title: SST, IP2, KO, Gabel, 733, C01, CGTCTAACAT, S4, R1, 001

city: St. Louis

first: Mati

middle: Tesfaye

last: Nemera

state: Missouri

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St. Louis School of Medicine

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

source_name: Cortex

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

value: Cortex

tag: strain

value: SST

value: Mecp2 KO

value: Male


title: GC055051_group_4_flying

status: Public on Jan 31 2025

type: SRA

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description: Library name: GC055051

library_source: transcriptomic

data_processing:
Raw sequencing data was pseudo-aligned against the D. melanogaster  transcriptome (Ensembl GRCh38.105) using kallisto (v0.45.0). Gene expression was summarized from the transcripts using tximport (v1.30.0).
Assembly: Ensembl drosophila melanogaster Release 113
Supplementary files format and content: Excel file with counts summarized to gene expression using tximport (v1.30.0).

molecule: total RNA

organism: Drosophila melanogaster

source_name: whole body

growth_protocol: One-day-old male flies were collected and tested for their flying ability. Flies were placed in an empty vial that was gently tapped. Flies able or unable to fly were scored one and zero, respectively [33]. For the sequencing analyses, the offspring of each parent pair that was able to fly (group 4) was separately collected from those that were not able to fly (group 3).

extract_protocol:
RNA was from whole flies using the innuPREP RNA Mini Kit 2.0.
Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: tissue

value: whole body

tag: Sex

value: male

tag: age

value: 1 day

tag: flying

value: Yes


title: MSI1 RRM2 RBNS, 500, rep2

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

country: USA

institute: UNC Chapel Hill

description: Counts were normalized for library size prior to enrichment against 20mer_RNA_input_2

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

organism: synthetic construct

source_name: RBNS

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

value: RBNS


title: SST, IP3, KO, Gabel, 795, E01, GTCGAGAAAT, S6, R1, 001

molecule: nuclear RNA

organism: Mus musculus

tag: cell type

tag: genotype


title: Control_Patient_3_Memb-2

city: Houston

first: Rachel

middle: A

last: Keuls

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

state: TX

address: One Baylor Plaza

department: MCB

institute: Baylor College of Medicine

description: sci-rna-seq3 run 3

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

organism: Homo sapiens

source_name: Chorionic Membranes

growth_protocol: Placentas were delivered via cesarian section

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

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

value: Chorionic Membranes

tag: treatment

value: Control


title: SST, IP1, KO, Gabel, 638, B01, AATCCAGCAT, S3, R1, 001


title: GC055047_group_2_notflying

description: Library name: GC055047

value: No


title: GC055048_group_2_notflying

description: Library name: GC055048


title: SST, IP4, WT, Gabel, 333-5, H01, GCACACAAAT, S9, R1, 001

value: WT


title: GC055046_group_2_notflying

description: Library name: GC055046


title: SST, IP3, WT, Gabel, 796, F01, ACAACAGCAT, S7, R1, 001


title: GC055045_group_2_notflying

description: Library name: GC055045


title: MSI1 RRM2 RBNS, 250, rep1

description: Counts were normalized for library size prior to enrichment against 20mer_RNA_input_1


title: SST, IP4, KO, Gabel, 333-4, G01, ATGACAGGAT, S8, R1, 001


title: SST, IP2, WT, Gabel, 734, D01, AACTCGGAAT, S5, R1, 001


title: MSI1 RRM2 RBNS, 1000, rep2


title: GC055044_group_2_notflying

description: Library name: GC055044


title: 20mer_RNA_input_1

description: Input control for MSI1 RRM1 and MSI1 RRM2 rep1 RBNS


title: SST, IP1, WT, Gabel, 637, A01, CGCTACATAT, S2, R1, 001


title: GC055042_group_2_notflying

description: Library name: GC055042


title: MSI1 RRM1 RBNS, 500, rep2


title: L5, Input3, KO, Gabel, 676-3, N, GACTACGA, S12, R1, 001


title: MSI1 RRM2 RBNS, 1000, rep1


title: GC055043_group_2_notflying

description: Library name: GC055043


title: L5, Input3, WT, Gabel, 676-4, N, ACTCCTAC, S13, R1, 001


title: L5, IP4, KO, Gabel, 681-5, IP, TCTTCGAC, S11, R1, 001


title: L5, IP3, KO, Gabel, 676-3, IP, ATGACAGG, S8, R1, 001


title: MSI1 RRM1 RBNS, 250, rep2


title: GC055040_group_1_flying

description: Library name: GC055040


title: MSI1 RRM2 RBNS, 500, rep1


title: MSI1 RRM1 RBNS, 250, rep1


title: MSI1 RRM1 RBNS, 500, rep1


title: GC055041_group_1_flying

description: Library name: GC055041


title: LB ECC R3

city: Marseille

first: Olivier

last: Zugasti

state: Provence-Alpes-Cote d'Azur

address: 163 Avenue de Luminy

country: France

institute: Institut de Biologie du Développement de Marseille

data_processing:
The RNAseq data were subjected to a series of bioinformatic analyses. Quality control of the sequenced reads was executed using HTSeq, with the removal of the first 18 nucleotides of each read. Subsequently, the reads were aligned to the Drosophila melanogaster reference genome (dmel6.31, FlyBase) utilizing HISAT2 version 2. Gene expression quantification was carried out with the featureCounts function from the Rsubread package. Normalization of read counts and the analysis of differential gene expression were conducted using the DESeq2 package via the SARTools pipeline.
Assembly: Drosophila melanogaster reference genome  : dmel6.31 (FlyBase)
Supplementary files format and content: Supplemental Data - RNA seq Processed file 1 Wild type Up.xlsx : tab delimited excel files includes raw counts, Gene Inducibility  (Control  vs. Infected conditions) and calculated p value
Supplementary files format and content: Supplemental Data - RNA seq Processed file 2 Wild type Down.xlsx : tab delimited excel files includes raw counts, Gene Repression (Control  vs. Infected conditions) and calculated p value
Supplementary files format and content: Supplemental Data - RNA seq Processed file 3 PGRP-LB Up.xlsx : tab delimited excel files includes raw counts, Gene Inducibility  (Control  vs. Infected conditions) and calculated p value
Supplementary files format and content: Supplemental Data - RNA seq Processed file 3 PGRP-LB Down.xlsx : tab delimited excel files includes raw counts, Gene Inducibility  (Control  vs. Infected conditions) and calculated p value

molecule: polyA RNA

source_name: Brain

extract_protocol:
The RNAseq analysis encompassed nine samples in total, consisting of three sample groups: brains from non-infected wild-type flies and brains from wild-type and PGRP-LB mutant flies orally infected with E.cc15 for 16 h. Each sample consisted of 20 brains isolated from adult females aged 4-6 days. RNA was extracted from each sample using the RNeasy Mini Kit (QIAGEN, cat. #74106). The extracted RNA samples were then sent to the GenomEast platform, located in Strasbourg, France, for further analysis.
RNA-Seq libraries were generated from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), following the manufacturer's instructions. During this process, only polyA RNAs were sequenced to focus on the mature messenger RNA fraction. The quality and quantity of the generated cDNA libraries were assessed using capillary electrophoresis. The sequencing was performed using Hiseq4000, producing 2x100 base pair reads, with all samples run in one lane. Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14, converting the raw data from the sequencer into a format ready for downstream bioinformatic analysis.

value: Brain

value: PGRP-LB mutant

value: Infected condition


title: MSI1 RRM2 RBNS, 250, rep2


title: L5, IP1, KO, Gabel, 653-4, IP, CGCTACAT, S2, R1, 001


title: LB ECC R4


title: L5, IP2, KO, Gabel, 653-6, IP, CGTCTAAC, S4, R1, 001


title: MSI1 RRM1 RBNS, 1000, rep1


title: MSI1 RRM1 RBNS, 1000, rep2


title: L5, IP4, WT, Gabel, 681-3, IP, CTCCTAGT, S10, R1, 001


title: W ECC R5

value: Wild Type


title: Fibroblasts-derived extracellular vesicles, FB-EVs sample5

city: Guangzhou

first: Miao

last: Zhen

address: No.58 Zhongshan Er Road

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

description:
Library name: Ctr5
Data.csv: Ctr5_TPM

data_processing:
All of the clean tags were aligned with small RNAs in GeneBank database (Release 209.0) and Rfam database(11.0) to identify and remove rRNA,scRNA,snoRNA,snRNA and tRNA.
Assembly: All of the clean tags were then searched against miRBase database(Release 21) to identify known miRNAs. All of the unannotated tags were aligned with reference genome. According to their genome positions and hairpin structures predicted by software Mireap_v0.2, the novel miRNA candidates were identified.
Supplementary files format and content: csv file includes TPM values for each samples

source_name: human foreskins

extract_protocol:
Total RNA was extracted by TRIzol
The RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel lectrophoresis(PAGE). Then the 3’ adapters were added and the 36-44nt RNAs were enriched. The 5’ adapters were then ligated to the RNAs as well. The ligation products were reverse transcripted by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co.

value: human foreskins

value: fibroblasts


title: Fibroblasts-derived extracellular vesicles, FB-EVs sample4

description:
Library name: Ctr4
Data.csv: Ctr4_TPM


title: W ECC R2


title: L5, IP3, WT, Gabel, 676-4, IP, GCACACAA, S9, R1, 001

value: Cortex


title: L5, IP1, WT, Gabel, 653-7, IP, AACTCGGA, S5, R1, 001

value: Male


title: W R9

value: Control condition


title: L5, IP2, WT, Gabel, 653-5, IP, AATCCAGC, S3, R1, 001


title: W ECC R1


title: L4, IP4, KO, Gabel, 338-7, CTCGAACA, S9, R1, 001

value: Mecp2 KO


title: DMSO, scRNAseq

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing basecalls were input into CellRanger V3.0.2 for demultiplexing and fastq generation. Alignment and gene quantification were first performed in tandem to a dual-species reference transcriptome for both hg19 (human) and mm10 (mouse), obtained from 10X Genomics (refdata-cellranger-hg19-and-mm10-3.0.0.). Using the R package Seurat (V4.0.1), the percentage of raw UMI counts within each cell aligning to either mm10 or hg19 transcriptomes was calculated and used in tandem with SNN clustering to separate out human GBM22 cells from contaminating mouse cells. GBM22 cell barcodes were then used to isolate these human cells from the data aligned to the GrCH38 (human) transcriptome for downstream gene expression analysis. Outlier cells were removed based on UMI count, detected gene count, and percent of mitochondrial transcript counts. Cells with less than 200 or more than 6000 detected genes, or with more than 10% of mitochondrial genome alignment were removed for downstream analysis.
Assembly: grch38
Supplementary files format and content: Tab-separated count file, UMI counts from filtered bc matrices output from Cell Ranger.

