title: MCF7 cells, control, PTN, biological rep1

city: Brno

first: Pavel

last: Bouchal

address: Kamenice 5

department: Biochemistry

country: Czech Republic

institute: Masaryk University, Faculty of Science

data_processing:
The raw reads were filtered to remove the adaptors and low-quality bases using Trimmomatic (v0.36) with Truseq2 s well as any reads that were shorter than 65 bases.
Filtered reads were aligned to the human genome (Homo_sapiens.GRCh38.dna.primary_assembly) using STAR (v2.5.2b) in end-to-end mode to scan splice junctions.
Counts in exon genomic features were calculated subread (v1.5.2).
Differential expression analysis was performed in R 3.5.3 under the Deseq2 package version 1.22.2.
BiomaRt package version 2.38.0. was used for annotation the results from differential expression analysis.
Assembly: genome: Ensembl GRCh38, annotation: Ensembl v94
Supplementary files format and content: excel file DESeq2.xlsx containing results from differential gene expression by DESeq2; raw_counts.xlsx, normalized_counts.xlsx - excel files containing information of raw and normalized counts for each gene, respectively

source_name: breast cancer cell line MCF7

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; high glucose) with 10% fetal bovine serum (Sigma-Aldrich, USA) at 37°C in 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated according to TRI reagent protocol (Sigma-Aldrich, T9424) and its concentration was determined using Qubit RNA BR assay kit (Q10210, Invitrogen). 240 ng of total RNA at 20ng/µl was used in RNA-Seq analysis.
The TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) was used to convert total RNA into a library of template molecules. Library was validated using Bioanalyzer (DNA 1000 Kit, Agilent) and quantified according to manufacturer instructions by qPCR (KAPA Library Quantification Kit Illumina platforms, Kapa Biosystems) using Quant studio (QuantStudio 5, Thermo Fisher Scientific).

treatment_protocol: 24 hrs after passage, cells were treated with parthenolide at IC50 concentration (12.8 µM) or DMSO and incubated for 24 hrs.

value: breast cancer cell line MCF7

value: epithelial cell

value: mock

value: parthenolide


title: 2736_P15_IP

status: Public on Sep 06 2023

type: SRA

city: Tokyo

first: Yukiko

last: Gotoh

state: Tokyo

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

country: Japan

institute: University of Tokyo

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 16.0 dpc stage of mouse NPCs (FAC-sorted, HMGA2 OE, replicate 1).

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: neural progenitor cells

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

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

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

tag: strain background

value: ICR

tag: genotype/variation

value: HMGA2 overexpression

tag: Stage

tag: cell type

value: neural progenitor cells (NPCs)

tag: chip antibody

value: H3K27me3 (Millipore, 07-449)


title: MCF7 cells, control, PTN, biological rep2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: genotype

tag: treatment


title: Ring1A -/-; Ring1B f/f -cre_RNAseq [Hiseq2000]

description: total RNA in 18.5 dpc stage of mouse NPCs (CD133high) deficient for Ring1A and floxed for Ring1B. Ring1A -/-,Ring1B fl/fl mice were subjected to tamoxifen treatment through maternal intraperitoneal injection at 15.5dpc.


title: endometrial biopsy, X210427

type: RNA

city: Parkville

first: Peter

last: Rogers

state: VIC

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

department: Department of Obstetrics and Gynaecology

country: Australia

institute: University of Melbourne

description: Sample X210427 from batch 7

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol with Illumina iScan Reader.

data_processing: Data generated by Illumina iScan Reader was processed by Illumina GenomeStudio software. The data was then normalized in R using background normalization and robust spline normalization with the lumi package and batch corrected with ComBat using the sva package.

label: biotin

source_name: Human endometrium

label_protocol: Biotinylated cRNA was prepared using the Ambion Illumina TotalPrep RNA amplification kit.

extract_protocol: Total RNA was extracted from homogenized endometrial tissues using RNA lysis solution (RLT buffer) and RNeasy Plus Mini Kit according to the manufacturer's instructions.

tag: tissue

value: Human endometrium

tag: age

tag: cycle stage

tag: pod

tag: batch

value: batch 7


title: MCF7 cells, control, biological rep2

value: DMSO


title: Human meningioma, FFPE [AM7]

city: San Francisco

first: William

last: Chen

state: CA

address: 1450 3rd Street, HD 402

country: USA

institute: UCSF

description: Nanostring nCounter

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

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

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

source_name: Human meningioma, FFPE

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

tag: disease

value: meningioma


title: 16.5_dpc_RNAseq rep2 [Hiseq2000]

description: total RNA in 16.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: MCF7 cells, DSC1, biological rep2

value: DSC1 overexpression


title: 16.5_dpc_RNAseq rep1 [Hiseq2000]


title: 14.5_dpc_RNAseq rep2 [Hiseq2000]

description: total RNA in 14.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: endometrial biopsy, X210099

description: Sample X210099 from batch 1

value: batch 1


title: MCF7 cells, control, biological rep1


title: MCF7 cells, DSC1, biological rep1


title: 12.5_dpc_RNAseq rep2 [Hiseq2000]

description: total RNA in 12.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: 14.5_dpc_RNAseq rep1 [Hiseq2000]


title: Human meningioma, FFPE [AM6]

description: Nanostring nCounter

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


title: MCF7 cells, DSC1, PTN, biological rep2


title: Human meningioma, FFPE [AM5]

description: Nanostring nCounter


title: 12.5_dpc_RNAseq rep1 [Hiseq2000]


title: MCF7 cells, DSC1, PTN, biological rep1


title: E12.5_HMGA2_ChIPseq [Hiseq2000]

description: Immunoprecipitated by anti-HMGA2 antibody in 12.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).

value: HMGA2 (Cell Signaling, #5629)


title: 18.5_dpc_input_ChIPseq [Hiseq2000]

description: Non-immunoprecipitated sample (=input) in 18.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: 14.5_dpc_input_ChIPseq [Hiseq2000]

description: Non-immunoprecipitated sample (=input) in 14.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: 16.5_dpc_H3K27me3_ChIPseq [Hiseq2000]

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 16.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: 12.5_dpc_input_ChIPseq [Hiseq2000]

description: Non-immunoprecipitated sample (=input) in 12.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: Spic-ChIP-seq-OE12-2iLd25_1

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

country: United Kingdom

institute: Queen's University Belfast

data_processing:
FASTQ reads were mapped against mouse mm9 reference genome using Bowtie2. Reads were filtered for high quality mapping with SAMtools q>15 and PCR duplicates were removed using PicardTools. SAM files were converted to BAM using SAMTools. BAM files were converted to BED files using BEDTools, and reads were extended by 160 nt and converted to BedGraph using bamCoverage tool from the deepTools suite. BedGraphs were converted to BigWig files using bedGraphToBigWig from UCSC tool suite for further visualization using Integrative Genomics Viewer browser.  Peak calling was performed using MACS2 58 and assigned peaks were filtered against the ENCODE black list regions. For read counting in assigned peaks, BAM files were first converted to BED files and read counting was performed using BEDTools. Read count across different samples were normalized for library size using DESeq2 (bioconductor.org) and values were used for differential peak analysis with the following criteria: minimum read number >20 reads per peak in at least one sample, P-Val<0.05, FC>=2). To identify genes in the vicinity to ChIP-seq/ ATAC-seq peaks, BEDTools window with -w 100,000 was used.
Assembly: mm9
Supplementary files format and content: xls, normalized ChIP-seq peaks
Supplementary files format and content: bigwig

source_name: embryonic

growth_protocol: mESCs (E14Tg2a) were routinely cultured in serum+LIF (SL) condition, on 0.1% gelatine-coated plates. To make SL medium, High glucose DMEM (Gibco) was supplemented with 14% heat-inactivated FBS (Gibco), 1% Glutamax (Gibco), 1% Na-pyruvate (Gibco), 1% penicillin/streptomycin (Gibco), 55 µM Bmercaptoetanol, and LIF (1,000 U ml−1, Millipore). For serum-free 2iL condition, cells were cultured on gelatine-coated dishes in NDiff 227 (TaKaRa) media supplemented with penicillin/streptomycin, LIF, and two inhibitors, GSK3 inhibitor CHIR99021 (Axon, 3 μM) and MEK inhibitor PD0325901 (Axon, 1 μM). For single inhibitors treatment experiments, only the noted inhibitor was omitted from the complete 2iL medium.

extract_protocol:
mESCs were cultured in SL or 2iL medium for 3 days. For each replicate, 15 million cells were fixed with 1% paraformaldehyde. Fixed cells were consecutively treated with buffers A (148mM NaCl, 1.48 mM EDTA, 0.74 mM EGTA, 74mM HEPES), Buffer-B (10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, 0.25% Triton-x100), and Buffer-C (150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES). Isolated nuclei were lysed in freshly made sonication buffer (150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, 0.15% SDS, 1% TritonX-100, 1X protease inhibitor) and samples were sonicated using Biorapture Pico (Diagenode). Sonicated chromatin was precleared using BSA blocked protein A/G beads (Invitrogen), and was further incubated with 10 µg of primary antibody (anti-FLAG from Sigma for NANOG ChIP, and anti-GFP from Abcam for SPIC-GFP ChIP). After overnight incubation, the immune complexes were captured by incubation with BSA blocked protein A/G beads for 2h on a rotating wheel at 4ºC. Beads were washed with ChIP wash buffer 1 (2 mM EDTA, 20 mM Tris pH:8 150 mM NaCl, 1% TritonX-100, 0.1% SDS), Buffer-2 (2 mM EDTA, 20 mM Tris pH:8 150 mM NaCl, 1% TritonX-100, 0.1% SDS, 500 mM NaCl) and Buffer-3 (1 mM EDTA, 10 mM Tris pH:8) for 10 minutes. Samples were then incubated with fresh ChIP elution buffer (0.1 M NaHCO3, 1% SDS) for 30 min at RT. Eluted chromatin was de-crosslinked overnight by adding 5M NaCl and proteinase K (final 10mg/ml) and incubating at 65ºC. DNA was purified using the MinElute PCR Purification Kit (Qiagen)
ChIP-Rx-seq libraries were subjected to library preparation using the KAPA HyperPrep kit (Roche) according to manufacturer’s instructions with dual indices and sequencing on an Illumina HiSeq 2500 sequencer (dual-indexed 50-bp paired-end reads).

