Per Kilobase of transcript sequence per Millions base pairs (FPKM) of each gene using the length of the gene and reads count mapped to this gene.   Differential expression analysis was performed using the DESeq2 R package (v. 1.20.0). DESeq2
The resulting p-values were adjusted using the Benjamini and Hochberg approach to control false discovery rate.
Assembly: Genome Reference Consortium Mouse Build; GRCm39

extract_protocol:
RNA was purified using the standard Trizol method in conjuntion with a Qiagen RNeasy kit
Messenger RNA (mRNA) was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in a First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was then performed using DNA Polymerase I and RNase H. Remaining overhangs were converted to blunt ends via exonuclease/polymerase activity. Following adenylation of 3’ ends of DNA fragments, adaptors with hairpin loop structures were ligated. To select cDNA fragments of 370~420 bp in length, library fragments were purified using AMPure XP beads (Beckman Coulter), as per the manufacturer’s instructions. PCR was then performed using Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) primers. Finally, PCR products were purified (AMPure XP system) using AMPure XP beads (Beckman Coulter), as per the manufacturer’s instructions, and library quality was assessed using a Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: 4 technical replicates per condition. Cells were treated for 24 h with either PBS or 100 ng of recombinant IL-17A

value: Fibroblast

value: 100 ng recombinant IL-17A


title: IL-17A_3


title: IL-17A_1


title: IL-17A_2


title: Control_2

source_name: Control

value: PBS


title: Control_4


title: Control_3


title: C005 B cell, young, replicate 2, scRNAseq


title: DMSO-1.Ser2.NET

description:
pNET-seq data
nuclear RNA

value: seedling


title: xrn3-1.Ser2.NET

description:
pNET-seq data
nuclear RNA


title: C005 B cell, young, replicate 1, scRNAseq


title: Control_1


title: C004 B cell, young, scRNAseq


title: Col-0-2.Ser2.NET

description:
pNET-seq data
nuclear RNA


title: Col-0-1.Ser2.NET

description:
pNET-seq data
nuclear RNA


title: Subject 53, Cohort A, visit 0

tag: subject

value: A

value: Baseline 1


title: MCF7 Y537S cells, no treatment 2

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description:
Madak_collatedCounts.txt
Vehicle_91

data_processing:
Fastqc files containing raw RNA-sequencing data were trimmed using Trimmomatic (version 0.38; RRID:SCR_011848)
Reads were mapped to the human reference genome (GRCh37) or mouse reference genome (GRCm38) from the Ensembl (RRID:SCR_002344) database and aligned using the STAR alignment tool
Read counts were generated from SUBREAD (version 1.6.3; RRID:SCR_009803), and feature counts were exported for statistical analysis in R.
Quality control and normalization were conducted in R using edgeR (version 3.24.3; RRID:SCR_012802).
Statistical analysis was conducted in R using limma
Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix.
Differentially expressed genes were then determined by fold change and P value with a Benjamini–Hochberg multiple testing correction for each gene for each treatment relative to the vehicle control.
We considered genes with a fold change of >1.5 and P value of <0.05 as significantly differentially expressed.
Assembly: mm10 and hg19
Supplementary files format and content: single table of counts

source_name: Liver tumor

growth_protocol: MCF7 ESR1Y537S mutant cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. The cells injected to mice as 10^6 cells per mice.

extract_protocol:
treated tumors were homogenized in 1 mL of TRIzol reagent (Life Technologies, Carlsbad, CA, USA), and total RNA was extracted according to the manufacturer’s protocol and cleaned using RNneasy mini kit (Qiagen, Hilden, Germany).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand

treatment_protocol: Fulv (Sigma-Aldrich) was dissolved in 10% dimethyl sulfoxide and 90% corn oil and was administrated via intramuscular injection (100 mg/kg) twice per week (Monday and Friday) for 4 weeks. Palb (50 mg/kg; Monday and Friday, twice per week), and KPT-9274 (100 mg/kg; Monday to Friday, daily) were dissolved in the corresponding solvent provided by Karyopharm Therapeutics and were administered by oral gavage.

