title: U87MG mRNA-seq

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

institute: National Institute of Technology

data_processing:
The reads obtained from the sequencing were quality checked and Phred scores were calculated. The reads were trimmed to remove adapter sequence using Cutadapt tool and then, were mapped to hg19 human genome followed by subsequent analysis predicting piRNAs and miRNAs.
For transcriptome data analysis, data was analysed by using Tuxedo software package. With the help of Hista2, the quality reads were mapped to the GRCh37 human reference genome and further analysed to identify transcripts such as PCG, lncRNAs and pseudogenes.
Genome_build: hg19 (small RNAs), GRCh37 (Transcriptome)
Supplementary_files_format_and_content: tab-delimited text files of annotated piRNA, miRNAs and transcripts predicted for each sample.

source_name: Glioblastoma cell line

extract_protocol:
U87MG cell line was procured and maintained in MEM growth media supplemented with 10% FBS and 1% antibiotics Pen-Strep at proper growth condition. Total RNA was extracted from the above cell line using trizol method. The purity of isolated RNA was evaluated using NanoDrop spectrophotometer (Thermo Scientific) by measuring absorbance at 260 nm and 280 nm. The integrity of isolated RNA was checked by running on an Agilent RNA Bioanalyzer to check for the RNA integrity number (RIN), which was found to be 8.7 of small RNAs and 9.3 of total RNAs.
For RNA libraries construction, the NEB Next Small RNA Sample Preparation protocol was used. Then, sequencing was done on HiSeq 2500 with a 1x50 bp read size to obtain 100 million  reads. After sequencing, small RNA seq data was processed to create FASTQ files.

value: cancer

value: Glioblastoma

value: untreated


title: T51_Exp2_RV16_plus_POPG_500_S74_L004

status: Public on Apr 04 2023

type: SRA

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

country: USA

institute: National Jewish Health

description:
count.matrix.txt
count.matrix.vst.txt

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed using skewer (v0.2.2) with the following parameters: end-quality=15, mean-quality=25, min=30.
Read alignment to the human reference genome GRCh38 was performed using HISAT2 (v2.1.0) with default parameters.
Gene quantification was performed using htseq-count (v0.9.1) and GRCh38 Ensemble v84 gene transcript model with the following parameters: stranded=reverse, a=20, mode=intersection-nonempty.
Raw count data were filtered for all genes with at least 6 counts in at least 10% of samples and then variance stabilized using the variance stabilizing transformation (VST) function implemented in DESeq2.
Assembly: Hg38
Supplementary files format and content: "count.matrix.raw.txt" - tab-delimited text file with raw counts for all seqeunced samples and genes
Supplementary files format and content: "count.matrix.vst.txt" - tab-delimited text file with VST-normalized counts for all sequenced samples and filtered genes

molecule: total RNA

organism: Homo sapiens

source_name: Differentiated human tracheal airway epithelial ALI cultures

growth_protocol: Primary AECs were isolated by the National Jewish Health (NJH) Live Cell Core from human lung specimens that were obtained from de-identified donors whose lungs were not suitable for transplantation by the International Institute for the Advancement of Medicine (Edison, NJ) and Donor Alliance of Colorado. The NJH Institutional Review Board (IRB) approved the research on lung cells (HS-3209), and the use and collection of cells and tissues by NJH Live Cell Core (HS-2240). Cells were differentiated and maintained using air-liquid interface (ALI) culture. We routinely performed three individual experiments using primary tracheal epithelial cells, obtained from four different non-smoking donors. Tracheal epithelial cells were expanded on collagen coated plates (Corning) initially using tracheal epithelial cell growth media (BEGM bullet kit from LONZA, (Walkersville, MD, USA)), and subsequently, cultured at ALI in 24-well plates with transwell inserts (Corning, ME, USA). After shift to ALI conditions, the cultures undergo differentiation for 14-16 days. H1-HeLa cells were ob-tained from Dr. Wai-Ming Lee (University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin) and cultured in DMEM/F12 medium (GIBCO, NY, USA) supplemented with 1% glutamine, 15mM HEPES, 1% penicillin and streptomycin (GIBCO, NY, USA), and 10% heat-inactivated bovine growth serum ((BGS), Cyti-va HyClone, Utah).

extract_protocol:
RNA extractions from cultured cells were performed by the RNeasy Mini kit (Qi-agen, Hilden, Germany).
Library preparation and RNA sequencing were conducted at National Jewish Health (Seibold Laboratory). RNA-seq libraries were generated on 81 ALI samples (3 replicates for 3 donors for 9 treatments). KAPA mRNA Hyper Prep (Roche) whole-transcriptome libraries were constructed on the Beckman Coulter FXP automation system with 500 ng RNA input per sample, and Illumina Dual Index Adapters (IDT Technologies) were used to barcode samples using 10 cycles of amplification. Barcoded libraries were pooled and sequenced on an Illumina NovaSeq 6000 system using 150bp paired end reads.

treatment_protocol: To examine anti-RV effects of the phospholipids, palmitoyl-oleoyl-phosphatidylglycerol (POPG) and phosphatidylinositol (PI) with inhibitory effects against the RV-A16 virus or the control lipid palmitoyl-oleoyl-phosphatidylcholine (POPC), unilamellar liposomes perpared by bath sonicatin were added to cells apically and incubated for 16 h at the concentration of 10 mg/ml (POPG), 4 mg/ml (PI) and 20 mg/ml (POPC). Subsequently, the virus, RV-A16, which was obtained from the ATCC (ATCC# VR-283), propagated in H1-HeLa cells and purified by ultracentrifugation, was added at a multiplicity of infection (moi) of 0.02 plaque-forming units (pfu) per cell for 4 h at 35 °C. Unbound virions were removed by washing with Dulbecco's phos-phate-buffered saline (DPBS) three times and the epithelial cells were next incubated for 48 hr at 35 °C either with, or without phospholipids in apical media. At 48 h, apical media was harvested. Ultimately, we generated three replicate ALI samples from each of three tracheal donors (T22, T51, T56) treated in each of the following ways: (1) mock (i.e., Control), (2) lipid only (PI, POPG, or PC), (3) RV-A16 infection alone at 4hr or 48hr (RV-A16_4hr, RV-A16_48h, respectively), or (4) lipid pretreatment followed by RV-A16 infection (RV-A16+PI, RVA-16+POPG, RV-A16+PC).

tag: cell type

value: Tracheal airway epithelial cultures

tag: donor

tag: phospholipid treatment

value: POPG

tag: virus treatment


title: MS37D2-062317-D2_Listeria

city: Cincinnati

first: Shouxiong

last: Huang

state: OH

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati College of Medicine

data_processing:
Sequence reads aligned to the genome and converted to intensity counts
edgeR to identify differentially expressed genes between Act and InAct subsets with defined fold change (>4 folds) and p-values (<0.05).
Supplementary files format and content: tab-delimited text files include intensity counts for each Sample

molecule: polyA RNA

source_name: blood

growth_protocol: human peripheral blood mononuclear cells were sorted using magnetic-conjugated anti-Va7.2 antibody and grew with RPMI1640 complete medium, and were further co-cultured with bacterial-incubated human MR1-overexpressed K562 cells for 16 hours.

extract_protocol:
mirVana kit (ThermoFisher)
NEBNext Ultra Directional RNA Library Prep 185 kit (New England BioLabs)

treatment_protocol: Cultured cells were sorted into two populations labeled by Va7.2+CD161+CD4-CD8+CD69+CD26++ (Act subset) and Va7.2+CD161+CD4-CD8+CD69+/-CD26+/- (InAct subset).

tag: tissue

value: blood

tag: cell line

value: mononuclear cells

value: MAIT

tag: agent

value: Listeria


title: T51_Exp2_RV16_plus_PI_200_S81_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PI


title: CRY_R3_60

city: Sevilla

first: Javier

last: Avalos

address: Faculty of Biology, Av. Reina Mercedes s/n

department: Genetics

country: Spain

institute: University of Seville

data_processing:
Raw reads for all samples were trimmed, filtered and quality controlled with AfterQC (Chen et al., 2017; doi:10.1186/s12859-017-1469-3)
Read mapping to the reference genome was performed using Tophat 2.1.1 (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (Roberts, 2011; doi:10.1093/bioinformatics/btr355. http://cole-trapnell-lab.github.io/cufflinks/)
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the RNAseq quantitation pipeline with the improved mRNA annotation generated by Cuffmerge, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which needs raw counts for quantitation, was used to compare among conditions.
Assembly: FMJU01
Supplementary files format and content: Processed data are described in a single tab-delimited text file that includes raw counts for all samples, indicating probe, chromosome, start and end positions, and feature. Transcripts with no equivalent in FFUJ annotation are indicated as "null"

organism: Fusarium fujikuroi

source_name: CryD mutant 60 min illumination, replicate 3

growth_protocol: the strains were grown in 100 ml of DG medium in 500 ml Erlenmeyer flasks, inoculated with 1000000 conidia. The flasks were kept in total darkness for three days at 30°C in an orbital shaker (150 rpm). Then, the cultures were transferred to four 25-ml Petri dishes under safe red light and kept in static conditions in the dark for 240 min. Subsequently, the Petri dishes were either kept in the dark or illuminated for 15, 60, or 240 min.

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols
400 bp libraries

treatment_protocol: Illumination was provided by a set of four fluorescent tubes (Philips TL-D 18 W/840) at a distance of 60 cm, yielding a light intensity of 7 W/m2.

tag: strain

value: cryD mutant SF237

tag: genotype

value: null cryD mutant

value: mycelium

tag: treatment

value: 60 min illumination


title: T51_Exp2_RV16_plus_PC_1000_S88_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PC


title: U87MG small RNA-seq

country: India

tag: disease state


title: CRY_R3_0

source_name: CryD mutant dark, replicate 3

value: dark


title: MS28D1-062317-D1_InActEcoli

value: InActEcoli


title: R_3

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), including the Q20, Q30 and GC-content of the clean data. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'.
Salmon was used to perform expression level for Unigenes by calculating TPM
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Morchella sextelata

source_name: fruitbody

growth_protocol: The cultivated fresh morels were collected from farm (119.199865, 26.712312) in Fujian province of China in March 2022 during fruiting period.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification.
Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp).

value: fruitbody

tag: group

value: red fruitbody


title: T51_Exp2_RV16_4h_S60_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Control


title: R_2


title: MS27D1-062317-D1_ActEcoli

value: ActEcoli


title: CRY_R2_60

source_name: CryD mutant 60 min illumination, replicate 2


title: T51_Exp2_RV16_0_2_S67_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures


title: CRY_R2_0

source_name: CryD mutant dark, replicate 2


title: T51_Exp2_POPG_500_S95_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: POPG


title: MS25D1-062317-D1_Listeria

value: blood

value: mononuclear cells


title: N_3

value: normal


title: CRY_R1_0

source_name: CryD mutant dark, replicate 1


title: N_2


title: R_1


title: T51_Exp2_PI_200_S102_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PI


title: GSK2-RNAi_oswrky53_CK_2

city: Harbin

first: Enyang

last: mei

address: haping street num 138

institute: Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences

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 kallisto was used to obtain TPM per transcript,  kallisto  v0.46.1.
DESeq2 ,version  1.26.0 was used to perform differential expression analysis
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include Count values for each Sample

organism: Oryza sativa

growth_protocol: Plants were grown in the growth chamber at 30°C for 10 h (day) and 24°C for 14 h (night). At the heading stage, the flag leaf  were harvested. Materials were collected and frozen in liquid nitrogen immediately.

extract_protocol:
Flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

tag: genotype/variation

tag: developmental stage

value: Heading stage

value: leaf


title: GSK2-RNAi_oswrky53_CK_1


title: T51_Exp1_RV16_plus_POPG_500_S94_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: CRY_R1_60

source_name: CryD mutant 60 min illumination, replicate 1

value: cryD mutant SF237

value: null cryD mutant

value: mycelium


title: GSK2-RNAi_oswrky53_CK_3


title: GSK2-RNAi_CK_3


title: N_1


title: T51_Exp2_PC_1000_S109_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PC


title: GSK2-RNAi_CK_2


title: T51_Exp1_RV16_plus_PI_200_S101_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Svitava-8_S1 non inoculated rep3

city: České Budějovice

first: Abdoallah

last: Sharaf

address: Branišovská 31

country: Czech Republic

institute: Biology Centre ASCR, v.v.i.

