title: Mycelium, CFS, replicate4

city: Castanet – Tolosan

first: Selma

middle: Pascale

last: Snini

address: Avenue Agrobiopole BP 32607

institute: Chemical Engineering Laboratory

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Aspergillus flavus SurePrint G3 Custom GE microarray (8X60K, Design 085497  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 085497_D_F_20180419). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We firstly selected control probes and probes targeting Aspergillus flavus transcripts (GeneNames begining by 'AFLA_') giving a dataset with 14374 entries. We next selected  the spots with a minimal weight of 1 for 7 out of 8 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 13005 spots out of 14374 were selected. Data were then stored in an ExpressionSet object and normalized by the qsmooth method using the qsmooth R library. The resulting matrix has 10009 rows each corresponding to a unique ProbeName (see 'Data table' below).

organism: Aspergillus flavus

source_name: Mycelium

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: The RNA was purified as recommended by the manufacturer from 100 mg of mycelium using a Qiagen RNeasy PlusMinikit (Qiagen, Hilden, Germany) and including a genomic DNA eliminator column. RNA concentrations were quantified using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Illkirch, France) and RNA integrity and purity were checked using the Experion RNA analysis kit and software (version 3.20, 2015, BioRad, Marnes-la-Coquette, France).

treatment_protocol: Petri dishes containing ISP2 supplemented with CFS4 at the final concentration of 1.5 g/L were covered with sterile cellophane sheets and inoculated with 10 µL of A. flavus spore suspension calibrayed at 10^6 spores/mL. As a control condition, Petri dishes containing ISP2 not supplemented were also inoculated in the same way. Then, fungal cultures were incubated at 28°C for five days. At the end of the incubation time, mycelia were separated from the medium and ground up under liquid nitrogen.

value: CFS

value: Mycelium


title: Human meningioma, Frozen [AP3]

status: Public on Sep 06 2023

type: RNA

city: San Francisco

first: William

last: Chen

state: CA

address: 1450 3rd Street, HD 402

country: USA

institute: UCSF

description: Nanostring nCounter

hyb_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.

scan_protocol: Cartridges were scanned on the nCounter Digital Analyzer with a FOV setting of 550

data_processing:
Samples here are unique meningiomas included in the study. Counts were positive control normalized using the spike-in positive control probes in the nSolver solftware, as per recommendations from the manufacturer (Nanostring).
Positive control normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: Human meningioma, Frozen

extract_protocol: Total RNA was extracted from frozen or FFPE meningioma tumor samples using Qiagen AllPrep or Qiagen FFPE RNAeasy kits.

tag: disease

value: meningioma


title: Human meningioma, Frozen [AP2]

description: Nanostring nCounter

label_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.


title: Mycelium, CTRL, replicate3

country: France

tag: treatment

value: CTRL

tag: tissue


title: Mycelium, CTRL, replicate4


title: 14.5_dpc_H3K27me3_ChIPseq [GAIIx]

type: SRA

city: Tokyo

first: Yukiko

last: Gotoh

state: Tokyo

address: 7-3-1 Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 14.5 dpc stage of mouse NPCs (manually dissected).

library_source: genomic

data_processing:
Basecalls performed using Illumina CASAVA version 1.4 at GAIIx and Illumina bcl2fastq-1.8.4 at Hiseq2000/Hiseq2500.
Sequenced reads were aligned to the mm9 reference genome using ELAND v2 software (Illumina).
The bigWig file generated by Homer software using makeTagDirectory and makeUCSCfile.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: neural progenitor cells

growth_protocol:
ChIP-seq: Neocortical NSCs were isolated either by fluorescent activated cell sorting (FACS) from mice expressing the NSC marker, Nestin-d4-Venus, or by manual dissection of the ventricular zone of the neocortex.
RNA-seq: Neocortical NSCs were isolated by fluorescent activated cell sorting (FACS) either from mice expressing the NSC marker, Nestin-d4-Venus or from Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/-

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared according to Illumina's instructions accompanying the Truseq ChIP Prep Kit.
RNA-seq: Total RNA was extracted from cell lysates.
RNA libraries were prepared according to Illumina' s instructions accompanying the Truseq RNA Prep Kit.

treatment_protocol: RNA-seq: For Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/-, cells were stained with CD133 antibody and highly positive fraction was isolated as neural stem cells.

tag: strain background

value: ICR

tag: Stage

tag: cell type

value: neural progenitor cells (NPCs)

tag: chip antibody

value: H3K27me3 (Millipore, 07-449)


title: r_BTK_inh_5

city: Rotterdam

first: Peter

middle: D.

last: Katsikis

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Department of Immunology

country: Netherlands

institute: Erasmus University Medical Center

library_source: transcriptomic

data_processing:
Reads were quality trimmed using Trim Galore! for bases with a Phred score lower than 30.
The reads were aligned for each sample seperately using STAR2.7.6a to the mouse reference genome (GRCm38).
BAM files were converted using Samtools 1.10.
Alignment files were annotated and counts were esimated with RSEM 1.3.1 using GRCm38.81.gtf from Ensembl file for gene annotation.
Differential expression analysis was perfomed by importing estimated counts into R 4.0.3 and DESeq2 1.30.0. (p-values were calculated with a Wald test, adjusted with the Benjamini-Hochberg multiple hypothesis testing method, Log2FoldChange was shrunk using the apeglm method)
Genes were indicated as differenetially expressed with an adjusted p-value <= 0.05.
Assembly: Ensembl GRCm38; Ensembl GRCm38.81.gtf
Supplementary files format and content: RSEM estimated gene counts for each sample
Supplementary files format and content: Exel file of all genes from r_BTK_inh vs r_DMSO. Sheet 1 has Ensembl Gene ID, annotation, differential expression values with r_DMSO asa reference. Sheet 2 has Ensembl Gene ID, annotation, and estimated counts
Supplementary files format and content: Exel file of significant differentially expressed genes from r_BTK_inh vs r_DMSO. Sheet 1 has Ensembl Gene ID, annotation, differential expression values with r_DMSO asa reference. Sheet 2 has Ensembl Gene ID, annotation, and estimated counts

source_name: purified CD8+ T cells

growth_protocol: CD8+ T cells purified from OT-I mice were stimulated daily for five days with 10ng/ml OVA(257-264) peptide in the presence of IL-15 and IL-7 (Repeat peptide stimulation). Cells were split on day 4. As controls, cells were  stimulated only once with OVA(257-264) peptide for 48 hours and then washed and cultured without peptide for an additional 3 days, from day5 different treatment was prescribed to the control cells (single stimualted) and exhasuted cells (repeat stimualted)

extract_protocol:
0.5-1*10^6 live CD8+ T cells were washed with PBS and immediately lysed with TRIzol LS reagent (Life Technologies) and stored at -80°C. RNA was extracted according to manufacturer’s instructions and a bioanalyzer (Agilent) was used to determine the integrity of the extracted RNA.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L).
mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

treatment_protocol: From day 5, the single peptide and repeat peptide stimulated cells were treated with the 1μM Ibrutinib (MedcheExpress, cat. No.HY10997) for 3 days. On day 8, the cells were harvested

value: purified CD8+ T cells

tag: strain

value: OT-1 mice WT

tag: genotype

value: btk KO-5

value: BTK inhitor 1uM

tag: condition

value: repeat peptide


title: Human meningioma, Frozen [AP6]

description: Nanostring nCounter


title: Mycelium, CTRL, replicate1


title: Mycelium, CFS, replicate3


title: Mycelium, CFS, replicate1


title: Mycelium, CTRL, replicate2


title: 12.5_dpc_H3K27me3_ChIPseq [GAIIx]

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 12.5 dpc stage of mouse NPCs (manually dissected).


title: RNAseq_autologous_tumor_cell_line_MEL12

city: Sapporo

first: Tomoyuki

last: Minowa

state: Hokkaido

address: west 17, south 1, Chuo-ku

department: Pathology

institute: Sapporo medical university school of medicine

data_processing:
The sequence data fo scRNAseq were processed with Cell Ranger software (version 6.1.2). Obtained raw reads of RNAseq were trimmed and quality-filtered using FastQC (version 0.11.7) and Trimmomatic (version 0.38). The reads were then mapped to the hg38 using HISAT2 (version 2.1.0), Bowtie2 (version 2.3.4.1), and STAR (version 2.6.0c). Transcripts per kilobase million (TPM) was calculated using StringTie (version 2.1.3b).
Assembly: GRCh38
Supplementary files format and content: scRNAseq: "matrix.mtx.gz" contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices. "features.tsv.gz" contains feature information that corresponds to the row index of matrix.mtx.gz. "barcodes.tsv.gz" contains cellular barcodes that correspond to column indices of matrix.mtx.gz. "filtered_contig_annotations.csv" is tab-delimited text files including TCR clonotype.
Supplementary files format and content: RNAseq: tab-delimited text files include TPM values for each samples

source_name: skin

extract_protocol:
Sample processing for scRNA-seq and scTCR-seq was performed using the Chromium Single Cell 5’ Library & Gel Bead Kit (10x Genomics). Total RNA for RNAseq was isolated using the RNeasy Mini Kit (Qiagen).
Single-cell cDNA libraries were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit (10x Genomics). The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was used for the fresh tumor tissues and its autologous tumor cell lines.
scRNA-seq and RNA-seq

value: skin

value: melanoma


title: RNAseq_autologous_tumor_cell_line_MEL09


title: Costal chondrocytes

city: Suita

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

institute: Osaka University

description: Gene expression data from mouse costal chondrocytes

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: biotin

source_name: Ribs from postnatal 4 days ICR mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: SFZ cells and costal chondrocytes were cultured with DMEM containing 10% FBS.

extract_protocol: Total RNA was extracted with Nucleospin RNA plus kit

value: Costal chondrocytes

value: ICR mice


title: SFZ cells

description: Gene expression data from mouse SFZ cells

source_name: Superficial zone of articular cartilage from postnatal 4 days ICR mice

value: SFZ cells


title: Human meningioma, Frozen [AP1]

description: Nanostring nCounter


title: r_DMSO_43

value: BTK KO-3

value: DMSO


title: Human meningioma, FFPE [KM10]

description: Nanostring nCounter

source_name: Human meningioma, FFPE

value: meningioma


title: Human meningioma, FFPE [KM9]

description: Nanostring nCounter


title: RNAseq_fresh_tumor_MEL12


title: Mycelium, CFS, replicate2

value: CFS

value: Mycelium


title: r_DMSO_37

value: BTK KO-1


title: RNAseq_fresh_tumor_MEL09


title: r_DMSO_23

value: OT-1 mice WT M2

value: ITK-PKC extra-2


title: Human meningioma, FFPE [KM5]

description: Nanostring nCounter


title: scTCRseq_MEL12

description: 10x Genomics

molecule: polyA RNA

value: lymphoycyte


title: r_DMSO_30

value: purified CD8+ T cells

value: OT-1 mice WT

value: btk KO-6


title: HEK293T SF3B1 MT Rep1

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

institute: City of Hope

description:
wt_vs_5_junctioncount_raw.txt
MT1

data_processing:
RNAseq: align with STAR, splicing analysis with StringTie, LeafCutter and rMATs
DRIPseq: mapping with BWA-MEM, R-loop narrow peaks called MCAC2
Assembly: GRCh38/hg38
Supplementary files format and content: RNAseq: junction count txt file for each sample
Supplementary files format and content: DRIPseq: narrowPeaks

source_name: embryonic kidney

extract_protocol:
DRIP-seq: DNA extracted from non-crosslinked cells using NucleoSpin® Tissue Kit (Macherey-Nagel, Duren, Germany). DNA were digested by HindIII EcoRI, BsrGI, XbaI, and SspI (New England BioLabs, Ipswich MA) re-striction enzymes cocktail. Half of the fragmented DNA was treated with RNase H (New England BioLabs, Ipswich MA) overnight at 37°C. DNA samples with or without RNase H treatment were then incubated with anti-DNA-RNA S9.6 monoclonal antibody (courtesy of Dr. Teresa V. Bowman, Albert Einstein College of Medicine) pre-blocked on Dynabeads™ Protein G beads (ThermoFisher Scientific, Waltham, MA) in immunoprecipiati-on buffer (50 mM Hepes/KOH at pH 7.5; 0.14 M NaCl; 5 mM EDTA; 1% Triton X-100; 0.1% Na-Deoxycholate, ddH2O) overnight at 4°C with rotation.
RNA-seq: Total RNA was isolated using the Macherey-Nagel NucleoSpin® RNA kit (Macherey-Nagel, Duren, Germany).
DRIP-seq: Next-generation sequencing library was constructed using SMARTer® ThruPLEX® DNA-Seq for sample prep kit (Takara Bio, Kusatsu, Japan)
RNA-seq: Library was constructed using KAPA stranded RNA-seq kit (Roche, San Francisco, CA) according to the manufacturer’s instructions.

