title: S17

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
Primers were trimmed from the raw fastq format sequence data using cutadapt software (v1.9.1; parameters -O 6 -m 16 -n 5 -q 20).
Only trimmed reads that contained the adapter, were 16nt or greater in length and were present at 2 or more copies per sample were retained.
Simple scripts were used to generate non-redundant sequence sets (collapsed) in fasta format from each sample.
Genome_build: ftp.ensembl.org/pub/release-88/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa10.2.dna.toplevel.fa
Supplementary_files_format_and_content: Non-redundant trimmed sequences in fasta format

organism: Sus scrofa

growth_protocol: Primary alveolar macrophages were obtained by bronchoalveolar lavage of three 3-week old pigs. Cells were plated out at a density of 1x10^7/ml in RPMI 1640 (with Glutamax™), supplemented with 10% porcine serum and 100 units/ml penicillin, 100μg/ml streptomycin.

extract_protocol:
RNA was harvested into QIAZOL reagent and subsequently extracted using QIAGEN miRNeasy mini kit, following the manufacturer’s protocol. Quality control was performed using Agilent Bioanalyzer (RNA 6000 nano kit) and Invitrogen Qubit (RNA high sensitivity assay).
Libraries were prepared using the CleanTag Small RNA Library Preparation Kit (TriLink Biotechnologies) following the manufacturer’s protocol, using index primers 1-18. The libraries were pooled and purified by gel extraction on a 6% Polyacrylamide gel.

treatment_protocol: Cells were infected or mock infected with African swine fever virus (Benin 97/1 strain) at a MOI of 10. The virus was left to absorb onto cells at 37°C for 1 hour, the virus was then removed, cells washed with PBS and the media replaced. RNA was extracted at 0, 6 and 16 hours post-infection.

tag: infection status

value: mock

tag: timepoint

tag: replicate


title: ac40

status: Public on Jul 28 2020

type: SRA

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

country: USA

institute: MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
transcript level counting with cell ranger v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: gene expression matrix

molecule: total RNA

organism: Homo sapiens

source_name: infusion product

extract_protocol: Libraries were prepared according to 10X Genomics Chromium Single Cell 5' Library Construction Kit (1000020) according to manufacturer's protocol.

treatment_protocol: CART cells were washed out from infusion bag by saline, and spin down at 500g for 30min. Cells were resuspended in PBS solution containing 0.4% ultrapure BSA and counted using haemocytometer to determine cell concentration and cell viability.

tag: cell type

value: CART cells


title: ac39


title: S16

value: infected


title: S15


title: HSC_Mysm1_Ko_2_3

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: rRNA-depleted stranded RNA. Both males and females were used, and sex-matched between experimental groups.

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
Low-quality bases were trimmed from read extremities using Trimmomatic v.0.33.
Trimmed reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithms.
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.1.2).
Pairwise comparisons were performed between samples across different mouse genotypes (Het and Sham samples were grouped together as WT) and genes with changes in expression ≥ |1.5| folds and Benjamini-Hochberg adjusted p values ≤ 0.01 were considered significant.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values after quantile normalization
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)

organism: Mus musculus

source_name: HSC

extract_protocol:
Mouse bone marrow was flushed from femurs, tibiae, humeri, and ilia of mice with a 26-G needle in PBS supplemented with 0.1% BSA and 2 mM EDTA, filtered through 40-μm cell strainers, and subjected to red blood cell lysis in ACK buffer (0.15 M NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA). The samples were stained with biotin anti-mouse Lineage Panel (BioLegend), PE-Cy7 cKit (clone 2B8, BioLegend), APC-Cy7 Sca-1 (D7, BioLegend), FITC CD48 (HM48-1, eBioscience), APC CD150 (TC15-12F12.2, BioLegend), PE Flt3 (A2F10, eBioscience), Brilliant Violet 421 CD34 (RAM34, BD Biosciences), and streptavidin-PECy5 (BioLegend). DAPI was added immediately before sorting for dead cell exclusion. Cell sorting was performed on FACSAria and analyzed with FACS Diva software (BD Biosciences). Specifically, the extracted BM cells were FACS sorted into primary HSC, MPP1, and MPP2 cells, gating on Lin-cKit+Sca1+CD150+Flt3-, and CD34-CD48- for HSCs, CD34+CD48- for MPP1, and CD34+CD48+ for MPP2 cells.
RNA was isolated from FACS-sorted HSCs and MPPs using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech).The libraries were sequenced on an Illumina HiSeq 2000 sequencer in paired-end 50bp configuration.

treatment_protocol: For tamoxifen-induced Mysm1 gene inactivation, the Mysm1 fl/fl CreERT2 mice were injected intraperitoneally with tamoxifen (Sigma T5648) in sterilized corn oil at 0.15mg/gram per injection, with 8 doses in total administered over 16 days. Successful deletion of Mysm1 exon 3 was validated by genotyping of the genomic DNA from hematopoietic and lymphoid organs, and the loss of Mysm1 transcript was further confirmed by qRT-PCR with Lin-cKit+Sca1+ HSC/MPP cells from mouse bone marrow. Mysm1 +/fl CreERT2 mice undergoing identical tamoxifen treatment, as well as Mysm1 fl mice treated with corn-oil only, were used as controls.

tag: strain

tag: age

value: Mice were 8-12 weeks of age.

tag: gender

value: pooled male and female

tag: tissue

value: Bone marrow

value: Hematopoietic Stem cells (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34-CD48-)

tag: genotype

value: Mysm1-KO (Tamoxifen-treated Mysm1fl/fl CreERT2 mice)


title: ac38


title: 6167b

city: Rehovot

first: Jedrzej Jakub Szymanski

middle: Jakub

last: Szymanski

address: 234 Herzl Street, POB 26

country: Israel

institute: Weizmann Institute of Science

description:
2027
Solanum lycopersicum-pennellii
Manually peeled skin tissue

data_processing:
The reads were mapped against a combined file that included the genomes from Solanum lycopersicum (ITAG 3.0) and Solanum pennellii (v2.0).
Mapping has been performed with STAR 2.4.2a.
The alignments in resulting SAM file were divided into genomes based on the alignment scores. If the highest scoring alignment is assigned to a certain genome, and is unique in that genome, then it is assigned as “lycopersicum-unique” or “pennellii-unique”. If there is no difference in the scores between the two genomes then the alignment to the S. lycopersicum genome is kept and categorized as “indistinguishable”.
Counting was performed on the TES (Transcript End Site) region of each gene. The TES region is defined as 200 bp downstream from the STOP codon of the gene, and at least 500 bases upstream to the STOP codon of the gene. The reads were counted using htseq-count using stranded method and union mode.
Genome_build: Solanum lycopersicum (ITAG 3.0) and Solanum pennellii (v2.0)
Supplementary_files_format_and_content: Using the htseq-count for each type of genome provide three complementary datasets:
Supplementary_files_format_and_content: (1) lyc-count - containing the count for the reads specific to S. lycopersicum genome (68% of all reads);
Supplementary_files_format_and_content: (2) pen-count - containing the count for the reads specific to S. pennellii genome (28% of all reads);
Supplementary_files_format_and_content: (3) ind-count - containing the count for the reads aligning to both genomes (4% of all reads).

organism: Solanum lycopersicum x Solanum pennellii

source_name: Skin fruit tissue

growth_protocol: Fruit at the breaker and red ripe stages were harvested from the field at the Western Galilee Experimental Station in Akko, Israel. Plants were grown in a randomized design with 4 plants per m2.

extract_protocol:
Standard tri-reagent protocol (Maniatis T., Fritsch E.F., Sambrook J. Cold Springs Harbor; NY: 1982. Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory).
Jaitin, Diego, Ido Amit, and Hadas Keren-Shaul. 2014. High throughput transcriptome analysis. WIPO 2014108850:A2. World Patent, filed January 9, 2014, and issued July 17, 2014. https://www.google.com.na/patents/WO2014108850A2?cl=en

treatment_protocol: Fruits were brought to the lab and skin tissue at the breaker and red, ripe stages was immediately separated from the flesh and frozen in liquid nitrogen.

value: Skin fruit tissue

tag: ripening stage

value: breaker stage of ripening

tag: population

value: BIL


title: 6461

description:
2321
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: S14


title: S18


title: 6476

description:
2336
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: S13


title: ac36


title: 6490

description:
2350
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: HSC_Mysm1_Ko_1


title: HSC_Mysm1_Het_2_3

value: Mysm1-Het (Tamoxifen-treated Mysm1+/fl CreERT2 mice)


title: S12


title: 6279

description:
2139
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac35


title: S11


title: ac34


title: ac33


title: IL10-2-2

description:
2626
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: S10


title: 6640

description:
2500
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac32


title: ac37


title: ac31


title: PCMV6-5-8F rep2

type: RNA

city: Nanning

first: Bo

last: Li

state: Guangxi

address: No. 22 Shuangyong road

department: Radiation oncology

country: China

institute: Guangxi Medical University

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Nasopharyngeal carcinoma

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: All cells were incubated at 37℃ in a humidified atmosphere containing 5% CO2 and cultured in Modified Eagles Medium/High glucose (DMEM) medium supplemented with 10% fetal bovine serum (FBS) in the presence of streptomycin and penicillin.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: The pCMV6-vector or ACAT1 plasmid was transferred into NPC cell line 5-8F by liposome transfection. After 3 weeks of selection in 4 μg/ml of G418 resistant cell clones were grown up and the transfection efficiency was validated for BDH2 expression by RT-qPCR.

tag: cell line

tag: treatment

value: transfected by PCMV6 (control)


title: 6641

description:
2501
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac30


title: S07


title: S06


title: ACAT1-5-8F rep3

value: transfected by ACAT1


title: PCMV6-5-8F rep1


title: PCMV6-5-8F rep3


title: 6572

description:
2432
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ACAT1-5-8F rep2


title: ac29


title: S05


title: 6462

description:
2322
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: S09


title: ACAT1-5-8F rep1


title: MCF-HK1LMP1exo-2

city: Tallahassee

first: li

last: sun

email: lsun2@fsu.edu, davidgmeckes@gmail.com

state: FL

address: 1115 west call st.