value: Liver tumor

value: MCF7 Y537S

value: metastatic tumor cells

value: NOD scid gamma


title: MCF7 Y537S cells, no treatment 3

description:
Madak_collatedCounts.txt
Vehicle_92


title: RHCOMP_plusIFN, 1

city: London

first: Philip

last: East

address: Midland Road

institute: The Francis Crick Institute

data_processing:
bcltofastq
RSEM quantification with STAR nfcore/rnaseq pipeline version 3.4
Assembly: GRCh38 with Ensembl annotation release version 95
Supplementary files format and content: tab delimited raw counts matrix

source_name: Human foreskin fibroblasts infected with RH Toxoplasma gondii

extract_protocol:
RNA was isolated using an RNeasy Mini Kit
mRNA libraries were prepared using the NEBNext Ultra II Directional PolyA mRNA kit with 100 ng of input

value: Human foreskin fibroblasts (HFF)

tag: infection

value: plus interferon gamma


title: RHCOMP_minusIFN, 3

value: minus interferon gamma


title: RHCOMP_plusIFN, 2


title: RHCOMP_plusIFN, 3


title: Subject 816, Cohort A, visit 0

tag: cohort

tag: visit


title: Empty vector control (LeGO-Ctl) FLC monoclone cell RNA-seq sample #2

description:
FLC tumor cells in culture, established from a patient-derived xenograft (PDX) mouse model
RNA-seq. FLC monoclones with LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
Clone E6
RKM5

source_name: FLC tumor cells

extract_protocol:
Libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina).
RNA was isolated from the new cohort using the Total RNA Purification Kit (Norgen Biotek).

tag: tissue

value: FLC tumor cells

value: tumor stage


title: Empty vector control (LeGO-Ctl) FLC monoclone cell RNA-seq sample #1

description:
FLC tumor cells in culture, established from a patient-derived xenograft (PDX) mouse model
RNA-seq. FLC monoclones with LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
Clone E5
RKM4


title: RHCOMP_minusIFN, 2


title: RHCOMP_minusIFN, 1


title: MCF7 Y537S cells, no treatment 1

description:
Madak_collatedCounts.txt
Vehicle_62


title: LINC00473-overexpression (LeGO-473ox) FLC monoclone cell RNA-seq sample #2

description:
FLC tumor cells in culture, established from a patient-derived xenograft (PDX) mouse model
RNA-seq. FLC monoclones with LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
Clone D4
RKM3


title: RHdGRA57, plusIFN, 3

value: Knockout RHdGRA57-infected


title: MCF7 Y537S cells, no treatment 4

description:
Madak_collatedCounts.txt
Vehicle_93


title: LINC00473-overexpression (LeGO-473ox) FLC monoclone cell RNA-seq sample #1

description:
FLC tumor cells in culture, established from a patient-derived xenograft (PDX) mouse model
RNA-seq. FLC monoclones with LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
Clone D3
RKM2


title: MCF7 Y537S cells, Palb treatment 4

description:
Madak_collatedCounts.txt
Palbo_90

value: Palbociclib


title: MCF7 Y537S cells, Palb treatment 3

description:
Madak_collatedCounts.txt
Palbo_28


title: MCF7 Y537S cells, Palb treatment 1

description:
Madak_collatedCounts.txt
Palbo_19


title: RHdGRA57, plusIFN, 1


title: MCF7 Y537S cells, Palb treatment 2

description:
Madak_collatedCounts.txt
Palbo_26


title: PGE2_cDC1_24h+polyIC_4h_B

description: PGE2 treated cDC1 24h + poly I:C activation for 4h

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 v1.14.1 R package was utilized to identify differentially expressed genes
Assembly: GRCm38.p6
Supplementary files format and content: tab delimited text file include sequence read counts of each sample

growth_protocol: In brief, bone marrow cells were isolated from murine femur and tibia by flushing the bones with RPMI using a syringe. After red blood cell lysis with hypotonic ACK buffer (ddH2O with 150mM ammonium chloride, 10mM potassium bicarbonate and 1um disodium EDTA) for 2 minutes at room temperature, 15x105 bone marrow cells/ml were incubated with GM-CSF (300pg/ml) and FLT3L (55ng/ml) in complete RPMI for 9 days. Cells were washed and reseeded in fresh medium with GM-CSF and FLT3L for 5 days. CD103+ cDC1 purified by cell sorting were used for functional assays

