title: HiC LCL D R1

description: HiC in cells treated with Dox for 24 h. Replicate 1 of 2

source_name: LCL D

value: mouse ES cells E14Tg2a

tag: genotype/variation

tag: kit

value: Dox


title: Normal Control Donor Serum Sample 15

status: Public on Apr 14 2020

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

country: USA

institute: UMDNJ-SOM

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters, PMT of 600, and a pixel size of 5um.

data_processing:
The GPR files were imported into Invitrogen's Prospector v5.2.3 microarray analysis software.  Individual results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.  Further significance analysis was performed using Random Forest (RF).
[Matrix files]  Normalized fluorescence intensities are presented in Relative Fluorescent Units (RFUs).

label: Alexa Fluor 647

molecule: other

organism: Homo sapiens

source_name: Normal Control Donor Serum Sample 15

label_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

extract_protocol: All STRIDE hip fracture repair plasma samples were provided by Johns Hopkins University, and all control serum samples were purchased from BioServe, a commercial biofluid repositiory. All samples were drawn and stored under proper conditions, and collected and used with IRB approval.

tag: individual

value: control

tag: age

tag: gender

value: MALE

tag: sample type

value: serum


title: ChIP CTCFL ID R1

type: SRA

city: New York

first: Nishana

last: Mayilaadumveettil

state: New York

address: 31st Street & East River DR, Receiving Department BLDG Smilow Floor 03, RM 307 (Jane Skok Laboratory)

department: Pathology

institute: NYU Langone health

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 48 h. Chromatin was treated with Rnase befpre ChIP.  Replicate 1 of 2

library_source: genomic

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the GRCm38/mm10 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ChIP-seq
Peaks were called using Macs/1.4
rwas counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

molecule: genomic DNA

organism: Mus musculus

source_name: CTCFL ID + Rnase treatment

growth_protocol: Mouse embryonic stem cells E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin (Sigma ES-006-B) coated dishes (Falcon, 353003) at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM (Thermo Fisher, 11965-118) supplemented with 15% fetal bovine serum (Thermo Fisher, SH30071.03), 100 U/ml penicillin - 100 μg/ml streptomycin (Sigma, P4458), 1 X GlutaMax supplement (Thermo Fisher, 35050-061), 1 mM sodium pyruvate (Thermo Fisher, 11360-070), 1 X MEM non-essential amino-acids (Thermo Fisher, 11140-50), 50 μM b-mercaptoethanol (Sigma, 38171), 104 U/ml leukemia inhibitory factor (Millipore, ESG1107), 3 μM CHIR99021 (Sigma, SML1046) and 1 μM MEK inhibitor PD0325901 (Sigma, PZ0162). The cells were passaged every alternate day by dissociation with TrypLE (Thermo Fisher, 12563011).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen 74104) as per the manufacturer's protocol.
ChIP-seq libraries were constructed using the Illumina Nextera DNA Sample prep kit. RNA seq libraries were prepared using standard Illumina protocols. Hi-C libraries were prepared as per the Arima kit guidelines.

treatment_protocol: For degradation of endogenous CTCF, 500 μM indole-3-acetic acid/IAA (Sigma, I5148) was added to the media. Expression of transgenes were achieved by the addition of doxycycline (Dox, 1 μg/ml) (Sigma, D9891) to the media. The cells were treated with IAA and/or Dox for 2 days for RNA seq and ChIP seq and 4 days for HiC.

tag: tissue

value: Mouse embryonic stem cells

tag: parental cell line

tag: strain

value: 129/Ola, XY

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre

value: Nextera

tag: chip antibody

value: Anti-Flag M2 Magnetic Beads; Sigma (M8823)


title: Dog 1: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract (D1C2)

city: Merelbeke

first: Michael

last: Pelst

address: Salisburylaan 133

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
Sequencing read quantity and quality was checked using FastQC (v0.11.8). Contamination was determined using FastQ Screen (v0.14.0). Adapter trimming and removal of reads having a quality score lower than 20 or containing any ambiguities, was done using cutadapt (v2.5). The remaining high-quality reads were mapped on the CanFam3.1 reference dog genome using STAR (v2.7.2) and features were count at the gene level using RSEM (v1.3.1).
Differential expression analyses of the RNA-sequencing data were done in R using the edgeR (v3.26.8) package. For each analysis, feature counts were normalized using edgeR’s standard normalization method.
To remove uninformative low-count features, those having less than 1 cpm (counts per million) in the number of samples equivalent to the size of the smallest group were discarded.
Statistical testing was done by fitting a general linear model, followed by a quasi-likelihood F-test.
Differentially expressed features were considered statistically significant when having a fold-change of at least 2 (doubling or halving between the compared groups) and a false discovery rate (FDR or adjusted p-value according to Benjamini-Hochberg) smaller than or equal to 0.05.
Genome_build: CanFam3.1 reference dog genome
Supplementary_files_format_and_content: xlsx

molecule: total RNA

organism: Canis lupus familiaris

source_name: Epithelial cells isolated from the sublingual mucosa

growth_protocol: Sublingual biopsies of approximately 0.5x0.5 cm were sampled within 3 hours after euthanasia from 6 privately-owned dogs that were euthanized for medical reasons unrelated to the study (Supplementary Table A). Oral consent to use the corpse for scientific purposes was given by all dog owners. Of one dog, one half of the sublingual biopsy was processed for immunohistochemistry. This sample was submerged in Methocel® MC (Merck), snap-frozen in liquid nitrogen and stored at -80°C. To isolate sublingual cells, biopsies were briefly submerged in 70% ethanol, washed 3 times with Ca2+- and Mg2+-free Dulbecco’s PBS (DPBS, Thermofisher Scientific, Waltham, MA, USA) and incubated in 4 mg/ml Dispase II (Thermofisher Scientific) in DPBS on ice. After 16-24h incubation, the epithelial layer was carefully separated from the underlying subepithelial tissue, followed by incubation of the epithelial and subepithelial tissue in DPBS with 0.25% trypsin (Thermofisher Scientific) and 2.65 mM EDTA for 20 min at room temperature (RT; 18-22°C). Subsequently, cell suspensions were resuspended, trypsin was neutralized with an equal volume of 5% fetal calf serum (FCS) (Merck, Burlington, MA, USA) in DPBS and the cells were filtered over a 70 µm cell strainer (Merck). After centrifugation (400g, 10 min, 18°C), cells were counted and 2.5x105 cells/cm2 were seeded in a culture flask in sublingual epithelial cell culture medium (SECCM; ¾ DMEM, ¼ nutrient mixture F12-Ham (Thermofisher Scientific), 5% FCS, 2 nM 3,3’,5-triiodo-L-thyronine sodium salt, 5 µg/ml recombinant human insulin, 10 ng/ml recombinant human epidermal growth factor, 0.4 µg/ml hydrocortisone, 100 nM L-isoproterenol hydrochloride (Merck), 100 U/ml penicillin, 100 µg/ml streptomycin and 100 µg/ml gentamicin (Thermofisher Scientific)) (27,28). During the first 7 days of culture, the SECCM was supplemented with 2.5 µg/ml amphotericin B (Thermofisher Scientific) and medium was changed daily. Thereafter, medium was replaced every 2-3 days. Cells were expanded, split (0.25% trypsin, 1 mM EDTA in DPBS) at 70-90% confluency and used at passage 2-7 for the experiments. The sublingual epithelial cells were shown to be free of Mycoplasma infection during routine testing using the LookOut® Mycoplasma PCR Detection Kit (Merck) according to the manufacturer’s instructions.

extract_protocol:
RNA extraction and DNase treatment of the samples was performed using the RNeasy mini kit (Qiagen) and RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions. Extracted RNA was stored at -80°C.
Total RNA concentration was measured using the Quant-iT RiboGreen RNA Assay Kit (Thermofisher Scientific). RNA quality was inspected using an RNA 6000 Nano chip on a BioAnalyser (Agilent Technologies, Santa Clara, CA, USA). For each sample, a sequencing library was constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) starting from 500 ng total RNA and amplified by 14 PCR cycles. Quality and size distribution of the libraries were checked on a BioAnalyser (Agilent Technologies) using the high sensitivity Quant-iT dsDNA Assay Kit (Thermofisher Scientific) and a High Sensitivity DNA chip. Library concentration was determined according to Illumina’s Sequencing Library qPCR Quantification Guide on a LightCycler 480 (Roche Life Science, Penzberg, Germany).

treatment_protocol: Canine primary sublingual epithelial cells were seeded in SECCM in a 24-well plate at 30,000 cells/well and incubated overnight at 37°C and 5% CO2. Thereafter, Dermatophagoides farinae extract, TLR ligands, calcitriol or control medium was added for 24h to the cultured cells, the supernatant was collected and stored at -20°C. The products, listed in Table 1, were added in a volume of 400 µl sublingual epithelial cell stimulation medium (SECSM) (¾ DMEM, ¼ Ham’s F-12, 100 U/ml penicillin, 100 µg/ml streptomycin and 100 µg/ml gentamicin). Since calcitriol was dissolved in ethanol, the control wells for calcitriol contained an equal volume of this solvent. To analyze the effect of D. farinae extract in combination with calcitriol, cells were incubated without stimulus, with 20 µg/ml D. farinae extract or with both D. farinae extract and 0.1 µM in SECSM. Additionally, after 6h incubation with 0.1 µM calcitriol and 20 µg/ml D. farinae extract, sublingual epithelial cells were lysed in RLT buffer (RNeasy mini kit, Qiagen, Hilden, Germany) and stored at -80°C.

tag: sample id

value: Dog 1

tag: treatment

value: 20 ug/ml D. farinae extract


title: Normal Control Donor Serum Sample 19

source_name: Normal Control Donor Serum Sample 19


title: JSC15-3 Untreated

type: RNA

city: Tokyo

first: Ryuhei

last: Kawakami

address: 3-8-31, Ariake,Koto-ku

country: Japan

institute: JFCR

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

label: biotin

source_name: Human Patient-derived Gastric Cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: Patient-derived gastric cancer cells were cultured in vitro in dishes and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: 5-FU: 3 mM, 7-day treatment (JSC15-3), 3 mM, 6-day treatment (JSC17-2) and 1 mM, 6-day treatment (JSC17-7) | SN38: 30 nM,  7-day treatment (JSC15-3) | shRNAs: introduced by using lentivirus and selected by 1 mg/mL puromycin for 8 days (JSC15-3)

tag: cell line

tag: cell type

value: Patient-derived Gastric Cancer

value: Untreated


title: JSC15-3 NC

value: NC (non-targeting shRNA)


title: HiC CLC ID R2

description: HiC in cells treated with IAA and Dox for 24 h. Replicate 2 of 2

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the GRCm38/mm10 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ChIP-seq
Peaks were called using Macs/1.4
raw counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: CLC ID

value: CTCF-AID, Tir1, Flag-CLC-mRuby 2 transgene at Tigre

value: Arima

tag: agent

value: IAA and Dox

tag: time point


title: Normal Control Donor Serum Sample 13

source_name: Normal Control Donor Serum Sample 13


title: Dog 5: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract (D5C2)

value: Dog 5

value: Epithelial cells isolated from the sublingual mucosa


title: Dog 4: Canine primary sublingual epithelial cells, no stimulus (D4C1)