department: College of medicine

institute: Florida State University

data_processing:
RAW data were uploaded to BaseSpace (Illumina) for quality control and base calling.
Qulified reads were aligned to the hg38 human reference genome.
Data was uploaded to NetworkAnalyst 3.0 for further analysis and network visualization.
Total counts were filtered by following specifications: counts less than 10, variance less than 10% and unannotated, and then normalized by Log2-counts per million.
IPA (Qiagen) software was used to generate potential interaction map between DE genes in the ECM pathway.
Genome_build: hg38
Supplementary_files_format_and_content: Processed counts file (xlsx) was generated and normalized by NetworkAnalyst.

source_name: Breast epithelial cell (non-tumorigenic)

growth_protocol: MCF10A cells were maintained in Dulbecco’s modified Eagle’s medium along with equivalent supplements as specified by ATCC (Lonza; MEGM kit; CC-3150) and Cholera toxin to a final concentration of 100ng/mL.

extract_protocol:
Cell total RNA was isolated with Trizol under manufacturer's protocol.
Isolated RNA was incubated with DNase I to remove trace genomic DNA contamination. Then, mRNA library was prepared by combination of NEBNext Ultra RNA Library Prep Kit (NEB, E7530) and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The library ran on Bioanalyzer with HS DNA chip (Agilent; 5067-4626) for quality control and quantified by KAPA library qPCR kit (KAPA; KR0405).

treatment_protocol: Each triplicate were treated with HK1-EV or HK1-LMP1-EV for 24h.

value: Breast epithelial cell line MCF10A

value: HK1-LMP1-EV for 24h


title: MCF-HK1LMP1exo-1


title: ac28


title: S08


title: 6520

description:
2380
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MCF-HK1LMP1exo-3


title: ac27


title: MCF-HK1exo-3

value: HK1-EV for 24h


title: 6253

description:
2113
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6486

description:
2346
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6235

description:
2095
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MCF-HK1exo-2


title: 6304

description:
2164
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MCF-HK1exo-1


title: ac25

value: CART cells


title: ac24


title: MCF-ctl-3

value: untreated


title: 6597

description:
2457
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MCF-ctl-2


title: S01

value: mock


title: ac23


title: 6552

description:
2412
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: S04

value: infected


title: ac21


title: 6212a

description:
2072
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6569

description:
2429
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: HK1-LMP1-EV-2

data_processing:
RAW data were uploaded to BaseSpace (Illumina) for quality control and base calling.
Raw data for miR-seq were submitted to OASIS online miR analysis tool to identify small RNAs on Human reference genome hg38.
Differential expressed miRs from HK1-LMP1 EVs were analyzed by both OASIS using default settings.
Genome_build: hg38
Supplementary_files_format_and_content: Process counts file (xls) was generated from OASIS.

source_name: Extracellular vesicles

growth_protocol: HK1 or HK1-LMP1 cells were RPMI-1640 cell culture medium with 10% final concentration of fetal bovine serum, 2 mM L-glutamine, 100 IU penicillin-streptomycin, and 100 µg/mL:0.25 µg/mL antibiotic/antimycotic.

extract_protocol:
EV samples were treated with RNase to final concentration of 50 ng/mL, at room temperature for 30 mins. RNase inhibitor and PCR grade water were added to EV sample to total volume of 200 µL. miRs were isolated by adding 600 µL Trizol LS according to manufacturer’s instruction. To increase the yield of small RNAs, two volume of 100% ethanol and linear acrylamide were used instead of isopropyl alcohol and incubation time was also increased to overnight at -20℃.
Small RNA libraries were generated with NEBNext Multiplex Small RNA Library Prep Set for Illumina. To increase yield and prevent primer/adaptor dimer, 3’ SR primer was diluted to 1:2 and increase ligation time to overnight at 16 ℃.

treatment_protocol: To induce LMP1 expression in the HK1-LMP1 cells, we added doxycycline to a final concentration of 1 μg/μL. Medium was changed to EV-free Medium and contiuned culture for 48h. EVs were isolated from approximately 500 mL of cell culture media.  The medium was centrifuged at 500 × g for 10 minutes in an Eppendorf 5804R using an S-4-104 rotor to pellet out the cells. The supernatant was then passed through a 0.22 µm VWR vacuum filtration. The conditioned media was further concentrated by Minimate® TFF Capsules (100KDa cut-off, Pall, OA100C12) to 50 mL. The remaining 50 mL supernatant was split in 50mL conical tubes where 1:1 volume of 16% (2X) polyethylene glycol (average Mn, 6000; Alfa Aesar; 25322-68-3) and 1 M sodium chloride was added to samples and incubated overnight at 4°C. The incubated samples were centrifuged at 3,214 × g for 1 hour in an S-4-104 rotor. The pellet from each tube was then washed with 1mL of 1X PBS, centrifuged at 100,000 × g for 70 min in a Beckman MAX-E using the TLA120.2 rotor. The collected EV Samples were resuspended in about 300 µL of particle-free PBS for RNA-seq.

value: nasopharyngeal carcinoma cell line HK1

tag: transfection

tag: sample type

value: EV


title: S02


title: ac22


title: ac26


title: ac20


title: 6167a

description:
2027
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MCF-ctl-1


title: S03


title: HK1-LMP1-EV-1


title: ac19


title: 6322

description:
2182
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac18


title: HK1-EV-3

value: control


title: IL8-2-1

description:
2611
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue


title: 6697

description:
2557
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: breaker stage of ripening


title: ac17


title: HK1-LMP1-EV-3


title: 6372

description:
2232
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: BIL


title: ac16


title: 6295

description:
2155
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac14


title: ac15


title: HK1-EV-1


title: IL12-3-1

description:
2637
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: HK1-EV-2


title: Copper_treated_replicate_3

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

data_processing:
Paired-end RNA-seq data were aligned to the human genome assembly (build hg38) using STAR (version 2.5a) with quantMode parameter set to ‘TranscriptomeSAM’.
Raw gene counts were calculated using RSEM (version 1.2.31) command rsem-calculate-expression.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table (.csv) with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for each Sample

source_name: Neuroblastoma cell line

extract_protocol:
RNA was isolated using RNeasy mini kit (Qiagen, cat#74104). Illumina TruSeq stranded mRNA Library prep was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: treated with copper for 4 hours


title: Copper_treated_replicate_1


title: Copper_treated_replicate_2


title: ac13


title: 6468

description:
2328
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: AMut3_S16

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

description: Mut

data_processing:
RNASeq data was mapped to Reference Consortium Zebrafish Build 10 (UCSC Genome GRCz10/danRer10; Sept 2014) using Olego (Wu, Anczukow et al., 2013)
featureCounts (Liao, Smyth et al., 2014) from subread package is used to compute the raw read counts for each gene.
TPM (Transcripts Per Millions)(Li & Dewey, 2011, Pachter, 2011) values were computed from the raw read counts using a custom perl script and log2(TPM+1) is used to compute the final log-reduced expression values.
DESeq2 1.26.0 (Love, Huber et al., 2014) R package is used to compute differentially expressed genes at 1% false discovery rate.
Genome_build: Reference Consortium Zebrafish Build 10 (UCSC Genome GRCz10/danRer10; Sept 2014)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

organism: Danio rerio

source_name: grna-/- mutant fish

growth_protocol: Zebrafish (Danio rerio) were raised as described (Westerfield, 2000) in a circulating aquarium system (Aquaneering) at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.

extract_protocol:
Zebrafish grna-/- and grna+/+ control siblings were anesthetized in tricaine, subjected to cardiocentesis and kidney dissection as previously described (Traver et al., 2003). The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy (Qiagen) following the manufacturer instructions.
Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, starting with 50 ng of RNA and modifying RNA shear time to five minutes.

treatment_protocol: Six kidney marrows were used to perform RNA-seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna-/- siblings

value: kidney marrow

value: grna-/-


title: 6268

description:
2128
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac12


title: AMut2_S15

description: Mut


title: 6226

description:
2086
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6469

description:
2329
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: AMut1_S14

description: Mut


title: ac10


title: IL2-2

description:
2574
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: TEPA+IFN_treated_replicate_3

value: treated with TEPA+IFN for 24 hours


title: ac09


title: TEPA+IFN_treated_replicate_2


title: ac08


title: WT3_S13

description: WT

source_name: grna+/+ control fish

value: WT


title: PC-3 prostata tumor cell line [E13D007c04]

type: genomic

city: Tuebingen

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2, Bioconductor 'methylumi' package
the non_normalized.txt contins unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: prostata cancer cell line

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from about 1 to 5 million cells reconstituted in 200 µL PBS using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany, Cat.-No. 51304) and following the recommendations of the manufacturer. DNA was eluted in 50-200 µL phosphate-buffered saline (PBS)

value: prostata tumor cell line

tag: disease

value: prostate cancer


title: LNCAP prostata tumor cell line [E13D007c03]

value: LNCAP


title: MPP1_Mysm1_Ko_1

description: rRNA-depleted stranded RNA. Both males and females were used, and sex-matched between experimental groups.

value: Mice were 8-12 weeks of age.