extract_protocol:
RNA from murine cDC1 was isolated using the NEB Monarch Total RNA Miniprep Kit.
As described previously (Macosko et al 2015), library construction for bulk 3’-sequencing of poly(A)-RNA was performed. In brief, Barcoded cDNA was produced from isolated RNA of each sample using a Maxima RT polymerase (Thermo Fisher), oligo-dT primers containing barcodes, and unique molecular identifiers (UMIs). Adaptor 5′ ends of the cDNAs were elongated using a template switch oligo (TSO). After pooling the samples, full-length cDNA was amplified using TSO site- and adaptor- specific primers. cDNA was supplemented with the Nextera XT kit (Illumina), 3′-end-fragments, as well as P5 and P7 Illumina overhangs. Barcoded cDNA libraries were sequenced using a NextSeq 500 system (Illumina). UMI tables were spawned for samples and genes using Drop-seq pipeline (https://github.com/broadinstitute/Drop-seq). We annotated reads using the GRCm38 reference genome (ENSEMBL annotation release 75). Using the DESeq2 R package (Love, Huber & Anders, 2014), differentially expressed genes were extracted. (DEGs, Log2 fold change of 1.5 and adjusted p-value (p.adj) <= 0.05).

treatment_protocol: 2x10e5 CD103+ cDC1 were seeded in 200ul RPMI supplemented with growth factors and the respective treatments for indicated periods of time.

value: bone marrow derived in vitro culture

value: PGE2 (100ng/ml) 24h + poly I:C (10ug/ml) 4h

value: B


title: PGE2_cDC1_24h+polyIC_4h_D

value: D


title: PGE2_cDC1_24h+polyIC_4h_C

value: C


title: RHdGRA57, minusIFN, 3


title: RHdGRA57, minusIFN, 2


title: MCF7 Y537S cells, Palb+NAMPTi treatment 1

description:
Madak_collatedCounts.txt
Palb_Kpt_50

value: Palbociclib+NAMPT inhibitor


title: MCF7 Y537S cells, Palb+NAMPTi treatment 2

description:
Madak_collatedCounts.txt
Palb_Kpt_54

value: Liver tumor


title: RHdGRA57, minusIFN, 1


title: NPC cells, RFX4 knock out, replicate 3

city: Seoul

first: Su Min

last: Kim

state: Gangnam-gu

address: Dogok-ro 237

institute: Severance Hospital

data_processing:
Sequence reads were mapped to GRCh38/hg38 using hisat2
Read count extraction and normalization were performed using subread package (featurecounts function)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: NPC

extract_protocol:
RNA was harvested using TRIZOL.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit following manufacturer's protocols.

value: NPC

value: RFX4 knock out

value: neurogenic differentiation


title: ESC cells, RFX4 knock out, replicate 2

source_name: ESC

value: ESC


title: RHdKu80, plusIFN, 3

value: Human foreskin fibroblasts (HFF)

value: Wildtype RHdKu80-infected

value: plus interferon gamma


title: ESC cells, RFX4 knock out, replicate 3


title: RHdGRA57, plusIFN, 2


title: NPC cells, RFX4 knock out, replicate 2


title: NPC cells, RFX4 knock out, replicate 1


title: Untreated_cDC1_24h+polyIC_4h_C

description: Untreated cDC1 24h + poly I:C activation for 4h

value: Untreated cDC1 24h + poly I:C (10ug/ml) 4h


title: Untreated_cDC1_24h+polyIC_4h_D


title: MCF7 Y537S cells, Palb+NAMPTi treatment 4

description:
Madak_collatedCounts.txt
Palb_Kpt_82

value: MCF7 Y537S

value: metastatic tumor cells

value: NOD scid gamma


title: MCF7 Y537S cells, NAMPTi treatment 4

description:
Madak_collatedCounts.txt
Kpt_42

value: NAMPT inhibitor


title: MCF7 Y537S cells, NAMPTi treatment 3

description:
Madak_collatedCounts.txt
Kpt_41


title: RHdKu80, plusIFN, 2


title: MCF7 Y537S cells, Palb+NAMPTi treatment 3

description:
Madak_collatedCounts.txt
Palb_Kpt_66


title: ESC cells, control, replicate 3

value: WT


title: Untreated_cDC1_24h+polyIC_4h_B

value: bone marrow derived in vitro culture

value: B


title: Untreated_cDC1_24h+polyIC_4h_A

value: A


title: PGE2_cDC1_24h_D

description: PGE2 treated cDC1 24h

value: D


title: RHdKu80, minusIFN, 3

value: minus interferon gamma


title: MCF7 Y537S cells, NAMPTi treatment 1

description:
Madak_collatedCounts.txt
Kpt_39

value: Liver tumor


title: MCF7 Y537S cells, NAMPTi treatment 2

description:
Madak_collatedCounts.txt
Kpt_40


title: ESC cells, RFX4 knock out, replicate 1

value: RFX4 knock out

value: neurogenic differentiation


title: PGE2_cDC1_24h+polyIC_4h_A

value: PGE2 (100ng/ml) 24h + poly I:C (10ug/ml) 4h


title: ESC cells, control, replicate 2

value: ESC


title: MCF7 Y537S cells, Fulv+Palb treatment 4

description:
Madak_collatedCounts.txt
Fulv_Palb_88

value: Fulvestrant+Palbociclib


title: RHdKu80, minusIFN, 2

value: Human foreskin fibroblasts (HFF)