source_name: PDX GBM22 orthotopic xenograft (frontal-cortex)

extract_protocol:
Tumor-bearing mice were perfused with PBS, and their brains were removed. Tumor was isolated and dissociated using the Worthington Biochem Papain dissociation kit. Cells were washed two times using ice-cold PBS with 0.1% BSA (w/v), checked for viability using AO/PI dye and a Nexcelom K2 Cellometer. Cells from dissociation suspension were loaded into a 10X Chromium chip using 10x Genomics NextGEM 3’ chemistry targeting the capture of approximately 10,000 cells per sample.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Following tumor implantation, mice recovered for a period of 7 days. GBM22 orthotopic tumor-bearing mice were treated intraperitoneally with either Alisertib (25mg/kg) (drug formulation: 5% DMSO / 30% PEG400 / 5% Tween-80 / 60% PBS) or vehicle control 5 days per week and monitored daily for signs of cognitive decline and body weight. Tumors were collected at the time of initial signs of cognitive decline or 15% of BW loss. Cells from tumors from three individual mice within each treatment group were captured and pooled for single cell RNA-sequencing.

tag: cell line

value: DMSO


title: Alisertib_02, scRNAseq

description: 10x Genomics

value: PDX GBM22 orthotopic xenograft (frontal-cortex)

value: Alisertib


title: LB ECC R1


title: Alisertib_01, scRNAseq

description: 10x Genomics


title: HaCaT,ALA-PDT-48h,3

city: Nantong

first: Zhinan

last: Shi

state: Jiangsu

address: Chongchuan district

institute: Nantong university

data_processing:
FASTQC for quality check
HISAT2 for reference mapping
StringTie  for transcript assembling
Genome_build:Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Excel file include FPKM values of each groups
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Excel file include fold change, p-value, FPKM values of each groups

source_name: skin

growth_protocol: HaCaT cells (AoYin Cell Center, Shanghai, China) were cultured with Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific, USA) containing 10% fetal bovine serum (FBS, Every Green, Zhejiang Tianhang Biotechnology Co., LtD) and 1% penicillin-streptomycin solution (New cell & Molecular Biotech Co., LtD), and placed in a 37°C, 5% CO2 cell culture incubator. HaCaT cells were digested using trypsinization (Gibco, Thermo Fisher Scientific, USA) for subsequent experiments.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Takara, Shiga, Japan) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
We performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Light treatment with low-dose ALA-PDT (0.5mmol/L 635±5nm, 3J/cm2) in human immortalized keratinocytes. There are two of experimental tries with differentiated post incubation time after low-dose ALA-PDT treatment. (n=3): Control, Low-dose ALA-PDT (treatment and post incubation for 12h), Low-dose ALA-PDT (treatment and post incubation for 48h).

value: skin

value: HaCaT

value: human immortalized keratinocytes


title: L4, IP3, KO, Gabel, 244-3, ATCGTCTC, S6, R1, 001


title: L4, IP2, KO, Gabel, 178-1, CGACCTAA, S4, R1, 001


title: Epidermal stem cell-derived extracellular vesicles, ESC-EVs sample3

description:
Library name: Case3
Data.csv: Case3_TPM

value: Epidermal stem cells


title: Epidermal stem cell-derived extracellular vesicles, ESC-EVs sample5

description:
Library name: Case5
Data.csv: Case5_TPM


title: Epidermal stem cell-derived extracellular vesicles, ESC-EVs sample4

description:
Library name: Case4
Data.csv: Case4_TPM


title: L4, IP1, KO, Gabel, 156-3, ACGAGAAC, S3, R1, 001


title: W R8

value: Brain


title: Fibroblasts-derived extracellular vesicles, FB-EVs sample1

description:
Library name: Ctr1
Data.csv: Ctr1_TPM


title: W R2


title: HaCaT,ALA-PDT-48h,2

value: Low-dose ALA-PDT (treatment and post incubation for 48h)


title: L4, IP4, WT, Gabel, 338-6, TCTAGGAG, S8, R1, 001

value: WT


title: Epidermal stem cell-derived extracellular vesicles, ESC-EVs sample2

description:
Library name: Case2
Data.csv: Case2_TPM


title: HaCaT,ALA-PDT-48h,1


title: Fibroblasts-derived extracellular vesicles, FB-EVs sample3

description:
Library name: Ctr3
Data.csv: Ctr3_TPM


title: Fibroblasts-derived extracellular vesicles, FB-EVs sample2

description:
Library name: Ctr2
Data.csv: Ctr2_TPM


title: Tumor mouse melanocytes cells Guadecitabine treated, rep5

type: RNA

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

hyb_protocol: Following IVT , the RNA biotinylated were hybridized for 16 hr at 45°C on Affymetrix GeneChip in GeneAtlas Hybridization Station. GeneChips were washed and stained using  GeneAtlas™ Hybridization, Wash, and Stain Kit for 3' IVT Arrays.

scan_protocol: GeneChip were finally scanned using GeneAtlas Scanner.

data_processing: Affymetrix® Transcriptome Analysis Console (TAC) Software.  Data were preprocessed following the RMA procedure using quantile normalization

label: biotin

source_name: tumor mouse cutaneous melanocytes cells treated with Guadecitabine

label_protocol: 500 ng of total of RNA was biotin labeled using the 3′ IVT Express Kit (Affymetrix) for array strips

growth_protocol:
B16F10 murine cutaneous melanoma cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin
B16F10 murine cutaneous melanoma cells were subcutaneously (SC) injected in Eight-week-old C57black6J mice and monitored for disease symptoms every other day, manually
B16F10 murine cutaneous melanoma cells were subcutaneously (SC) injected in Eight-week-old C57black6J mice and monitored for disease symptoms every other day, manually
Total RNA was extracted using Rneasy Plus mini kit (Qiagen) following the manufacturers protocol. RNA quantity and quality were determined using a Nanodrop-1000 spectrophotometer (Nanodrop Technology) and Agilent 2100 Bioanalyzer.

extract_protocol: Affymetrix standard protocol

treatment_protocol:
in vitro treatment with OTX015
OTX-015 was given to mice per OS
Guadecitabine was given to mice by Intra Peritoneal (IP) injections

value: tumor mouse cutaneous melanocytes cells

value: Guadecitabine

tag: group

value: Treated mouse tumor samples


title: L4, IP3, WT, Gabel, 244-4, CCAACACT, S7, R1, 001

value: Cortex


title: Tumor mouse melanocytes cells Guadecitabine treated, rep4


title: Epidermal stem cell-derived extracellular vesicles, ESC-EVs sample1

description:
Library name: Case1
Data.csv: Case1_TPM

value: human foreskins


title: L4, IP2, WT, Gabel, 178-3, TACATCGG, S5, R1, 001

value: Male


title: B13

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

data_processing:
Raw sequencing reads in the fastq files were mapped with STAR version 2.7.1a to the Gencode release 36 based on the GRCh38.p12 reference human genome with the corresponding GTF files.
Table counts was obtained with FeatureCounts function in the package subread, version 1.6.4
Assembly: hg38
Supplementary files format and content: Counts table

source_name: Cell line_3

growth_protocol: hMSLCs were isolated from teratomas by enzymatic digestion and hpMSCs were obtained from bone marrow aspirates. Cells were grown in Eagle’s medium supplemented with 10% FBS and bFGF (1ng/ml).

extract_protocol:
Total RNA from hMSLCs and hpMSC RNA was isolated with Genelute Total Mammalian RNA Kit (Sigma-Aldrich) and cDNA was obtained by using Transcriptor First Strand cDNA Synthesis Kit (Roche). cDNAs were subjected to Illumina TruSeq library preparation (Illumina). Libraries were sequenced on an Illumina HiSeq 2500.
RNA-Seq (polyA capture); NGS libraries with polyA capture were prepared according to the manual Protocol for use with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) (version 1.0, 7/20)

treatment_protocol: hMSLCs were transduced with lentiviral supernatants from 293T cells transfected with empty vector or flag-EWSFLI1 vector, in the presence of Polybrene at 4 µg/ml. Cell culture media was refreshed 24 hours later, and cells were collected 48 hours post-infection.

