title: ZR75_C3

status: Public on Nov 02 2022

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

growth_protocol: ZR-75 cells were cultured in Pheno red free RPMI medium supplemented with 10% charcoal stripped serum

extract_protocol:
Total RNA was isolated from ZR75 cells with and without 48 hours of 10μM SMIP34 treatment using the RNeasy mini kit according to the manufacturer’s protocol (Qiagen, Valencia, CA)
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

tag: cell-line

value: control


title: ZR75_SMIP34_2

type: SRA

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

country: USA

institute: UTHSA-GCCRI

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment


title: ZR75_C1


title: SSc patient 1

status: Public on Dec 09 2022

city: New Haven

first: Ian

last: Odell

state: CT

address: 330 Cedar St. LMP-5040

department: Dermatology

institute: Yale University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10x genomics Cell Ranger pipeline was used to align reads, perform clustering and gene expression analysis, and aggregate the samples with normalized read counts
Assembly: GRCh3.0.0
Supplementary files format and content: h5

source_name: skin

extract_protocol:
6 mm punch biopsy specimen was first incubated in RPMI 1640 medium (Gibco) containing 5% fetal bovine serum (5% FBS/RPMI) and 10 mg/ml Dispase II (Sigma D4693-1G) for 45 minutes at 37° C shaking at 200-250 rpm. The sample was then removed from the media and minced with sterile iris scissors, followed by digestion with Liberase TM (Sigma) 0.5 mg/ml and DNase I 30 Units/ml in 5% FBS/RPMI for 45 minutes at 37° C shaking at 200-250 rpm. The resulting single cell suspension was then filtered through a 70 mm nylon membrane and washed. Live cells were sorted on a FACSAria and their final concentration and viability quantified with Trypan blue on a hemacytomer. The cells were pelleted and suspended in phosphate buffered saline containing 0.04% bovine serum albumin between 500-1000 cells/ml. 3000-6000 cells with greater than 80% viability were submitted to the Yale DNA Sequencing facility for generation of single-cell cDNA libraries using the Chromium Single Cell Controller (10x Genomics).
per 10x Genomics protocol using Single Cell 3' v2. Each cDNA library was sequenced paired-end on 1 lane with 75 base-pair read length using the Illumina HiSeq 2500 System generating at least 75,000 reads per cell.

tag: cell type

value: all

tag: tissue

value: skin

tag: individual

value: SSc patient 1


title: ZR75_C2


title: ZR75_SMIP34_1


title: T47D_WT_Rep1_RNAseq

status: Public on Aug 01 2022

city: Miami

first: Liliana

last: Garcia-Martinez

state: Florida

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami

data_processing:
ChIP-seq: Single-end ChIP-seq fastq files were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4, and peaks with fold change > 3.5 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq). Reads were trimmed using cutadapt v2.3 with the following parameters: -j 4 --netseq-trim=20 -m 18. Reads were aligned to the hg19 genome using STAR v2.6.1a along default parameters, and RSEM v1.3.0 was used to obtain the expected gene counts against the human refseq also along default parameters.
RNA-seq differential expression was determined using DESeq2 v1.18.1 and R (version 3.4.1) with q-value <0.05. Ruvseq v1.12.0 was used for factor analysis to remove count based on ERCC spike-in. GSEA analysis was performed using gsea-3.0.jar. These additional analysis steps were included in the Diderote LSF-RNAseq Pipeline.
Bedtools v2.29.0 intersect was used to determine peak overlaps and assign target genes.
Homer v4.11 was used for peak annotation and motif analysis (http://homer.ucsd.edu/homer/data/software/homer.v4.11.1.zip)
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ).

extract_protocol:
Total RNA was isolated from frozen cell pellets using the TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions. RNA quantity and quality was measured on a nanodrop.2 ug of RNA were treated using the TURBO DNA-free Kit (Thermo Fisher AM1907) to remove DNA contamination and later on DNAse and divalent cations from the sample. 1ug of the treated RNA was used for library preparation. Quality was checked using a Bioanalyzer
Library preparation was perfromed on Dnase-treated RNA using the Illumina TruSeq Stranded Total RNA Library Prep Gold (Illumina 20020598). TruSeq RNA UD Indexes (Illumina 20022371) were used for the adapter ligation step. Samples were normalized to a concentration of ranging from 100-250ng for input, and 1 ul of ERCC spike-in Mix 1 (Thermo Fisher 4456740) diluted 1:200 was added to the samples.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications

value: Parental

tag: chip antibody


title: T47D_LTED8m_72h_DMSO_Rep1_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 8 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL). Cells were culture in  72h in the presence of DMSO.

extract_protocol:
Total RNA was isolated from frozen cell pellets using the TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions. RNA quantity and quality was measured on a nanodrop. 2 ug of RNA were treated using the TURBO DNA-free Kit (Thermo Fisher AM1907) to remove DNA contamination and later on DNAse and divalent cations from the sample. 1ug of the treated RNA was used for library preparation. Quality was checked using a Bioanalyzer
Library preparation was perfromed on Dnase-treated RNA using the Illumina TruSeq Stranded Total RNA Library Prep Gold (Illumina 20020598). TruSeq RNA UD Indexes (Illumina 20022371) were used for the adapter ligation step. Samples were normalized to a concentration of ranging from 100-250ng for input, and 1 ul of ERCC spike-in Mix 1 (Thermo Fisher 4456740) diluted 1:200 was added to the samples.

value: Parental estrogen deprived for 8 months


title: RL_C2

status: Public on Nov 16 2022

description: RL95-2 cells incubated with serum-free RPMI+DMEM media (1:1).

data_processing:
Illumina bcl2fastq software used for base-calling.
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene.
Gene count measurements were obtained using HTSeq-count.
Assembly: hg19
Supplementary files format and content: *_Genes_ReadCount.txt: The processed data files are in tabular format. The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count.

source_name: Endometrial cancer cell line-RL95-2

growth_protocol: RL95-2 cells were cultured in RPMI media supplemented with 10% FBS.

extract_protocol:
Total RNA from RL95-2 control, and ADP-CM cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing were done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide.

treatment_protocol: RL95-2 cells were incubated in serum-free RPMI medium with or without ADP-CM for 24 hrs.

tag: cell line

value: Endometrial cancer cell line

value: Control


title: Batch5_unsorted_water_F1_3

status: Public on Jul 21 2022

city: Los Angeles

first: Yen-Wei

last: Chen

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

data_processing:
Data quality checks were performed using the Cellranger tool
Reads passing quality control were further aligned to pre-mRNA reference transcriptome generated by replacing “transcript” to “exon” in annotation GTF file.
Assembly: ce10
Supplementary files format and content: filtered_feature_bc_matrix produced by Cellranger

organism: Caenorhabditis elegans

source_name: C. elegans whole worm body

growth_protocol: Worms were maintained on standard nematode growth medium (NGM) plates streaked with single colony Harvard OP50 E. coli. All experiments were grown at 20°C up until the generation right before sequencing during which they were moved at the L1 stage to 25°C and grown until day 2 of adulthood (i.e. 48 hours at 25°C). The JK560 (fog-1(q253) I.) strain used in this study was obtained from the C. elegans Genetics Center (CGC). This strain was chosen due to its defect in the last step of spermatogenesis. These mutants were observed to have a fully developed germline but not fertilized embryos.

extract_protocol:
All reagents except for Triton-X100, PBS-BSA 1%, and inhibitors were prepared the night before and all low retention 1.5mL microcentrifuge tubes were clearly labeled. The bench space and equipment used in this protocol were thoroughly sanitized with 70% ethanol and cleaned with RNaseZAP (AM9780 Fisher) before starting the dissociation. Reagents were prepared using RNase free water (BP2484100 Fisher). The FA lysis buffer was made using the following reagents: 50mM HEPES/NaOH pH 7.5, 1mM EDTA, 0.1% Triton X-100, 150mM NaCl, Protease inhibitor 0.5X (Roche 11697498001), RNase inhibitor 0.2U/μL (Thermo Fisher 10777019), and RNase free water and stored at 4°C or on ice. BSA was prepared to a final concentration of 1% in pH 7.4 1X PBS (AM9624 Thermo Fisher) using RNAse free water and RNAse free PBS. This solution was filtered using a 0.22μm pressure filter (Thermo Scientific 03-377-26, Fisher SLGP033RS). All equipment and reagents were moved to a 4°C cold room and subsequent steps were performed at 4°C.Homogenizers were stored pre-chilled in -20°C when not in use and moved to the 4°C room before starting the extraction. Each wheaton 1.5mL Dounce homogenizers (Z378623-1EA Sigma) was cleaned using 70% ethanol, RNaseZAP, and RNase free water. Homogenizers were rinsed twice with ethanol, twice with RNaseZAP, and 5 times with 1-2mL of RNase free water. The compact 30μL pellet of adult C. elegans was transferred to the dounce homogenizer and 400μL of ice cold FA buffer was used to rinse any remaining worms from the 1.5mL low bind microcentrifuge tube and 1000μL low bind pipette tip and added to the homogenizer. Worms were homogenized with 10 strokes of the dounce homogenizer using a corkscrew motion with a B (tight) pestle. Homogenized worms were transferred to a new low bind 1.5ml microcentrifuge tube and centrifuged at 100g for 1 minute to pellet debris. The supernatant containing the dissociated nuclei was removed using a 1000μL low bind tip and transferred to a fresh low bind 1.5mL microcentrifuge tube labeled pooled nuclei. 300μL of FA buffer was added to the debris remaining in the first microcentrifuge tube and homogenized using 10 strokes in a corkscrew fashion with an Eppendorf Dounce homogenizer. The newly homogenized sample was then centrifuged at 100g for 1 minute to pellet debris. The supernatant containing the newly dissociated nuclei was pooled with the previously dissociated nuclei and the previous steps with the Eppendorf Dounce homogenizer were repeated once more to further homogenize the sample. In total, worms were homogenized with 30 strokes: 10 strokes with the 1.5mL Wheaton Dounce homogenizer and 20 strokes with the Eppendorf dounce homogenizer. Between each homogenization step, debris was pelleted using 100g for 1 minute and the supernatant containing the dissociated nuclei was removed and added to a single 1.5mL microcentrifuge tube labeled pooled nuclei. Dissociated nuclei were removed after each set of 10 homogenization strokes to prevent overdigestion of nuclei. After homogenization, the pooled supernatant containing the dissociated nuclei was centrifuged at 100g for 1 minute to pellet any remaining or accidentally transferred debris. The top 900μL of supernatant containing nuclei was transferred to a clean low bind 1.5mL microcentrifuge tube, being careful not to disturb the debris pellet. These pooled nuclei were pelleted at 500g for 4 minutes. After pelleting, approximately 800μL of FA buffer was removed, being careful not to disrupt the nuclei pellet, and the pelleted nuclei was resuspended with 1000μL of PBS-BSA 1%. The nuclei was again centrifuged at 500g for 4 minutes and 1000μL of the PBS-BSA 1% supernatant was removed. Lastly, the nuclei pellet was resuspended in 750-850μL of PBS-BSA 1% (final volume was determined by examining the size of the nuclei pellet). After resuspension, the nuclei was filtered using a 40μm Flowmi tip filter (BAH136800040-50EA Sigma Aldrich). Filtered nuclei were transferred to a 1.5mL low retention microcentrifuge tube for FACS sorting or 10X sequencing.
Library preparation was performed by UCLA Technology Center for Genomics & Bioinformatics. Nuclei were isolated into single droplets and barcoded using the 10X platform. We sequenced using 50bp long paired end reads with the NovaSeq 6000 .