value: Dog 4

value: no stimulus


title: JSC15-3 shALDH1A3 #2

value: shALDH1A3 #2


title: Normal Control Donor Serum Sample 18

source_name: Normal Control Donor Serum Sample 18

value: control

value: MALE

value: serum


title: HiC LCL ID R1

description: HiC in cells treated with IAA and Dox for 24 h. Replicate 1 of 2

source_name: LCL ID

value: mouse ES cells E14Tg2a

value: 129/Ola, XY

value: CTCF-AID, Tir1, Flag-LCL-mRuby 2 transgene at Tigre


title: Normal Control Donor Serum Sample 11

source_name: Normal Control Donor Serum Sample 11


title: Normal Control Donor Serum Sample 16

source_name: Normal Control Donor Serum Sample 16


title: Normal Control Donor Serum Sample 17

source_name: Normal Control Donor Serum Sample 17


title: Dog 3: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract (D3C2)

value: Dog 3

value: 20 ug/ml D. farinae extract


title: HiC LCL D R2

description: HiC in cells treated with Dox for 24 h. Replicate 2 of 2

value: Dox


title: Dog 2: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract (D2C2)

value: Dog 2


title: Dog 1: Canine primary sublingual epithelial cells, no stimulus (D1C1)

value: Dog 1


title: Normal Control Donor Serum Sample 14

source_name: Normal Control Donor Serum Sample 14


title: Dog 5: Canine primary sublingual epithelial cells, no stimulus (D5C1)


title: JSC17-7 5-FU

value: Patient-derived Gastric Cancer


title: HiC CLC D R2

source_name: CLC D

value: CTCF-AID, Tir1, Flag-CLC-mRuby 2 transgene at Tigre

value: Arima


title: HiC CLC ID R1

value: IAA and Dox


title: Normal Control Donor Serum Sample 9

source_name: Normal Control Donor Serum Sample 9

value: FEMALE


title: Normal Control Donor Serum Sample 12

source_name: Normal Control Donor Serum Sample 12


title: Dog 3: Canine primary sublingual epithelial cells, no stimulus (D3C1)

value: Epithelial cells isolated from the sublingual mucosa

value: no stimulus


title: JSC17-7 DMSO

value: DMSO


title: JSC17-2 5-FU


title: HiC CTCFL D R2

source_name: CTCFL D

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre


title: HiC CTCFL D R1

value: mouse ES cells E14Tg2a


title: HiC CLC D R1

value: 129/Ola, XY


title: Dog 2: Canine primary sublingual epithelial cells, no stimulus (D2C1)


title: Normal Control Donor Serum Sample 7

source_name: Normal Control Donor Serum Sample 7

value: control

value: serum


title: JSC17-2 DMSO


title: HiC CTCFL ID R2

source_name: CTCFL ID


title: Normal Control Donor Serum Sample 6

source_name: Normal Control Donor Serum Sample 6


title: JSC15-3 SN38


title: Normal Control Donor Serum Sample 10

source_name: Normal Control Donor Serum Sample 10


title: JSC15-3 5-FU

source_name: Human Patient-derived Gastric Cancer


title: HiC CTCFL ID R1


title: Co4

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Adapter sequences were filtered out using the cutadapt software (Marcel Martin (2011)) (http://journal.embnet.org/index.php/embnetjournal/article/view/200)
Reads were aligned to the hg19 genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool.
Genome_build: hg19
Supplementary_files_format_and_content: The myCpG.txt is a tab-delimited text file that contains the location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The column headers are: chrBase, chr, base, strand, coverage, freqC, freqT.

source_name: control_CD34+ fraction of Bone marrow

growth_protocol: We used a two-dimensional “monolayer” system to differentiate human pluripotent stem cells (iPS) into “primitive” hematopoietic progenitor cells (hHPCs) as described (Mills et al. 2014). On day minus 1, iPS clones  were cultured in 100 x 20 mm petri dishes in the presence of 0.5 mM EDTA to reach a 5-10% confluency. On day 0, StemMACS iPS-Brew XF medium was replaced by complete hematopoietic differentiation medium supplemented with 5 ng/ml BMP4 (Peprotech), 50 ng/ml VEGF165 (Peprotech) and 1 μM GSK-3β inhibitor (CHIR99021, Sigma Aldrich). On day 2, this medium was replaced by hematopoietic differentiation medium serum free medium mixed 1:1 with complete StemPro34 medium and supplemented with 1% nonessential amino acids, 1mM L-glutamine, 0.5mg/ml Penicillin-Streptomycin, 0.1mM β-Mercaptoethanol, 1% Insulin-Transferrin-Selenium (ThermoFisher Scientific), 10% bovine serum albumin (BSA, Hyclone, ThermoFisher Scientific) fraction V, and 50 μg/ml ascorbic acid (Sigma Aldrich). This medium was further supplemented with 5ng/ml BMP4, 50ng/ml VEGF165 and 20ng/ml of bFGF. This medium was replaced on day 4 by hematopoietic differentiation medium supplemented with 50ng/ml VEGF165 and 5ng/ml bFGF, on day 6 by hematopoietic differentiation medium supplemented with 50ng/ml VEGF165, 50ng/ml bFGF, 50ng/ml SCF, and 5ng/ml Flt3LG, and on day 8 by hematopoietic differentiation medium supplemented with 50 ng/ml VEGF165, 50ng/ml bFGF, 50ng/ml SCF, 5ng/ml Flt3LG, 10ng/ml Interleukin-6 (IL-6, Peprotech) and 50ng/ml thrombopoietin (TPO, kindly provided by Kirin, Japon). hHPCs sorted at day 10-16 (depending on cell expension) were suspended in serum-free medium supplemented with 50ng/ml SCF, 5ng/ml FLT3LG, 10ng/ml IL-3, 10ng/ml IL-6, 50ng/ml TPO, 1U/ml EPO, 10ng/ml GM-CSF, 10ng/ml G-CSF and 10ng/ml M-CSF (all from Peprotech) for 10 days, with this medium being renewed every 2 days.

extract_protocol:
Twenty-five ng of high-molecular weight genomic DNA of CD34+ from control or patient A iPS clones were used to perform the ERRBS assay as described (Park et al. 2014) and sequenced on a HiSeq 3000 Illumina sequencer
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

tag: disease

value: Healthy Control

value: bone marrow

value: CD34+C43+ iPSCs


title: HPD3

first: Juan

last: Domínguez-Bendala

address: 1450 NW 10th Ave Miami

department: Department of Surgery

institute: Diabetes Research Institute, University of Miami, Miller School of Medicine

description: Cell specific Barcodes

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger v3.0.2 -mkfastq command
Subsequent UMI and cell barcode de-convolution along with mapping to respective genome was performed using 10X Genomics’ cellranger v3.0.2 software package to generate the final digital gene expression matrices
10X Output files were then converted into Seurat objects using Seurat v3.0.0, cells were thresholded, genes normalized and scaled.
Normalized data was used for principal component analysis and t-stochastic neighbour embedding analysis
Normalized data was integrated into a human pancreas single-cell transcriptome, and further comparitive analysis performed.
The barcode/UMI information is being captured in R1, while transcript/biological info is being captured in R2; UMI: 10bp + Barcode:16bp
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are tsv and mtx gene expression matrix files which are inputs for Seurat v3.0.0 for analysis
Supplementary_files_format_and_content: Supplementary files contain Cellranger output files, which have been renamed to ensure clarity. Change file names (of filtered information) to 'matrix.mtx.gz', 'barcodes.tsv.gz' and 'features.tsv.gz' after seperating files into donor specific folders. This is necessary, to allow Seurat to read these files. Seruat cannot read files named in their current form. Detailed information is available here: https://github.com/JDBLab/Pancreas_ductal_scRNAseq
Supplementary_files_format_and_content: alk3n3_gene_expression_matrix.csv: a gene expression count matrix of all the 3 samples compiled into one file.

source_name: Human Exocrine Pancreas

growth_protocol: Cells cultured overnight

extract_protocol:
Single live cells were extracted from cryopreservation buffer using a dead-cell removal kit (Miltenyi, USA)
Single cell RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA).
10x Genomics microfuidics mediated single cell RNA-seq

value: ALK3+ Cells

tag: number of cells

value: Exocrine Pancreas


title: Normal Control Donor Serum Sample 4

source_name: Normal Control Donor Serum Sample 4


title: QP-89 Model Nintedanib

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

country: Spain

institute: IDIBAPS

description: Gene expression from non-tumor liver tissue from chemically-induced model (DEN+CCl4) of HCC and fibrosis treated with Nintedanib for 5 weeks

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Raw expression data from microarrays were normalized using the robust multiarray algorithm (Irizarry RA et al, Nucleic Acids Res, 2003) with a custom probe set definition that mapped probes to Entrez Gene IDs (HTMG430PM_Mm_ENTREZG) (Dai M et al, Nucleic Acids Res, 2005).

source_name: Non-tumor liver tissue from chemically-induced model (DEN+CCl4) of HCC and fibrosis treated with Nintedanib for 5 weeks

label_protocol: Standard Affymetrix protocol

growth_protocol: Chemically-induced model of HCC and fibrosis in male C57BL/6J mice (Harlan Laboratories, n=58) generated by a single injection of N-nitrosodiethylamine (DEN) followed by weekly dosing with carbon tetrachloride (CCl4).Control mice were injected with saline and oil.

extract_protocol: Total RNA was extracted from 20 mg fresh-frozen non-tumoral liver tissue with Trizol reagent (Invitrogen) and purified with RNeasy columns (Qiagen, Valencia, CA). RNA sample concentration and quality were assessed by NanoDrop ND-1000 spectrometer (NanoDrop, Wilmington, DE) and bioanalyzer (Agilent, Palo Alto, CA), respectively.

treatment_protocol: Once fibrosis was established, mice were randomized to receive vehicle or nintedanib (50 mg/kg, Boehringer Ingelheim). Mice were then sacrificed at different time-points and liver and tumor tissue samples were collected and processed.

tag: liver damage

value: Chronic damage

value: Nintedanib


title: HiC CTCFL U R1

description: HiC in untreated cells. Replicate 1 of 2

source_name: CTCFL U

tag: genotype/variation

tag: kit

value: Arima

value: untreated


title: JSC15-3 DMSO

value: Patient-derived Gastric Cancer


title: QP-88 Model Nintedanib


title: HiC CTCFL I R2

description: HiC in cells treated with IAA for 24 h. Replicate 2 of 2

source_name: CTCFL I

value: IAA


title: QP-91 Model Nintedanib


title: QP-90 Model Nintedanib


title: HiC CTCFL I R1

description: HiC in cells treated with IAA for 24 h. Replicate 1 of 2


title: Normal Control Donor Serum Sample 8

source_name: Normal Control Donor Serum Sample 8

tag: individual

tag: age

tag: gender

value: FEMALE


title: QP-87 Model Nintedanib


title: ceRNA CONTROL7

city: Guangzhou

first: Qi

last: Guo

address: Yanjiangxi Road

country: China

institute: Sun Yat-sen University

description: Gene expression in healthy control plasma

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.

scan_protocol: After hybridization, slides were scanned on the Agilent Microarray Scanner (Agilent Technologies, Santa Clara, USA).

data_processing: Data were extracted with Feature Extraction software 12.0.3.1 (Agilent Technologies, Santa Clara, USA).

source_name: plasma, healthy controls

label_protocol: RNA samples from each group were then used to generate biotinylated cRNA targets for the LC Human ceRNA array (version 1.0).

extract_protocol: Total RNA was isolated using a Plasma RNA Purification Mini Kit (Norgen, Thorold, Canada) according to the manufacturer’s instructions and purified using an RNeasy Mini Kit (Qiagen, GmBH, Germany).