tag: sample group

value: Cell line_3

value: human MSLCs


title: Tumor mouse melanocytes cells Guadecitabine treated, rep3


title: Tumor mouse melanocytes cells Guadecitabine treated, rep2


title: Tumor mouse melanocytes cells Guadecitabine treated, rep6


title: B12

source_name: Cell line_2

value: Cell line_2


title: Female_SW_Pax_rfp_rep3

city: Madison

first: Zachary

middle: T

last: Campbell

state: WI

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

data_processing:
Raw files were downloaded from Illumina BaseSpace and subjected to quality assessment with FastQC 0.11.5 (Babraham Bioinformatics)
Sequence reads were trimmed for adaptor sequence
Strand specific mapping was conducted with TopHat 2.1.1 (with Bowtie 2.2.9) to the mouse reference genome (NCBI reference assembly GRCm38.p4) and reference transcriptome (Gencode vM10).
Processed bam files were quantified for each gene using Cufflinks 2.2.1 with gencode.vM10 genome annotation. Read counts were not normalized by length by the using the Cufflinks option -- no–length–correction.
Relative abundance was calculated using TPM
Assembly: mm10
Supplementary files format and content: excel file containing TPM values for processed data

source_name: DRG

extract_protocol:
MicroSpin S-400 columns (GE Healthcare) were used to isolate ribosome bound RNAs. After rRNA was removed using RiboCop rRNA depletion kit (Lexogen), footprints were dephosphorylated then size selected (28-34nt) by PAGE on 15% TBE-Urea gels (Bio-Rad). Footprints were generated by SMARTer smRNA-Seq kit for Illumina (TaKaRa).
RNA abundance was quantified using the Quantseq 3ʹ mRNA-Seq library kit (Lexogen). The concentrations of purified libraries were quantified using Qubit (Invitrogen)

treatment_protocol: Paclitxel at 4 mg/kg, i.p; given every other day, total of four treatments/injections

value: DRG

value: SW

value: Female


title: HaCaT,Control,3

value: skin

value: HaCaT

value: human immortalized keratinocytes

value: No treatment


title: L4, IP1, WT, Gabel, 156-1, GTACACCT, S2, R1, 001

value: WT


title: HaCaT,ALA-PDT-12h,1

value: Low-dose ALA-PDT (treatment and post incubation for 12h)


title: A13


title: HaCaT,Control,2


title: Female_SW_Pax_rfp_rep4

value: Paclitxel at 4 mg/kg, i.p; given every other day, total of four treatments/injections


title: Tumor mouse melanocytes cells Guadecitabine treated, rep1

value: tumor mouse cutaneous melanocytes cells

value: Guadecitabine

value: Treated mouse tumor samples


title: A12


title: Female_SW_Pax_rfp_rep2


title: HaCaT,Control,1


title: Tumor mouse melanocytes cells OTX015 treated, rep9

source_name: tumor mouse cutaneous melanocytes cells treated with OTX015


title: Female_SW_Pax_rfp_rep1


title: Female_SW_Pax_rna_rep4

extract_protocol:
Total RNA was isolated using TRIzol reagent and applied to a Phase Lock Gel-Heavy column. Eluted RNA was then rRNA depleted using the RiboCop  rRNA kit, according to the manufacturer’s protocols
Libraries were generated from 1mg of RNA using Lexogen’s QuantSeq 39mRNASeq library kit. The concentrations of purified  libraries were quantified using Qubit and the average size was determined by a fragment analyzer with a  high-sensitivity NGS fragment analysis kit

treatment_protocol: Treatment with saline as a control measurement


title: HCT116 cells, shEphexin1

city: Gwangju

first: Jeeho

last: Kim

address: Biotechnology Bldg. Rm210 309 Pilmundaero, Dong-gu

country: South Korea

institute: Chosun Univ.

data_processing:
Raw Data-Source type: Total RNA, Sequencing Platform: Novaseq
At first, reads for each sample were mapped to the reference genome by Tophat(v2.0.13) .
Trimmed sequence reads were mapped to human hg19
The aligned results were added to Cuffdiff(v2.2.0) to report differentially expressed genes. For library normalization and dispersion estimation , geometric and pooled (“blind” when each condition has single replicates, or “pooled” when multiple replicates are available) methods were applied.
Assembly: Human hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq Stranded Total RNA H/M/R Prep Kit following manufacturer's protocols.

value: Coloractal cancer cells

value: NO


title: HaCaT,ALA-PDT-12h,3


title: Tumor mouse melanocytes cells OTX015 treated, rep10


title: HCT116 cells, shControl


title: B11

source_name: Cell line_1

value: Cell line_1

value: human MSLCs


title: A11


title: HaCaT,ALA-PDT-12h,2


title: Tumor mouse melanocytes cells OTX015 treated, rep7


title: B10

value: Cell line_3

value: Control lentivirus


title: Female_SW_Pax_rna_rep3

value: DRG

value: SW

value: Female


title: Tumor mouse melanocytes cells OTX015 treated, rep8


title: Tumor mouse melanocytes cells OTX015 treated, rep6


title: REH cells

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

institute: Ulm University Medical Center

description: REH

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

source_name: REH

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

extract_protocol:
RNA was harvested using Allprep DNA/RNA Mini Kit (Qiagen).  500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared  NEB Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols using mRNA enrichment via oligo-dT magnetic beads.

value: REH

value: pre-B-cell acute lymphoblastic leukemia


title: A10


title: MCC13 cells

value: Merkel cell carcinoma

value: WT


title: Female_SW_Pax_rna_rep2


title: Female_SW_Pax_rna_rep1


title: WaGa cells

description: WaGa

source_name: WaGa

value: WaGa


title: A9

value: Cell line_2


title: Female_SW_control_rfp_rep3

data_processing:
Raw files were downloaded from Illumina BaseSpace and subjected to quality assessment with FastQC 0.11.5 (Babraham Bioinformatics)
Sequence reads were trimmed for adaptor sequence
Strand specific mapping was conducted with TopHat 2.1.1 (with Bowtie 2.2.9) to the mouse reference genome (NCBI reference assembly GRCm38.p4) and reference transcriptome (Gencode vM10).
Processed bam files were quantified for each gene using Cufflinks 2.2.1 with gencode.vM10 genome annotation. Read counts were not normalized by length by the using the Cufflinks option -- no–length–correction.
Relative abundance was calculated using TPM
Assembly: mm10
Supplementary files format and content: excel file containing TPM values for processed data separated by sex


title: MKL-2 cells


title: Tumor mouse melanocytes cells OTX015 treated, rep5

value: tumor mouse cutaneous melanocytes cells


title: B8


title: Tumor mouse melanocytes cells OTX015 treated, rep4

value: Treated mouse tumor samples


title: MKL-1 cells


title: Tumor mouse melanocytes cells OTX015 treated, rep3


title: HEK293 ARMC4

city: INDIANAPOLIS

first: Matthew

last: Martin

state: IN

address: 635 BARNHILL DR

institute: Indiana University School of Medicine

description: RNA collected from stable cell line generated with lentiviral vector overexpressing ARMC4

data_processing: All data was processed by the Center for Computational Biology & Bioinformatics at IUSM.

growth_protocol: The human embryonic kidney (HEK) 293 cells, also referred as 293 cells were cultured in Dulbecco’s modified Eagle’s media supplemented with 100 U/ml penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were constructed according to the protocols of the University of Chicago Genomics core.

treatment_protocol: Each treated sample was treated with IL-1B for 1 hour.

value: untreated

value: embryonic kidney cells

value: overexpression ODAD2/ARMC4


title: A8

value: Cell line_1

value: human MSLCs


title: HEK293 ARMC4 +IL1

description: RNA collected from stable cell line generated with lentiviral vector overexpressing ARMC4 stimulated with Il-1B

value: treated 1 hr IL-1B


title: B2

value: CTRL


title: Female_SW_control_rfp_rep2

value: DRG

value: SW


title: Tumor mouse melanocytes cells OTX015 treated, rep2


title: B9

value: Control lentivirus


title: A2


title: Female_SW_control_rfp_rep1

value: Female


title: B1

source_name: Cell line

value: Cell line

value: human pediatric MSCs


title: Tumor mouse melanocytes cells OTX015 treated, rep1


title: Male_SW_control_rfp_rep4

value: WT

value: Male


title: Tumor mouse melanocytes cells untreated Guadecitabine experiment, rep5

source_name: tumor mouse cutaneous melanocytes cells

value: tumor mouse cutaneous melanocytes cells

value: control (Guadecitabine expt)

value: Untreated mouse tumor samples


title: Male_SW_control_rfp_rep3


title: Tumor mouse melanocytes cells untreated Guadecitabine experiment, rep4


title: Female_SW_control_rfp_rep4


title: HEK293

description: RNA collected from wt cells

value: untreated

value: embryonic kidney cells

value: wt


title: Male_SW_control_rfp_rep2


title: A1


title: HEK293 +IL1

description: RNA collected from wt cells stimulated with il-1b


title: Tumor mouse melanocytes cells untreated Guadecitabine experiment, rep3


title: SCC7276B

city: Palo Alto

first: Andrew

last: Gentles

state: CA

address: 1265 Welch Rd

institute: Stanford University

description:
Library name: Sample 10
Metastatic lymph node

data_processing:
The gene expression quantification was done using Kallisto v0.46.1 to align reads to the GENCODE human transcripts v43. Transcript level expressions were summarized to gene level by TPM values using tximport.
Assembly: GENCODE human transcripts v43.
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.

source_name: Head and neck squamous cell carcinoma

extract_protocol:
A small slice of OCT tissue was placed in RNAlater and sent to Medgenome for RNA extraction and sequencing for each sample. RNA extraction was performed using the Takara SMARTer Stranded Total RNA-seq Kit v2 following manufacturer's protocols.
Library preparations were made using the Takara SMART-Seq v4 Ultra low input RNA kit following manufacturer's protocols. Quality controls were run on RNA and library preparations using the Qubit fluorometric quantitation.

value: Head and neck squamous cell carcinoma


title: SCC7267B

description:
Library name: Sample 9
Metastatic lymph node


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 24 hours post-stimulation, replicate 8

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

institute: Università di Pisa

description:
Library name: Recovery 8
Column "featureCounts on data 110 and data 109: Counts"

data_processing:
Default genomes and mouse annotation were Ensembl GRCm39. BAM data,  normalised gene count and differential expression (DE) analysis were performed on Galaxy platform (https://usegalaxy.eu/) with BWA-MEM, featureCounts ad DEseq2 tools, respectively.
nsembl GRCm39
Assembly: Ensembl GRCm39 (mm10)
Supplementary files format and content: Tabular format, normalised gene counts

source_name: Dorsal root ganglia

growth_protocol: P3-stage mouse pups were sacrificed and 30 DRGs were collected from each mouse in DPBS (Gibco, #14190-094) supplemented with 6.5 mg/ml D-glucose (Sigma, #G7021).  DRG neurons dissociation was performed as described in (https://doi.org/10.1016/j.celrep.2022.111912). Briefly, the cells were digested in DPBS containing 1.8 mg/ml D-glucose, 3 mg/ml Dispase II (Sigma, #D4693), 0.3 mg/ml Collagenase from Clostridium histolyticum (Sigma, #C7657). Subsequently, the cells were incubated in DPBS with 0.52 mg/ml trypsin inhibitor from glycine max (Sigma, #T9003) and 0.08 mg/ml Deoxyribonuclease I from bovine pancrease (Sigma, #DN25). Mechanical dissociation was carried out using a fire-polished glass Pasteur pipette, and the cell suspension was passed through a 40-um cell strainer (Corning, #352340). DRGs were then pelleted and resuspended in culture medium consisting of Neurobasal -A (Gibco, #12349015), 2% B27 (Gibco, #17504-044), 1% Glutamax (35050-038), 0.5% pen/strep (Gibco, #15140-122), supplemented with 100 ng/ml NGF (Sigma, #N5415) and 2.5 µM AraC (Sigma, #C1768). The cells were seeded inside XONA chambers (200,000 cells per chamber). After 2 hours, a chemical gradient of NGF (100 ng/ml in the axonal compartment and 50 ng/ml in the soma compartment) was established to promote axonal growth within the axonal compartment.

