title: Et52B in planta sample 3

city: Urbana

first: Mara

last: Krone

state: Illinois

address: 1102 S Goodwin Ave, Turner Hall

department: Crop Sciences

institute: University of Illinois

description: Library name: NLB5

data_processing:
Sequence quality control was performed and reads were trimmed. Reads were aligned to the reference genome using STAR and Bam files were output.
Multi-mapping reads and reads with ambiguous assignments were removed. Package "edgeR" was used for quality control and normalizations of read counts.
Assembly: Et52B genome assembly
Supplementary files format and content: csv file contains the raw counts for each sample

organism: Exserohilum turcicum

source_name: Infected leaf

growth_protocol: For in planta samples: Maize plants were inoculated with the Et52B strain at the V3 growth stage. Infected tissue was then collected 10 days after inoculation and flash frozen. For axenic samples: The cultures were grown on lactose-casein hydrolysate agar under 12 hour white light at 25C for 15 days. The cultures were transferd to potato dextrose broth and grown for 5 days. Mycelium was harvested by vacuum filtration.

extract_protocol:
RNA was extracted using TriZol (Thermo Fisher Scientific, Waltham, MA) following manufacturer instructions and cleaned using an RNA clean and concentrator kit (Zymo Research, Irvine, CA). The RNA quality and integrity were checked by running the RNA on a 1% agarose gel.
The RNA samples were submitted for library preparation and sequencing at Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. The RNA-seq libraries were prepared using a TruSeq Stranded mRNAseq Sample Prep kit (Illumina, San Diego, CA, United States) and quantified using qRT-PCR.

value: Infected leaf


title: Meningioma 930

status: Public on Jan 31 2025

type: genomic

city: Boston

first: Scott

middle: Thomas

last: Ryall

state: Massachusetts

address: 75 Francis Street

country: USA

institute: Brigham and Women's Hospital

description: Hybridized to OncoScanHD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were then washed using Affymetrix GeneChip Fluidics Station 450, and scanned using the Gene Chip Scanner 3000.

data_processing:
Data analysis was performed using Chromosome Analysis Suite software version 1.2.2
[primary data description] Fluorescent intensity values across SNP probes

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Meningioma Tissue

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Not applicable

extract_protocol: DNA was extracted using the QIAamp DNA FFPE Tissue Kit and stored at 4˚C

treatment_protocol: Not applicable

tag: tissue

value: Brain

tag: Sex

value: F

tag: age


title: Et52B axenic sample 3

type: SRA

description: Library name: Et52B_axenic_3

library_source: transcriptomic

molecule: total RNA

source_name: Mycelia

value: Mycelia


title: Et52B in planta sample 1

description: Library name: NLB1


title: Meningioma 931

description: Hybridized to OncoScanHD


title: Et52B in planta sample 2

description: Library name: NLB2


title: IP_srp54_control_U1.rep2

city: La Jolla

first: Cody

last: Ocheltree

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: Sample-147
IP_srp54_control_rep2_combined_Taildata.csv

library_source: other

data_processing:
FASTQ files were first subjected to 3’ adaptor, PCR duplicate removal, and gene-specific barcode and primer sequence removal using custom python scripts (https://pypi.org/project/jla-demultiplexer/).
Reads were aligned to small RNAs of interest using in-house alignment scripts.
Gene-specific 3’ end information and graphs were subsequently generated using in-house scripts.
For SLAMseq, gene-specific alignments were performed using in-house scripts which permitted T>C conversions. The number of conversions for each read was quantified and reads with two or more conversions were subsequently analyzed as nascently-labeled reads.
Assembly: human genome (version hg38)
Supplementary files format and content: comma separated variable table with RNA counts, 3' end position, and 3' post-transcriptional nucleotides

molecule: other

source_name: HEK 293T-REx

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:
RNA was isolated using TRIzol (Thermo Fisher) per manufacturer’s recommendation. RNA was subsequently treated with DNase I (1 U/µl; Zymo research) in DNase buffer (10 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 0.5 mM CaCl2) at 25˚ C for 15 minutes, followed by extraction with phenol:chloroform:isoamyl alcohol and ethanol precipitation. For RNA immunoprecipitations, cells were harvested by scraping into ice cold PBS and flash frozen in liquid nitrogen. Cells were resuspended in ice-cold isotonic lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% Triton X-100, 80 U/mL RNaseOut (Thermo Fisher), protease inhibitor tablet/10 mL (Roche)) and incubated with rotation for 20 minutes at 4°C. Cellular debris was pelleted at 13,000 g for 15 minutes at 4°C. The supernatant was briefly pre-cleared using Protein G beads (Thermo Fisher, 10004D) for 10 minutes at 4°C with rotation. Beads for immunoprecipitation were washed with bead wash buffer (PBS pH 7.4, 0.1% Tween 20) and subsequently incubated with anti-La antibody (Santa Cruz Biotechnology, sc-80656), anti-SRP54 antibody (Invitrogen, MA5-34835), rabbit IgG (Cell Signaling Technology, 2729), or mouse IgG1 (Cell Signaling Technology, 5415) antibody for 1 hour at 4°C with rotation, then washed with bead wash buffer. Sample protein was quantified with a BCA assay (Thermo Fisher). 1 mg of protein per sample was diluted 5-fold with ice-cold detergent dilution buffer (isotonic lysis buffer without Triton X-100) and incubated with antibody-bead complexes for 1 hour at 4°C with rotation. Samples were washed 5 times with ice-cold immunoprecipitation wash buffer (PBS pH 7.4, 0.1% Tween 20, 150 mM NaCl) at 4°C. RNA from input and immunoprecipitation material was extracted with TRIzol (Thermo Fisher) according to the manufacturer’s recommendation. For SLAMSeq, samples were treated with either iodoacetamide (IAA) or dimethylsulfoxide (DMSO) for 15 minutes at 50°C prior to 3' adaptor ligation. Gene-specific 3’-end sequencing libraries were prepared as described above.
RNA adapters containing barcodes and 10- to 16-nt randomers (AG10/AG11/AG15/AG16) were ligated to the 3′ ends of 2 μg of extracted RNA in a 10-μL reaction containing 1 μL of 10xT4 RNA ligase buffer (500 mM Tris-HCl, 100 mM MgCl2, 10 mM DTT at pH at 25°C), 0.2 mg/mL bovine serum albumin (BSA), 2 μM AG10 or AG11, 1 mM ATP, 10 U of T4 RNA ligase (NEB), and 40 units of RNaseOUT (Invitrogen) for 16 h at 16°C and extracted with phenol/chloroform/isoamyl alcohol. cDNA was generated using SuperScript III (SSRT III; Thermo Fisher) in a 20-μL reaction using 0.5 μM linker-specific primer AR-17. For sequencing, snRNA cDNA 3′ ends were amplified in 16–30 cycles of polymerase chain reaction (PCR) with small RNA gene-specific forward primers and AR17 primer using Q5 DNA polymerase (NEB), and then eight cycles with primers D50x and D70x. Libraries were sequenced on an Illumina MiSeq platform.

treatment_protocol: RNA interference was performed in HEK 293T Flp-In cells (FIRT, Thermo Fisher) with 40 nM small interfering (si)RNA targeting genes of interest, or luciferase as a control, using siLentFect (Bio-Rad) transfection reagent according to manufacturer’s recommendations at 72 and 24 hours before cell harvest. Transient transfection of plasmid (10 µg/15 cm plate) containing exogenous 7SL and U1 sequences was performed 18 hours prior to harvest with Lipofectamine 2000 (Thermo Fisher) according to manufacturer’s recommendations. Control or TENT2 KO 293 T-REx cell media was treated with 4-thiouridine [s4U] at a final concentration of 100 µM and incubated for 3 hours, then refreshed with 100 µM s4U-containing media and incubated for an additional 3 hours.

tag: cell line

value: HEK 293T-REx

tag: treatment


title: Et52B axenic sample 1

description: Library name: Et52B_axenic_1


title: IP_srp54_control_U1.rep1

description:
Library name: Sample-146
IP_srp54_control_rep1_combined_Taildata.csv


title: COVID_Patient_3_Plac

city: Houston

first: Rachel

middle: A

last: Keuls

email: Rachel.Keuls@bcm.edu, rkeuls@gmail.com

state: TX

address: One Baylor Plaza

department: MCB

institute: Baylor College of Medicine

description: sci-rna-seq3 run 2

data_processing:
Demultiplexing using the BBI pipeline command bbi-demux (https://github.com/bbi-lab/bbi-dmux)
Aligment and count matrix generation using the BBI pipeline command bbi-sci (https://github.com/bbi-lab/bbi-sci/)
Cells were clustered in Seurat using cells with 10PCs, >500 features per cell, 2000 variable features used to cluster cells, and samples in the control group were merged together while samples in the COVID-19 group were merged together and then the two groups were integrated together. The processed Seurat objects containing nuclei from all patients are included as follows: the file COVIDvControl_500Features_5pctmito_2000VariableFeature_Limit-Integrated-10PCs-CLEANED-clustsless5cellsremoved.rds was used for visualization and the file COVIDvControl_500Features_5pctmito_2000VariableFeature_Limit-Integrated-10PCs-CLEANED.rds was used for covid v control differential expression
Assembly: human GRCh38 build and annotation from Ensembl (release 99)
Supplementary files format and content: Filtered Feature Matrix Files
Supplementary files format and content: Monocle3 CDS and Seurat RDS file

molecule: nuclear RNA

source_name: Chorionic Villi

growth_protocol: Placentas were delivered via cesarian section

extract_protocol:
Tissue samples were manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at -80°C. Nuclei isolations were performed with the ‘hypotonic lysis buffer solution B’ [Martin et al. 2023]. Up to 200 mg of tissue was added to 5 mL of ‘hypotonic lysis buffer B’ for 5 to 25 minutes on ice with periodic agitation. For samples under 50 mg, 500 uL of ‘hypotonic lysis buffer B’ was added directly to the 1.5 mL sample tubes and a RNase-free pestle was used for 6 to 12 strokes to further dissociate the tissue. Released nuclei were passed through a 70-micron cell strainer, pelleted (500xg, 5 minutes, 4°C), and resuspended in 1 mL of cold ‘0.3 M SPBSTM’ (Martin et al. 2023). Pre-chilled fixative (5 mg of DSP resuspended in 100 uL DMSO per 4 mL of methanol) was incrementally added for every 1 mL of nuclei resuspended in ‘0.3 M SPBSTM’ and fixed on ice for 5 to 10 minutes. The nuclei were rehydrated by gradually adding 10 mL of ‘0.3 M SPBSTM’ for every 5 mL of fixed nuclei suspension prior to centrifugation (500xg, 5 minutes, 4°C) and resuspended in 1 mL of ‘0.3 M SPBSTM’. Nuclei suspensions processed in the third sci-RNA-seq3 experimental batch were additionally overlaid on 7 mL of a 1.4 M sucrose buffer (1.4 M sucrose, 1X phosphate buffered saline (8 mM Na2HPO4 (pH 7.4), 2 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl), 3 mM MgCl2) and centrifuged at 3,000xg, 20 minutes, 4°C to remove excess debris; the pelleted nuclei were again resuspended in 1 mL of ‘0.3 M SPBSTM’ and passed through a 20-micron cell strainer. After counting, nuclei aliquots were centrifuged (500xg, 5 minutes, 4°C), supernatant aspirated, and pelleted nuclei stored at -80°C until use.
Methods for the first two sci-RNA-seq3 experimental batches largely followed those described by Cao et al. [Cao et al. 2019] with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 2 μl of oligo(dT) primers were added to each well with 80,000 nuclei for reverse transcription, and tagmentation was performed using 1/40 μl per well of i7-loaded TDE1 enzyme prepared at the BAT-Lab following published protocols [Hennig et al. 2-18]. Libraries were sequenced on an Illumina Nextseq 200 cycles P3 kit with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Methods for the third sci-RNA-seq3 experimental batch largely followed the optimized protocol described by Martin et al. (Martin et al. 2023) with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 20,000 nuclei were loaded per reverse transcription well, tagmentation with N7 adaptor-loaded Tn5 transposases (Diagenode cat. no. C01070010-20) was performed at 1/80 uL per well across PCR plates, final library clean up was 0.5X AMPure XP supernatant followed by Qiagene GeneRead Size Selection purification column. The library was sequenced on an Illumina NovaSeq S4 flow cell at the University of Washington Northwest Genomics Center core sequencing facility with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Read alignment and gene count matrix generation was performed using the Brotman Baty Institute (BBI) pipeline for sci-RNA-seq3 (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci). The human GRCh38 build and annotation from Ensembl (release 99) was used as the reference genome. The 3’ UTR annotations of genes and transcripts were extended by 500 bp to avoid misclassifying genic reads as intergenic, and haplotype sequences were removed from the FASTA to avoid mapping inefficiencies due to multimapping.