treatment_protocol: Whole blood was collected in venous blood collection tubes containing EDTA after fasting overnight, and plasma was separated by centrifugation.

tag: tissue

value: plasma

tag: disease state

value: healthy

value: female


title: Normal Control Donor Serum Sample 2

source_name: Normal Control Donor Serum Sample 2

value: control

tag: sample type


title: ceRNA CONTROL4


title: ceRNA CONTROL2

value: male


title: ceRNA CONTROL6


title: ceRNA CONTROL5


title: ceRNA CONTROL3


title: ceRNA CONTROL1


title: HiC CTCFL U R2

description: HiC in untreated cells. Replicate 2 of 2

tag: parental cell line

value: mouse ES cells E14Tg2a

tag: strain

value: 129/Ola, XY

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre

tag: chip antibody


title: Normal Control Donor Serum Sample 5

source_name: Normal Control Donor Serum Sample 5

value: serum


title: Normal Control Donor Serum Sample 3

source_name: Normal Control Donor Serum Sample 3


title: Normal Control Donor Serum Sample 1

source_name: Normal Control Donor Serum Sample 1


title: HiC CTCF D R2

source_name: CTCF D

value: CTCF-AID, Tir1, Flag-CTCF-mRuby 2 transgene at Tigre

value: Dox


title: HiC CTCF ID R2

source_name: CTCF ID

value: IAA and Dox


title: ceRNA HCM15

description: Gene expression in hypertrophic cardiomyopathy patient plasma

source_name: plasma, hypretrophic cardiomyopathy

value: hypretrophic cardiomyopathy


title: CDR=0 Plasma Sample 18

source_name: CDR=0 Plasma Sample 18

value: hip fracture repair (HFR) patient

tag: clinical dementia ranking (cdr)


title: ceRNA HCM14


title: CDR=0 Plasma Sample 17

source_name: CDR=0 Plasma Sample 17


title: HiC CTCF D R1

value: Arima

tag: agent


title: HiC CTCF ID R1

tag: time point


title: HiC CTCF I R2

source_name: CTCF I

value: IAA


title: CDR=0 Plasma Sample 16

source_name: CDR=0 Plasma Sample 16

value: FEMALE


title: QP-85 Model Nintedanib

value: Chronic damage

tag: treatment

value: Nintedanib


title: QP-86 Model Nintedanib


title: QP-84 Model Nintedanib


title: HiC CTCF I R1


title: HiC CTCF U R2

source_name: CTCF U

value: untreated


title: CDR=0 Plasma Sample 15

source_name: CDR=0 Plasma Sample 15

value: plasma


title: CDR=0 Plasma Sample 14

description: DEL CON-9

source_name: CDR=0 Plasma Sample 14


title: QP-83 Model Nintedanib

source_name: Non-tumor liver tissue from chemically-induced model (DEN+CCl4) of HCC and fibrosis treated with Nintedanib for 5 weeks


title: ceRNA HCM13

value: male


title: HiC CTCF U R1

value: mouse ES cells E14Tg2a


title: QP-94 Model Vehicle

description: Gene expression from non-tumor liver tissue from chemically-induced model (DEN+CCl4) of HCC and fibrosis treated with vehicle for 5 weeks

source_name: Non-tumor liver tissue from chemically-induced model (DEN+CCl4) of HCC and fibrosis treated with vehicle for 5 weeks

value: Vehicle


title: CDR=0 Plasma Sample 13

description: DEL CON-7

source_name: CDR=0 Plasma Sample 13


title: QP-93 Model Vehicle


title: QP-82 Model Nintedanib


title: Wiz-del rep2 (Hi-C)

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive, CB 7100 3360 Genome Sciences Building

institute: UNC Chapel Hill

description: collisions_Wiz-del.txt; inter_30_Wiz-del.hic; merged_loops_Wiz-del.bedpe; contact_domains_25kb_Wiz-del.bedpe

data_processing:
Initial data processing, including merging of replicates, alignment, filtering, and generation of Hi-C contact maps, was perfomed using the Juicer wrapper from the Lieberman-Aiden lab.
Contact domains were called from merged, Knight-Ruiz balanced contact maps at 25kb resolution using the Arrowhead algorithm with default parameters.
Loops were called from merged, Knight-Ruiz balanced contact maps at 5kb, 10kb, and 25kb resolution using the HiCCUPs algorithm with default parameters except: -p 8,4,2 -i 14,10,6
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C matrices are provided in .hic format. Loop and domain calls are provided in .bedpe format.

source_name: Mouse embryonic stem cells v6.5

growth_protocol: V6.5 murine embryonic stem cells (mESCs) (male) were grown on irradiated murine embryonic fibroblasts under standard conditions, as previously described (Dowen et al, 2014)

extract_protocol:
Hi-C libraries were prepared using the Arima Hi-C kit (Arima Genomics) according to manufacturer's specifications, with one modification. Treatment with DNA ligase was performed for one hour instead of the recommended 15 minutes.
Dual-indexed Illumina sequencing libraries were prepared using Kapa Hyper Prep (Kapa Biosciences, cat.#KK8502) according to specifications provided by Arima Genomics, with one modification. Ligation of sequencing adapters was allowed to proceed for 1 hour instead of the recommended 15 minutes.

treatment_protocol: ESCs growing in exponential phase were placed in single cell suspension in 1x PBS with 1% formaldehyde. After 2 minutes, crosslinking was quenched with addition of glycine to 150mM

tag: genotype

value: WIZ deletion

tag: cell line

value: mESC v6.5


title: QP-81 Model Vehicle

tag: liver damage


title: CDR=0 Plasma Sample 12

description: DEL CON-5

source_name: CDR=0 Plasma Sample 12

value: MALE


title: ceRNA HCM10

value: female


title: ceRNA HCM11


title: ceRNA HCM12


title: ceRNA HCM9


title: WT rep1 (Hi-C)

description: collisions_WT.txt; inter_30_WT.hic; ; merged_loops_WT.bedpe; ; contact_domains_25kb_WT.bedpe

value: Wild Type


title: QP-80 Model Vehicle


title: CDR=0 Plasma Sample 11

description: DEL CON-4

source_name: CDR=0 Plasma Sample 11


title: CDR=0 Plasma Sample 10

description: DEL CON-3

source_name: CDR=0 Plasma Sample 10


title: RAD21 WIZdel Rep 2

description:
For RAD21 ChIPs, only the first read of the pair was used for analysis. Thus, the two samples with labels "R1" were concatenated, and the first 50 bp were used for subsequent analysis.
Rad21-WIZdel-ChIPseq.bw

data_processing:
Alignment:  reads were aligned to a hybrid mm10+hg38 genome with  bowtie v 1.2.2 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.9 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v 2016-02-15) with parameters -f BED -g mm -q 0.01
Spike-In Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = 1/(number human reads / 1,000,000)
Coverage File Generation: bigwig files were generated using bedtools (v 2.26) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normalization Factor) followed by ucsctools (v 320) bedGraphToBigWig
Genome_build: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary_files_format_and_content: For each ChIPped factor, a BigWig coverage track of merged replicates is provided for viewing in UCSC genome browser.

extract_protocol: mESCs were crosslinked in 1% formaldehyde (ThermoFisher, 28906) for 5 minutes in PBS and quenched by adding glycine. Cells were lysed using Lysis Buffers 1 and 2, and recovered nuclei resuspended in 1ml Covaris Sonication Buffer (50mM Tris pH 7.5, 10mM EDTA, 0.1% SDS). Human HEK293T nuclei prepared in the same manner were spiked-in to a final concentration of 5%, and nuclei were sheared for 12 minutes using a Covaris E220 water bath sonicator with device settings of duty factor 5, PIP/W of 140, and 200 cycles per burst. Insoluble material was cleared by spinning sonicated lysates for 10 minutes at 21,000rcf. 10µg anti-RAD21 antibody (Bethyl, A300-080A) was incubated for 8 hours with 30µl of Dynabeads in PBS, after which excess antibodies were washed from the beads. 107 cell equivalents of sheared chromatin were incubated overnight with the antibody-bound beads in 1 ml Sonication Buffer 1, washed with Wash Buffers 1, 2, and 3, and crosslinks were reversed overnight. DNA was purified using a ChIP DNA Clean and Concentrator Kit (Zymo, D5201) according to manufacturer’s instructions. Sequencing libraries were prepared using a Hyper Prep kit (Kapa Biosciences, KK8502) according to manufacturer’s instructions.

tag: antibody

value: anti-RAD21; Bethyl A300-080A


title: CDR=0 Plasma Sample 9

description: DEL CON-24

source_name: CDR=0 Plasma Sample 9

tag: individual

value: hip fracture repair (HFR) patient


title: RAD21 WIZdel Rep 1


title: ceRNA HCM7

value: hypretrophic cardiomyopathy

tag: age


title: QP-92 Model Vehicle


title: RAD21 Rep 2

description:
For RAD21 ChIPs, only the first read of the pair was used for analysis. Thus, the two samples with labels "R1" were concatenated, and the first 50 bp were used for subsequent analysis.
Rad21-ChIPseq.bw

extract_protocol: mESCs were crosslinked in 1% formaldehyde (ThermoFisher, 28906) for 5 minutes in PBS and quenched by adding glycine. Cells were lysed using Lysis Buffers 1 and 2, and recovered nuclei resuspended in 1ml Covaris Sonication Buffer (50mM Tris pH 7.5, 10mM EDTA, 0.1% SDS). Human HEK293T nuclei prepared in the same manner were spiked-in to a final concentration of 5%, and nuclei were sheared for 12 minutes using a Covaris E220 water bath sonicator with device settings of duty factor 5, PIP/W of 140, and 200 cycles per burst. Insoluble material was cleared by spinning sonicated lysates for 10 minutes at 21,000rcf. 10µg anti-RAD21 antibody (Bethyl, A300-080A) was incubated for 8 hours with 30µl of Dynabeads in PBS, after which excess antibodies were washed from the beads. 107 cell equivalents of sheared chromatin were incubated overnight with the antibody-bound beads in 1 ml Sonication Buffer 1, washed with Wash Buffers 1, 2, and 3, and crosslinks were reversed overnight. DNA was purified using a ChIP DNA Clean and Concentrator Kit (Zymo, D5201) according to manufacturer’s instructions. Sequencing libraries were prepared using a Hyper Prep kit (Kapa Biosciences, KK8502) according to manufacturer’s instructions, and 150bp paired-end sequencing reads were collected using the Illumina NovaSeq SP sequencing platform and reagents.


title: CDR=0 Plasma Sample 8

description: DEL CON-19

source_name: CDR=0 Plasma Sample 8

tag: gender


title: RAD21 Rep 1

extract_protocol: mESCs were crosslinked in 1% formaldehyde (ThermoFisher, 28906) for 5 minutes in PBS and quenched by adding glycine. Cells were lysed using Lysis Buffers 1 and 2, and recovered nuclei resuspended in 1ml Covaris Sonication Buffer (50mM Tris pH 7.5, 10mM EDTA, 0.1% SDS). Human HEK293T nuclei prepared in the same manner were spiked-in to a final concentration of 5%, and nuclei were sheared for 12 minutes using a Covaris E220 water bath sonicator with device settings of duty factor 5, PIP/W of 140, and 200 cycles per burst. Insoluble material was cleared by spinning sonicated lysates for 10 minutes at 21,000rcf. 10µg anti-RAD21 antibody (Bethyl, A300-080A) was incubated for 8 hours with 30µl of Dynabeads in PBS, after which excess antibodies were washed from the beads. 107 cell equivalents of sheared chromatin were incubated overnight with the antibody-bound beads in 1 ml Sonication Buffer 1, washed with Wash Buffers 1, 2, and 3, and crosslinks were reversed overnight as described above. DNA was purified using a ChIP DNA Clean and Concentrator Kit (Zymo, D5201) according to manufacturer’s instructions. Sequencing libraries were prepared using a Hyper Prep kit (Kapa Biosciences, KK8502) according to manufacturer’s instructions, and 150bp paired-end sequencing reads were collected using the Illumina NovaSeq SP sequencing platform and reagents.