value: embryonic

value: Embryonic-stem-cells

value: SPIC-GFP-OE


title: 18.5_dpc_H3K27me3_ChIPseq [Hiseq2000]

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 18.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: 16.5_dpc_input_ChIPseq [Hiseq2000]

description: Non-immunoprecipitated sample (=input) in 16.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: E14_Spic-KO_d20_Rep1

data_processing:
FASTQ reads were mapped against mouse mm9 reference genome using STAR and default setting. Genome_build: mm9
Assembly: mm9
Supplementary files format and content: processed_file_Spic_RNA_2iLd20_analysis.xls; xls, DESEQ results
Supplementary files format and content: bedgraph

extract_protocol:
RNA extraction was done using RNAsey mini kit (Qiagen) and according to the manufacturer’s instructions.
RNA-seq libraries were prepared using 1 µg of total RNA isolated with RNAeasy kit (Qiagen) and using polyA-RNA-seq profiling method (Novogene). The final libraries were sequenced on a HiSeq-2500 Illumina sequencer.

value: SPIC-KO


title: 14.5_dpc_H3K27me3_ChIPseq [Hiseq2000]

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 14.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: Human meningioma, FFPE [AM3]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM2]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM71]

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised according to manufacturer's instructions

scan_protocol: Arrays were imaged using Illumina iScan, using standard settingsusing standard settings

data_processing:
Refer to manuscript, Chen, Choudhury et al.
Average Beta or normalized (provide the normalization method) Average Beta

label: cy3, cy5

label_protocol: Standard Illumina protocol

extract_protocol: Qiagen FFPE Allprep or DNA extraction kits were used. Deparrafinization was performed with xylene.


title: Human meningioma, FFPE [RT103]

description: Nanostring nCounter


title: E14_Spic-OE_d20_Rep2


title: Human meningioma, FFPE [AM4]

description: Nanostring nCounter


title: E14_Spic-KO_d20_Rep2


title: Human meningioma, FFPE [AM69]


title: Human meningioma, FFPE [AM1]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT102]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM68]


title: Spic-ChIP-seq-OE12-2iLd25_2


title: E14_Spic-OE_d20_Rep1


title: Human meningioma, FFPE [AM67]


title: Human meningioma, FFPE [AM70]


title: Human meningioma, FFPE [RT101]

description: Nanostring nCounter


title: E14_WT_2i_d20_Rep2

value: WT


title: Human meningioma, FFPE [AM66]


title: Human meningioma, FFPE [RT100]

description: Nanostring nCounter


title: 12.5_dpc_H3K27me3_ChIPseq [Hiseq2000]

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 12.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: Human meningioma, FFPE [AM65]


title: Human meningioma, FFPE [AM64]


title: Human meningioma, FFPE [RT99]

description: Nanostring nCounter


title: E14_WT_2i_d20_Rep1


title: Human meningioma, FFPE [AM61]


title: Tumor #2 Tom+ cells

city: Madrid

first: Carmen

middle: Gómez-Escolar

last: Arias

state: Madrid

address: Calle Melchor Fernández Almagro 3

country: Spain

institute: CNIC

data_processing:
Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina
Trimmed sequence reads were mapped to GRCm38 using Salmon v1.9
Read count extraction and normalization were performed using tximport with flags: tx2gene = tx2gene and countsFromAbundance = "lengthScaledTPM"
Assembly: GRCm38
Supplementary files format and content: comma-separateb values file of TPMs

molecule: polyA RNA

source_name: λ-MYC Tom+/ki

extract_protocol:
B220+IgM+Tom+ (Tom+) and B220+IgM+Tom- (Tom-) spleen cells were purified using Sy3200 Cell Sorter (SonyBiotechnology). Total RNA was extracted using PicoPureTM RNA Isolation Kit (ThermoFisher Scientific)
Barcoded RNA-seq libraries using the NEBNext RNA Library preparation kit (Illumina). The size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip.

value: spleen

value: B220+ IgM+ Tom+


title: Human meningioma, FFPE [AM63]


title: Human meningioma, FFPE [RT98]

description: Nanostring nCounter


title: Tumor #2 Tom- cells

value: B220+ IgM+ Tom-


title: Human meningioma, FFPE [AM57]


title: Human meningioma, FFPE [AM58]


title: Human meningioma, FFPE [AM56]


title: Human meningioma, FFPE [RT97]

description: Nanostring nCounter


title: Tumor #1 Tom- cells


title: Human meningioma, FFPE [AM60]


title: Tumor #1 Tom+ cells


title: Human meningioma, FFPE [AM59]


title: Human meningioma, FFPE [AM55]


title: Adipo_KO_Tick_Rep3

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

country: China

institute: Zhejiang University

data_processing:
Partek Flow
RNAseq data were trimmed and aligned to the mouse genome ( from Ensembl), with associated annotation file using STAR (v2.7.3a).
The aligned reads were quantified to Ensembl transcripts using the Partek E/M algorithm and the subsequent steps were performed on gene-level annotation followed by total count normalization.
The counts generated were processed by gene set analysis (GSA).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes baseMean for each gene

source_name: Ear

extract_protocol:
Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit according to the manufacturer’s instructions (Qiagen, # 74704).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The adiponectin wildtype and knockout mice were challenged by ticks

value: Ear

value: Adipo-/-

value: Tick bite


title: Human meningioma, FFPE [RT95]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM54]


title: Human meningioma, FFPE [RT94]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM52]


title: Adipo_KO_Tick_Rep2


title: Human meningioma, FFPE [RT93]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM50]


title: Human meningioma, FFPE [AM62]


title: Human meningioma, FFPE [AM49]


title: Human meningioma, FFPE [AM48]


title: Adipo_KO_Tick_Rep1


title: Human meningioma, FFPE [RT92]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM47]


title: Human meningioma, FFPE [RT96]

description: Nanostring nCounter


title: Adipo_WT_Tick_Rep3

value: Adipo+/+


title: Human meningioma, FFPE [AM45]


title: Adipo_WT_Tick_Rep2


title: Human meningioma, FFPE [AM44]


title: Human meningioma, FFPE [RT91]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT90]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM43]


title: Human meningioma, FFPE [AM42]


title: Human meningioma, FFPE [RT89]

description: Nanostring nCounter


title: Adipo_WT_Tick_Rep1


title: Human meningioma, FFPE [AM41]


title: Human meningioma, FFPE [AM53]


title: Human meningioma, FFPE [AM40]


title: Human meningioma, FFPE [AM39]


title: Human meningioma, FFPE [RT87]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT88]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM51]


title: Human meningioma, FFPE [AM38]


title: Human meningioma, FFPE [RT86]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM36]


title: KO1-Liver

city: Hirakata

first: Rei

last: Yoshimoto

state: Osaka

address: 45-1 Nagaotoge-cho

department: Faculty of Agriculture

institute: Setsunan University

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using HISAT2
bedgraph files were generated using bedtools genomecov
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: Liver

extract_protocol:
Total RNAs were prepared with RNeasy Mini Kit (QIAGEN).
rRNA depletion was performed with NEBNext rRNA Depletion Kit v2 (NEB) The preparation of RNA libraries were performed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: Liver

tag: strain

value: CARNMT1 KO


title: Human meningioma, FFPE [AM35]

value: meningioma


title: Human meningioma, FFPE [AM34]


title: Human meningioma, FFPE [AM37]


title: Human meningioma, FFPE [AM33]


title: Human meningioma, FFPE [RT85]

description: Nanostring nCounter


title: WT2-Liver


title: Human meningioma, FFPE [AM31]


title: Human meningioma, FFPE [AM30]


title: Human meningioma, FFPE [RT84]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT83]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM32]


title: WT1-Liver


title: KO3-Liver


title: Human meningioma, FFPE [AM27]


title: Human meningioma, FFPE [AM29]


title: KO3-Brain

source_name: Brain

value: Brain


title: Human meningioma, FFPE [AM28]


title: Human meningioma, FFPE [RT81]

description: Nanostring nCounter


title: KO2-Liver


title: KO2-Brain


title: Human meningioma, FFPE [RT80]

description: Nanostring nCounter


title: KO1-Brain


title: Human meningioma, FFPE [AM26]


title: Human meningioma, FFPE [AM25]


title: WT3-Brain


title: WT2-Brain


title: Human meningioma, FFPE [AM19]


title: Human meningioma, FFPE [RT82]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT77]

description: Nanostring nCounter


title: WT3-Liver


title: Human meningioma, FFPE [AM17]


title: Human meningioma, FFPE [AM24]


title: Human meningioma, FFPE [AM23]


title: Human meningioma, FFPE [AM13]


title: dendritic cells, hypodermis, replicate 2

city: Bethesda

first: Keisuke

last: Nagao

state: MD

address: 10 Center Dr, Bldg 10, 12N240B

institute: National Institutes of Health

description: Hypodermal dendritic cells #2

data_processing:
The FASTQ files with 125bp paired-end reads were processed using Trimmomatic (v0.30) to remove adaptors and low-quality bases. The trimmed FASTQ data were aligned to mouse genome (GRCm38) with STAR (v2.4.2a) using GENCODE mouse gtf file version 4 (Ensembl 78). About 90% of ~42 million reads per sample were mapped to mouse genome uniquely for a total of 97% mapping rate. The STAR software was also used to generate the gene read counts. Statistical analysis was performed in R computing environment (https://www.r-project.org). The gene read count data from STAR for all samples were normalized with the R Package limma (v3.34.9).
Assembly: GRCm38
Supplementary files format and content: Excel files containing raw read counts.