value: pooled male and female

value: Bone marrow

value: Multipotent Progenitors 1 (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34+CD48-)

value: Mysm1-KO (Tamoxifen-treated Mysm1fl/fl CreERT2 mice)


title: ac06

value: CART cells


title: DU-145 prostata tumor cell line [E13D007c02]


title: CAKI-2 renal cell carcinoma cell line [E13D007b03]

source_name: renal cancer cell line

value: renal cell carcinoma cell line

value: renal cancer


title: ac11


title: ac04


title: TEPA_treated_replicate_1

value: treated with TEPA for 24 hours


title: HprEpC primary prostata cell line [E13D007c01]

description: P.N

source_name: primary prostate epithelial cells

value: HprEpC

value: primary prostata cell line

value: non-cancerous prostata cell line


title: CAL-54 renal cell carcinoma cell line [E13D007b04]


title: 6218

description:
2078
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue

value: breaker stage of ripening

value: BIL


title: IFN_treated_replicate_3

value: treated with IFN for 24 hours


title: TEPA_treated_replicate_2


title: ac03


title: J82 bladder tumor cell line [E13D007a04]

source_name: urothelial cancer cell line

value: bladder tumor cell line

value: bladder cancer


title: 6663

description:
2523
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: RCC-KP renal cell carcinoma cell line [E13D007b02]

value: RCC-KP


title: 5637 bladder tumor cell line [E13D007a03]


title: HREpC primary kidney cell line [E13D007b01]

description: K.N

source_name: primary renal epithelial cells

value: HREpC

value: primary kidney cell line

value: non-cancerous kidney cell line


title: E2F1Cr T1-44 cell line RNA-seq replicate 3

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing:
FASTQ files were trimmed to remove adaptors and low-quality bases with TrimGalore v0.4.3
Trimmed reads were aligned to the human reference genome (build hg19) with STAR aligner v2.7 with two mismatches allowed
Differential gene expression analysis was done with DESeq2 R Bioconductor package v1.25.17 using read count data provided by the aligner.
Genes were considered differentially expressed if the adjusted P-value, calculated using Benjamini-Hochberg method was less than 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts

molecule: polyA RNA

source_name: HCT116 stable cells with E2F1 knockdown

growth_protocol: HCT116 cell lines were grown in high glucose Dulbecco’s modified Eagle medium supplemented with 10% (v/v) FBS and 1% penicillin/streptomycin.

extract_protocol:
total RNA was extracted using TRIzol.
cDNA libraries were made using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: PRMT5 inhibition was induced with 1uM T1-44 for 48h

value: Colorectal carcinoma

tag: vector

value: E2F1 knockdown cell line treated with PRMT5 inhibitor

tag: conditions

value: PRMT5 inhibitor treatment:1uM, 48h


title: 6551

description:
2411
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac02

value: CART cells


title: IFN_treated_replicate_2


title: 6637

description:
2497
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: WT2_S12

description: WT

value: kidney marrow

value: WT


title: TEPA_treated_replicate_3

value: treated with TEPA for 24 hours


title: E2F1Cr T1-44 cell line RNA-seq replicate 1


title: ac01


title: IFN_treated_replicate_1


title: WT1_S11

description: WT


title: RT4 bladder tumor cell line [E13D007a02]


title: HBIEpC primary bladder cell line [E13D007a01]

description: B.N

source_name: primary urothelial epithelial cells

value: HBIEpC

value: primary bladder cell line

value: non-cancerous bladder cell line


title: TEPA+IFN_treated_replicate_1

value: treated with TEPA+IFN for 24 hours


title: 6443

description:
2303
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue

value: breaker stage of ripening

value: BIL


title: E2F1Cr cell line RNA-seq replicate 3

description: CRISPRDMSOC

value: E2F1 knockdown cell line


title: 6535

description:
2395
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: DC+IFN_treated_replicate_3

value: treated with DC+IFN for 24 hours


title: 6190a

description:
2050
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac05


title: DC+IFN_treated_replicate_2


title: 6610

description:
2470
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL12-4-1

description:
2639
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: E2F1Cr cell line RNA-seq replicate 1

description: CRISPRDMSOA

value: Colorectal carcinoma


title: WT T1-44 cell line RNA-seq replicate 3

source_name: HCT116 stable cells

value: empty vector cell line treated with PRMT5 inhibitor


title: E2F1Cr cell line RNA-seq replicate 2

description: CRISPRDMSOB


title: DC+IFN_treated_replicate_1


title: IL1-1

description:
2565
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: DC_treated_replicate_3

value: treated with DC for 24 hours


title: WT T1-44 cell line RNA-seq replicate 2

value: PRMT5 inhibitor treatment:1uM, 48h


title: DC_treated_replicate_2


title: 6267

description:
2127
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6500

description:
2360
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: WT cell line RNA-seq replicate 3

description: WTDMSOC

value: empty vector cell line


title: WT T1-44 cell line RNA-seq replicate 1


title: DC_treated_replicate_1


title: WT cell line RNA-seq replicate 2

description: WTDMSOB


title: WT cell line RNA-seq replicate 1

description: WTDMSOA


title: VeryLow_Adaptor_0024_Input

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: genomic

data_processing:
fastq files were demultiplexed on RELACS barcodes and aligned to dm6 (S2 cells) or hg38 (HepG2) using snakePipes v. 1.2.3. QC metrics and further downstream files (bigwig) were also generated using snakePipes (Bhardwaj et al. 2019)
default parameters used for the analysis are available at https://github.com/FrancescoFerrari88/AutoRELACS/tree/master/snakePipes_defaults
Genome_build: dm6 (S2 cells) and hg38 (HepG2)
Supplementary_files_format_and_content: bigWig, normalized coverage

source_name: HepG2 cells

growth_protocol: S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27 °C. HepG2 liver hepatocellular carcinoma (ATCC, HB-8065TM) were cultured in Eagle’s minimal essential medium (EMEM, Lonza, 06-174) supplemented with 10% fetal bovine serum (Sigma), 2 mM L-glutamine (Lonza), 1.8 mM CaCl2, 1 mM sodium pyruvate (Lonza) and penicillin–streptomycin mixture (100 units/mL, Lonza), at 37 °C at 5% CO2 in 10 cm plates, up to 70%-80% confluency.

extract_protocol:
HepG2 and S2 cells were fixed in 1% methanol-free formaldehyde (Thermo Scientific, 28906) in D-MEM (for HepG2 cells) or Express Five SFM (for S2 cells) for 15 min at room temperature under gentle shaking. Formaldehyde was quenched for 5 min by adding 125 mM glycine final concentration. Cells were rinsed twice with ice-cold PBS, harvested by scraping (HepG2) and pelleted (300 g, 10 min, 4 °C). Cells were processed according to RELACS / AutoRELACS protocols
Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After Illumina adapter ligation, library was PCR amplified. Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on NovaSeq 6000 machine, following manufacturer's protocol.
High-throughput RELACS ChIP-seq and automated high-throughput AutoRELACS ChIP-seq

treatment_protocol: No treatment was applied

tag: chip ab


title: 6460

description:
2320
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6576

description:
2436
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: VeryLow_Adaptor_0024_H3K4me3


title: 6263

description:
2123
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6473

description:
2333
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: VeryLow_Adaptor_0024_H3K27me3


title: 6284

description:
2144
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL7-2

description:
2602
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: VeryLow_Adaptor_0024_H3K27ac


title: E2F1Cr T1-44 cell line RNA-seq replicate 2

value: E2F1 knockdown cell line treated with PRMT5 inhibitor


title: VeryLow_Adaptor_0023_Input


title: IL3-3a

description:
2582
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL2-3a

description:
2575
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: VeryLow_Adaptor_0023_H3K4me3


title: F. robusta_2weeksLowCO2 2

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
Transcript de novol assemble using Trinity
Funcatonal annotation of transcripts by searching orhtolog in F. ramosissima gene reference.
mapping RNA-seq reads to assembled transcripts to quantify the abundance of transcript using RSEM
Call differentiall expressed genes between ctrl and ABA treatments using edgeR package.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Flaveria robusta

source_name: newly expanded mature leaf

growth_protocol: For low CO2 experiment, Plants were grown in growth chamber with light intensity to be 200 μmol m-2 s-1 and temperature to be 22oC, 16h/8h light/ dark duration, 70% humidity. . Plant were watered twice a week and fertilized weekly.

extract_protocol:
Total RNA was isolated following the protocol of the PureLInkTM RNA Mini (ThermoFisher Scientific)
Next-generation RNA-seq was performed in the Illumina platform in the pair-ended mode with read length150 bp.

treatment_protocol: The CO2 concentration of low CO2 condition is 100 μmol m-2 s-1, and that of control is 380 μmol m-2 s-1.

value: newly expanded mature leaf

value: 2 weeks Low CO2


title: 6205b

description:
2065
Solanum lycopersicum-pennellii
Manually peeled skin tissue

source_name: Skin fruit tissue


title: VeryLow_Adaptor_0023_H3K27me3


title: F. robusta_2weeksLowCO2 1


title: VeryLow_Adaptor_0023_H3K27ac


title: F. robusta_ctrl 3

value: control


title: VeryLow_Adaptor_0022_Input


title: 6228

description:
2088
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: ac07

source_name: infusion product

value: CART cells


title: VeryLow_Adaptor_0022_H3K4me3


title: 6278

description:
2138
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. robusta_ABA

data_processing:
Transcript de novol assemble using Trinity
Funcatonal annotation of transcripts by searching orhtolog in F. ramosissima gene reference.
mapping RNA-seq reads to assembled transcripts to quantify the abundance of transcript using RSEM
Call differentiall expressed genes between ctrl and ABA treatments using edgeR package.
Supplementary_files_format_and_content: txt file contains the transcript abundance of annotated genes

growth_protocol: Plants for ABA experiment were grown in green house of SIPPE, SIBS, CAS, the light intensity was controlled to be 500 μmol m-2 s-1, and temperature to be 25oC, 16h/8h light/ dark duration, 70% humidity. Plant were watered twice a week and fertilized weekly.

treatment_protocol: A concentration of 40 μM ABA dissolved in distill H2O was sprayed to mature leaf of one-month old plants, and the control was sprayed with distill H2O.

value: whole plant


title: 6276

description:
2136
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue


title: VeryLow_Adaptor_0022_H3K27me3


title: F. robusta_ctrl 1


title: 6538

description:
2398
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: breaker stage of ripening


title: 6659

description:
2519
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: BIL


title: F. robusta_2weeksLowCO2 3


title: F. robusta_ctrl 2


title: VeryLow_Adaptor_0022_H3K27ac


title: F. robusta_ctrl


title: VeryLow_Adaptor_0021_Input


title: 6417

description:
2277
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6487

description:
2347
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6488

description:
2348
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: VeryLow_Adaptor_0021_H3K4me3


title: F. sonorensis_6months_lowCO2 rep3

data_processing:
Transcript de novol assemble using Trinity
Funcatonal annotation of transcripts by searching orhtolog in F. ramosissima gene reference.
mapping RNA-seq reads to assembled transcripts to quantify the abundance of transcript using RSEM
Supplementary_files_format_and_content: txt file contains the transcript abundance of annotated genes
Supplementary_files_format_and_content: fastafile contains the transcript abundance of annotated genes

organism: Flaveria sonorensis

treatment_protocol: The CO2 concentration of low CO2 condition is 100 μmol m-2 s-1.

