title: T47D_D538G_clone2_E2_ChIPseq

value: 10 nM E2 1hr


title: BI16_89

status: Public on Apr 08 2020

type: SRA

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

country: USA

institute: University of California, Davis

library_source: transcriptomic

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0, B. cinerea ASM83294v1, F. acuminatum GGXD00000000, R. stolonifer GGWM00000000
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

molecule: total RNA

organism: Solanum lycopersicum

extract_protocol:
At 1 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, wounded, and infected fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as single-end 50-bp reads on an Illumina HiSeq 4000 platform by the DNA Technologies Core at the UC Davis Genome Center.

tag: genotype

value: rin

tag: ripening stage

value: MG-like

tag: treatment

value: Wounded

tag: tissue


title: T47D_D538G_clone1_E2_ChIPseq

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

library_source: genomic

data_processing:
Sequencing reads were aligned to the hg19 build of the human genome using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2.
MACS2 was used to call peaks with a p-value cutoff of 1*10-10 and a mfold parameter between 15 and 100. MACS2 also generated normalized bedgraphs.
Differential binding sites were identified by using DESeq2 to compare counts per million.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bedgraph files
Supplementary_files_format_and_content: narrowPeak files (from MACS2)

molecule: genomic DNA

organism: Homo sapiens

source_name: mammary gland ductal carcinoma

growth_protocol: WT and mutant T-47D cells were grown in RPMI 1640 media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1% penicillin-streptomycin (Thermo Fisher Scientific) (full media). MCF-7 WT and mutant cells were grown in Minimum Essential Media (MEM, Thermo Fisher Scientific) with 5% fetal bovine serum, 1% penicillin-streptomycin, 1x final concentration non-essential amino acids (NEAA, Thermo Fisher Scientific), and 1nM final concentration insulin (Sigma-Aldrich) (full media). Cells were grown at 37°C with 5% CO2. Five days before all experiments requiring a 17beta-estradiol (E2) induction, cells were placed in hormone-depleted media. Hormone-depleted media consisted of phenol-red free MEM (Thermo Fisher Scientific), 5% charcoal-stripped fetal bovine serum (Thermo Fisher Scientific), 1% penicillin-streptomycin, and NEAA and insulin as described above for MCF-7 cells and phenol-red free RPMI (Thermo Fisher Scientific), 10% charcoal-stripped fetal bovine serum, and 1% penicillin-streptomycin for T-47D cells. Hormone-depleted media was changed twice during each 5-day estrogen-deprivation period in order to ensure complete removal of estrogens from the media.

extract_protocol:
Fixation was performed by treating cells with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via cell scraping in Farnham lysis buffer supplemented with protease inhibitors.
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with either Anti-FLAG (Sigma-Aldrich M2) antibody that recognizes a FLAG tag on ESR1, Anti-CTCF (sc-5916, Santa Cruz Biotechnology), or Anti-OCT1 (A301-716A and A301-717A, Bethyl Laboratories Inc.) antibodies.

treatment_protocol: After 5 days of estrogen deprivation, cells were treated with 0.1% DMSO as a vehicle control (Fisher Scientific) or 10nM E2 (Sigma-Aldrich) for 1 hour.

tag: parental cell line

tag: esr1 genotype

tag: chip antibody

value: Anti-FLAG


title: in situ Hi-C 1

city: Shenzhen

first: Qing

last: Li

address: No 7,Pengfei Road,Dapeng District

country: China

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences,

data_processing:
Reads were quality filtered according to the Illumina pipeline
The reads mapping and filtering procedures were performed by HiC-Pro (v2.10.0) or HiCUP (v0.5.9).
Genome_build: mm9
Supplementary_files_format_and_content: The *_allValidPairs.txt file cotains uniquely mapped and non-redundent valid interactions. HiCPro_statics.xlsx cotains the mapping results and the noises distribution of different Hi-C libraries

organism: Mus musculus

source_name: mESC E14

growth_protocol: For mouse E14 embryonic stem cells (ATCC® CRL-1821™), they were cultured under the specific condition (KO-DMEM complete medium) in KO-DMEM (Invitrogen Life Technologies, 10829-018) supplemented with 15% fetal bovine serum (FBS, Invitrogen Life Technologies, 10099-141), 1% penicillin/streptomycin (GIBCO, 15140), 1% MEM nonessential amino acids (NEAA) (Invitrogen Life Technologies,  11140-122), 1% 2-Mercaptoethanol (BME) (Sigma, M-7522), 1% GlutaMAXTM (GIBCO, 35050061), 1‰ Vitamin C (L-ascorbicacid 2-phosphate, Sigma, A8960), 1 ‱ LIF (Chemicon, ESG-1107), 1 ‱ PD0325901 (Selleck), 3 ‱ CHIR-99021 (Selleck). Before the cells were thawed or passaged, firstly, 37°C warmed 0.1% gelatin was covered the bottom of the dish. Then, gelatin solution was removed and 0.5 million cells per 60 mm dish were seeded in the KO-DMEM complete medium. In subculture, the cell colony morphology, density, and size were initially observed. If average distribution of colonies were in size of 200–400 μm in diameter and space was around 400 μm apart in a 60-mm dish, the ESC cells would be split. After the cell clones were washed with 1 x DPBS (Invitrogen Life Technologies, 14190-144), the digestive enzyme Accutase (Invitrogen Life Technologies, A1110501) instead of trypsin was used.

extract_protocol:
Confluence of the cell should be around (80-90%).  Add HCHO to 1% the plate (280ul 37% HCHO to 10 ml medium) and incubate at 37°C for 10 min; Stop the cross linking by adding 0.89 ml 2.5M glycine to medium (final concentration 0.2M) at RT for 5 mins, aspirate the medium. Wash the cells twice with 10 ml of 1xPBS.Aspirate the buffer (keep 0.5 ml in the plate). Harvest cells by scraping. Wash the plate once with 0.5% BSA/PBS. Combine the cells from the plates. Spin down the cells at 500-1000g, 5 min, 4℃.
Following the proximity-ligation and linear noise elimination(exonuclease combination treatment), the chromosome conformation capture library was used for sonication and immunomagnetic interaction capturing of biotin labeled joint DNA. Hi-C library was submitting for next-generation sequencing.
Dilution Hi-C and in situ Hi-C

treatment_protocol: MEFs were isolated from E13.5 embryos carrying the Oct4-GFP transgene. “Flag/Jmjd3 treating day3” means MEFs transduced with the virus of Flag/Jmjd3 and OSKM, after cultured in mES medium including Vc for 3 days, cells were cross-linked with 2% formaldehyde for 10 min at room temperature and quenched by glycine at a final concentration of 0.125 M. Then, they were conducted with Hi-C library construction.

tag: cell type

value: Mouse embryonic stem cell

value: Wild type

tag: Stage

value: 0 day


title: LIC-in situ Hi-C 6


title: T47D_Y537S_clone2_E2_ChIPseq


title: Veh_2wk_4L

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: experiment: JQ1+palbociclib in vivo

data_processing:
Remove 3' adapter and discard reads shorter than 30 bp using fastx_clipper
Filter for reads matching the barcode pattern (alternating A/T and C/G) and with a Phred quality score of at least 10 for all base pairs and an average Phred score of 30
Genome_build: N/A
Supplementary_files_format_and_content: TSV files contain unique barcode sequences with corresponding number of reads.

source_name: breast cancer cells SUM159

growth_protocol: Cells were lentivirally infected with the ClonTracer barcode library (Bhang et al., 2015). Barcoded cells were passaged in vitro in the presence of drug or injected orthotopically into mammary fat pads of NOG mice to produce xenografts.

extract_protocol:
DNA was extracted from frozen cultured cells and xenografts using the AllPrep DNA/RNA Mini Kit or the QIAamp DNA Mini Kit (Qiagen).
PCR was used to amplify barcodes and introduce Illumina adaptors along with a 5 bp index sequence for multiplexing as described (Bhang et al., 2015). 2 µg of genomic DNA was used as template, and 15-16 samples were multiplexed. PCR products were run on 0.8% agarose NGS E-Gels (Invitrogen) to verify the correct library size, and bands were purified using the MinElute Gel Extraction Kit (Qiagen).

treatment_protocol: Cells were grown in vitro in the presence of DMSO, JQ1 (100 nM), paclitaxel (0.6 nM), palbociclib (160 nM), JQ1+paclitaxel, or JQ1+palbociclib, in triplicates, for up to 18 passages. Mice were treated for up to 2 weeks with vehicle, JQ1 (30-50 mg/kg daily), palbociclib (75 mg/kg daily), paclitaxel (10 mg/kg twice weekly), JQ1+palbociclib, or JQ1+paclitaxel, with 5 mice per group.

tag: cell line

tag: time point

value: 2 wk

tag: replicate


title: T47D_Y537S_clone1_E2_ChIPseq


title: BI16_65

value: fruit pericarp and epidermal tissue of the blossom end halves


title: T47D_WT_clone2_E2_ChIPseq

value: WT


title: Pre_0wk_2

description: experiment: JQ1+paclitaxel in vivo

value: pre-treatment

value: 0 wk


title: T47D_WT_clone1_E2_ChIPseq


title: BI16_41


title: Veh_2wk_2L

description: experiment: JQ1+palbociclib in vivo


title: T47D_D538G_clone2_DMSO_ChIPseq

value: 0.1% DMSO 1hr


title: LIC-in situ Hi-C 4


title: BI16_113


title: IIIIC-in situ Hi-C 6


title: Veh_2wk_1R

description: experiment: JQ1+palbociclib in vivo


title: Pal_2wk_3R

description: experiment: JQ1+palbociclib in vivo

value: palbociclib


title: BI16_6

value: RR-like

value: Healthy


title: T47D_Y537S_clone2_DMSO_ChIPseq


title: Pal_2wk_4L

description: experiment: JQ1+palbociclib in vivo


title: LRC-Hi-C 4


title: Pal_2wk_2L

description: experiment: JQ1+palbociclib in vivo


title: Veh_2wk_3R

description: experiment: JQ1+palbociclib in vivo


title: LRC-Hi-C 3


title: BI16_24


title: T47D_D538G_clone1_DMSO_ChIPseq


title: Pre_0wk_1

description: experiment: JQ1+paclitaxel in vivo


title: IIIIC-in situ Hi-C 4


title: LIC-in situ Hi-C 5


title: Pal_2wk_1R

description: experiment: JQ1+palbociclib in vivo


title: T47D_Y537S_clone1_DMSO_ChIPseq


title: BI16_34


title: LRC-Hi-C 2


title: BI16_58


title: JQ1_2wk_4L

description: experiment: JQ1+palbociclib in vivo


title: Hi-C 3


title: JQ1_2wk_3R

description: experiment: JQ1+palbociclib in vivo


title: T47D_WT_clone2_DMSO_ChIPseq


title: MCF7_WT_clone2_E2_25day_RNAseq

description: processed data file: MCF7_ESR1_WT_and_mutant_RNAseq_allsets_raw_counts.txt

data_processing:
Reads were aligned to the human genome using HISAT2.
Sam files were then converted to bam files and sorted via Samtools.
Read counts for each gene were determined from alignments to hg19 UCSC knownGene gene models using featuresCounts from the SubRead package.
Normalization and differential expression analysis were performed using DeSeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Gene counts in text files.