treatment_protocol: Worms were synchronized using a 10μm nylon mesh filter (NY1102500 EDM Millipore and SX00025000 EDM Millipore) which only allowed L1 staged worms to pass. The L1 worms were washed twice with M9 and centrifuged at 100g for 1 minute. These pellets were plated on fresh NGM plates and transferred to 25°C. Worms were grown for 62 hours at 25°C and were washed 5 times with M9. Between each wash, adult worms were centrifuged at 1300g for 1 minute to remove bacteria. After washing, worms were placed in 1mL of M9 in a 1.5mL low retention microcentrifuge tube and incubated in a rotator at 20°C for 30 minutes to remove residual OP50 from the worms gut. These microcentrifuge tubes were then set upright and the worms were allowed to settle by gravity for 5 minutes. The M9 supernatant was discarded and the final compact worm pellet volume was adjusted to 30μL.

tag: experitment design

value: water

tag: treatment group

tag: treatment details

value: Worms were synchronized using a 10Œºm nylon mesh filter (NY1102500 EDM Millipore and SX00025000 EDM Millipore) which only allowed L1 staged worms to pass. The L1 worms were washed twice with M9 and centrifuged at 100g for 1 minute. These pellets were plated on fresh NGM plates and transferred to 25¬∞C. Worms were grown for 62 hours at 25¬∞C and were washed 5 times with M9. Between each wash, adult worms were centrifuged at 1300g for 1 minute to remove bacteria. After washing, worms were placed in 1mL of M9 in a 1.5mL low retention microcentrifuge tube and incubated in a rotator at 20¬∞C for 30 minutes to remove residual OP50 from the worms gut. These microcentrifuge tubes were then set upright and the worms were allowed to settle by gravity for 5 minutes. The M9 supernatant was discarded and the final compact worm pellet volume was adjusted to 30ŒºL.

value: whole worm body

tag: generation


title: T47D_LTED8m_72h_DMSO_Rep2_RNAseq


title: T47D_WT_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL) and Glutamax (Life Technologies 35050-061 ).


title: Batch5_unsorted_water_F1_2


title: ZR75_SMIP34_3


title: RL_C1


title: Batch5_unsorted_ethanol0.5_F1_3

value: 0.5% ethanol

value: ethanol


title: Batch5_unsorted_ethanol0.5_F1_2


title: Batch5_unsorted_ethanol0.5_F1_1


title: Batch4_unsorted_water_F3_3


title: Batch5_unsorted_ethanol0.05_F1_1

value: 0.05% ethanol


title: Batch5_unsorted_ethanol0.05_F1_3


title: T47D_LTED5m_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 5 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL)

value: Parental estrogen deprived for 5 months


title: Batch4_unsorted_water_F3_2


title: Batch5_unsorted_ethanol0.05_F1_2


title: T47D_LTED5m_Rep1_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 5 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL)


title: Batch4_unsorted_ethanol0.5_F3_3


title: Batch4_unsorted_ethanol0.5_F3_2


title: Batch4_unsorted_ethanol0.5_F3_1


title: Batch4_unsorted_ethanol0.05_F3_1


title: Batch3_unsorted_normal_P0_3

value: normal


title: Batch4_unsorted_ethanol0.05_F3_2


title: Batch3_unsorted_normal_P0_2


title: Batch4_unsorted_ethanol0.05_F3_3


title: Batch4_unsorted_water_F3_1


title: Batch3_unsorted_normal_P0_1


title: Batch2_unsorted_water_F3_1


title: Batch2_unsorted_water_F1_1


title: Batch5_unsorted_water_F1_1


title: Batch2_unsorted_water_F1_2


title: Batch2_unsorted_water_F3_2


title: Batch2_unsorted_ethanol0.05_F1_2


title: Batch2_unsorted_ethanol0.05_F1_1


title: Batch2_unsorted_ethanol0.05_F3_2


title: Batch1_unsorted_normal_P0_1


title: Batch2_unsorted_ethanol0.05_F3_1


title: K562, empty vector controll, replicate 2

status: Public on Jul 19 2022

city: Düsseldorf

first: Julian

last: Schliehe-Diecks

address: Moorenstr. 5

country: Germany

institute: Uniklinik Düsseldorf

data_processing:
Upload into Galaxy
Adapters were trimmed with FASTQ Trimmer (9 bases of the 5' and 1 base of the 3')
Data quality was assesed via fastqc and aggregated with MultiQC
Reads were aligned to the hg38 reference genome via RNA STAR
Aligned reads were counted with featureCounts and aggregated into a count matrix
edgeR in combination with a gene annotation file was used to normalize the counts (log2 CPM) and to calculate the Fold Change and significance of the genes
Assembly: hg38
Supplementary files format and content: tsv of normalized counts

source_name: blood

growth_protocol: K562 were lentivirally transduced to express CAS9 and a guide RNA, sorted via a fluorescence marker & monoclonally selected

extract_protocol:
RNA was isolated utilizing the Maxwell® RSC simplyRNA Cells Kit (Promega, #AS1390).
Library preparation was carried out following supplier’s guidelines by using the VAHTs Stranded mRNA-Seq Library Prep Kit (Illumina Inc. San Diego, USA). Briefly, total RNA (500 ng) was used for capturing of mRNA, fragmentation, cDNA synthesis, ligation of the adapters and library amplification. Purified libraries were normalized and sequenced on the NextSeq550 (Illumina) with 1x76 bp read setup. Followed by using bcl2fastq2 tool to convert the bcl files to fastq files.

treatment_protocol: K562 were treated with increasing amounts of DMSO / PUH71 to gaine resistant clones. T´hese were monoclonally selected, then again selected and treated

value: blood

value: chronic myeloid leukemia

tag: genotype

value: WT


title: SKOV3_OCSCs_ LY500307_1

status: Public on Jul 13 2022

description: SKOV3 ovarian cancer stem cells (OCSCs) treated with ERβ agonist LY500307

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: SKOV3 ovarian cancer cell line

growth_protocol: OCSCs from SKOV3 cells were FACS sorted using the ALDEFLUOR kit. OCSCs were cultured as spheroids in DMEM-F12 medium supplemented with B27 serum free supplement, EGF (20ng/ml), bFGF (20ng/ml), hydrocortisone, and insulin.

extract_protocol:
OCSCs from SKOV3 cells were FACS sorted using the ALDEFLUOR kit. SKOV3-ALDH+ OCSCs were treated with vehicle or LY500307 (5 µM) for 24 h and the total RNA was isolated using RNeasy Mini Kit (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from SKOV3 OCSCs after treatmet with either vehicle or LY500307 for 24 hours.

value: Treatment


title: SKOV3_OCSCs_ LY500307_2


title: K562, empty vector controll, replicate 3


title: SKOV3_OCSCs_ Vehicle_1

description: SKOV3 ovarian cancer stem cells (OCSCs) treated with vehicle

value: Vehicle


title: SPOP F102C.2 shGLI3 -DHT repeat 2

status: Public on Jul 12 2022

description:
Clone 2 F102C LNCaP cells grown in hormone deprived media and treated with shGLI3 lentivirus
38_shGLI3_2

data_processing:
Illumina Casava v1.8.2 software used for base-calling for samples by HiSeq2000,  and Illumina bcl2fastq software used for base-calling for samples by HiSeq3000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: LNCaP prostate cancer cell line

growth_protocol: LNCaP were cultured at 37C and 5% CO2 in standard or phenol red–free RPMI-1640 medium containing 10% standard or dextran-charcoal treated fetal bovine serum respectively

extract_protocol:
Total RNA was isolated using Trizol and Direct-zol RNA Miniprep kit (Zymo Reserach) according to the manufacturer’s instructions.
Total RNA samples about 1-2 mg were used for sequencing library preparation according to Illumina TruSeq stranded mRNA-seq Sample Preparation Guide. Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SR) sequencing protocol.

treatment_protocol: All cells grown in hormone deprived media were transitioned to phenol red free and dextran-charcoal treated FBS containing media 10 days prior to RNA harvest. For all shGLI3 samples, cells were treated with shGLI3 lentivirus 6 days prior to transition to hormone deprived media.