value: leaf


title: 6378

description:
2238
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. sonorensis_6months_lowCO2 rep4


title: 6257

description:
2117
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. sonorensis_6months_lowCO2 rep2


title: VeryLow_Adaptor_0021_H3K27ac


title: 6565

description:
2425
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. sonorensis_6months_lowCO2 rep1


title: 6275

description:
2135
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Low_Adaptor_0024_Input


title: Low_Adaptor_0024_H3K4me3


title: 6439

description:
2299
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Antenna: untreated_A

city: Riverside

first: Christi Ann

last: Scott

state: CA

address: 3401 Watkins Drive

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

data_processing:
For HiSeq2000: RTA v1.7, CASAVA v1.7 used for basecalling. For NextSeq500: RTA 2.0 used for basecalling.
Reads aligned to the latest release of each of the genomes used (dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome) and quantified with kallisto (Version: kallisto 0.43.1, Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519) . Only libraries for which we obtained >75 % alignment were used for downstream analysis.
Transcript counts were summarized to gene-level using tximport package (version 1.4.0).
For any instances of detected batch effects, we removed unwanted variation using RuvR in the RuvSeq package (version_1.10.0).
Differentially expressed gene (DEG) analysis was performed with the edgeR package (version 3.18.1), using low count filtering (cpm >0.5) and TMM normalization.
Genome_build: dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome
Supplementary_files_format_and_content: tab-delimited .tsv files including counts TPM normalized read counts for each sample

organism: Drosophila melanogaster

source_name: Antenna

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit v2 was used with total RNA for the construction of sequencing libraries.

value: wCS

value: wild type

value: 5 days

tag: Sex

value: male

value: untreated (control)

value: 2nd and 3rd segment of the antenna


title: 6440

description:
2300
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. sonorensis_2weeksLowCO2 3


title: Low_Adaptor_0024_H3K27me3


title: Low_Adaptor_0024_H3K27ac


title: F. sonorensis_2weeksLowCO2 2


title: F. sonorensis_2weeksLowCO2 1


title: 6387

description:
2247
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6516

description:
2376
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Antenna: valproic_acid_B

value: 10mM valproic acid for 5 days


title: F. sonorensis_ctrl 3


title: Antenna: valproic_acid_A


title: F. sonorensis_ctrl 2


title: Low_Adaptor_0023_Input


title: VeryLow_Adaptor_0021_H3K27me3


title: Low_Adaptor_0023_H3K4me3


title: IL9-2

description:
2617
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: Antenna: sodium_butyrate_B

value: 10mM sodium butyrate for 5 days


title: F. sonorensis_ctrl 1

value: newly expanded mature leaf


title: 6277

description:
2137
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Low_Adaptor_0023_H3K27me3


title: Antenna: sodium_butyrate_A


title: Antenna: untreated_B


title: 6173

description:
2033
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. sonorensis_ABA


title: 6496

description:
2356
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Antenna: POR_B

value: 10 days

value: PO for 10 days (control)


title: F. ramosissima_6months_lowCO2 rep4

organism: Flaveria ramosissima


title: Low_Adaptor_0023_H3K27ac


title: 6205a

description:
2065
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Antenna: POR_A


title: F. sonorensis_ctrl

value: whole plant


title: F. ramosissima_6months_lowCO2 rep3


title: Low_Adaptor_0022_H3K27me3


title: Low_Adaptor_0022_Input


title: Antenna: d4onR_B

value: 1% diacetyl in PO for 5days, PO for 5 days


title: IL4-3

description:
2588
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue

value: breaker stage of ripening


title: IL9-3

description:
2620
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Low_Adaptor_0022_H3K4me3


title: F. ramosissima_6months_lowCO2 rep1

value: leaf


title: Antenna: d4onR_A

value: wCS


title: 6465

description:
2325
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: BIL


title: Low_Adaptor_0021_Input


title: Low_Adaptor_0022_H3K27ac


title: 6202

description:
2062
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Antenna: PO_B

value: wild type

value: 5 days

value: PO, 5 days (control)


title: Antenna: d4on_B

value: male

value: 1% diacetyl in PO, 5days

value: 2nd and 3rd segment of the antenna


title: IL12-4

description:
2638
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: Low_Adaptor_0021_H3K27me3


title: Low_Adaptor_0021_H3K4me3


title: F. ramosissima_2weeksLowCO2 2

value: newly expanded mature leaf

value: 2 weeks Low CO2


title: Antenna: d4on_A


title: Low_Adaptor_0021_H3K27ac


title: F. ramosissima_2weeksLowCO2 1


title: CSN8

city: Tel Aviv

first: Tamir

last: Tuller

address: Ramat Aviv

department: Biomedical Engineering

institute: Tel Aviv University

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted Arabidopsis TAIR 10 reference scaffold, allowing up to two mismatches per read. 100 base reads were divided in half and 50 base reads were processed as single reads. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
Identifying differential methylation between various samples was performed by Fisher Exact Test using the number of Cs (methylated cytosines) and Ts (unmethylated cytosines) of any pair of samples. A site was determined to be differentially differentially methylated using two statistical tests:
Fisher's Test type 1:  which was named External Fisher's Exact Test (EFET). This test is a Fisher's Exact Test where the input numbers to the test are: the ratio (#C/#T) in the position in the WT, the ratio (#C/#T) in the same position in the mutant, the  ratio (#C/#T) outside of the position (i.e. in all other positions) in the WT, the ratio (#C/#T) outside the position (i.e. in all other positions) in the mutant. We multiplied the numbers by 1000 and rounded so we have integer numbers.
Fisher's Test type 2:  which was named Internal Fisher's Exact Test (IFET). This is a Fisher's Exact when the input numbers to the test are:  #C  in the position in the WT, #T in the position in the WT, #C in the position in the mutant, #T in the position in the mutant.
Genome_build: TAIR 10
Supplementary_files_format_and_content: methylation ratio for each sample for all positions with nonzero methylation in at least one sample, and the max methylation ratio value among the samples

organism: Arabidopsis thaliana

source_name: light grown CSN8 seedlings batch 1

growth_protocol: Seedlings were grown for 12 days on agar plates containing MS salts, pH 5.7, under a light-and-dark cycle with 16 h of white light at 75 lmol m-2 s-1 and 8 h of darkness.

extract_protocol:
Tri-Reagent (Molecular Research Center, Inc., USA)  extraction of total RNA was performed according to the manufacturer's instructions.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing performed on the Illumina HiSeq 2000 platform.

treatment_protocol: After 12 days the seedlings were collected  for RNA extraction with no additional treatment

tag: ecotype

value: Wassilewskija

tag: genotype/variation

value: lethal csn8 mutant

value: whole seedlings


title: F. ramosissima_ctrl 3

value: control


title: F. ramosissima_6months_lowCO2 rep2


title: 6644

description:
2504
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue

value: breaker stage of ripening


title: 6484

description:
2344
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6482

description:
2342
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. ramosissima_ctrl 2


title: Wassilewskija

description: ws

source_name: light grown Wassilewskija seedlings batch 1

tag: age


title: Csn5a-1

source_name: light grown csn5a-1 seedlings

value: Columbia

value: non-lethal  csn5a-1 mutant


title: Antenna: PO_A

tag: strain

value: wCS

value: wild type


title: 6561

description:
2421
Solanum lycopersicum-pennellii
Manually peeled skin tissue

tag: tissue

value: BIL


title: Columbia

description: col

source_name: light grown Columbia seedlings


title: F. ramosissima_2weeksLowCO2 3


title: F. ramosissima_ctrl 1


title: F. ramosissima_ABA

value: whole plant


title: G4_d4_Cy5-PDS_1uM_plus_20uM_BMVC_comp_rep2

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: 1uM Cy5-PDS + 20uM BMVC G4 array experiment, ssDNA + 100mM KCl

hyb_protocol: Microarrays were blocked with 4% non-fat dry-milk in a potassium phosphate buffer before incubation with small molecules.   The binding reactions (Cy5-PDS, Cy5-PDS+BMVC, or Cy5-PDS+PDS)  were carried out in a hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: Molecule-bound microarrays were scanned with the G5761A SureScan Dx Microarray Scanner System (Agilent) to detect Cy5 signal at two laser settings (30 and 100PMT) to ensure signal intensities were below saturation.  Spot intensities from microarray images were extracted using the Agilent Feature Extraction Software and are reported as raw fluorescence units.  Microarrays with the fewest number of saturated spots were used for further analysis.

data_processing: An intensity value was calculated for each target sequence by computing the median signal intensity across probes containing an identical probe identifier (ProbeID)

molecule: other

organism: synthetic construct

source_name: 1uM Cy5-PDS + 20uM BMVC, G4 design 4

label_protocol: Synthesis of Cy5-labeled pyridostatin (Cy5-PDS) is described in (Ray et al., 2020).

treatment_protocol: Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation.  Binding experiments were then performed as previously described in Ray et al. ACS Chem Bio 2020.

tag: molecule name

value: 1uM Cy5-PDS + 20uM BMVC

tag: dna type

value: ssDNA

tag: array treatment

value: 100mM KCl


title: G4_d4_Cy5-PDS_1uM_plus_20uM_BMVC_comp_rep1


title: SRI-37330 treated #2

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
5583-011
Human islets incubated with 25mM glucose + 1uM SRI-37330 for 24h
Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

source_name: human islets

treatment_protocol: 24h incubation in 25mM glucose with or without 1uM SRI-37330

value: human islets


title: SRI-37330 treated #1

description:
5583-010
Human islets incubated with 25mM glucose + 1uM SRI-37330 for 24h
Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.