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen, #74034) from 8 replicates, resulting in 24 RNA extracts. Eighteen samples that passed the quality check (QC) were selected for RNA sequencing (RNAseq) (RNA integrity number, RIN>9).
The RNA library was prepared with polyA selection and paired-end (PE) sequencing, with a read length of 151 bp and 15 Gb of data generated per sample.

treatment_protocol: A chamber is generated by attaching a XONA silicon chip onto the poly-L-lysine/laminin-coated PDMS film. The chamber is mounted on a device that is equipped with micrometric screw to apply a precise strain into the PDMS film. Control group refers to DRG neurons grown on PDMS mounted in the cartridge in the pre-stretched position; Compressed/Recovery groups refers to DRG neurons grown on P PDMS mounted in the cartridge in the pre-stretched position and subjected to 20 cycles of stimulation from the pre-stretched to the resting position. The strain used was 5 %. The strain is applied and released at a constant speed (0.42%/s) and the resting time between application and release is 5 seconds.

value: Dorsal root ganglia

value: primary cells

value: neuron

value: mechanical stimulation, RNA extraction 24 h after stimulation


title: Tumor mouse melanocytes cells untreated Guadecitabine experiment, rep2


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 24 hours post-stimulation, replicate 7

description:
Library name: Recovery 7
Column "featureCounts on data 110 and data 108: Counts"


title: Female_SW_control_rna_rep4

value: DRG

value: SW


title: Male_SW_control_rfp_rep1


title: SCC7240B

description:
Library name: Sample 8
Metastatic lymph node


title: Tumor mouse melanocytes cells untreated Guadecitabine experiment, rep1


title: SCC7275

description:
Library name: Sample 6
Primary tumor


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep11

value: control (OTX-015 expt)


title: Female_SW_control_rna_rep2

value: Female


title: SCC7233B

description:
Library name: Sample 7
Metastatic lymph node


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 24 hours post-stimulation, replicate 3

description:
Library name: Recovery 3
Column "featureCounts on data 110 and data 106: Counts"


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 24 hours post-stimulation, replicate 2

description:
Library name: Recovery 2
Column "featureCounts on data 110 and data 105: Counts"


title: Female_SW_control_rna_rep1

value: WT


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep10


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep8


title: SCC7268

description:
Library name: Sample 5
Primary tumor


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 24 hours post-stimulation, replicate 1

description:
Library name: Recovery 1
Column "featureCounts on data 110 and data 104: Counts"


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep9


title: Male_SW_control_rna_rep4

value: Male


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 24 hours post-stimulation, replicate 4

description:
Library name: Recovery 4
Column "featureCounts on data 110 and data 107: Counts"


title: Female_SW_control_rna_rep3


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 6 hours post-stimulation, replicate 8

description:
Library name: Compressed 8
column "featureCounts on data 110 and data 101: Counts "

value: mechanical stimulation, RNA extraction 6 h after stimulation


title: SCC7267

description:
Library name: Sample 4
Primary tumor


title: SCC7240

description:
Library name: Sample 3
Primary tumor


title: Male_SW_control_rna_rep2


title: SCC7238

description:
Library name: Sample 2
Primary tumor


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep7

value: tumor mouse cutaneous melanocytes cells


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 6 hours post-stimulation, replicate 7

description:
Library name: Compressed 7
column "featureCounts on data 110 and data 100: Counts "


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 6 hours post-stimulation, replicate 4

description:
Library name: Compressed 4
column "featureCounts on data 110 and data 99: Counts "


title: SCC7233

description:
Library name: Sample 1
Primary tumor


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 6 hours post-stimulation, replicate 3

description:
Library name: Compressed 3
column "featureCounts on data 110 and data 98: Counts "


title: Male_SW_control_rna_rep1


title: pituitary tissue, B,9

city: beijing

first: Hongyan

last: Liu

address: No. 28 Fuxing Road, Haidian District, Beijing 100853, P.R. China

institute: Department of Endocrinology, Chinese PLA General Hospital

description: Sample 9

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: pituitary adenoma

extract_protocol:
RNA was extracted using TRIzol reagent
After the RNA sample is detected to be qualified, generally, the Ribo-Zero™ kit is used to remove rRNA from the total RNA sample (some lncRNAs have the same polyA tail structure as mRNA. The method of removing rRNA can retain lncRNAs containing polyA tails to the greatest extent). Add fragmentation buffer to the enriched RNA to break the RNA into small fragments. Then, using the fragmented RNA as a template, add 6bp random primers (random hexamers) to reverse transcribe and synthesize the first strand of cDNA. Then add buffer, dNTPs (dTTP in dNTP is replaced by dUTP), DNA polymerase I and RNase H to synthesize the second strand of cDNA. After purification, end repair, adding A, and ligating sequencing adapters to the synthesized double-stranded cDNA, use USER enzyme to degrade the second strand of cDNA containing U and perform PCR enrichment. Finally, purify the PCR product with AMPure XP beads to obtain the final strand-specific library. After the library is constructed, first use Qubit 2.0 for preliminary quantification and dilute the library. Then use Agilent 2100 to detect the insert fragment size of the library. After the insert fragment meets the expectation, use the Q-PCR method to accurately quantify the effective concentration of the library to ensure the library quality.

value: pituitary adenoma


title: pituitary tissue, B,10

description: Sample 10


title: SiLipids_2h_4

city: Cologne

first: Alga

last: Zuccaro

state: NRW

address: Zuelpicher Str. 47b

department: Institute for Plant Sciences

institute: University of Cologne

data_processing:
Trimmomatic (v. 0.39) (Bolger et al., 2014) was used for quality trimming and adapter clipping
quality of the reads was assessed using fastQC
Reads were  mapped to the barley Morexv3 pseudomolecules assembly cDNA (downloaded from ensembl plants on 18.08.2023) and quantified using kallisto (v. 0.46.1) (Bray et al., 2016), which resulted in estimated counts and transcripts per million (TPM) values.
The log2 fold difference of the gene expression between conditions was calculated using R and differential expression of genes was calculated using the R package “sleuth”.
Assembly: barley Morexv3 pseudomolecules assembly cDNA (downloaded from ensembl plants on 18.08.2023)
Supplementary files format and content: tab delimited text file containing TPM values, log2FC (compared to SC ) and means of expression of all genes for all samples

organism: Hordeum vulgare

source_name: root

growth_protocol: Seeds of Hordeum vulgare cv Golden Promise were surface sterilized with 6% sodium-hypochlorite, rotating for 1 h at 40 rpm and washed six times for 30 min with sterile milliQ-water. Seed coats were removed gently in sterile water using forceps and seeds were placed on wet filter paper (2 ml milliQ-water per 75 mm round filter paper) in a petri dish (eight seeds per filter paper). Plates were covered with aluminum foil and kept in the dark at 21 °C for three days before transfer to sterile WECK jars containing 100 ml solid 1/10 PNM (plant nutrition medium, pH 5.6) and 0.4 % Gelrite  in a growth chamber under long-day conditions (day/night cycle of 16/8 h, 22 °C/18 °C, light intensity of 108 μmol/m2*s) for an additional four days.

extract_protocol:
RNA extraction, cDNA synthesis and qRT-PCR were performed as described previously (Sarkar et al., 2019). Briefly, RNA was extracted using Trizol (Life Technologies, 15596018) and remaining DNA was removed by DNAseI (Thermo Scientific, EN0521) digestion at 37 °C for 30 min.
For Illumina-compatible RNAseq libraries at first an enrichment for poly-A RNAs was performed (NEBNext® Poly(A) mRNA Magnetic Isolation Module; New England Biolabs), followed by library generation with NEBNext Ultra™II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Next, sequencing-by-synthesis was done on a NextSeq 2000 device in 2 x 150 bp paired-end read mode

treatment_protocol: Prior to treatment, roots and shoots of seven days old barley seedlings were separated. The root tissue between 2 cm below the seed and 1 cm above the tip was cut into root pieces of 5 mm length and twenty-four randomly selected pieces were transferred into each well of a 24-well plate containing 1 ml 2.5 mM MES buffer. Plates were incubated ON at 21°C for recovery. On the next day, 500 µl buffer of each well were removed and replaced with two-fold concentrated elicitor solution ( 500 nM ergosterol or 1/80 S. indica lipid extract in 2.5 mM MES buffer containing 1/20 MeOH to allow  for lipid solubility) and gently mixed. At 2 hours post treatment, roots were removed from the treatment solution, gently dried on tissue paper and snap frozen in liquid nitrogen and homogenized with glass beads in the TissueLyserII (Qiagen) for 4 times 30 sec, 30 Hz in ice-cold holders. Roots from two wells with the same treatment were combined per replicate.