source_name: Hypodermis

extract_protocol:
Back skins from C57BL/6 female adult mice were harvested after shaving with an electric clipper. Subcutaneous fat was removed from hypodermis and hypodermal layers were physically isolated from the dermis with forceps. Dermis was isolated from epidermis after 45min of an enzymatic treatment with 0.15% Trypsin/0.75mM EDTA. Isolated dermis and hypodermis were each minced with scissors and digested for 2H at 37°C in RPMI supplemented with 5% FCS and containing 0.25mg/mL of liberase T-Flex and 1ug/mL of DNase I. Cells were isolated from each layer and stained with antibodies as well as with propidium iodide (PI) before being FACS sorted as dendritic cells (PI–, singlet, CD45+, CD11b+, Ly6c-lo, MHCII-hi, CD64–), CCR2+ macrophages (PI–, singlet, CD45+, CD11b+, Ly6c-lo, CD11c-mid/lo, CD64+, CCR2+) and CCR2– macrophages (PI–, singlet, CD45+, CD11b+, Ly6c-lo, CD11c-mid/lo, CD64+, CCR2–). Cells were then washed, counted and used for RNA-sequencing. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared using the SMART-Seq Ultra Low Input RNA kit with Nextera XT library prep protocol according to the manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: Hypodermis

value: Dendritic cells

value: 8-10 weeks

tag: Sex

value: Female

value: No treatment


title: Human meningioma, FFPE [AM22]


title: Human meningioma, FFPE [AM21]


title: Human meningioma, FFPE [AM11]


title: Human meningioma, FFPE [RT79]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM20]


title: Human meningioma, FFPE [RT73]

description: Nanostring nCounter


title: WT1-Brain

value: WT


title: Human meningioma, FFPE [AM18]


title: Human meningioma, FFPE [AM16]


title: dendritic cells, hypodermis, replicate 3

description: Hypodermal dendritic cells #3


title: Human meningioma, FFPE [RT76]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM8]


title: CCR2- macrophages, hypodermis, replicate 2

description: Hypodermal CCR2- macrophages #2

value: CCR2- macrophages


title: CCR2- macrophages, hypodermis, replicate 1

description: Hypodermal CCR2- macrophages #1


title: Human meningioma, FFPE [AM5]


title: Human meningioma, FFPE [RT74]

description: Nanostring nCounter


title: CCR2+ macrophages, hypodermis, replicate 3

description: Hypodermal CCR2+ macrophages #3

value: CCR2+ macrophages


title: Human meningioma, FFPE [AM14]


title: Human meningioma, FFPE [AM12]


title: Human meningioma, FFPE [AM10]


title: dendritic cells, hypodermis, replicate 1

description: Hypodermal dendritic cells #1


title: CCR2- macrophages, hypodermis, replicate 3

description: Hypodermal CCR2- macrophages #3


title: Human meningioma, FFPE [AM7]


title: Human meningioma, FFPE [RT69]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM2]


title: CCR2+ macrophages, hypodermis, replicate 2

description: Hypodermal CCR2+ macrophages #2


title: Human meningioma, FFPE [RT78]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM1]


title: CCR2+ macrophages, hypodermis, replicate 1

description: Hypodermal CCR2+ macrophages #1


title: Human meningioma, FFPE [AM9]


title: Human meningioma, FFPE [AM6]


title: Human meningioma, FFPE [AM15]


title: Human meningioma, FFPE [RT72]

description: Nanostring nCounter


title: dendritic cells, dermis, replicate 3

description: Dermal dendritic cells #3

source_name: Dermis

value: Dermis


title: Human meningioma, FFPE [RT71]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT98]


title: Human meningioma, FFPE [RT17]


title: dendritic cells, dermis, replicate 2

description: Dermal dendritic cells #2


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description: Nanostring nCounter


title: Human meningioma, FFPE [AM4]


title: Human meningioma, FFPE [RT70]

description: Nanostring nCounter


title: CCR2- macrophages, dermis, replicate 3

description: Dermal CCR2- macrophages #3


title: Human meningioma, FFPE [KM8]


title: Human meningioma, FFPE [RT75]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM3]


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title: Human meningioma, FFPE [RT6]


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description: Nanostring nCounter


title: Human meningioma, FFPE [G62]


title: Human meningioma, FFPE [RT95]


title: Human meningioma, FFPE [RT62]

description: Nanostring nCounter


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description: Nanostring nCounter


title: Human meningioma, FFPE [G96]


title: dendritic cells, dermis, replicate 1

description: Dermal dendritic cells #1


title: Human meningioma, FFPE [RT20]


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT78]


title: Human meningioma, FFPE [RT50]


title: Human meningioma, FFPE [G71]


title: Human meningioma, FFPE [RT59]


title: Human meningioma, FFPE [RT63]

description: Nanostring nCounter


title: Human meningioma, FFPE [G97]


title: CCR2- macrophages, dermis, replicate 2

description: Dermal CCR2- macrophages #2


title: p8m_aor

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Raw sequence data were processed to remove adapters from inserts of between 14 and 38 nt in length. Trimmed reads were mapped to human mature miRNA sequences, downloaded from miRBase (v21).  Only miRNAs with a read count higher than 10 in at least 1 sample were considered in the differential expression analysis.
Differential expression analyses were performed by DESeq2 using default parameters.
P-values were corrected using the Benjamini Hochberg procedure for the control of the False Discovery Rate.
Only genes showing a p-value <= 0.05 following the FDR adjustment were considered to be differentially expressed (DEGs).
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw reads counts for each Sample

source_name: aorta

growth_protocol: Procedures involving animals and their care were conducted in accordance with institutional guidelines, in compliance with national (D.L. No. 26, March 4, 2014, G.U. No. 61 March 14, 2014) and international laws and policies (EEC Council Directive 2010/63, September 22, 2010: Guide for the Care and Use of Laboratory Animals, United States National Research Council, 2011). The experimental protocol was approved by the Italian Ministry of Health.  C57BL/6J (Bl/6, RRID:MGI:5655668) male mice, Low-Density Lipoprotein receptor gene knock-out (Ldlr-KO, RRID:MGI:4443062) and Proprotein convertase subtilisin/kexin 9 gene knock-out (Pcsk9-KO, RRID:MGI:3577440) male mice in the C57BL/6 background were purchased from Charles River Laboratories (Calco, Italy).

extract_protocol:
Trizol protocol
Total RNA and miRNAs were extracted simultaneously with NucleoSpin® miRNA columns (Macherey-Nagel, Düren, Germany), according to the manufacturer’s instructions
Indexed cDNA libraries from the RNA fraction at low molecular weight were prepared using the TruSeq small RNA sample Preparation kit (Illumina, San Diego, CA) according to the manufacturer’s protocol and recommendations. Single end sequencing (1 × 50b), after fluorimetric quantification, was performed on an Illumina Hiseq II platform.

treatment_protocol: Mice were housed at constant temperature and relative humidity. From the sixth week from birth, mice had free access to either standard rodent chow containing 3% fat (4RF21, Mucedola, Settimo Milanese, Italy) or Western-type diet containing 0.2% cholesterol and 21% fat (TD.88137, Envigo, Bresso, Italy) and tap water to 22 weeks of age.

value: aorta

tag: subject

tag: diet

value: wd


title: Human meningioma, FFPE [RT58]

description: Nanostring nCounter


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description: Nanostring nCounter


title: p8f_aor


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title: CCR2- macrophages, dermis, replicate 1

description: Dermal CCR2- macrophages #1


title: Human meningioma, FFPE [RT64]

description: Nanostring nCounter


title: p7m_aor


title: Human meningioma, FFPE [RT61]

description: Nanostring nCounter


title: Human meningioma, FFPE [G99]


title: CCR2+ macrophages, dermis, replicate 2

description: Dermal CCR2+ macrophages #2


title: Human meningioma, FFPE [RT72]


title: Human meningioma, FFPE [KM6]


title: Human meningioma, FFPE [G122]


title: CCR2+ macrophages, dermis, replicate 1

description: Dermal CCR2+ macrophages #1


title: p7_liv

source_name: liver

value: liver


title: Human meningioma, FFPE [RT59]

description: Nanostring nCounter


title: p7_jej

source_name: jejunum

value: jejunum


title: Human meningioma, FFPE [RT47]


title: Human meningioma, FFPE [G67]


title: Human meningioma, FFPE [RT35]


title: Human meningioma, FFPE [RT53]


title: Human meningioma, FFPE [G108]


title: CCR2+ macrophages, dermis, replicate 3

description: Dermal CCR2+ macrophages #3


title: Human meningioma, FFPE [G116]


title: Human meningioma, FFPE [RT57]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT56]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT7]


title: Human meningioma, FFPE [RT55]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT82]


title: p7_ile

source_name: ileum

value: ileum


title: p7_duo

source_name: duodenum

value: duodenum


title: Human meningioma, FFPE [G60]

value: meningioma


title: Human meningioma, FFPE [G110]


title: Human meningioma, FFPE [RT37]


title: p7_wat

source_name: WAT

value: WAT


title: Human meningioma, FFPE [RT34]


title: p7_bra

source_name: brain

value: brain


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description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


title: p6_wat


title: Human meningioma, FFPE [RT63]


title: Human meningioma, FFPE [RT91]


title: Human meningioma, FFPE [RT52]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT47]

description: Nanostring nCounter


title: p6_jej


title: Human meningioma, FFPE [RT51]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT68]


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title: Human meningioma, FFPE [G64]


title: p6_ile


title: Human meningioma, FFPE [RT45]

description: Nanostring nCounter


title: p6_duo


title: Human meningioma, FFPE [RT44]

description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


title: p5_wat


title: Human meningioma, FFPE [RT42]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT48]


title: Human meningioma, FFPE [RT102]


title: Human meningioma, FFPE [KM2]


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT76]


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT77]


title: p6_bra


title: Human meningioma, FFPE [RT64]


title: Human meningioma, FFPE [RT33]


title: Human meningioma, FFPE [RT86]


title: Human meningioma, FFPE [RT12]


title: p5_duo


title: Human meningioma, FFPE [G76]


title: Human meningioma, FFPE [RT38]

description: Nanostring nCounter


title: p5_liv


title: Human meningioma, FFPE [G84]


title: p5_jej


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description: Nanostring nCounter