title: SRI-37330 treated #3

description:
5583-012
Human islets incubated with 25mM glucose + 1uM SRI-37330 for 24h
Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.


title: F. ramosissima_HighLight 3

data_processing:
Transcript de novol assemble using Trinity
Funcatonal annotation of transcripts by searching orhtolog in F. ramosissima gene reference.
mapping RNA-seq reads to assembled transcripts to quantify the abundance of transcript using RSEM
Call differentiall expressed genes between ctrl and ABA treatments using edgeR package.
Supplementary_files_format_and_content: xlsx file contains the transcript abundance of annotated genes
Supplementary_files_format_and_content: fasta file contains the de novo assembled transcripts

growth_protocol: For low high light experiment, Plants were grown in growth chamber with light intensity to be 200 μmol m-2 s-1 and temperature to be 22oC, 16h/8h light/ dark duration, 70% humidity. . Plant were watered twice a week and fertilized weekly.

treatment_protocol: The light intensity of hight light condition is 1400 μmol m-2 s-1, and that of control is 500 μmol m-2 s-1.

value: leaf


title: 6430

description:
2290
Solanum lycopersicum-pennellii
Manually peeled skin tissue

data_processing:
The reads were mapped against a combined file that included the genomes from Solanum lycopersicum (ITAG 3.0) and Solanum pennellii (v2.0).
Mapping has been performed with STAR 2.4.2a.
The alignments in resulting SAM file were divided into genomes based on the alignment scores. If the highest scoring alignment is assigned to a certain genome, and is unique in that genome, then it is assigned as “lycopersicum-unique” or “pennellii-unique”. If there is no difference in the scores between the two genomes then the alignment to the S. lycopersicum genome is kept and categorized as “indistinguishable”.
Counting was performed on the TES (Transcript End Site) region of each gene. The TES region is defined as 200 bp downstream from the STOP codon of the gene, and at least 500 bases upstream to the STOP codon of the gene. The reads were counted using htseq-count using stranded method and union mode.
Genome_build: Solanum lycopersicum (ITAG 3.0) and Solanum pennellii (v2.0)
Supplementary_files_format_and_content: Using the htseq-count for each type of genome provide three complementary datasets:
Supplementary_files_format_and_content: (1) lyc-count - containing the count for the reads specific to S. lycopersicum genome (68% of all reads);
Supplementary_files_format_and_content: (2) pen-count - containing the count for the reads specific to S. pennellii genome (28% of all reads);
Supplementary_files_format_and_content: (3) ind-count - containing the count for the reads aligning to both genomes (4% of all reads).

tag: ripening stage

tag: population


title: F. ramosissima_HighLight 2


title: F. trinervia_2weeksLowCO2 1

organism: Flaveria trinervia

value: newly expanded mature leaf

tag: treatment

value: 2 weeks Low CO2


title: Control #2

description:
5583-005
Human islets incubated with 25mM glucose for 24h
Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.


title: F. trinervia_2weeksLowCO2 2


title: G4_d4_Cy5-PDS_1uM_plus_3uM_BMVC_comp_rep1

description: 1uM Cy5-PDS + 3uM BMVC G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 3uM BMVC, G4 design 4

value: 1uM Cy5-PDS + 3uM BMVC


title: F. ramosissima_ctrl


title: F. ramosissima_ctrl (HighLight) 3


title: F. trinervia_ctrl 2

value: control


title: F. ramosissima_HighLight 1


title: G4_d4_Cy5-PDS_1uM_plus_3uM_BMVC_comp_rep2


title: Control #1

description:
5583-004
Human islets incubated with 25mM glucose for 24h
Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.


title: F. trinervia_ctrl 1


title: F. trinervia_ctrl 3


title: G4_d4_Cy5-PDS_1uM_plus_10uM_BMVC_comp_rep2

description: 1uM Cy5-PDS + 10uM BMVC G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 10uM BMVC, G4 design 4

value: 1uM Cy5-PDS + 10uM BMVC


title: F. trinervia_2weeksLowCO2 3


title: G4_d4_Cy5-PDS_1uM_plus_1uM_BMVC_comp_rep2

description: 1uM Cy5-PDS + 1uM BMVC G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 1uM BMVC, G4 design 4

value: 1uM Cy5-PDS + 1uM BMVC


title: G4_d4_Cy5-PDS_1uM_plus_1uM_BMVC_comp_rep1


title: INS-1 832/13 cells: NIKKA

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   F  PKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  Per  Kilobase  of  transcript  sequence  per   Millions  base  pairs  sequenced  ,  considers  the  effect  of  sequencing  depth  and  gene  length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression  levels (  Tr  apnell, Cole, et al., 2010  )
Genome_build: Ensemble_GRCm38.90

organism: Rattus norvegicus

source_name: INS-1 832/13 cells

extract_protocol: Not provided

value: INS-1 832/13 cells


title: INS-1 832/13 cells: NIK


title: Control #3

description:
5583-006
Human islets incubated with 25mM glucose for 24h
Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.


title: F. ramosissima_ctrl (HighLight) 1


title: F. trinervia_ABA


title: G4_d4_Cy5-PDS_1uM_plus_10uM_BMVC_comp_rep1


title: INS-1 832/13 cells: β-Gal


title: F. trinervia_ctrl


title: scRNA-Seq MICPCH-CASKdup45

status: Public on Jul 27 2020

city: Solna

first: Martin

last: Becker

address: Akademiska stråket 1

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

description: processed data file columns labeled by ungrouped cells: A1 to P22

data_processing:
Bulk RNA-Seq Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.4.0/RTA v3.3.3) with a 2x151 setup using 'S1' flow cell mode. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. The NGI-RNASeq pipeline was used to trim reads (TrimGalore), align to reference genome GRCh38/hg38 (STAR), perform quality control (FastQC, RSeQC, dupRadar, MultiQC) and count gene reads (featureCounts).
SMART-Seq2 samples were sequenced on Illumina HiSeq2000.The samples were analyzed by first demultiplexing the fastq files using  deindexer (https://github.com/ws6/deindexer) using the nextera index adapters and the 384 well  layout. Individual fastq files were then mapped to the hg38 genome assembly using the STAR  aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM file. The count matrix shows the individual counts aligning to each gene per cell.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include raw sequence counts per gene

source_name: in vitro neurons

growth_protocol: NES cells were seeded on plastic surface, pre-coated with 20 ug/ml poly-ornithine (Sigma Aldrich) and 1 ug/ml laminin (Sigma Aldrich) in DEMEM/F12+glutamax medium (Gibco) supplemented with 0.5X B-27 (Gibco), 1X N-2 (Gibco) and 10 U/ml Penicillin/Streptomycin (Gibco). Cells were maintained in a 5% CO2 atmosphere at 37°C. Two third of the medium was changed every second day of differentiation with 0.4 ug/ml laminin added.

extract_protocol:
For bulk RNA-Seq, cells were lysed in TRIzol reagent (Invitrogen), and RNA was isolated using the ReliaPrep RNA Cell Miniprep (Promega #A1222). For SMART-Seq2, cells were dissociated from culture surface with 2 min trypsin incubation and subsequent trypsin inhibition. After 3 minutes centrifugation at 300 rcf the cells were resuspended in cold Dulbecco’s PBS and single cells sorted by size into lysis-buffer using BD FACS Aria III.
Bulk RNA libraries were prepared using Tru-Seq at NGI Sweden, Stockholm. Smart-Seq2 library preparation and sequencing were done with the Eukaryotic Single Cell Genomics (ESCG) facility in the SciLifeLab, Stockholm according to published protocols (Picelli et al., 2013).

treatment_protocol: For siRNA-KD experiments, cells were seeded for differentiation and transfected the next day with 0.5µM Accell SMARTpool siRNA targeting CASK mRNA (Dharmacon #E-005311-00-0010) or 0.5µM Accell Green Non-targeting siRNA (Dharmacon #D-001950-01-20) according to standard protocol.

tag: days differentiation

tag: source

value: iPSC derived NES cells


title: G4_d4_Cy5-PDS_1uM_plus_3uM_PDS_comp_rep1

description: 1uM Cy5-PDS + 3uM PDS G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 3uM PDS, G4 design 4

value: 1uM Cy5-PDS + 3uM PDS


title: s.53

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

data_processing:
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore
Trimmed reads were aligned to the human genome (v.38) using HISAT2
Count matrix for genes was created using Kallisto
Differential expression analysis was done using the DESeq2 package available in R
Genome_build: human genome (v.38)

source_name: Bone

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen)
Strand-specific libraries constructed using the NEB mRNA library prep kit following manufacturer’s instructions

tag: cell type

value: High grade osteoblastic osteosarcoma met lesion

value: No treatment

value: Lung


title: s.28 ctc

value: High grade osteoblastic osteosarcoma circulating tumour cells in a cluster

value: Blood


title: s.54


title: F. ramosissima_ctrl (HighLight) 2

source_name: newly expanded mature leaf


title: s.23 ctc


title: s.22 ctc


title: s.20 ctc


title: G4_d4_Cy5-PDS_1uM_plus_0uM_BMVC_ctrl_rep2

description: 1uM Cy5-PDS + 0uM BMVC G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 0uM BMVC, G4 design 4

value: 1uM Cy5-PDS + 0uM BMVC

value: ssDNA

value: 100mM KCl


title: G4_d4_Cy5-PDS_1uM_plus_0uM_BMVC_ctrl_rep1


title: s.19 ctc


title: s.28 tmr

value: High grade osteoblastic osteosarcoma

value: Femur


title: s.22 tmr


title: s.29 tmr


title: s.23 tmr

value: Humerus


title: G4_d4_Cy5-PDS_1uM_plus_3uM_PDS_comp_rep2


title: s.21 tmr


title: s.20 tmr

value: Tibia


title: s.19 tmr


title: s.51

value: Scapula


title: EndoPanc46_Nsp

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

institute: Cancer Research UK

description:
PET12_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

hyb_protocol: Hybridisation was performed at 45°C for 16h in a hybridisation machine (Affymetrix).