value: LNCaP prostate cancer cell line

value: SPOP mutant

tag: media type

value: Hormone deprived media

value: shGLI3 specific lentivirus treated


title: SPOP F102C.2 shGLI3 -DHT repeat 1

description:
Clone 2 F102C LNCaP cells grown in hormone deprived media and treated with shGLI3 lentivirus
38_shGLI3_1


title: SPOP F102C.1 shGLI3 -DHT repeat 1

description:
Clone 1 F102C LNCaP cells grown in hormone deprived media and treated with shGLI3 lentivirus
7_shGLI3_1


title: SPOP WT shGLI3 -DHT repeat 2

description:
Wildtype LNCaP cells grown in hormone deprived media and treated with shGLI3 lentivirus
LNCaP_shGLI3_2

value: Wildtype


title: SPOP F102C.2 -DHT repeat 2

description:
Clone 2 F102C LNCaP cells grown in hormone deprived media
38_AI2

value: No treatment


title: SPOP F102C.1 shGLI3 -DHT repeat 2

description:
Clone 1 F102C LNCaP cells grown in hormone deprived media and treated with shGLI3 lentivirus
7_shGLI3_2


title: SPOP F102C.2 -DHT repeat 1

description:
Clone 2 F102C LNCaP cells grown in hormone deprived media
38_AI1


title: SPOP WT shGLI3 -DHT repeat 1

description:
Wildtype LNCaP cells grown in hormone deprived media and treated with shGLI3 lentivirus
LNCaP_shGLI3_1


title: SPOP F102C.1 +DHT repeat 1

description:
Clone 1 F102C LNCaP cells grown in hormone replete media
7_repl1

value: Hormone replete media


title: SPOP F102C.1 -DHT repeat 1

description:
Clone 1 F102C LNCaP cells grown in hormone deprived media
7_AI1


title: SPOP F102C.1 +DHT repeat 2

description:
Clone 1 F102C LNCaP cells grown in hormone replete media
7_repl2


title: SPOP F102C.1 -DHT repeat 2

description:
Clone 1 F102C LNCaP cells grown in hormone deprived media
7_AI2


title: SPOP F102C.2 +DHT repeat 1

description:
Clone 2 F102C LNCaP cells grown in hormone replete media
38_repl1


title: SPOP F102C.2 +DHT repeat 2

description:
Clone 2 F102C LNCaP cells grown in hormone replete media
38_repl2


title: SPOP WT -DHT repeat 2

description:
Wildtype LNCaP cells grown in hormone deprived media
LNCaP_AI2


title: SPOP WT +DHT repeat 2

description:
Wildtype LNCaP cells grown in hormone replete media
LNCaP_repl2


title: SPOP WT -DHT repeat 1

description:
Wildtype LNCaP cells grown in hormone deprived media
LNCaP_AI1


title: SPOP WT +DHT repeat 1

description:
Wildtype LNCaP cells grown in hormone replete media
LNCaP_repl1


title: K562, empty vector controll, replicate 1


title: SKOV3_OCSCs_ Vehicle_2

description: SKOV3 ovarian cancer stem cells (OCSCs) treated with vehicle


title: Three Day Neutrophil 2

status: Public on Jun 01 2022

city: Columbus

first: Andrew

last: Sas

state: OH

address: 395 W 12th Ave 7th Floor

department: Neurology

institute: Ohio State University

description: 10x Genomics

data_processing:
Cell Ranger 1.3 (https://10xgenomics.com/) was used to process Chromium single-cell 3′ RNA-seq output
The scRNA seq data was processed and visualized using the Seurat package (v.4.1.0) in R (4.1.0). The data was initially filtered for quality control through the removal of individual cells that detected less than 200 genes or more than 7000. Cells with less than 20 percent mitochondrial counts were retained.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Mus musculus

source_name: Intraperitoneal Fluid

extract_protocol:
Blood neutrophil isolation: Mice were euthanized by isoflurane overdose. Blood was collected from the left ventricle in an EDTA tube. PBMC were isolated over a lympholyte gradient (Cedarlane labs), and incidental red blood cells were lysed using an Ammonium-Chloride-Potassium (ACK) Lysing Buffer (Quality Biological).    Neutrophil isolation: Neutrophils were isolated from the i.p. lavaged cells with MACS Ly6G magnetic beads (Miltenyi Biotec) following the manufacturer’s instructions. Purity (95-99%) was verified using flow cytometry.
The cDNA libraries were constructed using the 10x Chromium Single cell 3′ Library Kit according to the manufacturer’s protocol. For quality control after library construction, 1 μl of sample was diluted 1:10 and ran on the Agilent Bioanalyzer High Sensitivity chip for qualitative analysis. For quantification, an Illumina Library Quantification Kit was used.

value: Neutrophil

value: Intraperitoneal Fluid

tag: strain

tag: age

value: 8-10 weeks

value: 3 days after zymosan injection


title: Naïve Blood 2

description: 10x Genomics

source_name: Blood

value: PBMC

value: Blood

value: untreated


title: Four Hour Neutrophil 2

description: 10x Genomics

value: 4 hours after zymosan injection


title: Four Hour Neutrophil 1

description: 10x Genomics


title: Young_4

status: Public on May 05 2022

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

description:
18527X1_201120_A00421_0259_BHM2V5DSXY_S1
processed data file: Young_matrix.txt.gz

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Human testicular tissue_young

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to collagenase IV and trypsin digestion for ~5 min at 37 C, respectively. The reaction was terminated by addition of FBS. Then, cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v3.1 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 2 X 150 cycle paired-end run via a Illumina Novaseq 6000 instrument. Each sample was sequenced in one separate sequencing lane.
10X Genomics single cell RNA sequencing

value: Testicle

value: young fertile adults (17-22 years old)


title: Three Day Neutrophil 1

description: 10x Genomics


title: Young_1

description:
18369X1_201002_A00421_0246_AHKMLGDSXY_S3
processed data file: Young_matrix.txt.gz


title: 231-P KD-2

status: Public on Mar 03 2022

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Breast cancer cell-line MDA-MB-231

growth_protocol: MDA-MB-231 control-shRNA and PELP1-shRNA cells were cultured in RPMI medium supplemented with 10% FBS

extract_protocol:
Total RNA from MDA-MB-231 control-shRNA and PELP1-shRNA cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

value: PELP1 shRNA

tag: shRNA

value: Stable tranfection were generated using puromycin selection


title: 231-P KD-3

tag: treatment


title: Young_2

description:
18328X1_201002_A00421_0246_AHKMLGDSXY_S2
processed data file: Young_matrix.txt.gz


title: Naïve Blood 1

description: 10x Genomics

tag: cell type


title: Young_3

description:
18434X1_201016_A00421_0249_BHKN3JDSXY_S1
processed data file: Young_matrix.txt.gz

tag: tissue


title: 231-Con-3

value: control non-targeted shRNA


title: 231-P KD-1


title: HFD 2

status: Public on Feb 16 2022

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

data_processing:
Bcl2fastq (v2.19.0.316) for demultiplexing and conversion to Fastq files
Raw reads were preprocessed for adapter trimming and quality check was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the reference genome (Ensembl Mus Musculus  release mm10) using the STAR algorithm (version 020201) (Dobin et al., 2013). The featureCounts package (version 1.6.4) implemented in the  Rsubread package was used to estimate read counts along genes. Differential expression analysis was performed using the GLM approach implemented in the R/Bionconductor edgeR (Robinson et al., 2010) package (R version 3.5; edgeR version 3.24.3).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: Tumor associated macrophages

growth_protocol: not applicable

extract_protocol:
Tumoral tissue was dissociated to single cell suspension. Briefly, tumors were digested for 1 hour and half in a Collagenase type V solution (1 mg/ml) at 37°C, 5% CO2 on a rocking platform. Cells digestion was then pelleted and incubated in 2.5% Trypsin for five minutes at 37°C, 5%CO2. Trypsin was then inactivated by complete medium with FBS and cells suspension was further passed through a syringe needle until complete dissociation and filtered through a 40 μm cell strainer. CD45+CD11b+F480+Ly6G- cells were sorted by flow cytometry, resuspended in 1ml PBS plus 0.04% BSA and washed two times by centrifugation at 450 rcf for 7min. After the second wash cells were resuspended in 250 ul of Trizol and RNA was extracted according to standard procedures
Total-RNA-sequencing library preparation was performed starting from 0.5 ng of total-RNA with the SMART-Seq Stranded Kit (Clontech-Takara). Libraries were obtained and qualitatively assessed by using TapeStation 4200 and quantified by Qubit Fluorimeter. Afterwards, they were multiplexed in an equimolar pool and sequenced on a NextSeq-500 Illumina Platform generating at least 40 million 75bp-PE reads per sample (i.e. 80 million reads per sample).

treatment_protocol: Mice were injected subcutaneously with 2.5x10^6 prostatic cancer cells (Pten -/-; Smad4 -/-). After tumor onset (10 days), mice randomly divided into two groups: NFD and HFD. After 45 days mice were sacrified.

value: Prostate tissue

tag: condition

value: High fat diet


title: HFD 1


title: NFD 2

value: Normal diet


title: Ptenpc-/-;Smad4pc-/- 2

data_processing:
Bcl2fastq (v2.19.0.316) for demultiplexing and conversion to Fastq files
Raw reads were preprocessed for adapter trimming and quality check was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the reference genome (Ensembl Mus Musculus  release mm10) using the STAR algorithm (Dobin et al., 2013). The featureCounts package (version 1.6.4) implemented in the  Rsubread package was used to estimate read counts along genes. Differential expression analysis was performed using the GLM approach implemented in the R/Bionconductor edgeR (Robinson et al., 2010) package (R version 3.5; edgeR version 3.24.3).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

extract_protocol:
murine prostates were dissociated to single cell suspension. Briefly, tumors were digested for 1 hour and half in a Collagenase type V solution (1 mg/ml) at 37°C, 5% CO2 on a rocking platform. Cells digestion was then pelleted and incubated in 2.5% Trypsin for five minutes at 37°C, 5%CO2. Trypsin was then inactivated by complete medium with FBS and cells suspension was further passed through a syringe needle until complete dissociation and filtered through a 40 μm cell strainer. CD45+CD11b+F480+Ly6G- cells were sorted by flow cytometry, resuspended in 1ml PBS plus 0.04% BSA and washed two times by centrifugation at 450 rcf for 7min. After the second wash cells were resuspended in 250 ul of Trizol and RNA was extracted according to standard procedure.
RNA quality control was performed with the Agilent 2200 Tape Station system and only RNAs having a RIN>8 were used for library preparation. Libraries for mRNA sequencing were prepared starting from 5 ng tot RNA for each sample by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). Libraries were obtained and qualitatively assessed by using TapeStation 4200 and quantified by Qubit Fluorimeter.  All samples were sequenced on an Illumina NextSeq 500 at an average of 40 million 75-bp single-end reads.
3'mRNA sequecing

treatment_protocol: not applicable


title: NFD 1


title: Ptenpc-/-;Smad4pc-/- 3


title: 231-Con-1


title: Ptenpc-/- 3

value: Ptenpc-/-


title: Ptenpc-/- 1


title: C11

status: Public on Jun 02 2022

type: genomic

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

description: methylation profiling using bisulfite converted

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing: Data was analysed using R version 4.1.0. Beta-values were extracted from ‘idat’ files by using the ‘Load’ module of the ‘ChAMP’ R package (v.2.22.0), with quality control options set as default. The quality control step retained 710029 probes, which were used for further analysis. Probes overlapped with SNP (93377) and with a detection pvalue < 0.01 (3387), beadcount <3 in at least 5% of samples in one or more samples (40275) were eliminated. X or Y chromosomes probes (16065), non-cg probes (2774), and probes aligning to multiple locations (11) and unannotated probes were also removed from analysis.BMIQ normalisation was applied, with the deafult ‘method’ option”. The BMIQ normalized samples were assigned with respective genome coordinates based on probe name and manifest file B4 annotation (Illumina Inc., USA). Batch correction was performed using Combat implemented in ‘ChAMP’ package.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.

