title: 48hpf_sibCTL_replicate_1

description:
Library name: C48_1_GRO1775A15
10x Genomics


title: Ins1Cre_NRK1_Islet_WT_13147

status: Public on Jan 31 2025

type: SRA

city: Lausanne

first: Carles

last: Canto

address: Ecole Polytechnique Fédérale de Lausanne

country: Switzerland

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: pancreatic islets

tag: cell line

tag: cell type

value: islets

tag: genotype

tag: treatment

value: HFD


title: Ins1Cre_NRK1_Islet_WT_13129

institute: Ecole Polytechnique Fédérale de Lausanne


title: Meningioma 797

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

value: Brain

tag: Sex

value: F

tag: age


title: fig4b_control_Y1.rep3

city: La Jolla

first: Cody

last: Ocheltree

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: Sample-18
fig4b_control_rep3_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.

value: HEK 293T-REx


title: fig4b_control_U1.rep3

description:
Library name: Sample-12
fig4b_control_rep3_combined_Taildata.csv


title: Meningioma 796

description: Hybridized to OncoScanHD


title: 72hpf_dmut_replicate_1

city: Pittsburgh

first: Shea

middle: Alexandra

last: Heilman

state: PA

address: 3501 Fifth Ave

department: Ophthalmology

institute: University of Pittsburgh

description:
Library name: D72_1_GRO1775A20
10x Genomics

library_source: transcriptomic single cell

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

molecule: polyA RNA

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: 72hpf_dmut_replicate_2

description:
Library name: 72-2_DMUT_Library_GRO2554A4
10x Genomics


title: fig4b_control_U2.rep1

description:
Library name: Sample-13
fig4b_control_rep1_combined_Taildata.csv


title: fig4b_control_U1.rep2

description:
Library name: Sample-11
fig4b_control_rep2_combined_Taildata.csv


title: Meningioma 795

description: Hybridized to OncoScanHD


title: fig4b_control_U1.rep1

description:
Library name: Sample-10
fig4b_control_rep1_combined_Taildata.csv


title: 72hpf_sibCTL_replicate_2

description:
Library name: 72-2_CTL_Library_GRO2554A3
10x Genomics

value: sibCTL


title: Ins1Cre_NRK1_Islet_WT13121


title: Ins1Cre_NRK1_Islet_WT_13159


title: 48hpf_dmut_replicate_1

description:
Library name: D48_1_GRO1775A16
10x Genomics


title: 72hpf_sibCTL_replicate_1

description:
Library name: C72_1_GRO1775A19
10x Genomics


title: Meningioma 800

description: Hybridized to OncoScanHD


title: Ins1Cre_NRK1_Islet_WT_13120


title: Meningioma 794

description: Hybridized to OncoScanHD


title: Meningioma 793

description: Hybridized to OncoScanHD


title: fig4b_control_U11.rep2

description:
Library name: Sample-8
fig4b_control_rep2_combined_Taildata.csv


title: Meningioma 792

description: Hybridized to OncoScanHD


title: Meningioma 791

description: Hybridized to OncoScanHD


title: fig4b_control_7sl.rep3

description:
Library name: Sample-6
fig4b_control_rep3_combined_Taildata.csv


title: Meningioma 790

description: Hybridized to OncoScanHD


title: Ins1Cre_NRK1_Islet_WT_13128


title: Ins1Cre_NRK1_Islet_KO_13146


title: 120hpf_dmut_replicate_1

description:
Library name: 120_1_DMUT_library_GRO2404A4
10x Genomics


title: 120hpf_sibCTL_replicate_3

description:
Library name: 120-3_CTL_Library_GRO2554A5
10x Genomics


title: Ins1Cre_NRK1_Islet_KO_13145


title: fig4b_control_7sl.rep2

description:
Library name: Sample-5
fig4b_control_rep2_combined_Taildata.csv


title: Meningioma 789

description: Hybridized to OncoScanHD


title: 120hpf_sibCTL_replicate_2

description:
Library name: 120_2CTL_LIBRARY_GRO2455A7
10x Genomics


title: fig4b_control_7sl.rep1

description:
Library name: Sample-4
fig4b_control_rep1_combined_Taildata.csv


title: Ins1Cre_NRK1_Islet_KO_13144


title: Meningioma 788

description: Hybridized to OncoScanHD


title: Ins1Cre_NRK1_Islet_KO_13130


title: Cited-UI_L004

first: Michael

last: Tsang

address: 3501 Fifth Ave. BST3-5062

department: Cell Biology

description: UI represents uninjured adult zebrafish

data_processing:
Raw FASTQ files were processed and aligned using the Cell Ranger (v. 7.0.0) “count” utility with automatic chemistry detection, aligning to the Danio reiro genome (GRCz11.108).
Processed counts were read into R (v4.2.0) using the Seurat package (v4.3.0). Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets.
Assembly: GRCz11.108
Supplementary files format and content: matrix.mtx.gz - Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample.
Supplementary files format and content: barcodes.tsv.gz - Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample.
Supplementary files format and content: features.tsv.gz - Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene-count matrix for the respective sample.

molecule: nuclear RNA

source_name: heart

extract_protocol:
Uninjured control hearts and 3 days post amputation (dpa) were extracted, washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor, PN-1000494.
Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) according to the manufacturer's protocol and using the 10X Chromium Controller.

value: heart

value: Uninjured heart


title: 120hpf_dmut_replicate_3

description:
Library name: 120-3_DMUT_Library_GRO2554A6
10x Genomics


title: Ins1Cre_NRK1_Islet_KO_13193


title: fig4b_control_7sk.rep2

description:
Library name: Sample-2
fig4b_control_rep2_combined_Taildata.csv


title: Ins1Cre_NRK1_Islet_KO_13127


title: Cited-UI_L003

description: UI represents uninjured adult zebrafish


title: Meningioma 786

description: Hybridized to OncoScanHD


title: Ins1Cre_NRK1_Islet_KO_13119


title: 48hpf_sibCTL_replicate_2

description:
Library name: C48_2_GRO1775A17
10x Genomics


title: Cited-UI_L001

description: UI represents uninjured adult zebrafish


title: Meningioma 785

description: Hybridized to OncoScanHD

value: M


title: Ins1Cre_NRK1_Islet_KO_13118


title: Cited-UI_L002

description: UI represents uninjured adult zebrafish


title: Meningioma 784

description: Hybridized to OncoScanHD


title: Cited-3dpa_L004

description: 3dpa represents 3 days post amputation of approxiamtely 20% of the heart ventricle in the adult zebrafish

value: 3 days post amputation


title: fig4b_control_U11.rep3

description:
Library name: Sample-9
fig4b_control_rep3_combined_Taildata.csv


title: fig4b_control_7sk.rep1

description:
Library name: Sample-1
fig4b_control_rep1_combined_Taildata.csv


title: Meningioma 783

description: Hybridized to OncoScanHD


title: Ins1Cre_NRK1_Islet_KO_131153


title: SK-N-BE(2)_DMSO_24h_rep3a

type: RNA

city: Chiba

first: XIAOYI

last: LAI

state: 千葉県

address: 666-2 Nitona-cho Chuo-ku

country: Japan

institute: Chiba Cancer Center Research Institute

description: Gene expression after 24h DMSO treatment in SK-N-BE(2) cells

hyb_protocol: Load each assembled chamber into the oven rotator rack. Start from the center of the rack according to the manufacture's instructions, for hybridize at 65°C for 17 hours.

scan_protocol: Arrays with sample were scanned on an Agilent SureScan microarray scanner. Put assembled slide holders into the scanner cassette. Select the  AgilentG3_HiSen_GX_1color. Verify that the Scanner status in the main window says Scanner Ready and click Start Scan.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: DMSO, 24h, replication3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: SK-N-BE(2) cells were supplemented with 15% fetal bovine serum. Additionally, penicillin/streptomycin (Thermo Fisher Scientific) was added and cells were cultured in a humidified atmosphere at 37 °C with 5% CO2.

extract_protocol: total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: SK-N-BE(2) cells were treated with CCC-002 for 1nM alone or in combination with AZD6738 1.5 μmM for 24 h

tag: gender

value: Male


title: SK-N-BE(2)_DMSO_24h_rep2a

source_name: DMSO, 24h, replication2


title: Meningioma 782

description: Hybridized to OncoScanHD


title: Cited-3dpa_L003


title: SK-N-BE(2)_DMSO_24h_rep1b

source_name: DMSO, 24h, replication1


title: BS cells PB-Tag untreated 1

first: Hatice

middle: Ulku

last: Osmanbeyoglu

address: 5117 Centre Ave

data_processing:
Reads were first processed with Trimmomatic to remove adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded.
Trimmed reads were then aligned to mm10 mouse genome with the STAR spliced-read aligner
For each gene from the RefSeq annotations, the number of uniquely mapped reads overlapping with the exons was counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/).
Genes with fewer than 50 read counts were considered as not expressed and filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: count data

source_name: Prostate cells

growth_protocol: All animal studies received received prior approval by the IACUC of MSKCC and were conducted in compliance with its recommendations.

extract_protocol:
Prostate glands from wild type C57BL/6J mice and prostate tumors from Pb-TAg, Hi-Myc, PTENpc/pc, and R26ERG Pten-/-mice were dissociated and sorted to purity into the different subpopulations. After RNA extraction, samples will be object of SMARTer amplification, followed by RNA sequencing using Illumina HiSeq/Agilent QC (Paired-end run with 40m of reads per sample).
RNA libraries were prepared for sequencing using standard Illumina protocols. Samples were sequenced PE50 on a HiSeq 2500.

value: prostate gland

tag: source

value: prostate tumor from Pb-TAg mouse

tag: sample type

value: Primary sorted cells

value: Transient amplifying cells


title: Meningioma 781

description: Hybridized to OncoScanHD


title: Cited-3dpa_L002


title: BS cells PB-TAg FAKinh treated 3


title: Meningioma 780

description: Hybridized to OncoScanHD


title: Cited-3dpa_L001


title: WT-UI_L004

description: UI represents uninjured adult zebrafish

value: WT


title: BS cells PB-TAg FAKinh treated 1


title: BS cells PB-TAg FAKinh treated 2


title: Meningioma 779

description: Hybridized to OncoScanHD


title: Meningioma 778

description: Hybridized to OncoScanHD


title: WT-UI_L003

description: UI represents uninjured adult zebrafish


title: SK-N-BE(2)_Comb_24h_rep3b

description: Gene expression after 24h Comb treatment in SK-N-BE(2) cells

source_name: CCC-002, 1nM, AZD6738, 1.5 μM, 24h, replication3


title: BS cells PB-Tag untreated 3


title: SK-N-BE(2)_Comb_24h_rep2b

source_name: CCC-002, 1nM, AZD6738, 1.5 μM, 24h, replication2


title: SK-N-BE(2)_DMSO_24h_rep1a


title: DPE+ cells PB-TAg untreated 3

value: Stem cells


title: SK-N-BE(2)_Comb_24h_rep3a


title: Meningioma 777

description: Hybridized to OncoScanHD


title: WT-UI_L002

description: UI represents uninjured adult zebrafish


title: DPE+ cells PB-TAg FAKihn treated 3


title: SK-N-BE(2)_Comb_24h_rep2a


title: Meningioma 776

description: Hybridized to OncoScanHD


title: WT-UI_L001

description: UI represents uninjured adult zebrafish


title: SK-N-BE(2)_Comb_24h_rep1b

source_name: CCC-002, 1nM, AZD6738, 1.5 μM, 24h, replication1


title: DPE+ cells PB-TAg FAKihn treated 2


title: WT-3dpa_L004


title: SK-N-BE(2)_Comb_24h_rep1a


title: Meningioma 775

description: Hybridized to OncoScanHD


title: Meningioma 774

description: Hybridized to OncoScanHD


title: DPE+ cells PB-TAg FAKihn treated 1


title: WT-3dpa_L003


title: WT-3dpa_L002


title: Meningioma 773

description: Hybridized to OncoScanHD


title: Meningioma 772

description: Hybridized to OncoScanHD


title: SK-N-BE(2)_CCC-002_24h_rep3b

description: Gene expression after 24h CCC-002 treatment in SK-N-BE(2) cells

source_name: CCC-002, 1nM, 24h, replication2


title: SK-N-BE(2)_CCC-002_24h_rep3a


title: DPE- cells PB-TAg untreated 3


title: DPE- cells PB-TAg FAKihn treated 3


title: WT-3dpa_L001


title: Meningioma 771

description: Hybridized to OncoScanHD


title: cited4a_5_S10

data_processing:
fastq files were processed with Cutadapt to remove adaptors
Trimmed seq files were mapped to the zebrafish geneome using HiSat2
Mapped files were processed within featureCount for gene expression counts
featureCount reads were imported into R package DeSeq2 for gene expression analysis. WT3 and cited4a_3 samples were omitted from the DeSeq2 analysis due to poor mapping. Normalized counts were calculated and log2 fold change and padj values were calculated using DeSeq2.
Assembly: Danio rerio GRC.z11
Supplementary files format and content: RFR_WTvsCited4aDeSeq2.xlsx
Supplementary files format and content: .csv files are raw counts from featureCount processing after HiSat2 mapping.