value: embryonic kidney

tag: cell line

value: human embrionic kindey

value: SF3B1 K700E


title: HEK293T SF3B1 MT Rep2

description:
wt_vs_5_junctioncount_raw.txt
MT2


title: HEK293T SF3B1 MT Rep3

description:
wt_vs_5_junctioncount_raw.txt
MT3


title: Human meningioma, FFPE [KM4]

description: Nanostring nCounter


title: scTCRseq_MEL11

description: 10x Genomics

value: skin


title: r_DMSO_18

value: OT-1 mice WT M1

value: repeat peptide


title: HEK293T SF3B1 WT Rep2

description:
wt_vs_5_junctioncount_raw.txt
WT2

value: SF3B1 K700K


title: Human meningioma, FFPE [KM2]

description: Nanostring nCounter

value: meningioma


title: H3K27ac ChIP-seq normal gastrocnemius 1 input

city: Houston

first: Zhaoyong

last: Hu

state: Texas

address: One Baylor Plaza

department: Nephrology

institute: Baylor college of medicine

description: CTL

data_processing:
The Raw reads were obtained after ChIP-seq sequencing, which was filtered to remove adapters and contamination, and then aligned to the reference genome. High-quality mapped reads (MPAQ greater than or equal to 30) were used for subsequent information analysis. Briefly,raw sequencing reads were trimmed to remove adaptors and low-quality sequences using Cutadapt and Trimmomatic. The Clean data were quality controlled with FastQC. Clean reads were aligned to the mouse reference genome (mm10) by bowtie2 (v2.3.5.1). The mapping data were analyzed with the MACS2 (v.2.2.7.1) peak-calling algorithm.
Assembly: mm10
Supplementary files format and content: bw files

source_name: Gastrocnemius muscle

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle

extract_protocol:
The ChIP seq was prepared using SimpleChIP® Chromatin Immunoprecipitation kit (Magnetic Beads, Cell signaling technology, Cat#9003). Briefly, whole gastrocnemius muscles (500mg) from mice with or without de sciatic denervation were homogenized with dunce grander to isolate myonuclei which were then cross-linked with 1% formaldehyde for 10 min. The myonuclei were treated with 0.5 µl Micrococcal Nuclease for 10 min followed by sonication for 15 min (1/8-inch probe, 30-sec pulses X15 with setting level at 3). After centrifuge, 50ug linked DNA was used for chromatin Immunoprecipitation using anti H3K27Ac antibody (#8173).
The pulled down DNA and input DNA were submitted to LC Sciences LLC (Houston, TX. lcsciences.com) for library preparation and the yield library was sequenced with Illumina platform.

treatment_protocol: Mice were anesthetized and the left sciatic nerve was removed for a 2-mm piece. Gastrocnemius (Gas) muscles were harvested 2 weeks after denervation. Gas muscles from left hind limb of normal mice served as controls.

value: Gastrocnemius muscle

tag: age

value: normal


title: scTCRseq_MEL09

description: 10x Genomics


title: DRIP Nalm-6 SF3B1 K700E RNH1 Rep2

description: Nalm-6 SF3B1 K700E RNH1 Rep2

data_processing:
library strategy: DRIP-seq
RNAseq: align with STAR, splicing analysis with StringTie, LeafCutter and rMATs
DRIPseq: mapping with BWA-MEM, R-loop narrow peaks called MCAC2
Assembly: GRCh38/hg38
Supplementary files format and content: RNAseq: junction count txt file for each sample
Supplementary files format and content: DRIPseq: narrowPeaks

source_name: blood

value: blood

value: human leukemic B cell

value: RNaseH1 treated


title: scTCRseq_MEL10

description: 10x Genomics

value: lymphoycyte


title: HEK293T SF3B1 WT Rep1

description:
wt_vs_5_junctioncount_raw.txt
WT1


title: r_DMSO_11

value: purified CD8+ T cells

value: INHB-1 left over

value: DMSO


title: Human meningioma, FFPE [KM1]

description: Nanostring nCounter


title: H3K27ac ChIP-seq normal gastrocnemius 1

description: CTL


title: Human meningioma, Frozen [QM374]

description: Nanostring nCounter


title: H3K27ac ChIP-seq denervation gastrocnemius 1 input

description: DENV

value: sciatic denervation


title: DRIP Nalm-6 SF3B1 K700E RNH1 Rep1

description: Nalm-6 SF3B1 K700E RNH1 Rep1


title: scTCRseq_MEL03

description: 10x Genomics


title: DRIP Nalm-6 SF3B1 K700E unt Rep2

description: Nalm-6 SF3B1 K700E unt Rep2

value: untreated


title: scRNAseq_MEL12

description: 10x Genomics

library_source: transcriptomic single cell


title: HEK293T SF3B1 WT Rep3

description:
wt_vs_5_junctioncount_raw.txt
WT3

value: embryonic kidney

value: human embrionic kindey


title: T-3

city: Nanjing

first: rui

last: duan

address: No.68 changle road

country: China

institute: Nanjing First Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases
which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further
filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as
follows:
1) removing reads containing adapters;
2) removing reads containing polyA and polyG;
3) removing reads containing more than 5% of unknown nucleotides (N);
4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases.
After that, a total of G bp of cleaned, paired-end reads were produced.
We use R to perform correlation analysis. Correlation of two parallel experiments provides the evaluation of the  reliability of experimental results as well as operational stability. The pearson correlation coefficient between two  replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1,  the better the repeatability between two parallel experiments.miRNAs
Assembly: mm9
Supplementary files format and content: FPKM

source_name: brain

extract_protocol:
Total RNA was extracted using Trizol reagent 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, 5067-1511)
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of <research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform.

value: microglia

value: Fed with 0.12%  TMAO once a day for 16 weeks

value: brain


title: H3K27ac ChIP-seq denervation gastrocnemius 1

description: DENV


title: DRIP Nalm-6 SF3B1 K700E unt Rep1

description: Nalm-6 SF3B1 K700E unt Rep1

value: SF3B1 K700E


title: scRNAseq_MEL10

description: 10x Genomics

value: skin


title: DRIP Nalm-6 SF3B1 K700K RNH1 Rep2

description: Nalm-6 SF3B1 K700K RNH1 Rep2

value: SF3B1 K700K


title: Human meningioma, Frozen [QM367]

description: Nanostring nCounter

value: meningioma


title: scRNAseq_MEL11

description: 10x Genomics


title: Human meningioma, Frozen [QM315]

description: Nanostring nCounter


title: Human meningioma, FFPE [KM3]

description: Nanostring nCounter


title: scTCRseq_MEL03_PBMC

description: 10x Genomics

value: blood


title: scRNAseq_MEL09_PMBC

description: 10x Genomics


title: Human meningioma, Frozen [QM245]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM127]

description: Nanostring nCounter


title: M-3

value: Fed with vehicle (water) for 16 weeks


title: scRNAseq_MEL09

description: 10x Genomics

value: lymphoycyte


title: T-1


title: DRIP Nalm-6 SF3B1 K700K unt Rep2

description: Nalm-6 SF3B1 K700K unt Rep2

value: human leukemic B cell


title: DRIP Nalm-6 SF3B1 K700K RNH1 Rep1

description: Nalm-6 SF3B1 K700K RNH1 Rep1

value: RNaseH1 treated


title: T-2


title: scRNAseq_MEL03_PBMC

description: 10x Genomics


title: DRIP Nalm-6 SF3B1 K700K unt Rep1

description: Nalm-6 SF3B1 K700K unt Rep1


title: Human meningioma, FFPE [G125]

description: Nanostring nCounter


title: Human meningioma, FFPE [G123]

description: Nanostring nCounter


title: M-1


title: M-2


title: scRNAseq_MEL03

description: 10x Genomics


title: iPSC, scRNA-seq

city: Palo Alto

first: Surag

last: Nair

address: 240 Pasteur Dr

department: Computer Science

institute: Stanford University

data_processing:
We used 10x Genomics Cell Ranger v6.0.2 for read mapping and quantification to obtain the counts matrix. We used the GRCh38 2020-A reference.
Assembly: hg38
Supplementary files format and content: unfiltered gene x barcode counts matrices in matrix market format, along with gene list and barcodes

source_name: iPSCs

growth_protocol: Fibroblasts were grown in DMEM with 10% fetal bovine serum at 37 °C, 20% O2, and 5% CO2 in a humidified incubator over two weeks

extract_protocol:
The cells were trypsinized for 5 minutes followed by the addition of fibroblast medium to inactivate the trypsin. Afterward, cells were spun down and washed with 1X PBS supplemented with 1%bovine serum albumin. To remove cell debris and large clumps, the cells were passed through a 40 micron filter. The number of cells was determined using a hemocytometer to a final concentration of 1000 cells/uL
Libraries were constructed using the 10X Genomics scRNA-seq kits

treatment_protocol: Sendai virons containing POU5F1, SOX2, KLF4 and cMYC genes were added to the well. After viral infection, fibroblasts were grown in fibroblast media every other day for 7 days. On day 7 after infection, fibroblasts were cultured in Essential 8 media.

value: iPSCs

value: Wildtype


title: Human meningioma, Frozen [QM292]

description: Nanostring nCounter


title: endometrial biopsy, X210071_2

city: Parkville

last: Rogers

state: VIC

address: Level 7, University Department, Royal Women's Hospital, Crn Grattan Street and Flemington Rd

department: Department of Obstetrics and Gynaecology

country: Australia

institute: University of Melbourne

description: Sample X210071_2 from batch 1

data_processing:
Sequence reads were trimmed for adaptor sequences and low quality sequences using Trimmomatic v0.36.
Trimmed reads were aligned against the human reference genome (Ensembl GRCh38 release 84) using HISAT2 v2.0.5.
Transcript quantification was performed using StringTie v1.3.1 and the Ensembl Homo sapiens GRCh8 release 91 reference annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file containing raw gene counts for all samples.

source_name: Human endometrium

extract_protocol:
Total RNA was isolated from endometrial tissue using the Qiagen Allprep DNA/RNA Mini Kit according to the manufacturer's instructions.
Stranded RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Gold protocol which includes ribosomal depletion.