source_name: mammary gland adenocarcinoma

extract_protocol:
Cells were harvested from 100mm dishes in 600mL RLT Plus (Qiagen) supplemented with 1% beta-mercaptoethanol after the induction with 10nM E2 or DMSO. RNA purification was performed using RNA Clean and Concentrator (Zymo Research) with the optional DNase I treatment.
The KAPA Stranded mRNA-seq kit (Kapa Biosystems) was used to create Poly(A) selected libraries from 500ng total RNA.

treatment_protocol: After 5 days of estrogen deprivation, cells were treated with 0.1% DMSO as a vehicle control (Fisher Scientific) or 10nM E2 (Sigma-Aldrich) for 8 hours. For the prolonged E2 treatment RNA-seq experiments, cells from T-47D and MCF-7 WT clones were grown in 100mm dishes in hormone-depleted media and were treated with 10nM E2 for 5, 10, 15, 20, or 25 days. E2 was added with media changes every 2 days to maintain E2 levels.

value: 10 nM E2 25 day


title: Hi-C 2


title: BI16_92

value: nor


title: MCF7_WT_clone2_E2_20day_RNAseq

value: 10 nM E2 20 day


title: JQ1_2wk_1R

description: experiment: JQ1+palbociclib in vivo


title: BI16_68

value: Wounded


title: IIIIC-in situ Hi-C 5


title: Hi-C 1


title: BI16_5

value: rin

value: MG-like


title: T47D_WT_clone1_DMSO_ChIPseq

value: Anti-FLAG


title: BI16_44


title: Elmsan1KO2_E2G7_rep2

city: Memphis

first: Hans-Martin

last: Herz

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were generated and mapped against mouse genome assembly NCBIM37.67 using the StrongArm pipeline described previously (Wu et al., 2016). Gene level quantification values were obtained with HT-seq based on the GENCODE annotation (vM20) and normalized by the TMM method with edgeR (version 3.16.5). Differential expression analysis was performed with the voom method applying the limma pipeline in R (version 3.3.1). Significantly up- and down- regulated genes were defined by at least a 1.5 fold change in gene expression and a p-value < 0.01. Reactome and gene set enrichment analysis (GSEA) were carried out using GSEA or EnrichR, respectively. Gene expression log2 CPM (counts per million) values were computed for heatmap and box plot visualization. Log2 FPKM gene expression values were applied for bar plot diagrams.
Genome_build: mm9

source_name: embryonic stem cells

growth_protocol: mESCs were grown in chemically defined 2iL medium (defined naïve culture conditions): 50% DMEM/F-12; 50% Neurobasal Medium (no L-glutamine); B-27 Supplement, minus vitamin A (1:100); N-2 Supplement (1:200); 2 mM L-Glutamine or GlutaMAX (1:100); 0.1 mM β-Mercaptoethanol (1:500); 3 µM CHIR 99021 (GSK3β inhibitor) (1:1000 from 3 mM stock in DMSO); 1 µM PD 0325901 (MEK inhibitor) (1:1000 from 1 mM stock in DMSO); 1000 U/ml LIF (1:10,000 from 107 U/ml stock); 50 U/ml Pen/Strep (1:100).

extract_protocol:
RNA was isolated from 3 x 10e6 cells with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer’s instructions with the following alterations. Cells were resuspended in 600 μl RLT buffer (with 2-Mercaptoethanol) and the homogenate further passed through a QiaShredder column (Qiagen, 79656) by centrifugation in a table top centrifuge for 2 minutes at full speed at room temperature (RT). The optional step after the second wash with RPE buffer was applied to dry the membrane. RNA was eluted with 85 μl H2O and supplied with 10 μl 10x DNAase buffer and 5 μl DNAse I (NEB, M0303S), mixed and incubated at RT for 20 min. After incubation RNA was purified by following the “RNA Cleanup” protocol in the RNeasy Mini Handbook. The optional step after the second wash with RPE buffer was applied to dry the membrane. RNA was eluted in 50 μl H2O and concentration determined with a NanoDrop 8000 Spectrophotometer.
RNA-seq Library Preparation and Sequencing:RNA was quantified using the Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific, R11490) and quality checked with the RNA 6000 Nano Kit (Agilent, 5067-1511) on a 2100 Bioanalyzer (Agilent, G2939BA) or High Sensitivity RNA ScreenTape Assay (Agilent, 5067-5579, 5067-5580, 5067-5581) on a 4200 TapeStation (Agilent, G2991AA) prior to library generation. Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, 20020599) according to the manufacturer’s instructions. Libraries were analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067-4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067-5584, 5067-5585, 5067-5587, 5067-5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Paired end 100 cycle sequencing was performed on a HiSeq 2500, HiSeq 4000, or NovaSeq 6000 System (all from Illumina) according to the manufacturer’s instructions.

value: Elmsan1 KO2 (E2G7)

value: embryonic stem cells

tag: ID


title: BI16_57

value: fruit pericarp and epidermal tissue of the blossom end halves


title: BI16_33


title: JQ1Pal_2wk_4L

description: experiment: JQ1+palbociclib in vivo

value: vehicle

value: 2 wk


title: Elmsan1KO2_E2G7_rep1


title: BI16_14


title: MCF7_WT_clone2_E2_15day_RNAseq

value: WT

value: 10 nM E2 15 day


title: MCF7_WT_clone2_E2_10day_RNAseq

value: 10 nM E2 10 day


title: JQ1Pal_2wk_3R

description: experiment: JQ1+palbociclib in vivo


title: MCF7_WT_clone2_E2_5day_RNAseq

value: 10 nM E2 5 day


title: Elmsan1KO1_E2E8_rep2

value: Elmsan1 KO1 (E2E8)


title: BI16_91


title: MCF7_WT_clone1_E2_25day_RNAseq

value: 10 nM E2 25 day


title: BI16_67

value: nor


title: MCF7_WT_clone1_E2_20day_RNAseq

value: 10 nM E2 20 day


title: Dnttip1KO2_D1E6_rep2

value: Dnttip1 KO2 (D1E6)


title: JQ1Pal_2wk_2L

description: experiment: JQ1+palbociclib in vivo


title: Elmsan1KO1_E2E8_rep1


title: JQ1_2wk_2L

description: experiment: JQ1+palbociclib in vivo


title: BI16_43

value: Wounded


title: MCF7_WT_clone1_E2_15day_RNAseq


title: BI16_13

value: MG-like


title: MCF7_WT_clone1_E2_10day_RNAseq


title: Dnttip1KO1_D2A7_rep2

value: Dnttip1 KO1 (D2A7)


title: Dnttip1KO2_D1E6_rep1


title: H3K36me2_EZH2i_qChIP-seq_rep2

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

data_processing:
Illumina RTAv2 software was used for basecalling
Raw reads trimmed using Trim Galore! (Galaxy version 0.4.2) to remove low-quality reads and adaptor sequence.
Libraries were mapped to the mm10 genome assembly using Bowtie2 (Galaxy version 2.2.6.2).
Duplicates and reads mapping to the Broad Institute's blacklist (Encode Project Consortium, 2012) were discarded. Remaining reads were extended by 250 bp for peak calling and downstream analyses.
Peak calling was done using SICERPeak calls were created with SICER (Zang et al., 2009) using redundancy threshold = 1, window size = 500, fragment size = 250, e˙ective genome fraction = 0.79, gap size = 1500 and an FDR threshold of 0.01. Input samples were used in peak calling to assess background and to determine true signal from IP enrichment.
Genome_build: mm10 and dm3
Supplementary_files_format_and_content: Bedgraph files contain corrected either RPM, n+1, log-transformed read counts for ChIP-seq datasets or RRPM, n+1, log-transformed read counts for qChIP-seq datasets from 1 kb windows with a 500 bp step.
Supplementary_files_format_and_content: Peak files include the mm10 coordinates for all peaks used in this study

source_name: E14 mESCs cells

growth_protocol: E14 mESCs were cultured at 37ºC and 5% CO2 on gelatin-coated plates in 2i/LIF medium (2i custom made medium (Thermo Fisher)) supplemented with Pen-Strep (Gibco), 2mM Glutamax (Gibco), 50µ β-mercaptoethanol (Gibco), 0.1mM nonessential amino acids (Gibco), 1mM sodium pyruvate (Gibco), N2+B27 (Thermo Fisher), GSK3i (CHIR99021), MEKi (PD0325901), Leukemia Inhibitor Factor (LIF; produced in Kristian Helin laboratory). Medium was supplemented with light, medium or heavy arginine and lysine (R0 Arginine hydrochloride (Sigma A6969), R6 Arginine 13C6 (CNLM-2265-H1), R10 Arginine 13C6 15N4 (CNLM-539-H1), K0 Lysine hydrochloride (Sigma L8662), K4 Lysine 4,4,5,5- d4 (DLM-2640-1 1gram), K8 Lysine 13C6 15N2 (CNLM-291-H-1 1gram) Cambridge isotope). Asynchronous Drosophila S2-DRSC cells were grown in suspension in spinners in M3+BPYE (Sigma-Aldrich) media with 10% HI-FBS and penicillin and streptomycin at 25ºC as described in Drosophila Genomics Resource Center.

extract_protocol:
Cells were processed using the truChIP Chromatin Shearing Kit (Covaris, 520127) following manufacturer’s instructions. 20 million nuclei were sonicated in 1mL tubes using a Covaris M220 to obtain chromatin frgament size of 250-500bp. Sonicated chromatin was centrifuged at 14,000 rpm at 4ºC for 10 minutes and the supernatant was isolated for subsequent steps. In parallel, Drosophila S2 cells were ﬁxed, lysed and sonicated as described above. For quantitative ChIP analysis E14 mESC input chromatin was mixed with Drosophila S2 chromatin (0.05% of total chromatin) after sonication. Chromatin associated to each histone mark was obtained by incubating sonicated chromatin with the corresponding antibody.
Libraries were costructed using the KAPA Hyperprep kit following manufacturer’s instruction, except that 1.25 µM of Illumina compatible indexed adapters (Pentabase) were ligated to A-tailed DNA.