source_name: heart ventricle

growth_protocol: Zebrafish adult at 6 months -1year of age

extract_protocol:
Adutls hearts were injured through ventricular resection and allowed to recover until 3 days post amputation.
Ventricles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit (Cat# 74004).

value: heart ventricle

value: cited4a pt38a/pt38a

value: 3 dpa


title: DPE- cells PB-TAg untreated 2


title: cited4a_4_S9


title: Meningioma 770

description: Hybridized to OncoScanHD

value: Brain


title: SK-N-BE(2)_CCC-002_24h_rep1b

source_name: CCC-002, 1nM, 24h, replication1


title: DPE- cells PB-TAg FAKihn treated 2


title: DPE+ cells PB-TAg untreated 1


title: cited4a_3_S8


title: Meningioma 769

description: Hybridized to OncoScanHD

value: F


title: SK-N-BE(2)_CCC-002_24h_rep1a


title: SK-N-BE(2)_CCC-002_24h_rep2a


title: DPE- cells PB-TAg FAKihn treated 1


title: Meningioma 768

description: Hybridized to OncoScanHD


title: SNU-16 clone D7 cells after 72 h of treatment with AZD4547

city: Suzuka

first: Kazuki

last: Kanayama

state: Mie

address: 1001-1 Kishioka

institute: Suzuka University of Medical Science

description: Library name: SNU-16cloneD7-R

data_processing:
featureCounts (ver. 2.0.3)
cutadapt (ver. 4.0) was used to remove adapter sequences, and then sickle (ver. 1.33) was used to remove bases with a quality score of less than 20 and paired reads with a quality score of less than 40 bases.
After converting sam format to bam format, sorting and indexing were performed using Samtools (ver. 1.17).
Reads mapped to the gene region of the reference sequence were counted using featureCounts(ver. 2.0.3).
Reads Per Kilobase Million (RPKM) normalization and Transcripts Per Million (TPM) to correct each read count for the total number of reads between samples and gene length.
Assembly: GRCh38
Supplementary files format and content: excel files includes raw counts, RPKM values and TPM values for each sample

source_name: Stomach

growth_protocol: The cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics (100 units/mL penicillin and 100 μg/mL streptomycin) in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted from clone D7, clone D7 after AZD4547 treatment and clone D7-R#0 using an RNeasy Mini kit (Qiagen, No. 74104).
DNB for RNA-seq were prepared using DNBSEQ G 400 RS High throughput Sequencing Kit (MGI Tech Co., Ltd) following manufactures protocols.

treatment_protocol: The concentration of AZD4547 started at 10 nM and was doubled with each second passage. We evaluated resistance to AZD4547 by comparing the proliferation of treated clone cells.

value: Stomach

value: Gastric cancer cells


title: Total Tissue PB-TAg untreated 3

value: Total tissue RNA extraction

value: Prostate tumor


title: SK-N-BE(2)_CCC-002_24h_rep2b


title: Total Tissue PB-TAg untreated 2


title: cited4a_1_S6


title: Meningioma 767

description: Hybridized to OncoScanHD

value: M


title: SNU-16 resistant clone D7 cells Replicate 1

description: Library name: SNU-16cloneD7-A


title: Total Tissue PB-TAg untreated 1


title: Meningioma 766

description: Hybridized to OncoScanHD


title: WT5_S5

value: AB*


title: SNU-16 clone D7 cells Replicate 1

description: Library name: SNU-16cloneD7


title: cited4a_2_S7


title: WT4_S4


title: Meningioma 765

description: Hybridized to OncoScanHD


title: Total Tissue PB-TAg FAKinh treated 3

value: prostate gland


title: WT3_S3


title: Meningioma 764

description: Hybridized to OncoScanHD


title: Total Tissue PB-TAg FAKinh treated 2

value: prostate tumor from Pb-TAg mouse


title: siBRD4_1

city: Singapore

first: Yoshiaki

last: Ito

address: 14 Medical Drive

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

description: RNA-Seq

data_processing:
The data were analyzed by using the online platform CSI NGS Portal (https://csibioinfo.nus.edu.sg/csingsportal) via RNA-Seq and Differential Expression pipelines.
Briefly, raw reads were trimmed for adapter sequences using Trimmomatic, and clean reads were mapped to the human reference genome (hg19) using STAR and gene expression quantification was done by HTSeq-count.
Differential gene expression analysis was done with DESeq2 followed by Pathway Enrichment analysis by using Reactome with the significantly differentially expressed genes and Gene Set Enrichment Analysis (GSEA) with the Molecular Signature Database v6.0 to identify enriched gene sets.
The online tool Metascape (http://metascape.org) was used for further Gene Ontology analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Spreadsheet includes raw and DESeq2 normalised counts for all the samples, as well as Reactome pathways, GSEA and Gene Ontology analyses of 3 comparisons: siRUNX1 vs siC, siBRD4 vs siC, and siRUNX1 & siBRD4 vs siC.

source_name: stomach cancer

extract_protocol:
RNA samples were extracted using QIAGEN RNeasy Mini Kit and subjected to DNase treatment to digest DNA.
RNA library preparation according to BGI protocol.

treatment_protocol: AGS cells were treated with specific siRNAs for 48 h to knockdown RUNX1 or BRD4.

value: AGS human gastric adenocarcinoma cells

value: BRD4 knockdown replicate 1


title: Meningioma 763

description: Hybridized to OncoScanHD


title: Total Tissue PB-TAg FAKinh treated 1


title: WT1_S1


title: siRUNX1_1

description: RNA-Seq

value: RUNX1 knockdown replicate 1


title: Meningioma 762

description: Hybridized to OncoScanHD


title: siBRD4_2

description: RNA-Seq

value: BRD4 knockdown replicate 2


title: 120hpf_dmut_replicate_2

description:
Library name: 120_2DMUT_LIBRARY_GRO2455A8
10x Genomics

value: eye


title: DNE- cells Normal 9

value: prostate gland from wild type C57BL/6J mouse

value: Primary sorted cells

value: Stromal cells


title: siC_2

description: RNA-Seq

value: non-targeting control siRNA replicate 2


title: Meningioma 760

description: Hybridized to OncoScanHD

value: Brain


title: DNE- cells Normal 8


title: DNE- cells Normal 7


title: HepG2-6d-Hypoxia-4

city: San Francisco

first: Li

last: Li

address: 1700 4th Street, MC 2540

institute: UCSF

description: Library name: HepG2-6d-Hypoxia-4

data_processing:
Fastq files were demultiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
Reads were mapped to GRCh38 using STAR v2.7.9a.
Count matrix was obtained using featureCounts v2.0.1 with reference gene annotations from Gencode v38.
DESeq2 v1.44.0 was used for normalization of count data and differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: normalized_counts.csv: normalized counts by sample.

growth_protocol: HepG2 cells (obtained from the UCSF Cell Culture Core Facility) in DMEM with 4.5 g/dL glucose (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Gemini Bio #100-106) and 1% penicillin/streptomycin (Thermo Fisher Scientific) were cultured in normoxia (21% Oxygen) or hypoxia (1% Oxygen).

extract_protocol:
RNA extraction were performed with the Qiagen RNeasy Mini Kit according to manufacturer instructions.
NEBNext Ultra II RNA Library Prep Kit was used for library preparation.

treatment_protocol: Cells were treated normoxia or hypoxia. Cells were washed with PBS and trypsinized before centrifuging to remove supernatant. The cell pellet was washed with PBS and stored at –80 °C until extraction.

value: Hepatocellular carcinoma cells

value: WT

tag: condition

value: Hypoxia (1% Oxygen) for 6d


title: Input, Total, Tg, B3, ACCATCCT

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

library_source: genomic

data_processing:
Sequenced reads were mapped to the mm9 genome using bowtie2 alignment, and reads were extended based on library sizes and deduplicated to consolidate PCR duplicate reads. Deduplicated reads were used to quantify read density normalized by the number of reads per sample and by read length in basepairs.
Bedtools coverage -counts was used to quantify ChIP-seq signal.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Cortex

extract_protocol:
Chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP libraries were generated using Ovation Ultralow Library System V2 (NuGEN). Libraries were pooled to a final concentration of 8-10nM and sequenced using Illumina HiSeq 3000 with GTAC to acquire 15-30 million single-end reads per sample.