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT36]

description: Nanostring nCounter


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description: Nanostring nCounter


title: Human meningioma, FFPE [G93]


title: Human meningioma, FFPE [G54]


title: p3m_aor

value: chow


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description: Nanostring nCounter


title: p3_wat


title: Human meningioma, FFPE [RT41]


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title: Human meningioma, FFPE [G120]


title: Human meningioma, FFPE [RT9]


title: Human meningioma, FFPE [RT25]


title: p4f_aor


title: Human meningioma, FFPE [G114]


title: p3_jej


title: Human meningioma, FFPE [G107]


title: p3_ile


title: Human meningioma, FFPE [G113]


title: Human meningioma, FFPE [G53]


title: Human meningioma, FFPE [RT69]


title: Human meningioma, FFPE [G125]


title: Human meningioma, FFPE [RT34]

description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT21]


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description: Nanostring nCounter


title: Human meningioma, FFPE [G123]


title: Human meningioma, FFPE [RT88]


title: p2_wat


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description: Nanostring nCounter


title: p3_duo


title: Human meningioma, FFPE [RT90]


title: Human meningioma, FFPE [RT58]


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description: Nanostring nCounter


title: p2_liv


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description: Nanostring nCounter


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description: Nanostring nCounter


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title: p2_duo


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description: Nanostring nCounter


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT4]


title: Human meningioma, FFPE [RT15]


title: Human meningioma, FFPE [G95]


title: p2_bra


title: Human meningioma, FFPE [RT52]


title: p1_wat


title: Human meningioma, FFPE [RT23]

description: Nanostring nCounter


title: Human meningioma, FFPE [G102]


title: p2_jej


title: Human meningioma, FFPE [KM-CM10]


title: Human meningioma, FFPE [RT21]

description: Nanostring nCounter


title: p1_liv


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description: Nanostring nCounter


title: Human meningioma, FFPE [G94]


title: Human meningioma, FFPE [G87]


title: Human meningioma, FFPE [KM1]


title: p2_ile


title: p1_jej


title: Human meningioma, FFPE [G48]


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description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT101]


title: p1_bra


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title: p1_duo


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title: Human meningioma, FFPE [G100]


title: Human meningioma, FFPE [RT94]


title: l8f_aor

value: Ldlr-KO


title: l7m_aor


title: Human meningioma, FFPE [RT65]


title: Human meningioma, FFPE [RT66]


title: Human meningioma, FFPE [G63]


title: l7_wat


title: l7_bra


title: Human meningioma, FFPE [RT16]

description: Nanostring nCounter


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description: Nanostring nCounter


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description: Nanostring nCounter


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title: l7_jej


title: Human meningioma, FFPE [G105]


title: Human meningioma, FFPE [RT11]

description: Nanostring nCounter


title: l7_ile


title: Human meningioma, FFPE [RT10]

description: Nanostring nCounter


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description: Nanostring nCounter


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title: Human meningioma, FFPE [RT5]


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title: l7_liv


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT9]

description: Nanostring nCounter


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title: Human meningioma, FFPE [RT8]

description: Nanostring nCounter


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT54]


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title: l6_jej


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title: Human meningioma, FFPE [RT6]

description: Nanostring nCounter


title: l6_ile


title: Human meningioma, FFPE [RT93]


title: Human meningioma, FFPE [G79]


title: Human meningioma, FFPE [RT5]

description: Nanostring nCounter


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title: l6_duo


title: Human meningioma, FFPE [RT4]

description: Nanostring nCounter


title: l6_liv


title: Human meningioma, FFPE [RT26]


title: Human meningioma, FFPE [G103]


title: Human meningioma, FFPE [RT92]


title: Human meningioma, FFPE [RT3]

description: Nanostring nCounter


title: Human meningioma, FFPE [RT24]


title: Human meningioma, FFPE [RT2]

description: Nanostring nCounter


title: l5_wat


title: Human meningioma, FFPE [RT44]


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description: Nanostring nCounter


title: l5_bra


title: Human meningioma, FFPE [RT81]


title: l6_bra


title: Human meningioma, FFPE [RT3]


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title: l5_jej


title: Human meningioma, Frozen [AP142]

description: Nanostring nCounter

source_name: Human meningioma, Frozen


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description: Nanostring nCounter


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description: Nanostring nCounter


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title: Human meningioma, FFPE [KM-M4]


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description: Nanostring nCounter


title: l4m_aor


title: Human meningioma, FFPE [RT51]


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description: Nanostring nCounter


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description: Nanostring nCounter


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title: Human meningioma, FFPE [RT42]


title: l3m_aor


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description: Nanostring nCounter


title: l3_wat


title: Human meningioma, Frozen [AP141]

description: Nanostring nCounter


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title: l4f_aor


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title: Human meningioma, Frozen [AP130]

description: Nanostring nCounter


title: l5_duo


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title: l3_jej


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description: Nanostring nCounter


title: Human meningioma, FFPE [G47 ]


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title: Human meningioma, FFPE [G111]


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description: Nanostring nCounter


title: Human meningioma, FFPE [RT84]


title: l3_duo


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description: Nanostring nCounter


title: l3_ile


title: Human meningioma, FFPE [RT79]


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description: Nanostring nCounter


title: l3_bra


title: ovary, BPA treated, biol rep3

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

data_processing:
The reads were first preprocessed with fastp (v 0.23.2), an ultra-fast all-in-one FASTQ preprocessor, which does quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data
The fastp-processed reads were then mapped on medaka genome (Oryzias_latipes.ASM223467v1) using STAR (2.7.7a)
Finally, DESeq2 (v1.34.0) was used to do the differential expression analysis
Assembly: Oryzias_latipes.ASM223467v1
Supplementary files format and content: pcos_rnaseq_normExp_diffExp_filtered-Padj.tsv : Normalized log2 expression values for all samples in tab-delimited text-file

organism: Oryzias latipes

source_name: ovary

extract_protocol:
The ovary of control and BPA lineage female fish (15 individuals from each lineage) were used for total RNA extraction by using Quick RNA/DNA Miniprep Plus Kit (#D-7003, Zymo Research, CA, USA) according to the manufacturer's protocol
The RNA of the ovary from three females were pooled as one biological replicate and there were three biological replicates per group. Transcriptome libraries were prepared using NEBNext Ultra II RNA Kit and manufacturer’s protocol.

value: ovary

value: BPA


title: ovary, BPA treated, biol rep2


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description: Nanostring nCounter


title: ovary, BPA treated, biol rep1


title: ovary, control, biol rep3

value: control


title: ovary, control, biol rep2


title: Human meningioma, Frozen [AP122]

description: Nanostring nCounter


title: l2_jej


title: ovary, control, biol rep1


title: Human meningioma, Frozen [AP121]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP119]

description: Nanostring nCounter


title: l2_ile


title: FigS4-siU1C-U1-rep3

city: La Jolla

first: Tiantai

last: Ma

address: 9500 Gilman Dr

department: Molecular Biology

institute: UCSD

data_processing:
Custom python scripts were used for demultiplexing, adaptor trimming, PCR duplicates removal, genome mapping, and 3' end information generation as previously described (Lardelli et al., Nat Genet, 2017).
Assembly: human genome (version hg38)
Supplementary files format and content: Taildata files containing reads mapped to each snRNA genes and the corresponding 3' end information.

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 nascent RNA sequencing, nascent RNA was captured as previously described (Lardelli and Lykke-Andersen, Genes Dev, 2020).
RNA adapters containing barcodes and 10- to 11-nt randommers (AG10/AG11) were ligated to the 3′ ends of 2.5 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 16–25 cycles of polymerase chain reaction (PCR) with snRNA 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 20 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. Plasmid transfections were performed using 2 μg plasmid per 3.5-cm well plates using Lipofectamine 2000 (Life Technologies) transfection reagent according to the manufacturer’s recommendations at 48 hours before harvest, unless specified otherwise.

value: HEK 293T-REx

tag: transfection


title: FigS4-siU1C-U1-rep1


title: l2_duo


title: FigS4-siU1A-U1-rep3


title: FigS4-siU1C-U1-rep2


title: Human meningioma, Frozen [AP117]

description: Nanostring nCounter


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description: Nanostring nCounter


title: l2_wat


title: l10m_aor


title: FigS4-si70K-U1-rep2


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title: Human meningioma, Frozen [AP116]

description: Nanostring nCounter


title: l2_liv


title: FigS3-siSmB-U4atac-rep1


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description: Nanostring nCounter


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description: Nanostring nCounter


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title: l1_jej


title: FigS3-siLuc-U4atac-rep2


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description: Nanostring nCounter


title: FigS2-TOE1-70K-rep3


title: l2_bra


title: FigS4-siU1A-U1-rep1


title: FigS3-siLuc-U4atac-rep1


title: FigS2-TOE1-70K-rep2


title: FigS2-TOE1-70K-rep1


title: l1_ile


title: FigS4-siU1A-U1-rep2


title: Human meningioma, Frozen [AP110]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP111]

description: Nanostring nCounter


title: l1_duo


title: FigS2-TOE1+70K-rep2


title: FigS3-siSmB-U4atac-rep2


title: FigS2-TOE1+70K-rep1


title: FigS2-TOE1+70K-rep3


title: Fig6-DE10-rep2


title: b8m_aor


title: Human meningioma, Frozen [AP107]

description: Nanostring nCounter


title: Fig6-DE10-rep1


title: Fig6-WT10-rep2


title: Fig6-WT1-rep2


title: Fig6-WT10-rep1


title: b8_liv


title: Human meningioma, Frozen [AP106]

description: Nanostring nCounter


title: Fig6-WT1-rep1


title: Fig6-WT0.1-rep2


title: Fig6-WT0.1-rep1


title: b8_jej


title: Human meningioma, Frozen [AP105]

description: Nanostring nCounter


title: Fig6-ctr-rep2

value: ctr


title: Fig6-ctr-rep1


title: Fig5-v15-super-rep3


title: l1_bra


title: b8_ile


title: b8_duo


title: Human meningioma, Frozen [AP103]

description: Nanostring nCounter


title: b8_bra


title: Human meningioma, Frozen [AP108]

description: Nanostring nCounter


title: Fig5-v15-super-rep2


title: b7f_aor


title: TBH-P4-2

city: Suzhou

first: Guihua

last: Jiang

address: Renai Road 199, Dushu Lake Higher Education Town

institute: Soochow University

data_processing:
Genome and gene model annotation referred to the silkworm database (http://metazoa.ensembl.org/Bombyx_mori/Info/Index).
The expression levels of genes and new transcripts were assessed by Transcripts Per Kilobase per Million mapped reads (TPM).
Conduct an overall quality evaluation of the comparison results of this sequencing, showcasing sequencing saturation, sequencing coverage, distribution of Reads in different regions, and distribution of Reads in different chromosomes.
On the basis of existing reference genomes, use software Cufflinks to assemble and splice mapped reads, compare them with known transcripts, obtain transcripts without annotated information, and perform functional annotation on potential new transcripts.
DESeq2 software was used to determine difference in gene expression between groups and the screening thresholds were |log2FC| ≥1 and p-adjust < 0.05.
Assembly: Bmori_2016v1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Bombyx mori