value: Wildtype RHdKu80-infected


title: NPC cells, control, replicate 3

value: NPC


title: RHdKu80, minusIFN, 1


title: MCF7 Y537S cells, Fulv+Palb treatment 3

description:
Madak_collatedCounts.txt
Fulv_Palb_83

value: MCF7 Y537S

value: metastatic tumor cells

value: NOD scid gamma


title: Uninfected, plusIFN, 3

source_name: Human foreskin fibroblasts

value: Uninfected

value: plus interferon gamma


title: NPC cells, control, replicate 2

value: WT


title: Uninfected, plusIFN, 2


title: NPC cells, control, replicate 1


title: RHdKu80, plusIFN, 1


title: MCF7 Y537S cells, Fulv+NAMPTi treatment 4

description:
Madak_collatedCounts.txt
Fulv_Kpt_9

value: Fulvestrant+NAMPT inhibitor


title: MCF7 Y537S cells, Fulv+Palb treatment 2

description:
Madak_collatedCounts.txt
Fulv_Palb_79


title: PGE2_cDC1_24h_A

description: PGE2 treated cDC1 24h

value: bone marrow derived in vitro culture

value: A


title: PGE2_cDC1_24h_B

description: PGE2 treated cDC1 24h

value: B


title: Untreated_cDC1_24h_D

description: Untreated cDC1 24h

value: none 24h

value: D


title: Uninfected, plusIFN, 1


title: MCF7 Y537S cells, Fulv+Palb treatment 1

description:
Madak_collatedCounts.txt
Fulv_Palb_21

value: Liver tumor


title: Untreated_cDC1_24h_C

description: Untreated cDC1 24h

value: C


title: Uninfected, minusIFN, 3

value: Human foreskin fibroblasts (HFF)

value: minus interferon gamma


title: Untreated_cDC1_24h_B

description: Untreated cDC1 24h


title: MCF7 Y537S cells, Fulv+NAMPTi treatment 2

description:
Madak_collatedCounts.txt
Fulv_Kpt_395


title: MCF7 Y537S cells, Fulv+NAMPTi treatment 3

description:
Madak_collatedCounts.txt
Fulv_Kpt_45


title: PGE2+EP2+EP4antagonist_cDC1_4h_D

description: PGE2 + EP2 + EP4 antagonist treated cDC1 4h


title: Uninfected, minusIFN, 1


title: ESC cells, control, replicate 1

value: ESC

value: neurogenic differentiation


title: Untreated_cDC1_24h_A

description: Untreated cDC1 24h


title: MCF7 Y537S cells, Fulv treatment 4

description:
Madak_collatedCounts.txt
Fulv_38

value: MCF7 Y537S

value: metastatic tumor cells

value: Fulvestrant


title: PGE2_cDC1_24h_C

description: PGE2 treated cDC1 24h


title: PGE2+EP2+EP4antagonist_cDC1_4h_C


title: MCF7 Y537S cells, Fulv treatment 3

description:
Madak_collatedCounts.txt
Fulv_36

value: NOD scid gamma


title: PGE2+EP2+EP4antagonist_cDC1_4h_B


title: MCF7 Y537S cells, Fulv treatment 2

description:
Madak_collatedCounts.txt
Fulv_34


title: PGE2+EP2+EP4antagonist_cDC1_4h_A


title: plasma exosomes, osteosarcoma patient [AA230-003]

city: Nanning

first: Yun

last: Liu

address: NO 6, Shuangyong Road, Nanning City, Guangxi Province, China

institute: The First Affiliated Hospital of Guangxi Medical University

description: lincRNA;circRNA;mRNA

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts and got clean data
Use the designated genome GRCh38 as a reference for sequence alignment
Cuffcompare program from the Cufflinks package v2.2.1 was used to predict Novel lncRNA gene
Two algorithms of CIRI2 and find_circ were used to predict circRNA,
Stringtiewas used to calculate FPKMs of all coding genes and lncRNA genes in each sample. Gene FPKMs was computed by summing the FPKMs of transcripts in each gene group.Junction reads were used as circRNA expression level. We used TPM to normalize the expression abundance quantification
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Peripheral blood