treatment_protocol: Placental biopsy tissue was washed extensively to remove maternal blood and maternal uterine tissue was largely removed and rolled membranebiopsies were washed to remove maternal blood

value: Chorionic Villi


title: Meningioma 929

description: Hybridized to OncoScanHD


title: IP_srp54_control_7sl.rep3

description:
Library name: Sample-145
IP_srp54_control_rep3_combined_Taildata.csv


title: IP_srp54_control_7sl.rep2

description:
Library name: Sample-144
IP_srp54_control_rep2_combined_Taildata.csv


title: Meningioma 928

description: Hybridized to OncoScanHD

value: M


title: 15St008 in planta sample 3

data_processing:
Sequence quality control was performed and reads were trimmed. Reads were aligned to the reference genome using STAR and Bam files were output.
Multi-mapping reads and reads with ambiguous assignments were removed. Package "edgeR" was used for quality control and normalizations of read counts.
Assembly: 15St008 genome assembly
Supplementary files format and content: csv file contains the raw counts for each sample

growth_protocol: For in planta samples: Sorghum plants were inoculated with the 15St008 strain at the V3 growth stage. Infected tissue was then collected 10 days after inoculation and flash frozen. For axenic samples: The cultures were grown on lactose-casein hydrolysate agar under 12 hour white light at 25C for 15 days. The cultures were transferd to potato dextrose broth and grown for 5 days. Mycelium was harvested by vacuum filtration.


title: 15St008 in planta sample 2


title: 15St008 in planta sample 1


title: Meningioma 927

description: Hybridized to OncoScanHD


title: IP_srp54_control_7sl.rep1

description:
Library name: Sample-143
IP_srp54_control_rep1_combined_Taildata.csv


title: 15St008 axenic sample 2


title: IP_la_tent2ko_U1.rep3

description:
Library name: Sample-142
IP_la_tent2ko_rep3_combined_Taildata.csv


title: 15St008 axenic sample 1


title: Meningioma 926

description: Hybridized to OncoScanHD


title: IP_la_tent2ko_U1.rep2

description:
Library name: Sample-141
IP_la_tent2ko_rep2_combined_Taildata.csv


title: ROI1

type: RNA

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

description: Spatial Transcriptomics

scan_protocol: Following a preliminary scan where regions of interest were manually defined, Barrett's esophagus sections underwent 40 sequential rounds of hybridization and image acquisition for Alexa Fluor 488, Cy3B, and Alexa Fluor 647 on the GenePS33. DAPI was also included in the experiment. Probes for target genes were designed and synthesized by Spatial Genomics. seqFISH images were exported as .tif files. Raw seqFISH images were thresholded using the SGAnalysis software (v0.6.1). The same thresholds were used for all regions of interest on the coverslip. seqFISH images were decoded in SGAnalysis to generate a count matrix for downstream analysis.

data_processing: Barrett's esophagus cells were identified in the tissue based on the expression of specific canonical genes, and cells lacking this signature were excluded. Following this selection, cells with zero counts were filtered from the dataset. The remaining cells underwent normalization based on total gene counts over all genes, followed by a natural logarithm transformation and scaling to achieve zero mean and unit variance. A neighborhood graph of the cells was then computed and visualized using UMAP. Concurrently, the scRNA-seq data of Barrett's esophagus cells was aligned with the genes from the spatial genomics dataset to form a correspondence matrix. Finally, the MaxFuse pipeline was used to integrate the spatial transcriptomics and scRNA-seq datasets35, improving the accuracy of cell type labeling. For distance measurements, the position of the lumen was determined by choosing the correct nodes from the convex hull that was found by using the Graham scan algorithm. We then calculated the distance of each cell to the line that represented the lumen.

label: FISH

source_name: Barrett's Esophagus

extract_protocol: Pinch biopsies used for seqFISH were embedded fresh in OCT (Fisher, 23730571) and snap-frozen in an isopentane (O35514, Fisher)-dry ice bath, after which they were transferred to -80 °C for storage. 10-um tissue sections were prepared from the OCT-embedded biopsies using a cryostat (Microm) set to -20 °C and transferred to functionalized coverslips (Spatial Genomics). Tissue sections were fixed in 3.7% formaldehyde (Fisher, BP531-500) solution in PBS (Invitrogen, AM9625) for 15 minutes at room temperature, followed by 3 PBS washes of 5 minutes each. Tissue sections were permeabilized in 70% ethanol at 4 °C overnight. Following permeabilization, the coverslip was dried completely before washing with 1 mL of Clearing Solution (Spatial Genomics) for 5 minutes. The coverslip was then rinsed with 70% ethanol for 60 seconds and let air dry. Once dry, the flow cell was assembled using the functionalized coverslip and Spatial Genomics flow cell top. 80 uL of Primary Wash Buffer (Spatial Genomics) was added to the flow cell and incubated for 5 minutes. 80 uL of primary probes were denatured at 90 °C for 3 minutes during the wash buffer incubation and subsequently added to the flow cell. The primary probe incubation took place overnight at 37 °C for 16 hours, after which the probe mix was removed and washed out with 2 washes of 80 uL of Primary Wash Buffer (Spatial Genomics). The flow cell was then incubated with 80 uL of Primary Wash Buffer for 30 minutes at 37 °C, repeating the washes and incubation a second time. Following the second incubation, the flow cell was rinsed three times with 80 uL of Rinse Buffer (Spatial Genomics) and loaded onto the Gene Positioning System (GenePS).

tag: disease state

value: Barrett's Esophagus


title: Meningioma 925

description: Hybridized to OncoScanHD


title: Et52B axenic sample 2

description: Library name: Et52B_axenic_2


title: ROI3


title: ROI2


title: IP_la_tent2ko_U1.rep1

description:
Library name: Sample-140
IP_la_tent2ko_rep1_combined_Taildata.csv


title: KO4700.3_bio rep 3

city: Guiyang

first: Muhammad

last: Asif

state: Guizhou

address: college of agriculture, Guizhou university

department: Plant Pathology

country: China

institute: Guizhou University

description:
Library name: Sample 9
Column name in  counts.txt: KO4700.3

data_processing:
After obtaining the sequencing data of the sample, it is first necessary to evaluate the sequencing data quality and filter the low-quality data to ensure the credibility of the subsequent analysis results. The software fastp was used for the quality control process, and the quality control standards were as follows: 1. The proportion of bases with quality value less than 15 was not higher than 40%; 2. Starting from the 5 'end of read, the average quality value in the sliding window of 4 bases is not lower than 20. If the quality value is lower than 20, the sequences in the sliding window and to the right of the window are discarded; 3. The read length after quality control should not be less than 75 bases; 4. The number of N bases in a single read should not exceed 5.
Bowtie2 software was used to compare the sequencing data after quality control with the ribosomal sequences in NCBI RefSeq database and Rfam database. samtools was used to calculate the alignment results and extract the sequences that were not aligned on both ends for subsequent analysis. Then, Bowtie 2 software was used to align the data after removing ribosomes to the reference genome and calculate the alignment results.
The expression levels of transcripts were quantified using quantitative software (RSEM, Kallisto, Salmon). After obtaining the readcounts of transcripts, the R package tximport was used to convert the readcounts of transcripts into the readcounts of genes.
Assembly: Shaanxi_M228 (GenBank accession number: CP032631.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include tpm value for each Sample

organism: Pseudomonas syringae pv. actinidiae

source_name: C_4700 Knockout

growth_protocol: Three single colonies of activated Psa wild type strain S26 and gene knockout strain Δ4700 and Δ22735 were selected and inoculated into LB medium. The strains were shaken at 25°C and 200 rpm overnight, and then inoculated into new LB medium at a ratio of 1: 100 the next day

extract_protocol:
Total RNA was extracted by Trizol method, and the quality of samples was checked by Thermo NanoDrop One and Agilent 4200 Tape Station.
After qualified RNA quality control, the EpicentreRibo Zero rRNA Removal Kit was used to remove ribosomal RNA. Strk-specific libraries were constructed using the NEBNext® Ultra II™Directional RNA Library Prep Kit for Illumina

treatment_protocol: The medium was removed by centrifugation at 5000 rpm for 5 min and the cells were resuspended in sterile water. The cells were collected by centrifugation at 5000 rpm for 5 min and resuspended in HDM. The cells were induced at 25°C and 200 rpm for 8 h before centrifugation and collection

tag: cell type

value: C_4700 Knockout


title: Meningioma 924

description: Hybridized to OncoScanHD


title: KO4700.1_bio rep 1

description:
Library name: Sample 7
Column name in  counts.txt: KO4700.1


title: IP_la_tent2ko_7sl.rep3

description:
Library name: Sample-139
IP_la_tent2ko_rep3_combined_Taildata.csv


title: KO4700.2_bio rep 2

description:
Library name: Sample 8
Column name in  counts.txt: KO4700.2


title: Meningioma 923

description: Hybridized to OncoScanHD


title: KO22735.3_bio rep 3

description:
Library name: Sample 6
Column name in  counts.txt: KO22735.3

source_name: C_22735 Knockout

value: C_22735 Knockout


title: KO22735.1_bio rep 1

description:
Library name: Sample 4
Column name in  counts.txt: KO22735.1


title: Meningioma 922

description: Hybridized to OncoScanHD


title: 15St008 axenic sample 3


title: KO22735.2_bio rep 2

description:
Library name: Sample 5
Column name in  counts.txt: KO22735.2


title: IP_la_tent2ko_7sl.rep1

description:
Library name: Sample-137
IP_la_tent2ko_rep1_combined_Taildata.csv


title: Meningioma 921

description: Hybridized to OncoScanHD


title: S26.3_bio rep 3

description:
Library name: Sample 3
Column name in  counts.txt: S26.3

source_name: WT

value: WT


title: IP_la_control_U1.rep3

description:
Library name: Sample-136
IP_la_control_rep3_combined_Taildata.csv


title: IP_la_tent2ko_7sl.rep2

description:
Library name: Sample-138
IP_la_tent2ko_rep2_combined_Taildata.csv


title: S26.2_bio rep 2

description:
Library name: Sample 2
Column name in  counts.txt: S26.2


title: S26.1_bio rep 1

description:
Library name: Sample 1
Column name in  counts.txt: S26.1


title: IP_la_control_U1.rep2

description:
Library name: Sample-135
IP_la_control_rep2_combined_Taildata.csv


title: Meningioma 920

description: Hybridized to OncoScanHD


title: G282_A_biol rep 2

description:
Library name: Sample8
Column name in gene_count.txt:G282_A_2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then 1 FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .
Assembly: CP032631.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: csv files include FPKM values for each Sample.