scan_protocol: The arrays were washed and stained on the Affymetrix fluidics Station 450 and the signal intensities were measured using the Affymetrix GeneChip® Scanner 3000.

data_processing: The raw images were analysed using the Affymetrix GCOS (Ver1.4) software. For genotyping analysis, we used the Affymetrix GTYPE (Ver4.1) software that implements an accurate genotyping algorithm, BRLMM.

source_name: tumour lesion of PET12 tissues

label_protocol: The experiments were performed according to the manufacturer's instructions (GeneChip® Mapping 250K Nsp or Sty Assay Kit). Briefly, 250 ng of tumour/reference DNA was digested by either Nsp or Sty restriction enzyme (New England Biolabs, Boston, MA, USA). After ligation to an appropriate adaptor for each enzyme, PCR reaction was carried out using a generic primer that recognises the adapter sequence. The PCR products from three reactions were pooled, concentrated, fragmented by DNase I and then, labelled with biotin.

extract_protocol: Tumour and reference genomic DNAs were extracted using Qiagen DNA extraction kit (Qiagen Ltd., Sussex, UK).

tag: Tumour lesion of PET12 tissues


title: EndoPanc45_Nsp

description:
PET11_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET11 tissues

tag: Tumour lesion of PET11 tissues


title: EndoPanc51_Nsp

description:
BON_cell line_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: BON cell line

tag: BON cell line


title: EndoPanc47_Nsp

description:
PET18_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET18 tissues

tag: Tumour lesion of PET18 tissues


title: EndoPanc36_Nsp

description:
PET27_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET27 tissues

tag: Tumour lesion of PET27 tissues


title: EndoPanc34_Nsp

description:
PET19_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET19 tissues

tag: Tumour lesion of PET19 tissues


title: EndoPanc52_Nsp

description:
CM_cell line_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: CM cell line

tag: CM cell line


title: EndoPanc35_Nsp

description:
PET27_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET27 tissues

tag: Non-neoplastic lesion of PET27 tissues


title: EndoPanc29_Nsp

description:
PET23_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET23 tissues

tag: Non-neoplastic lesion of PET23 tissues


title: EndoPanc40_Nsp

description:
PET2_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET2 tissues

tag: Tumour lesion of PET2 tissues


title: EndoPanc48_Nsp

description:
PET7_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET7 tissues

tag: Tumour lesion of PET7 tissues


title: EndoPanc39_Nsp

description:
PET2_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET2 tissues

tag: Non-neoplastic lesion of PET2 tissues


title: EndoPanc37_Nsp

description:
PET20_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET20 tissues

tag: Non-neoplastic lesion of PET20 tissues


title: EndoPanc43_Nsp

description:
PET5_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET5 tissues

tag: Tumour lesion of PET5 tissues


title: EndoPanc23_Nsp

description:
PET15_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET15 tissues

tag: Non-neoplastic lesion of PET15 tissues


title: EndoPanc50_Nsp

description:
QGP-1_cell line_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: QGP-1 cell line

tag: QGP-1 cell line


title: EndoPanc42_Nsp

description:
PET26_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET26 tissues

tag: Tumour lesion of PET26 tissues


title: EndoPanc25_Nsp

description:
PET13_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET13 tissues

tag: Non-neoplastic lesion of PET13 tissues


title: EndoPanc31_Nsp

description:
PET9_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET9 tissues

tag: Non-neoplastic lesion of PET9 tissues


title: EndoPanc28_Nsp

description:
PET4_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET4 tissues

tag: Tumour lesion of PET4 tissues


title: EndoPanc38_Nsp

description:
PET20_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET20 tissues

tag: Tumour lesion of PET20 tissues


title: EndoPanc44_Nsp

description:
PET14_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET14 tissues

tag: Tumour lesion of PET14 tissues


title: EndoPanc30_Nsp

description:
PET23_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET23 tissues

tag: Tumour lesion of PET23 tissues


title: EndoPanc26_Nsp

description:
PET13_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET13 tissues

tag: Tumour lesion of PET13 tissues


title: EndoPanc32_Nsp

description:
PET9_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET9 tissues

tag: Tumour lesion of PET9 tissues


title: EndoPanc24_Nsp

description:
PET15_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET15 tissues

tag: Tumour lesion of PET15 tissues


title: EndoPanc33_Nsp

description:
PET19_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET19 tissues

tag: Non-neoplastic lesion of PET19 tissues


title: EndoPanc41_Nsp

description:
PET29_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET29 tissues

tag: Tumour lesion of PET29 tissues


title: SAMPLE 328 DiEIn

city: Turku

first: Michael

last: Gabriel

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

description: Deep infiltrating endometriosis lesion intestine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Intestine

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, further purified with  QIAGEN Rneasy colums and treated with DNase I in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: Deep infiltrating endometriosis lesion

tag: age

tag: disease stage

tag: cycle phase

value: proliferative


title: SAMPLE 327 DiEIn

value: medication


title: SAMPLE 330 OMA

description: Ovarian endometrioma

source_name: Ovary

value: Ovarian endometrioma

value: unknown


title: SAMPLE 329 PE

description: Patient endometrium

source_name: Endometrium

value: Endometrium

value: secretory


title: EndoPanc27_Nsp

description:
PET4_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET4 tissues

tag: Non-neoplastic lesion of PET4 tissues


title: EndoPanc49_Nsp

description:
PET10_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET10 tissues

tag: Tumour lesion of PET10 tissues


title: SAMPLE 326 DiEIn


title: SAMPLE 325 PeLB

description: Peritoneal endometriosis black lesion

source_name: Peritoneal

value: Peritoneal endometriosis lesion


title: SAMPLE 323 CE

description: Control endometrium

value: Healthy


title: SAMPLE 322 DiEIn


title: SAMPLE 321 PE

description: Patient endometrium


title: SAMPLE 324 OMA

description: Ovarian endometrioma


title: SAMPLE 319 DiEIn


title: EndoPanc21_Nsp

description:
PET21_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET21 tissues

tag: Non-neoplastic lesion of PET21 tissues


title: SAMPLE 317 OMA

description: Ovarian endometrioma


title: SAMPLE 316 PP

description: Patient peritoneum

source_name: Peritoneum

value: Peritoneum


title: SAMPLE 320 SuL

description: Sacrouterine ligament lesion

source_name: Sacrouterine ligament

value: Sacrouterine ligament lesion


title: SAMPLE 315 CE

description: Control endometrium


title: SAMPLE 314 OMA

description: Ovarian endometrioma


title: SAMPLE 312 CE

description: Control endometrium


title: EndoPanc19_Nsp

description:
PET3_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET3 tissues

tag: Non-neoplastic lesion of PET3 tissues


title: SAMPLE 310 CE

description: Control endometrium


title: SAMPLE 309 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 313 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 308 PP

description: Patient peritoneum


title: SAMPLE 311 PP

description: Patient peritoneum


title: SAMPLE 307 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 331 DiEIn


title: EndoPanc18_Nsp

description:
PET1_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET1 tissues

tag: Tumour lesion of PET1 tissues


title: SAMPLE 306 PE

description: Patient endometrium


title: SAMPLE 305 DiEIn


title: SAMPLE 303 PP

description: Patient peritoneum


title: SAMPLE 302 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 301 PeLB

description: Peritoneal endometriosis black lesion


title: EndoPanc8_Nsp

description:
PET25_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET25 tissues

tag: Tumour lesion of PET25 tissues


title: SAMPLE 304 OMA

description: Ovarian endometrioma


title: EndoPanc20_Nsp

description:
PET3_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET3 tissues

tag: Tumour lesion of PET3 tissues


title: SAMPLE 300 REV

description: Rectovaginal lesion

source_name: Rectovaginal septum

value: Rectovaginal lesion


title: SAMPLE 298 CP

description: Control peritoneum


title: SAMPLE 299 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 297 CE

description: Control endometrium


title: SAMPLE 296 CP

description: Control peritoneum


title: EndoPanc17_Nsp

description:
PET1_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET1 tissues

tag: Non-neoplastic lesion of PET1 tissues


title: SAMPLE 294 CP

description: Control peritoneum


title: SAMPLE 291 CE

description: Control endometrium


title: SAMPLE 291 CE Replicate

description: Control endometrium


title: SAMPLE 290 PE

description: Patient endometrium


title: SAMPLE 288 DiEB

description: Deep infiltrating endometriosis lesion bladder

source_name: bladder


title: SAMPLE 287 PeLB

description: Peritoneal endometriosis black lesion

value: menstruation


title: SAMPLE 285 OMA

description: Ovarian endometrioma


title: SAMPLE 283 PE

description: Patient endometrium


title: EndoPanc9_Nsp

description:
PET8_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET8 tissues

tag: Non-neoplastic lesion of PET8 tissues


title: SAMPLE 295 CP

description: Control peritoneum


title: SAMPLE 284 PeLR

description: Peritoneal endometriosis red lesion


title: EndoPanc11_Nsp

description:
PET17_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET17 tissues

tag: Non-neoplastic lesion of PET17 tissues


title: SAMPLE 282 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 280 PE

description: Patient endometrium


title: SAMPLE 281 PE

description: Patient endometrium


title: SAMPLE 279 PP

description: Patient peritoneum


title: SAMPLE 278 PeLB

description: Peritoneal endometriosis black lesion


title: EndoPanc3_Nsp

description:
PET16_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET16 tissues

tag: Non-neoplastic lesion of PET16 tissues


title: EndoPanc10_Nsp

description:
PET8_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET8 tissues

tag: Tumour lesion of PET8 tissues


title: SAMPLE 276 PE

description: Patient endometrium

source_name: Endometrium


title: SAMPLE 293 PE

description: Patient endometrium


title: SAMPLE 275 DiEIn

source_name: Intestine


title: EndoPanc5_Nsp

description:
PET6_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET6 tissues