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000. The integrity of RNA was detected by agarose gel electrophoresis, and the RIN value was determined by Agilent 2100. Single database construction requires a total RNA amount of ≥ 1ug and a concentration of ≥ 35ng/ μ L. OD260/280 ≥ 1.8, OD260/230 ≥ 1.0.
The construction and sequencing of the transcriptional library was carried out by Shanghai Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China) using the Illumina Novaseq 6000 platform.

treatment_protocol: Ovary samples for RNA-sequencing (RNA-seq) were obtained by dissecting five female pupae at the P2 and P4 stages (n = 3).


title: TBH-P4-3


title: Human meningioma, Frozen [AP101]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP100]

description: Nanostring nCounter


title: b7_wat


title: TBH-P4-1


title: Fig5-v15-SmWT-rep2


title: Human meningioma, Frozen [AP109]

description: Nanostring nCounter


title: b7_liv


title: WT-P4-3


title: Human meningioma, Frozen [AP104]

description: Nanostring nCounter


title: Fig5-v15-SmWT-rep1


title: Fig5-v15-Sm-rep3


title: b7_jej


title: Human meningioma, Frozen [AP102]

description: Nanostring nCounter


title: WT-P4-1


title: Fig5-v15-Sm-rep2


title: b7_ile


title: Human meningioma, Frozen [AP99]

description: Nanostring nCounter


title: TBH-P2-3


title: Fig5-v15-super-rep1


title: b7_duo


title: Fig5-v15-SmWT-rep3


title: TBH-P2-2


title: Human meningioma, Frozen [AP97]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP96]

description: Nanostring nCounter


title: Fig5-v15-U1A-rep3


title: b7_bra


title: Human meningioma, Frozen [AP95]

description: Nanostring nCounter


title: Fig5-v15-Sm-rep1


title: WT-P2-3


title: Fig5-v15-U1A-rep2


title: Human meningioma, Frozen [AP94]

description: Nanostring nCounter


title: b6_liv


title: b6_wat


title: Human meningioma, Frozen [AP98]

description: Nanostring nCounter


title: WT-P2-2


title: Human meningioma, Frozen [AP93]

description: Nanostring nCounter


title: Fig5-v15-U1A-rep1


title: WT-P4-2


title: Human meningioma, Frozen [AP92]

description: Nanostring nCounter


title: Fig5-v15WT-rep3


title: WT-P2-1


title: b6_ile


title: Human meningioma, Frozen [AP91]

description: Nanostring nCounter


title: Fig5-v15WT-rep2


title: b6_jej


title: b6_duo


title: panda_RNA_rep2

city: Nanjing

first: Pengyue

last: Zhang

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argriculture University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to rice7 genome using hisat2 with default setting
The transcript abundance were calculated using stringtie with default settings
Genome_build: rice7
Supplementary_files_format_and_content: gtf with transcript abundance for each transcript

organism: Oryza sativa

source_name: seedling

growth_protocol: 13 hours daytime with the temperature of 23 oC, and 11 hours dark with  the temperate of 20 oC

extract_protocol:
Total RNA was extracted with Trizol (Sangon, China)
The cDNA libraries were constructed following Illumina standard protocols.

treatment_protocol: 2 replicates for RNA-seq

value: seedling

value: Taibei 309

value: panda-mutation


title: Human meningioma, Frozen [AP90]

description: Nanostring nCounter


title: panda_RNA_rep1


title: Human meningioma, Frozen [AP89]

description: Nanostring nCounter


title: TBH-P2-1


title: Fig5-v15WT-rep1


title: b4m_aor

value: aorta


title: Fig5-U1WT-rep3


title: WT_RNA_rep2

value: WT


title: Human meningioma, Frozen [AP88]

description: Nanostring nCounter


title: b6_bra

value: wd


title: WT_RNA_rep1


title: b8_wat


title: Human meningioma, Frozen [AP87]

description: Nanostring nCounter


title: Fig5-U1WT-rep2


title: Fig5-U1WT-rep1


title: PANDA anti-Flag Input

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the rice7 genome assembly using bowtie2 with default parameter
peaks were called using macs2 with follow settings : --extsize 200 -q 0.001 --nomodel
Genome_build: rice7
Supplementary_files_format_and_content: wig files were generated using deeptools; Scores represent enrichment

extract_protocol: The H3K27me3 ChIP-seq assay was performed using the panda mutant and its wild type cultivar ‘Taibei 309’. The PANDA ChIP-seq assay were performed using the plants expressing pUBI::PANDA-Flag in the japonica rice cultivar ‘Taibei 309’

treatment_protocol: 2 replicates for RNA-seq and 1 replicate for ChIP-seq

tag: antibody

value: anti-Flag (Cell Signaling, #14793


title: Fig4-SU1-70K-rep3


title: b3_wat


title: Human meningioma, Frozen [AP85]

description: Nanostring nCounter

value: meningioma


title: b4f_aor


title: Fig4-SU1-70K-rep2


title: Human meningioma, Frozen [AP86]

description: Nanostring nCounter


title: b3_liv

value: liver


title: PANDA anti-Flag

value: anti-Flag (Cell Signaling, #14793)


title: panda_Input


title: b3m_aor

value: chow


title: Fig4-SU1-70K-rep1


title: Fig4-superU1-rep3


title: panda_H3K27me3

value: H3K27me3 (Millipore 07-449)


title: Human meningioma, Frozen [AP84]

description: Nanostring nCounter


title: b3_jej

value: jejunum


title: WT_Input


title: Fig4-superU1-rep1


title: Human meningioma, Frozen [AP83]

description: Nanostring nCounter


title: b3_bra

value: brain


title: Human meningioma, Frozen [AP79]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP82]

description: Nanostring nCounter


title: Fig4-superU1-rep2


title: b2_wat

value: WAT


title: b3_ile

value: ileum


title: WT_H3K27me3


title: Human meningioma, Frozen [AP78]

description: Nanostring nCounter


title: b3_duo

value: duodenum


title: Human meningioma, Frozen [AP75]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP81]

description: Nanostring nCounter


title: Fig3-siSmB-U4-rep3

value: HEK 293T-REx


title: b2_liv


title: b2_ile


title: Fig3-siSmB-U5-rep3


title: Fig3-siSmB-U5-rep2


title: Fig3-siSmB-U5-rep1


title: Human meningioma, Frozen [AP76]

description: Nanostring nCounter


title: 253949444636-8

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: TRI reagent (Merck)

tag: cell type

value: human primary keratinocytes

tag: amount in (ug)

tag: rin number


title: Human meningioma, Frozen [AP73]

description: Nanostring nCounter


title: 253949444635-1

value: pre-miR-ctrl


title: Fig3-siSmB-U3-rep3

tag: cell line


title: b2_jej

tag: genotype


title: 253949444634-1

tag: treatment


title: Human meningioma, Frozen [AP71]

description: Nanostring nCounter


title: Fig3-siSmB-U3-rep2


title: 253949444635-8


title: b1_liv

tag: tissue


title: Fig3-siSmB-U4-rep2


title: Human meningioma, Frozen [AP74]

description: Nanostring nCounter


title: 253949444634-8


title: Fig3-siSmB-U2-rep2


title: Fig3-siSmB-U4-rep1


title: b2_duo


title: b2_bra


title: Human meningioma, Frozen [AP66]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP72]

description: Nanostring nCounter


title: b1_wat

value: aorta


title: Human meningioma, Frozen [AP70]

description: Nanostring nCounter


title: Fig3-siSmB-U3-rep1


title: Fig3-siSmB-U2-rep3


title: Human meningioma, Frozen [AP69]

description: Nanostring nCounter


title: b1_jej


title: 253949444636-1


title: b1_ile


title: mouse CD8, MEKi, 30hr, rep 2

city: Seattle

first: Hao

middle: Yuan

last: Kueh

state: WA

address: 3720 15th Ave NE

department: Bioengineering

institute: University of Washington

data_processing:
Raw fastq files from paired-end sequencing were aligned to the GRCm38/mm10 reference genome using Kallisto (v0.46.1) using the following code: kallisto quant -i transcriptome.idx -o kallisto -b 100 A4_1.fq.gz A4_2.fq.gz
Bootstrapped transcript-level abundance estimates generated by Kallisto were imported into R using sleuth (v0.30.0) for downstream analysis. Transcripts with low counts (<5) were removed.
Differentially expressed genes were identified with sleuth (v0.30.0) in R.
Assembly: GRCm38/mm10
Supplementary files format and content: The bootstrapped abundance.h5 file for each sample is a HDF5 binary file containing columns including Ensembl transcript ID and abundance estimates.
Supplementary files format and content: The abundance.tsv file for each sample is a plain text file containing columns including Ensembl transcript ID and abundance estimates.

source_name: Spleen

extract_protocol:
Cells were washed 1x in ice-cold PBS, resuspended in 350 ul Trizol (Invitrogen Cat # 15596018) and vortexed for 30 sec to lyse the cells and frozen at -80°C. RNA was then isolated with the RNeasy Micro kit (Qiagen Cat # 74004) starting from step 2.
RNA was eluted in RNase free water and shipped on dry ice to Novogene Corporation Inc. (Sacramento, CA) for library preparation and sequencing.