source_name: bacterial cell

growth_protocol: Wild-type strain G1 and mutant strains G126 and G282 were strewed on LB plate and cultured at 25 ℃ for 48 h. Single colonies were selected and cultured in LB liquid medium at 25 ℃ and 150 r/min for 16 h.

extract_protocol:
RNA was harvested using RNAprep Pure Cell/Bacteria Kit (TIANGEN). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using Fast RNA-seq Lib Prep Kit V2(ABClonal) following manufacturer's protocols.

treatment_protocol: The culture was removed and cleaned with sterile water for three times, then suspended with 200 μL sterile water. The bacterial suspension was added to 1 mL HDM medium at 25 ℃ and 150 r/min for 6 h at the rate of 1:50, and the bacteria were collected by centrifugation at 10 000× g

tag: strain

value: bacterial cell


title: Meningioma 919

description: Hybridized to OncoScanHD


title: IP_la_control_U1.rep1

description:
Library name: Sample-134
IP_la_control_rep1_combined_Taildata.csv


title: IP_la_control_7sl.rep3

description:
Library name: Sample-133
IP_la_control_rep3_combined_Taildata.csv


title: G126_A_biol rep 2

description:
Library name: Sample5
Column name in gene_count.txt:G126_A_2


title: G126_A_biol rep 3

description:
Library name: Sample6
Column name in gene_count.txt:G126_A_3


title: Meningioma 918

description: Hybridized to OncoScanHD


title: Meningioma 917

description: Hybridized to OncoScanHD


title: IP_la_control_7sl.rep2

description:
Library name: Sample-132
IP_la_control_rep2_combined_Taildata.csv


title: G1_A_biol rep 3

description:
Library name: Sample3
Column name in gene_count.txt:G1_A_3


title: G1_A_biol rep 2

description:
Library name: Sample2
Column name in gene_count.txt:G1_A_2


title: G1_A_biol rep 1

description:
Library name: Sample1
Column name in gene_count.txt:G1_A_1


title: G126_A_biol rep 1

description:
Library name: Sample4
Column name in gene_count.txt:G126_A_1


title: IP_la_control_7sl.rep1

description:
Library name: Sample-131
IP_la_control_rep1_combined_Taildata.csv


title: Brain, WT

city: St. Louis

first: Mati

middle: Tesfaye

last: Nemera

state: Missouri

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St. Louis School of Medicine

description: Vizgen MERSCOPE Instrument

hyb_protocol: Hybridization of the tissue to gene probes for MERFISH was performed according to instructions provided by Vizgen. Briefly, after aspiration of the 70% ethanol, the 10 μm-thick tissue section mounted onto the MERSCOPE slide was washed with Sample Prep Wash Buffer (Vizgen, PN 20300001) and Formamide Wash Buffer (Vizgen, PN 20300002) while placed in the petri dish, and incubated at 37°C for 30 min in a benchtop incubator (INCU-Line, VWR). The Formamide Wash Buffer was then aspirated, and 50 μL of a custom-designed MERSCOPE gene panel mix was delivered onto the tissue section. A 2 × 2 cm piece of Parafilm M (Fisher Scientific) was carefully placed onto the tissue so that the gene panel mix was evenly spread across the tissue and no bubbles were introduced between the tissue and the film. The petri dish was closed with a lid and sealed with Parafilm M, sterilized with 70% ethanol, and placed in a humidified benchtop incubator (INCU-Line, VWR) set at 37°C for 36–48 h.

data_processing:
Cells were segmented using the Watershed algorithm, using DAPI as the Seed Stain and PolyT as the Watershed Stain.
Single-cell expression matrices were produced from quantifying the number of RNA transcripts in segmented cells.
Cell-by-gene matrix csv files provide the RNA counts of each gene in each cell. Metadata csv files provide information about each cell such as cell volume and location.

organism: Mus musculus

extract_protocol: Brains were placed in O.C.T-containing molds and flash frozen in liquid nitrogen. 10 μm-thick coronal tissue sections were prepared from the O.C.T. compound-embedded brain using a cryostat. Tissue sections were mounted onto specialized MERSCOPE slides (Vizgen, PN 20400001), and maintained in 70% ethanol in a sealed petri dish until gene probe hybridization according to Vizgen's protocol.

tag: genotype

tag: gender

value: Female


title: Meningioma 915

description: Hybridized to OncoScanHD


title: Brain, Mecp2 KO/+, exp3

description: Vizgen MERSCOPE Instrument

value: Mecp2 KO/+


title: Brain, Mecp2 KO/+, exp4

description: Vizgen MERSCOPE Instrument


title: Brain, Mecp2 KO/+, exp1

description: Vizgen MERSCOPE Instrument


title: Brain, Mecp2 KO/+, exp2

description: Vizgen MERSCOPE Instrument


title: Meningioma 914

description: Hybridized to OncoScanHD


title: IP_input_tent2ko_U1.rep3

description:
Library name: Sample-130
IP_input_tent2ko_rep3_combined_Taildata.csv


title: G282_A_biol rep 3

description:
Library name: Sample9
Column name in gene_count.txt:G282_A_3


title: Xal treated ethanol (VOC-solvent), rep 4

city: Campinas

first: Joaquim

last: Martins Junior

state: SP

address: Rua Giuseppe Maximo Scolfaro 10000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
RNAseq reads were quality checked using FastQC.
Low-quality reads and adapters sequences were removed using Fastp 0.20
QC-filtered reads were aligned to Xanthomonas albilineans CFBP2553 genome (GCF_002939705.1_ASM293970v1) available at GenBank database using the STAR.
Reads counts of each gene were calculated using the featureCounts function from the Rsubread package.
Differential expression analysis was performed using the edgeR package.
Assembly: Xanthomonas albilineans CFBP2553 genome (GCF_002939705.1_ASM293970v1)
Supplementary files format and content: tab-delimited txt files include raw counts for each sample
Supplementary files format and content: tab-delimited txt files include TPM values for each sample
Supplementary files format and content: tab-delimited txt files include logFoldChange for each comparing

molecule: polyA RNA

organism: Xanthomonas albilineans

source_name: CFBP 2523

growth_protocol: Three milliliters of liquid sucrose-peptone medium and 100 µL of Xab inoculum were added to 10 mL-vials hermetically sealed. The experimental treatments were: (i) 0.5 mM of DMDS , (ii) 15 µL of ethanol (solvent control), and (iii) without DMDS/ethanol. The vials were incubated for 3 days at 28°C under constant agitation (200 rpm). The experiment was performed with four replicates.

extract_protocol:
RNA extraction was carried out with SV Total RNA Isolation System (Promega)
From 100 ng of RNA, we performed the ribosomal depletion with Tru-Seq Stranded Total RNA With Illumina Ribo-Zero Plus rRNA (Illumina Inc.), following the manufacturer's instructions. The sequencing libraries were prepared with TruSeq® Stranded mRNA Library Prep (Illumina Inc.), following the manufacturer's instructions. The size and quality of the libraries was evaluated using the 2100 Bioanalyzer Instrument (Agilent Technologies) with the 12000 DNA Assay Kit (Agilent Technologies). The libraries were quantified by real-time PCR with the QIAseq Library Quant Assay Kit (Qiagen) grouped in equimolar ratios and subsequently subjected sequencing on the Hiseq 2500 instrument (Illumina Inc.), with paired-end rapid run mode (2 X 100).

treatment_protocol: (i) 0.5 mM of DMDS, (ii)  ethanol (solvent control), and (iii) without DMDS/ethanol

value: CFBP 2523


title: Xal treated ethanol (VOC-solvent), rep 3


title: IP_input_tent2ko_U1.rep1

description:
Library name: Sample-128
IP_input_tent2ko_rep1_combined_Taildata.csv


title: Meningioma 912

description: Hybridized to OncoScanHD


title: G282_A_biol rep 1

description:
Library name: Sample7
Column name in gene_count.txt:G282_A_1


title: Xal treated ethanol (VOC-solvent), rep 2


title: Meningioma 911

description: Hybridized to OncoScanHD


title: Meningioma 916

description: Hybridized to OncoScanHD


title: IP_input_tent2ko_7sl.rep2

description:
Library name: Sample-126
IP_input_tent2ko_rep2_combined_Taildata.csv


title: IP_input_tent2ko_7sl.rep3

description:
Library name: Sample-127
IP_input_tent2ko_rep3_combined_Taildata.csv


title: Xal treated ethanol (VOC-solvent), rep 1


title: Xal treated with volatile dimethyl disulfide (DMDS), rep 1


title: Meningioma 910

description: Hybridized to OncoScanHD


title: Xal control, rep 4

value: untreated


title: Xal control, rep 3


title: Meningioma 913

description: Hybridized to OncoScanHD


title: Xal control, rep 2


title: IP_input_tent2ko_U1.rep2

description:
Library name: Sample-129
IP_input_tent2ko_rep2_combined_Taildata.csv


title: IP_input_control_U1.rep3

description:
Library name: Sample-124
IP_input_control_rep3_combined_Taildata.csv


title: Meningioma 908

description: Hybridized to OncoScanHD


title: Xal control, rep 1


title: IP_input_control_U1.rep2

description:
Library name: Sample-123
IP_input_control_rep2_combined_Taildata.csv


title: AGS_GNE_3

first: Sarah

last: Alp

address: 3601 Spruce Street

institute: The Wistar Institute

description: Library name: S12

data_processing:
Adapter trimming
Alignment with STAR
Counts called with RSEM
Assembly: hg38
Supplementary files format and content: RSEM output files

source_name: AGS

growth_protocol: Cells were plated at 70% confluency the day before treatment in 10% FBS RPMI media.

extract_protocol:
RNA was extracted with the Rneasy Mini Kit, Qiagen according to the manufacturer's protocol.
Libraries were constructed fro the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO or GNE6776 20uM

value: AGS

value: gastric cancer

value: EBV-

value: GNE


title: IP_input_control_U1.rep1

description:
Library name: Sample-122
IP_input_control_rep1_combined_Taildata.csv


title: AGS_GNE_2

description: Library name: S11


title: Meningioma 907

description: Hybridized to OncoScanHD

value: Brain

value: F


title: Meningioma 906

description: Hybridized to OncoScanHD


title: IP_input_control_7sl.rep3

description:
Library name: Sample-121
IP_input_control_rep3_combined_Taildata.csv

value: HEK 293T-REx


title: AGS_DSMO_2

description: Library name: S8

value: DMSO


title: Meningioma 905

description: Hybridized to OncoScanHD


title: Xal treated with volatile dimethyl disulfide (DMDS), rep 3


title: Meningioma 909

description: Hybridized to OncoScanHD


title: IP_input_tent2ko_7sl.rep1

description:
Library name: Sample-125
IP_input_tent2ko_rep1_combined_Taildata.csv


title: SNU719_GNE_3

description: Library name: S6

value: EBV+


title: Xal treated with volatile dimethyl disulfide (DMDS), rep 2


title: AGS_DMSO_1

description: Library name: S7


title: IP_input_control_7sl.rep2

description:
Library name: Sample-120
IP_input_control_rep2_combined_Taildata.csv


title: SNU719_GNE_2

description: Library name: S5


title: SNU719_GNE_1

description: Library name: S4


title: Meningioma 903

description: Hybridized to OncoScanHD


title: IP_input_control_7sl.rep1

description:
Library name: Sample-119
IP_input_control_rep1_combined_Taildata.csv


title: Meningioma 902

description: Hybridized to OncoScanHD


title: figS4g_IAA_U1.rep1

description:
Library name: Sample-118
figS4g_IAA_U1_rep1_counts.csv_SLAMseq_Taildata.csv


title: figS4g_IAA_7sl.rep1

description:
Library name: Sample-117
figS4g_IAA_7SL_rep1_counts.csv_SLAMseq_Taildata.csv


title: SNU719_DMSO_2

description: Library name: S2


title: 2D culture, SW480 cells cultured with J2 cells and hepatocytes, rep3

city: Minneapolis

first: Stephen

last: Jameson

state: MN

address: Wallin Medical Biosciences Bldg, MMC 641

department: Lab Medicine and Pathology

institute: University of Minnesota

data_processing:
adaptor trimming using trimmomatic (version 0.33)
reads mapped to GRCm38 mouse genome using HiSat2 (version 2.1.0)
counts generated using Subreads featureCounts tool (version 1.6.2) with Mus_musculus.GRCm38.100.gtf annotation
Counts were filtered to include only genes that were at least 300 nt in length with a counts per million value greater than 1 cpm in at least two sample replicates.
Assembly: GRCm38 v100
Supplementary files format and content: cpm_list_3DOrganoids.txt is a Gene x sample counts per million matrix for the 3D organoids samples.
Supplementary files format and content: cpm_list_2DCultures.txt is a Gene x sample counts per million matrix for the 2D cultures samples.