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 bowtie2
gene counts for every gene and every sample were calculated
Genome_build: IWGSC
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw sRNA counts for every miRNA and every sample

organism: Triticum aestivum

source_name: leaves

extract_protocol:
leaves were collected, flash-frozen on dry ice, and RNA was harvested using Trizol reagent. Lexogen Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Svitava

value: Non inoculated

value: leaves


title: T51_Exp1_RV16_plus_PC_1000_S108_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Svitava-8_S1 non inoculated rep2


title: GSK2-RNAi_CK_1


title: Svitava-8_S1 non inoculated rep1


title: T51_Exp1_RV16_4h_S80_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Control


title: ZH11_CK_3

value: wild type


title: Svitava-7_S15 non inoculated rep4


title: Sterne anthrose treated 2h replicate 3

city: Gainesville

first: Michael

middle: H

last: Norris

state: FL

address: 2055 Mowry Rd

institute: University of Florida

data_processing:
base calling
filtering
Bowtie
cufflink
cuffdiff
Assembly: GCF_000832645.1
Supplementary files format and content: tuxedo output table

organism: Bacillus anthracis

source_name: vegetative

growth_protocol: Growth in BHI

extract_protocol:
Zymo Direct-zol RNA Miniprep Plus kit including the optional bead beating steps as well as the on column DNAse treatment.
NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: mock treated or 10 ug anthrose treatment

value: Sterne

value: vegetative

value: 2 h anthrose


title: ZH11_CK_1


title: T51_Exp1_RV16_0_2_S87_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures


title: Svitava-8_S1 non inoculated rep4


title: Svitava-7_S15 non inoculated rep3


title: T51_Exp1_POPG_500_S115_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: POPG


title: HUVEC_palbociclib_3

city: Washington

first: Gregory

middle: T

last: Gallanis

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

description:
HUVEC_counts.csv
HUVEC_CPM.csv

data_processing:
iIllumina multiplex analysis -> fastq
salmon alignment and quantification of fastq -> salmonquant file
salmonquant file -> raw counts table
edgeR normalization filtering statistical analysis of raw counts table -> fitted table (CPM)
Assembly: Grcm39 (lungs) GRCh38.p13 (HUVEC)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: HUVEC + 2µM palbociclib 72hr (3)

extract_protocol:
Lungs were removed, preserved in RNA Later and stored at -80C until RNA collection. HUVEC cells were processed fresh after treatment. Total RNA from all tissues was harvested using the Rneasy kit (Qiagen). Sequencing results (fastq files) were provided by Novogene (Sacramento, CA) using Illumina Hiseq 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse experiment: A cohort of 24 female p16-INK-ATTAC mice were randomized into four groups (n=6 per group) for a 10-day treatment period: vehicle, AP20187 (AP) 2mg/kg every three days (four total doses) by intraperitoneal injection, palbociclib 150mg/kg daily by oral gavage (10 total doses), or combined palbociclib + AP. Following 10 days of treatment, three mice in each of groups were euthanized for analysis (“Immediate Effect” cohort). The remaining mice were treated with a 14-day holiday from palbociclib or with 14 days of continued AP 2mg/kg every three days (five additional doses) prior to collection (“Residual Effect” cohort). HUVEC experiment: Human umbilical vein endothelial cells were passaged once after cryorecovery, cultured for 24 hours, treated with 2µM palbociclib or water vehicle for 72 hours, and then collected for downstream processing.

value: Human umbilical vein endothelial cells

value: yes

tag: timepoint

value: 72 hours


title: Sterne anthrose treated 2h replicate 2


title: HUVEC_palbociclib_2

description:
HUVEC_counts.csv
HUVEC_CPM.csv

source_name: HUVEC + 2µM palbociclib 72hr (2)


title: Sterne anthrose treated 2h replicate 1


title: T51_Exp1_PI_200_S121_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PI


title: Svitava-7_S15 non inoculated rep1


title: Svitava-7_S15 non inoculated rep2


title: Svitava-6_S17 non inoculated rep4


title: Sterne mock treated 2h replicate 3

value: 2 h mock


title: T51_Exp1_PC_1000_S127_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: HUVEC_vehicle_3

description:
HUVEC_counts.csv
HUVEC_CPM.csv

source_name: HUVEC vehicle (3)

value: no


title: T51_Exp1_CONT_S73_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Sterne mock treated 2h replicate 2


title: HUVEC_vehicle_2

description:
HUVEC_counts.csv
HUVEC_CPM.csv

source_name: HUVEC vehicle (2)


title: Svitava-6_S17 non inoculated rep3


title: Sterne mock treated 2h replicate 1


title: T22_Exp3_RV16_plus_POPG_500_S114_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Svitava-6_S17 non inoculated rep2


title: Sterne anthrose treated 30 min replicate 3

value: 30 min anthrose


title: T22_Exp3_RV16_plus_PI_200_S126_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: HUVEC_vehicle_1

description:
HUVEC_counts.csv
HUVEC_CPM.csv

source_name: HUVEC vehicle (1)


title: Svitava-6_S17 non inoculated rep1

value: Svitava


title: T22_Exp3_RV16_plus_PC_1000_S59_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PC


title: COV318 ovarian cancer stem cells, control

city: San Giovanni rotondo

first: Valentina

last: Melocchi

state: Foggia

address: Viale Padre Pio 7

department: ISBReMIT - Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies

country: Italy

institute: Casa Sollievo della Sofferenza Hospital - IRCCS

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.7.5c with parameters  --runThreadN 8 --outFilterMultimapNmax 20 --alignIntronMax 500000 --quantMode TranscriptomeSAM GeneCounts --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate
Raw counts were determined by STAR v2.7.5c
STAR gene counts were normalized applying the median of ratios method implemented in DESeq2 R package
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include DESeq normalized reads
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Ascites

growth_protocol: Isolation, culture and processing of ovarian cancer cells:  Human ovarian carcinoma cell lines OVCAR3 were purchased from American Type Culture Collection (ATCC; cat# HTB-161), COV318 were acquired from Sigma (cat# 07071903). OVCAR3 cells were grown in RPMI 1640 medium (Euroclone, cat# ECM2001L) containing 20% fetal bovine serum (FBS, cat# RM10432), 2mM L-glutamine (Lonza, cat# 17-605E), 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone, cat# LODE17602E), 10 µg/ml bovine insulin (Merck, cat# 91077C). COV318 cells were cultured in DMEM (Euroclone, cat# ECM0103L) supplemented with 10% FBS, 100 μg/ml streptomycin and 100 U/mL penicillin. The immortalized human mesothelial cell line MeT5A was kindly provided by Prof. Aldieri (Turin) and maintained in Medium 199 (Sigma, cat# M4530) containing 10% FBS, 3.3 nM epidermal growth factor (Merck, cat# E4127), 400 nM hydrocortisone (Sigma, cat# H0888), 870 nM Bovine insulin and 20 mM HEPES (Sigma, cat# H0887). Cell lines were routinely tested for mycoplasma with a PCR-based method and authenticated via short tandem repeat profiling.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, cat# 217004) according to the manufacturer’s protocol and quantified using the 2100 Bioanalyzer (Agilent). RNA quality control was checked using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
Poly-A enriched strand-specific libraries were generated with the TruSeq mRNA V2 sample preparation kit (Illumina, cat# RS-122-2001), ribosomal RNA depleted strand-specific RNA libraries with the TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (Illumina, cat# RS-122-2301 and #RS-122-2302), and transcriptome capture based libraries with the TruSeq RNA Access Library Prep Kit (Illumina, cat# RS-301-2001).

value: Ascites

value: epithelial cell

tag: cell subtype

value: ovarian cancer stem cells

value: control

tag: passage

value: passage 18


title: Sterne anthrose treated 30 min replicate 1

value: Sterne

tag: cell type

value: vegetative


title: T22_Exp3_RV16_4h_S93_L004

description:
count.matrix.txt
count.matrix.vst.txt

source_name: Differentiated human tracheal airway epithelial ALI cultures

value: Tracheal airway epithelial cultures

tag: donor

tag: phospholipid treatment

value: Control


title: COV318 ovarian cancer stem cells, overexpressing MGP

tag: tissue

value: overexpressing MGP


title: COV318 bulk cells, control

tag: cell line

value: bulk


title: Svitava-3_S10 WDV infected rep3

value: WDV infected

value: leaves


title: HUVEC_palbociclib_1

description:
HUVEC_counts.csv
HUVEC_CPM.csv

source_name: HUVEC + 2µM palbociclib 72hr (1)

value: Human umbilical vein endothelial cells

value: yes

value: 72 hours


title: Svitava-3_S10 WDV infected rep2

value: Svitava


title: Sterne mock treated 30 min replicate 3

value: 30 min mock


title: COV318 bulk cells, overexpressing MGP

value: Ascites

value: epithelial cell


title: T22_Exp3_POPG_500_S120_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: POPG

tag: virus treatment


title: OVCAR3 ovarian cancer stem cells, control

value: ovarian cancer stem cells

value: control

value: passage 4


title: Svitava-3_S10 WDV infected rep1


title: Svitava-2_S8 WDV infected rep4


title: Sterne mock treated 30 min replicate 1

tag: strain

value: Sterne

value: vegetative


title: T22_Exp3_RV16_0_2_S107_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures

value: Control


title: T22_Exp3_PC_1000_S66_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PC


title: Sterne anthrose treated 30 min replicate 2

tag: genotype

value: 30 min anthrose


title: OVCAR3 ovarian cancer stem cells, KO for MGP

value: MGP KO


title: OVCAR3 bulk cells, control

value: bulk


title: Svitava-3_S10 WDV infected rep4

tag: treatment

value: WDV infected

value: leaves


title: Svitava-2_S8 WDV infected rep2

value: Svitava


title: Svitava-2_S8 WDV infected rep3


title: T22_Exp2_RV16_plus_POPG_500_S51_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: OVCAR3 bulk cells, KO for MGP

value: Ascites


title: Svitava-2_S8 WDV infected rep1


title: MM16 72 hr - LCL161

type: RNA

city: Hamilton

first: Jonathan

middle: L

last: Bramson

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

description: donor MM16 TAC T cells 72 hr stimulation in LCL161

hyb_protocol: Samples were hybridized using Applied Biosystems hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes • Transfer 90μl of hyb solution to each array, then tape holes. • Hybridize 16 hours at 45° at 60rpm (using GeneChip™ Hybridization Oven 645)• Fluidics washing is FS450_0007 (using GeneChip™ Fluidics Station 450)

scan_protocol: GeneChip Scanner 3000 7G System

data_processing:
Data were processed using ThermoFisher Transcriptome Analysis Console v4.0.2.15 software. Donor group was set as a repeated measure and pairwise differential expression was compared between the DMSO and LCL161 group using Gene Level - SST-RMA summarization.
meta-probeset file:  Clariom_S_Human.r1.na36.hg38.a1.transcript.csv

label: biotin

source_name: 72 hr stimulated T cells

label_protocol: cDNA was generated and the purified, sense-strand cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using a proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Primary human T cells were transduced with lentivirus encoding the TAC receptor and cultured for 14 days prior to cryopreservation in CryoStor10.