value: Spleen

value: CD8+ T cells

value: WT

tag: time

value: 30 hr

value: MEKi


title: mouse CD8, CsA, 30hr, rep 2

value: CsA


title: Nanog-ChIP-seq-KOF6-Rep1-SL

data_processing:
FASTQ reads were mapped against mouse mm9 reference genome using Bowtie2. Reads were filtered for high quality mapping with SAMtools q>15 and PCR duplicates were removed using PicardTools. SAM files were converted to BAM using SAMTools. BAM files were converted to BED files using BEDTools, and reads were extended by 160 nt and converted to BedGraph using bamCoverage tool from the deepTools suite. BedGraphs were converted to BigWig files using bedGraphToBigWig from UCSC tool suite for further visualization using Integrative Genomics Viewer browser.  Peak calling was performed using MACS2 58 and assigned peaks were filtered against the ENCODE black list regions. For read counting in assigned peaks, BAM files were first converted to BED files and read counting was performed using BEDTools. Read count across different samples were normalized for library size using DESeq2 (bioconductor.org) and values were used for differential peak analysis with the following criteria: minimum read number >20 reads per peak in at least one sample, P-Val<0.05, FC>=2). To identify genes in the vicinity to ChIP-seq/ ATAC-seq peaks, BEDTools window with -w 100,000 was used.
Assembly: mm9
Supplementary files format and content: xls, normalized ChIP-seq counts and peaks
Supplementary files format and content: bigwig

source_name: embryonic

growth_protocol: mESCs (E14Tg2a) were routinely cultured in serum+LIF (SL) condition, on 0.1% gelatine-coated plates. To make SL medium, High glucose DMEM (Gibco) was supplemented with 14% heat-inactivated FBS (Gibco), 1% Glutamax (Gibco), 1% Na-pyruvate (Gibco), 1% penicillin/streptomycin (Gibco), 55 µM Bmercaptoetanol, and LIF (1,000 U ml-1, Millipore). For serum-free 2iL condition, cells were cultured on gelatine-coated dishes in NDiff 227 (TaKaRa) media supplemented with penicillin/streptomycin, LIF, and two inhibitors, GSK3 inhibitor CHIR99021 (Axon, 3 μM) and MEK inhibitor PD0325901 (Axon, 1 μM). For single inhibitors treatment experiments, only the noted inhibitor was omitted from the complete 2iL medium.

value: embryonic

value: Embryonic stem cells

value: SPIC-KO+FLAG-NANOG

value: SL


title: Human meningioma, Frozen [AP68]

description: Nanostring nCounter

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

value: meningioma


title: b1_duo

value: chow


title: mouse CD8, MEKi+CsA, 30hr, rep 2

value: MEKi+CsA


title: b1_bra

value: brain


title: Fig3-siSmB-U1-rep3

value: HEK 293T-REx


title: Fig3-siLuc-U5-rep2


title: Nanog-ChIP-seq-OE6-Rep2-SL

value: SPIC-GFP-OE+FLAG-NANOG


title: Fig3-siSmB-U2-rep1


title: Human meningioma, Frozen [AP63]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP67]

description: Nanostring nCounter


title: Fig3-siSmB-U1-rep1


title: b11m_aor

value: WAT


title: Nanog-ChIP-seq-KOF6-Rep2-SL


title: Human meningioma, Frozen [AP56]

description: Nanostring nCounter


title: mouse CD8, DMSO, 30hr, rep 2

value: Spleen

value: DMSO


title: Human meningioma, Frozen [AP53]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP55]

description: Nanostring nCounter


title: Fig3-siLuc-U5-rep3


title: mouse CD8, MEKi+CsA, 30hr, rep 1

value: CD8+ T cells

value: WT


title: Nanog-ChIP-seq-OE6-Rep1-SL


title: Fig3-siLuc-U5-rep1


title: Human meningioma, Frozen [AP51]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP54]

description: Nanostring nCounter


title: Nanog-ChIP-seq-WT2-SL

value: WT+FLAG-NANOG


title: mouse CD8, DMSO, 30hr, rep 1

value: 30 hr


title: Fig3-siLuc-U4-rep2


title: Human meningioma, Frozen [AP52]

description: Nanostring nCounter


title: mouse CD8, MEKi, 30hr, rep 1

value: MEKi


title: mouse CD8, CsA, 30hr, rep 1

value: CsA


title: Nanog-ChIP-seq-KOF6-Rep2-2iLd3

description:
SPIC-KO+FLAG-NANOG-Rep2
ChIpseq_processed_data.xlsx (NANOG_ChIP_2id3_DESEQ)

value: embryonic

value: Embryonic stem cells

value: SPIC-KO+FLAG-NANOG


title: Human meningioma, Frozen [AP48]

description: Nanostring nCounter

value: meningioma


title: Nanog-ChIP-seq-OE6-Rep2-2iLd3

description:
SPIC-GFP-OE+FLAG-NANOG-Rep2
ChIpseq_processed_data.xlsx (NANOG_ChIP_2id3_DESEQ)


title: 24month_Ctrl

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Avenue

institute: Northwestern University

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw reads were aligned to mouse genome build mm10 using cellrange-atac v2.0.0
Assembly: refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: Filtered_peak_bc_matrix from cellranger-atac output with cell barcode as column name and peak as row name.

source_name: Skin

extract_protocol:
Total backskin from mice of indicated age was dissociated with collagenase treatment followed by trypsinization, single cell suspesion was obtained to load onto 10x Genomics single cell ATACseq profiling platform.
scATAC libraries were constructed following 10x Genomics single cell ATAC v1 protocol.

value: Skin

tag: age

value: Wildtype

value: No


title: Fig3-siLuc-U3-rep2

value: HEK 293T-REx


title: Fig3-siLuc-U4-rep1


title: Nanog-ChIP-seq-WT1-SL

value: SL


title: Human meningioma, Frozen [AP50]

description: Nanostring nCounter

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


title: Fig3-siLuc-U4-rep3


title: Human meningioma, Frozen [AP47]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP46]

description: Nanostring nCounter


title: TM4 cells,100nM AlCl3,Day30 rep3

first: Chen

last: junhan

address: Nanjing University, Hunan Road Street, Gulou District, Nanjing City

institute: Nanjing University

data_processing:
lllumina casava1.7 software used for basecalling.
The raw sequences were filtered to remove connector contamination, low-quality Reads, and reads with an N-content ratio greater than 5%.
The gene expression was calculated using FPKM (Fragments Per Kilobase Millon Mapped Reads) method.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: tab-limited text files include FPMK values for each sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: TM4 cells were cultured in DMEM-F12 medium containing 10% fetal bovine serum (FBS) at 37 ℃ and 5% CO2.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: TM4 cells were treated with 100nM AlCl3 for 30 days.

value: Sertoli Cell


title: TM4 cells,100nM AlCl3,Day30 rep2


title: Nanog-ChIP-seq-KOF6-Rep1-2iLd3

description:
SPIC-KO+FLAG-NANOG-Rep1
ChIpseq_processed_data.xlsx (NANOG_ChIP_2id3_DESEQ)

extract_protocol:
mESCs were cultured in SL or 2iL medium for 3 days. For each replicate, 15 million cells were fixed with 1% paraformaldehyde. Fixed cells were consecutively treated with buffers A (148mM NaCl, 1.48 mM EDTA, 0.74 mM EGTA, 74mM HEPES), Buffer-B (10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, 0.25% Triton-x100), and Buffer-C (150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES). Isolated nuclei were lysed in freshly made sonication buffer (150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, 0.15% SDS, 1% TritonX-100, 1X protease inhibitor) and samples were sonicated using Biorapture Pico (Diagenode). Sonicated chromatin was precleared using BSA blocked protein A/G beads (Invitrogen), and was further incubated with 10 µg of primary antibody (anti-FLAG from Sigma for NANOG ChIP, and anti-GFP from Abcam for SPIC-GFP ChIP). After overnight incubation, the immune complexes were captured by incubation with BSA blocked protein A/G beads for 2h on a rotating wheel at 4ºC. Beads were washed with ChIP wash buffer 1 (2 mM EDTA, 20 mM Tris pH:8 150 mM NaCl, 1% TritonX-100, 0.1% SDS), Buffer-2 (2 mM EDTA, 20 mM Tris pH:8 150 mM NaCl, 1% TritonX-100, 0.1% SDS, 500 mM NaCl) and Buffer-3 (1 mM EDTA, 10 mM Tris pH:8) for 10 minutes. Samples were then incubated with fresh ChIP elution buffer (0.1 M NaHCO3, 1% SDS) for 30 min at RT. Eluted chromatin was de-crosslinked overnight by adding 5M NaCl and proteinase K (final 10mg/ml) and incubating at 65ºC. DNA was purified using the MinElute PCR Purification Kit (Qiagen)
ChIP-Rx-seq libraries were subjected to library preparation using the KAPA HyperPrep kit (Roche) according to manufacturer’s instructions with dual indices and sequencing on an Illumina HiSeq 2500 sequencer (dual-indexed 50-bp paired-end reads).