tag: gender

value: F

value: Control

tag: batch

value: A


title: Bmp2 flox/floxed for 24h

status: Public on Jan 12 2022

description: dental papilla Bmp2 floxed cells

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were mapped to genome UCSC mm9 using TopHat v2.0.8b
Gene and Long_noncoding region count measurements were obtained using HTSeq-count based on refseq and gencode.mouse.v1.long_noncoding annotation
Genome_build: mm9-UCSC-Mus_musculus
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene/long_noncoding symbols and the second column contains the read counts of the gene/long_noncoding region using htseq-count

source_name: mouse dental papilla cells

extract_protocol: Total RNA samples about 1-2 mg were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from the dental papilla Bmp2 floxed and knock out cells and Samples were subjected to RNA seq analysis

value: Bmp2 floxed/floxed

value: mouse dental papilla cells

tag: culture time


title: Bmp2 flox/floxed for 72h

description: dental papilla Bmp2 floxed cells


title: C5

value: M

value: Blood


title: Bmp2 knock out for 24h

description: dental papilla Bmp2 knockout cells

value: Bmp2 KO


title: Bmp2 flox/floxed for 48h

description: dental papilla Bmp2 floxed cells


title: Ptenpc-/- 2


title: Bmp2 knock out for 48h

description: dental papilla Bmp2 knockout cells


title: Bmp2 knock out for 6h

description: dental papilla Bmp2 knockout cells


title: C1

value: B


title: Sample_02_tumor

data_processing:
Raw blc files were converted into fastq files using the Cell Ranger pipeline suite of 10X Genomics (version 3.0.2).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix starting from raw data.
Gene expression matrices were used as input for Seurat clustering (R version 3.5.1; Seurat version 3.0.2)
Genome_build: Pre-build Human genome (version GRCh38) was used as genome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell

source_name: tumor_CD45+ cells

extract_protocol:
Human prostatic tumoral and non tumoral tissue was dissociated to single cell suspension. Briefly, tumors were digested for 1 hour and half in a Collagenase type V solution (0.5 mg/ml) at 37°C, 5% CO2 on a rocking platform. Cells digestion was then pelleted and incubated in 2.5% Trypsin for five minutes at 37°C, 5%CO2. Trypsin was then inactivated by complete medium with FBS and cells suspension was further passed through a syringe needle until complete dissociation and filtered through a 40 μm cell strainer. CD45+ cells were sorted by flow cytometry, resuspended in 1ml PBS plus 0.04% BSA and washed two times by centrifugation at 450 rcf for 7min. After the second wash cells were resuspended in 30 ul and counted with an automatic cell counter (Countess II, Thermo Fisher) to get a precise estimation of total number of cells recovered.
CD45+ cells of each sample were loaded into one channel of the Single Cell Chip A using the Single Cell 3’ v2 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system.
Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq500 Illumina sequencing platform following 10x Genomics instruction for reads generation. A sequencing depth of at least ~ 20,000 reads/cell was obtained for each sample.

tag: subject status

value: prostatic adenocarcinoma (PCa) patient

tag: tissuee type

value: Tumor tissue

value: CD45+ cells


title: Sample_02_healthy

source_name: normal_CD45+ cells

value: Normal tissue adjcent to tumor


title: Sample_03_tumor

value: Prostate tissue


title: Sample_01_tumor


title: Bmp2 flox/floxed for 6h

description: dental papilla Bmp2 floxed cells


title: C8


title: P6

value: BWS


title: P2


title: C3


title: siSON_induction_1

status: Public on Dec 22 2021

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

data_processing:
RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 (2x150)
Reads were trimmed using cutadapt (v1.16) to remove adapters
Reads were aligned to the hg38 genome using STAR (v2.5.2a)
Gene counts were calculated using featureCounts (v1.6.2)
Differentially expressed genes were identified using DESeq2 (v1.28.1)
Changes in alternative splicing were identified using rMATS (v4.1.0) and MAJIQ (v1.1.7a)
GO terms were identified using gprofiler2 (v0.2.0)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file with raw counts for every sample and gene
Supplementary_files_format_and_content: bigwig files

source_name: RPE-1 cells

growth_protocol: RPE-1/Tet-PLK4 GFP-CETN were grown in DMEM/high glucose with Glutamine (Cytiva or Gibco) at 37°C with 5% CO2.

extract_protocol:
RNA was isolated with the Monarch Total RNA isolation miniprep kit (New England Biolabs)
Libraries were generated using the Nugen Universal Plus mRNA-seq library construction kit (part no. 0508)

treatment_protocol: Cells were treated with small interfering RNAs using Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher Scientific). PLK4 was induced with 1µg/mL doxycycline (Sigma-Aldrich).

tag: cell line

value: RPE-1 cells with Cetn2 tagged with GFP to identify centrioles, and PLK4 under control of the rtTA, doxycycline inducible promoter

value: expression of SON siRNA and induction of PLK4


title: siSON_induction_2


title: C4

value: F


title: Bmp2 knock out for 72h

description: dental papilla Bmp2 knockout cells


title: C9

value: Control


title: C7

value: A


title: P1


title: C6


title: Sample_01_healthy


title: siControl_induction_2

value: expression of scramble siRNA and induction of PLK4


title: Minus P 3

status: Public on Dec 15 2021

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description:
This sample is from medium minus P . It is the third of three biological replicates used in this experiment.
MMNminusP_6i

data_processing:
Illumina software was used by the Genotoul sequencing facilities (Toulouse, France) to generate fastq raw data files
Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. bicolor v2 reference transcripts available at the JGI database https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8. For read mapping the CLC genomic workbench parameters were the following: minimum length fraction 0.9, minimum similarity frac-tion 0.8, Mismatch cost = 2, insertion cost = 3, Deletion cost = 3 and the maximum number of hits for a read was set to 10. The unique and total mapped reads number for each transcript were determined and then normalized to RPKM (Reads Per Kilobase of exon model per Million mapped reads).
We calculated differential expression of genes with DESeq2
Genome_build: reference genome sequence of Laccaria bicolor  (https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html )
Supplementary_files_format_and_content: tab-delimited text file including JGI-Lacbi2 protein ID,  aligned reads (raw reads) and normalised expression values (rpkm).

organism: Laccaria bicolor

source_name: MMNminusP

growth_protocol: L. bicolor mycelium agar plugs (0.5 cm2) were inoculated on a cellophane membrane covering modified MMN medium   (Modified Melin Norkrans containing 0.45 mM CaCl2, 0.43 mM NaCl, 3.67 mM KH2PO4, 1.89 mM (NH4)2HPO4, 0.61 mM MgSO4·7H2O,    0.037 µM FeCl3·6H2O, 0.003 µM thiamine HCl, 0.5 mM KCl, 0.25 mM H3BO3, 50 µM MnSO4·7H2O, 20 µM ZnSO4·7H2O, 5 µM CuSO4·5H2O,    0.146 µM (NH4)6Mo7O24·4H2O, 0.5 % glucose, 0.5% malt extract, 1% casein hydrolysate, 2% agar and 0.1% MES    and pre-cultured for two weeks in dark at 25°C. After pre-culture, fungal colonies were transferred to new plates    containing control modified MMN medium or modified MMN medium adjusted for N (-N = all NH4 salts    removed and KH2PO4 supplemented to correct final PO4 concentration; +N = supplemented with 25 mM NH4Cl2),    P (-P = all PO4 salts removed and NH4Cl2 supplemented to correct final NH4 concentration; +P = supplemented with    25 mM KH2PO4) or C (-C = glucose reduced to 0.02%; +C = glucose supplemented to 2%) content to     induce nutrient deficiency or surplus. Plates were incubated in dark for an additional week at 25°C.     Subsequently, pictures were taken and mycelium was snap frozen in liquid nitrogen. Samples were stored     at -80°C until further RNA extraction.

extract_protocol:
Total RNA was extracted from fungal and mixed plant-fungal biomass (100 mg) using the RNeasy Plant Mini Kit (Qiagen). Biomass was ground in liquid nitrogen prior to extraction and an on column DNAse I treatment was included in the protocol
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 150 bp Illumina HiSeq3000 sequencing was performed at the GET platform (Gé-nopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.

tag: nutritional condition

value: Minus P


title: siSON_induction_3


title: C10

value: M


title: P4

value: Blood


title: C2


title: siControl_induction_3


title: Plus C 1

description:
This sample is from medium plus C . It is the first of three biological replicates used in this experiment.
MMNplusG_13

source_name: MMNplusG

value: Plus C


title: C12


title: siControl_induction_1


title: Minus P 2

description:
This sample is from medium minus P . It is the second of three biological replicates used in this experiment.
MMNminusP_5


title: Sample_03_healthy


title: Minus N 1

description:
This sample is from medium minus N . It is the first of three biological replicates used in this experiment.
MMNminusN_7i

source_name: MMNminusN

value: Minus N


title: Minus C 2

description:
This sample is from medium minus C . It is the second of three biological replicates used in this experiment.
MMNminusG_20

source_name: MMNminusG

value: Minus C


title: P5


title: Minus P 1

description:
This sample is from medium minus P . It is the first of three biological replicates used in this experiment.
MMNminusP_4


title: Minus C 1

description:
This sample is from medium minus C . It is the first of three biological replicates used in this experiment.
MMNminusG_19


title: P3

value: B


title: Control 1

description:
This sample is from control medium . It is the first of three biological replicates used in this experiment.
MMNCON_1i

source_name: MMNCON


title: Minus N 3

description:
This sample is from medium minus N . It is the third of three biological replicates used in this experiment.
MMNminusN_9i


title: Ptenpc-/-;Smad4pc-/- 1


title: Minus N 2

description:
This sample is from medium minus N . It is the second of three biological replicates used in this experiment.
MMNminusN_8i