growth_protocol: We maintained the microtissues in Human Hepatocyte Maintenance Media (HHM)(43.25mL 1x DMEM, 5mL Bovine Serum, 750uL HEPES, 1M, ph. 7.6, 500uL insulin/human transferring/selenous acid and linoleic acid premix, 500uL Penicillin-streptomycin, 0.5uL Dexamethasone, 0.5uL Glucagon). During the study, we provided fresh media changes every 48 hours by removing 300uL from each well and replacing it with 300uL of fresh media. We then removed the microtissues at their respective time point.

extract_protocol:
RNA was isolated from the sorted SW480 cells using a Qiagen RNeasy Mini Kit.
2x150-bp dual-indexed (UDI) TruSeq stranded mRNA libraries

treatment_protocol: For the 2D platform, cells were collected from the plates using 0.25% Trypsin-EDTA. For the 3D platform, microtissues were collected from the wells and dissociated by incubating at 37°C with 0.1mg/mL Collagenase Type IV in HBSS (+CaCl2, +MgCl2) for 30 minutes, then manually disrupted to form a single cell suspension. For both platforms, 8 wells were combined to form replicates, n=3 per group. The single cell suspensions were incubated with MicroBeads against human CD326 (EpCAM) and antibody against CD16/CD32 to block nonspecific binding, then isolated across Miltenyi LS magnetic separation columns.

value: Coculture with  3T3-J2 fibroblasts and Primary rat hepatocytes


title: Meningioma 901

description: Hybridized to OncoScanHD

value: M


title: 2D culture, SW480 cells cultured with J2 cells and hepatocytes, rep2


title: figS4g_DMSO_U1.rep1

description:
Library name: Sample-116
figS4g_DMSO_U1_rep1_counts.csv_SLAMseq_Taildata.csv


title: 2D culture, SW480 cells cultured with J2 cells and hepatocytes, rep1


title: AGS_GNE_1

description: Library name: S10


title: AGS_DMSO_2

description: Library name: S9


title: Meningioma 900

description: Hybridized to OncoScanHD


title: 2D culture, SW480 cells cultured with J2 cells, rep3

value: Coculture with  3T3-J2 fibroblasts


title: 2D culture, SW480 cells cultured with J2 cells, rep2


title: Meningioma 899

description: Hybridized to OncoScanHD


title: 2D culture, SW480 cells cultured with J2 cells, rep1


title: Meningioma 904

description: Hybridized to OncoScanHD


title: figS4f_slamseq_tent2ko_U2.rep3

description:
Library name: Sample-114
IP_input_tent2ko_rep3_combined_Taildata.csv


title: 2D culture, SW480 cells, rep3


title: 2D culture, SW480 cells, rep2


title: Meningioma 898

description: Hybridized to OncoScanHD


title: 2D culture, SW480 cells, rep1


title: Meningioma 897

description: Hybridized to OncoScanHD


title: SNU719_DMSO_3

description: Library name: S3


title: 3D organoid, SW480 cells cultured with J2 cells and hepatocytes, rep3


title: 3D organoid, SW480 cells cultured with J2 cells and hepatocytes, rep2


title: SNU719_DMSO_1

description: Library name: S1


title: Meningioma 896

description: Hybridized to OncoScanHD


title: figS4f_slamseq_tent2ko_7sl.rep3

description:
Library name: Sample-111
IP_input_tent2ko_rep3_combined_Taildata.csv


title: 3D organoid, SW480 cells cultured with J2 cells and hepatocytes, rep1


title: Meningioma 895

description: Hybridized to OncoScanHD


title: 3D organoid, SW480 cells, rep3


title: 3D organoid, SW480 cells, rep1


title: Meningioma 894

description: Hybridized to OncoScanHD


title: figS4f_slamseq_tent2ko_7sl.rep1

description:
Library name: Sample-109
IP_input_tent2ko_rep1_combined_Taildata.csv


title: EW2

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggretation were made using the Space Ranger software (v.3.0.0) (10x Genomics, CA, USA).
Assembly: hg38
Supplementary files format and content: Space Ranger software output files (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz).
Library strategy: Spatial Transcriptomics

source_name: Tumor mass

extract_protocol:
Paraffin-embedded mice sample tissues with transplanted human Ewing sarcoma tumors were used. A selection of FFPE tissue blocks with the best DV200 value was done performing RNA extraction from several slices of the different block tissues and calculating the percentage of total RNA fragments >200 nucleotides (DV200) with Agilent TapeStation. Kit used to assess the RNA Quality: Rneasy FFPE KIT (50)-RNA extraction kit from Qiagen (Ref. 73504). Tissue slides from selected FFPE blocks were located into Visium CytAssist FFPE Spatial Gene Expression 6.5mm slides through the CytAssist equipment following the Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide.
VISIUM Cytassist FFPE from 10X Genomics.

value: Tumor mass


title: EW1

source_name: Lung

value: Lung


title: Meningioma 893

description: Hybridized to OncoScanHD


title: Meningioma 892

description: Hybridized to OncoScanHD


title: figS4g_DMSO_7sl.rep1

description:
Library name: Sample-115
figS4g_DMSO_7SL_rep1_counts.csv_SLAMseq_Taildata.csv


title: figS4f_slamseq_control_U2.rep3

description:
Library name: Sample-108
IP_input_control_rep3_combined_Taildata.csv


title: figS4f_slamseq_control_U2.rep2

description:
Library name: Sample-107
IP_input_control_rep2_combined_Taildata.csv


title: Meningioma 891

description: Hybridized to OncoScanHD


title: figS4f_slamseq_tent2ko_U2.rep2

description:
Library name: Sample-113
IP_input_tent2ko_rep2_combined_Taildata.csv


title: figS4f_slamseq_control_7sl.rep3

description:
Library name: Sample-105
IP_input_control_rep3_combined_Taildata.csv


title: Meningioma 890

description: Hybridized to OncoScanHD


title: Meningioma 888

description: Hybridized to OncoScanHD


title: figS4f_slamseq_control_7sl.rep2

description:
Library name: Sample-104
IP_input_control_rep2_combined_Taildata.csv


title: figS4f_slamseq_control_U2.rep1

description:
Library name: Sample-106
IP_input_control_rep1_combined_Taildata.csv


title: figS4f_slamseq_tent2ko_U2.rep1

description:
Library name: Sample-112
IP_input_tent2ko_rep1_combined_Taildata.csv


title: Meningioma 889

description: Hybridized to OncoScanHD


title: figS4f_slamseq_control_7sl.rep1

description:
Library name: Sample-103
IP_input_control_rep1_combined_Taildata.csv


title: 3D organoid, SW480 cells, rep2


title: fig4d_tent2wt_addback_Y3.rep3

description:
Library name: Sample-102
fig4d_tent2wt_addback_rep3_combined_Taildata.csv


title: figS4f_slamseq_tent2ko_7sl.rep2

description:
Library name: Sample-110
IP_input_tent2ko_rep2_combined_Taildata.csv


title: Meningioma 886

description: Hybridized to OncoScanHD


title: MSI1 overlap nsRBNS, 100, rep1

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

institute: UNC Chapel Hill

description: Counts were normalized for library size prior to enrichment against overlap_nsRBNS_RNA_input

data_processing:
Reads were trimmed to library sequencing size (20 nt for RBNS, 33 nt for posRBNS and compPosRBNS, 100 nt for nsRBNS)
For non-nsRBNS: Duplicate reads were collapsed
Counts were generated as dictated per experiment: RBNS (6mers), posRBNS and compPosRBNS (3mers, positionally), nsRBNS (STAR mapping against .fa)
For non-nsRBNS: Counts were normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: hg38
Supplementary files format and content: RBNS: 6mer enrichments
Supplementary files format and content: posRBNS & compPosRBNS: 3mer enrichments, positionally
Supplementary files format and content: nsRBNS: sequence enrichments

source_name: RBNS

extract_protocol:
Bound RNA was eluted from streptavidin magnetic beads in 0.1% SDS with 0.3 mg/mL proteinase K. RNA was concentrated via phenol-chloroform extraction.
RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified.

value: RBNS


title: MSI1 overlap nsRBNS, 100, rep2


title: fig4d_tent2wt_addback_Y3.rep2

description:
Library name: Sample-101
fig4d_tent2wt_addback_rep2_combined_Taildata.csv


title: 28--28

city: Dallas

first: Lei

last: Guo

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

data_processing:
Blc2fastq2 Conversion software (Illumina) was used to generate demultiplexed Fastq files. The adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were aligned to the human genome (GRCH38) or mouse genome (mm10) using STAR (2.7.3a). Subsequently, the mapped reads were quantified using the featureCounts of the Subread (v1.6.3) package. Genes with low expression (genes with an expression value of zero in more than 30% of the samples) were removed before subsequent analysis. Gene expression was normalized using the Voom method in the R package “limma” (v 3.50.3). Differentially expressed genes were also identified using this software. Gene set enrichment analysis of differentially expressed genes was performed using the R package “clusterProfiler” (v4.2.2). Volcano plots were generated using R package ggplot2 (v3.5.1). Heat maps were generated using R package pheatmap (v1.0.12).
Assembly: hg38 & mm10
Supplementary files format and content: Text file for count tables

source_name: colon

growth_protocol: BMDM cells were generated by flushing bone marrow cells from femurs and tibia of wild type or Arhgef2-/-, Pglyrp-1-/- and Nod2-/- mice and red blood cells were removed by using ACK lysis buffer. Then, 70 µm cell strainers were used to filter BMDM cells, followed by resuspension in complete DMEM supplemented with 10% FBS and 0.5% penicillin/streptomycin mixture, and 200 ng M-CSF.