value: Human endometrium

tag: cycle stage

tag: pod

tag: batch

value: batch 1


title: Human meningioma, FFPE [G122]

description: Nanostring nCounter


title: endometrial biopsy, X210191

description: Sample X210191 from batch 1


title: D14, scRNA-seq

source_name: Fibroblasts Day 14

value: Fibroblasts Day 14


title: cortical hem(CH) cells, Lmx1a-/- embryo 5

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

data_processing:
FastQC-v0.11.8 was used to perform quality control of the RNA-Seq reads. Remaining adapters and low-quality bases were trimmed by Trimmomatic-v 0.36 with parameters: Adapters:2:30:10 SLIDINGWINDOW:4:15 MINLEN:30. Paired-end RNA-sequencing data was aligned to the mouse genome (GRCm38) with gene annotations from Ensembl (v102) using STAR-v2.7.1a with default parameters. Read count per gene was calculated using HTSeq-v0.11.2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count for each Sample

source_name: cortical hem(CH) cells

extract_protocol:
Pico Pure RNA purification kit (Arcturus), according to the manufacturer’s protocol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: cortical hem(CH) cells


title: Human meningioma, FFPE [G120]

description: Nanostring nCounter


title: cortical hem(CH) cells, Lmx1a-/- embryo 3


title: endometrial biopsy, X210255

description: Sample X210255 from batch 1


title: cortical hem(CH) cells, Lmx1a-/- embryo 4


title: cortical hem(CH) cells, Lmx1a-/- embryo 2


title: D8, scRNA-seq

source_name: Fibroblasts Day 8

value: Fibroblasts Day 8


title: D6, scRNA-seq

source_name: Fibroblasts Day 6

value: Fibroblasts Day 6


title: Human meningioma, FFPE [G116]

description: Nanostring nCounter


title: endometrial biopsy, X210127

description: Sample X210127 from batch 1


title: D10, scRNA-seq

source_name: Fibroblasts Day 10

value: Fibroblasts Day 10


title: Human meningioma, FFPE [G114]

description: Nanostring nCounter


title: endometrial biopsy, X210371

description: Sample X210371 from batch 1


title: endometrial biopsy, X210255_2

description: Sample X210255_2 from batch 1


title: Human meningioma, FFPE [G112]

description: Nanostring nCounter


title: endometrial biopsy, X210071

description: Sample X210071 from batch 1


title: cortical hem(CH) cells, Lmx1a-/- embryo 1


title: cortical hem(CH) cells, Control, wild type embryo 5

value: WT


title: endometrial biopsy, X210154

description: Sample X210154 from batch 1


title: D4, scRNA-seq

source_name: Fibroblasts Day 4

value: Fibroblasts Day 4


title: cortical hem(CH) cells, Control, wild type embryo 4


title: Human meningioma, FFPE [G108]

description: Nanostring nCounter

value: meningioma


title: Human meningioma, FFPE [G110]

description: Nanostring nCounter


title: D12, scRNA-seq

source_name: Fibroblasts Day 12

value: Fibroblasts Day 12


title: D2, scRNA-seq

source_name: Fibroblasts Day 2

value: Fibroblasts Day 2


title: endometrial biopsy, X210289

description: Sample X210289 from batch 1


title: cortical hem(CH) cells, Control, wild type embryo 3


title: endometrial biopsy, X210092

description: Sample X210092 from batch 1


title: Human meningioma, FFPE [G113]

description: Nanostring nCounter


title: iPSC, scATAC-seq

library_source: genomic single cell

data_processing:
We used Chromap (https://github.com/haowenz/chromap/tree/6e97125b9, https://doi.org/10.1038/s41467-021-26865-w) to perform barcode correction, alignment and filtering for each of our scATAC-seq samples.
Assembly: hg38
Supplementary files format and content: fragment (BED) files

extract_protocol:
The cells were dissociated using Tryple Express and resuspended in fibroblast medium. The cells with viability >90% were washed in ice-cold ATAC-seq resuspension buffer (RSB, 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2), spun down, and resuspended in 100 uL ATAC-seq lysis buffer (RSB plus 0.1% NP-40 and 0.1% Tween 20). Lysis was allowed to proceed on ice for 5 min, then 900 uL RSB was added before spinning down again and resuspending in 50 uL 1X Nuclei Resuspension Buffer (10x Genomics).
Libraries were constructed using the 10X Genomics scATAC-seq kits


title: D0, scRNA-seq

source_name: Fibroblasts

value: Fibroblasts


title: Human meningioma, FFPE [G107]

description: Nanostring nCounter


title: cortical hem(CH) cells, Control, wild type embryo 1


title: cortical hem(CH) cells, Control, wild type embryo 2


title: endometrial biopsy, X210224

description: Sample X210224 from batch 1


title: endometrial biopsy, X210209

description: Sample X210209 from batch 1


title: D12, scATAC-seq


title: Human meningioma, FFPE [G106]

description: Nanostring nCounter


title: D14, scATAC-seq


title: SMG7KO clone 12 replicate 2 lane 8

city: Bern

first: Oliver

last: Mühlemann

address: Freiestrasse 3

department: Chemistry, Biochemistry and Pharmaceutical Sciences

country: Switzerland

institute: University of Bern

data_processing:
Read mapping with STAR 2.7.8a to the full human genome GRCh38.10.9, annotation-agnostic
Read counting with featureCounts (Subread package) 2.0.1 on Ensembl GRCh38 release 109. Reverse strand (-s 2), multi-mapping allowed (-M), fractional assignment (--fraction)
Assembly: GRCh38.10.9
Supplementary files format and content: Ensembl gene counts

growth_protocol: HT1080 and SMG7KO cells were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Total RNA from cells in culture was isolated using the guanidium thiocyanate-phenol-chloroform extraction protocol followed by isopropanol precipitation
The library was prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit (chemistry v3), which also includes a ribo-zero depletion step

value: fibrosarcoma


title: endometrial biopsy, X210172

description: Sample X210172 from batch 1


title: endometrial biopsy, X210126

description: Sample X210126 from batch 1


title: D10, scATAC-seq


title: Human meningioma, FFPE [G105]

description: Nanostring nCounter


title: Human meningioma, FFPE [G103]

description: Nanostring nCounter


title: D8, scATAC-seq


title: SMG7KO clone 12 replicate 3 lane 8


title: Human meningioma, FFPE [G104]

description: Nanostring nCounter


title: SMG7KO clone 11 replicate 3 lane 8


title: SMG7KO clone 12 replicate 1 lane 8


title: endometrial biopsy, X210059

description: Sample X210059 from batch 1


title: D6, scATAC-seq


title: Human meningioma, FFPE [G102]

description: Nanostring nCounter


title: Human meningioma, FFPE [G109]

description: Nanostring nCounter


title: endometrial biopsy, X210229

description: Sample X210229 from batch 1


title: endometrial biopsy, X210373

description: Sample X210373 from batch 1


title: D4, scATAC-seq


title: SMG7KO clone 11 replicate 1 lane 8


title: D2, scATAC-seq


title: Human meningioma, FFPE [G101]

description: Nanostring nCounter


title: endometrial biopsy, X210108

description: Sample X210108 from batch 1


title: D2, Multiome

library_source: other

data_processing:
For ATAC, we used Chromap (https://github.com/haowenz/chromap/tree/6e97125b9, https://doi.org/10.1038/s41467-021-26865-w) to perform barcode correction, alignment and filtering for each of our scATAC-seq samples.
For RNA, we used 10x Genomics Cell Ranger v6.0.2 for read mapping and quantification to obtain the counts matrix. We used the GRCh38 2020-A reference.
Assembly: hg38
Supplementary files format and content: ATAC: fragment (BED) files
Supplementary files format and content: RNA: unfiltered gene x barcode counts matrices in matrix market format, along with gene list and barcodes
Supplementary files format and content: map between ATAC and RNA barcodes
Library strategy: Multiome (ATAC and RNA)

molecule: other

growth_protocol: Fibroblasts were grown in DMEM with 10% fetal bovine serum at 37 °C, 20% O2, and 5% CO2 in a humidified incubator

extract_protocol:
The cells were dissociated using Tryple Express and resuspended in fibroblast medium. The cells with viability >90% were washed in ice-cold ATAC-seq resuspension buffer (RSB, 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2), spun down, and resuspended in 100 uL ATAC-seq lysis buffer (RSB plus 0.1% NP-40 and 0.1% Tween 20). Lysis was allowed to proceed on ice for 5 min, then 900 uL RSB was added before spinning down again and resuspending in 50 uL 1X Nuclei Resuspension Buffer (10x Genomics).
Single nuclei libraries were prepared using the 10X Genomics Single Cell Multiome ATAC + Gene Expression kit


title: Human meningioma, FFPE [G95]

description: Nanostring nCounter


title: HT1080 replicate 1 lane 8


title: HT1080 replicate 3 lane 8


title: D1, Multiome

source_name: Fibroblasts Day 1

value: Fibroblasts Day 1


title: Human meningioma, FFPE [G97]

description: Nanostring nCounter

source_name: Human meningioma, FFPE


title: endometrial biopsy, X210219

description: Sample X210219 from batch 1


title: Human meningioma, FFPE [G94]

description: Nanostring nCounter


title: D0, scATAC-seq


title: endometrial biopsy, X210088

description: Sample X210088 from batch 1


title: endometrial biopsy, X210311

description: Sample X210311 from batch 1


title: HT1080 replicate 2 lane 8


title: SMG7KO clone 12 replicate 2 lane 7


title: SMG7KO clone 12 replicate 3 lane 7


title: endometrial biopsy, X210167

description: Sample X210167 from batch 1


title: Human meningioma, FFPE [G99]

description: Nanostring nCounter


title: endometrial biopsy, X210045

description: Sample X210045 from batch 1


title: Human meningioma, FFPE [G85]

description: Nanostring nCounter


title: ZNF652KO rep2

city: beijing

first: cheng

middle: yun

last: liu

address: 北京市海淀区学院路38号

institute: peking university

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using kallisto 0.46
Assembly: hg38
Supplementary files format and content: Abundance table with raw counts for each transcript and sample

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using QIAGEN Rneasy mini plus kit following manufacture’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MCF-7 cells

value: mammary adenocarcinoma cells

value: ZNF652 knockout


title: Human meningioma, FFPE [G83]

description: Nanostring nCounter


title: endometrial biopsy, X210170

description: Sample X210170 from batch 1

value: Human endometrium

value: batch 1


title: Human meningioma, FFPE [G80]

description: Nanostring nCounter


title: ZNF652KO rep3

address: 北京市海淀区学院路38号


title: SMG7KO clone 11 replicate 2 lane 8


title: endometrial biopsy, X210066

description: Sample X210066 from batch 1


title: endometrial biopsy, X210087

description: Sample X210087 from batch 1


title: ZNF652KO rep1

address: 北京市海淀区学院路38号


title: endometrial biopsy, X210028

description: Sample X210028 from batch 1


title: Human meningioma, FFPE [G84]

description: Nanostring nCounter


title: WT rep1

address: 北京市海淀区学院路38号


title: SMG7KO clone 12 replicate 1 lane 7


title: WT rep3

address: 北京市海淀区学院路38号


title: WT rep2

address: 北京市海淀区学院路38号


title: SMG7KO clone 11 replicate 3 lane 7


title: SMG7KO clone 11 replicate 2 lane 7


title: wu39,scRNA-seq

city: St. Louis

first: Erik

last: Storrs

state: MO

address: 660 S Euclid Ave

institute: Washington University

description: 10x Genomics

data_processing:
We aligned reads to the GRCh38 reference genome and obtained gene expression counts using 10x Cell Ranger 3.0.2 with default parameters. FASTQ files were aligned to the GRCh38 reference genome with the STAR aligner. Cell-specific unique molecular identifiers (UMIs) were then used to generate gene expression matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (RNA count matrices).