title: Minus C 3

description:
This sample is from medium minus C . It is the third of three biological replicates used in this experiment.
MMNminusG_21


title: ectomycorrhizal root tips 14d-3

description:
This sample is from ectomycorrhizal root tips  at 14d . It is the third of three biological replicates used in this experiment.
M14_39

source_name: ectomycorrhizal root tips 14d

growth_protocol: Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro co-cultures were made according to the sandwich   system , with small modifications. In brief, L. bicolor was pre-cultured in dark at 25°C for one week on sugar-reduced   Pachlewski agar medium P20. P. tremula x alba micro-cuttings were stimulated to root for 1 week on solid Murashige and Skoog    (MS) medium supplemented with 2 mg/L IBA (Indol-3-butyric acid) and subsequently transferred to cellophane covered    MS plates. After three weeks of incubation at 25°C with a 16h photoperiod, poplar explants were    transferred to cellophane covered P20 medium supplemented with 0.1% MES. To allow plant-fungal interaction,    the cellophane covered with L. bicolor pre-cultures was placed in an inverted position on the roots.    Control plates, containing no plants (i.e. free-living mycelium (FLM)) were prepared and handled the    same way as co-cultures. All plates were incubated at 20°C with a 16h photoperiod.    Samples (100 mg fresh weight) for RNA extraction were taken in triplicate at 0, 3, 7, 14 and 21 days of    (co-)culture from FLM, EcM (i.e. all fungal and mixed plant-fungal material within 0.5 cm distance of a root)    and extramatrical mycelium (i.e. all fungal material at a distance of > 0.5 cm of a root),    snap frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted from fungal and mixed plant-fungal biomass (100 mg) using the RNeasy Plant Mini Kit (Qiagen). Biomass was ground in liquid nitrogen prior to extraction and an on column DNAse I treatment was included in the protocol. For samples containing poplar roots (EcM), extraction buffer RLC was supplemented with 2% PEG (polyethylene glycol) 8000.
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 150 bp Illumina HiSeq3000 sequencing was performed at the GET platform (Gé-nopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.

value: ectomycorrhizal root tips

tag: time

value: 14 days


title: 231-Con-2

value: control non-targeted shRNA

value: Stable tranfection were generated using puromycin selection


title: ectomycorrhizal root tips 14d-1

description:
This sample is from ectomycorrhizal root tips at 14d . It is the first of three biological replicates used in this experiment.
M14_37


title: Control 3

description:
This sample is from control medium . It is the third of three biological replicates used in this experiment.
MMNCON_3


title: Control 2

description:
This sample is from control medium . It is the second of three biological replicates used in this experiment.
MMNCON_2


title: ectomycorrhizal root tips 7d-3

description:
This sample is from ectomycorrhizal root tips  at 7d . It is the third of three biological replicates used in this experiment.
M7_30

source_name: ectomycorrhizal root tips 7d

value: 7 days


title: ectomycorrhizal root tips 21d-2

description:
This sample is from ectomycorrhizal root tips  at 21d . It is the second of three biological replicates used in this experiment.
M21_47

source_name: ectomycorrhizal root tips 21d

value: 21 days


title: ectomycorrhizal root tips 7d-1

description:
This sample is from ectomycorrhizal root tips at 7d . It is the first of three biological replicates used in this experiment.
M7_28


title: ectomycorrhizal root tips 21d-1

description:
This sample is from ectomycorrhizal root tips at 21d . It is the first of three biological replicates used in this experiment.
M21_46


title: ectomycorrhizal root tips 7d-2

description:
This sample is from ectomycorrhizal root tips  at 7d . It is the second of three biological replicates used in this experiment.
M7_29


title: ectomycorrhizal root tips 3d-3

description:
This sample is from ectomycorrhizal root tips  at 3d . It is the third of three biological replicates used in this experiment.
M3_12

source_name: ectomycorrhizal root tips 3d

value: 3 days


title: ectomycorrhizal root tips 3d-2

description:
This sample is from ectomycorrhizal root tips  at 3d . It is the second of three biological replicates used in this experiment.
M3_11


title: ectomycorrhizal root tips 3d-1

description:
This sample is from ectomycorrhizal root tips at 3d . It is the first of three biological replicates used in this experiment.
M3_10


title: free-living mycelium 21d-1

description:
This sample is from free-living mycelium at 21d . It is the first of three biological replicates used in this experiment.
FLM21_40

source_name: free-living mycelium 21d

value: free-living mycelium


title: free-living mycelium 14d-3

description:
This sample is from free-living mycelium at 14d . It is the third of three biological replicates used in this experiment.
FLM14_33

source_name: free-living mycelium 14d


title: free-living mycelium 14d-1

description:
This sample is from free-living mycelium at 14d . It is the first of three biological replicates used in this experiment.
FLM14_31


title: free-living mycelium 7d-3

description:
This sample is from free-living mycelium at 7d . It is the third of three biological replicates used in this experiment.
FLM7_24

source_name: free-living mycelium 7d


title: free-living mycelium 7d-2

description:
This sample is from free-living mycelium at 7d. It is the second of three biological replicates used in this experiment.
FLM7_23


title: ectomycorrhizal root tips 21d-3

description:
This sample is from ectomycorrhizal root tips  at 21d . It is the third of three biological replicates used in this experiment.
M21_48


title: free-living mycelium 21d-3

description:
This sample is from free-living mycelium at 21d . It is the third of three biological replicates used in this experiment.
FLM21_42


title: free-living mycelium 14d-2

description:
This sample is from free-living mycelium at 14d. It is the second of three biological replicates used in this experiment.
FLM14_32


title: ectomycorrhizal root tips 14d-2

description:
This sample is from ectomycorrhizal root tips  at 14d . It is the second of three biological replicates used in this experiment.
M14_38


title: free-living mycelium 3d-2

description:
This sample is from free-living mycelium at 3d. It is the second of three biological replicates used in this experiment.
FLM3_14

source_name: free-living mycelium 3d


title: free-living mycelium T0-2

description:
This sample is from free living mycelium at T0 . It is the second of two biological replicates used in this experiment.
FLM0_50

source_name: free-living mycelium T0

value: Time 0


title: free-living mycelium 21d-2

description:
This sample is from free-living mycelium at 21d. It is the second of three biological replicates used in this experiment.
FLM21_41


title: free-living mycelium T0-1

description:
This sample is from free living mycelium at T0 . It is the first of two biological replicates used in this experiment.
FLM0_49


title: extramatrical mycelium 21d-2

description:
This sample is from extramatrical mycelium at 21d . It is the second of three biological replicates used in this experiment.
Extra21_44

source_name: extramatrical mycelium 21d

value: extramatrical mycelium


title: extramatrical mycelium 21d-3

description:
This sample is from extramatrical mycelium at 21d . It is the third of three biological replicates used in this experiment.
Extra21_45


title: free-living mycelium 7d-1

description:
This sample is from free-living mycelium at 7d . It is the first of three biological replicates used in this experiment.
FLM7_22


title: extramatrical mycelium 14d-2

description:
This sample is from extramatrical mycelium at 14d . It is the second of two biological replicates used in this experiment.
Extra14_35

source_name: extramatrical mycelium 14d


title: extramatrical mycelium 7d-3

description:
This sample is from extramatrical mycelium at 7d . It is the third of three biological replicates used in this experiment.
Extra7_27

source_name: extramatrical mycelium 7d


title: extramatrical mycelium 14d-1

description:
This sample is from extramatrical mycelium at 14d . It is the first of two biological replicates used in this experiment.
Extra14_34


title: extramatrical mycelium 21d-1

description:
This sample is from extramatrical mycelium at 21d . It is the first of three biological replicates used in this experiment.
Extra21_43


title: free-living mycelium 3d-3

description:
This sample is from free-living mycelium at 3d . It is the third of three biological replicates used in this experiment.
FLM3_15


title: extramatrical mycelium 7d-2

description:
This sample is from extramatrical mycelium at 7d . It is the second of three biological replicates used in this experiment.
Extra7_26


title: extramatrical mycelium 7d-1

description:
This sample is from extramatrical mycelium at 7d . It is the first of three biological replicates used in this experiment.
Extra7_25


title: extramatrical mycelium 3d-2

description:
This sample is from extramatrical mycelium at 3d . It is the second of three biological replicates used in this experiment.
Extra3_17

source_name: extramatrical mycelium 3d


title: extramatrical mycelium 3d-3

description:
This sample is from extramatrical mycelium at 3d . It is the third of three biological replicates used in this experiment.
Extra3_18


title: Plus N 3

description:
This sample is from medium plus N . It is the third of three biological replicates used in this experiment.
MMNplusN_18

source_name: MMNplusN

value: Plus N


title: extramatrical mycelium 3d-1

description:
This sample is from extramatrical mycelium at 3d . It is the first of three biological replicates used in this experiment.
Extra3_16


title: Plus P 2

description:
This sample is from medium plus P . It is the second of two biological replicates used in this experiment.
MMNplusP_12

source_name: MMNplusP

value: Plus P


title: Plus N 2

description:
This sample is from medium plus N . It is the second of three biological replicates used in this experiment.
MMNplusN_17


title: Plus P 1

description:
This sample is from medium plus P . It is the first of two biological replicates used in this experiment.
MMNplusP_11


title: free-living mycelium 3d-1

description:
This sample is from free-living mycelium at 3d . It is the first of three biological replicates used in this experiment.
FLM3_13


title: late fruiting body stipe-2

description:
This sample is from late stage L.bicolor fruiting body stipe . It is the second of three biological replicates used in this experiment.
LBFB3_stipe2

source_name: late fruiting body stipe

growth_protocol: L. bicolor fruiting bodies were harvested from a nursery experiment of inoculated Douglas fir seedlings as described by [24]. Cap and stipe were separated from early, medium and late stage mushrooms (see Figure 3A-C) and immediately frozen in liquid nitrogen and stored at -80°C .

extract_protocol:
Total RNA of basidiocarp stipes and caps was extracted using a CTAB (cetyltrime-thylammonium bromide)   based protocol including a LiCl precipitation of total RNA.   RNA concentration of all samples was determined spectrophotometrically and integrity was assessed   using the Biorad Experion and RNA StdSens kit and chips.
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 100 bp Illumina HiSeq2000 sequencing  was performed at the GET platform (Génopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.