tag: cultivar

value: Golden Promise

value: root

value: 7 days

value: S. indica lipid extract

tag: time

value: 2 h


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep4

value: Untreated mouse tumor samples


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 6 hours post-stimulation, replicate 2

description:
Library name: Compressed 2
column "featureCounts on data 110 and data 102: Counts "

value: Dorsal root ganglia

value: primary cells

value: neuron


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep2


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep3


title: SiLipids_2h_3


title: Compressed sample, cyclic stimulation, 5% strain, 20 cycles, 6 hours post-stimulation, replicate 1

description:
Library name: Compressed 1
column "featureCounts on data 110 and data 97: Counts "


title: pituitary tissue, B,8

description: Sample 8


title: SiLipids_2h_2


title: Control sample, no cyclic stimulation, replicate 8

description:
Library name: Control 8
column "featureCounts on data 110 and data 95: Counts"

value: no mechanical stimulation


title: Male_SW_control_rna_rep3

value: DRG

value: SW


title: pituitary tissue, B,7

description: Sample 7


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep1

value: control (OTX-015 expt)


title: Control sample, no cyclic stimulation, replicate 7

description:
Library name: Control 7
column "featureCounts on data 110 and data 94: Counts"


title: SiLipids_2h_1

value: WT


title: pituitary tissue, B,6

description: Sample 6


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep6


title: Control sample, no cyclic stimulation, replicate 4

description:
Library name: Control 4
column "featureCounts on data 110 and data 93: Counts"


title: B16F10 cell lines OTX015 treated, rep4

source_name: mouse cutaneous melanocytes cells lines treated with OTX015

value: OTX015 B16F10 treated cells


title: Tumor mouse melanocytes cells untreated OTX-015 experiment, rep5

value: tumor mouse cutaneous melanocytes cells


title: pituitary tissue, B,5

description: Sample 5

value: pituitary adenoma


title: Erg_2h_2

value: Golden Promise

value: Ergosterol


title: pituitary tissue, B,4

description: Sample 4


title: B16F10 cell lines OTX015 treated, rep3


title: Control sample, no cyclic stimulation, replicate 2

description:
Library name: Control 2
column "featureCounts on data 110 and data 90: Counts"


title: Control sample, no cyclic stimulation, replicate 3

description:
Library name: Control 3
column "featureCounts on data 110 and data 92: Counts"


title: pituitary tissue, B,3

description: Sample 3


title: Erg_2h_1

value: root

value: 7 days


title: B16F10 cell lines OTX015 treated, rep2


title: SC_2h_3

value: Solvent control

value: 2 h


title: SC_2h_2


title: pituitary tissue, B,2

description: Sample 2


title: B16F10 cell lines untreated, rep4

source_name: mouse cutaneous melanocytes cells lines

value: control

value: Control B16F10 cells


title: TME_Tom negative

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

description: 10X Genomics

data_processing:
The Cell Ranger package (version 7.0.1) was utilized to process unique molecular identifiers (UMIs) and barcodes and align the transcripts to a mm10 mouse reference genome, which was supplied with tdTomato and WPRE sequences manually.
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: Tumor

extract_protocol:
The mice were anesthetized with avertin (tribromoethanol) and further systemically perfused with PBS to remove the circulating cells in tumors. Tumors were collected, minced, and incubated for 20 minutes in 50 mg/mL Liberase DH (Roche), 10 mM HEPES, 2 kunitz/mL DNase in DMEM at 37oC and passed through 18-gauge needles followed by 21-gauge needles with a 20 min incubation in between. Cells were filtered through a 70 mm cell strainer and centrifuged at 400 g for 3 min. The pellet was resuspended into 10 mL ACK lysis buffer for 3 min at room temperature and washed with wash buffer. Cells were treated with an FcR blocking reagent on ice for 10 min, stained with fluorescence-labeled antibodies at 4oC for 30 min, washed, and analyzed or sorted using FACS SORPAria (BD Biosciences).
For the scRNA-seq library construction, we followed the manufacturer’s instructions of 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1.

value: Tumor

value: Stromal cells


title: pituitary tissue, B,1

description: Sample 1


title: TME_Tom positive

description: 10X Genomics


title: Erg_2h_3


title: B16F10 cell lines untreated, rep3


title: SC_2h_1


title: macaque cells sampling at embryonic 34 day_1_Hashtag

status: Public on Jan 30 2025

city: Beijing

first: Zhengyang

last: Xu

address: 8th Dongda street, Fengtai district

institute: Fifth Medical  Center of Chinese PLA General Hospital,

data_processing:
The raw data were aligned to the Mmul_10 and hg19 reference genome using cellranger count (Version 3.0), and the hashed cells were demultiplexed using HTODemux function in Seurat 3, the cells aligned to doublet and negative group were removed from further analysis.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every  cell

organism: Macaca mulatta

source_name: macaque embryonic yolk sac, dorsal aorta and liver

extract_protocol: Single-cell RNA-seq library was prepared and performed on the Chromium platform(10X Genomics), using the single cell expression 3’ profiling chemistry combined with cell hashing. Cell-hashing antibody (HTO)-labeled cells from 2~3 tissues were pooled together and washed with RPMI-1640 immediately before loading on the 10X controller.Then library was constructed following the manufacturer’s protocol, with some additional steps for the amplification of HTO barcodes.

tag: developmental stage

value: embryonic 34 day

value: wild type


title: macaque cells sampling at embryonic 30 day_Hashtag

value: embryonic 30 day


title: macaque cells sampling at embryonic 34 day _2_Hashtag


title: macaque cells sampling at embryonic 28 day_Hashtag

source_name: macaque embryonic yolk sac and dorsal aorta

value: embryonic 28 day


title: macaque cells sampling at embryonic 34 day_Fetal liver_KO

source_name: macaque embryonic liver


title: B16F10 cell lines untreated, rep1


title: macaque cells sampling at embryonic 30 day_Fetal liver_KO

value: knock out


title: B16F10 cell lines OTX015 treated, rep1

value: OTX015 B16F10 treated cells


title: macaque cells sampling at embryonic 30 day_Dorsal aorta-KO

source_name: macaque embryonic dorsal aorta


title: macaque cells sampling at embryonic 29 day_Dorsal aorta_KO

value: embryonic 29 day


title: macaque cells sampling at embryonic 30 day_Yolk sac_KO

source_name: macaque embryonicyolk sac


title: macaque cells sampling at embryonic 34 day_1


title: Control sample, no cyclic stimulation, replicate 1

description:
Library name: Control 1
column "featureCounts on data 110 and data 91: Counts"

value: Dorsal root ganglia

value: primary cells

value: neuron

value: no mechanical stimulation


title: macaque cells sampling at embryonic 34 day_2


title: macaque cells sampling at embryonic 28 day_Fetal liver_KO


title: macaque cells sampling at embryonic 30 day


title: rad51d xrcc3, 40 Gy, replicate 3

city: Yangzhou

first: Mingnan

last: Qu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

description: Library name: rad51d xrcc3-40 Gy-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100.
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: msu7.0
Supplementary files format and content: FPKM values for each Sample.

organism: Oryza sativa

source_name: leaf

growth_protocol: All the plant materials  were grown in 1/2MS medium under normal conditions.

extract_protocol:
Total RNA was extracted from rice leaves using a Trelief® RNApre Pure Plant Kit (tsingke, code: TSP411) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 3-week-old rice plants were treated by γ-irradiation of 40 Gy, rice leaves were collected at 20 h after the treatment.

value: leaf

value: rad51d xrcc3

value: γ-irradiation treatment of 40 Gy


title: macaque cells sampling at embryonic 28 day_Dorsal aorta_KO


title: macaque cells sampling at embryonic 29 day_Yolk sac_KO

source_name: macaque embryonic yolk sac


title: B16F10 cell lines untreated, rep2

value: control

value: Control B16F10 cells


title: rad51d xrcc3, CK, replicate 1

description: Library name: rad51d xrcc3-1

value: No treatment


title: sog1, 40 Gy, replicate 3

description: Library name: sog1-40 Gy-3


title: rad51d xrcc3, CK, replicate 2

description: Library name: rad51d xrcc3-2


title: rad51d xrcc3, CK, replicate 3

description: Library name: rad51d xrcc3-3


title: macaque cells sampling at embryonic 29 day_Fetal liver_KO


title: rad51d xrcc3, 40 Gy, replicate 2

description: Library name: rad51d xrcc3-40 Gy-2


title: sog1, 40 Gy, replicate 1

description: Library name: sog1-40 Gy-1


title: sog1, 40 Gy, replicate 2

description: Library name: sog1-40 Gy-2


title: sog1, CK, replicate 1

description: Library name: sog1-1


title: sog1, CK, replicate 3

description: Library name: sog1-3


title: ZH11, 40 Gy, replicate 3

description: Library name: ZH11-40 Gy-3

value: WT


title: macaque cells sampling at embryonic 30 day_Dorsal aorta

source_name: macaque embryonic dorsal aorta tissue

value: wild type


title: ZH11, 40 Gy, replicate 1

description: Library name: ZH11-40 Gy-1


title: sog1, CK, replicate 2

description: Library name: sog1-2


title: ZH11, CK, replicate 2

description: Library name: ZH11-2


title: ZH11, CK, replicate 1

description: Library name: ZH11-1


title: rad51d xrcc3, 40 Gy, replicate 1

description: Library name: rad51d xrcc3-40 Gy-1


title: primary human umbilical vein endothelial cells, untreated, biol rep 3

city: Los Angeles

first: Pablo

middle: Aldair

last: Alvarez

address: 615 Charles E Young Dr S

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

description:
Library name: HU3
Column name in allsamples_raw_counts.csv: HU3_1 and HU3_2
Column name in allsamples_rpkm.csv: HU3_1.ReadsPerGene.out.tab and HU3_2.ReadsPerGene.out.tab

data_processing:
The RNA-sequencing data were first processed to remove adapter sequences and low-quality reads using Trimmomatic
Trimmed and filtered reads were aligned to the human genome GCHr38 using STAR (v2.6+)
Count data was generated using HTSeq
Counts were calculated and normalized using DESeq2’s median of ratios method
Assembly: GCHr38
Supplementary files format and content: allsamples_raw_counts.csv is a comma separated values file that contains all the raw counts for each sample generated via HTSeq and DESeq2
Supplementary files format and content: allsamples_rpkm.csv is a comma separated values file that contains all the normalized read counts in RPKM format calculated using DESeq2

source_name: peripheral vasculature

growth_protocol:
iPSCs were cultured on matrigel coated flasks with mTeSR1 for one week prior to differentiation with DMEM/F12 supplemented with knockout serum replacer, L-glutamine, nonessential amino acids, and basic fibroblast growth factor. Cells were maintained on this medium for 5-7 days and then replaced with endothelial cell medium containing B-27, basic fibroblast growth factor, and retinoic acid for 2 days. Cells were lifted and seeded on collagen and fibronectin coated plates and maintained with endothelial cell media supplemented with B-27. All cells were cultured in a humidifed atmosphere with 5% CO2 at 37°C.
Primary human umbilical vein endothelial cell (HUVECs; ATCC, PCS-100-010) were cultured in complete Endothelial Cell Medium (Millipore Sigma, 211-500) at 37°C and 5% CO2.