treatment_protocol: When indicated, E14 mESCs were treated with 10µM of EPZ6438 EZH2 inhibitor (MedChem Express) or equivalent volume of DMSO for 7 days

value: EZH2 inhibitor (EPZ-6438)

tag: spike-in

value: YES

tag: antibody

value: H3K36me2:Abcam mAb #176921


title: H3K36me2_DMSO_qChIP-seq_rep2

value: DMSO


title: H3K36me2_EZH2i_qChIP-seq_rep1


title: Dnttip1KO1_D2A7_rep1

value: embryonic stem cells


title: H3K36me2_DMSO_qChIP-seq_rep1

value: H3K36me2:AbCam mAb #176921


title: MCF7_D538G_clone2_E2_RNAseq

value: 10 nM E2 8hr


title: MCF7_WT_clone1_E2_5day_RNAseq

value: WT


title: WT_rep2


title: H3K27me3_EZH2i_qChIP-seq_rep2

value: H3K27me3:Cell Signaling mAb #9733


title: BI16_84

value: RR-like

value: Healthy

value: fruit pericarp and epidermal tissue of the blossom end halves


title: H3K27me3_EZH2i_qChIP-seq_rep1


title: BI16_108

value: nor


title: BI16_36


title: MCF7_D538G_clone1_E2_RNAseq


title: WT_rep1


title: JQ1Pal_2wk_1R

description: experiment: JQ1+palbociclib in vivo

value: vehicle

value: 2 wk


title: MCF7_Y537S_clone2_E2_RNAseq


title: BI16_7

value: MG-like


title: H3K27me3_DMSO_qChIP-seq_rep2


title: MCF7_Y537S_clone1_E2_RNAseq


title: H3K27me3_DMSO_qChIP-seq_rep1


title: Eight_HPI_5

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

description:
Rep5
Eight_HPI_5

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were mapped to pig reference mRNA using the Bowtie1 software
Using R version 3.4.2 software to find differential genes
The CLOVER software (Frith et al. 2004) with JASPAR PWM database (Khan et al. 2018) were used to identify over-represented transcription factor binding motifs for each cluster of genes.
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: Reads count (tab deli text)

organism: Sus scrofa

source_name: Neutrophil samples infected by Salmonella

extract_protocol:
Total RNA was prepared from the neutrophil solutions using the RNeasy Mini Kit as per manufacturer instructions (Qiagen, Cat. no. 74104). The RNA quantity and quality were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with an RNA Integrity Number (RIN) < 7 or a yield < 10 μg were excluded from the experiment.
Sequencing libraries were prepared using the Illumina TruSeq RNA Sample Preparation kit according to the manufacturer protocol (Illumina Inc., USA).

value: Neutrophils

tag: infection

value: eight-hours post infection (hpi)

tag: breed

value: healthy crossbreed (Duroc x Landrace x Yorkshire)


title: Eight_HPI_6

description:
Rep6
Eight_HPI_6


title: BI16_59

tag: genotype


title: MCF7_WT_clone2_E2_RNAseq


title: BI16_35

tag: ripening stage


title: Eight_HPI_4

description:
Rep4
Eight_HPI_4


title: H3K36me3_ChIP-seq_rep2

tag: treatment

value: Non treated

value: NO

value: H3K36me3:Abcam pAb #9050


title: BI16_60

tag: tissue


title: MCF7_WT_clone1_E2_RNAseq

tag: parental cell line


title: BI16_107


title: H3K36me3_ChIP-seq_rep1


title: Eight_HPI_3

description:
Rep3
Eight_HPI_3


title: MCF7_D538G_clone2_DMSO_RNAseq

tag: esr1 genotype

value: 0.1% DMSO 8hr


title: MCF7_D538G_clone1_DMSO_RNAseq


title: H3K36me2_ChIP-seq_rep2

value: H3K36me2:Abcam mAb #176921


title: H3K36me2_ChIP-seq_rep1


title: BI16_64

value: Cnr

value: Wounded


title: MCF7_Y537S_clone2_DMSO_RNAseq


title: MCF7_Y537S_clone1_DMSO_RNAseq


title: Eight_HPI_2

description:
Rep2
Eight_HPI_2


title: BI16_88

value: RR-like


title: H3K27me3_ChIP-seq_rep2

value: H3K27me3:Cell Signaling mAb #9733


title: Zero_Hour_6

description:
Rep6
Zero_Hour_6

value: zero hour


title: H3K27me3_ChIP-seq_rep1


title: H3K27me2_ChIP-seq_rep2

value: H3K27me2:Cell Signalling mAb #9728


title: Zero_Hour_4

description:
Rep4
Zero_Hour_4


title: BI16_40

value: fruit pericarp and epidermal tissue of the blossom end halves


title: BI16_87


title: H3K27me2_ChIP-seq_rep1


title: Zero_Hour_5

description:
Rep5
Zero_Hour_5


title: MCF7_WT_clone2_DMSO_RNAseq

value: WT


title: H3K27me1_ChIP-seq_rep2

value: H3K27me1:Active Motif mAb #61015


title: T47D_WT_clone2_E2_20day_RNAseq

description: processed data file: T47D_ESR1_WT_and_mutant_RNAseq_allsets_raw_counts.txt

value: 10 nM E2 20 day


title: Zero_Hour_3

description:
Rep3
Zero_Hour_3

value: Neutrophils


title: Zero_Hour_2

description:
Rep2
Zero_Hour_2

value: healthy crossbreed (Duroc x Landrace x Yorkshire)


title: Eight_HPI_1

description:
Rep1
Eight_HPI_1

value: eight-hours post infection (hpi)


title: BI16_39

value: MG-like


title: BI16_63


title: BI16_112


title: T47D_WT_clone2_E2_25day_RNAseq

value: 10 nM E2 25 day


title: Zero_Hour_1

description:
Rep1
Zero_Hour_1


title: BI16_11


title: T47D_WT_clone2_E2_15day_RNAseq

value: 10 nM E2 15 day


title: H3K27me1_ChIP-seq_rep1

value: Non treated

value: NO


title: BI16_80

value: Cnr

value: Healthy


title: L2_B_S12_R1_001: Fbxl2 siRNA

city: Pittsburgh

first: Michael

middle: Emmet

last: O'Brien

state: PA

address: 200 Lothrop Street

department: Pulmonary, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

description: Timepoint: 48 h

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomics workbench (Qiagen).Genes with a mean raw count value < 10 were removed from further processing.
Differential gene expression was calculated with raw counts using DESeq2 in R Studio between the experimental groups using filters to select genes with an absolute fold change (FC) > 1.5 and a false discovery rate (FDR) P-value ≤ 0.05.
Genome_build: mm10

source_name: Myoblasts

growth_protocol: During myoblast proliferation, cells were supplemented daily with growth media (GM); DMEM with 10% FBS and 1% penicillin/streptomycin. Myogenic differentiation was induced when myoblasts reached 90-100% confluence by exchanging GM with differentiation media (DM), DMEM with 2% horse serum (Sigma) and 1% penicillin/streptomycin.

extract_protocol:
Total cellular RNA was collected from C2C12 cells using the RNeasy MiniKit (Qiagen). RNA integrity was determined with the Agilent 2100 Bioanalyzer prior to library preparation, RINs ranging from 9.7 to 10.0 were processed with an mRNA-Seq sample preparation kit (Illumina, Inc.; San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated cells were stimulated with TNF alpha (10ng/ml) for 48 hours during differentiation.

tag: strain

value: C2C12 cells

tag: passages


title: L2_C_S13_R1_001: Fbxl2 siRNA

description: Timepoint: 48 h

tag: cell type


title: T47D_WT_clone2_E2_5day_RNAseq

value: 10 nM E2 5 day


title: T47D_WT_clone2_E2_10day_RNAseq

value: 10 nM E2 10 day


title: T47D_WT_clone1_E2_25day_RNAseq


title: TNF_C_S17_R1_001: TNF alpha

description: Timepoint: 48 h


title: BI16_104

value: RR-like

value: fruit pericarp and epidermal tissue of the blossom end halves


title: MCF7_WT_clone1_DMSO_RNAseq

value: WT

value: 0.1% DMSO 8hr


title: BI16_4


title: L2_A_S2_R1_001: Fbxl2 siRNA

description: Timepoint: 48 h


title: T47D_WT_clone1_E2_20day_RNAseq

value: 10 nM E2 20 day


title: TNF_B_S16_R1_001: TNF alpha

description: Timepoint: 48 h


title: BI16_55


title: T47D_WT_clone1_E2_15day_RNAseq


title: TNF_A_S4_R1_001: TNF alpha

description: Timepoint: 48 h


title: T47D_WT_clone1_E2_10day_RNAseq


title: BI16_31


title: Con_C_S15_R1_001: Control

description: Timepoint: 48 h


title: Ler biological rep2

type: RNA

city: Bundoora, Melbourne

first: Song

middle: F

state: VIC

address: Kingsbury Dr

department: Botany

country: Australia

institute: La Trobe University

hyb_protocol: samples were hybridized to Affymetrix Arabidopsis

scan_protocol: scanned using the Genechip Scanner 3000

data_processing:
Microarray data were processed using the ArrayAssist 5.5.1 software provided by Stratagene
The Arabidopsis gene annotation data set was obtained from NetAffx
(Affymetrix) and GeneChip operating software was used to produce CEL files.
The normalized probe signals were obtained from CEL files using GeneSpringGX (RMA) (Agilent)

label: biotin

organism: Arabidopsis thaliana

source_name: wild-type Ler-7

label_protocol: biotin labeling of cRNA

growth_protocol: Developing seeds (globular to walking-stick stages) were isolated from the siliques

extract_protocol: RNAeasy plant kitr was used for RNA extraction

value: wild type Ler


title: Ler biological rep3

source_name: wild-type Ler-8

value: Developing seeds (globular to walking-stick stages)


title: Ler biological rep4

source_name: wild-type Ler-9


title: BI16_3

value: MG-like


title: BI16_56


title: T47D_WT_clone1_E2_5day_RNAseq


title: BI17_82

source_name: Ailsa Craig_RR_Wounded

value: Ailsa Craig

value: RR

value: Wounded


title: T47D_D538G_clone2_E2_RNAseq

value: 10 nM E2 8hr


title: ttg1 biological rep2

source_name: mutant ttg1-7

value: ttg1 mutant


title: Ler biological rep1

source_name: wild-type Ler-6


title: BI17_46


title: Con_A_S3_R1_001: Control

description: Timepoint: 48 h


title: ttg1 biological rep3

source_name: mutant ttg1-8


title: ttg1 biological rep1

source_name: mutant ttg1-6


title: T47D_D538G_clone1_E2_RNAseq


title: Day0_C_S11_R1_001: Proliferation (Day 0)