value: Stipe

tag: developmental stage

value: late


title: late fruiting body stipe-3

description:
This sample is from late stage L.bicolor fruiting body stipe . It is the third of three biological replicates used in this experiment.
LBFB3_stipe3


title: Plus C 3

description:
This sample is from medium plus C . It is the third of three biological replicates used in this experiment.
MMNplusG_15

source_name: MMNplusG

value: Plus C


title: Plus N 1

description:
This sample is from medium plus N . It is the first of three biological replicates used in this experiment.
MMNplusN_16


title: late fruiting body stipe-1

description:
This sample is from late stage L.bicolor fruiting body stipe . It is the first of three biological replicates used in this experiment.
LBFB3_stipe1


title: late fruiting body cap-3

description:
This sample is from late stage L.bicolor fruiting body cap . It is the third of three biological replicates used in this experiment.
LBFB3_cap3

source_name: late fruiting body cap

value: Cap


title: Plus C 2

description:
This sample is from medium plus C . It is the second of three biological replicates used in this experiment.
MMNplusG_14


title: medium fruiting body stipe-3

description:
This sample is from medium stage L.bicolor fruiting body stipe . It is the third of three biological replicates used in this experiment.
LBFB2_stipe3

source_name: medium fruiting body stipe

value: medium


title: late fruiting body cap-1

description:
This sample is from late stage L.bicolor fruiting body cap . It is the first of three biological replicates used in this experiment.
LBFB3_cap1


title: late fruiting body cap-2

description:
This sample is from late stage L.bicolor fruiting body cap . It is the second of three biological replicates used in this experiment.
LBFB3_cap2


title: medium fruiting body stipe-1

description:
This sample is from medium stage L.bicolor fruiting body stipe . It is the first of three biological replicates used in this experiment.
LBFB2_stipe1


title: medium fruiting body cap-3

description:
This sample is from medium stage L.bicolor fruiting body cap . It is the third of three biological replicates used in this experiment.
LBFB2_cap3

source_name: medium fruiting body cap


title: medium fruiting body stipe-2

description:
This sample is from medium stage L.bicolor fruiting body stipe . It is the second of three biological replicates used in this experiment.
LBFB2_stipe2


title: medium fruiting body cap-2

description:
This sample is from medium stage L.bicolor fruiting body cap . It is the second of three biological replicates used in this experiment.
LBFB2_cap2


title: medium fruiting body cap-1

description:
This sample is from medium stage L.bicolor fruiting body cap . It is the first of three biological replicates used in this experiment.
LBFB2_cap1


title: early fruiting body stipe-3

description:
This sample is from early stage L.bicolor fruiting body stipe . It is the third of three biological replicates used in this experiment.
LBFB1_stipe3

source_name: early fruiting body stipe

value: early


title: early fruiting body stipe-2

description:
This sample is from early stage L.bicolor fruiting body stipe . It is the second of three biological replicates used in this experiment.
LBFB1_stipe2


title: early fruiting body cap-1

description:
This sample is from early stage L.bicolor fruiting body cap . It is the first of three biological replicates used in this experiment.
LBFB1_cap1

source_name: early fruiting body cap


title: early fruiting body cap-3

description:
This sample is from early stage L.bicolor fruiting body cap . It is the third of three biological replicates used in this experiment.
LBFB1_cap3


title: L2_45C_3

status: Public on Dec 08 2021

description: Constructed by Yehong Huang

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with combined reference genome using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: Combined genome including Chlamydia trachomatis L2 434/Bu chromosome (GCF_000068585.1_ASM6858v1), C_trachomatis_pL2_plasmid_AM886278
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene names and the second column contain the read counts of the gene using htseq-count

organism: Chlamydia trachomatis

growth_protocol: L929 monolayers infected with CtL2, cultured with DMEM supplemented with 5% FBS at 37 °C, 5% CO2

extract_protocol:
Sigma TRI Reagent
Approximately 2000 ng Total RNA was used for RNA-seq library preparation using Illumina TruSeq stranded mRNA-seq sample preparation protocol with the modifications to remove rRNAs from both host and bacteria, and mRNAs from host.

treatment_protocol: 37 ℃ or 45 ℃ for 30 minutes.


title: early fruiting body cap-2

description:
This sample is from early stage L.bicolor fruiting body cap . It is the second of three biological replicates used in this experiment.
LBFB1_cap2


title: L2_45C_2

description: Constructed by Yehong Huang


title: L2_45C_1

description: Constructed by Yehong Huang


title: L2_37C_3

description: Constructed by Yehong Huang


title: L2_37C_2

description: Constructed by Yehong Huang


title: BT_549_EC359_2

status: Public on Dec 02 2021

description: BT-549 cells treated with EC359

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were mapped to Homo_sapiens genome UCSC hg19 using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count with RefSeq annotation
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: BT-549, triple negative breast cancer cell line

growth_protocol: BT-549 cells were cultured in RPMI media supplemented with 10% FBS

extract_protocol:
Total RNA from BT-549 cells treated with vehicle, EC359, HDACi, and EC359+HDACi was isolated using RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from BT-549 cells treated with vehicle (DMSO), EC359 (100nM), HDACi(Vorinostat-10µM), EC359+HDACi for 24 h and subjected to RNA-seq analysis

value: triple negative breast cancer


title: BT_549_SAHA(Vorinostat)_1

description: BT-549 cells treated with HDACi(SAHA/Vorinostat)

value: Treatment-HDACi (SAHA/Vorinostat)


title: BT_549_EC359_1

description: BT-549 cells treated with EC359


title: BT_549_SAHA(Vorinostat)_2


title: BT_549_Vehicle_2

description: BT-549 cells treated with Vehicle

value: Vehicle


title: BT_549_EC359+SAHA_1

description: BT-549 cells treated with EC359+HDACi


title: BT_549_Vehicle_1

description: BT-549 cells treated with Vehicle


title: BT_549_EC359+SAHA_2

description: BT-549 cells treated with EC359+HDACi


title: early fruiting body stipe-1

description:
This sample is from early stage L.bicolor fruiting body stipe . It is the first of three biological replicates used in this experiment.
LBFB1_stipe1


title: FD_33

status: Public on Nov 06 2021

description:
miRNA
pre treatment

data_processing:
Trimmomatic-0.36 (options: SE -phred33 -ILLUMINACLIP TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 CROP:24 MINLEN:21)
STAR-2.5.3a (options: --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 19 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1)
edgeR-3.16.5
Genome_build: Release 22.1 of miRBase
Supplementary_files_format_and_content: txt: (STAR mapped counts); fastq (fastq files obtained after Trimmomatic)

source_name: Fabry Patient

extract_protocol:
miRNasey mini kit to extract microRNAs from plasma
TruSeq SmallRNA Sample Prep Kit (Illumina)

value: Plasma

tag: disease state

value: Anderson Fabry disease

value: female


title: C_30

description:
miRNA
control

source_name: Healthy control

value: Healthy


title: 9_Fd

description:
miRNA
pre treatment

value: male


title: C_1

description:
miRNA
control


title: C_14

description:
miRNA
control

value: Healthy control


title: FD_32

description:
miRNA
pre treatment


title: 6_Fd

description:
miRNA
pre treatment


title: C_26

description:
miRNA
control


title: FD_38

description:
miRNA
pre treatment


title: L2_37C_1

description: Constructed by Yehong Huang

tag: strain


title: 4_Fd

description:
miRNA
pre treatment

tag: age


title: 11_Fd

description:
miRNA
pre treatment


title: 10_Fd

description:
miRNA
pre treatment


title: Treg_day13_rep1

status: Public on Oct 15 2021

city: Berlin

first: Julia

middle: K

last: Polansky

address: Augustenburger Platz 1

institute: Berlin Institute of Health @ Charité Universitätsmedizin Berlin

hyb_protocol: Bisulfite converted gDNA was fragmented,  hybridized, and stained according to the Infinium HD Methylation Assay Reference Guide.

scan_protocol: Bead arrays were scanned on the iScan.

data_processing: Idat files were processed using standard preprocessing steps with minfi (R/Bioconductor). Methylation values were quantile normalized and batch corrected using the ComBat function from the package sva (R/Bioconductor).

label: Cy3, Cy5

extract_protocol: Genomic DNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) or Quick-DNA Microprep Kit (Zymo Research) according to manufacturer's instructions. Bisulfite conversion was performed with EZ DNA Methylation Kit (Zymo Research) or EZ DNA Methylation Gold Kit (Zymo Research).

value: Treg

tag: donor

tag: time point (day)

tag: production run


title: Treg_day13_rep3

label_protocol: Infinium HD Methylation Assay Reference Guide.

tag: cell type


title: Treg_day23_rep2


title: Treg_day6_rep1


title: CD4mem_day23_rep3


title: Treg_day6_rep3


title: Treg_day0_rep1


title: Treg_day23_rep3


title: Treg_day13_rep2


title: CD4mem_day23_rep1


title: Treg_day6_rep2


title: Treg_day0_rep3


title: CD4mem_day23_rep4


title: CD4mem_day6_rep1


title: CD4mem_day6_rep2


title: CD4mem_day6_rep3


title: Treg_day0_rep5


title: Treg_day0_rep2


title: Treg_day0_rep4


title: CD4mem_day13_rep3


title: CD4mem_day13_rep1


title: CD4mem_day0_rep3


title: CD4mem_day23_rep7


title: CD4mem_day13_rep2


title: CD4mem_day23_rep6


title: CD4mem_day23_rep5


title: CD4mem_day0_rep4


title: CD4mem_day23_rep2


title: Treg_day23_rep1


title: CD4mem_day0_rep5


title: CD4mem_day0_rep1


title: 1stgen.Treg.product_Run2_day21_rep3


title: CD4mem_day0_rep2


title: 1stgen.Treg.product_Run2_day23_rep1


title: 2ndgen.Treg.product_day23_rep1


title: 2ndgen.Treg.product_day23_rep2


title: 1stgen.Treg.product_Run2_day14.5_rep3


title: 1stgen.Treg.product_Run2_day23_rep2


title: 1stgen.Treg.product_Run2_day20_rep3


title: 2ndgen.Treg.product_day23_rep4


title: 1stgen.Treg.product_Run2_day16.5_rep2


title: 1stgen.Treg.product_Run2_day20_rep2


title: 2ndgen.Treg.product_day23_rep3


title: 1stgen.Treg.product_Run2_day14.5_rep1


title: 1stgen.Treg.product_Run2_day9.5_rep2


title: 1stgen.Treg.product_Run2_day16.5_rep3


title: 1stgen.Treg.product_Run2_day0_rep3


title: 1stgen.Treg.product_Run2_day9.5_rep3


title: 1stgen.Treg.product_Run2_day16.5_rep1


title: 1stgen.Treg.product_Run2_day14.5_rep2


title: 1stgen.Treg.product_Run2_day6.5_rep1


title: 1stgen.Treg.product_Run2_day21_rep1


title: 1stgen.Treg.product_Run2_day21_rep2


title: 1stgen.Treg.product_Run2_day9.5_rep1


title: 1stgen.Treg.product_Run2_day12.5_rep2


title: 1stgen.Treg.product_Run2_day20_rep1


title: 1stgen.Treg.product_Run2_day12.5_rep3


title: 1stgen.Treg.product_Run2_day6.5_rep2


title: 1stgen.Treg.product_Run2_day23_rep3


title: miR182iWAT3

status: Public on Oct 13 2021

description: inguinal fat SVF isolation and differentiation

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: UCSC mouse genome build mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Primary cultured iWAT-miR182 overexpression