source_name: Pancreas

extract_protocol:
For EUS-FNB samples, endoscopic ultrasound was performed on patients with suspected solid pancreatic masses based on CT or MRI imaging. The diagnosis of pancreatic adenocarcinoma was confirmed by formal pathologic evaluation. After clinical diagnostic tissue acquisition was completed with 2-3 passes of a 22-gauge needle, an additional pass was obtained with a backfin “fine-needle biopsy” (FNB) needle.
Tissue was carefully washed with cold PBS, collected in RPMI 1640 media (Gibco) on ice when processed fresh, or collected in freezing media (90%FBS + 10% DMSO, when processed at a later time point) and dissociated into single cell suspension both mechanically and enzymatically as previously described40. Resected surgical tumor tissue was also dissociated in a similar way to obtain single-cell suspensions. Subsequently, single-cell suspensions were diluted to a final concentration of ~1,000 cells/μl and sequencing libraries prepared using the 10x Genomics Chromium Single Cell 5’ library platform. Complementary DNA libraries were then sequenced on an Illumina NovaSeq S4 flow cell with a target of 50,000 reads/cell.

value: Pancreas

tag: ajcc stage

value: Stage IB (T2N0M0)

tag: tumor location

value: Uncinate

tag: pathology

value: Adenocarcinoma

tag: vital status_(1_dead,_0_alive)

tag: survival time_(days)


title: Human meningioma, FFPE [G87]

description: Nanostring nCounter

data_processing:
Samples here are unique meningiomas included in the study. Counts were positive control normalized using the spike-in positive control probes in the nSolver solftware, as per recommendations from the manufacturer (Nanostring).
Positive control normalized counts

tag: disease


title: SMG7KO clone 11 replicate 1 lane 7


title: Human meningioma, FFPE [G79]

description: Nanostring nCounter


title: HT1080 replicate 3 lane 7

value: WT


title: Human meningioma, FFPE [G76]

description: Nanostring nCounter


title: Human meningioma, FFPE [G72]

description: Nanostring nCounter


title: endometrial biopsy, X210201

description: Sample X210201 from batch 1

tag: tissue


title: wu42,scRNA-seq

description: 10x Genomics

value: Head


title: HT1080 replicate 2 lane 7

tag: cell type


title: endometrial biopsy, X210074

description: Sample X210074 from batch 1


title: Human meningioma, FFPE [G71]

description: Nanostring nCounter

value: meningioma


title: Human meningioma, FFPE [G74]

description: Nanostring nCounter


title: endometrial biopsy, X210075

description: Sample X210075 from batch 1


title: WT Rep 1, Sodium Citrate buffer

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplex and convert reads to FASTQ format.
Trimmomatic (v0.30) was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie was used to align trimmed reads to the M. smegmatis MC2-155 (NCBI accession NC_008596.1) with the -S option to produce SAM files as output.
SAMtools was used to calculate coverage depth (>98% coverage across the genome for all samples).
HTSeq software suite was used to analyze aligned and determine counts per gene feature in the M. smegmatis MC2-155 genome.
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the edgeR package.
Qualimap was used to analyze coverage against the reference genome, sequence depth and Pearson's correlation coefficient between replicates.
Genome_build: M. smegmatis MC2-155 (NCBI accession NC_008596.1)
Supplementary_files_format_and_content: Table S1.xlsx: Processed file is an Excel spreadsheet and represents the average of 2 biological replicates.

organism: Mycolicibacterium smegmatis MC2 155

source_name: Bacterial Cell

growth_protocol: M. smegmatis was cultured starting in 30 mL of MMAT medium supplemented with 10 mM glycerol buffered to pH 7.0 with 100 mM MOPS to pre-adapt cells.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly, RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion). RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step.
After library quality control, sample libraries were pooled and sequenced in one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v1). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: M. smegmatis was cultured to an OD600 of ~0.6 before being washed twice in MOPS buffered MMAT medium twice and then split into 10 mL cultures of MMAT medium supplemented with 10 mM glycerol buffered to pH 7.0 with either 100 mM MOPS or sodium citrate in T25 flasks. Cultures were incubated for 3 hours standing at 37°C before RNA was extracted.

value: Wild Type

value: Sodium citrate buffer


title: endometrial biopsy, X210183

description: Sample X210183 from batch 1


title: Human meningioma, FFPE [G67]

description: Nanostring nCounter

extract_protocol: Total RNA was extracted from frozen or FFPE meningioma tumor samples using Qiagen AllPrep or Qiagen FFPE RNAeasy kits.


title: HT1080 replicate 1 lane 7


title: endometrial biopsy, X210223

description: Sample X210223 from batch 1


title: wu30,scRNA-seq

description: 10x Genomics

value: Stage III (T4N1M1)

value: Body


title: endometrial biopsy, X210216

description: Sample X210216 from batch 1


title: wu31,scRNA-seq

description: 10x Genomics

value: Stage IIB (T2N1M0)


title: wu38,scRNA-seq

description: 10x Genomics

value: Head/uncinate


title: WT Rep 2, Sodium Citrate buffer


title: wu32,scRNA-seq

description: 10x Genomics


title: Human meningioma, FFPE [G69]

description: Nanostring nCounter


title: endometrial biopsy, X210051

description: Sample X210051 from batch 1


title: endometrial biopsy, X210185

description: Sample X210185 from batch 1


title: wu29,scRNA-seq

description: 10x Genomics

value: Stage III (T4N0M0)


title: HA-VSMC cells, miRNA-Seq, 250nM, rep3

city: Beijing

first: Qiu

last: Xie

state: Beijing

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

institute: Peking Union Medical College Hospital

data_processing:
The quality of the samples, experiment, and the analysis data were completed by the Genesky Biotechnologies Inc.
The known mature miRNA expression profile was generated by using the quantifier module of the miRDeep2 package, which gives read counts for the known miRNAs.
The raw reads’ expression profiles generated for all the replicates of the samples were subjected to trimmed mean of M-values’ (TMM) normalization using the Bioconductor package edgeR.
Assembly: oryCun2
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Oryctolagus cuniculus

source_name: HA-VSMC

growth_protocol: HA-VSMC cells were cultured in RPMI1640 containing L-Glutamine ( C11875500BT, Gibco), and 10% FBS (10099141, Gibco), at 37℃ in a 5% CO2 incubator. Cells were seeded at a density of 2 × 105 viable cells /mL, and passaged every 3–4 days.

extract_protocol:
For RNA isolation, total RNA was isolated using TRIzol reagent.
A total of 2 μg of RNA/sample was used as input material for the miRNA library. The miRNA sequencing libraries were generated using a TruSeq Small RNA Sample Preparation Kit, and index codes were added to attribute sequences to each sample.

treatment_protocol: β-estradiol power (E2257,Sigma) was dissolved in DMSO with 3.7% filtered sodium hydrogen carbonate. After incubation of the final concentration of β-estradiol with 250nmol/L, cells were incubated at 37°C and 5% CO2 for 48 h before harvested.

value: HA-VSMC

tag: estrogen concentration

tag: treatment

value: estrogen


title: endometrial biopsy, X210221

description: Sample X210221 from batch 1

value: Human endometrium

value: batch 1


title: Human meningioma, FFPE [G64]

description: Nanostring nCounter


title: R354_CD4

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description:
R354
mapped to HG38

data_processing:
Aligned: STAR,  Ref.genome: Homo_sapiens.GRCh38.dna.primary_assembly.fa (Ensembl),
quantification: featureCounts
Assembly: HG38
Supplementary files format and content: matrix with ENS number and samples in each one column

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells,

extract_protocol: Total RNA purification (Norgen, Ontario, Canada)

treatment_protocol: culture activated with anti-CD3, 2h total

tag: agent

value: Rheumatoid arthritis

tag: Sex

value: female


title: HA-VSMC cells, miRNA-Seq, 250nM, rep2

tag: cell line


title: wu28,scRNA-seq

description: 10x Genomics

value: Pancreas

value: Stage IIB (T3N1M0)

value: Neck

value: Adenocarcinoma


title: wu26,scRNA-seq

description: 10x Genomics

value: Stage III (T2N2M0)


title: wu27,scRNA-seq

description: 10x Genomics


title: Human meningioma, FFPE [G63]

city: San Francisco

last: Chen

institute: UCSF

description: Nanostring nCounter

value: meningioma


title: HA-VSMC cells, miRNA-Seq, 50nM, rep3


title: WT Rep 1, MOPS buffer

tag: genotype

value: Wild Type

tag: condition

value: MOPS buffer


title: Human meningioma, FFPE [G62]

description: Nanostring nCounter


title: wu25,scRNA-seq

description: 10x Genomics

value: Stage III (T3N2M0)

value: Uncinate


title: R353_CD4

description:
R353
mapped to HG38


title: WT Rep 2, MOPS buffer


title: wu24,scRNA-seq

description: 10x Genomics

value: Stage III (T4N0M0)

value: Body


title: R352_CD4

description:
R352
mapped to HG38


title: HA-VSMC cells, miRNA-Seq, 50nM, rep1

value: HA-VSMC

value: estrogen


title: Human meningioma, FFPE [G61]

description: Nanostring nCounter


title: Human meningioma, FFPE [G66]

description: Nanostring nCounter


title: Human meningioma, FFPE [G60]

description: Nanostring nCounter


title: R351_CD4

description:
R351
mapped to HG38


title: wu23,scRNA-seq

description: 10x Genomics

value: Stage IIB (T2N1M0)


title: wu22,scRNA-seq

description: 10x Genomics

value: Stage IIB (T3 N1M0)

value: Head


title: R349_CD4

description:
R349
mapped to HG38

value: Rheumatoid arthritis

value: female


title: Human meningioma, FFPE [G59]

description: Nanostring nCounter


title: HA-VSMC cells, miRNA-Seq, Control, rep3

value: WT


title: R350_CD4

description:
R350
mapped to HG38


title: HA-VSMC cells, miRNA-Seq, 250nM, rep1


title: Human meningioma, FFPE [G54]

description: Nanostring nCounter


title: Human meningioma, FFPE [G58]

description: Nanostring nCounter


title: wu15,scRNA-seq

description: 10x Genomics

value: Pancreas

value: Stage IA (T1 N0 Mx)

value: Body/Tail

value: Adenocarcinoma


title: wu16,scRNA-seq

description: 10x Genomics

value: Stage IIA (cT3N0M0)


title: HA-VSMC cells, 250nM, rep2

data_processing:
Sequencing reads were trimmed using Trim Galore (parameter - Quality limit: 20)
Trimmed equencing reads were aligned to the rabbit reference genome (oryCun2) using TopHat2 (version 2.1.1).
The gene expression level was calculated by Cufflinks.
The differential expression between different groups was performed with the Cuffdiff module.
Assembly: oryCun2
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
For RNA isolation, total RNA was isolated using TRIzol reagent, in accordance with the manufacturer’s recommendations.
The mRNA sequencing libraries were generated using a TruSeq Small RNA Sample Preparation Kit, and index codes were added to attribute sequences to each sample.