description: Timepoint: 0 h


title: T47D_Y537S_clone2_E2_RNAseq


title: BI17_118


title: BI16_28

organism:
Solanum lycopersicum
Botrytis cinerea

source_name: rin_RR-like_B. cinerea

value: rin

value: B. cinerea


title: BI16_20


title: T47D_Y537S_clone1_E2_RNAseq

source_name: mammary gland ductal carcinoma


title: BI16_86


title: T47D_WT_clone2_E2_RNAseq


title: BI17_10


title: BI16_122


title: T47D_WT_clone1_E2_RNAseq


title: Con_B_S14_R1_001: Control

description: Timepoint: 48 h

value: C2C12 cells


title: Day0_B_S10_R1_001: Proliferation (Day 0)

description: Timepoint: 0 h


title: BI16_62


title: BI16_49

source_name: rin_MG-like_B. cinerea


title: BI16_98


title: ttg1 biological rep4

source_name: mutant ttg1-9


title: T47D_D538G_clone2_DMSO_RNAseq


title: BI16_110


title: T47D_D538G_clone1_DMSO_RNAseq


title: BI16_121


title: Day0_A_S1_R1_001: Proliferation (Day 0)

description: Timepoint: 0 h


title: BI16_76

source_name: nor_RR-like_B. cinerea

value: nor


title: BI16_73


title: BI17_9

source_name: Ailsa Craig_MG_Wounded

value: MG


title: BI16_52

value: RR-like

value: fruit pericarp and epidermal tissue of the blossom end halves


title: BI16_124


title: T47D_Y537S_clone1_DMSO_RNAseq

value: 0.1% DMSO 8hr


title: T47D_WT_clone1_DMSO_RNAseq

value: WT


title: BI16_100


title: BI17_117


title: BI16_9


title: T47D_WT_clone2_DMSO_RNAseq


title: T47D_Y537S_clone2_DMSO_RNAseq


title: BI16_19


title: BI16_10


title: BI17_81


title: BI16_85


title: The lliver from a HLJ1 knockout mouse, biological rep1

city: Taipei

first: Kang-Yi

last: Su

address: No.1, Jen-Ai Road

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from 6-8 week-old HLJ1 knockout male mice livers.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed by GeneSpring GX software (Agilent Technologies, Inc.). We used GC-RMA as normalization algorithm.

source_name: Livers from HLJ1 knockout mice.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Six to eight week-old wild-type and HLJ1 knokout mice were housed in the animal center at temperature 22±1℃ with 50±2 % humidity with 12 h light/ 12 h dark schedule and had free access to food and water.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were sacrified and livers were collected. After 1xPBS washing, livers were assessed for total RNA extraction.

value: Livers

value: knockout (HLJ1-/-)

tag: age

value: 6-8 weeks

tag: Sex

value: male


title: The liver from a wild-type mouse, biological rep2

description: Gene expression data from 6-8 week-old wild-type male mice livers.

source_name: Livers from wild-type mice.

value: wild-type (HLJ1+/+)


title: The lliver from a HLJ1 knockout mouse, biological rep2


title: Input_YPGly_repeat 3

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

institute: Academia Sinica

description: paired with ChIP G3

data_processing:
All sequencing protocols were carried out as per the manufacter's instructions using the Illumina NextSeq500 and NextSeq software: base calling was performed using NextSeq Control Software NCS 2.2.0 and Real-time Analysis software RTA 2.4.11 to generate BCL files. The Illumina bcl2fastq2 Conversion Software v2.17 was used to demultiplex sequencing data and convert BCL files into FASTQ files.
The quality control and adaptor trimming of sequencing reads were processed by FastQC version 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trimmomatic version 0.36 with the parameters “2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:3 CROP:68”.
Trimmed reads were mapped to the L. kluyveri CBS 3082 genome using Bowtie2 version 2.3.3.
Bowtie2 mapped BAM files were detected for the ChIP peaks using SPP version 1.13 with a false discovery rate (FDR) of 0.05.
The Sef1 binding peaks were compared and merged among three biological replicates by Diffbind version 2.10.0. Only peaks detected in all three biological repeats were used for the downstream analysis
Genome_build: Lachancea kluyveri CBS 3082 genome (Genebank: AACE00000000)
Supplementary_files_format_and_content: The text files, wig files, and narrowPeak files were generated from SPP. The bigwig files are generated by deepTools.

organism: Lachancea kluyveri

source_name: Yeast species

growth_protocol: Cells of SkSef1TAPNB1-1 (SEF1-TAP) and JYL1897 (no tag) were grown in the YPD medium at 30°C overnight, subsequently diluted into each indicated medium in a cell density of 0.2 OD600/ml, and then incubated at 30°C for 5.5 h.

extract_protocol:
For breaking cells, 500 OD600 of cells were thawed and resuspended in 4 ml of FA buffer (50 mM HEPES, pH 7.5; 140 mM NaCl; 0.1% SDS; 1 mM EDTA; 1% Triton X-100; 0.1% Deoxycholate, Na salt) with 1/100 PIC (Protease inhibitor cocktail Set IV, in DMSO; 539136, Merck) and 1 mM phenylmethanesulfonyl fluoride (PMSF, P7626, Sigma). The cell suspension was divided into four 2-ml breaking tubes (Biospec, 10832, Microtube 2 ml with cap) containing 1 ml volume of glass beads (11079105, BioSpec Products). The lysis was performed by three cycles of 5-min beating followed by 1-min chilling on ice (Biospec Mini-BeadBeater-16). Cell lysates and glass beads were separated by punching a hole on the bottom of the tube with a red-hot 18G needle and slow centrifugation (500 g, 3 min, 4°C; Eppendorf 5810R centrifuge, A-4-62 rotor). The collected lysates were combined into a 15-ml centrifuge tube and washed with two cycles of 5 ml FA buffer followed by centrifugation (12K rpm, 5 min, 4C; Eppendorf 5810R centrifuge, F-34-6-38 rotor). The washed lysates were completely resuspended in 2 ml FA buffer with 1/100 PIC and 1 mM PMSF in a new 15-ml centrifuge tube (CFT011150, BIOFIL). Chromatin was sheared by sonication in a Bioruptor water bath sonicator (Diagenode) with 15 ml tube-chip unit (High intensity; 30 sec on, 30 sec off, 15 min/cycle; total 3 cycles) at 4°C. The sheared lysate was centrifuged at 12000 g for 10 min at 4°C (Eppendorf 5810R centrifuge, F-34-6-38 rotor). About 25 ml of supernatant corresponding to 5 OD600 of cells was collected, mixed with 200 ml TES buffer (50 mM Tris-Cl, pH 8; 10 mM EDTA, pH 8; 1% SDS) plus 175 ml TE buffer (10 mM Tris-Cl; 1 mM EDTA, pH 8), and stored at -20°C as the input-DNA. Immunoprecipitation was performed by incubating all the rest sheared chromatins with 300 ml Dynabeads® Pan Mouse IgG (11041, human anti-mouse IgG, Invitrogen) in 6 ml of FA buffer with 1/100 PIC and 1 mM PMSF. The binding was performed in a 15-ml tube with mixing using an end-over-end rotator (Fntelli-Mixer, RM-2L, F1 mode, 30 rpm) at 4°C for 16 h. The magnetic beads were anchored with DynaMagTM-2 Magnet and the bound complexes were washed 4 times with 1 ml of each wash buffer for 5 min [FA buffer × 1, high-salt FA buffer (50 mM HEPES, pH 7.5; 500 mM NaCl; 0.1% SDS; 1 mM EDTA; 1% Triton X-100; 0.1% Deoxycholate, Na salt) × 1, DOC buffer (10 mM Tris·Cl; 1 mM EDTA, pH 8; 25 0mM LiCl; 0.5% IGEPAL® CA-630; 0.5% Deoxycholate, Na salt) × 1, and TE buffer × 1] with mixing (Fntelli-Mixer, RM-2L, F1 mode, 30 rpm) at room temperature. The bound complexes were eluted twice by heating at 65°C in 200 ml TES buffer for 20 min and in 200 ml TE buffer for 10 min. Two eluates were pooled as the ChIP-DNA. To remove RNA, both the input-DNA and ChIP-DNA (~400 ml each) were treated with 5 ml of 10 mg/ml RNase A (R5503, Sigma; 100 mM Tris-Cl, pH 7.4) at 37°C for 30 min. For de-crosslinking, both the RNase-treated input-DNA and ChIP-DNA were treated with 40 ml of 20 mg/ml Proteinase K (1.24568.0500, Merck; in 50 mM Tris-Cl, pH 8) at 42°C for 1 h and then 65°C for 16 h. De-crosslinked DNA was purified using the QIAquick DNA Purification Kit (28106, Qiagen) according to the manufacturer’s instruction, with a modification of a two-cycle wash step using the PE buffer. Final ChIP-DNA and input-DNA were eluted with 50 ml EB buffer. DNA concentrations were measured by using the Qubit™ dsDNA HS Assay Kit (Q32854, Invitrogen by Thermo Fisher Scientific).
ChIP-seq analysis was performed from three biological replicates of YPD- and YPGly-grown cells. The average fragment length of sonicated fragments was 150–1000 bp. For each condition, libraries were prepared from 3.96–20 ng of ChIP-DNA and input-DNA using the KAPA LTP Library Preparation Kit for Illumina® platforms (KK8232, KAPA Biosystems by Roche) according to the manufacturer’s instruction. Notably, after adapter ligation, double-sided size selection between 250–450bp for adapter-ligated fragments was performed using the KAPA Pure Beads (KK8000/07983271001, KAPA Biosystems by Roche). Size-selected fragments were then PCR-amplified for 12 cycles. The size of each library was assessed using a Bioanalyzer 2100 instrument (Agilent Technologies) with the High Sensitivity DNA Kit (Agilent Technologies). The concentration of each library was quantified by using the Qubit™ dsDNA HS Assay Kit (Q32854, Invitrogen by Thermo Fisher Scientific) and qPCR. Single-read sequencing (75 bp) of the libraries was performed using the NextSeq 500/550 high output reagent kit V2_75 cycle (FC-404-2005, Illumina) on an Illumina NextSeq500 sequencer.