title: TM4 cells,Control,Day30 rep2


title: Fig3-siSmB-U1-rep2


title: Human meningioma, Frozen [AP49]

description: Nanostring nCounter


title: Fig3-siLuc-U3-rep3


title: Fig3-siLuc-U2-rep2


title: Nanog-ChIP-seq-WT1-2iLd3

description:
WT+FLAG-NANOG-Rep1
ChIpseq_processed_data.xlsx (NANOG_ChIP_2id3_DESEQ)


title: ATAC-seq-SpicKO_H10-2iLd3

value: SPIC-KO


title: TM4 cells,100nM AlCl3,Day30 rep1


title: Nanog-ChIP-seq-WT2-2iLd3

description:
WT+FLAG-NANOG-Rep2
ChIpseq_processed_data.xlsx (NANOG_ChIP_2id3_DESEQ)


title: Nanog-ChIP-seq-OE6-Rep1-2iLd3

description:
SPIC-GFP-OE+FLAG-NANOG-Rep1
ChIpseq_processed_data.xlsx (NANOG_ChIP_2id3_DESEQ)

value: SPIC-GFP-OE+FLAG-NANOG


title: Fig3-siLuc-U3-rep1


title: ATAC-seq-SpicKO_F6-2iLd3


title: Human meningioma, Frozen [AP40]

description: Nanostring nCounter


title: TM4 cells,Control,Day30 rep3


title: Human meningioma, Frozen [AP43]

description: Nanostring nCounter


title: Fig3-siLuc-U2-rep3


title: TM4 cells,Control,Day30 rep1


title: Fig3-siLuc-U2-rep1


title: Human meningioma, Frozen [AP39]

description: Nanostring nCounter


title: Female 1 UI [X21649]

city: Minneapolis

first: Ling

last: Li

state: MN

address: Mcguire Translational Research Facility, 4-419

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

data_processing:
Raw sequencing reads were evaluated and trimmed using Trimmomatic
Trimmed reads were mapped to the mouse reference genome GRCm38 using HISAT2
RNA-seq raw counts for each gene were extracted using FeatureCounts
Assembly: GRCm38
Supplementary files format and content: xlsx file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from tissue homogenate using Trizol™ LS reagent (Thermo Fisher scientific) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions

value: brain

value: Wild-type C57BL/6

value: female

value: 10 month

value: Uninfected


title: Fig2-TOE1-_Sm-mut-rep3


title: ATAC-seq-SpicOE_cl5-2iLd3

value: embryonic

value: SPIC-GFP-OE


title: Fig3-siLuc-U1-rep1


title: ATAC-seq-WT_Rep2-2iLd3

value: Embryonic stem cells

value: WT


title: Human meningioma, Frozen [AP36]

description: Nanostring nCounter

value: meningioma


title: Human meningioma, Frozen [AP41]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP42]

description: Nanostring nCounter


title: Female 3 UI [X21226]


title: Fig3-siLuc-U1-rep3


title: Male 1 UI [X21646]

value: male


title: Female 2 UI [X21650]


title: Spic-ChIP-seq-OE12-2iLd3


title: Fig3-siLuc-U1-rep2


title: ATAC-seq-SpicOE_cl6-2iLd3


title: Female 3 SARS2 [X21212]


title: Spic-ChIP-seq-OE12-SL


title: Human meningioma, Frozen [AP35]

description: Nanostring nCounter


title: Male 3 UI [X21209]


title: Male 2 UI [X21648]


title: ATAC-seq-WT_Rep1-2iLd3


title: Spic-ChIP-seq-OE6-2iLd3


title: Fig2-TOE1+_Sm-mut-rep2


title: Fig2-TOE1-_Sm-mut-rep2


title: Male 3 SARS2 [X21193]


title: Fig2-TOE1+_Sm-mut-rep3


title: Human meningioma, Frozen [AP31]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP37]

description: Nanostring nCounter


title: RNA-seq-23-E14_2iD1_Rep1

data_processing:
FASTQ files against mouse rRNA, tRNA, snRNA, snoRNA, mtRNA sequences using Bowtie to deplete these small RNA contamination in sequenced libraries. We then mapped the cleaned files against mouse genome (mm9) using GSNAP and by applying the following parameters: -B 5 -t 15 -N 1 -E 100 -w 100000 -n 10 -s mm9refGene_splice. Genome_build: mm9
Assembly: mm9
Supplementary files format and content: processed_file_RNA-seq.xlsx; xls, DESEQ results
Supplementary files format and content: bigwig

extract_protocol:
RNA extraction was done using RNeasy mini kit (Qiagen) and according to the manufacturer’s instructions.
RNA-seq libraries were prepared using 1 µg of total RNA isolated with RNAeasy kit (Qiagen) and using KAPA RNA HyPerPrep Kit with RiboErase for rRNA depletion (Roche) according to manufacturer’s instructions. The final libraries were sequenced on a HiSeq-2500 Illumina sequencer.


title: Male 1 SARS2 [X21260]


title: Human meningioma, Frozen [AP33]

description: Nanostring nCounter


title: RNA-seq-24-E14_2iD1_Rep2


title: RNA-seq-22-spic_OE_2iD1_cl6


title: Human meningioma, Frozen [AP29]

description: Nanostring nCounter


title: Fig2-Sm-mut-rep2

value: Sm-mut


title: Female 1 SARS2 [X21252]


title: Human meningioma, Frozen [AP34]

description: Nanostring nCounter


title: Spic-ChIP-seq-OE6-SL


title: Fig2-TOE1+_Sm-mut-rep1

value: HEK 293T-REx


title: Fig2-70K-mut-rep3


title: Human meningioma, Frozen [AP32]

description: Nanostring nCounter


title: Fig2-TOE1-_Sm-mut-rep1


title: Human meningioma, Frozen [AP30]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP27]

description: Nanostring nCounter


title: Fig2-Sm-mut-rep1


title: BALB/c Murine Liver CD45+CD3-CD19-Siglec-F-Ly6g- cells, DOL17, BDL surgery, scRNA

first: Deborah

middle: R

last: Winter

address: 240 E. Huron Street, M300

description: 3' 10x Genomics

data_processing:
CITE-seq libraries were processed using the 10X GenomicsCell Ranger pipeline versions 3.1.0 (healthy and BA) and 6.0.0 (BDL) with mm10 3.0.0 as reference genome.  ADT reads were assigned to proteins using the included ADT_reference.csv.
Assembly: mm10
Supplementary files format and content: Matrix files with all data (raw)
Supplementary files format and content: Matrix files after filtering for cells (filtered)
Library strategy: CITE-seq

source_name: Whole Liver

extract_protocol:
On DOL 14 (healthy and BA) or 17 (BDL), whole liver tissue from 3 mice per experimental group was processed and pooled into a single-cell suspension. CD45+/CD3-/CD19-/Siglec-F-/Ly6g- immune cells were isolated by fluorescence-activated cell sorting (FACS)
CITE-seq libraries were prepared using the Single Cell 3’ v3 Reagent Kit on the 10x Genomics Chromium Controller.  Cellular mRNA and antibody-derived tag (ADT) oligos

treatment_protocol:
In the murine model of BDL, a midline incision was made to enter the peritoneal cavity and the common bile duct was exposed and separated from the adjacent portal vein and hepatic artery on BALB/c mice DOL 10.  An 8-0 nylon suture was used to tie two surgical knots and ligate the bile duct. The abdomen was then closed in two layers.  Sham surgery was performed on control mice at DOL 10 by creating an abdominal incision and closure without further manipulation.  All surgery was done using isoflurane inhalation for anesthesia, and efforts were made to minimize suffering.
In the murine model of BA, newborn BALB/c mice received intra-peritoneal injections of RRV at DOL 0 and developed sequelae of biliary obstruction by DOL 10-14.

value: Whole Liver

value: CD45+CD3-CD19-Siglec-F-Ly6g- cells

value: BALB/c

value: BDL surgery DOL10


title: Male 2 SARS2 [X21192]

value: brain


title: Female 2 SARS2 [X21195]

value: Wild-type C57BL/6


title: RNA-seq-21-spic_OE_2iD1_cl5


title: Human meningioma, Frozen [AP28]

first: William

last: Chen

address: 1450 3rd Street, HD 402

description: Nanostring nCounter


title: Human meningioma, Frozen [AP26]

description: Nanostring nCounter


title: BALB/c Murine Liver CD45+CD3-CD19-Siglec-F-Ly6g- cells, DOL17, BDL surgery, ADT

description: ADT 10x Genomics

library_source: other

molecule: protein

value: female


title: Macrophages, cKO, replicate 1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v 2.1.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hypodermis

extract_protocol:
Back skins from Igf1-flox and Csf1r-Cre x Igf1-flox female adult mice were harvested after shaving with an electric clipper. Subcutaneous fat was removed from hypodermis and hypodermal layers were physically isolated from the dermis with forceps. Hypodermis was minced with scissors and digested for 2H at 37°C in RPMI supplemented with 5% FCS and containing 0.25mg/mL of liberase T-Flex and 1ug/mL of DNAse I. Cells were isolated and immunostained with anti-CD45 and anti-CD64 antibodies as well as stained with Sytox-Red (SR) before being FACS sorted as live macrophages (SR–, CD45+, CD64+). Cells were lysed in cold lysis buffer (10 mM Tris–HCl (PH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1mM DTT and 1U/μl RNase inhibitor) for 5 min on ice for nuclei isolation. Upon washing the nuclei extracts, targeted nuclei recovery was processed for single-cell ATAC-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (Next GEM Single Cell Multiome ATAC + Gene expression (GEX) protocol, CGOOO338).

value: Hypodermis

value: Macrophages

value: Csf1r-cre x Igf1-flox

value: 8-10 weeks old

value: No treatment


title: FO-TC5

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

data_processing:
QC for fastq files was performed with FastQC.
Reads were mapped to the mouse genome (GRCm39) using STAR2 and aligned reads were quantified with htseq-counts to the M29 annotation.
Assembly: GRCm39
Supplementary files format and content: tab delimited read count files

source_name: follicular B cells

extract_protocol:
CD11c+ ABCs (CD19+B220+CD11c+CD21-CD23-AA4.1-) and FO B cells ( CD19+B220+CD11c-AA4.1-CD21-CD23+) were freshly isolated and snap-frozen
RNA purification, library preparation and sequencing were performed by Azenta (AZENTA life sciences). Library construction was performed by Azenta. Total RNA was purified, and mRNA was selected with polyA selection. QC of purified RNA and amplified cDNA were confirmed, and only high quality of samples were used for the sequencing.