extract_protocol:
RNA was extracted and DNAse-treated using the Qiagen mini RNA preparation kit (Maryland, USA) according to the manufacturer’s instructions. RNA concentration and quality was determined to match the guidelines of Novogene Corporation Inc. for RNA sequencing, concentration ≥20 ng/μL and RIN ≥7.
Final libraries were generated from total RNA using KAPA mRNA Hyper kit according to manufacturer's instructions.

treatment_protocol: All cells were untreated

value: peripheral vasculature

value: Primary HUVEC

value: endothelial cell

value: no treatment


title: ZH11, 40 Gy, replicate 2

description: Library name: ZH11-40 Gy-2


title: primary human umbilical vein endothelial cells, untreated, biol rep 2

description:
Library name: HU2
Column name in allsamples_raw_counts.csv: HU2_1 and HU2_2
Column name in allsamples_rpkm.csv: HU2_1.ReadsPerGene.out.tab and HU2_2.ReadsPerGene.out.tab


title: ZH11, CK, replicate 3

description: Library name: ZH11-3


title: human pluripotent stem cell derived brain microvascular endothelial like cells, untreated, biol rep 2

description:
Library name: ECM2
Column name in allsamples_raw_counts.csv: ECM2_1 and ECM2_2
Column name in allsamples_rpkm.csv: ECM2_1.ReadsPerGene.out.tab and ECM2_2.ReadsPerGene.out.tab

source_name: cerebral microvasculature

value: cerebral microvasculature

value: derived from iPS(IMR90)-4 cells

value: stem cell derived endothelial cells


title: macaque cells sampling at embryonic 28 day

value: embryonic 28 day


title: primary human umbilical vein endothelial cells, untreated, biol rep 1

description:
Library name: HU1
Column name in allsamples_raw_counts.csv: HU1_1 and HU1_2
Column name in allsamples_rpkm.csv: HU1_1.ReadsPerGene.out.tab and HU1_2.ReadsPerGene.out.tab


title: G4Switch_3h_PDS_4uM_treatment_B3

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome and only the reads within the whitelist have been retained.
bw files presented here were created using bamCoverage with counts per milion normalisation (CPM)  after extending the paired-end reads and accepting maximum mapped fragment length of 350nt.
Assembly: hg38
Supplementary files format and content: bigWig, bedgraph, counts

molecule: genomic DNA

growth_protocol:
Human osteosarcoma U2OS cells (ATCC, HTB-96) were cultured in phenol red free Dulbecco's Modified Eagle Medium (DMEM) (high glucose and L-glutamine plus, Gibco, catalogue no. 21063045) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS) (Gibco, catalogue no. 10082147) and 1 mM sodium pyruvate. Cells were grown at 37 ℃ in a humidified 5% CO2 atmosphere. After thawed, cells were passaged at least twice before being used in experiments. Cells were confirmed mycoplasma-free by periodic tests.
The protocol was adapted from that described previously40. U2OS cells were grown to 70-80% confluence at the time of harvesting. Cells were detached with Accutase (Gibco, catalogue no. A1110501), followed by quenching with full growth media, centrifugation (200 g, 5 min). Cell pellets were fixed in 0.1% (w/v) formaldehyde in PBS for 2 min at room temperature, following with quenching in a final concentration of ~110 mM added glycine. Cells were centrifuged (300 g, 5 min, 4 ℃), and cell pellets were either used directly by resuspending in cold wash buffer (20 mM HEPES, pH 7.5, 150 mM KCl, 0.5 mM spermidine, cOmplete EDTA-free protease inhibitor cocktail (Roche, catalogue no. 11836170001)) or kept frozen in wash buffer containing 10% (v/v) DMSO at -80 ℃ until use. The final density of 6 million cells per ml was used.

extract_protocol:
Cells were washed twice in 200 μl TAPS wash buffer (10 mM TAPS, 0.2 mM EDTA), and resuspended in 100 μl extraction buffer (10 mM Tris HCl, pH 8.0, 0.5 mg/ml proteinase K (Thermo Scientific, catalogue no. EO0491), 0.5% SDS) with vortexing, and incubated at 55 ℃ for 1.5 h at 800 rpm. DNA extraction was performed using the DNA Clean & Concentrator-5 kit (Zymo Research, catalogue no. D4013). DNA was eluted in 25 μl provided DNA Elution Buffer from the column after incubation at room temperature for 10 min.
To amplify DNA libraries, PCR was performed by mixing 21 μl tagmented DNA with 2 μl uniquely barcoded v2 Ad1.x primer (10 μM) and 2 μl uniquely barcoded v2 Ad2.x primer (10 μM)51, and 25 μl NEBNext Ultra II Q5 2× PCR Master mix (New England Biolabs, catalogue no. M0544) using the following cycle: 72 ℃ for 5 min; 98 ℃ for 30 s; 10 cycles of 98 ℃ for 10 s and 63 ℃ for 10 s; 72 ℃ for 1 min. Libraries were cleaned up by adding 1.3× volume (65 μl) of Ampure XP beads (Beckman Coulter, catalogue no. A63882), incubated at room temperature for 10 min, washed twice gently in 200 μl of 80% ethanol. DNA was eluted in 25 μl of 10 mM Tris HCl, pH 8.0.
The size distribution of libraries was confirmed by TapeStation analysis using High Sensitivity D1000 ScreenTape (Agilent, catalogue no. 5067–5584). The libraries were quantified using the NEBNext Library Quant Kit (New England Biolabs, catalogue no. E7630L). Libraries were balanced and pooled, followed by size selection by adding 0.4× volumn of Ampure XP beads and incubation at room temperature for 10 min. The supernatant was transferred to a new DNA LoBind tube, and 1.3× volumn of Ampure XP beads was then added and incubated at room temperature for 10 min. On-bead libraries were washed twice with 80% ethanol and eluted in 30 μl of 10 mM Tris HCl, pH 8.0. Paired-end sequencing of libraries was performed on an NextSeq 2000 sequencer (Illumina) using the NextSeq 1000/2000 P2 reagent kit (100 cycles) (Illumina, catalogue no. 20046811).
For chem-map competition experiments, U2OS cells were grown to a 70~80% confluence until treatment with PDS (4 μM or 20 μM) or vehicle DMSO at 37 ℃ for 3 h. Cells were washed twice with PBS, followed by performing standard G4switch Chem-map protocol.

value: epithelial osteosarcoma

tag: chip antibody


title: G4Switch_3h_PDS_4uM_treatment_B2


title: human pluripotent stem cell derived brain microvascular endothelial like cells, untreated, biol rep 1

description:
Library name: ECM1
Column name in allsamples_raw_counts.csv: ECM1_1 and ECM1_2
Column name in allsamples_rpkm.csv: ECM1_1.ReadsPerGene.out.tab and ECM1_2.ReadsPerGene.out.tab


title: G4Switch_3h_PDS_4uM_treatment_B1


title: G4Switch_3h_treatment_B2


title: G4Switch_3h_treatment_B1


title: No_antibody_B2


title: G4Switch_3h_PDS_20uM_treatment_B3


title: G4Switch_3h_PDS_20uM_treatment_B2


title: G4Switch_Chemmap_dark_2h_B3_t3


title: G4Switch_3h_PDS_20uM_treatment_B1


title: G4Switch_Chemmap_dark_2h_B3_t2


title: No_antibody_B3


title: G4Switch_3h_treatment_B3


title: G4Switch_Chemmap_dark_2h_B1_t2


title: G4Switch_Chemmap_dark_2h_B2_t1


title: G4Switch_Chemmap_405_2h_B3_t3


title: G4Switch_Chemmap_dark_2h_B1_t1


title: No_antibody_B1


title: G4Switch_Chemmap_405_2h_B3_t2


title: G4Switch_Chemmap_405_2h_B2_t2


title: G4Switch_Chemmap_405_2h_B2_t3


title: G4Switch_Chemmap_405_2h_B3_t1


title: G4Switch_Chemmap_405_2h_B2_t1


title: G4Switch_Chemmap_dark_2h_B2_t2


title: G4Switch_Chemmap_dark_2h_B3_t1


title: Bld37_Blood_Non demented control

city: Jerusalem

first: Nimrod

last: Madrer

address: The Edmond J. Safra Campus, Guvat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: Short RNA seq of post-mortem sample

data_processing:
FASTQ files were checked for quality using FastQC
Adaptors were removed using FLEXBAR according to the pipeline manual
Adaptor-less output FASTQ files were then aligned to tRFs using MINTmap
Assembly: Human NCBI genome build 37 (GRCh37)
Supplementary files format and content: Raw tRF counts (of SN or Blood), tRF names comply with MINTmap naming system

source_name: Blood

extract_protocol:
Brain and blood samples were obtained from the Netherlands Brain. Brain RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004), and blood RNA was extracted using the NucleoSpin RNA Blood Mini kit for RNA from blood (Machery-Nagel, 740200), both according to the manufacturer's protocol. This was followed by RNA concentration determination (NanoDrop 2000, Thermo Scientific), standard gel electrophoresis for quality assessment, and RIN determination (Bioanalyzer 6000, Agilent).
Libraries were generated (NEBNext Multiplex Small RNA library prep set for Illumina, New England Biolabs, NEB E7560S) and the small RNA fraction was sequenced

value: Blood

tag: brainid

value: Male

value: Ctrl

tag: diagnosis

value: Non demented control

tag: rin

tag: braak

tag: amyloid

value: B

tag: braaklb

tag: apoe

tag: pmd

tag: pd length

tag: sepsis


title: G4Switch_Chemmap_dark_2h_B2_t3

tag: cell line

tag: cell type


title: human pluripotent stem cell derived brain microvascular endothelial like cells, untreated, biol rep 3