treatment_protocol: After 5.5 h of incubation at 30°C, cultures of mid-log phase cells (1 OD600/ml in YPD and 0.5 OD600/ml in YPGly) were fixed with 1% formaldehyde at 25°C for 20 min with shaking at 180 rpm and then quenched with 125 mM glycine at 25°C for 10 min with shaking at 180 rpm. All the following steps were performed in an ice-cold or 4°C environment. Cells were harvested, washed twice with TBS (20 mM Tris-Cl, pH 7.5; 150 mM NaCl), and stored at −80°C until use.

tag: conditions

value: YPGly

tag: growth phase

value: log-phase, OD = ~0.10


title: The lliver from a HLJ1 knockout mouse, biological rep3


title: Input_YPGly_repeat 2

description: paired with ChIP G2

value: log-phase, OD = ~0.9


title: BI17_45

value: Ailsa Craig

value: Wounded


title: The liver from a wild-type mouse, biological rep3


title: BI16_21

source_name: nor_MG-like_B. cinerea

value: MG-like

value: B. cinerea


title: BI16_61

value: MG


title: Input_YPGly_repeat 1

description: paired with ChIP G1

value: log-phase, OD = ~0.8


title: BI16_123

value: nor

value: fruit pericarp and epidermal tissue of the blossom end halves


title: BI16_37


title: BI16_99


title: BI17_80

source_name: Ailsa Craig_RR_Healthy

value: RR

value: Healthy


title: ChIP_YPGly_repeat 3

description: paired with Input G3

value: log-phase, OD = ~0.7


title: The liver from a wild-type mouse, biological rep1

value: Livers

value: 6-8 weeks


title: ChIP_YPGly_repeat 2

description: paired with Input G2

value: log-phase, OD = ~0.6


title: BI16_96

source_name: Cnr_RR-like_B. cinerea

value: Cnr

value: RR-like


title: BI17_8


title: ChIP_YPGly_repeat 1

description: paired with Input G1

value: YPGly

value: log-phase, OD = ~0.5


title: Topotecan resistant, subpopulation 2, biological rep 1

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
07.1.W1TK2

hyb_protocol: Biotin-labeled miRNA were hybridized to Applied Biosystems™ miRNA 3.1 Array Strip (20 h, 48 °C). Then, the microarrays were subjected to a washing and staining procedure, according to the technical protocol, using the Affymetrix GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

source_name: Topotecan resistant, subpopulation 2

label_protocol: The complete procedure for preparing miRNA for hybridization was performed using the FlashTagTM Biotin HSR RNA Labeling Kit (ThermoFisher Scientific, Waltham, MA, USA). 150 ng of previously isolated miRNA was subjected to poly(A) tailing and biotin ligation procedure, according to producer protocol.

growth_protocol: The human primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc). All cell lines were maintained as monolayer in complete medium [RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum, 2 pMl-glutamine, penicillin (100 U/ml), streptomycin (100 U/ml) and amphotericin B (25 µg/ml)] at 37˚C in a 5% CO2 atmosphere.

extract_protocol: Total RNA with miRNA was purified with TRI Reagent solution according to the manufacturer’s protocol.

treatment_protocol: Cells grow as a monolayer, present epithelial morphology and adherent growth model. Sublines resistant to cisplatin (W1CR), doxorubicin (W1DR), topotecan (W1TR) and paclitaxel (W1PR1 and W1PR2) were obtained by exposure of the W1 cell line to stepwise increasing drug concentrations. Final concentration of each drug was twofold greater than the concentration in the plasma 2 hours after intravenous administration. The cells were 8-, 10-, 20-, 641- and 967-folds resistant to their selective drugs, respectively, as determined by Cell Proliferation Kit I (MTT).

tag: phenotype

value: Topotecan resistant

value: primary ovarian cancer cell line

tag: cell line


title: Doxorubicin resistant, biological rep 1

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
08.1.W1DK1

source_name: Doxorubicin resistant

value: Doxorubicin resistant


title: Doxorubicin resistant, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
08.3.W1DK1


title: BI17_44

value: Ailsa Craig


title: Topotecan resistant, subpopulation 2, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
07.3.W1TK2


title: Doxorubicin resistant, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
08.2.W1DK1


title: Input_YPD_repeat 3

description: paired with ChIP D3

value: YPD

value: log-phase, OD = ~1.0


title: Input_YPD_repeat 2

description: paired with ChIP D2


title: BI16_18

value: B. cinerea

value: fruit pericarp and epidermal tissue of the blossom end halves


title: BI17_116

value: RR

value: Healthy


title: Methotrexate resistant, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
06.3.W1MK1

source_name: Methotrexate resistant

value: Methotrexate resistant


title: BI16_78


title: BI16_120


title: Input_YPD_repeat 1

description: paired with ChIP D1


title: Methotrexate resistant, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
06.2.W1MK1


title: Topotecan resistant, subpopulation 2, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
07.2.W1TK2


title: BI16_54


title: ChIP_YPD_repeat 3

description: paired with Input D3


title: ChIP_YPD_repeat 2

description: paired with Input D2


title: BI16_17

source_name: Cnr_MG-like_B. cinerea

value: MG-like


title: Methotrexate resistant, biological rep 1

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
06.1.W1MK1


title: Cisplatin resistant, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
05.3.W1CK1

source_name: Cisplatin resistant

value: Cisplatin resistant


title: Cisplatin resistant, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
05.2.W1CK1


title: BI16_102


title: BI17_79

source_name: Ailsa Craig_MG_Healthy

value: MG


title: Cisplatin resistant, biological rep 1

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
05.1.W1CK1


title: BI16_70

source_name: Ailsa Craig_RR_B. cinerea


title: FC17_6

organism:
Solanum lycopersicum
Fusarium acuminatum

source_name: Ailsa Craig_RR_F. acuminatum

value: F. acuminatum


title: BI17_7


title: BI16_46


title: ChIP_YPD_repeat 1

description: paired with Input D1


title: FC17_18


title: BI17_43


title: BI16_71

value: Cnr


title: BI16_16


title: BI16_118


title: BI16_47


title: Vincristine resistant, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
04.3.W1VK1

source_name: Vincristine resistant

value: Vincristine resistant


title: BI17_115


title: BI16_2


title: BI16_93

source_name: Ailsa Craig_MG_B. cinerea


title: FC17_10


title: Vincristine resistant, biological rep 1

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
04.1.W1VK1


title: Vincristine resistant, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
04.2.W1VK1


title: Paclitaxel resistant, subpopulation 2, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
03.3.W1PR2

source_name: Paclitaxel resistant, subpopulation 2

value: Paclitaxel resistant


title: FC17_9

source_name: Ailsa Craig_MG_F. acuminatum


title: Paclitaxel resistant, subpopulation 2, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
03.2.W1PR2

value: primary ovarian cancer cell line


title: Paclitaxel resistant, subpopulation 2, biological rep 1

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
03.1.W1PR2


title: BI16_45


title: FC17_5


title: BI16_101


title: BI16_53


title: FC17_13


title: FC17_14


title: BI16_1


title: BI16_117


title: BI16_75

value: nor


title: Paclitaxel resistant, subpopulation 1, biological rep 1

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
02.1.W1PR1

source_name: Paclitaxel resistant, subpopulation 1


title: FC17_1

value: Ailsa Craig


title: P3root

city: Guiyang

first: Chunbo

last: Liang

state: Guizhou

address: Dongqingnan road

institute: Guizhou University of tradional Chinese Medicine

data_processing:
BGI500 own software used for basecalling.
The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA and snoRNA with Bowtie2 (2.2.9) [1]. Particularly, cmsearch (1.1.2) [2] was performed for Rfam mapping. The software miRA [3] was used to predict novel miRNA by exploring the secondary structure. The softwares including psRobot [4] , TAPIR [5] and TargetFinder [6] were used to predict target genes of miRNAs. The small RNA expression level was calculated by counting absolute numbers of molecules using unique molecular identifiers [7]. Differential expression analysis was performed using the DEGseq [8] , Q value ≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression difference. To annotate gene functions, all target genes were aligned against the Kyoto Encyclopedia of Genes (KEGG)and Gene Ontology (GO) database. GO enrichment analysis and KEGG enrichment analysis of target genes were performed using phyper, a function of R. The P-value was corrected using the Bonferroni method [9] , and a corrected P-value ≤ 0.05 was taken as a threshold. GO terms or KEGG terms fulfilling this condition were defined as significantly enriched terms.
Bowtie2 (2 2.2.9) [1] http://bowtie-bio.sourceforge.net/index.shtml  cmsearch (1.1.2) [2] https://omictools.com/cmsearch-tool  miRA [3] https://github.com/mhuttner/miRA  psRobot [4] http://omicslab.genetics.ac.cn/psRobot/  TAPIR [5] http://bioinformatics.psb.ugent.be/webtools/tapir/  TargetFinder [6] https://github.com/carringtonlab/TargetFinder  DEGseq [8] http://bioinfo.au.tsinghua.edu.cn/software/degseq/
Genome_build: Helianthus annuus (https://www.ncbi.nlm.nih.gov/genome/?term=Sunflower)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Helianthus annuus

source_name: PEG-treated drought stress

growth_protocol: R5 were sown into pots filled with soil and grown under controlled conditions (16h light, 25℃ and 95% ambient humidity) in a greenhouse at the industrial crops institute, Heilongjiang Academy of Agricultural Sciences (Harbin, China).