tag: Non-neoplastic lesion of PET6 tissues


title: SAMPLE 318 OMA

description: Ovarian endometrioma

source_name: Ovary

tag: tissue


title: SAMPLE 272 PE

description: Patient endometrium

tag: age


title: SAMPLE 271 DiEIn

tag: disease stage


title: SAMPLE 270 PP

description: Patient peritoneum

source_name: Peritoneum

tag: cycle phase


title: SAMPLE 273 SuL

description: Sacrouterine ligament lesion

source_name: Sacrouterine ligament


title: SAMPLE 266 DiEIn


title: SAMPLE 269 REV

description: Rectovaginal lesion


title: SAMPLE 268 DiEIn


title: SAMPLE 267 OMA

description: Ovarian endometrioma


title: EndoPanc16_Nsp

description:
PET22_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET22 tissues

tag: Tumour lesion of PET22 tissues


title: SAMPLE 289 PeLW

description: Peritoneal endometriosis white lesion

source_name: Peritoneal


title: SAMPLE 286 PE

description: Patient endometrium


title: EndoPanc13_Nsp

description:
PET24_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET24 tissues

tag: Non-neoplastic lesion of PET24 tissues


title: EndoPanc4_Nsp

description:
PET16_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET16 tissues

tag: Tumour lesion of PET16 tissues


title: SAMPLE 265 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 264 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 260 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 261 CE

description: Control endometrium


title: SAMPLE 258 PE

description: Patient endometrium


title: SAMPLE 274 PE

description: Patient endometrium


title: SAMPLE 256 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 257 DiEIn

description: Deep infiltrating endometriosis lesion intestine


title: SAMPLE 254 CE Replicate

description: Control endometrium


title: SAMPLE 254 CE

description: Control endometrium


title: SAMPLE 255 OMA

description: Ovarian endometrioma


title: SAMPLE 252 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 259 OMA

description: Ovarian endometrioma


title: SAMPLE 253 CP

description: Control peritoneum


title: SAMPLE 251 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 249 PeLR

description: Peritoneal endometriosis red lesion


title: EndoPanc7_Nsp

description:
PET25_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET25 tissues

tag: Non-neoplastic lesion of PET25 tissues


title: SAMPLE 248 REV

description: Rectovaginal lesion

source_name: Rectovaginal septum


title: SAMPLE 246 PE

description: Patient endometrium


title: SAMPLE 250 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 247 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 245 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 243 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 244 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 242 PE

description: Patient endometrium


title: SAMPLE 240 PE

description: Patient endometrium


title: SAMPLE 239 CP

description: Control peritoneum


title: SAMPLE 236 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 235 PE

description: Patient endometrium


title: SAMPLE 237 CP

description: Control peritoneum


title: SAMPLE 263 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 234 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 238 CP

description: Control peritoneum


title: SAMPLE 231 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 233 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 230 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 229 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 227 CP

description: Control peritoneum


title: SAMPLE 228 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 224 PE

description: Patient endometrium


title: SAMPLE 226 CP

description: Control peritoneum


title: SAMPLE 223 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 225 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 222 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 221 REV

description: Rectovaginal lesion


title: SAMPLE 220 CE Replicate

description: Control endometrium


title: SAMPLE 220 CE

description: Control endometrium


title: SAMPLE 232 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 218 DiEIn


title: SAMPLE 217 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 215 PE

description: Patient endometrium


title: SAMPLE 216 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 213 PP

description: Patient peritoneum


title: SAMPLE 219 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 211 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 208 REV

description: Rectovaginal lesion


title: SAMPLE 207 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 206 CE

description: Control endometrium


title: SAMPLE 205 PE

description: Patient endometrium


title: SAMPLE 241 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 203 PE

description: Patient endometrium


title: SAMPLE 202 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 204 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 209 PE

description: Patient endometrium


title: SAMPLE 199 PP

description: Patient peritoneum


title: SAMPLE 201 CE

description: Control endometrium


title: SAMPLE 200 PE

description: Patient endometrium


title: SAMPLE 214 PE

description: Patient endometrium


title: SAMPLE 198 DiEIn


title: SAMPLE 212 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 197 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 210 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 193 PE

description: Patient endometrium


title: SAMPLE 194 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 195 REV

description: Rectovaginal lesion


title: SAMPLE 192 REV

description: Rectovaginal lesion


title: SAMPLE 189 PeLW

description: Peritoneal endometriosis white lesion


title: EndoPanc14_Nsp

description:
PET24_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET24 tissues

tag: Tumour lesion of PET24 tissues


title: SAMPLE 188 CE

description: Control endometrium


title: SAMPLE 277 PE

description: Patient endometrium


title: SAMPLE 187 PeLR

description: Peritoneal endometriosis red lesion


title: EndoPanc22_Nsp

description:
PET21_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET21 tissues

tag: Tumour lesion of PET21 tissues


title: SAMPLE 185 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 182 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 292 CP

description: Control peritoneum


title: SAMPLE 181 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 180 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 179 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 178 DiEIn


title: EndoPanc12_Nsp

description:
PET17_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET17 tissues

tag: Tumour lesion of PET17 tissues


title: SAMPLE 176 PE

description: Patient endometrium


title: SAMPLE 177 REV

description: Rectovaginal lesion


title: SAMPLE 175 PeLW

description: Peritoneal endometriosis white lesion


title: EndoPanc2_Nsp

description:
PET28_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET28 tissues

tag: Tumour lesion of PET28 tissues


title: SAMPLE 196 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 174 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 190 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 173 PeLB

description: Peritoneal endometriosis black lesion


title: EndoPanc1_Nsp

description:
PET28_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET28 tissues

tag: Non-neoplastic lesion of PET28 tissues


title: SAMPLE 184 DiEIn


title: SAMPLE 172 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 191 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 186 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 168 REV

description: Rectovaginal lesion


title: SAMPLE 170 CP

description: Control peritoneum


title: SAMPLE 167 PE

description: Patient endometrium

source_name: Endometrium


title: SAMPLE 166 REV

description: Rectovaginal lesion


title: SAMPLE 169 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 164 REV

description: Rectovaginal lesion


title: SAMPLE 165 PeLR

description: Peritoneal endometriosis red lesion


title: EndoPanc6_Nsp

description:
PET6_tumour_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET6 tissues

tag: Tumour lesion of PET6 tissues


title: SAMPLE 262 CE

description: Control endometrium


title: SAMPLE 162 OMA

description: Ovarian endometrioma


title: SAMPLE 163 PE

description: Patient endometrium


title: SAMPLE 161 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 157 PE

description: Patient endometrium


title: EndoPanc15_Nsp

description:
PET22_ref_Nsp
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET22 tissues

tag: Non-neoplastic lesion of PET22 tissues


title: SAMPLE 158 OMA

description: Ovarian endometrioma

source_name: Ovary


title: SAMPLE 159 DiEIn

source_name: Intestine


title: SAMPLE 155 OMA

description: Ovarian endometrioma


title: SAMPLE 154 DiEB

description: Deep infiltrating endometriosis lesion bladder

source_name: bladder


title: SAMPLE 153 SuL

description: Sacrouterine ligament lesion

source_name: Sacrouterine ligament


title: SAMPLE 151 PE

description: Patient endometrium


title: SAMPLE 171 PeLW

description: Peritoneal endometriosis white lesion

source_name: Peritoneal


title: SAMPLE 150 DiEB


title: SAMPLE 148 REV

description: Rectovaginal lesion


title: SAMPLE 149 PP

description: Patient peritoneum

source_name: Peritoneum


title: SAMPLE 147 OMA

description: Ovarian endometrioma


title: SAMPLE 152 OMA

description: Ovarian endometrioma


title: SAMPLE 156 CE

description: Control endometrium


title: SAMPLE 145 CE

description: Control endometrium


title: SAMPLE 142 CP

description: Control peritoneum


title: SAMPLE 160 CE

description: Control endometrium


title: SAMPLE 143 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 141 CP

description: Control peritoneum


title: SAMPLE 140 PE

description: Patient endometrium


title: SAMPLE 136 REV

description: Rectovaginal lesion


title: SAMPLE 139 PE

description: Patient endometrium


title: SAMPLE 137 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 138 CP

description: Control peritoneum


title: SAMPLE 134 OMA

description: Ovarian endometrioma


title: SAMPLE 133 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 135 DiEIn