description:
Library name: ECM3
Column name in allsamples_raw_counts.csv: ECM3_1 and ECM3_2
Column name in allsamples_rpkm.csv: ECM3_1.ReadsPerGene.out.tab and ECM3_2.ReadsPerGene.out.tab

tag: tissue

tag: genotype

tag: treatment


title: G4Switch_Chemmap_dark_2h_B1_t3


title: G4Switch_Chemmap_405_2h_B1_t3


title: Bld36_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample

tag: Sex

tag: group

value: PD

value: Non demented Park. patient

tag: age

value: A


title: Bld34_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: brainid

value: Female

tag: diagnosis

value: O


title: G4Switch_Chemmap_405_2h_B1_t1

tag: chip antibody


title: Bld33_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: rin

tag: braak

tag: amyloid


title: Bld32_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: braaklb

tag: apoe

tag: pmd


title: Bld31_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: pd length

tag: sepsis


title: Bld35_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: tissue


title: Bld30_Blood_Non demented control

description: Short RNA seq of post-mortem sample


title: Bld29_Blood_Non demented control

description: Short RNA seq of post-mortem sample


title: Bld26_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

value: Park. dis. with dementia


title: Bld25_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

value: C


title: Bld24_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample


title: Bld22_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample


title: Bld21_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample


title: Bld20_Blood_Non demented control

description: Short RNA seq of post-mortem sample


title: Bld18_Blood_Non demented control

description: Short RNA seq of post-mortem sample


title: G4Switch_Chemmap_405_2h_B1_t2

tag: cell line

tag: cell type


title: Bld16_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: Sex


title: Bld14_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

tag: group


title: Bld15_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: age


title: Bld13_Blood_Non demented control

description: Short RNA seq of post-mortem sample

tag: brainid


title: Bld9_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

tag: diagnosis


title: Bld12_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample


title: Bld10_Blood_Non demented control

description: Short RNA seq of post-mortem sample


title: Bld11_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld4_Blood_Non demented control

description: Short RNA seq of post-mortem sample


title: Bld5_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld2_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld8_Blood_Non demented control

description: Short RNA seq of post-mortem sample


title: Bld7_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld23_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample


title: Bld28_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld27_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld17_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld19_Blood_Park. dis. with dementia

description: Short RNA seq of post-mortem sample


title: Bld6_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld1_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: Bld3_Blood_Non demented Park. patient

description: Short RNA seq of post-mortem sample


title: p57_KO_ex3

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

institute: Kyoto University

data_processing:
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-3.4.
The gene expression count matrix was generated using HTSeq (version 2.0.2) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RawCounts values for each Sample

source_name: testis

growth_protocol: GS cells established  from 3 day old mice of Cdkn1c conditional knockout. Cdkn1c(p57) floxed/floxed GS cells were treated with adenovirus cre recombinase.

extract_protocol:
At 2 days after adenovirus infection, GS cells were dissociated into single-cell suspension by trypsin. GS cells were purified using Sephadex G15 column. Total RNA samples were extracted by using TRIzol solution (Invitrogen) and purified by the RNeasy cleanup system (QIAGEN, Valencia, CA).
The library preparation was performed using a Illumina Stranded mRNA Prep Ligation Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: not applicable

value: testis

value: spermatogonia

tag: genotype

value: p57 flox/flox-Cre

tag: model


title: p57_KO_ex2


title: p57_KO_ex1


title: HEK293T, NUP98-PHF23 FA, rep3

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

institute: Duke University

data_processing:
For data analysis, RNA-seq reads were mapped to the reference genome followed by differential gene expression analysis as previously described. In brief, RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2-transformed. Raw read counts were used for differential gene expression analysis by DESeq. Gene Ontology analysis was done using the C5 gene set of Molecular Signature Database (MsigDB) collections available in GSEA website.
Assembly: hg38
Supplementary files format and content: tab-delimited text files for normalized read conunts and DEG
Supplementary files format and content: tab-delimited text files include FPKM for each sample

source_name: embryonic kidney

extract_protocol:
Total RNAs were purified using RNeasy Plus kit (Qiagen, 74136).
For RNA-seq, the RNA samples were processed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II RNA library Prep kit (NEB, E7770) as per the manufacturer’s instructions.

value: embryonic kidney


title: HEK293T, NUP98-PHF23 FA, rep2


title: Cont_ex1

value: p57 flox/flox


title: Cont_ex2


title: HEK293T, EV, rep2


title: NUP98_PHF23_WT,MLL1,ChIP-seq

data_processing:
ChIP–seq data alignment, filtration, peak calling and assignment, and cross-sample comparison were performed as previously described with slight modifications. In brief, ChIP–seq reads were aligned to human genome build GRCh38/hg38 or to mouse genome build GRCm38/mm10 using STAR version 2.7.1. The MACS2 software was used for peak identification with data from input as controls and default parameters. Homer (ver 4.10.0) ‘annotatePeaks’ and ‘findMotifsGenome’ functions were used to annotate the called peaks and to find enriched motifs in these called peaks. Alignment files in the bam format was also transformed into read coverage files (bigWig format) using DeepTools. Genomic binding profiles were generated using the deepTools ‘bamCompare’ functions with options [–operation ratio—pseudocount 1 -binSize 10–extendReads 250] and normalized to the matched input. The resulting bigWig files were visualized in the Integrative Genome Viewer (IGV). Heat maps for ChIP–seq signals were generated using the deepTools ‘computeMatrix’ and ‘plotHeatmap’ functions. ROSE were used for defining super-enhancers[14], with input signals used as control for normalization and peaks at ±2.5 kb from the transcriptional start site excluded. Homer mergePeaks was used to determine overlap of ChIP–seq peaks with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: human embryonic kindey

extract_protocol:
Cells were fixed in 1% formaldehyde (Thermo Scientific, 28908) for 10min, followed by quenching with 125mM glycine for 5min. Cells were then washed twice with cold PBS added with protease inhibitors (Sigma-Aldrich, 4693132001), and then subjected to resuspension and incubation in LB1 buffer (50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). The cell nuclei were collected for sonication using Bioruptor sonicator (Diagenode, B01020001; at high-energy setting for 45 cycles with 30s on and 30s off). Supernatant was collected after centrifugation (20,000g for 10min at 4 °C) for incubation with the dynabeads (Invitrogen, 11204D) that are pre-bound with antibodies for 8h at 4 °C. After a series of wash with LB1 buffer, LB2 buffer (10 mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and LB3 buffer (10 mM Tris-HCl pH 8.0, 100mM NaCl, 1 mM EDTA, 0.5mM  EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine), the chromatin–protein complexes bound to beads were eluted, subject to reverse crosslink overnight at 65 °C, and treated with RNase (Roche, 11119915001; 1 h at 37 °C) and then protease K (Roche, 03115828001; 2h at 55 °C).
The final DNA sample, as well as 1% of input chromatin, was recovered using PCR purification kit (Qiagen, 28106). The ChIP–seq library was prepared using NEBNext Ultra II kit (NEB, E7645L) following the manufacturer’s instructions.

value: human embryonic kindey


title: HEK293T, EV, rep1


title: HEK293T, NUP98-PHF23, rep2


title: HEK293T, NUP98-PHF23, rep3


title: HEK293T, NUP98-PHF23, rep1


title: HEK293T, NUP98-PHF23 FA, rep1


title: NUP98_PHF23_WT,H3K4me2,ChIP-seq


title: HEK293T, EV, rep3


title: Limbal-61y

city: Shanghai

first: Shiding

last: Li

address: 639 Zhizaoju Rd, Shanghai, China, 200011

institute: Department of Ophthalmology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
By using 10x Genomics' Space Ranger software (version 2.0.1), the FASTQ files were processed and aligned to the GRCh38 human reference genome.
Then, the Unique Molecular Identification (UMI) counts were summarized for each barcode. The tissue overlay points were detected based on the images to distinguish them from the background.
Subsequently, the filtered UMI count matrix was analyzed using the Seurat (version 4.1.0) R package
The data was normalized using Sctransform  to identify top 3000 highly variable genes. Principal component analysis (PCA) was used for reducing the dimension of the top-level variable gene-barcode matrices after logarithmic transformation.
Graph-based clustering was conducted to cluster cells according to their gene expression profile with the FindClusters function. The two-dimensional Uniform Manifold Approximation and Projection (UMAP) algorithm with RunUMAP function was used to visualize the cells. The FindAllMarkers function (test. use = bimod) was performed to identify the marker genes in each cluster.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz：list of spatial barcodes
Supplementary files format and content: features.tsv.gz:list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Martix Market Exchange Format
Library strategy: spatial transcriptomics

source_name: human limbus

extract_protocol:
After removal of the central buckle for corneal transplantation, two donor limbal rings (51-years-old and 61-years-old) were collected, and the conjunctiva and outer sclera at the limbal margin were removed under microscope.
The library was prepared by using 10x Genomics' Space Ranger software (version 2.0.1), the FASTQ files were processed and aligned to the GRCh38 human reference genome.