growth_protocol: Primary cultured iWAT in growth medium

extract_protocol:
total RNA was isolated by Trizol
Approximately 500ng Total RNA was used for RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide (Illumina, San Diego, CA). The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cautions under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final RNA-seq library.
stranded mRNA-Seq

treatment_protocol: Primary cultured iWAT was transfected with control and miR182 by electroporation

tag: Sex

value: Primary cultured iWAT

tag: genotype

value: miR182 overexpression


title: CtriWAT3

source_name: Primary cultured iWAT-control vector

value: control


title: miR182iWAT1


title: miR182iWAT2


title: 1stgen.Treg.product_Run2_day12.5_rep1


title: CtriWAT1


title: CtriWAT2


title: 1stgen.Treg.product_Run2_day0_rep1


title: Klinefelter1_rep2

status: Public on Sep 26 2021

source_name: Testicular cells

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane.
10X Genomics single cell RNA sequencing

tag: tissue

value: Testicle

tag: disease

value: Klinefelter syndrome


title: 1stgen.Treg.product_Run2_day0_rep2


title: 1stgen.Treg.product_Run1_day23_rep1


title: 1stgen.Treg.product_Run1_day23_rep2


title: Klinefelter2_rep2


title: DRG-L3-L5-4

status: Public on Sep 15 2021

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: UCSC mouse genome build mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: DRG L3-L5

extract_protocol:
Single-cell suspensions were genereated from sensory ganglia
Smart-Seq II protocol: RNA integrity was determined using Fragment Analyzer (Agilent, Santa Clara, CA) prior to library preparation. RNA-seq libraries were prepared according to SMART-seq2 protocol (Picelli S., 2014). RNA-seq libraries were sequenced using Illumina HiSeq 3000 system (Illumina, San Diego, CA) with 50bp single-read sequencing module.

value: Pirt1+ neurons

value: dorsal root ganglion


title: Klinefelter2_rep1


title: Klinefelter1_rep1


title: 1stgen.Treg.product_Run1_day21_rep2


title: DRG-L3-L5-3


title: 1stgen.Treg.product_Run1_day23_rep3


title: 1stgen.Treg.product_Run1_day15_rep3


title: DRG-L3-L5-2


title: ND4

source_name: NG-JG

value: nodose ganglion


title: 1stgen.Treg.product_Run1_day10_rep3


title: ND3


title: 1stgen.Treg.product_Run1_day20_rep1


title: ND2


title: ND1


title: DRG-T10-L1-1

source_name: DRG L1-T10


title: DRG-T10-L1-4


title: 1stgen.Treg.product_Run1_day20_rep2


title: TG3

source_name: TG

value: trigeminal ganglion


title: 1stgen.Treg.product_Run1_day15_rep2


title: DRG-L3-L5-1


title: DRG-T10-L1-3


title: TG1


title: TG2


title: 1stgen.Treg.product_Run1_day0_rep1


title: Tac_sfa.rep2

status: Public on Sep 01 2021

data_processing:
RNA-seq reads were aligned to the Ensembl GRCm38.87 genome assembly using STAR v2.5
Differentially expressed genes were identified using the edgeR R Biocondutor package
Genome_build: GRCm38.87
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.5

molecule: polyA RNA

source_name: Left ventricle

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Sample Validation:  -Standard RNA Reagent Kit (Perkin Elmer – Cat # CLS960010)  -HT DNA 5K/RNA/CZE LabChip (Perkin Elmer – Cat # 760435)  -LabChip GXTouch HT Instrument (Perkin Elmer)     -Sample Quantification  Qubit® RNA Assay Kit (LifeTechnologies – Cat# Q32852)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)     -Library Generation  TruSeq® Stranded mRNA Sample Prep Kit HT - (Illumina - Cat# RS-122-2103)   Purify and Fragment mRNA  Synthesize First/Second Strand cDNA  Adenylate 3' Ends  Ligate Adapters  - PCR Amplification  Plus: Agencourt AMPure XP (Beckman Coulter - Cat# A63881)    -Library Validation  HT DNA High Sens Reagent Kit (Perkin Elmer – Cat # CLS760672)  HT DNA 1K/12K/HI Sens Chip (Perkin Elmer – Cat # 760517)  LabChip GXTouch HT Instrument (Perkin Elmer)  Qubit® dsDNA HS Assay Reagent Kit (LifeTechnologies – Cat# Q32851)  Qubit® Assay Plastic Tubes (LifeTechnologies – Cat# Q32856)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)    -Normalization and Pool    -Denaturation and Dilution of Libraries    -Sequencing  NextSeq® 500/550 High Output v2 Reagent Kit (150 cycles) – Illumina – Cat# FC-404-2002)  NextSeq 500 Instrument

tag: diet

value: SFA

tag: treatment

value: TAC

value: Left ventricle


title: 1stgen.Treg.product_Run1_day0_rep3


title: 1stgen.Treg.product_Run1_day10_rep1


title: Tac_sfa.eaa.rep2

value: SFA-EAA


title: 1stgen.Treg.product_Run1_day21_rep1


title: Tac_sfa.rep1


title: Sham_sfa.eaa.rep2

value: sham


title: DRG-T10-L1-2

value: male


title: Sham_sfa.eaa.rep1


title: Sham_sfa.rep1


title: Donor 1 iNOA

status: Public on Aug 04 2021

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

institute: IRCCS, Ospedale San Raffaele

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
The whitelist of cell barcodes was identified with 'umi_tools whitelist --set-cell-number N --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNNNN' (umi_tools v1.0.0); with N = 2000 for donor1 and donor2, 5000 for donor3 and 1500 for donorOA.
Reads of the whitelisted cells were extracted with 'umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNNNN --filter-cell-barcode --whitelist=whitelist.txt' (umi_tools v1.0.0).
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of human genome (GRCh38) with parameter '--outFilterMultimapNmax 1' (to exclude multi-mapping reads).
Mapped reads were assigned to gene_name attributes from GENCODE basic annotation for GRCh38 (version 31) using Subread featureCounts (v1.6.4). Results were save in BAM files with option 'featureCounts -R BAM' and succesively sorted and indexed with samtools (v1.9).
Per gene counts were summarized for each cell using 'umi_tools count --per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell' (umi_tools v1.0.0).
Genome_build: hg38 (GRCh38 - v31)
Supplementary_files_format_and_content: Tab separated files of raw counts;  table with three columns: the gene_id, the cell barcode and the count of deduplicated UMIs. One file per sample, gzipped (.gz).

source_name: freshly isolated testis parenchyma

extract_protocol:
Fresh testes parenchyma was washed twice in PBS and subjected to enzymatic digestion (collagenase type I, collagenase type IV, hyaluronidase, trypsin, Deoxyribonuclease I; all enzymes at 1 mg/ml in DMEM-F12 without serum) for 10 minutes at 37°C with gentle agitation, repeated twice (1ml of digestion medium each time). The cell suspension was filtered through strainers with mesh size 70µm, washed twice with 0.4% BSA/PBS and filtered through a 40µm cell strainer to obtain single cell.
Chromium Single Cell 3′ Library & Gel Bead Kit v2 kit (10xGenomics).

value: testis

value: idiopathic non-obstructive azoospermia


title: 1stgen.Treg.product_Run1_day7_rep3


title: Donor 3 iNOA


title: Donor 2 iNOA


title: Il-6 Treated in vivo

status: Public on Jul 20 2021

data_processing:
Raw sequencing data (bcl-files) were converted to fastq files with Illumina bcl2fastq tool, integrated into the CellRanger (10X Genomics) suite (version 3.1.0).
R1 = cellular barcode (CB) (16 bp) + molecular barcode (MB) (umi) 10bp
The CellRanger analysis pipeline was used to generate a digital gene expression matrix staring from raw data.
The raw digital gene expression matrix (UMI counts per gene per cell) was imported in R (version 3.6.1) using Seurat R package (version Seurat_3.1.1)
Genome_build: Genome_build: Pre-build mouse genome (version mm10-3.3.0) was used as genome reference.

source_name: Embryonic Hippocampal tissue

growth_protocol: WT pregnant mice were housed in in a Specific Pathogen Free (SPF) facility under constant temperature (22 ± 1 °C) and humidity (50%) conditions with a 12 h light/dark cycle and were provided with food and water ad libitum.

extract_protocol: ~5,000 cells were loaded into one channel of the Single Cell Chip A for each sample using the Single Cell 3’ v3 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, we synthesized cDNA and amplified it for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries.  Sequencing was performed on the NextSeq550 Illumina sequencing platform following 10x Genomics instruction for reads generation; at least 50.000 reads per cell were produced.