extract_protocol:
RNeasy Mini Plus kit (Qiagen)
Libraries were synthesized using TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adapters according to the manufacturer’s protocol (Illumina). The final libraries were quantified using a Qubit fluorometer (Agilent Technologies), and RT-qPCR was performed using the Kapa Biosystems library quantification kit according to the manufacturer’s protocol. Pooled libraries were subjected to 35 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NextSeq 500). The targeted sequencing depth was set at 30 million paired-end reads per sample

value: colon

value: biopsies

value: active


title: UNK overlap nsRBNS, 100, rep1


title: Meningioma 884

description: Hybridized to OncoScanHD


title: Meningioma 885

description: Hybridized to OncoScanHD


title: 27--27


title: fig4d_tent2wt_addback_Y3.rep1

description:
Library name: Sample-100
fig4d_tent2wt_addback_rep1_combined_Taildata.csv


title: fig4d_tent2wt_addback_Y1.rep3

description:
Library name: Sample-99
fig4d_tent2wt_addback_rep3_combined_Taildata.csv


title: 26--26


title: Meningioma 883

description: Hybridized to OncoScanHD


title: 25--25


title: 24--24


title: Meningioma 882

description: Hybridized to OncoScanHD


title: fig4d_tent2wt_addback_Y1.rep2

description:
Library name: Sample-98
fig4d_tent2wt_addback_rep2_combined_Taildata.csv


title: 23--23


title: Meningioma 881

description: Hybridized to OncoScanHD


title: 22--22


title: fig4d_tent2wt_addback_Y1.rep1

description:
Library name: Sample-97
fig4d_tent2wt_addback_rep1_combined_Taildata.csv


title: overlap_nsRBNS_RNA_input

description: Input control for overlap nsRBNS


title: fig4d_tent2wt_addback_U1.rep3

description:
Library name: Sample-96
fig4d_tent2wt_addback_rep3_combined_Taildata.csv


title: 20--20


title: Meningioma 887

description: Hybridized to OncoScanHD


title: 21--21


title: Meningioma 880

description: Hybridized to OncoScanHD


title: 18--18


title: fig4d_tent2wt_addback_U1.rep2

description:
Library name: Sample-95
fig4d_tent2wt_addback_rep2_combined_Taildata.csv


title: Meningioma 879

description: Hybridized to OncoScanHD


title: 17--17


title: 19--19


title: UNK overlap nsRBNS, 100, rep2


title: fig4d_tent2wt_addback_U1.rep1

description:
Library name: Sample-94
fig4d_tent2wt_addback_rep1_combined_Taildata.csv


title: fig4d_tent2wt_addback_7sl.rep3

description:
Library name: Sample-93
fig4d_tent2wt_addback_rep3_combined_Taildata.csv


title: 15--15

value: inactive


title: Meningioma 878

description: Hybridized to OncoScanHD


title: 16--16


title: 14--14


title: 12--12


title: 13--13


title: Meningioma 877

description: Hybridized to OncoScanHD


title: Meningioma 876

description: Hybridized to OncoScanHD


title: 11--11


title: fig4d_tent2wt_addback_7sl.rep2

description:
Library name: Sample-92
fig4d_tent2wt_addback_rep2_combined_Taildata.csv


title: Meningioma 875

description: Hybridized to OncoScanHD


title: 10--10

value: Healthy


title: fig4d_tent2wt_addback_7sk.rep3

description:
Library name: Sample-90
fig4d_tent2wt_addback_rep3_combined_Taildata.csv


title: fig4d_tent2wt_addback_7sl.rep1

description:
Library name: Sample-91
fig4d_tent2wt_addback_rep1_combined_Taildata.csv


title: 9--9


title: 7--7


title: 8--8


title: Meningioma 873

description: Hybridized to OncoScanHD


title: 6--6


title: Meningioma 874

description: Hybridized to OncoScanHD


title: fig4d_tent2wt_addback_7sk.rep2

description:
Library name: Sample-89
fig4d_tent2wt_addback_rep2_combined_Taildata.csv


title: 5--5


title: Meningioma 872

description: Hybridized to OncoScanHD


title: fig4d_tent2dead_addback_Y3.rep3

description:
Library name: Sample-87
fig4d_tent2dead_addback_rep3_combined_Taildata.csv


title: fig4d_tent2wt_addback_7sk.rep1

description:
Library name: Sample-88
fig4d_tent2wt_addback_rep1_combined_Taildata.csv


title: 2--2


title: 4--4


title: 3--3


title: Meningioma 871

description: Hybridized to OncoScanHD


title: Meningioma 870

description: Hybridized to OncoScanHD


title: EZH2 H3K27ac

city: Rehovot

first: Ofir

last: Griess

address: Hetzel

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Assesment of quality with Fastqc
Alignment to the reference genome using Bowtie2.0
Peak calling using SEACR
Assembly: Hg39
Library strategy: CUT&Run

source_name: Pleaural effrision

growth_protocol: Samples were grown in IMDM supplemented in 20% FBS and 1% P/S and maintained at 1-2*10^6 million cells/ml

extract_protocol:
0.2m cells were extracted for chromatin-bound DNA of the approproate marks as depicted, quality was checked with tapestation and concentration was examined by qubit
All of total DNA obtained ligated with barcodes using T4 DNA polymerase (NEB). DNA was cleaned with Ampsure XP beads, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

value: Pleaural effrision

value: OCI-Ly7 EZH2 GOF

value: B

value: EZH2 Y646N

value: No


title: OCI-Ly7 HRP

value: WT


title: fig4d_tent2dead_addback_Y3.rep1

description:
Library name: Sample-85
fig4d_tent2dead_addback_rep1_combined_Taildata.csv

value: HEK 293T-REx


title: Meningioma 869

description: Hybridized to OncoScanHD

value: Brain

value: F


title: EZH2 H3K27me2


title: fig4d_tent2dead_addback_Y1.rep3

description:
Library name: Sample-84
fig4d_tent2dead_addback_rep3_combined_Taildata.csv


title: EZH2 H3K27me3


title: Meningioma 868

description: Hybridized to OncoScanHD


title: OCI-Ly7 H3K27ac


title: OCI-Ly7 H3K27me2


title: fig4d_tent2dead_addback_Y1.rep2

description:
Library name: Sample-83
fig4d_tent2dead_addback_rep2_combined_Taildata.csv


title: OCI-Ly7 H3K27me3


title: Meningioma 867

description: Hybridized to OncoScanHD


title: Meningioma 866

description: Hybridized to OncoScanHD


title: fig4d_tent2dead_addback_Y1.rep1

description:
Library name: Sample-82
fig4d_tent2dead_addback_rep1_combined_Taildata.csv


title: Meningioma 865

description: Hybridized to OncoScanHD

value: M


title: fig4d_tent2dead_addback_U1.rep3

description:
Library name: Sample-81
fig4d_tent2dead_addback_rep3_combined_Taildata.csv


title: Meningioma 864

description: Hybridized to OncoScanHD


title: fig4d_tent2dead_addback_U1.rep2

description:
Library name: Sample-80
fig4d_tent2dead_addback_rep2_combined_Taildata.csv


title: fig4d_tent2dead_addback_7sl.rep3

description:
Library name: Sample-78
fig4d_tent2dead_addback_rep3_combined_Taildata.csv


title: Meningioma 863

description: Hybridized to OncoScanHD


title: Meningioma 862

description: Hybridized to OncoScanHD


title: fig4d_tent2dead_addback_7sl.rep1

description:
Library name: Sample-76
fig4d_tent2dead_addback_rep1_combined_Taildata.csv


title: Meningioma 861

description: Hybridized to OncoScanHD


title: fig4d_tent2dead_addback_Y3.rep2

description:
Library name: Sample-86
fig4d_tent2dead_addback_rep2_combined_Taildata.csv


title: fig4d_tent2dead_addback_U1.rep1

description:
Library name: Sample-79
fig4d_tent2dead_addback_rep1_combined_Taildata.csv


title: fig4d_tent2dead_addback_7sl.rep2

description:
Library name: Sample-77
fig4d_tent2dead_addback_rep2_combined_Taildata.csv


title: Meningioma 860

description: Hybridized to OncoScanHD


title: fig4d_tent2dead_addback_7sk.rep3

description:
Library name: Sample-75
fig4d_tent2dead_addback_rep3_combined_Taildata.csv


title: 1--1


title: fig4d_tent2dead_addback_7sk.rep1

description:
Library name: Sample-73
fig4d_tent2dead_addback_rep1_combined_Taildata.csv


title: Meningioma 857

description: Hybridized to OncoScanHD


title: fig4d_tent2dead_addback_7sk.rep2

description:
Library name: Sample-74
fig4d_tent2dead_addback_rep2_combined_Taildata.csv


title: Meningioma 856

description: Hybridized to OncoScanHD


title: Meningioma 858

description: Hybridized to OncoScanHD


title: Meningioma 855

description: Hybridized to OncoScanHD


title: fig4c_siTent2_Y3.rep2

description:
Library name: Sample-71
fig4c_siTent2_rep2_combined_Taildata.csv


title: fig4c_siTent2_Y3.rep1

description:
Library name: Sample-70
fig4c_siTent2_rep1_combined_Taildata.csv


title: Meningioma 853

description: Hybridized to OncoScanHD


title: fig4c_siTent2_Y1.rep3

description:
Library name: Sample-69
fig4c_siTent2_rep3_combined_Taildata.csv


title: Meningioma 852

description: Hybridized to OncoScanHD


title: fig4c_siTent2_Y3.rep3

description:
Library name: Sample-72
fig4c_siTent2_rep3_combined_Taildata.csv


title: fig4c_siTent2_Y1.rep2

description:
Library name: Sample-68
fig4c_siTent2_rep2_combined_Taildata.csv


title: Meningioma 851

description: Hybridized to OncoScanHD


title: Meningioma 854

description: Hybridized to OncoScanHD


title: fig4c_siTent2_Y1.rep1

description:
Library name: Sample-67
fig4c_siTent2_rep1_combined_Taildata.csv


title: fig4c_siTent2_U1.rep3

description:
Library name: Sample-66
fig4c_siTent2_rep3_combined_Taildata.csv


title: Meningioma 850

description: Hybridized to OncoScanHD


title: fig4c_siTent2_U1.rep2

description:
Library name: Sample-65
fig4c_siTent2_rep2_combined_Taildata.csv


title: fig4c_siTent2_U1.rep1

description:
Library name: Sample-64
fig4c_siTent2_rep1_combined_Taildata.csv


title: Meningioma 859

description: Hybridized to OncoScanHD


title: Meningioma 848

description: Hybridized to OncoScanHD


title: F2_RNA_EV_RBCs

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation method was . RNA Isolation kit was miRNeasy (Qiagen).
Library construction kit was Other. Samples were not multiplexed. Type of Starting Material was total RNA.

tag: individual

value: Plasma

value: RBCs

tag: condition

value: Healthy Control

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: miRNeasy (Qiagen)


title: M2_RNA_EV_RBCs


title: Meningioma 847

description: Hybridized to OncoScanHD

source_name: Meningioma Tissue


title: Meningioma 849

description: Hybridized to OncoScanHD


title: M2_RNA_EV_Neut

value: Neut


title: F2_RNA_EV_Plat

value: Plat


title: fig4c_siTent2_7sl.rep3

description:
Library name: Sample-63
fig4c_siTent2_rep3_combined_Taildata.csv


title: Meningioma 846

description: Hybridized to OncoScanHD


title: fig4c_siTent2_7sl.rep2

description:
Library name: Sample-62
fig4c_siTent2_rep2_combined_Taildata.csv


title: fig4c_siTent2_7sl.rep1

description:
Library name: Sample-61
fig4c_siTent2_rep1_combined_Taildata.csv


title: M1_RNA_EV_RBCs


title: F1_RNA_EV_Neut


title: M2_RNA_EV_Plat


title: fig4c_siTent2_7sk.rep3

description:
Library name: Sample-60
fig4c_siTent2_rep3_combined_Taildata.csv


title: Meningioma 845

description: Hybridized to OncoScanHD


title: F2_RNA_EV_Neut


title: Meningioma 844

description: Hybridized to OncoScanHD


title: M1_RNA_EV_Plat


title: Meningioma 843

description: Hybridized to OncoScanHD


title: fig4c_siTent2_7sk.rep1

description:
Library name: Sample-58
fig4c_siTent2_rep1_combined_Taildata.csv


title: M1_RNA_EV_Neut


title: F1_RNA_EV_Plat


title: Non Treated EC miR 409 mimic-3

city: BOSTON

first: BASAK

last: ICLI

address: 800 Washington St Box 80

department: MOLECULAR CARDIOLOGY RESEARCH INSTITUTE

institute: TUFTS MEDICAL SCHOOL

data_processing:
Qiagen RNA-Seq Analysis Portal
First, all annotated transcripts are extracted (using anmRNAtrack). If there are several annotated splice variants, they are all extracted.
Next, the reads are mapped against all the transcripts plus to the whole genome. From this mapping, the reads are categorized and assigned to the genes using the EM estimation algorithm , and expression values for each gene and each transcript are calculated.
Each gene is modeled by a separate Generalized Linear Model (GLM) assuming that the read counts follow a Negative Binomial distribution.
The final GLM fit and dispersion used to calculate the total likelihood of the model given the data, and the uncertainty on each fitted coefficient. The two statistical tests, Wald test and Likelihood Ratio test, each make use of one of these values.
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: Tab-delimited text (.txt) files include Identifier (Ensembl ID numbers) and TPM (Transcript per Million) values for each gene