value: Cortex

tag: strain

value: Whole cortex

value: Mecp2 OE

value: Male

value: 8-10 weeks

tag: chip antibody


title: siC_1

description: RNA-Seq

value: AGS human gastric adenocarcinoma cells

value: non-targeting control siRNA replicate 1


title: HepG2-6d-Hypoxia-3

description: Library name: HepG2-6d-Hypoxia-3


title: Meningioma 759

description: Hybridized to OncoScanHD

source_name: Meningioma Tissue

value: F


title: SS cells Normal 12

value: prostate gland

value: Epithelial cell


title: siRUNX1_2

description: RNA-Seq

value: RUNX1 knockdown replicate 2


title: WT2_S2

value: heart ventricle

value: AB*

value: 3 dpa


title: Meningioma 758

description: Hybridized to OncoScanHD

value: Brain


title: Input, Total, Tg, B1, CTATCTTG


title: HepG2-6d-Hypoxia-2

description: Library name: HepG2-6d-Hypoxia-2

value: Hepatocellular carcinoma cells

value: WT


title: SS cells Normal 11

value: prostate gland from wild type C57BL/6J mouse

value: Primary sorted cells


title: HepG2-6d-Hypoxia-1

description: Library name: HepG2-6d-Hypoxia-1

value: Hypoxia (1% Oxygen) for 6d


title: Input, Total, WTtg, B3, ACAACAGC

value: Cortex

value: Whole cortex

value: Male


title: Meningioma 761

description: Hybridized to OncoScanHD

value: M


title: HepG2-6d-Hypoxia-5

description: Library name: HepG2-6d-Hypoxia-5


title: Meningioma 757

description: Hybridized to OncoScanHD

value: F


title: Meningioma 756

description: Hybridized to OncoScanHD


title: SS cells Normal 10

value: prostate gland


title: DNE+ cells Normal 12

value: Epithelial cell


title: HepG2-24h-Hypoxia-6

description: Library name: HepG2-24h-Hypoxia-6

value: Hypoxia (1% Oxygen) for 24hr


title: Meningioma 755

description: Hybridized to OncoScanHD


title: Input, Total, WT, B1, ATGTCGGC

value: 8-10 weeks


title: HepG2-24h-Hypoxia-5

description: Library name: HepG2-24h-Hypoxia-5


title: Input, Total, KO, B3, AACCGAAC

value: Mecp2 KO


title: Input, Total, KO, B2, CCAACACT


title: HepG2-24h-Hypoxia-4

description: Library name: HepG2-24h-Hypoxia-4


title: DNE+ cells Normal 11


title: Meningioma 754

description: Hybridized to OncoScanHD


title: HepG2-24h-Hypoxia-3

description: Library name: HepG2-24h-Hypoxia-3


title: Input, Total, WTKO, B3, CCTTAGGT


title: DNE+ cells Normal 10


title: Meningioma 753

description: Hybridized to OncoScanHD


title: BS cells Normal 12

value: Transient amplifying cells


title: HepG2-24h-Hypoxia-2

description: Library name: HepG2-24h-Hypoxia-2


title: Input, Total, WTKO, B2, ATCGTCTC


title: Input, PV, Tg, B3, ACTCCTAC

value: PV

value: Mecp2 OE


title: HepG2-24h-Hypoxia-1

description: Library name: HepG2-24h-Hypoxia-1

value: Hepatocellular carcinoma cells

value: WT


title: BS cells Normal 11

value: prostate gland from wild type C57BL/6J mouse

value: Primary sorted cells


title: Meningioma 750

description: Hybridized to OncoScanHD

value: Brain


title: Meningioma 751

description: Hybridized to OncoScanHD


title: HepG2-Normoxia-6

description: Library name: HepG2-Normoxia-6

value: Normoxia


title: Input, PV, Tg, B1, CTTCCCAT

value: Cortex

value: Male


title: DPE+ cells PB-Tag 4

value: prostate tumor from Pb-TAg mouse

value: Stem cells


title: Meningioma 749

description: Hybridized to OncoScanHD

value: M


title: HepG2-Normoxia-5

description: Library name: HepG2-Normoxia-5


title: DPE+ cells PB-Tag 3

value: prostate gland


title: HepG2-Normoxia-4

description: Library name: HepG2-Normoxia-4


title: Meningioma 748

description: Hybridized to OncoScanHD

value: F


title: DPE+ cells PB-Tag 2


title: Meningioma 747

description: Hybridized to OncoScanHD


title: Input, PV, KO, B3, TCTAGGAG

value: Mecp2 KO

value: 8-10 weeks


title: Input, PV, WT, B1, TCGCGAGG

value: PV


title: HepG2-Normoxia-3

description: Library name: HepG2-Normoxia-3


title: HepG2-Normoxia-2

description: Library name: HepG2-Normoxia-2


title: Meningioma 746

description: Hybridized to OncoScanHD


title: DPE+ cells Pten f/f 3

value: prostate tumor from PTENpc/pc mouse


title: Meningioma 752

description: Hybridized to OncoScanHD


title: Input, PV, WTKO, B3, CTCGAACA


title: DPE+ cells Pten f/f 2


title: BS cells Normal 10

value: Transient amplifying cells


title: HepG2-Normoxia-1

description: Library name: HepG2-Normoxia-1

value: Hepatocellular carcinoma cells

value: WT


title: Input, PV, WTtg, B3, AACTCGGA


title: 120hpf_sibCTL_replicate_1

description:
Library name: 120_1_CTL_library_GRO2404A3
10x Genomics

value: eye

value: sibCTL


title: Meningioma 745

description: Hybridized to OncoScanHD

value: Brain


title: DPE+ cells Pten f/f 1

value: Primary sorted cells


title: Input, PV, WTKO, B2, CGACCTAA

value: Cortex

value: Male


title: fig4b_control_7sk.rep3

description:
Library name: Sample-3
fig4b_control_rep3_combined_Taildata.csv

source_name: HEK 293T-REx

value: HEK 293T-REx


title: DPE+ cells Normal 6

value: prostate gland from wild type C57BL/6J mouse

value: Stem cells


title: H3K27ac, Total, Tg, B3, CTATCTTG

value: Whole cortex

value: Mecp2 OE

value: H3K27ac (Abcam, #ab4729)


title: Meningioma 744

description: Hybridized to OncoScanHD

value: F


title: Ins1Cre_NRK1_Islet_KO_13161

source_name: pancreatic islets

value: pancreatic islets

value: islets

value: HFD


title: fig4b_control_U11.rep1

description:
Library name: Sample-7
fig4b_control_rep1_combined_Taildata.csv


title: Day_21_sample_2

city: Santa Cruz

first: Susan

last: Carpenter

address: Biomedical Sciences Building First Floor, Red Hill Road

department: MCD

institute: UC Santa Cruz

data_processing:
fastq.gz files were analyzed using the https://github.com/quasiben/gRNA_Tool
all guide RNA (sgRNA) + barcode reads were collapsed to obtain sgRNA counts
Counts were normalized to the median sgRNA count
Fold changes were calculated for for each sgRNA
Mann Whitney U test was performed comparing sgRNA
Assembly: Hg38
Supplementary files format and content: CRISPRi gRNA library
Supplementary files format and content: Mann-Whitney U score and significance p-values for each gene.

source_name: human leukemia monocytic cells

growth_protocol: All THP1 cell lines were cultured in RPMI 1640 supplemented with 10% low-endotoxin fetal bovine serum (ThermoFisher), 1X penicillin/streptomycin, and incubated at 37°C in 5% CO2.

extract_protocol:
Cell pellets from samples were resuspended in 20 mL P1 buffer (Qiagen) with 100 μg/mL RNase A and 0.5% SDS followed by incubation at 37C for 30 min. After that, Proteinase K was added (100 μg/mL final) followed by incubation at 55C for 30 min. After digest, samples were homogenised by passing them three times through a 18G needle followed by three times through a 22G needle. Homogenised samples were mixed with 20 mL Phenol:Chlorophorm:Isoamyl Alcohol (Invitrogen #15593–031), transferred into 50 mL MaXtract tubes (Qiagen) and thoroughly mixed. Samples were then centrifuged at 1500 g for 5 min at room temperature (RT). The aqueous phase was transferred into ultracentrifuge tubes and thoroughly mixed with 2 mL 3 M sodium acetate plus 16 mL isopropanol at RT before centrifugation at 15,000 g for 15 min. The gDNA pellets were carefully washed with 10 mL 70% ethanol and dried at 37C. Dry pellets were resuspended in H2O and gDNA concentration was adjusted to 1 μg/uL. The degree of gDNA shearing was assessed on a 1% agarose gel and gDNA was sheared further by boiling at 95C until average size was between 10 and 20 kb.
Multiple PCR reactions were prepared to allow amplification of the total harvested gDNA from a 1000x cell coverage for each sample. For the first round of two nested PCRs, the total volume was 100 μL containing 50 μg sheared gDNA, 0.3 μM forward (5′-ggcttggatttctataacttcgtatagca-3) and reverse (5′-cggggactgtgggcgatgtg-3′) primer, 200 μM each dNTP, 1x Titanium Taq buffer and 1 μL Titanium Taq (Clontech). PCR cycles were: 1x (94C - 3 min), 16x (94C - 30 s, 65C – 10 s, 72C – 20 s), 1x (68C – 2 min). All first round PCRs were pooled and a fraction was used as template for the second round PCR. The total volume of the second round PCR was 100 μL containing 2 μL pooled first round PCR, 0.5 μM forward (5’-AATGATACGGCGACCACCGAGATCCACAAAAGGAAACTCACCCTAAC-3′) and reverse (5’-CAAGCAGAAGACGGCATACGAGAT-(N)6-GTGACTGGAGTTCAGACGTG-3′) primer where (N)6 is a 6 nt index for sequencing on the Illumina HiSeq platform, 200 μM each dNTP, 1x Titanium Taq buffer and 1 μL Titanium Taq (Clontech). PCR cycles were: 1x (94C - 3 min), 16x (94C - 30 s, 55C – 10 s, 72C – 20 s), 1x (68C – 2 min). The resulting PCR product (344 bp) was extracted from a 1% agarose gel. Gel extracted bands were submitted for sequencing on an Illumina HiSeq 2500 platform using paired end 50 kits with the custom sequencing primer 5’-GAGACTATAAGTATCCCTTGGAGAACCACCTTGTTGG-3′ for reading the sgRNA sequence and the standard Truseq Illumina reverse primer to read out 20 nt unique barcode sequences and library IDs.
sequencing of amplicon

treatment_protocol: Library infected and selected THP1-NFkB-EGFP-CRISPRi-sgRNA cells were expanded to 2000X coverage. Cells were selected for 10 days and then let grow for 11 days before isolation

value: human leukemia monocytic cells


title: Meningioma 743

description: Hybridized to OncoScanHD

value: M


title: Day_21_sample_3


title: Meningioma 787

description: Hybridized to OncoScanHD


title: H3K27ac, Total, Tg, B1, TGCATGTA

value: 8-10 weeks


title: DPE+ cells Normal 5

value: prostate gland


title: Day_21_sample_1


title: Meningioma 742

description: Hybridized to OncoScanHD

value: Brain


title: H3K27ac, Total, WTtg, B3, ATGTCGGC

value: Cortex

value: WT


title: plasmid


title: DPE+ cells Normal 4

value: Primary sorted cells


title: Meningioma 741

description: Hybridized to OncoScanHD


title: Input, PV, KO, B2, TACATCGG

value: PV

value: Mecp2 KO

value: Male


title: DPE+ cells Normal 12

value: prostate gland from wild type C57BL/6J mouse

value: Stem cells


title: H3K27ac, Total, WT, B1, CTCAGGGC

value: Whole cortex

value: H3K27ac (Abcam, #ab4729)


title: DPE+ cells Normal 11


title: Meningioma 740

description: Hybridized to OncoScanHD


title: UM-RC-2, ChIP-seq, RNA, VHL, Rep 2

city: Cleveland

first: Abhishek

last: Chakraborty

state: OH

address: 9620 Carnegie Ave NB4-120

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
featureCounts
Assembly: hg19
Supplementary files format and content: ChIP-seq: bigwig, tdf, tabular, mean log2-FC at set of genomic intervals ([HOMER] identified superenhancers)
Supplementary files format and content: RNA-seq: tabular, per gene read counts, normalized FPKM gene counts

source_name: UM-RC-2 (RRID:CVCL_2739)

growth_protocol: UM-RC-2, and 786-O cells were maintained in Dulbecco’s Modified Eagles Medium (DMEM) (Life Technologies 11995073) supplemented with 10% Fetal Bovine Serum (FBS) (Life Technologies 10437-028), and 1X Penicillin-Streptomycin (Life Technologies 15140163)

extract_protocol:
RNA was harvested using Trizol reagent. ChIP samples were fixed for 10' in 1% formaldehyde, lysed in SDS buffer, and sonicated.
Illumina Tru-Seq RNA Library Preparation Kit, Illumina Tru-Seq ChIP Library Preparation Kit

treatment_protocol: Cells stably expressing VEC or VHL were generated by lentiviral infection followed by selection with Blasticidin (10 µg/ml)