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: Four-leaf stage seedlings which showed appropriate growth status were rinsed with sterilized distilled water and placed into culture bottles filled with 15% PEG 6000 in water for 24 h to serve as drought-stressed plants. Seedlings placed in distilled water were used as control plants and were grown in parallel and collected at the same time points.

tag: cultivar

value: roots


title: RPA_ChIPSeq-rep2

city: Guangzhou

first: Tian

last: Zheng

address: No. 135 West Xingang Road

institute: Sun Yat-sen University

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie2 with default parameters.
Reads were converted to normalized BigWig files for genomic visualization using Deeptools (version 3.4.1), with reads coverage for each window of 100bp was normalized by CPM (Counts per million mapped reads).
MACS2 (version 2.2.4) was used to call peaks between IP and input samples with the parameters ‘-p 1e-12 –nomodel –nolambda’.
Genome_build: hg38
Supplementary_files_format_and_content: xls files include peaks for each sample were generated using MACS.

source_name: 293T cells

growth_protocol: 293T cells were grown in DMEM (GIBCO) with 10% fetal bovine serum (GIBCO) and 100 U per ml penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C and 5% CO2.

extract_protocol:
Cell lysates were sonicated and protein-DNA complexes were isolated with Flag-beads (Sigma Aldrich).
Libraries were prepared using Paired-End DNA Sample Prep kit (Illumina).

treatment_protocol: Cells were transfected with either Flag-RBMX or Flag-RPA1, and treated with Camptothecin(CPT) for 24 hours.

value: Embryonic kidney cell line

tag: transfection

tag: chip antibody

value: Anti-Flag


title: Paclitaxel resistant, subpopulation 1, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
02.2.W1PR1


title: LNR3

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

description: N Replete Root

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Spinacia_oleracea whole genome using hisat2-2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts
Differeantial expression analysis with DEseq2
Genome_build: Spinacia_oleracea V1.0
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

organism: Spinacia oleracea

source_name: N Replete Root

growth_protocol: Samples collected from 6-week old plants were frozen in liquid nitrogen and stored at −80 °C until subsequent analyses. Three independent plants were used for metabolic analysis, total RNA extractions, physiological and biochemical analysis. The seeds of spinach variety ‘Banjo’ were grown in plastic containers containing Turface ® based growing medium under 200 μmol·m-·s-1light intensity(12 hours each light and dark period) at 23°C and 60-70% relative humidity. Two treatments, High N and low N, where N was added in the form of Ca(NO3)2 , were used to maintain the concentration of 200 ppm for High N and 50 ppm for low N. CaCl2 was compensated to keep the same concentration of calcium in both treatments. The concentrations of remaining macro- and micro-elements were kept constant using N-free Hoagland’s nutrient solution

extract_protocol:
The flash-frozen plant samples in liquid nitrogen were ground to a fine powder using a paint shaker (Harbil, Wheeling, IL, USA) and 3-mm-diameter steel balls (Abbott Ball, West Hartford, CT, USA). Total RNA was extracted using an RNeasy® Plant Mini Kit (QIAGEN Sciences, Germantown, MD, USA) as per the manufacturer’s protocol and treated with DNase1 (QIAGEN Sciences, Germantown, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Banjo

value: Leaf

value: Low N


title: Paclitaxel resistant, subpopulation 1, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
02.3.W1PR1


title: BI16_77

tag: genotype

tag: ripening stage

value: Healthy

value: fruit pericarp and epidermal tissue of the blossom end halves


title: P3leaf

tag: tissue

value: leaves


title: LNR2

description: N Replete Root

tag: treatment


title: RBMX_ChIPSeq-rep2

value: Flag-RBMX


title: Input-RPA-rep2


title: BI16_69

value: MG

value: B. cinerea


title: Control line, biological rep 2

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
01.2.W1

source_name: Control line

value: Control line


title: LNR1

description: N Replete Root


title: P2root


title: GMR-GAL4_UAS-NERFIN-HA

city: Leuven

first: Carmen

last: Bravo González-Blas

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

description: Omni-ATAC-seq protocol as described by Corces et al. (2017)

data_processing:
ATAC-seq reads were first cleaned for adapters using fastq-mcf. (ea-utils v1.12) and a list of sequencing primers. Cleaned reads (FastQC v0.1) were then mapped to the 3rd 2017 FlyBase release (D. melanogaster r6.16) genome using Bowtie2 (v2.2.5) with default parameters, with the single end option (to compare with the WT sample, which was single-end sequenced).
Sorted bam files were produced using using SAMtools (v1.2). Normalized bigwigs were generated using the Kent software (UCSC). Peaks were called on mapped reads using MACS2 (v2.1.2.1) with the following options: -g dm –nomodel –bdg -t Sample/Control -c Sample/Control (depending on whether we want to determine upregulated or downregulated peaks).
Genome_build: dm6
Supplementary_files_format_and_content: Bigwig files containing the normalized coverage profiles of each experiment.

organism: Drosophila melanogaster

source_name: L3 Drosophila eye-antennal disc

growth_protocol: All flies were raised and crossed at 25°C on a yeast based medium.

extract_protocol:
Briefly, ~10 eye-antennal discs were dissected and lysed using 50 µl of cold ATAC-Resupension Buffer (RSB) (see Corces et al. for composition) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubating the cells for 3 min on ice. The lysis was washed out by adding 1 mL of cold ATAC-RSB containing 0.1% Tween-20 and inverting the tube three times.
Nuclei were pelleted at 500 RCF for 10 min at 4°C, the supernatant was carefully removed and nuclei were resuspended in 50 µl of transposition mixture (25 µl 2x TD buffer (see Corces et al. for composition), 2.5 µl transposase (100 nM), 16.5 µl DPBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O) by pipetting six times up and down, followed by 30 minutes incubation at 37°C at 1000 RPM mixing rate. After MinElute clean-up and elution in 21 µl elution buffer, the transposed fragments were pre-amplified with Nextera primers by mixing 20 µl of transposed sample, 2.5 µl of both forward and reverse primers (25 µM) and 25 µl of 2x NEBNext Master Mix (program: 72°C for 5 min, 98°C for 30 sec and 5 cycles of [98°C for 10 sec, 63 °C for 30 sec, 72°C for 1 min] and hold at 4°C). To determine the required number of additional PCR cycles, a qPCR was performed (see Buenrostro et al.83 for the determination of the number of cycles to be added). The final amplification was done with the additional number of cycles, samples were cleaned-up by MinElute and libraries were prepped using the KAPA Library Quantification Kit as previously described82. Samples were sequenced on a NextSeq500 High Output chip, with 50bp single-end reads.
Omni-ATAC-seq (Corces et al., 2017)

tag: sequencing method

value: Omni-ATAC-seq


title: BI16_15

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0, B. cinerea ASM83294v1, F. acuminatum GGXD00000000, R. stolonifer GGWM00000000
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

extract_protocol:
At 1 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, wounded, and infected fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as single-end 50-bp reads on an Illumina HiSeq 4000 platform by the DNA Technologies Core at the UC Davis Genome Center.


title: P2leaf


title: Control line, biological rep 1

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
01.1.W1

value: primary ovarian cancer cell line


title: Input-RBMX-rep2


title: LNL3

description: N Deplete Leaf

source_name: N Deplete Leaf

value: High N


title: FC17_8

organism:
Solanum lycopersicum
Rhizopus stolonifer

source_name: Ailsa Craig_RR_R. stolonifer

value: Ailsa Craig

value: RR

value: R. stolonifer


title: LNL2

description: N Deplete Leaf


title: P1root

value: roots


title: FC17_4


title: Control line, biological rep 3

description:
primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc)
total miRNA
Gene expression data
01.3.W1


title: P1leaf


title: GMR-GAL4_UAS-LOV

tag: strain


title: LNL1

description: N Deplete Leaf

value: Banjo


title: HNR3

description: N Replete Root

value: Leaf


title: FC17_16


title: C3leaf

source_name: control


title: FC17_20


title: C3root


title: HNR2

description: N Replete Root

value: Low N


title: FC17_12


title: C2root


title: HNR1

description: N Replete Root


title: FC17_7

source_name: Ailsa Craig_MG_R. stolonifer


title: GMR-GAL4_UAS-NERFIN-CC


title: HNL3

description: N Replete Leaf

source_name: N Replete Leaf


title: C2leaf


title: 21_94-09_Day_0

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Natural Killer (NK) cells

growth_protocol: Frozen primary cells were used for this experiment. Cells were frozen in 90%FBS + 10% DMSO and stored in LN2 vapor phase

extract_protocol:
NK cells were sorted directly into cold (4ºC) RPMI. The sorted NK cells were pelleted (500 x g, for 10 minutes) and lysed by vortexing for 1 minute in cold supplemented RLT buffer (RLT + β-MeOH) using the following ratio: 50µL cells in R10 and 350µL RLT buffer, 4ºC. Samples were then immediately frozen at -80ºC. RNA was extracted from these samples using the RNeasy Micro kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer.
Five (5) nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina HiSeq3000 at 100SR, yielding 20-25 million reads per sample.

treatment_protocol: Cells were thawed quickly in complete R10 media and immediately stained using antibodies to identify NK cells.

value: Natural Killer (NK) cells


title: 32_144-07_Day_0


title: 7_283-09_Day_0


title: 26_349-09_Day_0


title: FC17_15

first: Barbara

address: One Shields Avenue

institute: University of California, Davis

value: fruit pericarp and epidermal tissue of the blossom end halves


title: FC17_3


title: 13_231-09_Day_0


title: C1root


title: HNL1

description: N Replete Leaf


title: C1leaf

value: leaves


title: HNL2

description: N Replete Leaf


title: 1_173-09_Day_0


title: Blood Serum_MI3_rep1

status: Public on Apr 07 2020

city: Wuhan

first: xiang

last: nie

address: 1095# Jiefang Ave.

institute: Tongji Hospital, Tongji Medical College

description: miRNA expression in  myocardial infarction patients  blood serum

hyb_protocol: The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 4 out of 28 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.
Fold Change >= 2.0，P-value <= 0.05

source_name: Peripheral Blood

label_protocol: Total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology)

extract_protocol: Total RNA was extracted from blood serum（750μl）by Trizol Ls（250μl）/chloroform/isopropanol.