title: CDR=0 Plasma Sample 7

description: DEL CON-18

source_name: CDR=0 Plasma Sample 7


title: ceRNA HCM6

source_name: plasma, hypretrophic cardiomyopathy

tag: tissue


title: QP-78 Model Vehicle


title: QP-79 Model Vehicle


title: QP-76 Model Vehicle


title: BisSeq_infect_3T3_rep2

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
bisulfite-treated, rRNA-depleted RNA from infected NIH3T3 cells
BisSeq_pNCA_proviral.txt
viral_m5C_position_fraction.txt
total RNA

data_processing:
Adapter sequences and reads less than 30 bases were removed using the program FastX clipper.
Reads were mapped to a bisulfite-converted version of the pNCA proviral sequence (i.e., all cytosines were changed to thymines) using Bowtie 1, allowing for up to three mismatches. To more easily visualize on the IGV browser, a randomly selected subset of 10 million clipped reads was aligned to the MLV sequence.Candidate m5C sites were identified using the bam-readcount tool and visually inspected on the IGV browser.
Supplementary_files_format_and_content: tab-delimited text file showing the m5C fraction of candidate m5C sites on the MLV genome; text file of bisulfite-converted MLV proviral sequence used for alignment

organism:
Mus musculus
Murine leukemia virus

source_name: mouse fibroblasts (NIH3T3 cells)

growth_protocol: Mouse embryonic fibroblasts (NIH3T3 cells; ATCC) were cultured in DMEM containing 100 U/mL penicillin-streptomycin, 10% fetal bovine serum, and 2 mM L-glutamine.

extract_protocol:
To prepare virus for bisulfite sequencing, viral particles were first concentrated by sedimenting filtered media from infected cells through 2-mL cushions of 20% sucrose and viral RNAs isolated using Trizol (Invitrogen. For infected cellular samples, total RNA was extracted in Trizol.
Cellular and viral RNAs were DNase treated. Additionally, cellular samples were subjected to RiboMinus (Thermo) treatment to deplete ribosomal RNAs. The Zymogen EZ RNA Methylation kit protocol was followed to convert unmethylated cytosines to uracil. Recovered RNA was used to generate sequencing libraries with the TruSeq Stranded mRNA kit (Illumina). cDNA libraries were amplified by 12 cycles of PCR, loaded onto a HiSeq 2000 Illumina sequencer, and sequenced for 100 bases at The University of Chicago Genomics Facility.
RNA bisulfite sequencing

treatment_protocol: NIH3T3 cells were infected (20:1 multiplicity of infection) with murine leukemia virus (MLV) particles produced from HEK293T cells in media containing 8 μg/mL hexadimethrine bromide (Polybrene; American Bioanalytical).

tag: passages


title: QP-77 Model Vehicle


title: Mouse_term_myometrial_cell_5_RNAseq

city: Nashville

first: Dhivya

last: Sudhan

state: TN

address: 777 Preston Research Building

department: Hematology/Oncology Division

institute: Vanderbilt University

data_processing:
Quality control on raw reads was performed using FastQC.
STAR v2.5.3a used for reads mapping.
FeatureCounts v1.15.2 was used to count the number of mapped reads to each gene.
BiomaRt package was used to map mouse genes to human genes, and only uniquely mapped genes between human and mouse were kept.
Significantly differentially expressed genes with FDR-adjusted p-value≤0.01 and absolute fold-change≥2.0 were detected by DESeq2 (v1.18.1).
Genome Ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package.
Gene set enrichment analysis was performed using the GSEA package.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: Term primary myometrial cell rep 5

growth_protocol: Primary human and mouse myometrial cells, as well as PHM1 cells were cultured in DMEM (Corning MT17205CV) supplemented with 10% fetal bovine serum (FBS), 2mM L-Glutamine, 100 U/ml penicillin-streptomycin. hTERT-HM cells were cultured in DMEM-F12 (Gibco 11-039-021) supplemented with 10% FBS and 100 U/ml penicillin-streptomycin. Primary adult aorta cells were cultured in  vascular cell basal medium (ATCC® PCS-100-030™). Fetal aorta and DA cells were cultured in DMEM (Gibco 11965-092) supplemented with 10% FBS and 100 U/ml penicillin-streptomycin.

extract_protocol:
Flash frozen tissues stored in -80oC were homogenized in TRIzolTM reagent (Invitrogen) using a bead homogenizer (Fisherbrand™ Bead Mill 24) for two 20sec cycles at 5000 rpm. Near-confluent cells were lysed using 1mL TRIzolTM reagent. Total RNA was isolated per the Trizol’s manufacturer instructions,  DNase-treated (DNA-free kit, Ambion) and then sent to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core for quality control and cDNA library preparation. The RNA was analyzed with an Agilent Bioanalyzer 2100, which showed that all samples had an RIN>8.
The coding RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and paired end libraries were generated using the NEBNext Ultra II Directional RNA Library Kit for Illumina (7760).

tag: gestational age

value: day 19

tag: cell type

value: Term primary myometrial cell


title: CDR=0 Plasma Sample 5

description: DEL CON-16

source_name: CDR=0 Plasma Sample 5

value: FEMALE

tag: sample type


title: QP-50 Control Vehicle

description: Gene expression from healthy liver tissue

source_name: Healthy liver tissue

value: Healthy


title: ceRNA HCM8

tag: disease state


title: ceRNA HCM4


title: ceRNA HCM3


title: WT_Pa_monoculture_rep3

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Basecalls - Illumina native app
Trimming - Illumina native app to trim adapter sequences
Quality Control CLC Genomics Workbench: quality score = 0.05, ambiguous bases = 2, auto adapter trim = NO, trim bases 5' and 3', filter length above =  NO,  filter length below = NO
Alingment to Pseudomonas aeruginosa strain PA14  genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
Extraction of unmapped reads - CLC Workbench
Allignment to Ca SC5314  genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
Reporting - CLC Workbench export raw counts, TPM, CPM and RPKM
Genome_build: UCBPP-PA14 (www.pseudomonas.com)  and SC5314 (www.candidagenome.org , Assembly22)
Supplementary_files_format_and_content: csv including TPM

organism: Pseudomonas aeruginosa

source_name: single species colony biofilm

growth_protocol: C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µ of P. aeruginosa overnight culture from LB was spotted on top. Co-culture colony biofilms were incubated at 30℃ for 16 hours before cells were collected.

extract_protocol:
Cell pellets were dissolved in Trizol and cells were lysed by bead beating. Lysate was phase separated by centrifugation and from the aqueous phase RNA was precipitated by linear acrylimide. Centrifugation collected the RNA into a pellet that was, after supernatent removal, washed with ethanol and resuspended into deionized, nuclease-free water.
RNA was treated with Dnase using the Rneasy MinElute protocol and ribo-depletion using RiboZero (bacteria). Library prep was done as the Illumina TrueSeq Stranded RNAseq.

treatment_protocol: P. aerguinosa was grown on WT and adh1∆/∆ C. albicans. P. aeruginosa and C. albicans were also grown alone.

tag: strain

tag: taxonomy id


title: ceRNA HCM5


title: CDR=0 Plasma Sample 4

description: DEL CON-15

source_name: CDR=0 Plasma Sample 4

tag: clinical dementia ranking (cdr)


title: WT_Pa_monoculture_rep2


title: Mouse_term_myometrial_cell_2_RNAseq

source_name: Term primary myometrial cell rep 2


title: BisSeq_infect_3T3_rep1


title: Mouse_term_myometrial_cell_3_RNAseq

source_name: Term primary myometrial cell rep 3


title: QP-4 Control Vehicle

tag: treatment


title: ceRNA HCM1


title: QP-49 Control Vehicle


title: WT_Pa_monoculture_rep1


title: CDR=0 Plasma Sample 6

description: DEL CON-17

source_name: CDR=0 Plasma Sample 6


title: CDR=0 Plasma Sample 2

description: DEL CON-11

source_name: CDR=0 Plasma Sample 2


title: Mouse_term_myometrial_cell_1_RNAseq

source_name: Term primary myometrial cell rep 1


title: CDR=0 Plasma Sample 1

description: DEL CON-1

source_name: CDR=0 Plasma Sample 1


title: ceRNA HCM2


title: MYB30-OE rep2

city: Bei Jing

first: Yan

last: Yan

address: 2 yuanmingyuan west road, haidian district,

institute: china agriculture university

description:
GENE_19-1_vs_1303_featurediff.txt
GENE_Col-1_vs_19-1_featurediff.txt

data_processing:
Sequencing was carried out with the Illumina HiSeq 2000 platform and the resulting reads were mapped to the reference genome of Arabidopsis thaliana (TAIR10) with TopHat (http://tophat.cbcb.umd.edu).
Transcript expression was evaluated by cuffdiff (http://cufflinks.cbcb.umd.edu),
transcript abundance was estimated by fragments per kilobase of exon model per million mapped fragments (FPKM)
Differentially expressed genes were selected using Student’s t-test with P<0.05.
Supplementary_files_format_and_content: tab-delimited text files include logFC   logCPM

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Plants were grown on MS mediated plates under white light condition for 4 days

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings using the RNeasy Plant Mini kit (TIANGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT, MYB30-OE, and myb30 mutant  under continue white light condition for 4 days

tag: genotype

value: MYB30- over expression

value: whole seedling

tag: ecotype

value: Col

value: 4 days old seedling


title: MYB30-OE rep3


title: Mouse_term_myometrial_cell_4_RNAseq

source_name: Term primary myometrial cell rep 4


title: Shield_Elavl1a_MO_NAIN3.rep1

city: Beijing

first: Jinsong

last: Zhang

state: Beijing

department: Life Science

institute: Tsinghua University

description: processed data file: shield-elavl1a-mo.icshape.out.txt

data_processing:
Library strategy: icSHAPE
trimmed 3' adaptor from reads by cutadapt
trimmed low quality bases by trimmomatic
collapsed duplicated reads as icSHAPE pipeline
trimmed the leading 13nt UMI
mapping reads to zebrafish reference transcriptome(z10) by bowtie2 using the same parameters in icSHAPE pipeline
calculate rpkm as icshape pipeline
calulate reverse transcription stop sites(RT stop) as icshape pipeline
RT stop was normalized by using sliding window, then icSHAPE score was calculated as icshape pipeline
Genome_build: z10
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Refseq ID, second is transcript length, third is RPKM, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab-delimited text files for read counts and rpkm files. First column is the Refseq ID, second is  transcript length, third is the unique mapped reads count, fourth is the mulitple mapped reads count, fifth is the RPKM.

molecule: polyA RNA

organism: Danio rerio

growth_protocol: Zebrafish wild-type strain AB was raised in system water at 28.5°C under standard conditions.