title: HA-VSMC cells, miRNA-Seq, Control, rep1


title: wu18,scRNA-seq

description: 10x Genomics


title: R348_CD4

description:
R348
mapped to HG38


title: R346_CD4

description:
R346
mapped to HG38


title: R345_CD4

description:
R345
mapped to HG38


title: HA-VSMC cells, miRNA-Seq, 50nM, rep2


title: HA-VSMC cells, 250nM, rep3


title: R347_CD4

description:
R347
mapped to HG38


title: Human meningioma, FFPE [G53]

description: Nanostring nCounter

value: meningioma


title: Human meningioma, FFPE [G52]

description: Nanostring nCounter


title: HA-VSMC cells, miRNA-Seq, Control, rep2


title: wu07,scRNA-seq

description: 10x Genomics

value: Stage IV (cT2N0M1)

value: Adenosquamous


title: wu09,scRNA-seq

description: 10x Genomics

value: Stage IB (cT2N0M0)

value: Head/Neck/Uncinate


title: HA-VSMC cells, 50nM, rep2

value: HA-VSMC

value: estrogen


title: Human meningioma, FFPE [G57]

description: Nanostring nCounter


title: Human meningioma, FFPE [G49]

description: Nanostring nCounter


title: Human meningioma, FFPE [G51]

description: Nanostring nCounter


title: HA-VSMC cells, 50nM, rep3


title: R344_CD4

description:
R344
mapped to HG38


title: R342_CD4

description:
R342
mapped to HG38


title: HA-VSMC cells, 50nM, rep1


title: HA-VSMC cells, 250nM, rep1


title: R343_CD4

description:
R343
mapped to HG38


title: Human meningioma, FFPE [G47]

description: Nanostring nCounter


title: wu05,scRNA-seq

description: 10x Genomics


title: HA-VSMC cells, Control, rep3


title: Human meningioma, FFPE [G48]

description: Nanostring nCounter


title: R341_CD4

description:
R341
mapped to HG38


title: Human meningioma, FFPE [G46]

description: Nanostring nCounter


title: R340_CD4

description:
R340
mapped to HG38


title: Human meningioma, FFPE [G45]

description: Nanostring nCounter


title: wu03,scRNA-seq

description: 10x Genomics

value: Stage IIB (cT2N1M0)


title: HA-VSMC cells, Control, rep1


title: HA-VSMC cells, Control, rep2


title: Human meningioma, FFPE [G43]

description: Nanostring nCounter


title: wu02,scRNA-seq

description: 10x Genomics


title: wu14,scRNA-seq

description: 10x Genomics


title: Human meningioma, FFPE [G42]

description: Nanostring nCounter


title: wu01,scRNA-seq

description: 10x Genomics


title: Human meningioma, FFPE [G44]

description: Nanostring nCounter


title: SGLT2_V_3

city: ChongQing

first: Jianlin

last: Du

address: No.1, medical college road, ChongQing, China

institute: ChongQing Medical University

data_processing:
SOAPnuke (v1.5.2)
Sequenced reads were trimmed for adaptor sequence by SOAPnuke (v1.5.2), afterwards clean reads were obtained and stored in FASTQ format.
Clean reads were mapped to rattus norvegicus genome using HISAT2(v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to rattus norvegicus genome
Sequenced Fragments Per Kilobase of exon per Million fragments mapped to rattus norvegicus genome (FPKM) were calculated using RESEM(v1.2.12).
Assembly: Rattus_norvegicus NCBI GCF_000001895.5_Rnor_6.0
Supplementary files format and content: Excel files include FPKM values for each sample.

organism: Rattus norvegicus

source_name: Spontaneous hypertension rat, treated with a sodium-glucose cotransporter 2 (SGLT2) inhibitor

growth_protocol: Spontaneous hypertension rats were housed in groups of 3-4 rats/cage in a controlled environment (22 ± 2°C, 12-h/12-h light/dark cycle with lights on at 7:00 am) and ad libitum access to water and standard rat chow.

extract_protocol:
Total RNA was extracted from the rat tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.1.3 ug of total RNA was used for the construction of sequencing libraries.
the final library was generated by heated denaturing and circularizing the above double stranded PCR products using the splint oligo sequence, then followed by formatting the single strand circle DNA (ssCir DNA). DNA nanoballs (DNBs) were generated by library amplification and loaded into the patterned nanoarray and single end 50 bases reads on BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: Spontaneous hypertension rats were treated with empaglifozin by gavage at the dose of 10 mg/kg/d or saline vehicle control daily for a period of 30 days.

value: Liver

tag: age

value: 8 weeks


title: SGLT2_LU_3

value: Lung


title: SGLT2_V_1


title: R339_CD4

description:
R339
mapped to HG38

value: Rheumatoid arthritis

value: female


title: SK-N-BE(2)c xenograft, MOXD1 OE, replicate 5

city: Lund

first: Stina

last: Andersson

address: Sölvegatan 19

institute: Lund University

data_processing:
Demultiplexing: organizing the FASTQ files based on the sample index information, and generating the statistics and reporting files. This task was performed using the bcl2fastq2 software with default settings.
Raw Quality Control (QC): FastQC provides quality control analyses and checks on raw sequence data coming from the above Demultiplexing step of the pipeline. For each analysis it provides a graphical plot and a suggestive warning if the data has any problems.
Read Mapping: alignment of reads to a specified reference genome. This task was performed using the HISAT2 software, and the reference genome sequence was from the Ensemble database, the Human GRCh38, and the annotation (GTF) from the release 94 or 99.
Mapping QC: mapping quality control checks such as evaluating the distribution of reads mapped by the above mapping step.
Expression counts: assembly of the alignments into full transcripts and quantification of the expression levels of each gene and transcript. This task was performed using the StringTie software.
DE analysis: Differentially expressed genes (DEG) analysis was performed using DESeq2.
Assembly: Ensemble database (Human GRCh38, GTF 94 (cells) or 99 (xenograft tumors))
Supplementary files format and content: STRINGTIE_2019_97_R1_All_Gene_rcount_Data.txt file contains raw read count of all genes.
Supplementary files format and content: STRINGTIE_2019_97_R1_GeneData_TPM.txt file contains TPM normalized values of all genes.
Supplementary files format and content: STRINGTIE_2020_53_R1_All_Gene_rcount_Data.txt file contains raw read count of all genes.
Supplementary files format and content: STRINGTIE_2020_53_R1_GeneData_TPM.txt file contains TPM normalized values of all genes.

growth_protocol: Cells were cultured at 37°C, 21% O2, and 5% CO2 in MEM suplemented with 10% FBS, 100 units Penicillin and 10 μg/mL streptomycin. For the xenografts 0.8 × 10^6 cells were subcutaneously injected in a 100 μL 2:1 mixture of cell culture media and growth factor reduced Matrigel (BD, 354230) to the right flank of mice. Mice were euthanized when tumors reached a size of >1800 mm3 in diameter or 12 months after experiment start (endpoint, 365 days).

extract_protocol:
Total RNA from cells was extracted using RNAqueous Micro Kit (Ambion RNAqueous™-Micro Kit, ThermoFisher, #AM1931). Total RNA from tumors was extracted using QIAshredder (Qiagen, cat. no. 79656) and RNeasy® Midi Kit (Qiagen, cat. no. 75142). The total RNA input to library preparation was 500 ng
The library preparation was performed according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.

value: Neuroblastoma cell line

value: MOXD1 OE


title: SK-N-BE(2)c xenograft, MOXD1 OE, replicate 3


title: SK-N-BE(2)c xenograft, MOXD1 OE, replicate 2


title: SGLT2_V_2


title: Human meningioma, FFPE [G39]

first: William

address: 1450 3rd Street, HD 402

description: Nanostring nCounter


title: SK-N-BE(2)c xenograft, MOXD1 OE, replicate 4


title: SK-N-BE(2)c xenograft, MOXD1 OE, replicate 1


title: Human meningioma, FFPE [G40]

description: Nanostring nCounter


title: R333_CD4

description:
R333
mapped to HG38


title: SGLT2_LU_1


title: R337_CD4

description:
R337
mapped to HG38


title: R334_CD4

description:
R334
mapped to HG38


title: R335_CD4

description:
R335
mapped to HG38


title: SGLT2_WF_3

value: White fat tissue


title: R338_CD4

description:
R338
mapped to HG38


title: Human meningioma, FFPE [G36]

description: Nanostring nCounter


title: wu04,scRNA-seq

description: 10x Genomics

value: Pancreas

value: Body/Tail

value: Adenocarcinoma


title: SK-N-BE(2)c xenograft, CTRL, replicate 5

value: WT


title: SK-N-BE(2)c xenograft, CTRL, replicate 4


title: Human meningioma, FFPE [G35]

description: Nanostring nCounter

value: meningioma


title: R336_CD4

description:
R336
mapped to HG38


title: R329_CD4

description:
R329
mapped to HG38


title: Human meningioma, FFPE [G38]

description: Nanostring nCounter


title: SGLT2_WF_2


title: Human meningioma, FFPE [G33]

description: Nanostring nCounter


title: SGLT2_WF_1


title: R331_CD4

description:
R331
mapped to HG38


title: SGLT2_LU_2


title: SGLT2_BF_2

value: Brown fat tissue


title: SK-N-BE(2)c xenograft, CTRL, replicate 1


title: Human meningioma, FFPE [G34]

description: Nanostring nCounter


title: SK-N-BE(2)c xenograft, CTRL, replicate 2


title: SGLT2_BF_3


title: SK-N-BE(2)c cells, MOXD1 OE, replicate 3


title: SGLT2_BF_1


title: R330_CD4

description:
R330
mapped to HG38


title: SK-N-BE(2)c cells, MOXD1 OE, replicate 2


title: Human meningioma, FFPE [G30]

description: Nanostring nCounter


title: Human meningioma, FFPE [G37]

description: Nanostring nCounter


title: Human meningioma, FFPE [G32]

description: Nanostring nCounter


title: R328_CD4

description:
R328
mapped to HG38


title: SGLT2_BR_2

value: Brain


title: R332_CD4

description:
R332
mapped to HG38


title: Human meningioma, FFPE [G31]

description: Nanostring nCounter


title: Human meningioma, FFPE [G27]

description: Nanostring nCounter


title: R325_CD4

description:
R325
mapped to HG38


title: SGLT2_BR_3


title: R326_CD4

description:
R326
mapped to HG38


title: R324_CD4

description:
R324
mapped to HG38


title: R323_CD4

description:
R323
mapped to HG38


title: Human meningioma, FFPE [G24]

description: Nanostring nCounter


title: SK-N-BE(2)c cells, CTRL, replicate 1


title: R322_CD4

description:
R322
mapped to HG38


title: SK-N-BE(2)c cells, CTRL, replicate 3


title: SGLT2_BR_1


title: Human meningioma, FFPE [G25]

description: Nanostring nCounter


title: SK-N-BE(2)c cells, CTRL, replicate 2


title: TOE1- rep2

city: La Jolla

first: Tiantai

last: Ma

address: 9500 Gilman Dr

department: Molecular Biology

institute: UCSD

description:
RNA 3' end was ligated to AG11 adaptor
TOE1_M_Nascent_2_S11_L001_R1_001.fastq.trimmed.fastq.All.smRNA.Aligned.out_tail.csv

data_processing:
FASTQ files were first subjected to 3’ adaptor and PCR duplicate removal using custom python scripts (https://pypi.org/project/jla-demultiplexer/).
For highly abundant small RNAs (U1, U2, U3, 7SL and 7SK), 100,000 reads were selected for subsequent analyses by averaging three random samplings using seqtk (https://github.com/lh3/seqtk). This was done to prevent undercounting of these RNAs since their abundance in the full library exceeded the depth of the randomer used for detecting PCR duplicates. For all other RNAs, the entire library was used. Reads were mapped to the human genome (version hg38) using STAR 2.7.8a
Gene-specific 3’ end information and graphs were subsequently generated using Tailer (https://github.com/TimNicholsonShaw/tailer) (Nicholson-Shaw, RNA, 2022) using the global alignment mode.
Assembly: human genome (version hg38)
Supplementary files format and content: comma separated variable table with RNA tail length change, read counts, and statistics

source_name: HEK 293T-REx TOE1-degron

growth_protocol: All cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS, Gibco) and 1% penicillin/streptomycin (Gibco) at 37°C, 5% CO2.

extract_protocol:
Small RNA (100 to 500 nucleotides) was isolated from total RNA by a 9% polyacrylamide/6M urea denaturing gel. Genomic DNA was removed using Turbo DNA-free kit (Thermo Fisher) and ribosomal (r)RNAs were depleted using RiboCOP rRNA depletion kit (Lexogen) per manufacturer’s recommendations. The rRNA-depleted small RNA samples were subsequently subjected to FastAP/PNK treatment to remove RNA 5' and 3' phosphates. AG10N or AG11N RNA adaptors were ligated to the RNA 3' ends using T4 RNA ligase (NEB). RNA samples were subjected to nascent RNA extraction using Click-it nascent RNA capture kit (Thermo Fisher). Reverse transcription was perfromed using AffinityScript RT (Agilent) and AR17 primer per manufacturer's recommendations. cDNA was cleaned by ExoSAP-IT (Thermo Fisher) and NaOH treatment. 3Tr3 adaptor was ligated to cDNA 5' end using T4 RNA. ligase (NEB)
The cDNA was amplified in two stages of Polymerase Chain Reaction (PCR) using Q5 DNA polymerase (NEB). For the first PCR reaction, the cDNA library was amplified using 3’ adaptor primer (AR17) and a primer complementary to the 5’ adaptor (RC_3Tr3) for 8 cycles. The PCR product was purified by AMPure XP beads (Beckman Coulter) per manufacturer’s recommendation. The second PCR reaction was performed using Illumina Trueseq D50X and D70X primers for 18 cycles. Amplified cDNA was subsequently isolated by separation in a 3% agarose gel and isolation of cDNAs 200 to 600 base pairs in length (corresponding to 100 to 500 nucleotide RNAs plus adaptors) using QIAquick gel extraction kit (Qiagen) according to manufacturer's recommendation.

treatment_protocol: TOE1 was depleted in HEK 293T-REx-derived TOE1-degron cells by incubation with 600 μM auxin hormone Indole-3-Acetic Acid (IAA, Sigma) for 8 hours. Cells were incubated with 0.2 mM Ethynyl Uridine (EU; Thermo Fisher) for 8 hours and harvested in 1 ml TRIzol reagent (Thermo Fisher).

value: HEK 293T-REx TOE1-degron


title: SGLT2_AV_3

value: Aortic blood vessel


title: TOE1- rep1

description:
RNA 3' end was ligated to AG10 adaptor
TOE1_M_Nascent_1_S10_L001_R1_001.fastq.trimmed.fastq.All.smRNA.Aligned.out_tail.csv


title: SGLT2_AV_2


title: R320_CD4

description:
R320
mapped to HG38


title: R327_CD4

description:
R327
mapped to HG38


title: SK-N-BE(2)c xenograft, CTRL, replicate 3


title: SGLT2_A_3

value: Atrium


title: TOE1+ rep3

description:
RNA 3' end was ligated to AG10 adaptor
TOE1_P_Nascent_3_S9_L001_R1_001.fastq.trimmed.fastq.All.smRNA.Aligned.out_tail.csv


title: Human meningioma, FFPE [G23]

description: Nanostring nCounter


title: R318_CD4

description:
R318
mapped to HG38


title: TOE1- rep3

description:
RNA 3' end was ligated to AG11 adaptor
TOE1_M_Nascent_3_S12_L001_R1_001.fastq.trimmed.fastq.All.smRNA.Aligned.out_tail.csv


title: SGLT2_AV_1

value: 8 weeks


title: Human meningioma, FFPE [G22]

description: Nanostring nCounter


title: SK-N-BE(2)c cells, MOXD1 OE, replicate 1


title: Human meningioma, FFPE [G20]

description: Nanostring nCounter


title: R321_CD4

description:
R321
mapped to HG38


title: Human meningioma, FFPE [G19]

description: Nanostring nCounter


title: TOE1+ rep1

description:
RNA 3' end was ligated to AG10 adaptor
TOE1_P_Nascent_1_S7_L001_R1_001.fastq.trimmed.fastq.All.smRNA.Aligned.out_tail.csv


title: Human meningioma, FFPE [G21]

description: Nanostring nCounter


title: SGLT2_K_2

value: Kidney


title: SGLT2_A_2


title: R319_CD4

description:
R319
mapped to HG38

value: Rheumatoid arthritis


title: Human meningioma, FFPE [G13]

description: Nanostring nCounter


title: SGLT2_A_1


title: kd_3

city: Guangzhou

first: Zhi

last: Song

address: No. 56, Lingyuan West Road, Guangzhou 510055, China

institute: Sun Yat-Sen University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.12.4 was subsequently employed to convert aligned short reads into read counts for each gene model.
Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated for each sample. 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.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include TPM/counts for each Sample

source_name: PDLSCs, LV-sh-TRX1

extract_protocol:
Total RNA was harvested using a RNA quick purification kit (Esunbio). 1.3μg of total RNA was used for the construction of the sequencing libraries.
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

value: mesenchymal stem cells

value: TRX1 knockdown

value: osteogenic differentiation


title: Human meningioma, FFPE [G11]

description: Nanostring nCounter


title: R316_CD4

description:
R316
mapped to HG38

value: female


title: Human meningioma, FFPE [G12]

description: Nanostring nCounter


title: TOE1+ rep2

description:
RNA 3' end was ligated to AG10 adaptor
TOE1_P_Nascent_2_S8_L001_R1_001.fastq.trimmed.fastq.All.smRNA.Aligned.out_tail.csv


title: SGLT2_K_1


title: R315_CD4

description:
R315
mapped to HG38


title: kd_1


title: SHR_V_3

source_name: Spontaneous hypertension rat

value: Liver


title: R314_CD4

description:
R314
mapped to HG38


title: SGLT2_K_3


title: kd_2


title: con_3

source_name: PDLSCs, LV-NC


title: Human meningioma, FFPE [G6]

description: Nanostring nCounter


title: R312_CD4

description:
R312
mapped to HG38


title: Human meningioma, FFPE [G5]

description: Nanostring nCounter


title: SHR_V_1


title: con_2


title: R317_CD4

description:
R317
mapped to HG38


title: R311_CD4

description:
R311
mapped to HG38


title: con_1


title: SHR_LU_3

value: Lung


title: Human meningioma, FFPE [G3]

description: Nanostring nCounter


title: Human meningioma, FFPE [G2]

description: Nanostring nCounter


title: R309_CD4

description:
R309
mapped to HG38


title: CAF, 52N

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

country: South Korea

institute: Asan Medical Center

description: gene expression

data_processing:
Sample demultiplexing, barcode processing and UMI counting were performed by using the official 10x Genomics pipeline Cell Ranger (v6.1.1).
Assembly: GRCh38
Supplementary files format and content: UMI_count_matrix.mtx, barcodes.tsv, and features.tsv files

source_name: pancreas

growth_protocol: CAFs were isolated from endoscopic ultrasound (EUS)-guided biopsy samples from pancreatic cancer patients, and then were maintained Dulbecco’s modified Eagle’s medium (HyClone Laboratories) supplemented with 10% FBS, 1% penicillin, and streptomycin.

extract_protocol:
Along with the reverse transcription master mix, cell suspensions were loaded onto 10x Genomics Single Cell 30 Chips. During this step, cells were partitioned into the GEMs along with gel beads coated with oligonucleotides. These oligonucleotides enable mRNA capture inside the droplets by 30 bp oligo-dT after cell lysis and provide barcodes to index cells (16 bp) as well as transcripts (12 bp UMI).
Single Cell 3’ Reagent Kit (v3.1 chemistry)
The 10x Genomics Chromium platform

treatment_protocol: Primary CAFs were incubated in normoxia (21% O2) or hypoxia (0.1% O2) for 72 hours. Hypoxia was achieved by incubation of the cells in a hypoxia chamber in which there was 0.1% O2 and 5% CO2 and the remainder was N2. This chamber was then placed in an incubator at 37°C.

tag: disease state

value: pancreatic cancer

value: pancreas

value: CAF

tag: stress

value: normoxia


title: SHR_LU_2


title: SHR_LU_1


title: SHR_WF_3

value: White fat tissue


title: CAF, 52H

description: gene expression

value: hypoxia


title: R313_CD4

description:
R313
mapped to HG38


title: Dicer-dsRBD-deletion single cleavage replicate 3

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description: Each-variant-DICER-deldsRBD.bed

data_processing:
First, we used cutadapt (-a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 10) to remove the adapters from the raw reads.
Next, we joined the pair-end reads using fastq-join, and then filtered out the low-quality reads using fastq_quality_filter (-q 20 -p 90).
We removed any duplicated reads containing the same 4 nt or 6 nt randomized barcodes in both ends using fastx_collapser. We then processed the control RNA (OS), double cleavage (DC), and single cleavage (SC) samples separately.
For the OS libraries, we used cutadapt (cutadapt -u 4 -u -6) to remove the 4-nt randomized barcodes in the 5'-end and 6-nt randomized barcodes in the 3'-end of the OS reads. We split the resulting read into two segments (FL-OS and 32N) using cutadapt (cutadapt -g GCTTGC…GCAAGC -m 32 -M 32 --discard-untrimmed). We discarded any shRNA/32N pairs that contained the 32N barcode shared by two or more shRNAs. We aligned the resulting FL-OS sequences with the reference sequences containing 23,296 possible variants of 6 shRNA subgroups using BWA. We selected only the perfectly aligned FL-OS sequences for further analysis. The raw counts of each FL-OS were the sum of read counts of the FL-OS in the unique FL-OS/32N-dictionary.
For DC and SC, we used cutadapt to remove randomized barcodes in both ends (cutadapt -u 4 -u -4: 4 nt in both ends for DC reads; cutadapt -u 4 -u -6: 4 nt in 5'-end and 6 nt in 3'-end for SC reads). We then split the processed reads into two fragments, including a cleaved shRNA product (CP) and a 32N barcode, using cutadapt (cutadapt -g GCTTGC…GCAAGC -m 32 -M 32 --discard-untrimmed). For each pair of CP and 32N, we used the 32N barcode sequence to assign the CP to the OS sequence in a pair with the barcode in the dictionary. We determined the cleavage sites by mapping the CP and OS using the local alignment mode of pairwise2 from Biopython. We labeled the modes of DICER cleavage as SC-5p (single cleavage on 5'-strand), SC-3p (single cleavage on 3'-strand), or DC (double cleavage) based on the reported mapping coordinates (x, y), where x and y are the 5p and 3p cleavage sites counting from the first nt of shRNA variants.
Assembly: home-made reference shRNA sequences
Supplementary files format and content: Bed files of control samples contain the raw read count of each shRNA in the control library.
Supplementary files format and content: Bed files of the single cleavage and double cleavage samples contains the assigned cleavage sites, cleavage accuracy, positional cleavage efficiency, global cleavage efficiency.

organism: synthetic RNA

source_name: ligated RNA

extract_protocol: We first ligated the control RNA and single cleavage products to the 4N-RA3 adapter using T4 RNA Ligase 2, truncated KQ enzyme (NEB, M0373L). The resulting 4N-RA3-ligated RNA were then gel-purified. Next, we mixed the purified RNAs in a reverse transcription (RT) mixture containing cirRTP primer and Superscript IV Reverse Transcriptase (Invitrogen) and incubated the mixture for 60 min at 50°C. To degrade the RNAs, we added 0.1 M NaOH to the RT mixture and incubated it at 98°C for 10 min. We then purified the resulting cDNAs and circularized them using CircLigase ssDNA ligase (Epicentre). After separating the circularized cDNAs from linear cDNAs in an 18% urea-PAGE gel and gel-purifying them, we amplified the purified circularized DNAs by PCR using RP1 and RPI1 and one of the RPIx primers, respectively. We used the RP1 and RPIx primer systems from the Truseq Illumina primers.  For the double cleavage (DC) fragments, we ligated them to the 4N-RA3 adapter and separated the resulting 4N-RA3-ligated DC from unligated DC and free 4N-RA3 in a 12% Urea-PAGE gel, which we then gel-purified. We ligated the purified 4N-RA3-ligated DC with the 4N-RA5 primer using T4 RNA ligase 1, and reverse-transcribed the double-ligated DC using Superscript IV Reverse Transcriptase and RTP primer. Finally, we amplified the resulting cDNA by PCR using RP1 and RPIx.

value: ligated RNA

value: mutant DICER


title: CAF, 27N

description: gene expression


title: R308_CD4

description:
R308
mapped to HG38


title: SHR_V_2

value: 8 weeks


title: Dicer-dsRBD-deletion single cleavage replicate 2

description: Each-variant-DICER-deldsRBD.bed


title: Human meningioma, FFPE [G9]

description: Nanostring nCounter

value: meningioma


title: Dicer-dsRBD-deletion single cleavage replicate 1

description: Each-variant-DICER-deldsRBD.bed


title: R310_CD4

description:
R310
mapped to HG38

value: Rheumatoid arthritis


title: SHR_WF_2


title: R307_CD4

description:
R307
mapped to HG38


title: CAF, 27H

description: gene expression


title: R306_CD4

description:
R306
mapped to HG38


title: SHR_WF_1


title: P229

city: Tianjin

first: Kuan

last: Li

state: Tianjin

address: Jingu road 890

institute: Tianjin Key Laboratory of Pulmonary Regenerative Medicine

description: 10x Genomics

data_processing:
The raw sequencing data of PBMCs were processed by Cell Ranger (version 6.1.1)
Assembly: human reference genome (GRCh38)
Supplementary files format and content: barcodes, features and matrix files

source_name: PBMCs, healthy group, scRNAseq

extract_protocol:
Venous blood samples (4 mL) were collected from each participant into a BD Vacutainer EDTA tube (BD, Cat#:367861). The Ficoll-Paque medium was used for density gradient centrifugation to obtain peripheral blood mononuclear cells (PBMCs). After trypan blue staining, cells in each sample for the construction of a single-cell RNA library should exceed the cell viability of 80%. Cell suspension with the concentration of 700-1200 cells/μL was prepared for 10x Genomics ChromiumTM.
The single-cell library was conducted using Chromium Next GEM Automated Single Cell 3ʹ Library and Gel Bead Kit v3.1 (10×Genomics, Cat#: PN-1000141) according to the manufacturer's protocol. Briefly, cell suspension, enzymes and partitioning oil loaded onto Chromium Next GEM Automated Chip G (10×Genomics, Cat#: PN-1000136) to generate single-cell gel beads in emulsion (GEMs). Barcoded cDNA was generated from poly-adenylated mRNA of captured cells in GEMs. cDNA was PCR-amplified prior to library construction. The constructed libraries were sequenced with 150-bp paired-end reads on an Illumina NovaSeq 6000 platform.

value: Plasma

value: PBMCs


title: SHR_BF_2

value: Brown fat tissue


title: P225

description: 10x Genomics

value: male


title: R304_CD4

description:
R304
mapped to HG38

value: female


title: Dicer-dsRBD-deletion double cleavage replicate 3

description: Each-variant-DICER-deldsRBD.bed


title: R305_CD4

description:
R305
mapped to HG38


title: SHR_BF_1


title: R303_CD4

description:
R303
mapped to HG38


title: Dicer-dsRBD-deletion double cleavage replicate 1

description: Each-variant-DICER-deldsRBD.bed


title: Dicer-WT single cleavage replicate 2

description: Each-variant-DICER-WT.bed

value: WT


title: Dicer-WT single cleavage replicate 1

description: Each-variant-DICER-WT.bed


title: P214

description: 10x Genomics


title: P216

description: 10x Genomics


title: Dicer-WT single cleavage replicate 3

description: Each-variant-DICER-WT.bed


title: SHR_BR_3

value: Brain


title: P217

description: 10x Genomics


title: P215

description: 10x Genomics


title: R299_CD4

description:
R299
mapped to HG38


title: R302_CD4

description:
R302
mapped to HG38


title: P125

description: 10x Genomics

source_name: PBMCs, SARS survivor 18 years after discharge, scRNAseq


title: Dicer-WT double cleavage replicate 1

description: Each-variant-DICER-WT.bed


title: SHR_BF_3


title: P118

description: 10x Genomics


title: SHR_AV_3

value: Aortic blood vessel


title: Dicer-dsRBD-deletion double cleavage replicate 2

description: Each-variant-DICER-deldsRBD.bed


title: SHR_AV_2


title: SHR_AV_1


title: SHR_BR_2


title: R301_CD4

description:
R301
mapped to HG38


title: SHR_BR_1


title: R297_CD4

description:
R297
mapped to HG38


title: R300_CD4

description:
R300
mapped to HG38


title: P117

description: 10x Genomics


title: Control sample 3


title: Dicer-WT double cleavage replicate 3

description: Each-variant-DICER-WT.bed


title: R295_CD4

description:
R295
mapped to HG38


title: R298_CD4

description:
R298
mapped to HG38


title: Dicer-WT double cleavage replicate 2

description: Each-variant-DICER-WT.bed


title: Control sample 2


title: P129

description: 10x Genomics


title: R296_CD4

description:
R296
mapped to HG38


title: SN87_NCS2_KO_41_Rep2_RPF

status: Public on Sep 05 2023

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

institute: ETH

data_processing:
Ribosome profiling reads were processed by clipping the adapter sequence and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13
Processed reads were uniquely mapped to non-dubious ORF (Allele A, C_albicans_SC5314_version_A22) extended by 18 nt into the UTRs
Assembly: C_albicans_SC5314_version_A22
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Candida albicans

source_name: Yeast

growth_protocol: C. albicans cultures were grown to mid-exponential phase (optical density 600 [OD600], ~0.4) at 30°C, 37°C or 41°C, 200 revolutions per minute in yeast extract peptone dextrose (YPD).

extract_protocol:
The cells were lysed using a Freezer-Mill (SPEX SamplePrep) with the settings: 2 cycles of 2 min precooling, 2 min at 5 CPS and 1 min intermittent cooling. 10 A260 units of cleared lysates were digested with 250 U Ambion RNase I for 1 h at 22 °C and 1400 rpm agitation. The reaction was stopped by adding 15 μl SuperaseIn. Lysates were thawed in lysis buffer (20 mM Tris-HCl pH 7.4, 5 mM MgCl2, 100 mM NaCl, 1 % Triton, 2 mM DTT, 100 μg/ml CHX and clarified by two rounds of centrifugation (3 min; 4 °C; 3000 g and 5 min, 4 °C and 10000 g).
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.

treatment_protocol: Cells were harvested by vacuum filtration using a 0.45 µm nitrocellulose filter and immediately flash frozen in liquid nitrogen.

tag: strain

value: SN87 - ncs2delta/ncs2delta

tag: growth temperature


title: SN87_NCS2_KO_41_Rep1_RPF


title: SHR_K_3

value: Kidney


title: P115

description: 10x Genomics


title: P114

description: 10x Genomics


title: SHR_K_2


title: Donor6-CAR13-NKT-8h

city: Philadelphia

first: Antonia

last: Rotolo

state: PA

address: 3900 Chestnut Street, Apt 521

institute: University of Pennsylvania

hyb_protocol: Gene expression profiling was performed using NanoString Canine Immuno-Oncology panel and nCounter instrument (Wistar Institute) according to the manufacturer’s instructions.

scan_protocol: standard protocol

data_processing:
NanoString data were normalized based on NanoString housekeeping probes and the geNorm algorithm using Rosalind® Software (https://rosalind.onramp.bio/). Fold-changes and p-values were calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment was performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Pathway enrichment analysis was performed using default settings with reference to built-in gene sets as defined in public databases (table S4). Enrichment was calculated relative to a set of background genes relevant for the experiment.
Differential gene expression and pathway enrichment were considered significant with fold-change cutoff of ±1.5 and adjusted p-value of ≤0.05.

label: unlabeled pure CAR iNKT

organism: Canis lupus familiaris

source_name: 8h bead stimulation, donor 6

label_protocol: Purity of End of expansion CAR-iNKT was >90%. No further label/purification step was required

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: End-of-expansion, resting CAR-iNKTs were stimulated for 4-8 hours with anti-CD3/CD28-coated beads at 1:1 ratio.

value: CAR13.{delta}CD19 engineered

value: 8h bead stimulation


title: Control sample 1

value: ligated RNA


title: SHR_K_1


title: Donor5-CAR13-NKT-4h

source_name: 4h bead simulation, donor 5

value: 4h bead simulation


title: Donor5-CAR13-NKT-8h

source_name: 8h bead stimulation, donor 5


title: SN87_WT_37_Rep2_RPF

value: SN87 - wild type


title: Donor6-CAR13-NKT-0

source_name: baseline, donor 6

value: baseline


title: SN87_WT_41_Rep1_RPF


title: SN87_WT_37_Rep1_RPF


title: 47_ CD25- B4-1,MHCII-Block,IL2 (3x)

city: South San Francisco

first: Shining

address: 1120 Veterans Blvd

institute: Amgen Inc.

data_processing:
RNA-Seq sequencing reads were aligned using OSA aligner embedded in v10.0 of the Omicsoft Array Suite (Qiagen) to mouse genome version B38 based on gene model GENCODE v19.
Gene level expression were quantified based on Omicsoft implementation of RSEM, and represented as normalized fragments per kilobase per million reads (FPKM).
Genes that were expressed at very low levels (counts per million mapped reads > 0.5 in less than 4 samples), genes that did not code for protein and those that transcribed long non-coding RNAs (lncRNAs) were filtered out before downstream differential expression analysis by DESeq2 (v1.30.1) with default parameters
Assembly: mouse B38 genome reference
Supplementary files format and content: gene_FPKM_Matrix.txt (Note: this is Supplementary files format and content)
Supplementary files format and content: gene_Counts_Matrix.txt (Note: this is Supplementary files format and content)

source_name: Spleen

extract_protocol:
Treg and Tcon cells were purified from total splenocytes using a commercial mouse Treg isolation kit (Miltenyi # 130-091-041) following the manufacturer’s protocol. Individual mice were processed as separate samples. Tcons were collected as the flow-through fraction in the CD25 positive selection step. The bound fraction was eluted and collected as the Treg cells.
Sorted CD25 or Treg cell RNA was extracted by using Qiagen RNeasy mini kit (Qiagen #74106). The concentration and quality of the isolated RNA samples were assessed and determined on ThermoFisher NanoDrop 8000 spectrophotometer and Agilent 4200 TapeStation system, respectively, and had RNA integrity numbers at least 9.1. 200ng or 500ng RNA was used to prepare cDNA library by using a protocol modified from the Illumina TruSeq Stranded mRNA kit (Illumina #20020595).
The constructed libraries were amplified and barcoded using the PCR program: a denaturation step at 98oC for 30 seconds, 15 cycles of 95 oC for 10 seconds, 60 oC for 30 second, 72oC for 30 seconds, and a 72 oC extension cycle for 5 minutes followed by a hold step at 4 oC. The amplified products were subjected to a clean-up step using AMPure XP bean (Beckman Coulter #63881) at the 0.85x ratio of beads to the PCR reaction volumes.
The final barcoded libraries were sequenced to a minimum depth of 30 million paired-end reads at the 150nt read length on an Illumina Nextseq2000.

treatment_protocol: C57BL/6 mice were treated twice with isotype control or MHC class II blocking antibody (500µg per dose by i.p. injection) on day -1 and d0 and dosed with IL-2 on d0 (25µg by s.c. injection). Spleens were harvested on d4 post IL-2 dosing.

value: Female

value: 8-12 week old

value: Spleen

value: CD4-Positive CD25-Negative T-Lymphocyte

tag: drug treatment

value: Normal (Undiseased)

tag: sample treatment

value: MHCII-Block


title: 45_ CD25- B3-1,MHCII-Block,IL2 (H16R)

tag: disease


title: Donor6-CAR13-NKT-4h

source_name: 4h bead simulation, donor 6


title: SN87_NCS2_KO_37_Rep3_RPF


title: SN87_NCS2_KO_37_Rep2_RPF


title: SN87_NCS2_KO_30_Rep2_RPF


title: SN87_NCS2_KO_37_Rep1_RPF


title: SN87_NCS2_KO_30_Rep1_RPF


title: 44_CD25- B2-2,MHCII-Block,WT

tag: tissue

value: WT


title: 41_CD25- B1-1,MHCII-Block,PBS

tag: cell type

value: PBS


title: 40_CD25- A4-2,Isotype,IL2 (3x)

value: Isotype


title: 34_CD25- A1-2,Isotype,PBS


title: 36_CD25- A2-2,Isotype,WT


title: Donor5-CAR13-NKT-0

source_name: baseline, donor 5


title: 29_B4-1 Treg,MHCII-Block,IL2 (3x)

value: Regulatory T-Lymphocytes


title: SN87_WT_37_Rep3_RPF


title: 46_CD25- B3-2,MHCII-Block,IL2 (H16R)


title: 48_CD25- B4-2,MHCII-Block,IL2 (3x)


title: 43_CD25- B2-1,MHCII-Block,WT


title: 42_CD25- B1-2,MHCII-Block,PBS


title: 23_B2-3 Treg,MHCII-Block,WT


title: SN87_WT_41_Rep2_RPF


title: 25_B3-1 Treg,MHCII-Block,IL2 (H16R)


title: 24_B2-4 Treg,MHCII-Block,WT


title: 37_CD25- A3-1,Isotype,IL2 (H16R)


title: 39_CD25- A4-1,Isotype,IL2 (3x)


title: 35_CD25- A2-1,Isotype,WT


title: 33_CD25- A1-1,Isotype,PBS


title: 31_B4-3 Treg,MHCII-Block,IL2 (3x)


title: 32_B4-4 Treg,MHCII-Block,IL2 (3x)


title: 14_A4-2 Treg,Isotype,IL2 (3x)


title: 30_B4-2 Treg,MHCII-Block,IL2 (3x)


title: 13_A4-1 Treg,Isotype,IL2 (3x)


title: 26_B3-2 Treg,MHCII-Block,IL2 (H16R)


title: 27_B3-3 Treg,MHCII-Block,IL2 (H16R)


title: 28_B3-4 Treg,MHCII-Block,IL2 (H16R)


title: 21_B2-1 Treg,MHCII-Block,WT


title: 22_B2-2 Treg,MHCII-Block,WT


title: 20_B1-4 Treg,MHCII-Block,PBS


title: 38_CD25- A3-2,Isotype,IL2 (H16R)


title: 18_B1-2 Treg,MHCII-Block,PBS


title: 19_B1-3 Treg,MHCII-Block,PBS


title: 4_A1-4 Treg,Isotype,PBS


title: 7_A2-3 Treg,Isotype,WT


title: 5_A2-1 Treg,Isotype,WT


title: 16_A4-4 Treg,Isotype,IL2 (3x)


title: 17_B1-1 Treg,MHCII-Block,PBS


title: 12_A3-4 Treg,Isotype,IL2 (H16R)


title: 15_A4-3 Treg,Isotype,IL2 (3x)


title: olive-derived microRNAs

city: Pamplona

first: Fermín

middle: Ignacio

last: Milagro Yoldi

state: Navarra

department: Department of Nutrition, Food Science and Physiology/Center for Nutrition Research

country: Spain

institute: University of Navarra

data_processing:
Adapter were removed from data using skewer.
Read with a size ranging from 15 to 30 bases were aligned to the reference genome with microRNA annotation from miRBase (maximum 2 mismatches in the seed area) using ShortStack.
Mapped tags were counted using htseq-count.
Reads were normalized with DESeq2.
Assembly: Prunus Persica (NCBIv2 and annotation NCBIv2.52 restricted to microRNAs)
Supplementary files format and content: text files that include raw counts for each sample
Supplementary files format and content: text file that includes normalized counts for each Sample

organism: Olea europaea

source_name: edible portion

extract_protocol:
0.1 of fruits (apple, olive, orange, pear, tomato), 0.1 of vegetables (spinach) and 0.5 g of nuts (almond and nut) were ground in QIAzol Lysis Reagent for 1 min using Ultra-Turrax T25 Basic (Basic IKA- WerkeTotal RNA). Total RNA was isolated with miRNeasy Serum/Plasma Kit (Qiagen) according to manufacturer protocol.
Libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina kit

value: edible portion


title: 10_A3-2 Treg,Isotype,IL2 (H16R)


title: 6_A2-2 Treg,Isotype,WT


title: spinach-derived microRNAs

organism: Spinacia oleracea


title: 3_A1-3 Treg,Isotype,PBS


title: 2_A1-2 Treg,Isotype,PBS


title: 9_A3-1 Treg,Isotype,IL2 (H16R)


title: 8_A2-3 Treg,Isotype,WT


title: 1_A1-1 Treg,Isotype,PBS


title: walnut-derived microRNAs

organism: Juglans regia


title: n12_DRS_2

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: Direct RNA Nanopore sequencing

data_processing:
Basecalling was performed using Guppy (version 3.2.10)
Alignment was performed using Minimap2 https://github.com/lh3/minimap2
Bedgraph coverage files generated using protocol described in Current Protocols in Microbiology, 57, e99. doi: 10.1002/cpmc.99
Supplementary files format and content: Hg38 human genome build, Dm3 drosophila genome build, HSV-1 KOS in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: Strand-specific bedgraph files
Library strategy: Direct RNA Nanopore sequencing

growth_protocol: HEp-2 cells were maintained in DMEM supplemented with 10% NBS and pen/strep

extract_protocol:
mRNA was isolated from infected cells using Dynabeads mRNA DIRECT purification kit (Invitrogen)
Libraries generated using the SQK-RNA002 kit (Oxford Nanopore Technologies)

treatment_protocol: Cells were infected with HSV-1 n12  or repair at a MOI of 5 and infection allowed to proceed for 1.5h. Performed in duplicates.

value: lung epithelial carcinoma cells

tag: hour post-infection

tag: viral infection

value: infected with HSV-1 ICP4 null mutant n12

tag: virus strain

value: HSV-1 KOS


title: n12_repair_DRS_2

description: Direct RNA Nanopore sequencing

value: infected with HSV-1 ICP4 null mutant repair


title: n12_repair_DRS_1

description: Direct RNA Nanopore sequencing


title: 11_A3-3 Treg,Isotype,IL2 (H16R)

state: CA

tag: Sex


title: tomato-derived microRNAs

organism: Solanum lycopersicum


title: n12_DRS_1

description: Direct RNA Nanopore sequencing

tag: cell line


title: EAE_mouse_rep6

city: Rochester

first: Charles

middle: L

last: Howe

state: MN

address: 200 First St SW

department: Neurology

institute: Mayo Clinic

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays following manufacturer's instructions by the University of Illinois at Chicago Core Genomics Facility.

scan_protocol: Arrays were scanned on the Affymetrix GeneTitan System following manufacturer's instructions by the University of Illinois at Chicago Core Genomics Facility.

data_processing: Raw data (CEL files) were imported into Transcriptome Analysis Console (Affymetrix) and normalized by robust multiarray average (RMA).

source_name: neuron-specific polyribosomal RNA

label_protocol: RNA was labeled following manufacturer's instructions by the University of Illinois at Chicago Core Genomics Facility.

growth_protocol: All mice were housed and maintained in standard facilities in accordance with the guidelines of the Mayo Clinic Institutional Animal Care and Use Committee.

extract_protocol: RNA was extracted from anti-HA antibody immunoprecipitates using the RNeasy micro plus kit (Qiagen).

treatment_protocol: EAE = experimental autoimmune encephalomyelitis induced by MOG(35-55) peptide; CUP = Purina Test Diet 5LG6 containing 0.3% bis(cyclohexanone)oxaldihydrazone; CON = mice fed control chow.

value: brain

value: adult

tag: genotype

tag: treatment

value: MOG-EAE mice at peak disease (18 days post-induction)


title: cuprizone_mouse_rep6

tag: age

value: Cuprizone chow mice at 6 weeks on chow.


title: DU145-Treated 01

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
PE150 high throughout data
C_vs_D.deseq2.annot
DB02T1

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 h38.p10 whole genome using bowtie v 0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text files include TPM values and counts for each Sample

source_name: Human prostate cancer cells

growth_protocol: Prostate cancer cells were routinely cultured and passaged (typically 0.5–1 × 10^6 cells in a T25 flask) in DMEM media supplemented with 10% FBS.

extract_protocol:
At the end of cell culture, media were removed, cells were lysed with Trizol reagent and total RNA was harvested. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101, RS-122-2102) 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: Upon 80% confluency, cancer cells were treated for 3 days with conditioned media derived from prostate stromal cells, either naive (control) or ectopically expressing human PDK4.

value: prostate cancer cells

tag: cell source

value: Carcinoma, derived from the metastatic site, brain of a prostate cancer patient

tag: passage

tag: name

value: DU145 treated (PSC27-PDK4 CM)

value: conditioned media from prostate stromal cells, ectopically expressing human PDK4


title: M12-Treated 01

description:
PE150 high throughout data
E_vs_F.deseq2.annot
DC02T1

value: Carcinoma, derived from BPH1 but phenotypically neoplastic and metastatic

value: M12 treated (PSC27-PDK4 CM)


title: DU145-Treated 02

description:
PE150 high throughout data
C_vs_D.deseq2.annot
DB02T2


title: cuprizone_mouse_rep3


title: DU145-CTRL 01

description:
PE150 high throughout data
C_vs_D.deseq2.annot
DB01C1

value: DU145 control (PSC27 CM)

value: conditioned media from prostate stromal cells, naive (control)


title: EAE_mouse_rep1


title: EAE_mouse_rep4


title: cuprizone_mouse_rep5


title: M12-CTRL 02

description:
PE150 high throughout data
E_vs_F.deseq2.annot
DC01C2

value: M12 control (PSC27 CM)


title: M12-Treated 02

description:
PE150 high throughout data
E_vs_F.deseq2.annot
DC02T2


title: cuprizone_mouse_rep4


title: cuprizone_mouse_rep2


title: DU145-CTRL 02

description:
PE150 high throughout data
C_vs_D.deseq2.annot
DB01C2


title: M12-CTRL 01

description:
PE150 high throughout data
E_vs_F.deseq2.annot
DC01C1


title: EAE_mouse_rep3


title: cuprizone_mouse_rep1


title: EAE_mouse_rep5


title: PC3-Treated 02

description:
PE150 high throughout data
A_vs_B.deseq2.annot
DA02T2

value: Carcinoma, derived from the metastatic site, bone of a prostate cancer patient

value: PC3 treated (PSC27-PDK4 CM)


title: EAE_mouse_rep2


title: control_mouse_rep3

value: Unmanipulated control mice.


title: control_mouse_rep4