treatment_protocol: Systematic and comprehensive treatment (such as mechanical life support, immunological modulation, antiviral reagents, etc.) based on the Chinese society of cardiology expert consensus statement on the diagnosis and treatment of adult fulminant myocarditis (PMID:30519877)

tag: individual

value: myocardial infarction patient

value: blood serum

tag: gender

value: male

tag: time

value: at the onset


title: Blood Serum_MI2_rep1


title: Blood Serum_FM3_13 days_rep1

description: miRNA expression in  FM patients  blood serum

value: FM patient

value: female

value: mechanical life support, immunological modulation, antiviral reagents

value: thirteen days


title: Blood Serum_MI5_rep1


title: Blood Serum_MI4_rep1


title: Blood Serum_FM9_15 days_rep1

value: fifteen days


title: Blood Serum_FM1_14 days_rep1

value: fourteen days


title: Blood Serum_MI6_rep1


title: Blood Serum_FM2_13 days_rep1


title: Blood Serum_FM10_1 day_rep1


title: Blood Serum_FM19_1 day_rep1


title: Blood Serum_FM16_9 days_rep1

value: nine days


title: Blood Serum_FM19_1 month_rep1

value: one month


title: Blood Serum_FM10_12 days_rep1

value: twelve days


title: Blood Serum_FM5_6 months_rep1

value: six months


title: Blood Serum_FM3_1 day_rep1


title: Blood Serum_FM9_1 day_rep2


title: Blood Serum_FM5_1 day_rep2


title: Blood Serum_FM16_1 day_rep2


title: Blood Serum_control8_rep2

description: miRNA expression in  healthy controls blood serum

value: healthy control


title: Blood Serum_FM2_1 day_rep2


title: Blood Serum_FM1_2 days_rep2


title: Blood Serum_control5_rep2


title: Blood Serum_control7_rep2


title: BI16_72

city: Davis

last: Blanco-Ulate

source_name: Cnr_RR-like_B. cinerea

value: Cnr

value: RR-like

value: B. cinerea

value: fruit pericarp and epidermal tissue of the blossom end halves


title: Blood Serum_control2_rep1

value: blood serum

value: male


title: Blood Serum_control4_rep2

value: at the onset


title: Blood Serum_control3_rep1


title: Blood Serum_control1_rep1


title: Ncstn KO 3

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

data_processing:
4 RNA-seq reads files per sample were merged
RNA-seq reads were aligned to rmm10 using hisat2 version 2.1.0 using the default parameters
Counts were obained using htseq-count function of HTSeq 0.11.1 using the parameters -a 20 -s no
Counts were normalized using DESeq2 R package
Genome_build: mm10
Supplementary_files_format_and_content: counts table using mm10refGene.gtf ( prepared from ://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz)

source_name: urinary bladder

extract_protocol:
Dissected urothelia seperated from muscularis propria were frozen in liquid nitrogen, pulverized with a mortar and pestle and total RNA was isolated ising TRI-Reagent (Merck). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder (urothelial tissue)

tag: age

value: 10 weeks


title: Mst1KO_S3_rep3

first: Hongbo

last: Chi

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: iNKT cell developmental subsets

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Total thymocytes were enriched for iNKT cells using the CD8+ microbeads positive-selecting kit (Miltenyi) and iNKT developmental stages were sorted using the Sony SY3200 sorter as follows: (S1, TCRb+CD1d-PBS57-tet+CD24–CD44–NK1.1–; S2, TCRb+CD1d-PBS57-tet+CD24–CD44+NK1.1–; or S3, TCRb+CD1d-PBS57-tet+CD24–CD44+NK1.1+) .

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from RNeasy Micro kit from Qiagen.

value: thymus

tag: inkt developmental stage


title: Mst1KO_S1_rep1


title: Mst1KO_S1_rep3


title: Ncstn KO 1


title: Ncstn KO 2


title: Mst1KO_S3_rep2


title: Mst1KO_S1_rep2


title: WT_S2_rep1

value: WT


title: Mst1KO_S3_rep1


title: Mst1KO_S2_rep1


title: WT_S3_rep3


title: Mst1KO_S2_rep3


title: WT_S1_rep3


title: WT_S2_rep3


title: WT_S3_rep1


title: WT_S3_rep2


title: WT 2


title: WT_S2_rep2


title: Mst1KO_S2_rep2


title: WT_S1_rep1


title: WT_S1_rep2


title: DCreg_2

city: Palo Alto

first: Xiangyue

last: Zhang

address: 3373 Hillview ave

department: Pathology

institute: Stanford University

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: oligo package in R  was used to read cel files and RMA data was calculated at transcript level by setting target argument to core.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monoctyes were cocutured with human Th or Treg or together in the presence of anti-CD3 for 3-4 days

extract_protocol: Qiagen RNAeasy micro kit

treatment_protocol: Myeloid cells were sorted by flow cytometry as HLA-DR+CD2-

tag: cell type

value: Dcreg


title: DCgm_2

value: DCgm


title: WT 1


title: DCgm_1


title: MFtreg_2

value: Mftreg


title: MALT1_823

city: Beijing

first: Qinghua

last: Zou

address: No.38, Xueyuan Rd

institute: Peking university health science center

data_processing:
Basecalls performed using CASAVA version 1.4
The sequenced data were filtered by removing adaptor sequences, reads in which unknown bases are more than 10%, and low quality reads (the percentage of low quality bases is over 50% in a read, we defined a low quality base asa base whose sequencing quality is no more than 5).We used Bowtie2  to map clean reads to the reference gene and used HISAT  to map reads to the reference genome hg19.
The FPKM method was used to calculate the expression level
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: gastric carcinoma undifferentiated cell line

growth_protocol: The cell lines were cultured in RPMI 1640 supplemented with 10% FBS at 37 °C in an atmosphere of 5% CO2. The cells were washed with PBS three times and then infected with H. pylori at an MOI of 100

extract_protocol:
Total RNA was extracted using Trizol
RNA with an RNA integrity number > 8 according to the 2100 Bioanalyzer (Agilent, USA) was used to prepare cDNA libraries with the  Illumina TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA). Oligo (dT) magnetic beads were used to select mRNA with polyA tail.

treatment_protocol: After 4 h, the cells were washed, harvested, and total RNA and proteins were extracted for transcriptomic analysis.

tag: agent

value: MALT1 stimulated


title: H879_823

value: H879 stimulated

tag: cell line


title: BCG823

value: unstimulated


title: RP mock - Lactimidomycin - Rep 1

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

description:
Ribosome protected RNA fragments (29-30nt)
Human.A.tsv,HSV.A.tsv

data_processing:
3' sequencing adapter sequence were removed from the 50 nt long reads by computing a prefix-suffix sequence alignment
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use.
Bowtie 1.0 was used to align all reads to the human genome, Ensembl transcripts (v75), ribosomal rRNA, the HSV1 genome (JN555585, terminal repeats masked), the HSV1 transcripts as well as novel junctions identified in the 4sU data by ContextMap. Only reads aligning to at most 3 distinct genome positions with at most 2 mismatches were kept for further analyses.
At each alignment position a greedy algorithm successively discarded alignments such that no read sequence remained that has hamming distance 1 to any other read. The total number of unique sequences was taken as the conservative fragment count.
Mapped reads were further processed by Price 1.0.1, once with standard parameters for cellular ORFs, and once with -novelTranscripts to identify novel viral transcripts.
Genome_build: hg19, JN555585

source_name: Ribosome profiling

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 13 were infected at 60% confluency 24h after the last split.

extract_protocol:
Cells were snap frozen followed by cell lysis in presence of cycloheximide. Following removal of cell nuclei by centrifugation and stringent RNAse digest, ribosomes were pelleted through a sucrose cushion. Translated RNA fragments were recovered by size selection.
Translated RNA fragments were cloned following the protocol described by Stern-Ginossar N et al. Science 2012. rRNA depletion involved additional biotinylated oligos to improve depletion. To efficiently remove all biotinylated oligos complementary to specific rRNA sequences, two rounds of streptavidin depletion were performed. cDNA libraries were amplified by PCR and sequenced (HiSeq 50nt reads).

treatment_protocol: Cells were infected for 10 min with HSV-1 strain 17 at an MOI of 10 followed by PBS wash and media replacement. 500µM 4-thiouridine was added to the cell culture at the indicated time points.

value: human foreskin fibroblasts

tag: time post infection

value: mock

tag: infection with

tag: barcode

value: NNNTTGTNN


title: MCF-7 Cyto Input

city: Brisbane

first: Selene

middle: Lizbeth

last: Fernandez-Valverde

state: QLD

address: Goddard Building 8 University of Queensland

department: School of Biological Sciences

institute: University of Queensland

description: Cytoplasmic Input Control small RNAs. Cytoplasmic and nuclear RNA were separated as described previously (Hwang et al. 2007). Briefly, the cell pellets were resuspended in 400 ml/plate lysis buffer A (10 mM Tris-HCl (pH 8), 140 mM NaCl, 1.5 mM MgCl2, 0.5% Nonidet P-40), incubated on ice for 5 min, and then centrifuged at 1,000 rpm for 3 minutes at 4°C. The cytoplasmic fraction remained in the supernatant, while the nuclear fraction was in the pellet. The cytoplasmic fraction was collected and spun again to remove any contaminating nuclear pellet. The nuclear pellet was washed twice in buffer A, and finally with buffer A containing 1% Tween-40 and 0.5% deoxycholic acid.

data_processing:
Adaptors were trimmed and sequences collapsed and counted using the fastx_toolkit version 0.0.13.
The raw counts in the IgG were subtracted from the abundance of identical sequences in the Nuclear and AGO2 RIP samples.
Sequences were mapped to the human genome using bowtie without allowing for mismatches.
The abundance of all reads was normalized by the dividing it by the depth of the library (counts) multiplied by a factor of 10^6.
Genome_build: hg19
Supplementary_files_format_and_content: Count files cointain two columns, the sequence and it's raw counts after trimming the adapter.

source_name: human breast adenocarcinoma cell line

growth_protocol: MCF-7 cells were grown at 140 mm dishes in Invitrogen Gibco Minimal Essential Media (MEM – Invitrogen - 12360-038) supplemented with 10% heat inactivated FCS, 2 mM L-Glutamax (Invitrogen-35050-061), 50 units/mL of penicillin and 50 mg/mL of Streptomycin (Invitrogen-15070-063), 0.1 mM of non essential aminoacids (Invitrogen-11140-050), 1.0 mM Sodium Pyruvate (Invitrogen – 11360-070) and 10 mg/mL human insulin solution (Sigma – I9278).

extract_protocol:
RNA was extracted using the standard Invitrogen TRIzol procedure. RNA quality and yield was assessed on an Agilent 2100 Bioanalyzer using total RNA Pico Chip kit (Agilent). Cell equivalent amounts of RNA from nuclear and cytoplasmic fractions were used for all analyses, unless stated otherwise.
Libraries were prepared using the TruSeq Small RNA kit v1.5

treatment_protocol: See sample description.

value: MCF-7 human breast adenocarcinoma cell line

tag: ip antibody

tag: adaptor

value: TGGAATTCTCGGGTGCCAAGG


title: MCF-7 Nuc AGO2

description: AGO2-bound nuclear small RNAs. Cytoplasmic and nuclear RNA were separated as described previously (Hwang et al. 2007). Briefly, the cell pellets were resuspended in 400 ml/plate lysis buffer A (10 mM Tris-HCl (pH 8), 140 mM NaCl, 1.5 mM MgCl2, 0.5% Nonidet P-40), incubated on ice for 5 min, and then centrifuged at 1,000 rpm for 3 minutes at 4°C. The cytoplasmic fraction remained in the supernatant, while the nuclear fraction was in the pellet. The cytoplasmic fraction was collected and spun again to remove any contaminating nuclear pellet. The nuclear pellet was washed twice in buffer A, and finally with buffer A containing 1% Tween-40 and 0.5% deoxycholic acid.