extract_protocol: Stimulated T cells were washed in 1x PBS, then T cells were homogenized using the QIAGEN QIAshredder column and total RNA was extracted using the QIAGEN RNEasy Plus mini RNA extraction kit. RNA was quantified by NanoDrop OneC and qualified by Agilent Bioanalyzer.

treatment_protocol: Cryopreserved BCMA-specific TAC T cells were thawed and rested for 24 hrs. After rest, T cells were stimulated 1:1 with BCMA-coated polystyrene microbeads for 24 or 72 hrs in the presence of DMSO or 0.625 μM LCL161. For 24 hr timepoint: after stimulation apoptotic cells were removed using the Miltyeni Dead Cell removal kit as per manufactureres instructions.

value: T cell

tag: time point

value: 72 hrs


title: Sterne mock treated 30 min replicate 2

value: 30 min mock


title: T22_Exp2_RV16_plus_PI_200_S65_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PI


title: T22_Exp3_PI_200_S52_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T22_Exp2_RV16_plus_PC_1000_S79_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: MUM2B-sh2

city: Shanghai

first: Jie

last: Yu

address: No. 639, Zhizaoju road, Huangpu district

department: Department of Ophthalmology

institute: Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology

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 (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Hg38
Supplementary files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig, (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

source_name: Uveal melanoma cells/uveal region

growth_protocol: The cell line MUM2B were cultured in Dulbecco's modified Eagle medium (DMEM;Gibco,USA) supplemented with 10% certified heat-inactivated fetal bovine serum (FBS; Gibco, USA), penicillin (100 U/ml) and streptomycin (100μg/ml) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
MUM2B cells samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated


title: MUM2B-sh1


title: Svitava-1_S9 WDV infected rep3


title: L10 72 hr - LCL161

description: donor L10 TAC T cells 72 hr stimulation in LCL161


title: T22_Exp2_RV16_4h_S113_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: MUM2B-control2


title: T22_Exp2_RV16_0_2_S125_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T22_Exp3_CONT_S100_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: MM16 72 hr - DMSO

description: donor MM16 TAC T cells 72 hr stimulation in DMSO

value: DMSO


title: MUM2B-control1


title: Svitava-1_S9 WDV infected rep1


title: T22_Exp2_POPG_500_S58_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: POPG


title: HN18 72 hr - LCL161

description: donor HN18 TAC T cells 72 hr stimulation in LCL161


title: L10 72 hr - DMSO

description: donor L10 TAC T cells 72 hr stimulation in DMSO


title: 50_KP4-Verteporfin_rep2

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference genome assembly mm10 or hg19 using STAR mapping tool (Dobin et al, 2013l; PMID: 23104886).
Assembly: mm10 or hg19
Supplementary files format and content: Differentially expressed genes were analyzed using Cufflinks tools (Trapnell et al, 2012; PMID: 22383036)

source_name: human PDA cells

growth_protocol: Above cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: Treated with drugs as indicated.

value: KP4 cell line

tag: biological replicate

value: Verteporfin


title: Fengyou-9_S4 non inoculated rep4

tag: cultivar

value: Fengyou

value: Non inoculated


title: T22_Exp2_PI_200_S72_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures

value: Control


title: Svitava-1_S9 WDV infected rep4


title: 49_KP4-Verteporfin_rep1


title: Fengyou-9_S4 non inoculated rep3


title: MM16 24 hr - LCL161

description: donor MM16 TAC T cells 24 hr stimulation in LCL161

source_name: 24 hr stimulated T cells

value: 24 hrs


title: 48_KP4-DMSO_rep2


title: Fengyou-9_S4 non inoculated rep2


title: T22_Exp2_PC_1000_S86_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PC


title: 47_KP4-DMSO_rep1


title: T22_Exp2_CONT_S119_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Svitava-1_S9 WDV infected rep2

value: WDV infected

value: leaves


title: Fengyou-9_S4 non inoculated rep1


title: L10 24 hr - LCL161

description: donor L10 TAC T cells 24 hr stimulation in LCL161


title: T22_Exp1_RV16_plus_POPG_500_S71_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: 46_RNA-seq_SUIT2

value: SUIT2 cell line


title: 45_RNA-seq_PANC0403

value: PANC0403 cell line


title: Fengyou-5_S11 WDV infected rep4


title: 20010R-02-09

city: Medellin

first: Sneider

middle: Alexander

last: Gutierrez Guarnizo

state: Antioquia

department: Biology

country: Colombia

institute: Universidad de Antioquia

data_processing:
FastQC (reads quality control)
Trim galore! Script (read quality filtering and trimming)
BWA-MEM (Mapping to the genome of reference)
SortSam (coordinate sorting .Bam files from mapping)
MarkDuplicates (remove PCR duplicates)
Samtools flagstat (mapping quality)
featureCounts (Counting matrix)
DESeq2 (Read counnt normalization and differential expression analysis)
Assembly: LmajorFriedlin Tritryps DB release-46 2019-11-04 14:07

organism: Leishmania tropica

source_name: promastigotes

growth_protocol: Leishmania promastigotes were grown at a density of 5×105 cells/mL, in Schneider Insect medium, supplemented with 10% Fetal Bovine Serum (FBS), 10 units/mL Penicillin and 0.1 mg/mL Streptomycin (P0781-Sigma Aldrich).

extract_protocol:
RNA isolation using Direct-zolTM RNA MiniPrep (R2050) following the kit instructions. The RNA was recovered in 50 µL nuclease-free water and quantified by Qubit 3.0 and compared to reference samples.
Library preparation was performed with 2 μg polysome-bound RNA by NEBNext Ultra II RNA library prep non-directional (New England BioLabs Inc., Ipswich, MA) following manufacturer instructions.

treatment_protocol: HR strain was treated with 100 µg/mL of SbIII for 12 hours after 36 hours of culture to induce the mechanism active to combat the drug.

value: promastigotes

value: HRSbIII

tag: polysome fraction

value: Total RNA input

tag: replicate


title: Fengyou-5_S11 WDV infected rep3


title: 20010R-02-08

value: HR


title: T22_Exp1_RV16_plus_PC_1000_S99_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Fengyou-5_S11 WDV infected rep2


title: L10 24 hr - DMSO

description: donor L10 TAC T cells 24 hr stimulation in DMSO

value: T cell

value: DMSO


title: HN18 24 hr - LCL161

description: donor HN18 TAC T cells 24 hr stimulation in LCL161


title: MM16 24 hr - DMSO

description: donor MM16 TAC T cells 24 hr stimulation in DMSO


title: T22_Exp1_RV16_4h_S50_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: 43_RNA-seq_AsPC

value: AsPC cell line


title: 20010R-02-06


title: T22_Exp1_RV16_0_2_S64_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Fengyou-3_S13 WDV infected rep4

value: Fengyou


title: 42_RNA-seq_HPAFII

value: HPAFII cell line


title: Fengyou-3_S13 WDV infected rep3


title: 20010R-02-05


title: T22_Exp1_POPG_500_S78_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures

value: POPG


title: 41_RNA-seq_T3M4

value: T3M4 cell line


title: T22_Exp1_PI_200_S92_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PI

value: Control


title: 44_RNA-seq_SNU2571

value: SNU2571 cell line


title: Fengyou-3_S13 WDV infected rep2

value: WDV infected

value: leaves


title: 20010R-02-03

value: promastigotes


title: T22_Exp1_CONT_S57_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: 20010R-02-02


title: Fengyou-5_S11 WDV infected rep1


title: 38_RNA-seq_KP4

value: KP4 cell line


title: Fengyou-3_S13 WDV infected rep1


title: 37_RNA-seq_KP2

value: KP2 cell line


title: 40_RNA-seq_SNU2469

value: SNU2469 cell line


title: T22_Exp1_RV16_plus_PI_200_S85_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: 20010R-02-07

value: WT

value: Total RNA input


title: 20010R-02-04


title: 39_RNA-seq_KLM1

value: KLM1 cell line


title: Fengyou-1_S16 WDV infected rep3

value: Fengyou


title: 20010R-01-27

data_processing:
FastQC (reads quality control)
Trim galore! Script (read quality filtering and trimming)
BWA-MEM (Mapping to the genome of reference)
SortSam (coordinate sorting .Bam files from mapping)
MarkDuplicates (remove PCR duplicates)
Samtools flagstat (mapping quality)
featureCounts (Counting matrix)
DESeq2 (Read counnt normalization and differential expression analysis)
Genome_build: LmajorFriedlin Tritryps DB release-46 2019-11-04 14:07

value: HR

value: HP


title: Fengyou-1_S16 WDV infected rep2


title: 20010R-01-26

value: LP


title: 21_ChIP-seq_H3K27ac_PANC0403

library_source: genomic

data_processing:
Raw reads were mapped to the reference mouse (mm9) or human (hg19) genome assembly using Bowtie2 allowing two-mismatches for only unique alignment. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net). HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Assembly: mm9 or hg19
Supplementary files format and content: bigWig files were generated using makeBigwig.pl script of HOMER suite.

molecule: genomic DNA

extract_protocol:
Lysates were prepared from 5-10 millon single cell dissociated of organoid cultures or monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared using the NEXTflex ChIP-seq kit (Cat# NOVA-5143-02; PerkinElmer) according to the manufacturer's instructions.

value: PANC0403 cell line

tag: antibody

value: H3K27ac (ab4729, Abcam)


title: 25- BC25/27, RH30 w/o BV6

city: Frankfurt a.M.