extract_protocol:
a procedure of ultracentrifuged and size exclution chromatography methods  were used to isolate exosomes. Total RNA was extracted and purified from plasma exosome using miRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204) according to the kit instruction. RNA concentration and purity were evaluated using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 250pg—10ng RNA per sample was used as input material for sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit V2 (Takara Bio USA, Inc.) following manufacturer’s ecommendations and index codes were added to attribute sequences to each sample.Sequencing libraries were generated using QIAseq miRNA Library Kit (Qiagen, Frederick, MD) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Reverse transcription (RT) primers with unique molecular indices (UMIs) were introduced to analyze the quantification of miRNA expressions during cDNA synthesis and PCR amplification. At last, library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR. The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated

value: Peripheral blood

value: plasma exosomes

tag: disease state

value: osteosarcoma

tag: patient

tag: group

tag: Sex

value: Male

tag: location

value: Distal femur

tag: grade

value: III


title: plasma exosomes, osteosarcoma patient [AA230-004]

description: lincRNA;circRNA;mRNA

tag: cell type

value: II B


title: MCF7 Y537S cells, Fulv treatment 1

description:
Madak_collatedCounts.txt
Fulv_33

value: Liver tumor

tag: cell line

tag: treatment


title: plasma exosomes, osteosarcoma patient [AA230-001]

description: lincRNA;circRNA;mRNA


title: plasma exosomes, control volunteer [A503-11]

description: circRNA_control.txt;lncRNA_control.txt;mRNA_control.txt

value: control

value: Female


title: PGE2+EP4antagonist_cDC1_4h_C

description: PGE2 + EP4 antagonist treated cDC1 4h

tag: strain

value: bone marrow derived in vitro culture

tag: biological replicate

value: C


title: PGE2+EP4antagonist_cDC1_4h_D

description: PGE2 + EP4 antagonist treated cDC1 4h

value: D


title: PGE2+EP4antagonist_cDC1_4h_B

description: PGE2 + EP4 antagonist treated cDC1 4h

value: B


title: Uninfected, minusIFN, 2

value: Human foreskin fibroblasts (HFF)

value: Uninfected

value: minus interferon gamma


title: plasma exosomes, osteosarcoma patient [AA230-002]

description: lincRNA;circRNA;mRNA

value: Peripheral blood

value: Proximal fibula

value: I B


title: plasma exosomes, control volunteer [A503-09]

value: plasma exosomes

tag: genotype


title: plasma exosomes, control volunteer [A503-10]


title: plasma exosomes, osteosarcoma patient [AA230-005]

description: lincRNA;circRNA;mRNA

value: osteosarcoma

value: Distal femur


title: plasma exosomes, control volunteer [A503-07]


title: Zn-3

first: Lincheng

last: Han

address: Guangzhou Higher Education Mega Center

institute: South China University of Technology

data_processing:
Quality Control: Raw Data are processed with Perl scripts to ensure the quality of data used in following analysis. The adopted filter criteria are: 1) Filter out adaptor-polluted reads. (Reads contains more than 5 adapter-polluted bases are regarded as adaptor-polluted reads and are filtered out. As for paired-end sequencing data, reads from two ends are filtered out if any read of the paired-end reads are adaptor-polluted); 2) Filter out low-quality reads. (Reads with the number of bases whose phred Quality value was no more than 19 accounting for more than 15% are regarded as low-quality reads and are filtered out.) 3) Filter out reads with the number of N basesaccounting for more than 5 %. As for paired-end sequencing data, reads from two ends are filtered out if any read of the paired-end reads should be filtered out according to the abovecriteria. The Clean Data is abotained after filtering, and statistics analyses are performed on its quantity and quality, including Q30 statistics, data quantity statistics, base content statistics, etc.
Mapping the Sequencing Reads to Reference Genomes: The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). And Clean Data were mapped to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml). HISAT2 is a specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again. Moreover, HiSAT2 is more accurater and faster.
Assembly: GRCm38.90

source_name: ovaries

extract_protocol:
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. RNA degradation and contamination was detected by 1% agarose gels; RNA purity was checked using the Qubit® 3.0 Flurometer(Life Technologies, CA, USA); RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The ovaries from 3 dpp mice were cultured in the medium (control, Ct) or the medium supplemented with 200 μM MnCl2 (Mn) or 35 μM ZnSO4  (Zn) for 1 day. The ovaries were collected to extract total RNA for RNA-sequencing assay.