value: Anti-Ago2 / eIF2C2 antibody - ChIP Grade (ab57113)


title: 26695_823

value: 26695 stimulated


title: MCF-7 Cyto AGO2

description: AGO2-bound cytoplasmic small RNAs. Cytoplasmic and nuclear RNA were separated as described previously (Hwang et al. 2007). Briefly, the cell pellets were resuspended in 400 ml/plate lysis buffer A (10 mM Tris-HCl (pH 8), 140 mM NaCl, 1.5 mM MgCl2, 0.5% Nonidet P-40), incubated on ice for 5 min, and then centrifuged at 1,000 rpm for 3 minutes at 4°C. The cytoplasmic fraction remained in the supernatant, while the nuclear fraction was in the pellet. The cytoplasmic fraction was collected and spun again to remove any contaminating nuclear pellet. The nuclear pellet was washed twice in buffer A, and finally with buffer A containing 1% Tween-40 and 0.5% deoxycholic acid.


title: cRNA-seq mock R1

description: cRNA.tsv

data_processing:
3' sequencing adapter sequence were removed from the 50 nt long reads by computing a prefix-suffix sequence alignment (cRNA-seq only)
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use. (cRNA-seq only)
Bowtie 1.0 was used to align all reads to the human genome, Ensembl transcripts (v75), ribosomal rRNA, the HSV1 genome (JN555585, terminal repeats masked), the HSV1 transcripts as well as novel junctions identified in the 4sU data by ContextMap. Only reads aligning to at most 3 distinct genome positions with at most 2 mismatches were kept for further analyses.
Peaks were called by identifying significant enrichment in a sliding-window approach.
Genome_build: JN555585
Supplementary_files_format_and_content: FPKM

source_name: human foreskin fibroblasts (HFF)

growth_protocol: Primary human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 15 were infected with HSV-1 strain 17 at an MOI of 10

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated.
Sequencing libraries were prepared using the cRNA-seq and dRNA-seq inhouse protocols.

treatment_protocol: Cells were infected for 15 min using an MOI of 10. 15min after infection (time point 0h), cell culture media was replaced with fresh media. Cells were harvested prior to or at 8h p.i. cRNA-seq and dRNA-seq libraries were prepared.

value: primary fibroblasts

value: Mock

tag: replicate

value: Replicate 1

tag: enrichment

value: 5' RNA ends enriched


title: MCF-7 Nuc Input

description: Nuclear Input Control small RNAs. Cytoplasmic and nuclear RNA were separated as described previously (Hwang et al. 2007). Briefly, the cell pellets were resuspended in 400 ml/plate lysis buffer A (10 mM Tris-HCl (pH 8), 140 mM NaCl, 1.5 mM MgCl2, 0.5% Nonidet P-40), incubated on ice for 5 min, and then centrifuged at 1,000 rpm for 3 minutes at 4°C. The cytoplasmic fraction remained in the supernatant, while the nuclear fraction was in the pellet. The cytoplasmic fraction was collected and spun again to remove any contaminating nuclear pellet. The nuclear pellet was washed twice in buffer A, and finally with buffer A containing 1% Tween-40 and 0.5% deoxycholic acid.


title: DCTh_1

value: DCTh


title: MCF-7 Nuc

description: Nuclear mall RNAs. Cytoplasmic and nuclear RNA were separated as described previously (Hwang et al. 2007). Briefly, the cell pellets were resuspended in 400 ml/plate lysis buffer A (10 mM Tris-HCl (pH 8), 140 mM NaCl, 1.5 mM MgCl2, 0.5% Nonidet P-40), incubated on ice for 5 min, and then centrifuged at 1,000 rpm for 3 minutes at 4°C. The cytoplasmic fraction remained in the supernatant, while the nuclear fraction was in the pellet. The cytoplasmic fraction was collected and spun again to remove any contaminating nuclear pellet. The nuclear pellet was washed twice in buffer A, and finally with buffer A containing 1% Tween-40 and 0.5% deoxycholic acid.


title: MCF-7 Cyto

description: Cytoplasmic small RNAs. Cytoplasmic and nuclear RNA were separated as described previously (Hwang et al. 2007). Briefly, the cell pellets were resuspended in 400 ml/plate lysis buffer A (10 mM Tris-HCl (pH 8), 140 mM NaCl, 1.5 mM MgCl2, 0.5% Nonidet P-40), incubated on ice for 5 min, and then centrifuged at 1,000 rpm for 3 minutes at 4°C. The cytoplasmic fraction remained in the supernatant, while the nuclear fraction was in the pellet. The cytoplasmic fraction was collected and spun again to remove any contaminating nuclear pellet. The nuclear pellet was washed twice in buffer A, and finally with buffer A containing 1% Tween-40 and 0.5% deoxycholic acid.


title: cRNA-seq mock R2

description: cRNA.tsv

value: Replicate 2


title: MCF7 IgG

description: Small RNAs associated with an IgG control antibody.

value: yes


title: MCF-7 Total

description: Total small RNA component. Small RNAs were size selected during library preparation by gel purification of ligation products comprising small RNAs between 12 and 37 bp.


title: RP mock - Lactimidomycin - Rep 2

description:
Ribosome protected RNA fragments (29-30nt)
Human.B.tsv,HSV.B.tsv

value: NNNCGGANN


title: MFtreg_1

value: Mftreg


title: DCTh_2


title: DCreg_1

value: Dcreg


title: Normal tissue URCONT48Nsp

type: genomic

city: Johannesburg

first: Jacqueline

last: Brown

state: Gauteng

address: 7 York Rd Parktown

department: Molecular Medicine and Haematology

country: South Africa

institute: National Health Laboratory Services

description:
URCONT48Nsp
Hybridized to 250K Nsp SNP array.

hyb_protocol: As per manufacturer (Affymetrix) in GeneChip 640 ovens.

scan_protocol: The arrays were washed using Affymetrix GeneChip 450 Fluidics Stations, and scanned using the GeneChip Scanner 3000 7G.

data_processing: CEL files were generated using the Affymetrix algorithm and were then imported into Partek Genomics Suite for DNA copy number analysis. The copy number data were segmented using the circular binary algorithm in GenePattern (Broad Institute) To assess the significance of gains and losses, the segmentation file was analysed using GISTIC 2.0 (Genomic Identification of Significant Targets in Cancer).

label: Biotin

source_name: normal tissue URCONT48

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: DNA was extracted using a phenol/chloroform protocol from 80% tumour cells that were macrodissected from the tissue blocks. The reference samples were also extracted in the same way. DNA quality was assessed using the Nanodrop, standard gel electrophoresis and a multiplex PCR.

tag: disease state

value: normal

tag: tissue

value: liver

value: male

tag: sample identifier


title: Normal tissue URCONT47Nsp

description:
URCONT47Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT47

value: epididymis

tag: gender


title: Normal tissue URCONT46Nsp

description:
URCONT46Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT46

value: omentum


title: Normal tissue URCONT44Nsp

description:
URCONT44Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT44

value: appendix


title: Normal tissue URCONT43Nsp

description:
URCONT43Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT43

value: larynx


title: Normal tissue URCONT42Nsp

description:
URCONT42
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT42

value: skin


title: Normal tissue URCONT33Nsp

description:
URCONT33Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT33


title: Normal tissue URCONT34Nsp

description:
URCONT34Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT34

value: sigmoid


title: Normal tissue URCONT39Nsp

description:
URCONT39Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT39

value: kidney


title: Esophageal squamous carcinoma 2136_04Nsp

description:
2136_04Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma 2136_04

value: esophageal squamous carcinoma

value: esophageal squamous epithelium

value: female


title: Normal tissue URCONT32Nsp

description:
URCONT32Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT32


title: Esophageal squamous carcinoma 1805_04Nsp

description:
1805_04Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma 1805_04


title: Normal tissue URCONT38Nsp

description:
URCONT38Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT38

value: lymph node


title: Normal tissue URCONT37Nsp

description:
URCONT37Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT37

value: small bowel


title: Normal tissue URCONT29Nsp

description:
URCONT29Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT29


title: Normal tissue URCONT35Nsp

description:
URCONT35Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT35


title: Normal tissue URCONT11Nsp

description:
URCONT11Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT11

value: uterus


title: Esophageal squamous carcinoma 2134_04Nsp

description:
2134_04Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma 2134_04


title: Normal tissue URCONT6Nsp

description:
URCONT6Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT6

value: Fallopian tube


title: Normal tissue URCONT13Nsp

description:
URCONT13Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT13

value: normal


title: Normal tissue URCONT25Nsp

description:
URCONT25Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT25


title: Normal tissue URCONT26Nsp

description:
URCONT26Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT26

value: ovary and tube


title: Normal tissue URCONT28Nsp

description:
URCONT28Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT28


title: Normal tissue URCONT14Nsp

description:
URCONT14Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT14


title: Normal tissue URCONT16Nsp

description:
URCONT16Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT16


title: Normal tissue URCONT27Nsp

description:
URCONT27Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT27


title: Normal tissue URCONT8Nsp

description:
URCONT8Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT8

value: oral biopsy


title: Esophageal squamous carcinoma UROC172Nsp

description:
UROC172Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC172


title: Normal tissue URCONT22Nsp

description:
URCONT22Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT22


title: Normal tissue URCONT3Nsp

description:
URCONT3Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT3


title: Normal tissue URCONT4Nsp

description:
URCONT4Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT4

value: ovary


title: Esophageal squamous carcinoma UROC158Nsp

description:
UROC158Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC158


title: Esophageal squamous carcinoma UROC171Nsp

description:
UROC171Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC171

value: male


title: Esophageal squamous carcinoma UROC151Nsp

description:
UROC151Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC151


title: Normal tissue URCONT5Nsp

description:
URCONT5Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT5


title: Esophageal squamous carcinoma UROC156Nsp

description:
UROC156Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC156


title: Esophageal squamous carcinoma UROC133Nsp

description:
UROC133Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC133

value: unknown


title: Esophageal squamous carcinoma 1708_04Nsp

description:
1708_04Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma 1708_04


title: Esophageal squamous carcinoma UROC144Nsp

description:
UROC144Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC144


title: Esophageal squamous carcinoma UROC142Nsp

description:
UROC142Nsp_2
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC142


title: Esophageal squamous carcinoma UROC167Nsp

description:
UROC167Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC167


title: Normal tissue URCONT19Nsp

description:
URCONT19Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT19

value: endometrium


title: Esophageal squamous carcinoma UROC128Nsp

description:
UROC128Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC128


title: Esophageal squamous carcinoma UROC148Nsp

description:
UROC148Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC148


title: Esophageal squamous carcinoma UROC132Nsp

description:
UROC132Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC132


title: Esophageal squamous carcinoma UROC131Nsp

description:
UROC131Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC131