title: MgCl2_day3_10h_3

status: Public on Feb 13 2018

city: Potsdam

first: Joachim

last: Kopka

state: Brandenburg

address: Am Muehlenberg 1

department: Infrastructure Groups and Service Units

country: Germany

institute: Max Planck Institute For Molecular Plant Physiology

description: Sample AS

data_processing:
Sequence data of all samples were mapped with STAR v2.5.2a using default parameters (Dobin et al. 2013). Ensembl version 31 (TAIR10) genome reference in FASTA format and Ensembl version 31 cDNA Annotation in GTF format were used for genome indexing
Anti-strand read counts from the ReadsPerGene files of all 18 samples were merged in order to perform a differential expression analysis with DeSeq2 (Love et al. 2014) as guided by the rnaseqGene Bioconductor workflow (https://www.bioconductor.org/help/workflows/rnaseqGene/). Briefly, samples were grouped by their three replicate parameters, read count data were then loaded with DESeqDataSetFromMatrix to create a DeSeqDataSet object to subsequently run the standard analysis consisting of the functions DESeq and Results. Transcript abundance data were expressed as log2-transformed fold changes (log2fc) of mature primed versus mock-treated leaves from single plants.
Genome_build: EnsemblPlants version 31 of Arabidopsis thaliana
Supplementary_files_format_and_content: Default STAR output files (ASCII format): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

organism: Arabidopsis thaliana

source_name: MgCl2_day3_10h_single young systemic leaf

growth_protocol: Arabidopsis Col-0 plants were germinated on half-strength MS medium. After 10 days plants were individually transferred to single pots with peat substrate. Plants were grown in a growth chamber with a 16 h light phase at 150 µmol m-2s-2, 20°C at night, 22°C during the day, and relative air humidity of 70%. 4 week old plants were used for the experiment.

extract_protocol:
Leaf harvests at day 3 were done at 10 h and 15 h after dawn and at day 4 at 9 h after dawn. Frozen leaf tissue (40 - 100 mg) from three independent replicates each of bacteria-primed and mock treated plants was ground (2 x 45 s, maximum frequency) by a Retsch mill (MM 400, Retsch, Haan, Germany). Each harvest was a single young systemic leaf from a single rosette. The harvested systemic leaves were all developmentally younger than the previously locally infected leaves. RNA was extracted with the RNeasy Plant Mini Kit according to the manual (QIAGEN GmbH, Hilden, Germany). RNA was quantified with a Qubit® RNA HS Assay Kit (ThermoFisher Scientific Life Technologies GmbH, Darmstadt, Germany) and RNA quality was further assessed by agarose gel electrophoresis.
Library preparation and sequencing was done at the Max-Planck-Genome Centre (Cologne, Germany) according to the manufacturer's protocols. Briefly 500 ng of mRNA was poly-A enriched by applying the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra directional RNA library prep kit for Illumina was used to construct the library before amplification in 12 PCR cycles. Sequencing was performed on a Illumina HiSeq 3000 sequencer.

treatment_protocol: Three lower mature leaves per plant were inoculated 5 h before the end of the light phase, i.e. 11 h after light on (dawn), by syringe-infiltration with ~15 µl of P. syringae avrRpm1 (PstRpm1) in 10 mM MgCl2 at OD600= 0.02 (107 cfu/ml), mock treatment consisted of 10 mM MgCl2.

tag: ecotype background

tag: age

value: 4 week old plants

value: 10 mM MgCl2 (mock treatment)

tag: harvest time after treatment

value: single young systemic leaf


title: MgCl2_day3_10h_2

type: SRA

description: Sample AR

library_source: transcriptomic

molecule: polyA RNA

tag: treated with

tag: tissue


title: Rpm1_day3_10h_3

description: Sample AN

source_name: Rpm1_day3_10h_single young systemic leaf

value: P. syringae avrRpm1 (PstRpm1) in 10 mM MgCl2


title: Panax-notoginseng-whole-plant-sample-M1

status: Public on Feb 14 2018

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

description: small RNA

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequences whose lengths are greater than or equal to 18 bp (the 3' adapter sequences of reads had been removed by the sequencing facility)
Sort and remove repetitive sequences
Calculate the counts of unique sequences
The unique sequences were aligned to a self-assembled transcriptome with SOAP2
Supplementary_files_format_and_content: sequences and count values

molecule: total RNA

organism: Panax notoginseng

source_name: grow in Wenshan, Yunnan, China

growth_protocol: The Panax notoginseng were grown in field in Wenshan, Yunnan ,China

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Small RNA libraries were prepared by following the Illumina's protocol.

treatment_protocol: no treatment

value: whole plant


title: MgCl2_day3_10h_1

description: Sample AQ


title: MgCl2_day4_9h_3

description: Sample AD

source_name: MgCl2_day4_9h_single young systemic leaf


title: Rpm1_day4_9h_3

description: Sample X

source_name: Rpm1_day4_9h_single young systemic leaf


title: Gwiazda_D0_3

city: Poznań

first: Marcin

middle: Andrzej

last: Pieczynski

address: Wieniawskiego 1

country: Poland

institute: Adam Mickiewicz University

description:
Processed data file: res_gd0_gd6_deseq_full.tsv
Processed data file: res_gd0_gd10_deseq_full.tsv
Processed data file: res_gd0_ob0_deseq_full.tsv