value: UM-RC-2 (RRID:CVCL_2739)

value: Clear cell renal cell carcinoma, VHL; Simple; p.Arg82Pro (c.245G>C)


title: Meningioma 739

description: Hybridized to OncoScanHD

value: F


title: DPE+ cells Hi-Myc 5

value: prostate tumor from Hi-Myc mouse


title: UM-RC-2, ChIP-seq, RNA, VEC, Rep 2


title: H3K27ac, Total, KO, B2, TGCATGTA

value: 8-10 weeks


title: UM-RC-2, ChIP-seq, RNA, VHL, Rep 1


title: H3K27ac, Total, WTKO, B3, CTATCTTG


title: UM-RC-2, ChIP-seq, RNA, VEC, Rep 1

data_processing:
data processed by Syros
featureCounts
Assembly: hg19
Supplementary files format and content: ChIP-seq: bigwig, tdf, tabular, mean log2-FC at set of genomic intervals ([HOMER] identified superenhancers)
Supplementary files format and content: RNA-seq: tabular, per gene read counts, normalized FPKM gene counts


title: Meningioma 738

description: Hybridized to OncoScanHD


title: Meningioma 737

description: Hybridized to OncoScanHD


title: Meningioma 736

description: Hybridized to OncoScanHD

value: M


title: H3K27ac, Total, WTKO, B2, CTCAGGGC


title: DPE+ cells Hi-Myc 3

value: prostate gland


title: UM-RC-2, ChIP-seq, H3k27ac, VHL

data_processing:
data processed by Syros
bigWigAverageOverBed
bamCompare
bigwig file of log2-FC H3K27ac deposition between read count normalized [--scaleFactorsMethod readCount] .bam files (comparison = VHL/VEC)
bamCoverage
Assembly: hg19
Supplementary files format and content: ChIP-seq: bigwig, tdf, tabular, mean log2-FC at set of genomic intervals ([HOMER] identified superenhancers)
Supplementary files format and content: RNA-seq: tabular, per gene read counts, normalized FPKM gene counts

tag: antibody

value: ChIP-seq on H3K27ac


title: H3K27ac, PV, Tg, B3, TGCATGTA

value: Cortex

value: Mecp2 OE


title: Meningioma 735

description: Hybridized to OncoScanHD

value: Brain


title: DPE+ cells Hi-Myc 2

value: Primary sorted cells


title: UM-RC-2, ChIP-seq, H3k27ac, VEC

data_processing:
data processed by Syros
bamCoverage
Assembly: hg19
Supplementary files format and content: ChIP-seq: bigwig, tdf, tabular, mean log2-FC at set of genomic intervals ([HOMER] identified superenhancers)
Supplementary files format and content: RNA-seq: tabular, per gene read counts, normalized FPKM gene counts


title: Meningioma 734

description: Hybridized to OncoScanHD


title: H3K27ac, PV, Tg, B2, GACTACGA

value: PV

value: Male


title: 786-O, ChIP-seq, H3k27ac, VHL

value: Clear cell renal cell carcinoma, VHL; Simple; p.Gly104Alafs*55 (c.311delG)


title: DPE+ cells Hi-Myc 1

value: Stem cells


title: Meningioma 733

description: Hybridized to OncoScanHD


title: H3K27ac, PV, Tg, B1, GCTGAGTC

value: H3K27ac (Abcam, #ab4729)


title: 786-O, ChIP-seq, H3k27ac, VEC


title: H3K27ac, Total, KO, B3, ATGTCGGC

value: Whole cortex

value: Mecp2 KO


title: DPE+ cells R26-ERG PTENf/f 4

value: prostate tumor from R26ERG PTEN-/- mouse


title: 160_953_E030_TCZ+ IL1B_24h [0700837051]

city: Doha

first: nico

last: marr

email: nico_marr@outlook.com, tkhan@sidra.org

address: AL RAYYAN

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
Raw RNA-seq reads were aligned with UCSC human genome assembly version hg38, with STAR aligner (Dobin et al., 2013).
HTseq-count (Anders et al., 2015) was used to count the reads mapping to each gene feature. Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Assembly: hg38
Supplementary files format and content: HTSeq-count is used to get the count files, followed by quantile  normalization.

source_name: PBMCs

extract_protocol: RNeasy plus micro kit (Qiagen): cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation and used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively

value: PBMCs

tag: donor

value: Healthy control

value: WT/WT

value: Tocilizumab + IL1B

tag: timepoint


title: DPE+ cells Hi-Myc 4

value: prostate gland

value: prostate tumor from Hi-Myc mouse


title: 159_953_E030_TCZ + LPS _24h [0700837041]

value: Tocilizumab + LPS


title: Meningioma 732

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

value: Brain

value: F


title: Meningioma 731

description: Hybridized to OncoScanHD


title: H3K27ac, PV, WTtg, B2, CGTCTAAC

value: Cortex

value: PV

value: WT

value: 8-10 weeks


title: DPE- cells PB-Tag 4

value: prostate tumor from Pb-TAg mouse

value: Primary sorted cells

value: Stem cells


title: 158_953_E030_TCZ + RPMI_24h [0700837031]

value: Tocilizumab + RPMI


title: H3K27ac, PV, WT, B1, AAGGAGTC

value: Male

value: H3K27ac (Abcam, #ab4729)


title: Meningioma 730

description: Hybridized to OncoScanHD


title: DPE- cells PB-TAg 3


title: H3K27ac, PV, KO, B3, TCGCGAGG

value: Mecp2 KO


title: 157_953_E029_TCZ+ IL1B_24h [0700837021]

value: PBMCs

value: Healthy control

value: WT/WT

value: Tocilizumab + IL1B


title: DPE+ cells R26-ERG PTENf/f 5

value: prostate gland

value: prostate tumor from R26ERG PTEN-/- mouse


title: 156_953_E029_TCZ + LPS _24h [0700837011]

value: Tocilizumab + LPS


title: Meningioma 728

description: Hybridized to OncoScanHD

value: Brain

value: F


title: H3K27ac, PV, KO, B2, GCTGAGTC

value: Cortex

value: PV

value: 8-10 weeks


title: Meningioma 727

description: Hybridized to OncoScanHD


title: H3K27ac, PV, KO, B1, GCTGAGTC


title: 155_953_E029_TCZ + RPMI_24h [0700837001]


title: DPE- cells Pten f/f 2

value: prostate tumor from PTENpc/pc mouse

value: Primary sorted cells

value: Stem cells


title: H3K27ac, PV, WTKO, B3, CTTCCCAT

value: WT

value: Male

value: H3K27ac (Abcam, #ab4729)


title: H3K27ac, PV, WTtg, B3, TCGCGAGG


title: 154_953_E028_TCZ+ IL1B_24h [0700836991]

value: PBMCs

value: Healthy control


title: Meningioma 726

description: Hybridized to OncoScanHD

value: M


title: DPE+ cells R26-ERG PTENf/f 3

value: prostate gland


title: DPE- cells Pten f/f 1


title: H3K27ac, PV, WTKO, B2, AAGGAGTC


title: Meningioma 725

description: Hybridized to OncoScanHD


title: 153_953_E028_TCZ + LPS _24h [0700836981]

value: WT/WT


title: DPE- cells Normal 6

value: prostate gland from wild type C57BL/6J mouse


title: Meningioma 724

description: Hybridized to OncoScanHD

value: Brain


title: Meningioma 729

description: Hybridized to OncoScanHD

value: F


title: 152_953_E028_TCZ + RPMI_24h [0700836971]

value: Tocilizumab + RPMI


title: DPE- cells Normal 5


title: H3K27ac, PV, WTko, B1, AAGGAGTC

value: Cortex

value: PV


title: run, 2916, s, 1, withindex, sequence.txt, GTACACCT

description: Input

data_processing:
FASTQ files were trimmed with Trim Galore and rRNA sequences were filtered out with Bowtie.
Remaining reads were aligned to mm9 using STAR with the default parameters
Reads were assigned to genes using bedtools coverage -counts.
Exonic reads were filtered for non- and lowly-expressed coding genes (minimum of 5 counts across samples) and then DESeq2 performed using adaptive shrinkage.
RUVg was used to normalize data from each cell type on “in silico” defined negative control genes.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include TPM values for each INTACT-isolated cell type.

extract_protocol:
Nuclear RNA was extracted using RNeasy micro kit (QIAGEN) following manufacturer instruction.
RNA libraries for RNA-seq were prepared using the Nugen/Tecan Ovation SoLo RNA-Seq Library Preparation Kit.

value: Mecp2 KO


title: 151_953_E002_TCZ+ IL1B_24h [0700836961]

value: Tocilizumab + IL1B


title: run, 2916, s, 1, withindex, sequence.txt, ACGAGAAC

description: Input


title: Meningioma 723

description: Hybridized to OncoScanHD


title: Meningioma 722

description: Hybridized to OncoScanHD


title: 150_953_E002_TCZ + LPS _24h [0700836951]

value: Tocilizumab + LPS


title: DPE- cells Normal 12

value: Primary sorted cells

value: Stem cells


title: DPE- cells Pten f/f 3

value: prostate tumor from PTENpc/pc mouse


title: DPE- cells PB-TAg 2

value: prostate tumor from Pb-TAg mouse


title: 149_953_E002_TCZ + RPMI_24h [0700836941]

value: PBMCs

value: Healthy control


title: PV, Input3, WT, 598, run, 2916, s, 1, withindex, sequence.txt, CGTCCATT

value: WT

value: Male


title: 148_091_S05_TCZ+ IL1B_24h [0700836931]

value: Sibling

value: WT/mut


title: Meningioma 720

description: Hybridized to OncoScanHD

value: Brain

value: F


title: Meningioma 721

description: Hybridized to OncoScanHD


title: DPE- cells Hi-Myc 6

value: prostate gland

value: prostate tumor from Hi-Myc mouse


title: PV, IP4, KO, 603, run, 2916, s, 1, withindex, sequence.txt, GCACACAA

value: Cortex

value: PV

value: Mecp2 KO


title: 147_091_S05_TCZ + LPS _24h [0700836921]

value: Tocilizumab + LPS


title: Meningioma 719

description: Hybridized to OncoScanHD


title: 146_091_S05_TCZ + RPMI_24h [0700836911]

value: Tocilizumab + RPMI


title: PV, IP3, KO, 600, run, 2916, s, 1, withindex, sequence.txt, ACAACAGC


title: DPE- cells Hi-Myc 5

value: Primary sorted cells

value: Stem cells


title: Meningioma 718

description: Hybridized to OncoScanHD

value: M


title: PV, IP2, KO, 597, run, 2916, s, 1, withindex, sequence.txt, AACTCGGA


title: DPE- cells Normal 4

value: prostate gland from wild type C57BL/6J mouse


title: 145_091_S03_TCZ+ IL1B_24h [0700836901]

value: PBMCs

value: Tocilizumab + IL1B


title: DPE- cells Hi-Myc 4


title: PV, Input3, KO, 600, run, 2916, s, 1, withindex, sequence.txt, AACTTGCC

value: Male


title: DPE- cells R26-ERG PTENf/f 6

value: prostate tumor from R26ERG PTEN-/- mouse


title: Meningioma 716

description: Hybridized to OncoScanHD

value: Brain


title: DPE- cells R26-ERG PTENf/f 5


title: PV, IP4, WT, 602, run, 2916, s, 1, withindex, sequence.txt, ATGACAGG

value: WT


title: 143_091_S03_TCZ + RPMI_24h [0700836881]