extract_protocol:
The  RNA or modified RNA was extracted or cleaned up and eluted in RNase-free water by using TRIzol® Reagent (invitrogen).To enrich polyA RNA, the total RNA was subjected to polyA selection.
For icSHAPE, the in vivo modified RNA and unmodified RNA were biotinylated by copper-free click reaction, followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix (70 mM Tris 7.0, 18mM MgCl2, 5mM DTT, 4 U/µl RiboLock, 0.1 U/µl FastAP (Life Technology), 2 U/µl T4 PNK(NEB)) before 3’ adapter ligation with addition of 10 µl ligation mix (5mM DTT, 0.5µM 5’ adenylated and 3’-blocked linker (3’-bio for unmodified, 3’-ddc for modified), 0.66 U/µl T4 RNA ligase (NEB, M0437M), 15% PEG8000, 1X RNA ligase buffer) and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP, 0.2µl SSB (Promega), 0.8µl Ribolock and 1µl 5’ Deadenylase (NEB) in 1X NEB buffer 2 (NEB) at 30℃ for 90 min. And then 1µl RecJf (NEB) was added with another incubation at 37℃ for 1 hour. The following procedures, including reverse transcription, biotin-streptavadin enrichment, size selection of cDNA, circularization and PCR amplification, were the same as described in the standard protocol. For RNA-seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA) according to manufacturer’s protocol.

treatment_protocol: For Elavl1a morphants generation, morpholino oligonucleotides of elavl1a were injected into one-cell stage embryos, then embryos were harvested at desired stages. For in vivo treatment, cells was incubated with NAI-N3 or DMSO at 28.5°C for 5min

tag: strain background

value: AB

value: elavl1a morphants zebrafish embryos cells


title: myb30 rep3

description:
GENE_Col-1_vs_1303_featurediff.txt
GENE_19-1_vs_1303_featurediff.txt

value: myb30 mutant


title: Shield_Elavl1a_MO_NAIN3.rep2


title: Shield_Elavl1a_MO_DMSO.rep2

value: DMSO


title: myb30 rep2


title: CDR=0.5 Plasma Sample 20

description: DEL CON-22

source_name: CDR=0.5 Plasma Sample 20

extract_protocol: All STRIDE hip fracture repair plasma samples were provided by Johns Hopkins University, and all control serum samples were purchased from BioServe, a commercial biofluid repositiory. All samples were drawn and stored under proper conditions, and collected and used with IRB approval.

value: MALE

value: plasma


title: CDR=0 Plasma Sample 3

description: DEL CON-14

source_name: CDR=0 Plasma Sample 3


title: CDR=0.5 Plasma Sample 19

description: DEL CON-21

source_name: CDR=0.5 Plasma Sample 19


title: Shield_Elavl1a_MO_DMSO.rep1


title: myb30 rep1


title: CDR=0.5 Plasma Sample 18

description: DEL CON-20

source_name: CDR=0.5 Plasma Sample 18


title: Col rep3

description:
GENE_Col-1_vs_1303_featurediff.txt
GENE_Col-1_vs_19-1_featurediff.txt

value: WT


title: Sphere_Elavl1a_MO_NAIN3.rep2

description: processed data file: sphere-elavl1a-mo.icshape.out.txt


title: RNase H1

city: GuangZhou

first: Zhang

middle: Can

last: Feng

address: Graduate school, building 493, 135 xingang west road

description: RNase H1

data_processing:
Adaptor sequences were trimmed off by Cutadapt (version 2.8).
Reads aligned to the hg19 reference genomes by using Bowtie2 (version 2.3.3.1) with default parameters
Low mapping quality reads and duplicated reads were removed by Samtools
The remaining reads were converted to normalized BigWig files for genomic visualization using Deeptools (version 3.4.1), with reads coverage for each window of 100 bp was normalized by CPM (Counts Per Million mapped reads).
R-loop peaks were identified between IP and input using MACS2 (version 2.2.4) with the parameters '--nomodel –nolambda'.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files include CPM values for each Sample ...

extract_protocol:
Fragmentary DNA were isolated with S9.6 antibody
DNA libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit and standard Illumina protocols

value: Human Embryonic Kidney

tag: rnase h treatment

value: no

tag: antibody


title: NC, Input DNA

description: Input DNA

value: yes


title: siMETTL3+I-PpoI


title: siMETTL3


title: siMETTL3, Input DNA

description: Input DNA


title: NC+I-PpoI

description: NC+I-PpoI


title: Sphere_Elavl1a_MO_NAIN3.rep1

tag: age


title: CDR=0.5 Plasma Sample 17

description: DEL CON-13

data_processing:
The GPR files were imported into Invitrogen's Prospector v5.2.3 microarray analysis software.  Individual results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.  Further significance analysis was performed using Random Forest (RF).
[Matrix files]  Normalized fluorescence intensities are presented in Relative Fluorescent Units (RFUs).

source_name: CDR=0.5 Plasma Sample 17

tag: individual

value: hip fracture repair (HFR) patient

tag: gender


title: MYB30-OE rep1

tag: tissue


title: Col rep2


title: NC

description: NC


title: Sphere_Elavl1a_MO_DMSO.rep2


title: CDR=0.5 Plasma Sample 21

description: DEL CON-23

source_name: CDR=0.5 Plasma Sample 21

value: FEMALE


title: Sphere_Elavl1a_MO_DMSO.rep1


title: Col rep1


title: 15C

city: Deyang

first: Ning

last: Zou

state: Sichuan

address: No. 173, Taishan North Road, Jingyang District

institute: People's Hospital of Deyang City

data_processing:
By using Base Calling version 0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), the FASTQ sequence data were obtained from the RNA-sequencing data.
Reads with low quality (adaptor sequences, sequences with a quality score <20, and sequences with an N base rate of raw reads >10%) were removed with Cutadapt version 1.9.1 (https://cutadapt.readthedocs.io/en/stable/) to obtain the clean reads.
TopHat release 2.2.1 (http://tophat.cbcb.umd.edu/) was used to align the clean reads with the human reference genome, Ensemble GRCh38.p7 (ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens).
With Cuffquant version 2.2.1 (http://cufflinks.cbcb.umd.edu/), expression of mRNAs and lncRNAs was normalized and outputted.
Fragments per Kilobase of exon per million fragments mapped (FPKM) was used to determine the transcription abundance of lncRNAs and mRNAs. With Cuffdiff version 2.2.1 (http://cufflinks.cbcb.umd.edu/), FPKMs of lncRNAs and mRNAs were calculated.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: fpkm value

source_name: Luminal-B breast cancer adjacent tissue samples

extract_protocol:
RNA isolation was conducted on the manufacturer’s protocol with PAXgene blood RNA kit (PreAnalytiX GmbH, Hombrechtikon, CH, Switzerland).
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: CDR=0.5 Plasma Sample 15

description: DEL CON-10

source_name: CDR=0.5 Plasma Sample 15


title: F3_LB_BETA-N102F2N2C

city: Toronto

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

data_processing:
Sequenced reads were aligned to cavPor3 genome assembly using TOPHAT2 and default settings
Gene read counts were generated using Genomic Alignemnts (version 1.6.3) and outliers removed using Cook's distance with default cutoffs.
Count data were normalized by residuals using RUVSeq (version 3.12.1)
Differential gene expression was assessed using EdgeR's (version 3.12.1) genral linear model likelihood ratio test and FDR-corrected p< 0.05 was considered significant.
Bisulfite treated DNA Seq reads were trimmed using Trimmomatic-0.32, then aligned to the guinea pig genome (cavPor3) using bsmap-2.74 v0.12.5. Picard-tools-1.93 was used to remove duplicates. Methylation levels were determined for individual CpG sites using bsmap-2.74 with a minimal coverage of 10 reads.
Changes in methylation for 100bp windows (50bp apart) and individual CpGs were detected using the calculateDiffMeth() function from MethylKit (v.1.4.0) in R (version 3.2.3). Data were annotated using Homer v4.6 with the annotatePeaks script and CavPor3 genome.
Genome_build: cavPor3
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample- EdgeR output, Methylkit output 100bp methylatio output and single nucleotide resolution (SNR) methylation output

organism: Cavia porcellus

source_name: Hippocampus

extract_protocol:
Brains were removed, and hippocampus was surgically extracted and flash frozen on dry ice. RNA was harvested using AllPrep RNA/DNA/microRNA Universal Extraction Kit (Qiagen Cat#80224).TruSeq RNA Library Preparation Kit V2 (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; Bisulfite DNA libraries were prepared from purified DNA, using the KAPA Library Prep Kit Illumina (Roche) according SeqCap Epi Enrichment System User’s guide

tag: generation

value: Beta

value: post natal day 40

tag: Sex

value: Female


title: CDR=0.5 Plasma Sample 14

first: Robert

last: Nagele

description: DEL CON-8

source_name: CDR=0.5 Plasma Sample 14

tag: sample type


title: 9C

value: Luminal-B breast cancer adjacent tissue samples


title: shield NAIN3_icSHAPE

description:
shield NAIN3
shield.icshape.out

data_processing:
Library strategy: icSHAPE
icSHAPE computational pipeline reference: PubMedID: 26766114, DOI: 10.1038/nprot.2016.011
trimmed 3' adaptor from reads by cutadapt
trimmed low quality bases by trimmomatic
collapsed duplicated reads as icSHAPE pipeline
trimmed the leading 13nt UMI
mapping reads to zebrafish reference transcriptome(z10) by bowtie2 using the same parameters in icSHAPE pipeline
calculate rpkm as icshape pipeline
calculate reverse transcription stop sites(RT stop) as icshape pipeline
RT stop was normalized by using sliding window, then icSHAPE score was calculated as icshape pipeline
Genome_build: z10
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Refseq ID, second is transcript length, third is RPKM, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab-delimited text files for read counts and rpkm files. First column is the Refseq ID, second is  transcript length, third is the unique mapped reads count, fourth is the mulitple mapped reads count, fifth is the RPKM.

source_name: shield NAIN3

extract_protocol:
The  RNA or modified RNA was extracted or cleaned up and eluted in RNase-free water by using TRIzol® Reagent (invitrogen).To enrich polyA RNA, the total RNA was subjected to polyA selection.
For icSHAPE, the in vivo modified RNA and unmodified RNA were biotinylated by copper-free click reaction, followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix (70 mM Tris 7.0, 18mM MgCl2, 5mM DTT, 4 U/µl RiboLock, 0.1 U/µl FastAP (Life Technology), 2 U/µl T4 PNK(NEB)) before 3’ adapter ligation with addition of 10 µl ligation mix (5mM DTT, 0.5µM 5’ adenylated and 3’-blocked linker (3’-bio for unmodified, 3’-ddc for modified), 0.66 U/µl T4 RNA ligase (NEB, M0437M), 15% PEG8000, 1X RNA ligase buffer) and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP, 0.2µl SSB (Promega), 0.8µl Ribolock and 1µl 5’ Deadenylase (NEB) in 1X NEB buffer 2 (NEB) at 30°C for 90 min. And then 1µl RecJf (NEB) was added with another incubation at 37°C for 1 hour. The following procedures, including reverse transcription, biotin-streptavadin enrichment, size selection of cDNA, circularization and PCR amplification, were the same as described in the standard protocol. For RNA-seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA) according to manufacturer’s protocol.

treatment_protocol: For in vivo treatment, cells was incubated with NAI-N3 or DMSO at 28.5  C for 5min.