value: follicular B cells

value: Sle 1/2/3 triple congenic mice

value: 8 months


title: Fig2-70K-mut-rep2


title: FO-TC2


title: Macrophages, cKO, replicate 2

description: 10x Genomics


title: Fig2-Sm-mut-rep3

value: Sm-mut


title: FO-TC4


title: Human meningioma, Frozen [AP23]

institute: UCSF

description: Nanostring nCounter

value: meningioma


title: Fig2-70K-mut-rep1

value: HEK 293T-REx


title: Fig2-U1A-mut-rep2


title: Human meningioma, Frozen [AP24]

description: Nanostring nCounter


title: FO-TC3


title: Macrophages, WT, replicate 1

description: 10x Genomics


title: FO-TC1


title: ABC-TC5

source_name: age associated B cells

value: age associated B cells


title: Fig2-U1A-mut-rep1


title: Fig2-U1WT-rep2


title: Human meningioma, Frozen [AP25]

description: Nanostring nCounter


title: Prostate tip luminal cells 2

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
Different library size has been corrected by picard DownsampleSam
After transcripts assembling, gene level counts were obtained using Htseq with annotations Grcm38.87 and normalized to 20 millions of aligned reads.
Assembly: Grcm38 / mm10
Supplementary files format and content: .csv / Normalized gene expression

source_name: Prostate

extract_protocol:
Minced tissues were digested in 5mg/ml Collagenase Type I (Sigma-Aldrich, diluted in HBSS) for 2 h at 37 °C under agitation.  Cells were rinsed in HBSS supplemented with 10% FBS and the cell suspensions were filtered through a 70um cell strainers (BD Bioscience), followed by 2 successive washes in HBSS supplemented with 2% FBS. Samples were incubated in 200 μl PBS supplemented with 2% FBS with fluorochrome-conjugated antibodies for 30 min on ice protected from light. Antibodies were washed with 2% FBS/PBS and cells were resuspended in 2.5 mg/ml DAPI (Invitrogen, D1306) before analysis. The following antibodies were used: PE-conjugated anti-CD45 (rat, clone 30-F11, dilution 1:100, BD Biosciences Cat#553081), PE-conjugated anti-CD31 (rat, clone MEC 13.3, dilution 1:100, BD Biosciences Cat#553373), PE-conjugated anti-CD140a (rat, clone APA5, dilution 1:100, BD Biosciences Cat#624049), APC-conjugated anti-CD49f (rat, clone GoH3, dilution 1:100, eBioscience Cat#17-0495), APC-Cy7-conjugated anti-EpCAM (rat, clone G8.8, dilution 1:100, BioLegend Cat#118218). Living cells were selected by forward and side scatter, doublets discriminating and DAPI dye exclusion. CD45+, CD31+ and CD140a+ cells were excluded (Lin+) before analysis of the epithelial basal (EpCamhigh/CD49fhigh) and luminal (EpCamhigh/CD49flow) cells. Fluorescence-activated cell sorting and analysis were performed using FACSAria and LSRFortessa, using FACSDiva software (BD Bioscience). Sorted cells were collected in lysis buffer for RNA extraction (RLT buffer, QIAGEN). RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer´s recommendations. Prior to sequencing the quality of RNA was evaluated by Bioanalyzer 2100 (Agilent).
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: Prostate

value: primary epithelial cells (EpCAM CD326 positive)

value: Luminal cells (CD49f low expression)

value: Postnatal day 10-13


title: Fig2-U1WT-rep3


title: Human meningioma, Frozen [AP22]

city: San Francisco

description: Nanostring nCounter


title: Prostate tip luminal cells 3


title: Human meningioma, Frozen [AP20]

description: Nanostring nCounter


title: ABC-TC4


title: Human meningioma, Frozen [AP21]

description: Nanostring nCounter


title: Macrophages, WT, replicate 2

description: 10x Genomics


title: Prostate tip basal cells 1

value: Basal cells (CD49f high expression)


title: Fig2-U1A-mut-rep3


title: Prostate tip basal cells 3


title: Human meningioma, Frozen [AP19]

description: Nanostring nCounter


title: 2849_P15_input

city: Tokyo

first: Yukiko

last: Gotoh

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

institute: University of Tokyo

description: Non-immunoprecipitated sample (=input) in 16.0 dpc stage of mouse NPCs (FAC-sorted, HMGA2 OE, replicate 2).

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

source_name: neural progenitor cells

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

tag: strain background

value: ICR

tag: genotype/variation

value: HMGA2 overexpression

tag: Stage

value: neural progenitor cells (NPCs)

tag: chip antibody


title: Fig2-U1WT-rep1

data_processing:
Custom python scripts were used for demultiplexing, adaptor trimming, PCR duplicates removal, genome mapping, and 3' end information generation as previously described (Lardelli et al., Nat Genet, 2017).
Assembly: human genome (version hg38)
Supplementary files format and content: Taildata files containing reads mapped to each snRNA genes and the corresponding 3' end information.

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 nascent RNA sequencing, nascent RNA was captured as previously described (Lardelli and Lykke-Andersen, Genes Dev, 2020).
RNA adapters containing barcodes and 10- to 11-nt randommers (AG10/AG11) were ligated to the 3′ ends of 2.5 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 16–25 cycles of polymerase chain reaction (PCR) with snRNA gene-specific forward primers and AR17 primer using Q5 DNA polymerase (NEB), and then eight cycles with primers D50x and D70x. Libraries were sequenced on an Illumina MiSeq platform.


title: ABC-TC2


title: 2849_P12_input

description: Non-immunoprecipitated sample (=input) in 16.0 dpc stage of mouse NPCs (FAC-sorted, control, replicate 2).


title: s_BTK_inh_35

city: Rotterdam

first: Peter

middle: D.

last: Katsikis

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Department of Immunology

country: Netherlands

institute: Erasmus University Medical Center

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

source_name: purified CD8+ T cells

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

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

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

value: purified CD8+ T cells

tag: strain

value: OT-1 mice WT

value: BTK KO-1

value: BTK inhitor 1uM

tag: condition

value: single peptide


title: 1 dpf itgb4+ embryonic basal precursors (rep1)

city: Yokohama

first: Zhengcheng

last: Liu

state: Kanagawa

address: Midori-ku, Nagatsuta-cho, 4259

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

description:
Em_itgb4+.1
Raw_gene_counts_matrix.txt

data_processing:
High-quality reads were mapped using hisat2 (ver. 2.2.1)
Trimmed sequence reads were mapped to GRCz11 using hisat2.
Read count extraxction and normalization were performed using featureCounts (ver. 2.0.3)
Assembly: GRCz11
Supplementary files format and content: tab delimited text file includes basic gene information (gene id, length, Genebank id, RNA type, gene name, product), raw count, RPKM and TPM values.

organism: Danio rerio

source_name: epidermal cells

growth_protocol: Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild-type zebrafish (Danio rerio) strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.

extract_protocol:
The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit (Qiagen)
RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.

treatment_protocol: Different types of cells were sorted by the fluorescence-activated cell sorter SH800S (SONY).

value: embryonic epidermal basal cells


title: Adult itgb4+ basal cells

description:
Ad_itgb4+.1
Raw_gene_counts_matrix.txt

value: adult fin epidermal basal cells


title: 1 dpf itgb4+ embryonic basal precursors (rep2)

description:
Em_itgb4+.2
Raw_gene_counts_matrix.txt


title: Human meningioma, Frozen [AP15]

description: Nanostring nCounter

tag: disease

value: meningioma


title: Human meningioma, Frozen [AP14]

description: Nanostring nCounter


title: s_BTK_inh_8

value: INHB-1 left over


title: s_DMSO_46

value: PKC igoni-2

value: DMSO


title: 2849_P15_IP

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 16.0 dpc stage of mouse NPCs (FAC-sorted, HMGA2 OE, replicate 2).

value: H3K27me3 (Millipore, 07-449)


title: 1 dpf krt4+ embryonic periderm cells (rep2)

description:
Em_krt4+.2
Raw_gene_counts_matrix.txt

value: embryonic periderm cells


title: Human meningioma, Frozen [AP10]

description: Nanostring nCounter


title: 2849_P12_IP

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 16.0 dpc stage of mouse NPCs (FAC-sorted, control, replicate 2).


title: Human meningioma, Frozen [AP11]

description: Nanostring nCounter


title: Human meningioma, Frozen [AP16]

description: Nanostring nCounter


title: s_BTK_inh_27

value: btk KO-6


title: 19.5_dpc_input_ChIPseq [GAIIx]

description: Non-immunoprecipitated sample (=input) in 19.5 dpc stage of mouse NPCs (manually dissected).

value: ICR


title: s_DMSO_34


title: s_DMSO_40

value: BTK KO-3


title: s_BTK_inh_41


title: Human meningioma, Frozen [AP8]

description: Nanostring nCounter


title: ABC-TC1

value: age associated B cells

value: Sle 1/2/3 triple congenic mice

value: 8 months


title: s_DMSO_26b

value: purified CD8+ T cells

value: OT-1 mice WT


title: Human meningioma, Frozen [AP13]

description: Nanostring nCounter


title: s_DMSO_7

value: single peptide


title: 1 dpf krt4+ embryonic periderm cells (rep1)

description:
Em_krt4+.1
Raw_gene_counts_matrix.txt


title: Human meningioma, Frozen [AP5]

description: Nanostring nCounter


title: 16.5_dpc_input_ChIPseq [GAIIx]

description: Non-immunoprecipitated sample (=input) in 16.5 dpc stage of mouse NPCs (manually dissected).

value: neural progenitor cells (NPCs)


title: Human meningioma, Frozen [AP4]

description: Nanostring nCounter


title: 14.5_dpc_input_ChIPseq [GAIIx]

description: Non-immunoprecipitated sample (=input) in 14.5 dpc stage of mouse NPCs (manually dissected).


title: 19.5_dpc_H3K27me3_ChIPseq [GAIIx]

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 19.5 dpc stage of mouse NPCs (manually dissected).


title: 12.5_dpc_input_ChIPseq [GAIIx]

description: Non-immunoprecipitated sample (=input) in 12.5 dpc stage of mouse NPCs (manually dissected).


title: r_BTK_inh_38

value: BTK KO-1

value: BTK inhitor 1uM

value: repeat peptide


title: r_BTK_inh_44


title: r_BTK_inh_31


title: 16.5_dpc_H3K27me3_ChIPseq [GAIIx]

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 16.5 dpc stage of mouse NPCs (manually dissected).


title: Human meningioma, Frozen [AP7]

description: Nanostring nCounter

value: meningioma


title: r_BTK_inh_12b

value: INHB-1 left over