value: Sibling

value: WT/mut


title: 144_091_S03_TCZ + LPS _24h [0700836891]


title: DPE- cells Normal 11

value: prostate gland


title: PV, IP3, 598, wt, run, 2916, s, 1, withindex, sequence.txt, GTCGAGAA

value: Cortex

value: PV


title: DPE- cells R26-ERG PTENf/f 4


title: Meningioma 714

description: Hybridized to OncoScanHD

value: F


title: DPE- cells R26-ERG PTENf/f 3


title: 141_091_P12_TCZ + LPS _24h [0700836861]

value: Patient

value: mut/mut

value: Tocilizumab + LPS


title: Meningioma 713

description: Hybridized to OncoScanHD

value: M


title: PV, IP2, WT, 594, run, 2916, s, 1, withindex, sequence.txt, CGTCTAAC


title: PV, IP1, WT, 586, run, 2916, s, 1, withindex, sequence.txt, CGCTACAT


title: 140_091_P12_TCZ + RPMI_24h [0700836851]

value: Tocilizumab + RPMI


title: Meningioma 712

description: Hybridized to OncoScanHD


title: PV, IP1, KO, 587, run, 2916, s, 1, withindex, sequence.txt, AATCCAGC

value: Mecp2 KO


title: 142_091_P12_TCZ+ IL1B_24h [0700836871]

value: PBMCs

value: Tocilizumab + IL1B


title: 139_091_P07_TCZ+ IL1B_24h [0700836841]


title: Meningioma 711

description: Hybridized to OncoScanHD


title: LC_FEMALE_02

city: Seattle

state: WA

address: 1959 NE Pacific St J181-Health Sciences

department: Anesthesiology & Pain Medicine

institute: University of Washington

description: 10x Genomics

data_processing:
sequence alignment to mouse genome done with 10x Genomics Cell Ranger Count v6.1.2 pipeline
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Adult mice were euthanized with 0.01 ml/kg of phenytoin/pentobarbitol solution, and perfused transcardially with cold NMDG-aCSF (96 mM NMDG, 2.5 mM KCl, 1.35 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na+ ascorbate, 3 mM Na+ pyruvate, 2 mM N-acetyl-cysteine, 0.5 mM CaCl2, 10 mM MgSO4, 0.6 mM glutathione-ethyl-ester; pH 7.35-7.40, 300-305 mOsm, oxygenated with 95% O2 and 5% CO2) with the following inhibitors: 500 nM TTX, 10 μM APV, 10 μM DNQX, 5 μM actinomycin, 22.7 μM anisomycin. Extracted brains were sliced using a vibratome (Leica, VT1200), the locus coeruleus and its neighboring regions dissected out, and the tissue flash frozen on dry ice and stored at -80°C. Later, coerulear sections were lysed, homogenized with glass pestle, filtered via a 40 μm strainer, centrifuged initially to remove cellular debris, and again in differing density solvents (50% and 30% OptiPrep) in which the pelleted nuclei were collected. Nuclei were resuspended in PBS as needed for >400 nuclei/μl.
The cDNA libraries were constructed using the Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 Dual Index, 10x Genomics. Briefly, ~10,000 nuclei were load into the chip, single nuclear mRNAs were captured by barcoded beads, and the transcripts were reverse transcribed. The resulting cDNAs were then PCR amplified, fragmented, ligated with adaptors, and added with sample index.

value: peri-LC and LC

value: wild type

value: female

value: 2-3 months


title: Meningioma 717

description: Hybridized to OncoScanHD

value: Brain


title: 138_091_P07_TCZ + LPS _24h [0700836831]


title: LC_FEMALE_01

description: 10x Genomics

value: 4-5 months


title: Res+PD1_2

city: Houston

first: Qi

last: Wang

state: TX

address: 7007 Bertner Ave

institute: UT MD Anderson Cancer Center

description: Resistant cells, treated with anti-PD-1

hyb_protocol: Samples were hybridized with GeneChip Mouse genome 430 2.0 arrays (Affymetrix) at the MDACC Sequencing and ncRNA Program.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Normalized data analysis and statistical evaluations were performed with customized R codes.

source_name: lung adenocarcinoma

label_protocol: Biotin-labeled cRNA was generated using in vitro transcription with T7 RNA polymerase (Affymetrix), then purified, fragmented, and hybridized to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix).

extract_protocol: Total RNA was isolated from tumors  with Triazol (Life Technologies) according to the manufacturer’s protocol.

treatment_protocol: 344SQ_Parental (Sen) or 344SQ_anti-PD-1 resistant (Res) cells were subcutaneously inoculated into the right flank of 129sv/ev mice (female mice, 5 mice per group). Anti-PD-1 or control IgG (10mg/kg, Merck) antibodies were given on days 4 and 7 after tumor inoculation. On day 11, tumor tissues were collected for RNA preparation. There are four groups in this study: (1) parental tumors+control IgG treatment, (2) parental tumors+anti-PD-1 treatment, (3) resistant tumors+control IgG treatment, and (4) resistant tumors+anti-PD-1.


title: Meningioma 715

description: Hybridized to OncoScanHD

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


title: Res+PD1_3

description: Resistant cells, treated with anti-PD-1


title: LC_MALE_02

description: 10x Genomics

value: male

value: 3-4 months


title: Meningioma 710

description: Hybridized to OncoScanHD

value: F


title: Res+PD1_1

description: Resistant cells, treated with anti-PD-1


title: 136_953_E030_IL1B _24h [0700836811]

value: Healthy control

value: WT/WT


title: Meningioma 709

description: Hybridized to OncoScanHD


title: LC_MALE_01

description: 10x Genomics

value: 2-5 months


title: Meningioma 708

description: Hybridized to OncoScanHD

value: M


title: Res+IgG_2

description: Resistant cells, treated with control IgG


title: 22-02953

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

data_processing:
fastp was used to trim adaptors and filter the reads by quality and length
reads were aligned to the zebrafish genome (GRCz11, Ensembl release 104) using STAR
PCR duplicates were de-duplicated using the dedup function of umi-tools
The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts
Assembly: GRCz11, Ensembl release 104
Supplementary files format and content: csv file containing the output from featurecounts (raw counts)

source_name: whole brain

extract_protocol:
RNA was extracted using the Qiagen Rneasy mini kit, then DNase treated using the DNAfree kit
Libraries were generated according to the Nugen Universal Plus mRNA-seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity

value: whole brain

value: EOfAD-like

tag: hometank

tag: rin


title: Meningioma 707

description: Hybridized to OncoScanHD

tag: tissue


title: Res+IgG_3


title: Res+IgG_1


title: 134_953_E030_RPMI_24h [0700836791]

tag: cell type

value: PBMCs

value: RPMI


title: 135_953_E030_LPS_24h [0700836801]

tag: genotype

value: LPS


title: Meningioma 706

description: Hybridized to OncoScanHD


title: 22-02952


title: Meningioma 704

description: Hybridized to OncoScanHD


title: 22-02949

value: MPS IIIB


title: 132_953_E029_LPS_24h [0700836771]

tag: treatment


title: 133_953_E029_IL1B _24h [0700836781]


title: Meningioma 705

description: Hybridized to OncoScanHD

tag: Sex


title: 22-02951

value: wt


title: Sen+PD1_3

description: Parental cells, treated with anti-PD-1


title: 137_091_P07_TCZ + RPMI_24h [0700836821]

value: Patient

value: mut/mut

value: Tocilizumab + RPMI


title: Meningioma 702

description: Hybridized to OncoScanHD

value: Brain

tag: age


title: 22-02947


title: 131_953_E029_RPMI_24h [0700836761]


title: 129_953_E028_LPS_24h [0700836741]


title: 128_953_E028_RPMI_24h [0700836731]


title: Meningioma 701

description: Hybridized to OncoScanHD


title: Sen+PD1_1

description: Parental cells, treated with anti-PD-1


title: Sen+IgG_3

description: Parental cells, treated with control IgG


title: Sen+PD1_2

description: Parental cells, treated with anti-PD-1


title: 22-02948


title: Sen+IgG_2


title: Meningioma 700

description: Hybridized to OncoScanHD


title: Meningioma 699

description: Hybridized to OncoScanHD


title: Sen+IgG_1


title: 127_953_E002_IL1B _24h [0700836721]


title: 22-02942


title: 22-02946


title: 126_953_E002_LPS_24h [0700836711]


title: SNU-16 clone E8 cells Replicate 2

description: Biological replicate 1

hyb_protocol: Mix the components according to the microarray format to prepare the Hybridization Master Mix. Add the appropriate volume of the Hybridization Master Mix to the 1.5-mL RNase-free Microfuge Tube, 200-μL Thin-Wall Tube, Tall Chimney PCR plate well or 96-well PCR plate well that contains the labeled gDNA. Then, heat to 98℃ for 3 minutes and 37℃ for 30 minutes. Samples were applied to microarrays enclosed in the Agilent Microarray Hybridization Chamber. After hybridization at 67℃, slides were washed sequential.

scan_protocol: Scanned on an Agilent G4900DA SureScan Microarray Scanner. Scanned images were processed by Feature Extraction S/W with default settings(background subtraction and LOWESS normalization).

data_processing: CGH data were extraction from scanned images using Agilent Feature Extraction software(v.11.0.1.1) which was used for background subtraction and LOWESS normalization.

source_name: SNU-16 gastric cancer cells isolated by single cell cloning

label_protocol:
Add 2.5 μL of Random Primers to each reaction tube that contains 13 μL of gDNA to make a total volume of 15.5 μL.Then, heat to 98℃ for 3minutes.
Add 9.5 μL of Labeling Master Mix to each reaction tube that contains the gDNA to make a total volume of 25 μL. Then, heat to 37℃ for 2 hours and 65℃ for 10 minutes.

extract_protocol: Genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen).

tag: cell line

value: Stomach

source_name: Normal DNA NA10851

value: Agilent control NA10851(Male)


title: 22-02941

value: F


title: Meningioma 698

description: Hybridized to OncoScanHD


title: Meningioma 697

description: Hybridized to OncoScanHD


title: SNU-16 resistant clone D7 cells Replicate 2

description: Biological replicate 1

source_name: Clone D7 cells with treatment resistant


title: 22-02938


title: Meningioma 696

description: Hybridized to OncoScanHD


title: 124_091_S05_IL1B _24h [0700836691]

value: Sibling

value: WT/mut


title: 125_953_E002_RPMI_24h [0700836701]

value: Healthy control

value: WT/WT


title: SNU-16 cloneD7 cells Replicate 1

description: Biological replicate 1


title: 22-02937

value: whole brain


title: 22-02945

value: M


title: Meningioma 695

description: Hybridized to OncoScanHD


title: 22-02936


title: Meningioma 694

description: Hybridized to OncoScanHD


title: 121_091_S03_IL1B _24h [0700836661]

value: PBMCs


title: SNU-16 clone E8 cells Replicate 1

description: Biological replicate 1


title: 123_091_S05_LPS_24h [0700836681]

value: LPS


title: 120_091_S03_LPS_24h [0700836651]


title: Meningioma 693

description: Hybridized to OncoScanHD


title: Meningioma 692

description: Hybridized to OncoScanHD


title: 22-02935


title: F2T1R2

first: exRNA

last: BRL

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

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: Blood

extract_protocol:
RNA Isolation method was RNA was isolated from serum using QiaZol/Chloroform and cleaned using Qiagen miRNeasy Mini Kit. RNA Isolation kit was Serum and Plasma kit (Qiagen).
Library construction kit was TruSeq Small RNA library prep kit (Illumina). Samples were not multiplexed. Type of Starting Material was total RNA.