value: ovaries

value: all cells in mouse ovaries

value: WT

value: The ovaries from 3 dpp mice were cultured in the DMEM/F12 medium supplemented with 35 μM ZnSO4 for 1 day


title: Mn-1

value: The ovaries from 3 dpp mice were cultured in the DMEM/F12 medium supplemented with 200 μM MnCl2 for 1 day


title: Mn-3


title: Mn-2


title: Zn-2


title: Zn-1


title: Ct-3

value: The ovaries from 3 dpp mice were cultured in the DMEM/F12 medium for 1 day


title: plasma exosomes, osteosarcoma patient [A503-06]

description: circRNA_patient.txt;lncRNA_patient.txt;mRNA_patient.txt

value: Female

value: Proximal tibia

value: II B


title: plasma exosomes, osteosarcoma patient [A503-05]

value: Proximal femur

value: II A


title: PGE2+EP2antagonist_cDC1_4h_D

description: PGE2 + EP2 antagonist treated cDC1 4h

value: bone marrow derived in vitro culture

value: D


title: MCF7 Y537S cells, Fulv+NAMPTi treatment 1

description:
Madak_collatedCounts.txt
Fulv_Kpt_27

value: Liver tumor

value: MCF7 Y537S

value: metastatic tumor cells

value: NOD scid gamma

value: Fulvestrant+NAMPT inhibitor


title: Ct-2

value: ovaries

value: all cells in mouse ovaries


title: Ct-1

value: WT


title: PGE2+EP3antagonist_cDC1_4h_B

description: PGE2 + EP3 antagonist treated cDC1 4h

value: B


title: PGE2+EP3antagonist_cDC1_4h_A

description: PGE2 + EP3 antagonist treated cDC1 4h

value: A


title: PGE2+EP4antagonist_cDC1_4h_A

description: PGE2 + EP4 antagonist treated cDC1 4h


title: PGE2+EP3antagonist_cDC1_4h_D

description: PGE2 + EP3 antagonist treated cDC1 4h


title: plasma exosomes, control volunteer [A503-08]

value: Peripheral blood

value: plasma exosomes

value: control

value: Male


title: plasma exosomes, osteosarcoma patient [A503-03]

value: osteosarcoma

value: Distal femur

value: II B


title: AG_CPI, biol replicate 2, scRNAseq

city: New Haven

first: Martina

last: Damo

address: 300 Cedar St

department: Immunobiology

institute: Yale University

description: 10x Genomics

data_processing:
All scRNAseq datasets were processed with CellRanger 3.1 using mm10 mouse genome indices from 10X
Libraries were further preprocessed using the scprep package, removing cells with library size lower than 1500 unique molecular identifiers (UMI) per cell and more than 15000 UMI per cell
Cells with high mitochondrial content (>85th percentile per sample) were removed, and genes not detected in any of the six samples were removed.
The resulting data matrix was then normalized by library size to 1000 counts per cell
Finally, the matrix was log-transformed.
Assembly: mm10
Supplementary files format and content: Gzipped CSV files, where rows are cells and columns are measures genes after pre-processing.

source_name: Skin

extract_protocol:
Confirmed all experimental animals had expected phenotypes based on presence/absence of overt macroscopic skin pathology, and skin infiltration and functional properties of P14 CD8 T cells recovered from each moouse. Then prepared single-cell suspensions from 4-OH-Tam-treated skin area for sequencing.
Libraries were prepared by the Yale Center for Genome Analysis using Chromium Single Cell 5' Reagent Kit (10X Genomics), according to manufacurer's instructions

value: Skin

value: NINJA

tag: age

value: 6-12 weeks old


title: AG, biol replicate 2, scRNAseq

description: 10x Genomics

value: AG


title: plasma exosomes, osteosarcoma patient [A503-04]

value: Female

value: Proximal femur


title: plasma exosomes, osteosarcoma patient [A503-02]

value: Proximal tibia


title: PGE2+EP2antagonist_cDC1_4h_A

description: PGE2 + EP2 antagonist treated cDC1 4h

source_name: CD103+ cDC1

value: bone marrow derived in vitro culture


title: PGE2+EP2antagonist_cDC1_4h_B

description: PGE2 + EP2 antagonist treated cDC1 4h

value: B


title: PGE2+EP2antagonist_cDC1_4h_C

description: PGE2 + EP2 antagonist treated cDC1 4h

value: C