first: Meike

last: Vogler

address: Komturstraße 3a

country: Germany

institute: Goethe-Universität Frankfurt

data_processing:
Custom pipeline
The reads were mapped against the human genome (build GRCh38.95) using STAR (version 2.6.1d).
We obtained gene counts using a union model of isoforms of transcripts per gene based on the ENSEMBL (GRCh38.95) known genes database.
Assembly: GRCh38.95
Supplementary files format and content: tab-delimited text file including raw counts per gene for all samples

source_name: cancer

growth_protocol: RH30 cells were cultuvated in RPMI-1640 GlutaMax-I media (Life Technologies), supplemented with 10% FCS (Life Technologies), 1% penicillin/streptomycin (Life Technologies), at 37°C at 5% CO2 enriched humidified atmosphere.

extract_protocol:
Total RNA was extracted using either Qiagen's Rneasy Mini or Micro Kit.
mRNA-focused RNA libraries were prepared using Illumina’s TruSeq stranded RNA library prep kit with input amounts of 200 or 400 ng total RNA. Poly(A)-positive mRNA transcripts were isolated from total RNA by binding to magnetic oligo(d)T beads and subsequently fragmented and reverse transcribed during first and second strand synthesis to yield double-stranded cDNA. The fragmented cDNA was then end-repaired and adenylated followed by ligation of the appropriate eight-nucleotide NEXTFLEX DNA barcode adapter (PerkinElmer). The final ligation product was amplified via PCR. Intermediate and final library purification steps were done using AMPure XP beads (Beckman Coulter). Final library quantity and quality was assessed using the Qubit dsDNA HS AssayKit (Invitrogen) and the Agilent High Sensitivity DNA kit.

treatment_protocol: RH30 cells were treated with 5 µM BV6 (Genentech) added to complete RH30 growth medium for 24 h at 37°C, 5% CO2 enriched humidified atmosphere.

value: cancer

value: rhabdomyosarcoma

value: wt

value: untreated


title: 26- BC25/27, RH30 +5µM BV6

value: 5 uM BV6, 24h


title: Fengyou-1_S16 WDV infected rep1

value: WDV infected

value: leaves


title: 22 - RH30+BV6 (BC14)


title: 22_ChIP-seq_H3K27ac_SUIT2

value: SUIT2 cell line


title: 20010R-01-25

value: promastigotes

value: MS


title: 21- RH30 (BC14)


title: Fengyou-1_S16 WDV infected rep4


title: T22_Exp1_PC_1000_S106_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures

value: PC

value: Control


title: 20_ChIP-seq_H3K27ac_SNU2571

value: SNU2571 cell line


title: 20010R-01-24

value: HR

value: HP


title: 19_ChIP-seq_H3K27ac_AsPC1

value: AsPC cell line

value: H3K27ac (ab4729, Abcam)


title: 20010R-02-01

value: WT

value: Total RNA input


title: Fengyou-11_S18 non inoculated rep3

value: Fengyou

value: Non inoculated


title: HN18 72 hr - DMSO

description: donor HN18 TAC T cells 72 hr stimulation in DMSO

value: T cell

value: DMSO

value: 72 hrs


title: 12- RH30+BV6 (BC13)

value: cancer

value: rhabdomyosarcoma

value: wt

value: 5 uM BV6, 24h


title: 11- RH30 (BC13)

value: untreated


title: 20010R-01-23

value: promastigotes

value: LP


title: Fengyou-11_S18 non inoculated rep2

value: leaves


title: 18_ChIP-seq_H3K27ac_HPAFII

value: HPAFII cell line


title: 20010R-01-22

value: HR

value: MS


title: 5- RH30  (BC11)


title: MUM2B-shPD-L1_rep3

data_processing:
library strategy: CUT&Tag
Using Bowtie2 (2.3.5.1) to map the raw reads against the genome with the options
Read redundancy was removed by the rmdup command of SAMtools
using macs2 (2.2.7.1) to call peaks and selected peaks with −log10 p values larger than 8
Assembly: hg38
Supplementary files format and content: bigWig: DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig, (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

extract_protocol:
p-STAT3-DNA complexes were isolated with antibody. DNA was purified using the phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
The libraries were amplified by mixing the DNA with 2μL of a universal i5 and uniquely barcoded i7 primer.

value: PD-L1 knockdown


title: 17_ChIP-seq_H3K27ac_T3M4

value: T3M4 cell line

value: H3K27ac (ab4729, Abcam)


title: 20010R-01-21

value: WT

value: HP


title: Fengyou-10_S6 non inoculated rep4

value: Fengyou

value: Non inoculated


title: Fengyou-11_S18 non inoculated rep1


title: 20010R-01-20


title: 16_ChIP-seq_H3K27ac_SNU2469

value: SNU2469 cell line


title: MUM2B-shPD-L1_rep2


title: Fengyou-10_S6 non inoculated rep3


title: Fengyou-11_S18 non inoculated rep4


title: 14_ChIP-seq_H3K27ac_KP4

value: KP4 cell line


title: 20010R-01-19


title: MUM2B-shPD-L1_rep1


title: Fengyou-10_S6 non inoculated rep2


title: 20010R-01-18


title: Fengyou-10_S6 non inoculated rep1


title: 20010R-01-17


title: 13_ChIP-seq_H3K27ac_KP2

value: KP2 cell line


title: MUM2B-nc_rep2

value: untreated


title: Akteur-9_S3 non inoculated rep4

value: Akteur


title: MUM2B-nc_rep1


title: WM_7_2

city: Los Angeles

first: Brent

last: Fogel

state: CA

address: 710 Westwood Plaza

department: Neurology

institute: UCLA

data_processing:
Sequence reads were aligned to the mouse mm10 reference genome and RefSeq GTFusing the Spliced Transcripts Alignment to a Reference (STAR).
Mapped reads were counted with HTSeq.
RPKM were calculated using a custom script in R based on the GenomicFeatures library and rtracklayer library.
Assembly: mm10
Supplementary files format and content: comma separated text files include RPKM values for each sample

organism: Mus musculus

source_name: subcortical white matter

extract_protocol:
Following immunoprecipitation, ribosomal-bound RNA was isolated using the Nucleospin miRNA isolation kit (Clontech) allowing purification of large and small RNA species. Bulk RNA from miR-142-null and heterozygote mice as well as rTg4510 mice was generated by fresh dissection of the frontal cortex (rTg4510) or prefrontal cortex (miR-142-null), homogenization in lysis buffer and RNA isolation using the Nucleospin miRNA isolation kit. RNA quality was measured using an Aligent Bioanalyzer generating RINs between 6.1-9.5 for all samples.
RNA-sequencing was carried out using either the NuGEN RNA amplification with RiboZero treatment with 50 bp paired end reads (M dataset) or the Illumina TruSeq Stranded RNA library kit with RiboZero Gold treatment with 75 bp paired end reads (T and P datasets).

value: subcortical white matter

value: mature oligodendrocytes


title: WM_8_2


title: 20010R-01-15

value: promastigotes


title: MUM2B-IgG_rep2

data_processing:
Using Bowtie2 (2.3.5.1) to map the raw reads against the genome with the options
Read redundancy was removed by the rmdup command of SAMtools
using macs2 (2.2.7.1) to call peaks and selected peaks with −log10 p values larger than 8
Assembly: hg38
Supplementary files format and content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig, (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

extract_protocol:
PD-L1-DNA complexes were isolated with antibody. DNA was purified using the phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
The libraries were amplified by mixing the DNA with 2μL of a universal i5 and uniquely barcoded i7 primer.
CUT&Tag

value: Uveal melanoma cells


title: WM_6_2


title: Akteur-9_S3 non inoculated rep2

source_name: leaves

value: leaves


title: 15_ChIP-seq_H3K27ac_KLM1

value: KLM1 cell line


title: 20010R-01-14

value: HR

value: LP


title: HN18 24 hr - DMSO

description: donor HN18 TAC T cells 24 hr stimulation in DMSO

value: T cell

value: DMSO

value: 24 hrs


title: Akteur-9_S3 non inoculated rep1

value: Non inoculated


title: WM_3_2


title: WM_2_2


title: Akteur-8_S5 non inoculated rep4


title: WM_5_2


title: 20010R-01-13

value: MS


title: MUM2B-PD-L1_rep2


title: 20010R-01-12

value: WT

value: HP


title: MUM2B-PD-L1_rep1


title: Akteur-8_S5 non inoculated rep2


title: SC_8_4

source_name: spinal cord

value: spinal cord


title: 20010R-01-16


title: Akteur-8_S5 non inoculated rep3

value: Akteur


title: 20010R-01-10


title: 20010R-01-09


title: 20010R-01-11


title: Akteur-9_S3 non inoculated rep3


title: MUM2B-nc_rep3

value: untreated


title: MUM2B-IgG_rep1


title: Akteur-3_S14 WDV infected rep3

value: WDV infected


title: 20010R-01-08

value: promastigotes


title: SC_7_4

value: mature oligodendrocytes


title: SC_5_4


title: SC_4_4


title: SC_3_4


title: 20010R-01-06


title: Akteur-3_S14 WDV infected rep2

value: leaves


title: 72 hs post-transfection with tRNA Replicate 1

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: Biological replicate 1 of 1.

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
Global analysis of nuclearly encoded tRNAs
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on mean fluorescence signal (background fluorescence substraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the  tRNA standards e.g. tRNA standards E. coli tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios.

source_name: cultivated cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; E. coli tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) were added to 2 µg extracted total RNA prior to deacetylation.
2. For  abundance arrays total RNA was deacylated for 45 min at 37°C with 100 mM Tris-HCl (pH 9)
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 16h at 16°C in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
Cells were grown in MEM supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco)
Cells were grown independently for each biological experiment in 6-well plates previously coated

extract_protocol: Total RNA for total tRNA arrays was extracted using TriReagent (Sigma-Aldrich) and for arrays to determine the charged fraction with acidic phenol (pH 4.5) according to manufacturer's protocol

treatment_protocol: Cells were trransfected with suppressor tRNA and samples were withdrawn at 5, 24, 36, 48 and 72 hs post tranfection

value: CFF-16HBEge CFTR R553X transfected with suppressor tRNA

tag: patient identifier

value: CFF-16HBEge CFTR R553X


title: 20010R-01-05

value: HR

value: LP


title: Akteur-8_S5 non inoculated rep1


title: cortex_7_1

source_name: frontal cortex

value: frontal cortex


title: cortex_8_1


title: Akteur-2_S12 WDV infected rep4


title: 20010R-01-04


title: 48 hs post-transfection with tRNA Replicate 1

description: Biological replicate 1 of 1.


title: HGSOC_OCSC_rep2

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

hyb_protocol: Each pool was labeled and hybridized to Affymetrix® Human Gene 2.1 ST according to the manufacturer instructions (Affymetrix).

scan_protocol: Scan protocol was carried out according to the manufacturer instructions (Affymetrix).

data_processing: Quality control and normalization of Affymetrix.CEL files using the Robust Multi-array Average (RMA) were performed by Expression Console software (Affymetrix; version: 1.4.1.46).

growth_protocol: Primary cell cultures were established from peritoneal ascites of high-grade serous ovarian cancer (HGSOC) patients. Tissue samples were incubated with dispase and red blood cells were eliminated. All primary epithelial cells were cultured on collagen-I-coated plates for a maximum of three passages.

extract_protocol: Total RNA was isolated using the miRNeasy Micro kit (Qiagen, cat# 217084) according to manufacturer’s protocol and quantified using a NanoDrop 2000 (Thermo Scientific). The Ovation® Pico WTA System V2 (Nugen, cat# 3302-60) was used to amplify 5 ng of total RNA according to manufacturer’s protocol. Quality control of the RNA samples was performed using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Samples were untreated.

tag: diagnosis

value: Ovarian cancer, high-grade serous ovarian carcinoma (HGSOC)

value: Ovarian cancer stem cells (OCSC) (peritoneal ascites)

tag: Sex

value: Female


title: Akteur-3_S14 WDV infected rep1


title: Akteur-3_S14 WDV infected rep4


title: HGSOC_BULK_rep2

label_protocol: Each pool was labeled and hybridized to Affymetrix® Human Gene 2.1 ST according to the manufacturer instructions (Affymetrix).

tag: cell type

value: Bulk ovarian cancer epithelial cells (peritoneal ascites)


title: cortex_6_1


title: 36 hs post-transfection with tRNA Replicate 2

description: Biological replicate 2 of 2.


title: cortex_5_1


title: 20010R-01-03

value: WT

value: HP


title: 20010R-01-07

value: MS


title: Akteur-2_S12 WDV infected rep3

value: Akteur


title: HGSOC_OCSC_rep1


title: Akteur-2_S12 WDV infected rep2

value: WDV infected


title: 20010R-01-02

value: promastigotes


title: 36 hs post-transfection with tRNA Replicate 1

description: Biological replicate 1 of 2.


title: 24 hs post-transfection with tRNA Replicate 2

description: Biological replicate 2 of 2.


title: cortex_4_1

value: mature oligodendrocytes


title: Akteur-2_S12 WDV infected rep1

value: leaves


title: 24 hs post-transfection with tRNA Replicate 1

description: Biological replicate 1 of 2.

value: CFF-16HBEge CFTR R553X transfected with suppressor tRNA


title: HGSOC_BULK_rep1


title: cortex_3_1


title: Akteur-1_S2 WDV infected rep4


title: 5 hs post-transfection with tRNA Replicate 2

description: Biological replicate 2 of 2.

value: CFF-16HBEge CFTR R553X


title: cortex_2_1


title: Akteur-1_S2 WDV infected rep3


title: CBL_7_3

source_name: cerebellum

value: cerebellum


title: 5 hs post-transfection with tRNA Replicate 1

description: Biological replicate 1 of 2.


title: vhl-1 mutant, biological rep 3

city: Freiburg

first: Athina

last: Ganner

address: Hugstetterstr. 55

department: Nephrology

institute: University hospital Freiburg

data_processing:
All the samples were analyzed on Galaxy  platform.
Quality check was assessed with FastQC v0.71.
Trim Galore! version 0.4.3.1 was used for trimming.
STAR v2.6.0b  was used for alignment.
FeatureCounts v1.6.3 was used for counting the reads and DESeq2 v2.2.12.40.3  for differential expression analysis.
Assembly: Ce11
Supplementary files format and content: counts

organism: Caenorhabditis elegans

source_name: whole animals

extract_protocol:
All strains were maintained at 20°C without starvation prior to experiment. Total RNA purified from age-synchronized young adult C. elegans was prepared using TRI Reagent (Sigma-Aldrich) and a RNA clean and concentrator kit (Zymo Research Corp.). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Eurofins  GATC Biotech GmbH
Illumina 1.9

value: whole animals

value: vhlk-1 mutant

tag: developmental stage

value: young adult


title: CBL_8_3

tag: tissue


title: Akteur-1_S2 WDV infected rep1

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 bowtie2
gene counts for every gene and every sample were calculated
Genome_build: IWGSC
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw sRNA counts for every miRNA and every sample


title: ∆staRPZnstaR strain, +Zn, +novobiocin, rep2

city: Madrid

first: Pablo

last: Hernandez

state: Madrid

address: Ramiro de Maeztu 9

department: Cellular and Molecular Biology

institute: Centro de Investigaciones Biologicas (CSIC)

data_processing:
Analysis of RNA-Seq data was carried out using the web-based platform Galaxy (European server UseGalaxy.eu).
Quality of raw sequence data from Illumina NovaSeq 6000 was analysed with FastQC tool. Trimming for quality control was conducted with Trimmomatic (Galaxy Version 0.38.1).
Sequencing reads were mapped against the S. pneumoniae R6 genome (ASM704v1) using BWA software package (Galaxy version 0.7.17.4) in simple Illumina mode.
BAM files from BWA were analyzed to obtain the number of reads overlapping each protein-coding gene using program featureCount (Galaxy Version 2.0.1+galaxy2).
Assembly: ASM704v1 RefSeq GCF_000007045.1
Supplementary files format and content: Tab-delimited text files obtained from featureCounts (protein-coding genes), including Reference assembly, Gene ID, Gene name, Start, End and Counts.

organism: Streptococcus pneumoniae

source_name: Bacterial cell

growth_protocol: S. pneumoniae was grown as static cultures at 37ºC in a casein hydrolysate-based liquid medium (AGCH) containing 0.2% yeast extract and 0.3% sucrose (C+Y).

extract_protocol:
RNA (about 5 µg) was obtained from samples containing 2-4E8 cells using the RNeasy mini kit (Quiagen). It was depleted of ribosomal RNA using the Ribo-Zero (Bacteria) Magnetic Kit (Illumina).
Libraries for RNA-Seq were prepared from 1 µg RNA using the ScriptSeq v2 RNA-Seq system (Illumina).

treatment_protocol: Cultures were grown to OD620nm = 0.2, diluted 50-fold in medium either without ZnSO4 or with 150 µM ZnSO4 and grown to OD620nm = 0.4.To analyze the effect of novobiocin, the antibiotic was added (0.5 x MIC) to the cultures and they were grown for 30 additional min, while the same ZnSO4 concentration was maintained.

value: Bacterial cell

tag: cell line

value: deltastaRPZnstaR

value: 150 microM ZnSO4, novobiocin 0.5 x MIC


title: ∆staRPZnstaR strain, -Zn, -novobiocin, rep2

value: Untreated


title: ∆staRPZnstaR strain, +Zn, -novobiocin, rep2

value: 150 microM ZnSO4


title: Akteur-1_S2 WDV infected rep2

extract_protocol:
leaves were collected, flash-frozen on dry ice, and RNA was harvested using Trizol reagent. Lexogen Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ∆staRPZnstaR strain, -Zn, +novobiocin, rep2

value: novobiocin 0.5 x MIC


title: CBL_6_3


title: vhl-1 mutant, biological rep 1


title: CBL_5_3


title: Akteur-10_S7 non inoculated rep4

value: Akteur

value: Non inoculated


title: wild type control, biological rep 3

value: wild type animal


title: 20010R-01-01

value: promastigotes

value: WT

value: MS


title: ∆staRPZnstaR strain, +Zn, +novobiocin, rep1


title: wild type control, biological rep 2


title: ∆staRPZnstaR strain, +Zn, -novobiocin, rep1


title: CBL_3_3

value: mature oligodendrocytes


title: Akteur-10_S7 non inoculated rep2

value: leaves


title: Akteur-10_S7 non inoculated rep3


title: wild type control, biological rep 1

value: whole animals


title: ∆staRPZnstaR strain, -Zn, +novobiocin, rep1


title: CBL_2_3

value: cerebellum


title: Akteur-10_S7 non inoculated rep1


title: genomic DNA from tumor cNF56

status: Public on Apr 03 2023

type: genomic

city: Toronto

first: Jeff

last: Liu

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

description: tumor sample

hyb_protocol: Methylation profiling was performed on bisulfite-treated DNA using the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, USA) at the PMGC (Toronto, Canada).

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw methylation files were imported and preprocessed with the statistical programming language R using the minfi package (Bioconductor).

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Samples were collected fresh from the patients at the time of surgical resection and stored at -80ºC. DNA was extracted from fresh-frozen tumor tissue and normal tissue using the DNeasy Blood and Tissue Kit (Qiagen, USA).

tag: gender

value: F

tag: sample type

value: tumor extract

tag: disease state

value: Cutaneous NF_G7


title: genomic DNA from tumor cNF34

description: tumor sample

value: M


title: vhl-1 mutant, biological rep 2

tag: genotype

value: vhlk-1 mutant

value: young adult


title: genomic DNA from tumor CN88

description: tumor sample


title: Pancreatic tumor, Tgm2-edited, rep2

city: Boston

first: Bruno

last: Gegenhuber

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

library_source: transcriptomic single cell

data_processing:
Data were processed using the Cell Ranger pipeline v6.0.0. CellBender (v0.2.2) was used to remove ambient RNA from the count matrices.
Assembly: mm10
Supplementary files format and content: The H5 file contains the feature-barcode matrix after removing ambient RNA. The csv file contains the cell barcodes for each sample.

source_name: Pancreatic tumor

growth_protocol: 6-week-old C57/Bl6 male mice were ordered from Jackson Laboratory.

extract_protocol:
Orthotopic tumors were collected, minced, and incubated at 37°C in digestion buffer [RPMI (Gibco), 2% FBS, 0.2 mg/mL Collagenase P (Roche), 0.2 mg/mL Dispase (Gibco), and 0.1 mg/mL DNase I (Roche)] with low agitation (300 rpm) for 45 min, vortexing every 15 min. Released cells were collected from the supernatant and quenched with cold flow cytometry buffer (PBS, 2% FBS, 20 mM HEPES). The remaining tumor pieces underwent a second round of digestion. Released cells from the two rounds were combined, filtered through 70-um mesh, and concentrated by centrifugation (300 rcf, 5 minutes, 4°C). The single cell suspension was then subjected to ACK lysis and a series of negative selection for removal of dead cells (Miltenyi Dead Cell Removal Kit, cat No. 130-090-101), immune cells (Miltenyi CD45 microbeads, cat No. 130-052-301), and epithelial cells (Miltenyi EPCAM microbeads cat No. 130-105-958). Remaining cells were used for single cell sequencing on the 10X Genomics platform.
Libraries were prepared with the Chromium Single Cell 3' Reagent Kit (v3.1), following the manufacturer's instructions.

treatment_protocol: 10,000 2D cultured PDA cells were injected in 20 ul of 50% Matrigel (Corning, 356231) into the pancreas. Tumors were harvested 2 weeks following injection for scRNA-seq.

value: Pancreatic tumor


title: ∆staRPZnstaR strain, -Zn, -novobiocin, rep1

value: Bacterial cell

value: deltastaRPZnstaR

tag: treatment

value: Untreated


title: Pancreatic tumor, Tgm2-scr, rep1

value: scramble


title: Pancreatic tumor, Krt19-edited, rep2


title: genomic DNA from tumor CN76

description: tumor sample


title: genomic DNA from tumor CN77

description: tumor sample


title: Pancreatic tumor, Tgm2-edited, rep1


title: genomic DNA from tumor CN91

description: tumor sample


title: genomic DNA from tumor CN75

description: tumor sample


title: genomic DNA from tumor CN82

description: tumor sample


title: Pancreatic tumor, Tgm2-scr, rep2


title: genomic DNA from tumor CN97

description: tumor sample


title: Pancreatic tumor, Krt19-scr, rep2


title: Pancreatic tumor, Krt19-edited, rep1


title: genomic DNA from tumor CN96

description: tumor sample


title: Pancreatic tumor, Krt19-scr, rep1


title: genomic DNA from tumor CN95

description: tumor sample


title: genomic DNA from tumor CN90

description: tumor sample


title: genomic DNA from tumor CN85

description: tumor sample


title: PDX1-2 ChIP-seq

city: Chicago

first: Benjamin

middle: J

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10
Supplementary files format and content: bigWig files (*.bw.gz)
Supplementary files format and content: HiCPro validPair files (*.validPairs)
Supplementary files format and content: Homer peak files (*peaks.txt)

growth_protocol: DMEM + 15% FBS (cells), RPMI + 10% FBS or human AB serum (islets)

extract_protocol:
Omni-ATAC protocol for bulk ATAC-seq, 10X Protocol for snATAC-seq, DirectZol MicroPrep (Zymo) for RNA, AQuA HiChIP for HiChIP
10X Protocol for snATAC-seq. NEBNext Ultra II for RNA, ChIP, and HiChIP-seq. Nextera (Tn5) for ATAC-Seq

treatment_protocol: Cells synchronized using 1 hour 10 micromolar forskolin pulse

value: beta cell

value: WT


title: PDX1_input


title: BTC-WT-sin3a-input


title: genomic DNA from tumor CN74

description: tumor sample


title: PDX1-1 ChIP-seq


title: BTC-WT-sin3a-2 ChIP-seq

value: SIN3A (Cell Signaling #8056S)


title: genomic DNA from tumor CN84

description: tumor sample


title: BTC-WT-sin3a-1 ChIP-seq


title: genomic DNA from tumor CN98

description: tumor sample


title: genomic DNA from tumor CN79

description: tumor sample


title: genomic DNA from tumor cNF37

description: tumor sample

value: Cutaneous  NF_G6


title: genomic DNA from tumor CN72

description: tumor sample


title: Abeta + Acetate biol rep 1

city: Daejeon

first: C Justin

last: Lee

address: 55, Expo-ro, Doryong-dong, Yuseong-gu

department: Center for Cognition and Sociality

institute: Institute for Basic Science

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
AceAbeta_2_S3

data_processing:
BCL files obtained from Illumina HiSeq2500 were converted to fastq and demultiplexed based on the index primer sequences. The data was imported to Partek Genomic Suite (Copyright 2009, Partek Inc., St. Louis, MO, USA), where further processing was carried out.
Read quality was checked for each sample using FastQC (Flow version 10.0.21.0328)
High-quality reads were aligned using STAR (2.7.3a)
Aligned reads were quantified to the mouse genome assembly (mm10, Ensemble transcripts release 99) and normalised to the counts per million (CPM) value for each gene in each biological replicate.
The average CPM value from all 3 replicates was subtracted from each raw count value and then divided by the stadard deviation ((raw score minus population average) divided by standard deviation) to obtain the Z-Score for plotting in the heatmap.
Assembly: Alignment was to the mouse genome assembly (mm10, GRCm39).
Supplementary files format and content: CPM values obtained and the calculations performed to obtain Z Score (CPM and calculations.xlsx).

source_name: Brain (Cortex)

growth_protocol: Primary astrocyte cultures were grown in Dulbecco’s modified Eagle’s medium (DMEM, Corning) supplemented with 4.5 g/L glucose, L-glutamine, sodium pyruvate, 10% heat-inactivated horse serum, 10% heat-inactivated fetal bovine serum, and 1000 units/ml of penicillin–streptomycin. Cultures were maintained at 37oC in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from the cell culture using Rnasy Mini Kit (Qiagen, #74104).
1μg of total RNA was enriched for Poly-mRNA (Dynabeads mRNA purification kit, Invitrogen) and reverse transcribed to double-stranded cDNA. The cDNA was end-repaired, adenylated and ligated to Illumina indices prior to 14 cycles of PCR amplification (Ultra RNA library prep kit, NEBNext). Sequencing was performed using 20pM libraries hybridization to  a 2x100 paired-end flow cell in HiSeq2500 (Illumina).

treatment_protocol: At DIV8, cells were washed and treated with 1μM Aβ (Abcam). At DIV11, media was replaced with glucose-free DMEM and 10mM sodium acetate (Sigma Aldrich) was added to the culture. Cells were harvested for RNA isolation on DIV12

value: Brain (Cortex)

value: Primary culture

value: Cortical astrocytes

tag: strain

value: C57BL/6 (P1 pups)

value: Aβ (1μM, 5days) + sodium acetate (10mM, 1day) + 1day glucose-free


title: genomic DNA from tumor cNF19

description: tumor sample

value: M

value: tumor extract


title: Abeta + Acetate biol rep 3

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
AbetaAce4_S3


title: Acetate biol rep 3

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
Acetate4_S4

value: Sodium Acetate (10mM, 1day) + 1day glucose-free


title: genomic DNA from tumor CN83

description: tumor sample

value: F

value: Cutaneous NF_G7


title: genomic DNA from tumor CN80

description: tumor sample


title: Acetate biol rep 1

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
Acetate_2_S4


title: genomic DNA from tumor CN89

description: tumor sample


title: Acetate biol rep 2

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
Acetate3_S4


title: Abeta + Acetate biol rep 2

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
AbetaAce3_S3


title: genomic DNA from tumor CN94

description: tumor sample


title: Control biol rep 3

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
Control3_S1

value: Naïve + 1day glucose-free


title: Control biol rep 2

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
Ctl_2_S1


title: Control biol rep 1

description:
mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)
Ctl_S1


title: genomic DNA from tumor CN100

description: tumor sample


title: genomic DNA from tumor CN78

description: tumor sample


title: genomic DNA from tumor CN99

description: tumor sample


title: genomic DNA from tumor CN87

description: tumor sample


title: genomic DNA from tumor CN86

description: tumor sample


title: genomic DNA from tumor CN92

description: tumor sample


title: CPZ-12+12wk-2 (F), C57BL/6, cortex, rep2

city: College Station

first: Jianrong

last: Li

state: TX

address: VBEC Receiving, VICI Bldg Rm127, 4458 TAMUS

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

description:
ctx-11
Supple_Chronic_Expression Data-CTX-11

data_processing:
Acute (Illumina HiSeq 2500 used for base calling) Chronic (Illumina NovaSeq 6000 for base calling)
Reads were mapped to the mouse genome (GRCm38/mm10) using TopHat version 2.0.13 with default settings.
DEseq2 normalized fold-changes of all samples were done using DESeq2 and were then used to estimate differential gene expression between samples.
Assembly: mm10
Supplementary files format and content: Excel files include log-transformed values

source_name: brain cortex

extract_protocol:
Mice were anesthetized followed by transcardial perfusion with 20mL of sterile PBS (Kim et al., 2012, Steelman et al., 2012). The brain was removed, and the corpus callosum, cortex, and hippocampus were microdissected. Each piece of tissue was flash frozen in liquid nitrogen and stored at -80°C until use. RNA was extracted with Tri Reagent.
Messenger RNA sequencing libraries were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina). Libraries were pooled and sequenced on a one hundred fifty  base pair, paired-end sequencing run on an Illumina NovaSeq 6000.

value: brain cortex

value: wild type

value: Cuprizone-Chronic

tag: treatment period

value: 12wk+12 wk recovery


title: 8Mo naïve (M), C57BL/6 control cortex, rep 3

description:
ctx-14
Supple_Chronic_Expression Data-CTX-14

value: untreated-Chronic


title: 8Mo naïve (M), C57BL/6 control cortex, rep2

description:
ctx-13
Supple_Chronic_Expression Data-CTX-13


title: 8Mo naïve (F), C57BL/6 control cortex, rep 1

description:
ctx-12
Supple_Chronic_Expression Data-CTX-12


title: 8Mo naïve (F), C57BL/6 control cortex, rep 4

description:
ctx-15
Supple_Chronic_Expression Data-CTX-15


title: genomic DNA from tumor CN93

description: tumor sample

value: Cutaneous  NF_G6


title: genomic DNA from tumor CN70

description: tumor sample


title: CPZ-12+8wk-3 (M), C57BL/6, cortex, rep 3

description:
ctx-9
Supple_Chronic_Expression Data-CTX-9

value: 12wk+8 wk recovery


title: genomic DNA from tumor NF2414

description: tumor sample

source_name: Neurofibroma

value: Sporadic Spinal NF_G5


title: CPZ-12+12wk-1 (F), C57BL/6, cortex, rep 1

description:
ctx-10
Supple_Chronic_Expression Data-CTX-10


title: CPZ-12+8wk-2 (F), C57BL/6, cortex, rep2

description:
ctx-8
Supple_Chronic_Expression Data-CTX-8


title: CPZ-12+8wk-1 (F), C57BL/6, cortex, rep 1

description:
ctx-7
Supple_Chronic_Expression Data-CTX-7


title: genomic DNA from tumor NF1869

description: tumor sample


title: genomic DNA from tumor NF1890

description: tumor sample


title: CPZ-12+4wk-2 (F), C57BL/6, cortex, rep2

description:
ctx-5
Supple_Chronic_Expression Data-CTX-5

value: 12wk+4 wk recovery


title: CPZ-12+4wk-3 (M), C57BL/6, cortex, rep 3

description:
ctx-6
Supple_Chronic_Expression Data-CTX-6


title: genomic DNA from tumor NF2314

description: tumor sample


title: genomic DNA from tumor NF882

description: tumor sample


title: CPZ-12+4wk-1 (F), C57BL/6, cortex, rep 1

description:
ctx-4
Supple_Chronic_Expression Data-CTX-4


title: genomic DNA from tumor NF1547

description: tumor sample


title: CPZ-12wk-3 (M), C57BL/6, cortex, rep 3

description:
ctx-3
Supple_Chronic_Expression Data-CTX-3


title: genomic DNA from tumor NF3175

description: tumor sample


title: CPZ-12wk-2 (F), C57BL/6, cortex, rep2

description:
ctx-2
Supple_Chronic_Expression Data-CTX-2


title: genomic DNA from tumor NF2300

description: tumor sample


title: CPZ, 5+1wk (M), C57BL/6, corpus callosum, rep 3

description:
aCC-7
Supple_Acute_Expression Data-aCC-7

source_name: brain corpus callosum

value: brain corpus callosum

value: Cuprizone-Acute

value: 5wk+1wk recovery


title: genomic DNA from tumor NF1397

description: tumor sample

value: tumor extract


title: CPZ, 5+1wk (M), C57BL/6, corpus callosum, rep 2

description:
aCC-6
Supple_Acute_Expression Data-aCC-6

value: M


title: genomic DNA from tumor NF1674

description: tumor sample


title: genomic DNA from tumor NF2525

description: tumor sample

value: F


title: genomic DNA from tumor CN71

description: tumor sample


title: CPZ, 5+1wk (F), C57BL/6, corpus callosum, rep 1

description:
aCC-5
Supple_Acute_Expression Data-aCC-5


title: CPZ, 3wk (F), C57BL/6, corpus callosum, rep 2

description:
aCC-3
Supple_Acute_Expression Data-aCC-3


title: genomic DNA from tumor NF2978

description: tumor sample


title: genomic DNA from tumor NF2173

description: tumor sample


title: genomic DNA from tumor NF1738

description: tumor sample


title: 2Mo naïve (F), C57BL/6 control corpus callosum

description:
aCC-1
Supple_Acute_Expression Data-aCC-1

value: untreated-Acute


title: genomic DNA from tumor NF2166

description: tumor sample


title: zmpshh1-br2 (B)

city: Riverside

first: Brandon

last: Le

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

data_processing:
Raw single end reads were subjected to adapter trimming using a custom Perl script.
Trimmed reads (≥ 18nt) were aligned to a custom index containing Arabidopsis rRNA/tRNA/snoRNA regions using Bowtie v1.1.0 (Langmead et al., 2009) with the parameters "-v 2 -k 1", and  reads that aligned to the 45S rRNA regions were counted.
Subsequently, all aligned reads were discarded and the remaining unaligned reads were mapped to the Arabidopsis genome (TAIR10) using ShortStack  v3.4(Johnson et al., 2016) with parameters (--mismatches 0 --mmap u --bowtie_m 1000 --ranmax 50).
Mapped reads were normalized by calculating the RPMR value (reads per million of 45S rRNA reads) (Li et al., 2016).
Genome_build: Arabidopsis thaliana (TAIR10 genome), Araport11 annotations
Supplementary_files_format_and_content: Tab-delimited text file containing the raw and normalized read counts per 100-bp non-overlapping windows for each sample. The column headers for each file are as follows: Window_ID, chromosome, start position, end position, raw read count, reads per million (RPM) normalization, reads per million of 45S rRNA reads (RPMR) normalization,  read size. Windows without any raw read count are omitted. The start and end positions are 0-based coordinates and can be formatted into bed files for further downstream analysis.

organism: Arabidopsis thaliana

source_name: Inflorescences

growth_protocol: Plants (Col-0 ecotype) were grown in a growth room under long-day conditions (16 hr light/8 hr dark) at 23oC.

extract_protocol:
Inflorescences were collected and frozen in liquid nitrogen and kept at -80oC unitl use.  Total RNA was extracted using TRI reagent (MRC) according to the manufacturer's protocol, and resolved in 15% urea-polyacrylamide gels, from which gel pieces corresponding to the 10-50 nt small RNA fraction were excised. The small RNAs were recovered by soaking the gel slices in 0.4 N NaCl followed by ethanol precipitation. The resulting small RNAs were then used for library preparation.
Extracted small RNAs were used for library preparation with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturer's protocol. The final library products were resolved on a 12% polyacrylamide gel, from which the 150 bp band as determined by the pBR322 DNA-MspI Digest ladder (New England Biolabs, E7323AA, provided in NEB 7300) was excised. The libraries were pooled and sequenced.

value: Inflorescences

value: zmp-2 shh1-1

tag: sequencing batch

value: B

tag: ecotype


title: zmpshh1-br1 (B)

tag: replicate


title: zmpnrpd1-br3 (B)

value: zmp-2 nrpd1-3


title: zmpshh1-br3 (B)


title: genomic DNA from tumor NF2162

description: tumor sample


title: genomic DNA from tumor NF2149

description: tumor sample


title: genomic DNA from tumor NF1693

description: tumor sample


title: zmpnrpd1-br2 (B)


title: genomic DNA from tumor NF1560

description: tumor sample


title: genomic DNA from tumor NF1059

description: tumor sample


title: zmpnrpd1-br1 (B)


title: CPZ-12wk-1 (F), C57BL/6, cortex, rep 1

description:
ctx-1
Supple_Chronic_Expression Data-CTX-1

value: brain cortex

value: wild type

value: Cuprizone-Chronic


title: genomic DNA from tumor NF1847

description: tumor sample


title: zmp-2-br3 (B)


title: genomic DNA from tumor NF2042

description: tumor sample


title: zmp-2-br2 (B)


title: CPZ, 3wk (M), C57BL/6, corpus callosum, rep 3

description:
aCC-4
Supple_Acute_Expression Data-aCC-4


title: genomic DNA from tumor NF2474

description: tumor sample


title: zmp-2-br1 (B)


title: genomic DNA from tumor NF2249

description: tumor sample


title: WT-br3 (B)

value: WT


title: WT-br2 (B)


title: genomic DNA from tumor NF2301

description: tumor sample


title: CPZ, 3wk (M), C57BL/6, corpus callosum, rep 1

description:
aCC-2
Supple_Acute_Expression Data-aCC-2


title: WT-br1 (B)


title: ZMP-YFP-zmp-2-br3 (A)

value: ZMP-YFP zmp-2

value: A


title: genomic DNA from tumor NF1742

description: tumor sample


title: genomic DNA from tumor NF3011

description: tumor sample


title: genomic DNA from tumor NF1537

description: tumor sample


title: ZMP-YFP-zmp-2-br2 (A)


title: genomic DNA from tumor NF1783

description: tumor sample


title: genomic DNA from tumor NF2401

description: tumor sample


title: ZMP-YFP-zmp-2-br1 (A)


title: zmp-2-br2 (A)


title: zmp-2-br1 (A)


title: genomic DNA from tumor NF1832

description: tumor sample


title: genomic DNA from tumor NF1301

description: tumor sample


title: genomic DNA from tumor NF1886

description: tumor sample


title: genomic DNA from tumor NF781

description: tumor sample


title: genomic DNA from tumor NF453

description: tumor sample


title: genomic DNA from tumor NF1377

description: tumor sample


title: zmp-2-br2 (methylation)

data_processing:
Raw  paired-end reads were trimmed using Trim Galore (Krueger, 2015) with parameters "--paired --fastqc --trim1". Trimmed reads alignment, de-duplication, and methylation calling were processed using bismark v0.17.0 (Krueger and Andrews, 2011).
Methylation calls were generated using the bismark_methylation_extractor function and the CX_report file was used to calculate methylation level per cytosine
Genome_build: Arabidopsis thaliana (TAIR10 genome), Araport11 annotations
Supplementary_files_format_and_content: Tab-delimited perC text file containing counts and methylation level per cytosine with greater than one read. The column headers for each file are as follows: Chromosome,  position, strand, methylation level [C/(C+T)], total_C, total_T, sequence context, actual sequence

source_name: 12-day-old seedlings

extract_protocol:
Genomic DNA was isolated using the Dneasy Plant Mini Kit (Qiagen)
5 ug of genomic DNA was used to generate the MethylC-seq libraries as described by Lister et al. 2008 with minor modifications. genomic DNA was fragmented to approximately 200 bp by sonication with a Covaris sonicator according to manufacturer’s instructions (Covaris, S220), then subjected to end repair and ligation of methylated adapters provided by Illumina (Illumina, FC-121-2001) per manufacturer’s instructions for gDNA library construction. 100-200 ng of adapter-ligated gDNA was subjected to sodium bisulfite treatment using the MethylCode Bisulfite conversion kit (Thermo Fisher, MECOV50). Converted and adapter-ligated DNA fragments were enriched by 12 cycles of PCR amplification with PfuTurboCx Hotstart DNA polymerase (Thermo Fisher) . The library was purified with the PCR purification kit (Invitrogen, K310001) and quantified on a Bioanalyzer Instrument (Agilent).

value: 12-day-old seedlings


title: WT-br3 (A)


title: genomic DNA from tumor NF1682

description: tumor sample


title: nrpd1-br1 (A)


title: WT-br2 (A)


title: WT-br1 (A)


title: zmp-2-br1 (methylation)


title: nrpd1-br2 (A)


title: genomic DNA from tumor NF1720

description: tumor sample


title: zmp-2-br3 (A)


title: WT-br2 (methylation)


title: genomic DNA from tumor NF1856

description: tumor sample


title: genomic DNA from tumor NF1874

description: tumor sample


title: genomic DNA from tumor NF2797

description: tumor sample


title: WT-br1 (methylation)


title: genomic DNA from tumor NF1467

description: tumor sample


title: nrpd1-br2 (methylation)


title: nrpd1-br1 (methylation)


title: WT-H3K4me3-IP

data_processing:
Raw paired-end reads were first trimmed using Trim Galore v0.4.3 (Krueger, 2015) with parameters "--paired --fastqc --trimn". Remaining high quality trimmed reads were aligned to the Arabidopsis reference genome (TAIR10) using bowtie2 v2.2.9 (Langmead and Salzberg, 2012).
Peak calling was carried out using MACS v2.2.6  with parameters "-BAMPE -g 1.19e8 --keep-dup auto --bdg" for respective IP and input control
Genome_build: Arabidopsis thaliana (TAIR10 genome)
Supplementary_files_format_and_content: narrowPeak: narrowPeak format of called peaks from the MACS2 output; bigwig: ChIP-seq coverage in 50bp bin generated from deeptools bamCoverage tool

source_name: inflorescences

extract_protocol:
2 g of inflorescences was collected, ground to a fine powder in liquid nitrogen and cross-linked with 1% formaldehyde (Sigma Aldrich) for 20 min at room temperature with slow rotation. The chromatin was then fragmented to 300bp by sonication and the lysate was incubated with anti-HA polyclonal antibody (Sigma Aldrich, H6908) at 4 °C overnight. Subsequently, Dynabeads protein A and protein G were added followed by incubation for an additional 2 hr at 4 °C. The beads were washed five times for 5 min each at 4 °C and eluted twice by incubation in elution buffer (1% SDS, 0.1 M NaHCO3) at 65°C under rotation for 15 min each time. The cross-linking was reversed by incubation at 65 °C overnight, and the DNA was purified using a phenol:chloroform:isoamyl alcohol kit (Thermo Scientific, 17908)
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer's protocol.

value: inflorescences

tag: transgene

tag: chip antibody

value: Anti-H3k4me3 (Abcam, ab8580)


title: genomic DNA from tumor NF2179

description: tumor sample

value: tumor extract


title: genomic DNA from tumor NF1117

description: tumor sample


title: WT-H3K4me3-input


title: genomic DNA from tumor NF1349

description: tumor sample


title: ZMP-HA-IP-br2 (B)

value: Anti-HA (Sigma Aldrich, H6908)


title: genomic DNA from tumor NF1083

description: tumor sample

value: F


title: genomic DNA from tumor NF1543

description: tumor sample


title: genomic DNA from tumor NF2178

description: tumor sample

value: M


title: ZMP-HA-IP-br1 (B)


title: genomic DNA from tumor NF2503

description: tumor sample


title: ZMP-HA-input-br1 (B)


title: genomic DNA from tumor NF1799

description: tumor sample


title: genomic DNA from tumor NF990

description: tumor sample


title: WT-IP-br2 (B)


title: WT-IP-br1 (B)


title: genomic DNA from tumor NF2130

description: tumor sample


title: WT-input-br2 (B)


title: WT-input-br1 (B))


title: zmp-NRPD1-HA-IP-br2


title: genomic DNA from tumor NF2138

description: tumor sample


title: zmp-NRPD1-HA-IP-br1


title: genomic DNA from tumor NF1729

description: tumor sample


title: genomic DNA from tumor M2297

description: tumor sample

source_name: Low-Grade MPNST


title: zmp-NRPD1-HA-input-br1


title: genomic DNA from tumor M9413

description: tumor sample

source_name: MPNST


title: genomic DNA from tumor M1508

description: tumor sample


title: WT-NRPD1-HA-IP-br2


title: WT-NRPD1-HA-input-br1


title: genomic DNA from tumor M4719

description: tumor sample


title: WT-NRPD1-HA-input-br2


title: ZMP-HA-input-br2 (B)


title: genomic DNA from tumor M2491

description: tumor sample


title: genomic DNA from tumor NF1901

description: tumor sample


title: genomic DNA from tumor M2377

description: tumor sample


title: genomic DNA from tumor NF2477

description: tumor sample


title: WT-IP-br2


title: WT-IP-br1


title: WT-input-br2


title: WT-input-br1


title: genomic DNA from tumor M803

description: tumor sample


title: PSCs, control, rep2

data_processing:
Fastq files were aligned to the GRCm38/mm10 reference genome using STAR (v2.5.2b-1), with the parameters: Filter by number of mismatches=2; Maximum number of alignments allowed=2. Read counts over gene exons were detected using featureCounts (version 1.4.6.p5). Differential gene expression was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing normalized transcript values from DESeq2.

growth_protocol: Pancreatic stellate cell line PSC4 (a gift from David Tuveson’s lab) were cultured in DMEM with 5% FBS (Seradigm, 1500-500), 100 units/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Four wells of cells cultured in the same condition were pooled for RNA extraction. RNA extraction was performed using the RNeasy Mini kit (Qiagen, 74106). Cultured cells were directly lysed in RLT buffer (Qiagen).
Sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep kit (20020594). Briefly, 4 μg total RNA per sample were used to prepare cDNA libraries. cDNA was amplified with 12 PCR cycles to minimize duplicate reads. Libraries were pooled and sequenced with single-end 76 bp reads on an Illumina NextSeq 500, using the High Output kit.

treatment_protocol: One day prior to treatment, 100,000 cells were resuspended in 50ul Matrigel (Corning, 356231) and plated on a 12 well plate. After solidifying, Matrigel domes were grown in culture media. On the day of treatment, cells were treated with fresh control media or media containing recombinant cytokines for 6 hr.

value: control


title: PSCs, TNFa-/IFNg-treated, rep2

value: TNFa-/IFNg-treated


title: genomic DNA from tumor M1933

description: tumor sample


title: genomic DNA from tumor M1677

description: tumor sample


title: genomic DNA from tumor M2240

description: tumor sample


title: zmp-NRPD1-HA-input-br2


title: genomic DNA from tumor M6712

description: tumor sample


title: genomic DNA from tumor M3398

description: tumor sample


title: WT-NRPD1-HA-IP-br1


title: genomic DNA from tumor M3048

description: tumor sample


title: genomic DNA from tumor M2346

description: tumor sample


title: genomic DNA from tumor M2372

description: tumor sample


title: genomic DNA from tumor M2252

description: tumor sample


title: PSCs, control, rep1


title: genomic DNA from tumor M2325

description: tumor sample


title: genomic DNA from tumor M1014

description: tumor sample


title: genomic DNA from tumor M9450

description: tumor sample


title: PSCs, TNFa-/IFNg-treated, rep1


title: Cultured corneal endothelial cells, PRGF 3

city: Debrecen

first: Noemí

last: Caballero-Sánchez

address: Egyetem tér 1

department: Biochemestry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
bcl2fastq2 Conversion Software v2.20
Sequence reads were mapped to hg38 using STAR v2.5.4 (default parameters)
Read count extraction was performed by featureCounts (Subread-v2.0.2)
Normalization was preformed using DEseq2 version 1.38.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Cornea

growth_protocol: Corneal endothelial cells were cultured in humidified atmosphere with 5% CO2 at 37C using Optimem-1 supplemented with (A) 8 %v/v FBS, 0.3 mM ascorbic acid 2-phosphate, 200 mg/L calcium chloride, 0.04% chondroitin sulfate, 10 U/mL penicillin, 10 µg/mL streptomycin, 20 ng/mL nerve growth factor, and 5 ng/mL epidermal growth factor (B) 10 %v/v PRGF, 200 mg/L calcium chloride and 10 U/mL penicillin and 10 µg/mL streptomycin.

extract_protocol:
Total RNA from confluent cultures was extracted using the Pico Pure™ RNA isolation kit. Sample quality was checked on Agilent BioAnalyzer using Eukaryotic Total RNA Nano Kit according to the Manufacturer’s protocol. The samples with RNA integrity number (RIN) value > 8 were accepted for the library preparation.
The libraries were prepared from total RNA with NEBNext® Ultra™ II RNA Library Prep for Illumina according to the manufacturer’s protocol.  Sequencing runs were executed on Illumina NextSeq500 instrument using single-end 75 cycles sequencing.

value: Primary culture

value: Cornea

value: Endothelial  cells

value: Cultured PRGF

tag: Sex

value: Female


title: Cultured corneal endothelial cells, PRGF 4

value: Male


title: Cultured corneal endothelial cells, PRGF 2


title: Cultured corneal endothelial cells, FBS 4

value: Cultured FBS


title: Cultured corneal endothelial cells, PRGF 1


title: Cultured corneal endothelial cells, FBS 3


title: Cultured corneal endothelial cells, FBS 2


title: Cultured corneal endothelial cells, FBS 1


title: Donor 1, Time 8

city: Oxford

first: Philippa

last: Hulley

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: mini organotypic culture

data_processing:
Reads were trimmed using trimmomatic
Reads were pseaudoaligned using kallisto with an index built from the hg38 cDNA fasta reference sequence
Differential gene expression was performed using the sleuth package in R
Assembly: hg38
Supplementary files format and content: Tab separated values files containing transcript lengths, estimated counts and tpm as calculated by kallisto

source_name: Trabecullar Bone

growth_protocol: Osteoblasts from 4 donors were seeded onto 20 constructs. Constructs were constructed as described: Calcium phosphate (brushite / β-TCP) posts were pinned into a Sylgard 184 silicone elastomer (base and curing agent, Dow Corning Corporation) base layer in 6-well dishes. Cells were seeded in fibrinogen onto a thrombin gel and subsequently cultured in 3ml of proliferation media (osteoblast media, 50 μg/ml ascorbate-2-phosphate, 40 μg/ml proline) per well until cells had fully contracted the gel between the support posts.

extract_protocol:
Snap frozen constructs were pulverised in a Cryo-Cup grinder on dry ice and RNA extracted using Trizol and cleaned up with a Direct-Zol RNA miniprep kit and RNA clean and concentrator (Zymo Research, Cambridge, UK) according to the manufacturer’s instructions.
RNA libraries were constructed using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biosystems, Ipswich, UK) and then the NEBNext ultra-directional RNA library prep kit was used to create the final library.
The sample was sequenced using 41bp paired end configuration with an Illumina NextSeq 500 sequencing device.

treatment_protocol: Week 0 constructs were harvested and snap-frozen at this point with the remainder transferred to osteogenic media (proliferation media, 10 mM β-glycerophosphate, 10 nM dexamethasone) and harvested at 2, 4, 6 and 8 weeks.

tag: age

tag: passage

value: Trabecullar Bone

value: primary

tag: cell type

value: osteoblast

tag: time

value: 8 weeks

value: osteogenic - differentiation


title: Donor 2, Time 0

description: mini organotypic culture

tag: tissue

tag: cell line

value: 0 weeks


title: Donor 2, Time 4

description: mini organotypic culture

value: 4 weeks


title: Donor 2, Time 2

description: mini organotypic culture

value: 2 weeks


title: Donor 1, Time 4

description: mini organotypic culture


title: Donor 1, Time 2

description: mini organotypic culture


title: Donor 1, Time 0

description: mini organotypic culture


title: Progenitor Endothelial Cells, 30 hours, Replicate 1

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Standard Affymetrix procedures using a Hewlett-Packard scanner

data_processing: Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the Robust Multichip Average (RMA) method.

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

growth_protocol: Progenitor SMCs were grown to confluence in M231 medium supplemented with smooth muscle growth supplement (SMGS; Cascade Biologics Inc.), 1x antibiotic/antimycotic (AA) mix and 20% FCS. Progenitor ECs were cultured in phenol red free endothelial basal medium (EBM-2; Lonza) supplemented with 1x AA, endothelial growth supplement (EGM-2 bullet kit; Lonza) and 20% FCS.

extract_protocol: Total RNA was extracted from vehicle-treated and estradiol-treated samples using QIA shredder and RNAeasy Mini kit (Qiagen) according to manufacturer’s instruction. The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only the samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2.0 were further processed.

treatment_protocol: When P-SMC and P-EC reached 80% confluence, the cells washed thrice with phenol red free DMEM/F12 medium and subsequently fed medium (DMEM/F12 supplemented with 2.5% steroid free serum and 1x AA) containing either vehicle (DMSO 1ul/ml) or 17β-estradiol (10nM). Following  treatment with estradiol for the prescribed times (0, 4 and 30 hours) the cells were washed with PBS and processed for total RNA isolation.

value: Progenitor Endothelial Cells

tag: estradiol treatment


title: Donor 4, Time 8

description: mini organotypic culture


title: Progenitor Endothelial Cells, 30 hours, Replicate 3


title: Progenitor Endothelial Cells, 0 hours, Replicate 3

description: Endothelial Cells, 0 hours, Replicate 3


title: Progenitor Endothelial Cells, 0 hours, Replicate 2

description: Endothelial Cells, 0 hours, Replicate 2


title: Donor 4, Time 6

description: mini organotypic culture

value: 6 weeks


title: Progenitor Smooth Muscle Cells, 30 hours, Replicate 2

value: Progenitor Smooth Muscle Cells


title: Progenitor Endothelial Cells, 0 hours, Replicate 1

description: Endothelial Cells, 0 hours, Replicate 1


title: Progenitor Smooth Muscle Cells, 30 hours, Replicate 3


title: Progenitor Smooth Muscle Cells, 0 hours, Replicate 3