value: Female 2

tag: time

value: Blood

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Serum and Plasma kit (Qiagen)


title: SNU-16 resistant clone D7 cells Replicate 1

description: Biological replicate 1

value: Stomach


title: F3T1R1

value: Female 3

tag: condition


title: 22-02933

value: wt

value: F


title: SNU-16 clone D7 cells Replicate 1

description: Biological replicate 1


title: Meningioma 691

address: 75 Francis Street

description: Hybridized to OncoScanHD

value: Brain


title: F3T2R2


title: SNU-16 parental cells Replicate 1

description: Biological replicate 1

source_name: SNU-16 gastric cancer cell lines

value: Agilent control NA10851(Male)


title: 118_091_P12_IL1B _24h [0700836631]

value: Patient

value: mut/mut


title: 22-02932

value: whole brain

value: MPS IIIB

value: M


title: 117_091_P12_LPS_24h [0700836621]

value: PBMCs

value: LPS


title: 22-02931


title: 116_091_P12_RPMI_24h [0700836611]

value: RPMI


title: F3T3R1

value: Blood

value: Healthy Subject

value: Entire cardiovascular system


title: Meningioma 690

description: Hybridized to OncoScanHD


title: F4T1R2

value: Female 4

value: total cell-free biofluid RNA

value: Serum and Plasma kit (Qiagen)


title: 22-02930

value: EOfAD-like


title: 115_091_P07_IL1B _24h [0700836601]


title: Meningioma 688

description: Hybridized to OncoScanHD

value: Brain

value: F


title: F4T2R1


title: Meningioma 687

description: Hybridized to OncoScanHD


title: 22-02934


title: 22-02929


title: 119_091_S03_RPMI_24h [0700836641]

value: Sibling

value: WT/mut


title: 114_091_P07_LPS_24h [0700836591]

value: Patient

value: mut/mut


title: 22-02928

value: whole brain

value: MPS IIIB


title: Meningioma 686

description: Hybridized to OncoScanHD


title: 22-02927

value: wt

value: M


title: 111_953_E030_TCZ + LPS _6h [0700836561]

value: PBMCs

value: Healthy control

value: WT/WT

value: Tocilizumab + LPS


title: M2T2R1

value: Male 2

value: Blood

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: Meningioma 689

description: Hybridized to OncoScanHD

value: Brain

value: F


title: F1T3R2

value: Female 1

value: Serum and Plasma kit (Qiagen)


title: Meningioma 684

description: Hybridized to OncoScanHD


title: 110_953_E030_TCZ + RPMI_6h [0700836551]

value: Tocilizumab + RPMI


title: Meningioma 685

description: Hybridized to OncoScanHD


title: Meningioma 682

description: Hybridized to OncoScanHD


title: M2T1R2


title: 109_953_E029_TCZ+ IL1B_6h [0700836541]

value: Tocilizumab + IL1B


title: F4T1R1

value: Female 4


title: 108_953_E029_TCZ + LPS _6h [0700836531]


title: M1T1R1

value: Male 1


title: Meningioma 680

description: Hybridized to OncoScanHD

value: M


title: Meningioma 681

description: Hybridized to OncoScanHD


title: F5T1R2

value: Female 5


title: 107_953_E029_TCZ + RPMI_6h [0700836521]

value: PBMCs

value: Healthy control

value: WT/WT


title: 113_091_P07_RPMI_24h [0700836581]

value: Patient

value: mut/mut

value: RPMI


title: F5T2R1

value: Blood

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: Meningioma 679

description: Hybridized to OncoScanHD

value: Brain

value: F


title: pre_B-cell_acute-lymphoblastic_cell_line_REH

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University Medical Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC (EPIC) array Beadchip using standard Illumina protocol

scan_protocol: EPIC arrays were scanned using the Illumina iScan and all samples passed the MethylAid data quality assessment by using the corresponding R script (version R-3.6.2)

data_processing: GenomeStudio software (v2011.1; methylation module 1.9.0; Illumina Inc., USA)

label: Cy5 and Cy3

source_name: cell line

label_protocol: Standard Illumina Protocol

growth_protocol: cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol: genomic DNA was harvested using Allprep DNA/RNA Mini Kit (Qiagen).

tag: sample type

value: pre B-cell acute-lymphoblastic cell line


title: 22-02925

value: whole brain

value: EOfAD-like


title: 112_953_E030_TCZ+ IL1B_6h [0700836571]

tag: donor

value: Tocilizumab + IL1B


title: Meningioma 683

first: Scott

last: Ryall

description: Hybridized to OncoScanHD

value: M


title: Meningioma 678

description: Hybridized to OncoScanHD


title: 22-02924


title: F1T1R1

value: Female 1

value: Serum and Plasma kit (Qiagen)


title: 105_953_E028_TCZ + LPS _6h [0700836501]

value: PBMCs

value: Healthy control

value: WT/WT

value: Tocilizumab + LPS

tag: timepoint


title: F1T3R1

value: Blood


title: Meningioma 677

description: Hybridized to OncoScanHD


title: F2T2R1

value: Female 2

value: Healthy Subject


title: 104_953_E028_TCZ + RPMI_6h [0700836491]

value: Tocilizumab + RPMI


title: 103_953_E002_TCZ+ IL1B_6h [0700836481]


title: Meningioma 675

description: Hybridized to OncoScanHD

value: Brain


title: 102_953_E002_TCZ + LPS _6h [0700836471]


title: 106_953_E028_TCZ+ IL1B_6h [0700836511]


title: F1T1R2

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: Merkel_cell carcinoma_cell_line_MKL-2

value: Merkel cell carcinoma cell line


title: Meningioma 676

description: Hybridized to OncoScanHD

value: F


title: F2T3R2


title: Meningioma 674

description: Hybridized to OncoScanHD


title: 101_953_E002_TCZ + RPMI_6h [0700836461]


title: F2T1R1


title: Meningioma 673

description: Hybridized to OncoScanHD


title: Meningioma 672

description: Hybridized to OncoScanHD


title: 98_091_S05_TCZ + RPMI_6h [0700836431]

value: Sibling

value: WT/mut


title: 100_091_S05_TCZ+ IL1B_6h [0700836451]

value: Tocilizumab + IL1B


title: M5T2R2

value: Male 5

value: Serum and Plasma kit (Qiagen)


title: F1T2R1

value: Female 1


title: Merkel_cell carcinoma_cell_line_MKL-1


title: 96_091_S03_TCZ + LPS _6h [0700836411]

value: PBMCs


title: M3T2R2

value: Male 3


title: Meningioma 669

description: Hybridized to OncoScanHD


title: F3T1R2

value: Female 3

value: Blood


title: M3T3R1

value: Healthy Subject


title: Meningioma 671

description: Hybridized to OncoScanHD


title: F3T2R1


title: Merkel_cell carcinoma_tissue_L-MCC17

source_name: skin

value: Merkel cell carcinoma tissue


title: 97_091_S03_TCZ+ IL1B_6h [0700836421]


title: Meningioma 668

description: Hybridized to OncoScanHD

value: Brain

value: M


title: Merkel_cell carcinoma_cell_line_WaGa


title: 99_091_S05_TCZ + LPS _6h [0700836441]

value: Tocilizumab + LPS


title: M4T3R2

value: Male 4

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: M5T3R1


title: 93_091_P12_TCZ + LPS _6h [0700836381]

value: Patient

value: mut/mut


title: F1T2R2


title: 92_091_P12_TCZ + RPMI_6h [0700836371]

value: Tocilizumab + RPMI


title: 95_091_S03_TCZ + RPMI_6h [0700836401]

value: Sibling

value: WT/mut


title: Meningioma 665

description: Hybridized to OncoScanHD

value: F


title: Meningioma 664

description: Hybridized to OncoScanHD


title: M4T2R2

value: Serum and Plasma kit (Qiagen)


title: Meningioma 667

description: Hybridized to OncoScanHD


title: Merkel_cell carcinoma_tissue_L-MCC7

source_name: skin face


title: 90_091_P07_TCZ + LPS _6h [0700836351]

value: PBMCs


title: Meningioma 663

description: Hybridized to OncoScanHD

source_name: Meningioma Tissue


title: Akata Induced, 1

city: New Orleans

first: Truong

middle: D

last: Nguyen

state: Louisiana

address: 1700 Tulane Avenue

department: Pathology

institute: Tulane University, School of Medicine

description: Library name: Sample1

data_processing:
HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Servant N., Varoquaux N., Lajoie BR., Viara E., Chen CJ., Vert JP., Dekker J., Heard E., Barillot E. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x http://www.genomebiology.com/2015/16/1/259
Assembly: hg38_plus_EBV
Supplementary files format and content: The BEDPE file containing loops was generated using our Python script.

source_name: Akata

growth_protocol: EBV+ Burkitt's Lymphoma lines, Akata (gift from Kenzo Takada) were cultured in RPMI (Fisher Scientific, cat no. SH30027) supplemented with 10% FBS (ThermoFisher Scientific, cat no. 10437) at 37°C with 5% CO2. Akata cells harboring the pCEP4-BMRF1p-GFP reporter plasmid were cultured in the presence of 250 ug/ml hygromycin to retain the episomal reporter.

extract_protocol: Dovetail® Micro-C Kit

treatment_protocol: BCR crosslinking: Affinipure goat α-Human IgG (Jackson ImmunoResearch, cat no. 109-005-003) was added to cell culture media of Akata cells harboring the pCEP4-BMRF1p-GFP reporter plasmid to a final concentration of 10 μg/ml. Cells were incubated for 24 h prior to harvesting for FACS isolation.

value: Akata

value: B-cells

value: IgG


title: Merkel_cell carcinoma_cell_line_MCC13

value: Merkel cell carcinoma cell line


title: Merkel_cell carcinoma_tissue_L-MCC16

source_name: inguinal lymph node

value: Merkel cell carcinoma tissue


title: Meningioma 666

institute: Brigham and Women's Hospital

description: Hybridized to OncoScanHD

value: Brain

value: M


title: Meningioma 670

description: Hybridized to OncoScanHD


title: Merkel_cell carcinoma_tissue_L-MCC18

source_name: axillary lymph node


title: M4T3R1

value: Male 4

value: Blood

value: Healthy Subject

value: Entire cardiovascular system


title: Merkel_cell carcinoma_tissue_L-MCC11

source_name: gluteus area


title: M4T1R1

value: total cell-free biofluid RNA


title: Merkel_cell carcinoma_tissue_L-MCC13


title: 91_091_P07_TCZ+ IL1B_6h [0700836361]

source_name: PBMCs

value: Patient

value: mut/mut

value: Tocilizumab + IL1B


title: 89_091_P07_TCZ + RPMI_6h [0700836341]

value: Tocilizumab + RPMI


title: Meningioma 662

description: Hybridized to OncoScanHD

value: F


title: Merkel_cell carcinoma_tissue_L-MCC12


title: M5T1R2

value: Male 5

value: Serum and Plasma kit (Qiagen)


title: A549 shDUSP23 SUS rep1

city: Seoul

first: Sangmyung

last: Rhee

state: State...