value: zebrafish embryos

tag: genotype/variation

value: normal zebrafish embryos cells


title: shield DMSO_icSHAPE

description:
shield DMSO
shield.icshape.out

source_name: shield DMSO

tag: strain

value: AB


title: CDR=0.5 Plasma Sample 13

description: DEL CON-6

source_name: CDR=0.5 Plasma Sample 13


title: 5C


title: sphere NAIN3_icSHAPE

description:
sphere NAIN3
sphere.icshape.out

source_name: sphere NAIN3


title: F3_LB_BETA-N143F1N2A


title: F3_LB_BETA-N162F3-N1A


title: sphere DMSO_icSHAPE

description:
sphere DMSO
sphere.icshape.out

source_name: sphere DMSO


title: 15A

source_name: Luminal-B breast cancer tissue samples

value: Luminal-B breast cancer tissue samples


title: CDR=0.5 Plasma Sample 12

description: DEL CON-2

source_name: CDR=0.5 Plasma Sample 12


title: 11A


title: CDR=0.5 Plasma Sample 10

source_name: CDR=0.5 Plasma Sample 10


title: F3_LB_VEH-N125F1N3D

value: Control


title: F3_LB_BETA-N100F1N3C


title: 2h NAIN3_icSHAPE

description:
2h NAIN3
2h.icshape.out

source_name: 2h NAIN3


title: 9A


title: 11C


title: CDR=0.5 Plasma Sample 9

source_name: CDR=0.5 Plasma Sample 9


title: 4-cell NAIN3_icSHAPE

description:
4-cell NAIN3
4-cell.icshape.out

source_name: 4-cell NAIN3


title: 2h DMSO_icSHAPE

description:
2h DMSO
2h.icshape.out

source_name: 2h DMSO


title: 5A


title: F3_LB_VEH-N146F4N2B


title: CDR=0.5 Plasma Sample 8

source_name: CDR=0.5 Plasma Sample 8


title: adh1_Ca_monoculture_rep3

organism: Candida albicans

source_name: single species colony biofilm

tag: taxonomy id


title: F3_LB_VEH-N166F4N1B


title: 4-cell DMSO_icSHAPE

description:
4-cell DMSO
4-cell.icshape.out

source_name: 4-cell DMSO


title: F3_LB_EPI-BETA-N152-34

source_name: Hippocampus


title: CDR=0.5 Plasma Sample 7

source_name: CDR=0.5 Plasma Sample 7

tag: clinical dementia ranking (cdr)


title: CDR=0.5 Plasma Sample 6

source_name: CDR=0.5 Plasma Sample 6


title: adh1_Ca_monoculture_rep2


title: F3_LB_VEH-N166F4N3B

tag: treatment


title: CDR=0.5 Plasma Sample 5

source_name: CDR=0.5 Plasma Sample 5

value: MALE


title: 1-cell DMSO_icSHAPE

description:
1-cell DMSO
1-cell.icshape.out

source_name: 1-cell DMSO


title: fertilized egg NAIN3_icSHAPE

description:
fertilized egg NAIN3
fertilized_egg.icshape.out

source_name: fertilized egg NAIN3


title: CDR=0.5 Plasma Sample 4

source_name: CDR=0.5 Plasma Sample 4

value: plasma


title: F3_LB_VEH-N173F3N1C


title: F3_LB_VEH-N137F3N2C


title: F2_LB_BETA-170F2N2


title: WT_Ca_monoculture_rep3


title: WT_Ca_monoculture_rep1


title: F2_LB_BETA-N187F2N1


title: shield Flag-Elavl1a iCLIP rep2

description: shield Flag-Elavl1a iCLIP rep2

data_processing:
The proceesing procedure is similar to CTK tool(https://zhanglab.c2b2.columbia.edu/index.php/ICLIP_data_analysis_using_CTK). First, we trimmed 3' adaptor from reads by cutadapt
collapsed duplicated reads by fastq2collapse.pl in CTK tool
stripped  5’ degenerated barcode
mapped clean reads to zebrafish reference genome(z10) by bwa(v0.7.17).
data from replicates was merged for peak calling
We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters -big -s -maxgap "-1"
peaks are identified using tag2peak.pl with parameters -big -ss -v --prefix "CITS" -gap 25 -p 0.05
Genome_build: z10
Supplementary_files_format_and_content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0-based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus, peak height(PH), expected PH/background(PH0) and pvalue(P). The fifth  column represents the peak height.

source_name: zebrafish embryos

extract_protocol:
iCLIP-seq was carried out as previously described (Despic et al., 2017). Breifly, flag-elavl1a mRNA injected embryos were collected at 4 h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 (Stratalinker 2400, Stratagene), lysed, and subjected to mild RNA fragmentation. Crosslinked RNA-proteins complexes were immunopurified using Anti-FLAG M2 Magnetic Beads (Merck, M8823) for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted
Library construction was performed by using Smarter smRNA-Seq kit (Clontech Laboratories Inc)

tag: cell type


title: CDR=0.5 Plasma Sample 2

source_name: CDR=0.5 Plasma Sample 2


title: WT_Ca_monoculture_rep2


title: CDR=0.5 Plasma Sample 3

source_name: CDR=0.5 Plasma Sample 3


title: shield Flag-Elavl1a iCLIP rep1

description: shield Flag-Elavl1a iCLIP rep1


title: adh1_Ca_monoculture_rep1


title: sphere Flag-Elavl1a iCLIP rep2

description: sphere Flag-Elavl1a iCLIP rep2


title: sphere Flag-Elavl1a iCLIP rep1

description: sphere Flag-Elavl1a iCLIP rep1


title: fertilized egg DMSO_icSHAPE

description:
fertilized egg DMSO
fertilized_egg.icshape.out

source_name: fertilized egg DMSO


title: 1-cell NAIN3_icSHAPE

description:
1-cell NAIN3
1-cell.icshape.out

source_name: 1-cell NAIN3


title: F3_LB_BETA-N170F2N1C


title: Cap_Meth 3 rep2

first: Rashim Pal

last: Singh

address: 101, College Street

institute: Princess Margaret Cancer Centre, UHN

data_processing:
ATAC: Differentially accessible regions were calculated using the DiffBind and EdgeR packages in R. Regions with an absolute fold-change >= 1.5 and an FDR value <= 0.05 were defined as significantly differentially accessible regions.
RNA seq: After removing genes whose cpm (counts per million reads) were less than 0.5 to remove noise, edgeR was used to estimate differential expression by applying a generalized linear model between the control samples and the cells isolated after MB6 treatment and MB6 and PEN treatment. A score that ranks genes from top up regulated in the MB6 samples and MB6PEN samples to top down regulated when compared to control samples was calculated using the formula `-log10(pvalue) * sign(logFC)`.
Cap meth seq: Data is analyzed using the MethylKit R package. Differentially methylated sites were identified and ranked based on percentage of methylation difference >25% and q-value <0.01. Differentially methylated sites were mapped and associated to their nearby genes (5kb upstream, 1kb downstream of transcription start site) for annotation purpose. Gene Ontology (GO) and pathway analysis were performed using default parameters of Bioconductor package rGREAT
Genome_build: Human
Supplementary_files_format_and_content: bigwig for ATAC seq, tsv for RNA and cap meth seq

source_name: OCI-AML2 cells

growth_protocol: Cells were grown in IMDM+10% FCS and passaged every 3 days.

extract_protocol:
For cap meth seq DNA was extracted with Dneasy kit for qiagen (Cat 67506), For RNA seq RNA was isolated with RNeasy kit (Cat 74134). ATAC seq was performed as described previously (Corces, R., Trevino, A.E., Hamilton, E.G., Greenside, P.G., Sinnott-Armstrong, N.A., Vesuna, S., Satpathy, A.T., Rubin, A.J., Montine, K.S., Wu, B., et al. (2017). An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962.)
For RNA seq: Prior to analysis, read adapters and low quality ends were removed using Trim Galore v. 0.4.0. Reads were aligned against hg19 using Tophat v. 2.0.11. Read counts per gene were obtained through htseq-count v.0.6.1p2 in the mode “intersection_nonempty”.    Gene read counts were normalized using the TMM method available from the edgeR_3.24.3 package.
For ATAC seq: ATAC samples were preprocessed according to the ENCODE ATAC-seq pipeline. Single-end reads were aligned to the hg19 genome using Bowtie2 with the --local parameter, reads with MAPQ scores < 30 were filtered out with Samtools, duplicates were removed using Sambamba, and TN5 tagAlign shifted files were created. MACS2 was used to call peaks with the following parameters: -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR –keep-dup all --call-summits. Peaks were later filtered at a q-value threshold of 0.0001 for further analyses.  Peak counts and sizes for each replicate were calculated using a custom Python script, and Jaccard indices for similarities between called peaks was calculated using BEDTools.
For cap meth seq: Following company’s protocol (TruSeq-Methyl Capture EPIC, cat # FC-151-1002, Illumina Inc., San Diego, CA) libraries were prepared using 500 ng of genomic DNA. DNA was sonicated using a Covaris LE220 sonicator (Covaris, Woburn, MA) to obtain products of 180–220 bp. DNA was end-repaired, A-tailed and ligated with methylated indexed-adapters to create pre-capture DNA libraries. All pre-capture libraries were hybridized to the EPIC oligos. Hybridized products were subjected to bisulfite conversion. The bisulfite-treated libraries were PCR-amplified. Libraries were sequenced 100 bp paired-end on Illumina NovaSeq-6000

treatment_protocol: Cells were treated with drugs for 48 hrs before processing

value: Acute Myeloid leukemia cell line

value: mitoblock-6 and penicillamine


title: F2_LB_VEH-N181F3N4


title: CDR=0.5 Plasma Sample 1

address: 2 Medical Center Drive

institute: UMDNJ-SOM

source_name: CDR=0.5 Plasma Sample 1


title: F2_LB_BETA-N75F3N1


title: F2_LB_VEH-N196F1N3


title: F2_LB_VEH-N188F4N2


title: 786-0_VSVD51+Herceptin

city: Ottawa

first: Mohammed

last: Selman

state: ON

address: 501 Smyth Road

department: Cancer Center

institute: Ottawa Hospital

hyb_protocol: cRNA  was Hybridized for 16 hr at 45°C to Affymetrix Human PrimeView Array. Performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing:
Microarray data was processed using Transcriptome Analysis Console (TAC) 3.0 under default parameters of Gene Level Differential Expression Analysis.
The value definition was carried out with the Affymetrix Expression Console Software.

source_name: 786-0, drug treated and infected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 786-0 cells were grown in in HyQ high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10 % fetal calf serum and incubated at 37 °C in a 5% CO2 humidified incubator.

extract_protocol: Twenty-four hours post infection, RNA was collected using an RNA-easy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Cells were pretreated for 4hours with Kadcyla, Herceptin, colchicine or the vehicle. Following pre-treatment, the cells were infected with VSVΔ51 at an MOI of 0.01 or left uninfected.

tag: cell line

value: renal cell adenocarcinoma cells

tag: time point

value: 24 hour after treatment


title: F2_LB_VEH-N191F1N1


title: 786-0_VSVD51+Colchine


title: elavl1a morphant 6h rna-seq rep1

description: elavl1a morphant 6h rna-seq rep1

data_processing:
trimmed 3' adaptor from reads by cutadapt
trimmed low quality bases by trimmomatic
collapsed duplicated reads as icSHAPE pipeline
trimmed the leading 13nt UMI
mapping reads to zebrafish reference transcriptome(z10) by bowtie2 using the same parameters in icSHAPE pipeline
calculate rpkm as icshape pipeline
calculate reverse transcription stop sites(RT stop) as icshape pipeline
RT stop was normalized by using sliding window, then icSHAPE score was calculated as icshape pipeline
Genome_build: z10
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Refseq ID, second is transcript length, third is RPKM, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab-delimited text files for read counts and rpkm files. First column is the Refseq ID, second is  transcript length, third is the unique mapped reads count, fourth is the mulitple mapped reads count, fifth is the RPKM.