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (Lonza, CC-2519) passaged three times were used for all experiments and cultured in growth media EGM®-2 (Lonza, CC-3162)

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen, #74104). 500ng of total RNA was used for the construction of sequencing libraries.
From 500ng starting material, the mRNA was enriched and fragmented using enzymatic fragmentation. After first and second strand synthesis, the cDNA was end-repaired and 3’ adenylated. Sequencing adapters were ligated to the overhangs.
Adapted molecules were enriched using by 13 cycles or PCR and purified by a bead based cleanup. The libraries size distribution was validated and quality inspected on a TapeStation (Agilent Technologies). High quality libraries are pooled based in equimolar concentrations based on the Bioanalyzer automated electrophoresis system (Agilent Technologies).
The library pool(s) were quantified using qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on a NextSeq500/550 instrument (1x75 cycles) according to the manufacturer instructions (Illumina Inc.).

treatment_protocol: For transfection studies, HUVECs plated at 50,000 cells/ml were cultured overnight before being transfected with Lipofectamine™ 2000 transfection reagent (Invitrogen, 52887) and either 50nM miR-409-3p mimic (Thermo Scientific, 4464066) or non-specific control (Thermo Scientific, 4464058) in accordance with manufacturer’s instructions.

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: miR-409-3p mimic

tag: time

value: 48 hours

tag: replicate

value: Biological Replicate 3


title: Non Treated EC miR 409 mimic-2

value: WT

value: Biological Replicate 2


title: fig4c_siLuc_Y3.rep3

description:
Library name: Sample-57
fig4c_siLuc_rep3_combined_Taildata.csv

source_name: HEK 293T-REx

value: HEK 293T-REx


title: Non Treated EC miR 409 mimic-1

value: Biological Replicate 1


title: Non Treated EC Control-3

value: non-specific control


title: Meningioma 841

description: Hybridized to OncoScanHD

data_processing:
Data analysis was performed using Chromosome Analysis Suite software version 1.2.2
[primary data description] Fluorescent intensity values across SNP probes

tag: tissue

value: Brain

value: M


title: Meningioma 840

description: Hybridized to OncoScanHD

tag: Sex

value: F


title: fig4c_siLuc_Y3.rep2

description:
Library name: Sample-56
fig4c_siLuc_rep2_combined_Taildata.csv

data_processing:
FASTQ files were first subjected to 3’ adaptor, PCR duplicate removal, and gene-specific barcode and primer sequence removal using custom python scripts (https://pypi.org/project/jla-demultiplexer/).
Reads were aligned to small RNAs of interest using in-house alignment scripts.
Gene-specific 3’ end information and graphs were subsequently generated using in-house scripts.
For SLAMseq, gene-specific alignments were performed using in-house scripts which permitted T>C conversions. The number of conversions for each read was quantified and reads with two or more conversions were subsequently analyzed as nascently-labeled reads.
Assembly: human genome (version hg38)
Supplementary files format and content: comma separated variable table with RNA counts, 3' end position, and 3' post-transcriptional nucleotides


title: Meningioma 842

description: Hybridized to OncoScanHD

tag: age


title: Non Treated EC Control-1

tag: cell line


title: Non Treated EC Control-2

tag: treatment


title: F1_RNA_EV_RBCs

value: Plasma

value: RBCs

value: Healthy Control

value: Entire cardiovascular system

value: extracellular vesicle


title: fig4c_siLuc_Y3.rep1

description:
Library name: Sample-55
fig4c_siLuc_rep1_combined_Taildata.csv


title: GBM53, scRNAseq

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: grch38
Supplementary files format and content: Tab-separated count file, UMI counts from filtered bc matrices output from Cell Ranger.

source_name: resected glioblastoma

extract_protocol:
Tissue collection was performed under approved IRB study 20170887 (MODCR00002196). University of Miami Hospital pathologists separated resected tissue into three spatially distinct groups, namely the necrotic core, enhancing edge, and infiltrating tumor. The tissue was transferred from the operating suite to the laboratory on ice. Tissue from the enhancing edge was used for dissociation and single-cell RNA sequencing. Tumor samples were dissociated using the Worthington Biochemical Papain Dissociation System.16 Tumor tissue was finely minced with a sterile surgical blade and incubated in sterile Earl’s Balanced Salt Solution (EBSS) containing 20 units of papain per mL in 1 mM L-cysteine with 0.5mM EDTA and DNase for 45 minutes at 37 °C while shaking. Following papain incubation, the tissue was gently triturated with a 5 mL serological pipette until it was adequately dissociated. The resulting suspensions were pelleted and resuspended in EBSS with ovomucoid protease inhibitor, bovine serum albumin (BSA), and DNase. This suspension was layered on top of ovomucoid protease inhibitor solution with BSA to form a gradient, which was centrifuged at 70xg for 6 minutes. The supernatant, which contained cellular debris, was removed. The pellets were resuspended, and the gradient centrifugation was repeated. The resulting pellet was then washed 2 times with ice cold PBS with 0.1% BSA, passed through a 0.45 μM cell strainer, and resuspended in ice cold PBS with 0.1% BSA. This resulting suspension was then checked for cell viability by staining an aliquot with acridine orange and propidium iodide (AO/PI) and counted on a Nexcelom K2 Cellometer. All samples had cell viability greater than 90% prior to loading of the single-cell chips.
Single cells were captured using a 10X Genomics Chromium Controller, and patient single-cell gene expression libraries were prepared using 10X Genomics 5’ Gene Expression chemistry.

value: resected glioblastoma


title: Meningioma 839

description: Hybridized to OncoScanHD

extract_protocol: DNA was extracted using the QIAamp DNA FFPE Tissue Kit and stored at 4˚C


title: fig4c_siLuc_Y1.rep3

description:
Library name: Sample-54
fig4c_siLuc_rep3_combined_Taildata.csv

extract_protocol:
RNA was isolated using TRIzol (Thermo Fisher) per manufacturer’s recommendation. RNA was subsequently treated with DNase I (1 U/µl; Zymo research) in DNase buffer (10 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 0.5 mM CaCl2) at 25˚ C for 15 minutes, followed by extraction with phenol:chloroform:isoamyl alcohol and ethanol precipitation. For RNA immunoprecipitations, cells were harvested by scraping into ice cold PBS and flash frozen in liquid nitrogen. Cells were resuspended in ice-cold isotonic lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% Triton X-100, 80 U/mL RNaseOut (Thermo Fisher), protease inhibitor tablet/10 mL (Roche)) and incubated with rotation for 20 minutes at 4°C. Cellular debris was pelleted at 13,000 g for 15 minutes at 4°C. The supernatant was briefly pre-cleared using Protein G beads (Thermo Fisher, 10004D) for 10 minutes at 4°C with rotation. Beads for immunoprecipitation were washed with bead wash buffer (PBS pH 7.4, 0.1% Tween 20) and subsequently incubated with anti-La antibody (Santa Cruz Biotechnology, sc-80656), anti-SRP54 antibody (Invitrogen, MA5-34835), rabbit IgG (Cell Signaling Technology, 2729), or mouse IgG1 (Cell Signaling Technology, 5415) antibody for 1 hour at 4°C with rotation, then washed with bead wash buffer. Sample protein was quantified with a BCA assay (Thermo Fisher). 1 mg of protein per sample was diluted 5-fold with ice-cold detergent dilution buffer (isotonic lysis buffer without Triton X-100) and incubated with antibody-bead complexes for 1 hour at 4°C with rotation. Samples were washed 5 times with ice-cold immunoprecipitation wash buffer (PBS pH 7.4, 0.1% Tween 20, 150 mM NaCl) at 4°C. RNA from input and immunoprecipitation material was extracted with TRIzol (Thermo Fisher) according to the manufacturer’s recommendation. For SLAMSeq, samples were treated with either iodoacetamide (IAA) or dimethylsulfoxide (DMSO) for 15 minutes at 50°C prior to 3' adaptor ligation. Gene-specific 3’-end sequencing libraries were prepared as described above.
RNA adapters containing barcodes and 10- to 16-nt randomers (AG10/AG11/AG15/AG16) were ligated to the 3′ ends of 2 μg of extracted RNA in a 10-μL reaction containing 1 μL of 10xT4 RNA ligase buffer (500 mM Tris-HCl, 100 mM MgCl2, 10 mM DTT at pH at 25°C), 0.2 mg/mL bovine serum albumin (BSA), 2 μM AG10 or AG11, 1 mM ATP, 10 U of T4 RNA ligase (NEB), and 40 units of RNaseOUT (Invitrogen) for 16 h at 16°C and extracted with phenol/chloroform/isoamyl alcohol. cDNA was generated using SuperScript III (SSRT III; Thermo Fisher) in a 20-μL reaction using 0.5 μM linker-specific primer AR-17. For sequencing, snRNA cDNA 3′ ends were amplified in 16–30 cycles of polymerase chain reaction (PCR) with small RNA gene-specific forward primers and AR17 primer using Q5 DNA polymerase (NEB), and then eight cycles with primers D50x and D70x. Libraries were sequenced on an Illumina MiSeq platform.


title: fig4c_siTent2_7sk.rep2

description:
Library name: Sample-59
fig4c_siTent2_rep2_combined_Taildata.csv


title: GBM49, scRNAseq

description: 10x Genomics


title: GBM47, scRNAseq

description: 10x Genomics


title: GBM41, scRNAseq

description: 10x Genomics


title: Meningioma 838

description: Hybridized to OncoScanHD


title: fig4c_siLuc_Y1.rep2

description:
Library name: Sample-53
fig4c_siLuc_rep2_combined_Taildata.csv


title: GBM21, scRNAseq

description: 10x Genomics


title: L-MCC18

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University Medical Center

data_processing:
Bcl2fastq v2.20
The sequencing output (fastq.gz-files) was aligned using the splice-aware aligner STAR (version:2.4.5b) by using hg19 as reference for the alignment (GRCh37.87).
The obtained fastq.gz files  for the tissues were merged together.
The alignment was done as 2-pass experiment as described in the TCGA project (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline).
The free available transcript assembly and RNA sequencing quantification tool StringTie (1.3.5) was used with the default parameters and a reference gtf-file of hg19 (GRCh37.87) to identify known and potential new isoforms. This information was utilized to extract the genomic regions of all identified isoforms from PAX5. The samtools (0.1.19) functions “view” and “depth” were then applied to extract the sequencing depth value for each position from the alignment output (bam-files). The normalized counts were extracted for the eleven PAX5 exons for the three MCC cell lines and plotted in box plots using the python 3 package seaborn 0.11.256. The significance of the exon count difference was estimated by using scikit_posthoc 0.6.7 t-test and was illustrated using the sign_plot feature57. Moreover, StringTie was used to calculate the TPM-values for the expression of each identified gene for each sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each sample
Supplementary files format and content: tab-delimited text files include normalized PAX5 exon count values for each Sample

source_name: axillary lymph node

extract_protocol:
RNA was harvested using Allprep DNA/RNA Mini Kit (Qiagen).  500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared  NEB Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols using rRNA depletionThe tissue sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB, Great Britain). Briefly, rRNA was depleted from total RNA using the rRNA depletion kit (NEB, Great Britain).