address: 84, Heukseok-ro

country: South Korea

institute: Chung-ang university

description:
Library name: A549_shDUSP23_1
H-R-ShDU2_TS-N3_S30

data_processing:
mRNA-Seq reads were aligned using STAR 2.7.1a, with reference indices generated from genome assembly or representative transcript sequences. Transcript assembly, quantification, and differential expression analysis were performed using FPKM values processed in the DESeq2 package (version 1.32.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: Lung tumor

extract_protocol:
Total RNA was isolated from cells using the RNAiso Plus reagent (#9109; TaKaRa, Tokyo, Japan) according to the manufacturer’s instructions.
Total RNA was extracted from A549 shMock and shDUSP23 tumor cluster cells. RNA quality was assessed using a bioanalyzer (RNA 600 Nano kit; Agilent Technologies, Santa Clara, CA, USA). Library construction was performed using an mRNA-seq Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. High-throughput sequencing was performed using the NovaSeq 6000 platform (Illumina).

value: Lung tumor

value: Lung adenocarcinoma cell line

value: DUSP23 knockdown


title: Merkel_cell carcinoma_tissue_L-MCC14

source_name: upper arm

value: Merkel cell carcinoma tissue


title: 94_091_P12_TCZ+ IL1B_6h [0700836391]

value: PBMCs


title: Meningioma 661

city: Boston

description: Hybridized to OncoScanHD

value: Brain


title: 88_953_E030_IL1B _6h [0700836331]

value: Healthy control

value: WT/WT


title: M5T2R1

value: Blood

value: Healthy Subject

value: Entire cardiovascular system


title: A549 shMock SUS rep2

description:
Library name: A549_shMock_2
H-R-shM_TS-N4_S29

value: Wild type


title: 87_953_E030_LPS_6h [0700836321]

value: LPS


title: A549 shDUSP23 SUS rep2

description:
Library name: A549_shDUSP23_2
H-R-ShDU2_TS-N4_S31


title: Meningioma 660

description: Hybridized to OncoScanHD


title: M5T3R2

value: total cell-free biofluid RNA


title: Merkel_cell carcinoma_tissue_L-MCC10

source_name: subcutis


title: Meningioma 659

description: Hybridized to OncoScanHD

value: M


title: Merkel_cell carcinoma_tissue_L-MCC15


title: F5T3R2

value: Female 5


title: Merkel_cell carcinoma_tissue_L-MCC8

source_name: skin upper leg


title: A549 shMock SUS rep1

description:
Library name: A549_shMock_1
H-R-shM_TS-N3_S28


title: 86_953_E030_RPMI_6h [0700836311]

value: RPMI


title: Subject_12_Nasal

city: Cambridge

first: Menna

last: Clatworthy

address: Cambridge Biomedical Campus, Francis Crick Ave, Trumpington

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description:
Library name: MC9785407
GEX

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v6.0.1 (10x Genomics)
Assembly: GRCH38
Supplementary files format and content: Compressed tab-separated values files, unfiltered single cell barcode gene expression matrix

source_name: Nasal

extract_protocol:
Nasal tissue samples were minced, digested in a DNAse/Liberase solution for 30 minutes, strained and washed to create a single cell suspension. Paired whole blood was centrifuged layered on Histopaque 1077, with PBMC layer extracted and washed. Nasal and PBMC samples were loaded as single cell suspensions without sorting
ScRNAseq gene expression libraries were contructed in accordance with the manufacturer protocol (Single cell 5' v2 protocol, 10x Genomics)

value: Nasal

value: Conval COVID


title: 85_953_E029_IL1B _6h [0700836301]


title: Meningioma 658

description: Hybridized to OncoScanHD


title: M1T2R2

value: Male 1

value: Serum and Plasma kit (Qiagen)


title: Subject_12_Blood

description:
Library name: MC9785374
GEX


title: Meningioma 657

description: Hybridized to OncoScanHD

value: F


title: M1T3R1


title: Subject_11_Blood

description:
Library name: MC9785373
GEX


title: 84_953_E029_LPS_6h [0700836291]

value: PBMCs


title: Meningioma 656

description: Hybridized to OncoScanHD

value: Brain


title: 83_953_E029_RPMI_6h [0700836281]

value: Healthy control

value: WT/WT


title: M2T3R2

value: Male 2

value: Blood

value: Healthy Subject


title: 82_953_E028_IL1B _6h [0700836271]


title: Subject_10_Nasal

description:
Library name: MC9785372
GEX


title: Meningioma 655

description: Hybridized to OncoScanHD


title: Merkel_cell carcinoma_tissue_L-MCC4

source_name: face (temporal)

value: Merkel cell carcinoma tissue


title: M5T1R1

source_name: Blood

value: Male 5

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: 81_953_E028_LPS_6h [0700836261]

value: LPS


title: Subject_10_Blood

description:
Library name: MC9785371
GEX


title: Merkel_cell carcinoma_tissue_L-MCC5

source_name: lower leg


title: F4T2R2

value: Female 4


title: 80_953_E028_RPMI_6h [0700836251]

value: RPMI


title: 79_953_E002_IL1B _6h [0700836241]


title: F4T3R1


title: Meningioma 653

description: Hybridized to OncoScanHD

value: M


title: Subject_9_Nasal

description:
Library name: MC9785370
GEX

value: Nasal

value: Conval COVID


title: Subject_9_Blood

description:
Library name: MC9785369
GEX


title: Subject_8_Nasal

description:
Library name: MC9785368
GEX


title: Meningioma 651

description: Hybridized to OncoScanHD

value: F


title: 78_953_E002_LPS_6h [0700836231]

value: PBMCs


title: Meningioma 654

description: Hybridized to OncoScanHD

value: Brain


title: Meningioma 652

description: Hybridized to OncoScanHD


title: F5T3R1

value: Female 5

value: Serum and Plasma kit (Qiagen)


title: Merkel_cell carcinoma_tissue_L-MCC2

source_name: para-aortic lymph node


title: Subject_8_Blood

description:
Library name: MC9785367
GEX

value: Blood


title: 77_953_E002_RPMI_6h [0700836221]

value: Healthy control

value: WT/WT


title: M2T1R1

value: Male 2

value: Healthy Subject


title: Meningioma 650

description: Hybridized to OncoScanHD


title: F5T2R2

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: 76_091_S05_IL1B _6h [0700836211]

value: Sibling

value: WT/mut


title: Meningioma 649

description: Hybridized to OncoScanHD


title: M2T2R2


title: Subject_7_Blood

description:
Library name: MC9785365
GEX

value: Active COVID


title: Meningioma 648

description: Hybridized to OncoScanHD


title: Meningioma 647

description: Hybridized to OncoScanHD


title: 74_091_S05_RPMI_6h [0700836191]

value: RPMI


title: Subject_6_Nasal

description:
Library name: MC9785364
GEX

value: Nasal


title: M2T3R1


title: M3T1R2

value: Male 3


title: Subject_6_Blood

description:
Library name: MC9785363
GEX


title: M3T2R1


title: 72_091_S03_LPS_6h [0700836171]

value: PBMCs

value: LPS


title: Meningioma 646

description: Hybridized to OncoScanHD

value: Brain

value: M


title: Meningioma 645

description: Hybridized to OncoScanHD

value: F


title: M3T3R2

value: Blood

value: Serum and Plasma kit (Qiagen)


title: Subject_5_Blood

description:
Library name: MC9785361
GEX


title: 73_091_S03_IL1B _6h [0700836181]


title: Meningioma 644

description: Hybridized to OncoScanHD


title: 71_091_S03_RPMI_6h [0700836161]


title: 70_091_P12_IL1B _6h [0700836151]

value: Patient

value: mut/mut


title: Subject_4_Nasal

description:
Library name: MC9785360
GEX


title: Meningioma 643

description: Hybridized to OncoScanHD


title: F5T1R1

value: Female 5

value: Healthy Subject

value: Entire cardiovascular system


title: Subject_7_Nasal

description:
Library name: MC9785366
GEX


title: M3T1R1

value: total cell-free biofluid RNA


title: 69_091_P12_LPS_6h [0700836141]


title: Subject_4_Blood

description:
Library name: MC9785359
GEX

value: Active COVID


title: Meningioma 642

description: Hybridized to OncoScanHD


title: M4T1R2

value: Male 4


title: 75_091_S05_LPS_6h [0700836201]

value: Sibling

value: WT/mut


title: Subject_3_Blood

description:
Library name: Sample_Fq6_COVID
GEX


title: 68_091_P12_RPMI_6h [0700836131]

value: PBMCs

value: RPMI


title: Meningioma 641

description: Hybridized to OncoScanHD

value: Brain


title: Subject_5_Nasal

description:
Library name: MC9785362
GEX

value: Nasal


title: M4T2R1


title: 67_091_P07_IL1B _6h [0700836121]


title: Meningioma 640

description: Hybridized to OncoScanHD

value: F


title: Subject_3_Nasal

description:
Library name: Sample_Fq5_COVID
GEX


title: F2T2R2

value: Female 2

value: Blood


title: 66_091_P07_LPS_6h [0700836111]

value: Patient

value: LPS


title: 65_091_P07_RPMI_6h [0700836101]

value: mut/mut


title: Subject_2_Nasal

description:
Library name: Sample_Fq4_COVID
GEX


title: Meningioma 638

description: Hybridized to OncoScanHD


title: Subject_1_Nasal

description:
Library name: Sample_Fq2_COVID
GEX


title: Meningioma 636

description: Hybridized to OncoScanHD


title: F4T3R2

value: Female 4

value: Healthy Subject

value: Serum and Plasma kit (Qiagen)


title: F3T3R2

value: Female 3

value: Entire cardiovascular system

value: total cell-free biofluid RNA


title: Meningioma 637

description: Hybridized to OncoScanHD


title: 64_953_E030_TCZ+ IL1B_2h [0700836091]

value: Healthy control

value: WT/WT

value: Tocilizumab + IL1B


title: Subject_1_Blood

description:
Library name: Sample_Fq1_COVID
GEX

value: Active COVID


title: M1T1R2

value: Male 1


title: 63_953_E030_TCZ + LPS _2h [0700836081]

value: PBMCs

value: Tocilizumab + LPS


title: Meningioma 635

description: Hybridized to OncoScanHD

value: Brain

value: M


title: SK-N-BE(2) cell, RA+NEN, 24h, Replicate3

city: palo alto

first: Jiangbin

last: ye

state: California

address: 269 Campus Drive CCSR-South 1245

institute: Stanford university

description: Library name: RA+NEN3

data_processing:
kallisto
slueth
Assembly: hg19
Supplementary files format and content: csv files include TPM for each sample

source_name: bone marrow

growth_protocol: SK-N-BE(2)l cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS), extra 1mM and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The total RNA from treatment groups were extracted using Trizol reagent (#15596026) according to the manufacture's instructions
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA

treatment_protocol: Proper number of cells were plate in 10cm dishes before  treatment by 1µM RA or 1µM RA and RA+ NEN for 24h.  Each group contain 3 biological replicates.

value: bone marrow

value: neuroblastoma cell

value: RA+NEN


title: M1T2R1

value: Blood

value: Healthy Subject


title: 61_953_E029_TCZ+ IL1B_2h [0700836061]


title: 62_953_E030_TCZ + RPMI_2h [0700836071]

value: Tocilizumab + RPMI


title: Meningioma 634

description: Hybridized to OncoScanHD


title: SK-N-BE(2) cell, RA+NEN, 24h, Replicate2

description: Library name: RA+NEN2


title: M1T3R2

value: Entire cardiovascular system

value: Serum and Plasma kit (Qiagen)


title: Meningioma 639

description: Hybridized to OncoScanHD

value: F


title: SK-N-BE(2) cell, RA+NEN, 24h, Replicate1

description: Library name: RA+NEN1


title: F2T3R1

value: Female 2

value: total cell-free biofluid RNA


title: Meningioma 631

description: Hybridized to OncoScanHD


title: Subject_2_Blood

description:
Library name: Sample_Fq3_COVID
GEX

value: Active COVID


title: 59_953_E029_TCZ + RPMI_2h [0700836041]

value: Healthy control

value: WT/WT


title: KO P2 #7620 biol rep 4

city: OKLAHOMA CITY

middle: E

last: Kovats

state: OK

address: 825 NE 13TH ST.