title: SAMPLE 132 CP

description: Control peritoneum


title: SAMPLE 144 REV

description: Rectovaginal lesion


title: SAMPLE 130 PE

description: Patient endometrium


title: SAMPLE 125 CE

description: Control endometrium


title: SAMPLE 127 PE

description: Patient endometrium


title: SAMPLE 128 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 129 REV

description: Rectovaginal lesion


title: SAMPLE 124 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 121 CE

description: Control endometrium


title: SAMPLE 146 DiEIn


title: SAMPLE 121 CE Replicate

description: Control endometrium


title: SAMPLE 123 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 116 PP

description: Patient peritoneum


title: SAMPLE 119 PP

description: Patient peritoneum


title: SAMPLE 112 PP

description: Patient peritoneum


title: SAMPLE 113 CE

description: Control endometrium


title: SAMPLE 115 REV

description: Rectovaginal lesion


title: SAMPLE 114 OMA

description: Ovarian endometrioma


title: SAMPLE 117 CE

description: Control endometrium


title: SAMPLE 111 REV

description: Rectovaginal lesion


title: SAMPLE 131 PE

description: Patient endometrium


title: SAMPLE 110 CE

description: Control endometrium

value: No disease


title: SAMPLE 107 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 109 PP

description: Patient peritoneum


title: SAMPLE 108 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 104 PE

description: Patient endometrium


title: SAMPLE 126 CP

description: Control peritoneum


title: SAMPLE 105 DiEIn


title: SAMPLE 106 CE

description: Control endometrium


title: SAMPLE 101 PP

description: Patient peritoneum


title: SAMPLE 120 PE

description: Patient endometrium


title: SAMPLE 103 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 99 PE

description: Patient endometrium


title: SAMPLE 98 CE

description: Control endometrium


title: SAMPLE 102 DiEIn


title: SAMPLE 97 REV

description: Rectovaginal lesion


title: SAMPLE 100 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 95 OMA

description: Ovarian endometrioma


title: SAMPLE 118 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 122 PE

description: Patient endometrium


title: SAMPLE 90 CE

description: Control endometrium


title: SAMPLE 94 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 93 OMA

description: Ovarian endometrioma


title: SAMPLE 92 PE

description: Patient endometrium


title: SAMPLE 91 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 89 PE

description: Patient endometrium


title: SAMPLE 88 OMA

description: Ovarian endometrioma


title: SAMPLE 87 CE

description: Control endometrium


title: SAMPLE 86 DiEIn


title: SAMPLE 85 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 83 REV

description: Rectovaginal lesion


title: SAMPLE 82 PE

description: Patient endometrium


title: SAMPLE 79 PP

description: Patient peritoneum


title: SAMPLE 84 OMA

description: Ovarian endometrioma


title: SAMPLE 81 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 80 CE

description: Control endometrium


title: SAMPLE 77 PE

description: Patient endometrium


title: SAMPLE 78 PE

description: Patient endometrium


title: SAMPLE 75 DiEIn


title: SAMPLE 76 OMA

description: Ovarian endometrioma


title: SAMPLE 74 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 71 DiEIn


title: SAMPLE 73 PE

description: Patient endometrium


title: SAMPLE 96 DiEIn


title: SAMPLE 70 PE

description: Patient endometrium


title: SAMPLE 72 PP

description: Patient peritoneum


title: SAMPLE 69 OMA

description: Ovarian endometrioma


title: SAMPLE 68 PE

description: Patient endometrium


title: SAMPLE 66 PP

description: Patient peritoneum


title: SAMPLE 65 PE

description: Patient endometrium


title: SAMPLE 64 PE

description: Patient endometrium


title: SAMPLE 62 PP

description: Patient peritoneum


title: SAMPLE 60 DiEIn


title: SAMPLE 67 CP

description: Control peritoneum


title: SAMPLE 59 SuL

description: Sacrouterine ligament lesion


title: SAMPLE 58 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 56 CE

description: Control endometrium


title: SAMPLE 57 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 54 PE

description: Patient endometrium


title: SAMPLE 52 DiEIn


title: SAMPLE 53 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 55 CE

description: Control endometrium


title: SAMPLE 51 CE

description: Control endometrium


title: SAMPLE 50 PP

description: Patient peritoneum


title: SAMPLE 49 CE

description: Control endometrium


title: SAMPLE 47 CE

description: Control endometrium


title: SAMPLE 48 PE

description: Patient endometrium


title: SAMPLE 45 CE

description: Control endometrium


title: SAMPLE 44 CP

description: Control peritoneum


title: SAMPLE 46 PP

description: Patient peritoneum


title: SAMPLE 43 PP

description: Patient peritoneum


title: SAMPLE 42 PE

description: Patient endometrium


title: SAMPLE 39 CE

description: Control endometrium


title: SAMPLE 61 PE

description: Patient endometrium


title: SAMPLE 40 CE

description: Control endometrium


title: SAMPLE 63 PP

description: Patient peritoneum


title: SAMPLE 37 PP

description: Patient peritoneum


title: SAMPLE 36 PE

description: Patient endometrium


title: SAMPLE 33 PE

description: Patient endometrium


title: SAMPLE 35 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 38 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 34 PP

description: Patient peritoneum


title: SAMPLE 32 CE

description: Control endometrium


title: SAMPLE 27 PE

description: Patient endometrium


title: SAMPLE 31 CP

description: Control peritoneum


title: SAMPLE 26 CE

description: Control endometrium


title: SAMPLE 30 OMA

description: Ovarian endometrioma


title: SAMPLE 25 CP

description: Control peritoneum


title: SAMPLE 23 DiEIn


title: SAMPLE 41 PE

description: Patient endometrium


title: SAMPLE 20 CE

description: Control endometrium


title: SAMPLE 22 PeLB

description: Peritoneal endometriosis black lesion


title: SAMPLE 18 OMA

description: Ovarian endometrioma


title: SAMPLE 19 CP

description: Control peritoneum


title: SAMPLE 21 PE

description: Patient endometrium


title: SAMPLE 17 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 24 PP

description: Patient peritoneum


title: SAMPLE 16 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 15 CE

description: Control endometrium


title: SAMPLE 12 CP

description: Control peritoneum


title: SAMPLE 14 PE

description: Patient endometrium


title: SAMPLE 11 REV

description: Rectovaginal lesion


title: SAMPLE 32 CE Replicate

description: Control endometrium


title: SAMPLE 9 DiEIn


title: SAMPLE 6 CP

description: Control peritoneum


title: SAMPLE 7 PP

description: Patient peritoneum


title: SAMPLE 28 REV

description: Rectovaginal lesion


title: SAMPLE 5 REV

description: Rectovaginal lesion


title: SAMPLE 29 PeLR

description: Peritoneal endometriosis red lesion


title: SAMPLE 2 PP

description: Patient peritoneum


title: SAMPLE 3 PE

description: Patient endometrium


title: SAMPLE 1 OMA

description: Ovarian endometrioma


title: SAMPLE 4 DiEIn


title: SAMPLE 183 OMA

description: Ovarian endometrioma


title: SAMPLE 13 PP

description: Patient peritoneum


title: SAMPLE 10 OMA

description: Ovarian endometrioma


title: SAMPLE 8 PE

description: Patient endometrium


title: 8mon_br_wt

city: Stony Brook

first: Shao-Jun

last: Tang

state: New York

address: 101 Nicolls Road

institute: Renaissance School of Medicine at Stony Brook University

data_processing:
Illumina OLB software was used for basecalling
Sequences were processed using the Drop-seq toolkit. Briefly, adaptor sequences and poly-A tails were trimmed
Processed reads were mapped to mm10 genome using Drop-seq_tools v1.12 and STAR v 2.5
Gene expression of each cell was summarized in a gene expresison matrix generated by DigitalExpression, with parameter NUM_CORE_BARCODES=10000
Genome_build: mm10
Supplementary_files_format_and_content: Digital Expression matrix/counts

source_name: brain cortex

extract_protocol:
Brain cortex and whole spinal cord tissue were removed. Tissue was processed using papain and was slowly triturated and filtered using 70μm strainer. Microglia were enriched using density centrifugation. Briefly, A 4mL desnity gradient was prepared in a 15m falcon tube. 6ML of cell suspension was added on top of the OptiPrep media and centrifuged at 800g for 30 minutes. The bottom fraction, enriched with Microglia, was collected, resuspended in HABG media.
Library cDNA was fragmented and amplified using a Nextera XT DNA Sample prep kit with three separate reactions of 600, 1200 and 1800 pg input cDNA. The libraries were pooled and purified twice using 0.7X volume of SPRIselect beads. The purified libraries were sequenced on the Illumina HiSeq 2500

value: brain cortex

tag: genotype

value: wt

value: 8 months


title: 4mon_br_wt

value: 4 months


title: 2mon_br_gp120

value: 2 months


title: 4mon_sp_gp120

source_name: Whole spine

value: Whole spine


title: 2mon_sp_gp120


title: 4mon_br_gp120


title: 2mon_sp_wt


title: 8mon_br_gp120


title: scRNAseq_d2_EpiLC

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

data_processing:
The 10x Genomics scRNA-seq data was generated across different stages of PGCLC differentiation and can be easily explored by opening the cloupe file with the Loupe Cell Browser (https://www.10xgenomics.com). UMIs were counted using NCBI:GCA_000001635.6 and cellranger-2.1.0103. The resulting UMI values were aggregated into a single matrix with default normalization (‘‘–normalize=mapped’’) (UMI_counts).
Genome_build: mm10
Supplementary_files_format_and_content: UMI_counts;cloupe_file

source_name: epiblast-like cells

growth_protocol: ESC were cultured on gelatin-coated plates using Knock-out DMEM supplemented with 15% FBS and LIF. Before each PGCLC differentiation, ESC were adapted to 2i+LIF media (serum-free N2B27 medium supplemented with MEK inhibitor PD0325901 [0.4 μM], GSK3β inhibitor CHIR99021 [3 μM], and LIF) for at least four days in gelatin-coated tissue culture plates. For the EpiLC differentiation, 6-well plates were coated with 15 µg ml-1 Fibronectin and 2 x 105 2i ESC were differentiated in N2B27 media supplemented with 20 ng ml-1 Activin A, 12 ng ml-1 bFGF and 10 µl ml-1 KSR for two days. For EpiSC differentiation, 2i ESC were plated at a density of 2.5 x 105 cells ml-1 on plates coated with 15 µg ml-1 Fibronectin and differentiated into EpiSC by passaging them in N2B27 media supplemented with 20 ng ml-1 Activin A and 12 ng ml-1 bFGF for at least eight days. For the PGCLC differentiation, d2 EpiLC were plated at a density of 2 x 104 cells ml-1 and cultured as embryoid bodies (EB) on Ultra-Low attachment multiwell plates (Corning® Costar®) in GK15 medium supplemented with growth factors (0.5 µg ml-1 BMP4, 0.1 µg ml-1 SCF, 1000 U ml-1 LIF and 50 ng ml-1 EGF, no BMP8a) for four days.

extract_protocol:
For single cell RNA sequencing, EpiSC were dissociated with Accutase and all other cell types with TripleExpress. Cells were then centrifuged and resuspended in PBS containing 0.04 % BSA. Next, cells were passed through a strainer, the cell concentration was determined and the single cell RNA sequencing libraries were prepared using the Chromium Single Cell Gene Expression (10x Genomics) according to the Single Cell 3’ Reagents Kit (v2 chemistry) protocol.
10x Genomics - Single Cell 3’ Reagents Kit (v2)

tag: cell line

value: d2 EpiLC

tag: strain

value: wild type


title: scRNAseq_d3_EpiLC

value: d3 EpiLC