source_name: elavl1a morphant 6h rna-seq rep1

treatment_protocol: For Elavl1a morphants generation, morpholino oligonucleotides of elavl1a were injected into one-cell stage embryos, then embryos were harvested at desired stages

value: elavl1a morphants zebrafish embryos cells


title: 786-0_VSVD51+Kadcyla


title: elavl1a morphant 6h rna-seq rep2

description: elavl1a morphant 6h rna-seq rep2

source_name: elavl1a morphant 6h rna-seq rep2


title: Hep3B cells, shPSPC1

city: Taipei, Taiwan

first: Tang

middle: K

last: Tang

state: Taiwan

address: 28 Sec. 2, Academia Rd. Nankang, Taipei 115

department: Institute of biomedical science

country: Taiwan

institute: Academia Sinica

description: Knockdown of PSPC1 from Hep3B cells

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC contentthe clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Qualified reads after filtering low-quality data were analyzed using   TopHat  v2.0.  12. and HTSeq v0.6.1 for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Hep3B cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted from cancer cell lines by NucleoSpin RNA XS (Macherey Nagel, Duren, Germany).
A total amount of 3 μg RNA per sample was used as in put material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out. using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H. Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: genotype

value: PSPC1 knockdown


title: 786-0_Kadcyla

source_name: 786-0, drug treated

value: Kadcyla


title: elavl1a morphant 4h rna-seq rep2

description: elavl1a morphant 4h rna-seq rep2

source_name: elavl1a morphant 4h rna-seq rep2


title: F2_LB_VEH-N128F1N2

source_name: Hippocampus

value: post natal day 40


title: 786-0_Herceptin

value: Herceptin


title: Cap_Meth 3 rep1


title: F2_LB_BETA-N171F2N3

value: Beta

value: Female


title: control 6h rna-seq rep2

description: control 6h rna-seq rep2

source_name: control 6h rna-seq rep2

value: zebrafish embryos

value: normal zebrafish embryos cells


title: F2_LB_BETA-N175F1N2


title: Cap_Meth 2 rep3


title: 786-0_VSVD51_1

source_name: 786-0, infected


title: Cap_Meth 2 rep1


title: 786-0_VSVD51_2


title: 786-0_Colchine

value: Colchine


title: F2_LB_BETA-N194F2N2


title: Hep3B cells, shLaz

description: Knockdown of control shLaz from Hep3B cells

value: control


title: Cap_Meth 2 rep2


title: elavl1a morphant 4h rna-seq rep1

description: elavl1a morphant 4h rna-seq rep1

source_name: elavl1a morphant 4h rna-seq rep1

value: AB


title: H_PANC1 sgBAP1_IR

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip® scanner

data_processing: Affymetrix console, PrimeView Human Gene Expression Array, RMA normalization

label: Biotin

source_name: PANC1, sgBAP1 + IR

label_protocol: biotin

growth_protocol: DMEM 10% fetal bovine serum

extract_protocol: RNeasy Mini Kit (Qiagen)

value: pancreatic cancer cell line PANC-1

value: BAP1 deletion (sgBAP1)

value: IR (10Gy)


title: CDR=0.5 Plasma Sample 16

city: Stratford

description: DEL CON-12

source_name: CDR=0.5 Plasma Sample 16

value: hip fracture repair (HFR) patient

value: FEMALE

value: plasma


title: F2_LB_VEH-N173F3N2

value: Control


title: control 6h rna-seq rep1

description: control 6h rna-seq rep1

source_name: control 6h rna-seq rep1


title: F1_LB_EPI-BETA-N14F3-11


title: 786-0_Untreated_1

source_name: 786-0, untreated

value: renal cell adenocarcinoma cells

value: none (untreated)

value: 24 hour after treatment


title: control 4h rna-seq rep2

description: control 4h rna-seq rep2

source_name: control 4h rna-seq rep2


title: Cap_Meth 1 rep2

value: Acute Myeloid leukemia cell line

value: untreated


title: 786-0_Untreated_2


title: ATAC 3  rep2

value: mitoblock-6 and penicillamine


title: Cap_Meth 1 rep1


title: control 4h rna-seq rep1

description: control 4h rna-seq rep1

source_name: control 4h rna-seq rep1

value: zebrafish embryos

value: normal zebrafish embryos cells


title: E_PANC1_IR

source_name: PANC1, IR (10Gy)

value: Wildtype


title: Cap_Meth 1 rep3

source_name: OCI-AML2 cells


title: control 2h rna-seq rep1

description: control 2h rna-seq rep1

source_name: control 2h rna-seq rep1

value: AB


title: F1_LB_VEH-N181F1

value: post natal day 40

value: Female


title: F_PANC1_IR

value: pancreatic cancer cell line PANC-1

value: IR (10Gy)


title: G_PANC1 sgBAP1_IR

value: BAP1 deletion (sgBAP1)


title: ATAC 2  rep3


title: ATAC 2  rep2


title: ATAC 3  rep1


title: C_PANC1 sgBAP1

source_name: PANC1, sgBAP1


title: F1_LB_VEH-N147F2


title: control 2h rna-seq rep2

description: control 2h rna-seq rep2

source_name: control 2h rna-seq rep2


title: ATAC 2  rep1


title: F1_LB_BETA-N97F3

value: Beta


title: F1_LB_EPI-VEH-N109F1-9

value: Control


title: F1_LB_BETA-N96F2


title: TS3_Tumor Plasma

city: Boston

first: Sunita

middle: R

last: Setlur

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital

description: Nanostring miRNA V1.5 Assay

hyb_protocol: Following this, the ligated targets were hybridized with capture and reporter probes at 65°C for 18 hours.

scan_protocol: The next day, the hybridized probes were purified on nCounter Prep Station and counted on nCounter Digital Analyzer.

data_processing: The data was analyzed using nSolver. Briefly, miRNA normalization was carried out using the top 100 expressed miRNAs (i.e. top 10% of miRNAs expressed above background) for tissue samples without any background subtraction. A similar strategy was used to normalize the data from plasma samples. The metastatic tumor sample M5 failed the normalization QC and was excluded from further analysis. Similarly, the control plasma sample CS1 was excluded from the analysis.

source_name: Test serum from individuals with tumors

label_protocol: Plasma and tissue extracted miRNAs were subjected to nCounter miRNA sample preparation according to the manufacturer’s instructions. Briefly, 100ng and 10ng miRNA from tissue and plasma samples respectively, were ligated with unique oligonucleotide tags (miR-tag).  The label used is a digital molecular barcode in this platform

growth_protocol: Samples were frozen in -80°C freezer prior to extraction

extract_protocol: Norgen’s Animal Tissue RNA Purification Kit and Plasma/Serum RNA Purification Kits, respectively as per manufacturer’s instructions. The samples were subjected to an on-column Dnase digestion step during extraction

treatment_protocol: Tissue samples were placed on dry ice and the tissue was excised for RNA extraction

value: Plasma


title: F1_LB_VEH-N92F1


title: TS4_Tumor Plasma

description: Nanostring miRNA V1.5 Assay


title: F1_LB_BETA-N41F2


title: D_PANC1 sgBAP1


title: ATAC 1  rep2


title: ATAC 1  rep3


title: B_PANC1


title: F1_LB_BETA-N54F1


title: TS1_Tumor Plasma

description: Nanostring miRNA V1.5 Assay


title: TS2_Tumor Plasma

description: Nanostring miRNA V1.5 Assay


title: A_PANC1


title: ATAC 1  rep1


title: CS3_Control Plasma

description: Nanostring miRNA V1.5 Assay

source_name: Control sample


title: F1_LB_BETA-N21F2

source_name: Hippocampus


title: CDR=0.5 Plasma Sample 11

source_name: CDR=0.5 Plasma Sample 11

value: hip fracture repair (HFR) patient

value: FEMALE

value: plasma


title: F1_LB_VEH-N173F4


title: T250_4-d growth_rep3

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom Array 4x44K (GPL22578) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Mycroarray Scanner System (Agilent) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (GE1_105_Dec08 and Grid: 076115_D_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Zea mays

source_name: T250 seedlings grown for 4d in a NS withou N

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol:
Maize (Zea mays L.) seeds of two inbred lines (Lo5 and T250) previously soaked in water for 24 h, were allowed to germinate in the dark at 26°C for 4d. The seedlings were then transferred in pots containing 2.2 L of 0.5 mM CaSO4
CaSO4 aerated solution for 48h under controlled climatic conditions (day/night photoperiod, 16 h/8 h; Photosynthetically Active Radiation, PAR, 220 µE m-2s-1; temperature 27 °C). .

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol:
Seedling of Lo5 and T250 were then grown in the same conditions for 4d using a nutrient solution without N with the following composition: 100 µM MgSO4, 200 µM K2SO4, 400 µM CaSO4, 175 µM KH2PO4, 5 µM KCl, 0.05 µM
NaMoO4, 2.5 µM H3BO3, 0.2 µM MnSO4, 0.2 µM ZnSO4, 0.05 µM CuSO4, and 2 µM Fe‐EDTA, pH= 6.0.

value: root


title: F3_Control6_SGM31


title: CS4_Control Plasma

description: Nanostring miRNA V1.5 Assay


title: CS2_Control Plasma

description: Nanostring miRNA V1.5 Assay


title: M6_Metastasis

description: Nanostring miRNA V1.5 Assay

source_name: Ovarian tumor

value: Ovarian tumor


title: F3_Control5_SGM29


title: M4_Metastasis

description: Nanostring miRNA V1.5 Assay

source_name: Peritoneal Metastatic sample

value: Perinoteal metastasis


title: T250_4-d growth_rep2


title: T250_1-d growth_rep2

source_name: T250 seedlings grown for 1d in a NS withou N


title: F3_Control4_SGM27


title: M3_Metastasis

description: Nanostring miRNA V1.5 Assay


title: M2_Metastasis

description: Nanostring miRNA V1.5 Assay


title: T250_4-d growth_rep1


title: T250_1-d growth_rep3


title: F3_Control3_SGM25


title: M1_Metastasis

description: Nanostring miRNA V1.5 Assay


title: F1_LB_VEH-N144F2


title: FT5_Doxycycline induced FT

description: Nanostring miRNA V1.5 Assay

source_name: Doxycycline induced tube

value: Fallopian tube


title: F3_Control2_SGM24


title: FT4_Doxycycline induced FT

description: Nanostring miRNA V1.5 Assay


title: T250_0-d growth_rep3

source_name: T250 seedlings grown for 0d in a NS withou N


title: F3_Control1_SGM23


title: Human_term_tissue_2_RNASeq

data_processing:
Quality control on raw reads was performed using FastQC.
STAR v2.5.3a used for reads mapping.
FeatureCounts v1.15.2 was used to count the number of mapped reads to each gene.
BiomaRt package was used to map mouse genes to human genes, and only uniquely mapped genes between human and mouse were kept.
Significantly differentially expressed genes with FDR-adjusted p-value≤0.01 and absolute fold-change≥2.0 were detected by DESeq2 (v1.18.1).
Genome Ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package.
Gene set enrichment analysis was performed using the GSEA package.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: Term myometrial tissue rep 5