value: axillary lymph node

tag: primary or_metastasis

value: metastasis


title: L-MCC17

source_name: skin

value: skin

value: primary


title: Meningioma 836

first: Scott

last: Ryall

address: 75 Francis Street

institute: Brigham and Women's Hospital

description: Hybridized to OncoScanHD


title: fig4c_siLuc_Y1.rep1

first: Cody

last: Ocheltree

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: Sample-52
fig4c_siLuc_rep1_combined_Taildata.csv


title: L-MCC15

source_name: upper arm

value: upper arm


title: fig4c_siLuc_U1.rep2

description:
Library name: Sample-50
fig4c_siLuc_rep2_combined_Taildata.csv

value: HEK 293T-REx


title: Meningioma 834

description: Hybridized to OncoScanHD


title: fig4c_siLuc_U1.rep3

description:
Library name: Sample-51
fig4c_siLuc_rep3_combined_Taildata.csv


title: L-MCC12


title: L-MCC14


title: Meningioma 835

description: Hybridized to OncoScanHD


title: L-MCC16

description:
L-MCC16
MCC8 and MCC16 from the same patient

source_name: inguinal lymph node

value: inguinal lymph node


title: GBM51, scRNAseq

description: 10x Genomics


title: L-MCC8

description:
L-MCC8
MCC8 and MCC16 from the same patient

source_name: upper leg

value: upper leg


title: fig4c_siLuc_U1.rep1

description:
Library name: Sample-49
fig4c_siLuc_rep1_combined_Taildata.csv


title: L-MCC13

source_name: face

value: face


title: L-MCC11

source_name: gluteal area

value: gluteal area


title: fig4c_siLuc_7sl.rep3

description:
Library name: Sample-48
fig4c_siLuc_rep3_combined_Taildata.csv


title: Meningioma 833

description: Hybridized to OncoScanHD

value: Brain

value: F


title: Meningioma 837

description: Hybridized to OncoScanHD

value: M


title: L-MCC6

description:
L-MCC6
MCC5 and MCC6 from the same patient


title: L-MCC5

description:
L-MCC5
MCC5 and MCC6 from the same patient

source_name: lower leg

value: lower leg


title: fig4c_siLuc_7sl.rep1

description:
Library name: Sample-46
fig4c_siLuc_rep1_combined_Taildata.csv


title: L-MCC4


title: L-MCC7

description:
L-MCC7
MCC7 and MCC10 from the same patient


title: Meningioma 830

description: Hybridized to OncoScanHD


title: fig4c_siLuc_7sl.rep2

description:
Library name: Sample-47
fig4c_siLuc_rep2_combined_Taildata.csv


title: Meningioma 831

description: Hybridized to OncoScanHD


title: L-MCC2

source_name: para-aortic lymph node

value: para-aortic lymph node


title: AREx4

city: Tsukuba

first: Takehito

last: Sugasawa

state: Select State

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
RNA-seq reads were using CLC genomics workbench 24.0 with the default settings.
Assembly: GRCm39
Supplementary files format and content: Excel file of statistic test and expression data

source_name: Synovial membrane and fat pad complex

extract_protocol:
RNA were extracted from synovial membrane and fad pad complex tissue, using Rneasy Plus Mini Kit (Cat#74134; QIAGEN)
Llibrary was constracted using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext Poly(A) mRNA Magnetic Isorlation Module (Cat# E7770L and E7490; New England Biolabs).

value: Synovial membrane and fat pad complex

value: tissue

tag: cell type

value: synovial cell, adipocyte


title: Meningioma 829

description: Hybridized to OncoScanHD


title: fig4c_siLuc_7sk.rep3

description:
Library name: Sample-45
fig4c_siLuc_rep3_combined_Taildata.csv


title: Meningioma 828

description: Hybridized to OncoScanHD


title: fig4c_siLuc_7sk.rep2

description:
Library name: Sample-44
fig4c_siLuc_rep2_combined_Taildata.csv


title: AREx3


title: fig4c_siLuc_7sk.rep1

description:
Library name: Sample-43
fig4c_siLuc_rep1_combined_Taildata.csv


title: AREx2


title: Meningioma 827

description: Hybridized to OncoScanHD


title: L-MCC10

description:
L-MCC10
MCC7 and MCC10 from the same patient

source_name: subcutis

value: subcutis

value: metastasis


title: fig4b_tent2ko_Y3.rep3

description:
Library name: Sample-42
fig4b_tent2ko_rep3_combined_Taildata.csv


title: AREx1


title: Meningioma 826

description: Hybridized to OncoScanHD


title: Xenograft from HeLa cells, 11

city: Ciudad de México

first: Alfredo

last: Hidalgo-Miranda

state: CDMX

address: Periferico Sur #4809

department: Cancer Genomic

country: Mexico

institute: INMEGEN

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). GeneChips were scanned using The Genechip Scanner 3000 7G (Affymetrix , Santa Clara, USA).

data_processing: Array signal intensitive were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.

label: biotin

source_name: Mouse treated with vehicle (water) by 24 days, 2

label_protocol: The GeneChip™ WT Pico Reagent Kit used to generate the biotinylated cRNA starting from 100 pg of total RNA according to the manufacturer (Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays).

growth_protocol: NOD-SCID mice were xenotransplanted subcutaneously with HeLa cells 1.5X106 cells) and after 2 weeks of inoculation, were treated with metformin 525mg/kg/day for 11 days and for 24 days, the control group received drinking water. Tumor size was measured twice every third day and tumor volume was calculated. After completion of the metformin treatment, all NOD-SCID mice were euthanized in a compressed CO2 chamber, and tumors were extracted through a cut made in the skin and they were measured, weighed and photo-documented. One part of the tumor tissue was dissected and frozen in liquid nitrogen for RNA extraction.

extract_protocol: Total RNA was extracted from snap frozen tumor tissue using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer´s recommendations.

treatment_protocol: The NOD-SCID mice with xenotransplant were treated with metformin 525mg/kg/day for 11 days (2s) and for 24 days (4s), the control group received drinking water (Vehicle).

tag: metformin treatment

value: Vehicle, 24 days


title: fig4b_tent2ko_Y3.rep2

description:
Library name: Sample-41
fig4b_tent2ko_rep2_combined_Taildata.csv


title: Xenograft from HeLa cells, 12

source_name: Mouse treated with vehicle (water) by 24 days, 3


title: AR4


title: Meningioma 825

city: Boston

description: Hybridized to OncoScanHD

source_name: Meningioma Tissue


title: Xenograft from HeLa cells, 9

source_name: Mouse treated with metformin 525mg/kg/day by 24 days, 3

value: Treated, 24 days


title: Meningioma 824

description: Hybridized to OncoScanHD


title: fig4b_tent2ko_Y1.rep3

city: La Jolla

description:
Library name: Sample-39
fig4b_tent2ko_rep3_combined_Taildata.csv

source_name: HEK 293T-REx

value: HEK 293T-REx


title: Xenograft from HeLa cells, 10

source_name: Mouse treated with vehicle (water) by 24 days, 1


title: AR3


title: fig4b_tent2ko_Y3.rep1

description:
Library name: Sample-40
fig4b_tent2ko_rep1_combined_Taildata.csv


title: fig4b_tent2ko_Y1.rep2

description:
Library name: Sample-38
fig4b_tent2ko_rep2_combined_Taildata.csv


title: AR2


title: Meningioma 823

description: Hybridized to OncoScanHD


title: Meningioma 822

description: Hybridized to OncoScanHD


title: Xenograft from HeLa cells, 7

source_name: Mouse treated with metformin 525mg/kg/day by 24 days, 1


title: fig4b_tent2ko_Y1.rep1

description:
Library name: Sample-37
fig4b_tent2ko_rep1_combined_Taildata.csv


title: Meningioma 821

description: Hybridized to OncoScanHD


title: Sedentary3


title: Meningioma 820

description: Hybridized to OncoScanHD


title: Xenograft from HeLa cells, 6

source_name: Mouse treated with vehicle (water) by 11days, 3

value: Vehicle, 11 days


title: Xenograft from HeLa cells, 5

source_name: Mouse treated with vehicle (water) by 11days, 2


title: Sedentary2


title: fig4b_tent2ko_U2.rep1

description:
Library name: Sample-34
fig4b_tent2ko_rep1_combined_Taildata.csv


title: Xenograft from HeLa cells, 3

source_name: Mouse treated with metformin 525mg/kg/day by 11days, 3

value: Treated, 11 days


title: Meningioma 832

description: Hybridized to OncoScanHD


title: Meningioma 819

description: Hybridized to OncoScanHD


title: Xenograft from HeLa cells, 4

source_name: Mouse treated with vehicle (water) by 11days, 1


title: Sedentary1


title: Meningioma 818

description: Hybridized to OncoScanHD


title: Xenograft from HeLa cells, 2

source_name: Mouse treated with metformin 525mg/kg/day by 11days, 2


title: AR1


title: fig4b_tent2ko_U1.rep2

description:
Library name: Sample-32
fig4b_tent2ko_rep2_combined_Taildata.csv


title: Xenograft from HeLa cells, 8

source_name: Mouse treated with metformin 525mg/kg/day by 24 days, 2


title: A2

city: nanjing

first: wenbo

last: zhang

state: jiangsu

address: jiangning longmiandadao 639

institute: China Pharmaceutical University

description: Library name: Sample 11

data_processing:
Data Quality Control: Utilize fastp to filter the raw sequencing data, focusing on the removal of reads containing adapters.Discard paired reads if the N content in any sequencing read exceeds 10% of the total base count.Remove paired reads if the number of low-quality bases (with a quality score Q<=20) in any sequencing read surpasses 50% of the total bases.All subsequent analyses are conducted using the cleaned reads.
Reads Mapping to the Reference Genome: Following quality control, the clean reads are mapped to a reference genome. The reference genome and its annotation files are downloaded from a designated website, and HISAT is used to construct an index for efficient read alignment.
New Transcript Prediction: StringTie is employed for the prediction of new transcripts. This tool uses network streaming algorithms and can perform de novo splicing to assemble transcripts. It is chosen for its ability to produce more accurate and complete transcripts compared to other software like Cufflinks, and for its faster processing speed.
Quantification of Gene Expression Levels: Gene expression levels are quantified using featureCounts, which tallies the number of reads aligned to each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) is then calculated for each gene, taking into account the gene length, to estimate gene expression levels. FPKM is a common metric for gene expression analysis.
Differential Expression Analysis: DESeq2 is used to identify genes that are differentially expressed between two groups. The analysis corrects for multiple testing using the Benjamini & Hochberg method, and significant differential expression is determined by thresholds set for the corrected P value and the absolute value of the log2 fold change. This step helps to identify genes with expression levels that significantly differ between the compared groups.
Assembly: ftp://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/
Supplementary files format and content: "Processed data file" include FPKM values and raw counts for each Sample

extract_protocol:
RNA was were extracted by Trizol method；
A total amount of 1 ug RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ul USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: Mouse melanoma cells


title: A3

description: Library name: Sample 12


title: Meningioma 817

description: Hybridized to OncoScanHD


title: Sedentary4


title: Meningioma 816

description: Hybridized to OncoScanHD


title: fig4b_tent2ko_U2.rep3

description:
Library name: Sample-36
fig4b_tent2ko_rep3_combined_Taildata.csv


title: Trbp-cKO; TAC Surgery;Rep3

city: Los Angeles

first: Yao Wei

last: Lu

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

description: Library name: TT1_3

data_processing:
FASTQ files were extracted and the TruSeq sequencing adapters and low-quality reads were removed from FASTQ files with Cutadapt (v.2.3). The cleaned FASTQ files were quality checked using FastQC (Babraham Bioinformatics), then aligned to the genome (GRCm38 obtained from GENCODE) using HISAT2 (v.2.1.0). Subsequently, transcript assembly was performed using StringTie (v.1.3.4) with the annotated transcriptome as a reference.
Assembly: GRCm38
Supplementary files format and content: csv; raw gene count matrix for each sample

source_name: heart ventricle

extract_protocol:
RNA from mouse hearts ~8-week after either sham or TAC surgery was prepared for gene expression profiling (4 biological replicates for each group). Total cardiac RNAs were isolated from fresh ventricular tissue using TRIzol (ThermoFisher Scientific).
The RNA-sequencing was processed by GENEWIZ using Illumina platform (paired-ended, 150bp read-length)

treatment_protocol: Mice were anesthetized with isoflurane delivered using a scavenger-equipped calibrated vaporizer. Induction was performed in an induction chamber with an initial vaporizer setting of 3-5%. Animals were removed from the chamber after induction and placed on a rodent-specific nose cone apparatus with maintenance anesthesia provided using an isoflurane vaporizer setting of 1-2%. The chest was shaved and cleaned with alcohol. A suture was placed around the front upper incisors and pulled taut so that the neck was slightly extended. The tongue was retracted and held with forceps, and a 20-gauge catheter was inserted into the trachea. The catheter was then attached to the mouse ventilator via a Y-shaped connector. Ventilation was performed with a tidal volume of 220 to 240 μl for a 25–30 g mouse and a respiratory rate of 130 to 140 breaths per minute. 100% oxygen was provided to the inflow of the ventilator. The chest was opened through a left second intercostal thoracotomy. The 26-gauge needle without its sharp tip was placed on the ascending aorta. The needle and the ascending aorta were tightly ligated together using a 7-0 nylon suture (Ethicon) at the position between the brachiocephalic artery and the common carotid artery, and the 26-gauge needle was removed immediately after ligation. In the sham operation, no ligation was performed. Isoflurane was stopped, and the lungs were slightly overinflated to assist in removal of air in the pleural cavity. Dissected intercostal space and chest skin were closed using a 6-0 silk suture (Ethicon). All manipulations were performed by an operator without knowledge of the genotype.

value: heart ventricle

tag: genotype

value: aMHC-MerCreMer;Trbp-Flox/Flox

value: Tamoxifen


title: A1

description: Library name: Sample 10


title: fig4b_tent2ko_U2.rep2

description:
Library name: Sample-35
fig4b_tent2ko_rep2_combined_Taildata.csv


title: Meningioma 815

description: Hybridized to OncoScanHD

value: Brain

value: F


title: Trbp-cKO; TAC Surgery;Rep2

description: Library name: TT1_2


title: fig4b_tent2ko_U11.rep3

description:
Library name: Sample-30
fig4b_tent2ko_rep3_combined_Taildata.csv


title: Meningioma 814

description: Hybridized to OncoScanHD


title: Q3

description: Library name: Sample 9


title: fig4b_tent2ko_U1.rep3

description:
Library name: Sample-33
fig4b_tent2ko_rep3_combined_Taildata.csv


title: Trbp-cKO; TAC Surgery;Rep1

description: Library name: TT1_1


title: fig4b_tent2ko_U11.rep2

description:
Library name: Sample-29
fig4b_tent2ko_rep2_combined_Taildata.csv


title: Trbp-cKO; TAC Surgery;Rep4

description: Library name: TT1_4


title: Meningioma 813

description: Hybridized to OncoScanHD


title: Q2

description: Library name: Sample 8


title: Trbp-cKO; Sham Surgery;Rep4

description: Library name: TS3_4


title: Q1

description: Library name: Sample 7


title: fig4b_tent2ko_U1.rep1

description:
Library name: Sample-31
fig4b_tent2ko_rep1_combined_Taildata.csv


title: fig4b_tent2ko_7sl.rep3

description:
Library name: Sample-27
fig4b_tent2ko_rep3_combined_Taildata.csv


title: Trbp-cKO; Sham Surgery;Rep3

description: Library name: TS3_3


title: fig4b_tent2ko_U11.rep1

description:
Library name: Sample-28
fig4b_tent2ko_rep1_combined_Taildata.csv


title: Meningioma 811

description: Hybridized to OncoScanHD


title: P3

description: Library name: Sample 6


title: Xenograft from HeLa cells, 1

source_name: Mouse treated with metformin 525mg/kg/day by 11days, 1


title: Trbp-cKO; Sham Surgery;Rep2

description: Library name: TS3_2


title: Meningioma 810

description: Hybridized to OncoScanHD

value: M


title: fig4b_tent2ko_7sl.rep2

description:
Library name: Sample-26
fig4b_tent2ko_rep2_combined_Taildata.csv


title: fig4b_tent2ko_7sl.rep1

description:
Library name: Sample-25
fig4b_tent2ko_rep1_combined_Taildata.csv


title: Trbp-cKO; Sham Surgery;Rep1

description: Library name: TS3_1


title: Control;TAC Surgery:Rep4

description: Library name: CT2_4

value: Corn oil


title: fig4b_tent2ko_7sk.rep3

description:
Library name: Sample-24
fig4b_tent2ko_rep3_combined_Taildata.csv


title: Meningioma 808

description: Hybridized to OncoScanHD


title: V3

description: Library name: Sample 3


title: Meningioma 809

description: Hybridized to OncoScanHD


title: Control;TAC Surgery:Rep3

description: Library name: CT2_3


title: fig4b_tent2ko_7sk.rep2

description:
Library name: Sample-23
fig4b_tent2ko_rep2_combined_Taildata.csv


title: V2

description: Library name: Sample 2


title: Meningioma 807

description: Hybridized to OncoScanHD


title: Control;TAC Surgery:Rep2

description: Library name: CT2_2


title: Meningioma 812

description: Hybridized to OncoScanHD


title: fig4b_tent2ko_7sk.rep1

description:
Library name: Sample-22
fig4b_tent2ko_rep1_combined_Taildata.csv


title: V1

description: Library name: Sample 1


title: Control;TAC Surgery:Rep1

description: Library name: CT2_1


title: fig4b_control_Y3.rep3

description:
Library name: Sample-21
fig4b_control_rep3_combined_Taildata.csv


title: Meningioma 805

description: Hybridized to OncoScanHD


title: 36hpf_dmut_replicate_2

city: Pittsburgh

first: Shea

middle: Alexandra

last: Heilman

address: 3501 Fifth Ave

department: Ophthalmology

institute: University of Pittsburgh

description:
Library name: 36-2_DMUT_Library_GRO2554A2
10x Genomics

data_processing:
Generation of base count matrices were generated using cellRanger(version 6.1.2). Low quality cells were removed and ambient RNA correction was performed. After ambient RNA correction, normalized logcounts were calcluated
Assembly: Danio rerio.GRCz11.106
Supplementary files format and content: matrix files

organism: Danio rerio

source_name: eye

extract_protocol:
Whole sibCTL and tet2-/-tet3-/- eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin, with genotype and timepoint-specific protocols utilized
Library was generated using manaufacturer's instructions (scRNAseq v2 3' Paired-End). For each experiment, in 2 separate wells, sibCTL and  tet2-/-tet3-/-  dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS.  Each GEM contained sufficient priming material to enable cDNA amplification of poly-adenylated mRNA molecules with cell-specific(10x barcode) and transcript-specific(UMI) tags. Pooled cDNA was then cleaned up with silane beads, and PCR amplified. After PCR amplification, cDNAs were size-selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.

value: eye


title: P2

description: Library name: Sample 5


title: Control;Sham Surgery;Rep3

description: Library name: CS4_3


title: Control;Sham Surgery;Rep4

description: Library name: CS4_4


title: 36hpf_dmut_replicate_1

description:
Library name: 36_1DMUT_LIBRARY_GRO2455A6
10x Genomics


title: fig4b_control_Y3.rep2

description:
Library name: Sample-20
fig4b_control_rep2_combined_Taildata.csv


title: P1

description: Library name: Sample 4


title: Meningioma 803

description: Hybridized to OncoScanHD


title: 36hpf_sibCTL_replicate_2

description:
Library name: 36-2_CTL_Library_GRO2554A1
10x Genomics

value: sibCTL


title: Control;Sham Surgery;Rep2

description: Library name: CS4_2


title: Meningioma 802

description: Hybridized to OncoScanHD


title: Control;Sham Surgery;Rep1

description: Library name: CS4_1


title: fig4b_control_Y1.rep2

description:
Library name: Sample-17
fig4b_control_rep2_combined_Taildata.csv


title: fig4b_control_Y3.rep1

description:
Library name: Sample-19
fig4b_control_rep1_combined_Taildata.csv


title: 36hpf_sibCTL_replicate_1

description:
Library name: 36_1CTL_LIBRARY_GRO2455A5
10x Genomics


title: 48hpf_dmut_replicate_2

description:
Library name: D48_2_GRO1775A18
10x Genomics


title: Meningioma 806

description: Hybridized to OncoScanHD


title: fig4b_control_Y1.rep1

description:
Library name: Sample-16
fig4b_control_rep1_combined_Taildata.csv


title: fig4b_control_U2.rep3

description:
Library name: Sample-15
fig4b_control_rep3_combined_Taildata.csv


title: Ins1Cre_NRK1_Islet_WT_13155

city: Lausanne

first: Carles

last: Canto

address: Ecole Polytechnique Fédérale de Lausanne

country: Switzerland

data_processing:
mapping to the mouse reference genome using STAR v2.5.2
counting using Htseq-count v0.6.1
DEG analysis using edgeR R package
Assembly: mus musculus GRCm38
Supplementary files format and content: log2_norm_HFD.csv, normalized gene expression matrix on the log2 scale

source_name: pancreatic islets

extract_protocol:
For RNA extraction, islets were placed in a Matrix D tube (MP Biomedicals) with 600ul of lysis buffer from Agencourt RNAdvance Tissue Kit (Beckman Coulter). Samples were homogenized twice for 1 minute at speed 6 on FastPrep-24™ (MP Biomedicals). Total RNA was extracted using the Agencourt RNAdvance Tissue Kit (Beckman Coulter) following the manufacturer’s instruction. Total RNA was quantified using the Quant-iT™ RiboGreen™ RNA Assay Kit (Invitrogen) on a Spectramax M2 (Molecular Devices). Total RNA quality was assessed with Fragment Analyzer-96 using DNF-471-0500 Standard Sensitivity RNA Analysis Kit (Agilent Technologies).
Next, 50ng of total RNA (8.9<RQN<10) were used to generate the libraries using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following 20 cycles of PCR amplification. Libraries were quantified using the Quant-iT™ Picogreen (Invitrogen) on a Spectramax M2 (Molecular Devices). Size pattern was assessed with Fragment Analyzer-96 using DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies). Libraries (average size of 242bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pmol on a single read sequencing flow cell. 65 cycles of sequencing were performed on an Illumina HiSeq 2500 in rapid mode using a 50 cycles SBS kit (Illumina) according to manufacturer’s instruction.

treatment_protocol: Both WT and NRK1 Ins1Cre KO mice were submitted on high fat diet for 12 weeks. Pancretic islets were collected at the sacrifice and used to extract RNA for transcriptomic analysis.

value: pancreatic islets

value: islets

value: HFD


title: Meningioma 799

description: Hybridized to OncoScanHD


title: Meningioma 804

description: Hybridized to OncoScanHD


title: Meningioma 801

description: Hybridized to OncoScanHD


title: Ins1Cre_NRK1_Islet_WT_13154

institute: Ecole Polytechnique Fédérale de Lausanne


title: fig4b_control_U2.rep2

description:
Library name: Sample-14
fig4b_control_rep2_combined_Taildata.csv


title: Meningioma 798

description: Hybridized to OncoScanHD