treatment_protocol: Pregnant mothers were intraperitoneally injected with either vehicle or 5 µg of IL-6 (Peprotech) at E15 and embryonic hippocampi collected at E16

tag: tag

value: mothernal IP injection of IL-6 at GD15


title: Peat_S17_single

status: Public on Jul 12 2021

description: This sample is from O.maius free-living mycelium grown on modified MMN supplemented with peat. It is from single-read sequencing

data_processing:
Illumina software was used by the company to generate fastq raw data files
Raw fastq file reads were trimmed for quality and adapter using CLC Genomics Workbench 9. Trimmed reads were aligned to the Oidiodenron maius v1 (https://genome.jgi.doe.gov/Oidma1/Oidma1.home.html) reference transcripts using CLC Genomics Workbench 9 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Oidiodendron maius Zn v1 (https://genome.jgi.doe.gov/Oidma1/Oidma1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Oidiodendron maius Zn

growth_protocol: In all cases, fungal cultures were grown for 45 days on Modified Melin Norkrans (MMN) plates, overlaid with sterile cellulose membranes (autoclaved in ddH20 twice, with 24 hours in between), with a range of amendments (glucose (1g L-1), BSA (0.1 g L-1) or peat (~10 g dry weight)). The MMN medium contained: 0.075 g L-1 (NH4)2HPO4 (filter sterilized, 0.2 μm, added after autoclaving), 1 g L-1 glucose, 0.5 g L-1 KH2PO4, 0.066 g L-1 CaCl2.2H2O, 0.025 g L-1 NaCl, 0.15 g L-1 MgSO4.7H2O,  0.1 g L-1 thiamine HCl (filter sterilized, 0.2 μm, added after autoclaving), 1 mg L-1 FeCl3.6H2O and 10 g L-1 agar; pH was adjusted to 4.7.

extract_protocol:
Fungal tissue was removed from cellulose membrabes with a sterile scalpel, placed in pre-weighed RNase-free 1.5 mL Eppendorf tubes and flash-frozen in liquid nitrogen. Up to 100 mg of flash-frozen fungal tissue was mechanically disrupted by grinding in liquid nitrogen in a sterile mortar and pestle and placed in RNase-free 1.5 mL Eppendorf tubes on ice. To each tube, 700 μL extraction buffer (100 mM Tris-HCl pH 8, 100 mM NaCl, 20 mM Na-EDTA, 0.1% PVP, 1% sodium-lauryl sarcosine, prepared in diethylpyrocarbonate (DEPC) water) and 700 μL acid phenol were added prior to gently inverting the tubes. Tubes were centrifuged for 5 minutes at 14000 rpm (4 °C); all subsequent centrifugation was also performed at 14000 rpm (4 °C). The uppermost phase of the supernatants was transferred to new Eppendorf tubes on ice, to which an equal volume of acid phenol-chloroform-isoamyl alcohol (25:24:1) was added. Tubes were gently inverted several times, then centrifuged for 5 minutes. Supernatants were transferred to new tubes containing an equal volume of chloroform, tubes were gently inverted several times and then centrifuged for 5 minutes. This chloroform extraction and centrifugation was repeated once. Total nucleic acids were precipitated by addition of an equal volume of isopropyl alcohol to the supernatant and gentle inversion. Tubes were incubated for 30 minutes at -80 °C, then centrifuged 30 minutes. Supernatant was discarded and the pellet was resuspended in 500 μL DEPC water. To each tube 500 μL 6 M LiCl was added, then the tubes were gently inverted and kept overnight in ice at 4 °C. Tubes were centrifuged 30 minutes, then the supernatant was discarded and the remaining pellet was washed with 150 μL 70% ethanol (prepared with DEPC water). The tubes were centrifuged for an additional 5 minutes, the supernatant discarded and the pellet was dried on ice in the fume hood. Once completely dry, the pellet was resuspended in 25 μL DEPC water, then the concentration and quality were determined using a NanoDrop ND-1000 UV-visible light spectrophotometer (NanoDrop, Wilmington, DE, USA). Only RNA samples with 260/280 nm wavelength ratio of approximately 2 and 260/230 nm wavelength ratio of approximately 2 were retained. RNA solutions were treated with PerfeCTa® DNase I according to manufacturer’s instructions (Quanta Biosciences™, Beverly, MA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols for MiSeq

tag: carbon source

value: Peat

value: mycelium


title: Control Vehicle in vivo

value: mothernal IP injection of Vehicle at GD15


title: Peat_S1_paired

description: This sample is from O.maius free-living mycelium grown on modified MMN supplemented with peat. It is from paired-read sequencing


title: BSA_S2_paired

description: This sample is from O.maius free-living mycelium grown on modified MMN supplemented with BSA. It is from paired-read sequencing

value: BSA


title: 1stgen.Treg.product_Run1_day15_rep1


title: NH4_S19_single

description: This sample is from O.maius free-living mycelium grown on modified MMN supplemented with glucose. It is from single-read sequencing

value: Glucose


title: TG4

value: Pirt1+ neurons


title: 1stgen.Treg.product_Run1_day21_rep3


title: 1stgen.Treg.product_Run1_day20_rep3


title: Sham_sfa.rep2


title: NH4_S3_paired

description: This sample is from O.maius free-living mycelium grown on modified MMN supplemented with glucose. It is from paired-read sequencing


title: 1stgen.Treg.product_Run1_day7_rep2


title: 1stgen.Treg.product_Run1_day0_rep2


title: Tac_sfa.eaa.rep1


title: 1stgen.Treg.product_Run1_day10_rep2


title: BSA_S18_single

description: This sample is from O.maius free-living mycelium grown on modified MMN supplemented with BSA. It is from single-read sequencing


title: 1stgen.Treg.product_Run1_day7_rep1


title: RS8_HrcA_IND12-16hpi-1

status: Public on Jul 08 2021

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with combined reference genome using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: Combined genome including Chlamydia trachomatis 434/Bu chromosome (GCF_000068585.1_ASM6858v1), C_trachomatis_pL2_plasmid_AM886278 and mKate gene
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene names and the second column contain the read counts of the gene using htseq-count

source_name: Constructed by Wurihan Wurihan

growth_protocol: L929 monolayers infected with CtL2 transformed with a GrgA, Euo or HrcA expression plasmid, cultured with DMEM supplemented with 5% FBS and 1 µg/ml cycloheximide at 37 °C, 5% CO2

extract_protocol:
Sigma TRI Reagent
Approximately 1250 – 2000 ng Total RNA was used for RNA-seq library preparation using Illumina TruSeq stranded mRNA-seq sample preparation protocol with the modifications to remove rRNAs from both host and bacteria, and mRNAs from host.

treatment_protocol: 10 nM anhydrotetracycline (IND) or noninduced (NI)

value: L2 Transformed with HrcA expression plasmid

tag: protocol

value: Induced with ATC between 12 and 16 hpi


title: RS7_Euo_NI-2

value: L2 Transformed with Euo expression plasmid

value: Noninduced


title: RS8_HrcA_NI-1


title: RS8_HrcA_IND12-16hpi-2


title: RS8_HrcA_NI-2


title: RS7_Euo_NI-1


title: RS7_Euo_IND12-16hpi-1


title: RS7_Euo_IND12-16hpi-2


title: RS6_GrgA_NI-2

value: L2 Transformed with full length GrgA expression plasmid


title: RS6_GrgA_IND30m-3

value: Induced with ATC between 15.5 and 16 hpi


title: RS6_GrgA_NI-1


title: RS6_GrgA_IND30m-2


title: RS6_GrgA_IND2h-3

value: Induced with ATC between 14 and 16 hpi


title: RS6_GrgA_IND2h-2


title: RS6_GrgA_IND2h-1


title: RS6_GrgA_IND1h-1

value: Induced with ATC between 15 and 16 hpi


title: RS5_dl138-165GrgA_NI-1

value: L2 Transformed with delta138-165 GrgA expression plasmid


title: RS5_dl138-165GrgA_IND12-16hpi-2


title: RS6_GrgA_IND1h-3


title: RS4_dl1-64GrgA_NI-2

value: L2 Transformed with delta1-64 GrgA expression plasmid


title: RS4_dl1-64GrgA_NI-1


title: RS6_GrgA_IND1h-2


title: RS4_dl1-64GrgA_IND12-16hpi-1


title: RS4_dl1-64GrgA_IND12-16hpi-2


title: RS3_GrgA_NI-1


title: RS3_GrgA_IND12-16hpi-1


title: RS3_GrgA_IND12-16hpi-2


title: RS1_GrgA_NI


title: RS6_GrgA_NI-3


title: RS3_GrgA_NI-2


title: RS2_GrgA_IND17-21hpi

value: Induced with ATC between 17 and 21 hpi


title: RS2_GrgA_NI


title: RS1_GrgA_IND12-16hpi


title: RS6_GrgA_IND30m-1


title: RS5_dl138-165GrgA_NI-2


title: RS5_dl138-165GrgA_IND12-16hpi-1


title: EUF16

status: Public on Jul 01 2021

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

institute: Fondazione Human Technopole

description:
Successful implantation after transfer
counts_exp2.txt.gz

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode version 26 for samples 1-20;  Gencode version 27 for samples 21-93)
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: Uterine fluid derived Extracellular Vesicles

extract_protocol:
Endometrial tissue biopsies were obtained with the use of a Pipelle, immediately after UF sampling. Uterine fluid samples were obtained by lavage of the endometrial cavity with 2.5 of physiologic solution using a balloon hysterosonosonography catheter to avoid vaginal contamination. Extracellular vesicles were isolated- after mucus disgregation by vortexing- using standard ultracentrifugation protocol.  RNA was harvested using  RNase micro KIT of QIAGEN with DNAse treatment step in coloumn.
To compare the transcriptomic profile of tissues and UF-Evs (samples 1-20), cDNA libraries were generated from total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen GmbH, Vienna, Austria). To perform transcriptome sequencing on UF-EVs collected from fertile women and ART patients during the window of implantation (samples 21-93), cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan)

tag: population

value: Women undergoing ART and transfer of an euploid blastocyst

tag: menstrual cycle phase

value: secretory

tag: mentrual cycle day (counted from the first day of menstrual bleeding and expressed as n or from the day of urinary lh surge detection and expressed an lh+n)

value: LH+7 (within window of implantation)


title: EUF4

description:
Failed implantation after transfer
counts_exp2.txt.gz

value: Uterine fluid derived Extracellular Vesicles


title: EUF12


title: EUF17


title: EUF2


title: EUF9


title: EUF15


title: EUF1


title: EUF11


title: EUF51


title: EUF50


title: EUF49


title: EUF48


title: EUF7


title: EUF42


title: EUF5


title: EUF40


title: EUF45


title: EUF44


title: EUF43


title: EUF41


title: EUF39


title: EUF38


title: EUF37


title: EUF36


title: EUF35


title: EUF8


title: EUF33


title: EUF14


title: EUF32


title: EUF52


title: EUF31


title: EUF24


title: EUF46


title: EUF47


title: EUF27


title: EUF20


title: EUF13


title: EUF28


title: EUF26


title: EUF22