tag: gestational age

value: Term myometrial tissue


title: T250_0-d growth_rep2


title: T250_0-d growth_rep1


title: F3_Beta7_SGM30

tag: age


title: FT3_Doxycycline induced FT

description: Nanostring miRNA V1.5 Assay


title: Lo5_4-d growth_rep2

source_name: Lo5 seedlings grown for 4d in a NS withou N


title: Human_term_tissue_1_RNASeq

source_name: Term myometrial tissue rep 4


title: Lo5_4-d growth_rep3


title: T250_1-d growth_rep1


title: F3_Beta6_SGM34


title: FT2_Doxycycline induced FT

description: Nanostring miRNA V1.5 Assay


title: Human_term_tissue_3_RNASeq

source_name: Term myometrial tissue rep 3


title: FT1_Doxycycline induced FT

description: Nanostring miRNA V1.5 Assay


title: Lo5_4-d growth_rep1


title: Human_term_tissue_4_RNASeq

source_name: Term myometrial tissue rep 1


title: Human_term_tissue_5_RNASeq

source_name: Term myometrial tissue rep 2


title: F3_Beta5_SGM36


title: CT5_Control FT

description: Nanostring miRNA V1.5 Assay

source_name: Control tube


title: F3_Beta2_SGM22


title: Lo5_1-d growth_rep3

source_name: Lo5 seedlings grown for 1d in a NS withou N


title: CT4_Control FT

description: Nanostring miRNA V1.5 Assay


title: Lo5_1-d growth_rep2


title: F3_Beta3_SGM26


title: Human_term_myometrial_cell_2_RNASeq

source_name: Term primary myometrial cell rep 5

value: Term primary myometrial cell


title: Human_term_myometrial_cell_4_RNASeq

source_name: Term primary myometrial cell rep 4


title: Human_term_myometrial_cell_3_RNASeq

source_name: Term primary myometrial cell rep 3


title: CT2_Control FT

description: Nanostring miRNA V1.5 Assay


title: F2_Control6_SGM17

source_name: Hippocampus

value: post natal day 40


title: Lo5_0-d growth_rep3

source_name: Lo5 seedlings grown for 0d in a NS withou N


title: CT3_Control FT

description: Nanostring miRNA V1.5 Assay


title: F3_Beta1_SGM21

value: Female


title: Human_term_myometrial_cell_5_RNASeq

source_name: Term primary myometrial cell rep 2


title: Lo5_1-d growth_rep1


title: F3_Beta4_SGM28


title: Lo5_0-d growth_rep2


title: Male1

city: Los Angeles

first: Gage

last: Crump

state: CA

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

description: fresh 5uM 4-oh tamoxifen added at 4 hours post fertilization embryos,  washed after 2h

data_processing:
10X Genomic Cellranger v3.0.0 was used for demultiplexing, alignment, and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences (EGFP, mCherry, and TagBFP). QC step for the library was performed along with the Cellranger alignment process.
The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed.
To reduce the batch effects caused by the different strategies, we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library.
The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes.
With the aligned  CCA space, we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited file with cell barcode information, tab-delimited file with gene names, sparse matrix file with raw count associated with previous two files

source_name: Pituitary

growth_protocol: 6months old animals (Males and Male1) and 3month old animal for transplant

extract_protocol:
Single cell was partitioned through Chromium platform (10X Genomic) which encapsulate each cell in individual GEMs. The cell lysis, polyA pull down, tagging with cell barcode, and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell 3' Reagent Kits was used for this RNA extraction step.
After cell-barcoding the extracted RNA, the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell 3' Reagent Kits. Two size selections were performed for long fragments (> 1000 bps) and short fragments (< 1000 bps) before fragmentation and after finalization respectively.

value: Pituitary

value: 6 months


title: F2_Control5_SGM16


title: Human_term_myometrial_cell_1_RNASeq

source_name: Term primary myometrial cell rep 1

extract_protocol:
Flash frozen tissues stored in -80oC were homogenized in TRIzolTM reagent (Invitrogen) using a bead homogenizer (Fisherbrand™ Bead Mill 24) for two 20sec cycles at 5000 rpm. Near-confluent cells were lysed using 1mL TRIzolTM reagent. Total RNA was isolated per the Trizol’s manufacturer instructions,  DNase-treated (DNA-free kit, Ambion) and then sent to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core for quality control and cDNA library preparation. The RNA was analyzed with an Agilent Bioanalyzer 2100, which showed that all samples had an RIN>8.
The coding RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and paired end libraries were generated using the NEBNext Ultra II Directional RNA Library Kit for Illumina (7760).


title: Males


title: Human_PHM1_cell_4_RNASeq

source_name: PHM1 cell rep 4

tag: passage

value: PHM1 cell


title: Transplant

description: donor cells (ubi:loxP-EGFP-loxP-mCherry) were injected with mRNA taram-a and grafted into host (bact:loxP-TagBFP-loxP-dsRed)

value: mosaic animal:(ubi:loxP-EGFP-loxP-mCherry) + (bact:loxP-TagBFP-loxP-dsRed)

value: graft transplantation during early embryogenesis

value: 3 months


title: Lo5_0-d growth_rep1


title: F2_Control2_SGM13

value: Control


title: Human_PHM1_cell_3_RNASeq

source_name: PHM1 cell rep 3


title: Human_PHM1_cell_2_RNASeq

source_name: PHM1 cell rep 2


title: F2_Control3_SGM14


title: DKO_3

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Liver-specific Tsc1/Depdc5 DKO

data_processing:
Each sample produced more than 20M clean reads, that were mapped to the mm9 reference genome using STAR.
Then, Cufflinks was used to generate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) table.
Genome_build: mm9
Supplementary_files_format_and_content: A csv file including FPKM values for all samples.

source_name: Liver-specific Tsc1/Depdc5 DKO

growth_protocol: Normal rearing condition

extract_protocol:
Total liver RNA was extracted using Trizol. mRNA was enriched through Oligo dT Selection.
Library was constructed at BGI following their standard protocol (Library construction + Sequencing (20M reads, BGISeq 50SE)); DNA nanoball synthesis and sequencing on BGISEQ platform

treatment_protocol: Normal rearing condition

value: Liver

value: 8 weeks


title: DKO_1

description: Liver-specific Tsc1/Depdc5 DKO


title: CD8+Cho 0.75 [Yi-Q17007]

city: Houston

first: xingzhe

last: ma

state: TX

address: 6565 fannin street

department: cancer center

institute: houston methodist hospital

hyb_protocol: GeneChip Hybridization

scan_protocol: AGCC

data_processing: Affymetrix GeneChip Command Console (AGCC) Software

label_protocol: WT Sense Target Labeling

growth_protocol: T cell culture

extract_protocol: Trizol RNA extration

treatment_protocol: CD8 under Tc1 cytokine condition and CD8 under Tc1 cytokine condition with 0.5 or 0.75 cholesterol treatment

tag: protocol

value: Tc1 cytokine condition with 0.75 microgram per ml cholesterol treatment


title: F2_Beta6_SGM33

value: Beta


title: THP-1 macrophages, acLDL

city: New York City

first: Coen

last: van Solingen

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

description: cholesterol loaded

data_processing:
provided data sheet from SABiosciences
CT-values, 2^deltadeltaCT

label: SYBR

growth_protocol: RPMI + FCS and PS

extract_protocol: RNA isolation by miRNA Isolation kit (SABiosciences)

treatment_protocol: loading: acLDL (37.5 ug/mL) for 24 hours. Depletion; 5 uM simvastatin for 24 hours

value: thp-1 macrophages

value: acLDL to load with cholesterol


title: Human_PHM1_cell_1_RNAseq

city: Nashville

first: Dhivya

last: Sudhan

address: 777 Preston Research Building

institute: Vanderbilt University

source_name: PHM1 cell rep 1


title: Depdc5_2

description: Liver-specific Depdc5 knockout

source_name: Liver-specific Depdc5 knockout

tag: tissue


title: F2_Control1_SGM12

tag: generation


title: Human_hTERT_cell_4_RNASeq

source_name: hTERT-HM cell rep 4

value: hTERT-HM

value: hTERT-HM cell


title: Depdc5_1

description: Liver-specific Depdc5 knockout


title: PAC414_2

city: Atlanta

first: Joanna

middle: B

last: Goldberg

state: Georgia

address: O. Wayne Rollins Research Center, Room 3009 1510 Clifton Road NE

institute: Emory University

data_processing:
RNAseq reads were trimmed using cutadapt v2.3 with a minimum length cutoff of 18bp. The reads were then mapped to PAO1 refseq genome NC_002516.2 using bowtie2 v2.3.5 with end-to-end alignment.  The number of reads mapped to each genomic feature was calculated using HTSeq v11.1 and features with less than 10 mapped reads were discarded
Genome_build: PAO1 refseq genome NC_002516.2
Supplementary_files_format_and_content: .count.txt files contain the number of reads mapped to each genomic feature calculated using HTSeq

growth_protocol: Overnight cultures of the P. aeruginosa strains were grown in 3ml MOPS-succinate, cultures were back diluted to an OD600 of 0.01 in 20 ml MOPS-succinate and allowed to grow to exponential phase, shaking at 200 rpm.

extract_protocol:
Cells were lysed by bead beating and RNA was precipitated using chloroform and isopropanol. Pellets were washed with ethanol and quantified using NanoDrop.
mRNA was enriched using Ambion MICROBExpress kit. Enriched mRNA was fragmented using NEBNext Fragmentation Module kit and libraries were prepared using NEBNext Multiplex Small RNA Library Prep kit.

treatment_protocol: 2 ml aliquots from each culture were added directly to 10ml of RNAlater, stored at 4°C for 24 hours, and then transferred to -80°C until samples were processed.

value: mucA22 algP-

tag: group

value: mucoid


title: PAC412_2

value: Wild Type algP-

value: non-mucoid


title: PAC414_1


title: F2_Beta5_SGM20

value: post natal day 40

tag: Sex

value: Female


title: F2_Control4_SGM15


title: CD8 [Yi-Q17005]

value: Tc1 cytokine condition


title: Tsc1_2

description: Liver-specific Tsc1 knockout

source_name: Liver-specific Tsc1 knockout


title: F2_Beta4_SGM19


title: Human_hTERT_cell_1_RNASeq

source_name: hTERT-HM cell rep 3


title: Human_hTERT_cell_3_RNASeq

source_name: hTERT-HM cell rep 2


title: CD8+Cho 0.5 [Yi-Q17006]

source_name: CD8+Cho 0.5

value: Tc1 cytokine condition with 0.5 microgram per ml cholesterol treatment


title: PAC412_1


title: Human_hTERT_cell_2_RNASeq

source_name: hTERT-HM cell rep 1


title: F2_Beta2_SGM10

source_name: Hippocampus


title: PDO300_2


title: Con_3

description: Control

source_name: Control


title: F2_Beta3_SGM18


title: THP-1 macrophages, statin

state: New York

description: cholesterol depleted

value: statin to deplete cholesterol


title: PDO300_1


title: Human_fetal_da_cell_2_RNASeq

source_name: Immortalized fetal DA cell rep 6

value: Immortalized fetal DA cell


title: F2_Beta1_SGM11


title: PAO1_2

value: Wild Type


title: Human_fetal_da_cell_6_RNASeq

source_name: Immortalized fetal DA cell rep 5


title: Con_1

description: Control

value: Liver

value: 8 weeks


title: Human_fetal_da_cell_5_RNASeq

source_name: Immortalized fetal DA cell rep 3


title: Human_fetal_da_cell_4_RNASeq

source_name: Immortalized fetal DA cell rep 4


title: F1_Control5_SGM8

value: Control