institute: OKLAHOMA MEDICAL RESEARCH FOUNDATION

description:
Library name: 22B
KO_7620_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx

data_processing:
Raw sequencing reads were trimmed, and aligned using the Bluebee FWD-UMI Mouse (GRCm38) Lexogen QuantSeq 2.6.1 Pipeline. Gene annotation was done using biomaRt in R. Principal component analysis of the sample groups were made for further quality control using R.
Differentially expressed analyses were performed using the empirical Bayes approach implemented in the R package DESeq2. Genes were removed from analysis if all reads from any sample were 0 or the sum across samples was less than 10. Genes were considered differentially expressed if the absolute value of the fold-change ≥ 2 and the False Discovery Rate (FDR) P-value adjusted ≤ 0.05.
Assembly: Bluebee FWD-UMI Mouse (GRCm38)
Supplementary files format and content: normalized counts for each sample after DESeq2, plus DESeq2 analysis results

source_name: lung

extract_protocol:
Arcturus PicoPure RNA isolation kit, Ovation Pico SL WTA system V2 kit (Nugen)
Lexogen Quantseq RNAseq 3' mRNA kit

treatment_protocol: cells isolated from collagenase-digested lungs on day 5 post IAV infection, stained with fluorochrome-labeled Abs specific for surface proteins, and sorted on a FACS ARIA

value: lung

value: dendritic cell cDC2B

value: IAV infection


title: 58_953_E028_TCZ+ IL1B_2h [0700836031]

value: PBMCs

value: Tocilizumab + IL1B


title: Meningioma 629

description: Hybridized to OncoScanHD

source_name: Meningioma Tissue

value: Brain


title: KO P2 #7589 biol rep 2

description:
Library name: 26A
KO_7589_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx


title: Meningioma 626

description: Hybridized to OncoScanHD


title: Meningioma 625

description: Hybridized to OncoScanHD

value: M


title: Meningioma 627

description: Hybridized to OncoScanHD


title: CH5_1

city: Chongqing

first: Jingzhen

last: Zhu

address: Xinqiaozhengjie

department: Department of Urology, Urologic Surgery Center

country: China

institute: Xinqiao Hospital, Third Military Medical University (Army Medical University)

description:
Library name: CH5_1
PC-3cells,cepharanthine hydrochloride(5μM),Day3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: excel files include RPKM values for each Sample

growth_protocol: PC-3 prostate cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37

extract_protocol:
RNA was harvested using TRIzol™.  1.2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: All cells in the presence of 10% FBS ,after which they were fed every other day with DMEM containing 10% FBS,until day 3

value: prostate cancer cell

value: WT

value: Cepharanthine hydrochloride(5μM),Day3


title: WT P2 #7624 biol rep 3

description:
Library name: 15A
WT_7624_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx


title: KO P2 #7617 biol rep 3

description:
Library name: 18B
KO_7617_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx


title: KO P2 #7576 biol rep 1

description:
Library name: 18A
KO_7576_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx


title: 54_953_E002_TCZ + LPS _2h [0700835991]

value: Tocilizumab + LPS


title: SK-N-BE(2) cell, RA, 24h, Replicate1

description: Library name: RA1

value: bone marrow

value: neuroblastoma cell

value: RA


title: WT P2 #7618 biol rep 4

description:
Library name: 11B
WT_7618_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx


title: CH5_3

description:
Library name: CH5_3
PC-3cells,cepharanthine hydrochloride(5μM),Day3


title: Meningioma 630

description: Hybridized to OncoScanHD

value: F


title: 55_953_E002_TCZ+ IL1B_2h [0700836001]

value: Healthy control


title: SK-N-BE(2) cell, RA, 24h, Replicate2

description: Library name: RA2


title: 56_953_E028_TCZ + RPMI_2h [0700836011]

value: WT/WT

value: Tocilizumab + RPMI


title: CH5_2

description:
Library name: CH5_2
PC-3cells,cepharanthine hydrochloride(5μM),Day3


title: WT P2 #7580 biol rep 2

description:
Library name: 7A
WT_7580_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx

value: lung

value: dendritic cell cDC2B


title: 60_953_E029_TCZ + LPS _2h [0700836051]

value: PBMCs


title: NC_3

description:
Library name: NC_3
PC-3cells,control,Day3


title: WT P2 #7579 biol rep 1

description:
Library name: 3A
WT_7579_P2
DESeq2_DE_KO_P2_vs_WT_P2.xlsx

value: IAV infection


title: 52_091_S05_TCZ+ IL1B_2h [0700835971]

value: Sibling

value: WT/mut

value: Tocilizumab + IL1B


title: Meningioma 623

description: Hybridized to OncoScanHD

value: Brain


title: 53_953_E002_TCZ + RPMI_2h [0700835981]


title: SK-N-BE(2) cell, RA, 24h, Replicate3

description: Library name: RA3


title: 57_953_E028_TCZ + LPS _2h [0700836021]


title: Meningioma 628

description: Hybridized to OncoScanHD

value: M


title: Meningioma 622

description: Hybridized to OncoScanHD


title: KO CD103 #7620 biol rep 4

description:
Library name: 21B
KO_7620_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx

value: dendritic cell cDC1


title: 51_091_S05_TCZ + LPS _2h [0700835961]

value: Tocilizumab + LPS


title: Meningioma 621

description: Hybridized to OncoScanHD


title: NC_1

description:
Library name: NC_1
PC-3cells,control,Day3

value: prostate cancer cell

value: WT


title: Meningioma 620

description: Hybridized to OncoScanHD

value: F


title: Meningioma 619

description: Hybridized to OncoScanHD


title: Meningioma 618

description: Hybridized to OncoScanHD


title: NC_2

description:
Library name: NC_2
PC-3cells,control,Day3


title: smallRNA_3end_globalseq_totalRNA_rep2

city: La Jolla

first: Cody

last: Ocheltree

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: totalRNA_2
D501, D702

data_processing:
FASTQ files were first subjected to 3’ adaptor and PCR duplicate removal using custom python scripts (https://pypi.org/project/jla-demultiplexer/).
Residual Illumina adaptor sequence was removed with Cutadapt (62).
Reads were mapped to the human genome (version hg38) using STAR 2.7.11b (63).
Gene-specific 3’ end information and graphs were subsequently generated using Tailer (https://github.com/TimNicholsonShaw/tailer) (Nicholson-Shaw, RNA, 2022) using the global alignment mode.
A three-pass alignment strategy against a small RNA genome which was developed in the lab and described previously (Ma et. al. 2024), but with a modification in order to improve the local alignment step which provides post-transcriptional nucleotide modification information. After performing a three-pass end-to-end alignment, which includes a 5’-hard clip of 10 nucleotides to facilitate alignment of reads with post-transcriptional nucleotide modifications, the aligned reads were grouped by gene and re-converted into individual fastq files for each gene detected using bedtools and samtools. Individual-gene fastq files were then re-aligned with a three-pass local alignment to single-gene genomic sequences corresponding to the gene each file was previously aligned to in the end-to-end alignment. Gene-specific 3’ end information and graphs were subsequently generated using Tailer (https://github.com/TimNicholsonShaw/tailer) using the global alignment mode.
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

source_name: HEK 293T-REx

extract_protocol:
Small RNA (100-500 bp) was isolated with a 9% polyacrylamide/6M urea denaturing gel. Ribosomal (r)RNAs were depleted using RiboCOP rRNA depletion kit (Lexogen) per manufacturer’s recommendations. A 3' adaptor containing a 15 or 16 bp randomer was ligated to RNAs. Nascent RNA was isolated with Click-it nascent RNA capture kit (Thermo Fisher). A fraction of material was prepared as total RNA and was not processed with nascent capture. A 5' adaptor was ligated following reverse transcription using a primer against the 3' adaptor.
The cDNA was amplified in two stages of Polymerase Chain Reaction (PCR) using Q5 DNA polymerase (NEB). For the first PCR reaction, the cDNA library was amplified using 3’ adaptor primer (AR17) and a primer complementary to the 5’ adaptor (RC_3Tr3) for 8 cycles. The PCR product was purified by AMPure XP beads (Beckman Coulter) per manufacturer’s recommendation. The second PCR reaction was performed using Illumina Trueseq D50X and D70X primers for 18 cycles.

treatment_protocol: HEK293 T-REx cells were incubated with either 0.5 mM 5-ethynyl uridine (EU; Thermo Fisher) or an equivalent volume of DMSO for 2 hours and harvested in TRIzol reagent (Thermo Fisher).

value: HEK 293T-REx

tag: molecule type

value: totalRNA


title: KO CD103 #7576 biol rep 1

description:
Library name: 17A
KO_7576_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx


title: smallRNA_3end_globalseq_nascent_rep3

description:
Library name: nascent_3
D502, D703

value: nascent


title: 50_091_S05_TCZ + RPMI_2h [0700835951]

value: Tocilizumab + RPMI


title: Meningioma 617

description: Hybridized to OncoScanHD


title: 47_091_S03_TCZ + RPMI_2h [0700835921]


title: Meningioma 616

description: Hybridized to OncoScanHD


title: KO CD103 #7617 biol rep 3

description:
Library name: 17B
KO_7617_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx

value: lung


title: KO CD103 #7587 biol rep 2

description:
Library name: 21A
KO_7587_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx


title: 49_091_S03_TCZ+ IL1B_2h [0700835941]

value: PBMCs


title: WT CD103 #7580 biol rep 2

description:
Library name: 5A
WT_7580_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx

value: IAV infection


title: 48_091_S03_TCZ + LPS _2h [0700835931]

value: Sibling


title: smallRNA_3end_globalseq_totalRNA_rep1

description:
Library name: totalRNA_1
D501, D701


title: WT CD103 #7618 biol rep 4

description:
Library name: 9B
WT_7618_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx


title: WT CD103 #7588 biol rep 3

description:
Library name: 9A
WT_7588_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx


title: smallRNA_3end_globalseq_nascent_rep2

description:
Library name: nascent_2
D502, D702


title: smallRNA_3end_globalseq_nascent_rep1

description:
Library name: nascent_1
D502, D701


title: 45_091_P12_TCZ + LPS _2h [0700835901]

value: Patient

value: mut/mut


title: Meningioma 615

description: Hybridized to OncoScanHD

value: Brain


title: WT CD103 #7579 biol rep 1

description:
Library name: 1A
WT_7579_CD103
DESeq2_DE_KO_CD103_vs_WT_CD103.xlsx


title: P4O2 COVID-19, stimulation, patient 3 post-COVID

city: Amsterdam

first: Anke-Hilse

last: Maitland-van der Zee

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description:
Library name: S06
S4.300 (PE150)

data_processing:
To remove low quality reads/read-ends and sequencing adapters, readouts were trimmed using Trim-Galore v0.6.10, which acts as a wrapper around FastQC v0.12.1 and cutadapt v4.3
Transcripts were aligned against the human genome (GRCh38.p14) using Salmon v1.10.1
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: nasal epithelial cells

extract_protocol:
RNA was harvested using the Bioline ISOLATE II mini kit.
KAPA mRNA Hyperprep capture according to the manufacturer's protocol

value: nasal epithelial cells

value: 3-6 months post-COVID