value: human limbus

value: limbal epithelial stem cells


title: M2 RAW264.7 BMH-21 2

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

data_processing:
adatptor removal: /trimmomatic-0.38
alignment: HISAT2
duplicate removal, sorting: SAMtools
Assembly: MM10
Supplementary files format and content: tab delimited text file, quantification using MM10 transcriptome

growth_protocol: RAW 264.7 cells were cultured in DMEM  supplemented with 10% heat-inactivated FBS

extract_protocol:
RNA was extracted using the Qiagen RNAeasy mini kit (qiagen).
The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA)

treatment_protocol: BMDMs (M0) were stimulated with either 20 ng/ml IL-4 or 50 ng/ml IFNγ and 50 ng/ml LPS  to polarize these macrophages to alternatively polarized. In order to assess the effects of inhibiting RNA Pol I on macrophage polarization, medium containing 500 nM BMH-21  was added to the macrophage cultures 24 hours post-polarization, for an additional 24 hours

value: macrophage

value: male

tag: treatment


title: NUP98_PHF23_FA,MLL1,ChIP-seq


title: M2 RAW264.7 BMH-21 1


title: NUP98_PHF23_FA,H3K4me2,ChIP-seq


title: M2 RAW264.7 DMSO 2

value: DMSO


title: Limbal-51y


title: NUP98_PHF23_FA,H3K27ac,ChIP-seq


title: NUP98_PHF23_WT,H3K4me3,ChIP-seq


title: NUP98_PHF23_WT,INPUT,ChIP-seq


title: NUP98_PHF23_WT,H3K27ac,ChIP-seq


title: mES cells, mt2, d3

city: Paris

first: Guillaume

last: Velasco

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

institute: Université Paris Cité

data_processing:
Reads were trimmed to remove low-quality bases with Trim Galore v0.4.2 and aligned to the mm10 genome with BSMAP v2.74. Methylation scores were calculated using methratio.py in BSMAP v2.74 and filtered CpGs covered by a minimum of eight reads.
DMRs were identified using eDMR from the methylKit R package with a minimum of seven differentially methylated CpGs, a difference in methylation >20% and a q-value <0.001.
Assembly: mm10
Supplementary files format and content: IGV files containing methylation scores for all CGs with at least 8X sequencing depth

source_name: ESCs

growth_protocol: mESCs  were maintained in the absence of feeder cells, on plates coated with 1x Laminin in serum-free 2i medium containing  Dulbecco’s modified Eagle’s medium (DMEM) F12 Glutamax supplemented with  50% Neurobasal medium , N2 and B27 Supplements, penicillin/streptomycin, non-essential amino acids, 2-mercaptoethanol, CHIR99201, PD032552 inhibitors and Leukemia Inhibitory Factor. Cells were passaged every two days and maintained at 37ºC with 8% CO2 in a humidified chamber. Huamn Lymphoblastoid cell lines (LCLs) from healthy donors and ICF2 patients were cultured in RPMI 1640 supplemented with 15% FCS and antibiotics.

extract_protocol: RRBS libraries were prepared by MspI digestion from 50 to 100 ng genomic DNA and sequenced in paired-end 2 × 75 bp on an Illumina HiSeq4000

treatment_protocol: For in vitro differentiation, mESCs were grown in bacteriological Petri dish with differentiation medium containing 25% Advanced DMEM, 25% DMEM/F12 GlutaMAX, 50% Neurobasal medium, penicilline/streptavidin, β-mercatoethanol and 11% of knock out serum, at 37ºC with 5% CO2. The differentiation medium was changed every day and embryoid bodies were collected by centrifugation and resuspended in fresh medium.

value: ESCs

value: embryonic stem cells

value: ZBTB24 mutant

value: ESCs differentiation

tag: time

value: Day 3

tag: strain

value: Male


title: NUP98_PHF23_FA,H3K4me3,ChIP-seq


title: NUP98_PHF23_FA,INPUT,ChIP-seq


title: mES cells, WT2, d3

value: WT


title: M2 RAW264.7 DMSO 3


title: NUP98_PHF23_WT-2,GFP,ChIP-seq


title: mES cells, mt2, 2i

value: Day 0


title: M2 RAW264.7 BMH-21 3


title: Cont_ex3

value: testis

value: spermatogonia


title: M2 RAW264.7 DMSO 1


title: NUP98_PHF23_W362A,GFP,ChIP-seq


title: NUP98_PHF23_W362A,INPUT,ChIP-seq


title: NUP98_PHF23_WT-1,GFP,ChIP-seq


title: mES cells, WT2, 2i


title: mES cells, WT1, d3


title: mES cells, mt1, 2i


title: NUP98_PHF23_FA-1,GFP,ChIP-seq


title: AL12, scATAC-seq

city: Seodaemun-gu

first: Insuk

last: Lee

state: Seoul

address: 50 Yonsei-ro

department: Biotechnology

institute: Yonsei University

description: 10x Genomics

data_processing:
scRNA-seq: Barcoded processing, gene counting and aggregation were made using CellRanger v6.1.1. scTCR-seq: barcoded processing, V(D)J sequences and annotations were made using the CellRanger v7.0.0. scATAC-seq: barcoded processing, CellRanger ATAC v2.0.0 for scATAC-seq
Assembly: GRCh38
Supplementary files format and content: raw and filtered matrix file for scRNA-seq, filtered contigs for scTCR-seq, filtered peaks, cell list, peak list, and fragments for scATAC-seq

source_name: Lung

extract_protocol:
We collected fresh tumor tissues which was mechanically and enzymatically dissociated using a gentleMACS dissociator (Miltenyi Biotec, Gladbach Bergisch, Germany, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929) following the manufacturer's instructions. After incubation for 1 h at 37℃, the resuspended samples were filtered through a 70-µm MACS SmartStrainer (Miltenyi Biotec, Cat# 130-098-462) into RPMI-1640 medium (Corning, Inc. Corning, NY, USA) supplemented with 10% fetal bovine serum (Biowest, Riverside, MO, USA) and centrifuged at 300 ×g for 10 min.
Single-cell RNA and TCR libraries were generated using the Chromium controller in accordance with the 10x Chromium Next GEM Single Cell 5-v2_CellSurfaceProtein_UserGuide (CG000330). Cell suspensions were initially diluted with nuclease-free water to a target concentration of 10,000 cells. These suspensions were then combined with the master mix, Single Cell 5′ Gel Beads, and Partitioning Oil, and loaded into a Next GEM Chip K. Within the droplets, RNA transcripts from individual cells were barcoded and reverse-transcribed. The resulting cDNA was pooled and subjected to PCR enrichment. Following amplification, the cDNA was size-selected to generate three distinct library types: 5ʹ Gene Expression, V(D)J Enriched, and Cell Surface Protein. For the Cell Surface Protein Library, the cDNA pool underwent further enrichment using index PCR. The V(D)J Enriched Library required two rounds of amplification with specific primers. The 5’ Gene Expression Library was processed through end repair, addition of a single ‘A’ base, adapter ligation, and subsequent purification and PCR enrichment. Quantification of the purified libraries was performed using qPCR as outlined in the qPCR Quantification Protocol Guide (KAPA), and quality assessment was conducted using the Agilent Technologies 4200 TapeStation. Finally, sequencing was carried out on the HiSeq platform (Illumina) according to the read length specifications provided in the user guide. Single-cell ATAC Libraries were generated using the Chromium controller in accordance with the 10x Single Cell ATAC protocol (CG000168). Initially, nuclei were isolated and incubated with Transposase in a Transposition Mix. These transposed nuclei were then combined with master mix, Single Cell ATAC gel beads, and Partitioning Oil in a Chip E, where DNA fragments are barcoded in droplets during thermal incubation. The resulting barcoded DNA fragments were pooled and underwent sample index PCR. Quantification of the purified libraries was performed using qPCR as described in the qPCR Quantification Protocol Guide (KAPA), and quality assessment was conducted with the Agilent Technologies 4200 TapeStation. Finally, sequencing was carried out on the HiSeq platform (Illumina) following the read length specifications provided in the user guide.

value: Lung

value: Total

tag: tumor type

value: ALK-positive LUAD


title: NUP98_PHF23_WT-HD,GFP,ChIP-seq

value: human embryonic kindey


title: AL11, scATAC-seq

description: 10x Genomics

value: WT LUAD


title: mES cells, WT1, 2i


title: AL10, scATAC-seq

description: 10x Genomics


title: NUP98_PHF23_FA-2,GFP,ChIP-seq


title: Oral submucous Fibrosis_2

city: Manipal

first: Raghu

last: Radhakrishnan

state: Karnataka

address: Madava Nagar, Manipal

department: Oral and Maxillofacial Pathology and Microbiology

country: India

institute: Manipal College of Dental Sciences, Manipal

data_processing:
Quality control and adapter trimming using tool Trimmomatic
contamination removal using Bowtie2( version 2.2.4)
Assembly: Alignment of preprocessed data with human reference genome (hg19) using HISAT2
Supplementary files format and content: text file includes the Read counts for each sample

source_name: Oral submucous Fibrosis

extract_protocol:
The isolation of total RNA  was performed utilizing the mirVana™ miRNA Isolation Kit (Cat. No. AM1560, Invitrogen, Carlsbad, CA, US)
Library preparation was performed using NEBNext RNA Ultra II (NEB #E7775, Massachusetts, US).

value: Oral submucous Fibrosis


title: Oral Submucous Fibrosis_1

source_name: Oral Submucous Fibrosis

value: Oral Submucous Fibrosis


title: Oral Sqaumous cell carcinoma_1

source_name: Oral Sqaumous cell carcinoma

value: Oral Sqaumous cell carcinoma


title: Oral Squamous cell carcinoma_2

source_name: Oral Squamous cell carcinoma

value: Oral Squamous cell carcinoma


title: Normal_2

source_name: Normal

value: Normal


title: Normal_1


title: AL12, scTCR-seq

description: 10x Genomics


title: AL08, scATAC-seq

description: 10x Genomics


title: mES cells, mt1, d3

value: ESCs

value: embryonic stem cells

value: ZBTB24 mutant

value: ESCs differentiation


title: AL10, scTCR-seq

description: 10x Genomics


title: MCF-7 PR si-PDGFB-2 cells

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

institute: George Washington University

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

source_name: Breast

growth_protocol: All cells were maintained in DMEM supplemented with 10% FBS at 37 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen). 2ug of the total RNA was used for the construction of sequencing libraries
Total RNA was extracted and prepared for cDNA libraries within Illumina TruSeq Stranded mRNA sample preparation kit

value: Breast

value: MCF-7 PR si-PDGFB

value: Breast cancer cells

value: PR PDGFB knockdown

value: siPDGFB


title: AL06, scTCR-seq

description: 10x Genomics

value: Lung

value: Total

value: ALK-positive LUAD


title: AL11, scTCR-seq

description: 10x Genomics

value: WT LUAD


title: MCF-7 PR si-PDGFB-3 cells


title: AL08, scTCR-seq

description: 10x Genomics


title: MCF-7 PR si-PDGFB-1 cells


title: AL05, scTCR-seq

description: 10x Genomics


title: AL04, scTCR-seq

description: 10x Genomics


title: MCF-7 PR-1 cells

value: MCF-7 PR

value: PR

value: Palbociclib