data_processing:
Clean reads were first tested for quality with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then, as the quality was not questionable, mapped to the reference potato genome (Solanaceae Genomics Resource, S. tuberosum Group Phureja DM1-3 Assembly Version 3 DM, PGSC Version 4.03 Pseudomolecule Sequence) using TopHat2 [PMID: 23618408] software. Number of mapped reads was obtained using FluxCapacitor v. 1.6.1 [PMID: 20220756] and a Python script - fluxgtf2counts.py, which retrieves and concatenates transcripts counts from flux capacitor GTF files (available at https://github.com/lpryszcz/bin/blob/master/fluxgtf2counts.py). FluxCapacitor is a program that predicts abundances for transcript molecules and alternative splicing events from RNA-seq experiments. The input for the FluxCapacitor is the annotation of a reference transcriptome (Solanaceae Genomics Resource, PGSC_DM_V403_genes.gtf - Gene annotation for the v4.03 Pseudomolecules in GFF3 format) and reads from RNA-seq technologies aligned to the genome. The tables prepared in such a way are then ready to be used for statistical analysis. Statistical analysis was performed to identify gene expression differences between samples studied (package R [R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/ ]). FluxCapacitor was run for each fastq file for every biological replicate from every condition. Afterwards, all the results were gathered in tables using mentioned scripts - one table per one comparison (e.g., a table with 3 biological replicates from one variety stressed with drought for 6 days and 3 replicates for the same variety in control conditions). These tables were then fed in DESeq - R package suitable for analysis of differential gene expression based on the negative binomial distribution [PMID: 20979621].
Genome_build: S. tuberosum Group Phureja DM1-3 Assembly Version 3 DM, PGSC Version 4.03 Pseudomolecule Sequence
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include data before (mean value for each sample) and after statistical analysis.

organism: Solanum tuberosum

source_name: Gwiazda, leaves, day 0 control

growth_protocol: Plants were grown in 14 liter pot filled with thin layer of gravel at the bottom and 12 liter of universal vegetable soil substrate with the addition of chalk, pH range 5.5-6.5 (Hollas company). The gum pipe was installed inside of each pot for better soil aeration. Pest and diseases control was carried out according to the needs. Plants were watered everyday with optimal water amount according to volumetric water content (VWC) in soil measured using 5TM Decagon sensors. For control conditions, VWC was 0.361 m3/m3.

extract_protocol:
During the drought experiment, leaves-samples were taken everyday from three different plants for each variety at given time point, and immediately frozen in liquid nitrogen for storage and further use. Third, fourth and fifth whirl from the top of the plant complex leaves were taken from each plant.
Total RNA was extracted from plant tissue using TRIzol and chloroform reagents followed by ethanol precipitation. Quality of RNA samples was tested with the use of Agilent RNA 6000 Nano Kit Guide (Agilent Technologies), only samples with: 28S:18S > 1.0, RIN≥ 6.5, OD 260/280 ≥1.8 and OD 260/230 ≥ 1.8 were used.
Strand-specific library constructions and RNA-seq (PE100) using Illumina HiSeq 2500 were conducted by BGI Tech Solutions Co. Ltd. (Hong Kong).

treatment_protocol: Three weeks after the initiation of the tuberisation process, half of the plant population was subjected to soil drought stress by withdrawal of irrigation, while control plants were still watered. Results of VWC measurements in subsequent days of drought were as follows: 0.121, -0.040, -0.066 and -0.106 at 3rd, 6th, 9th and 13th day of drought, respectively. After rewatering the plants, VWC was increased to control level. All experiments were performed in three biological replicates.

tag: cultivar

value: Gwiazda

tag: condition

value: control

tag: day of drought

value: leaf


title: MgCl2_day4_9h_2

description: Sample AC


title: MgCl2_day3_15h_3

description: Sample L

source_name: MgCl2_day3_15h_single young systemic leaf


title: Rpm1_day3_15h_3

description: Sample F

source_name: Rpm1_day3_15h_single young systemic leaf


title: MgCl2_day3_15h_1

description: Sample J


title: Panax-notoginseng-root-sample-r15

description: small RNA

value: root tuber


title: MgCl2_day4_9h_1

description: Sample AB


title: MgCl2_day3_15h_2

description: Sample K


title: Rpm1_day4_9h_1

description: Sample V


title: Rpm1_day4_9h_2

description: Sample W


title: Gwiazda_D0_2


title: Rpm1_day3_10h_2

description: Sample C


title: Rpm1_day3_15h_1

description: Sample D


title: Pool of samples from strain R: 16, 19, 20 (R-15-26, R-15-24, R-15-21)

city: Swansea

first: Rebecca

middle: Jane

last: Pawluk

address: Swansea Univeristy

department: Biosciences

country: United Kingdom

institute: Swansea Univeristy

data_processing:
Raw sequences were processed using Trimmomatic, version 0.33
De novo transcriptome assembly was conducted with reads from all combined samples using Trinity version r2013-02-25
With in silico normalisation with an optimised K value of 40
Annotation: BlastX (ensembl:Zebrafish, Human, Mouse, Medaka, Stickleback) and Blastn, see optimized join all file and http://www.ensembl.org/index.html
Three sequences pools made to ensure equal pool numbers. Alignment using Bowtie2 and read count generation with samtools
Supplementary_files_format_and_content: Expression (cacluated with EdgeR) data set 1: Combined strain treatment groups. 2. Strain R data 3. Strain DAN data

organism: Kryptolebias marmoratus

source_name: Whole fish tissue RNA

extract_protocol:
Bioline Isolate II RNA mini kit (Bioline, London, United Kingdom) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Twenty fish of each line were individually infected with one single Argulus foliaceus raised in brackish water, whereas the other twenty from each line were unexposed to serve as controls. Fish were exposed to the parasite for 48 hours

tag: sample type

value: C4 strain control

tag: line

value: R


title: Rpm1_day3_10h_1

description: Sample A


title: Uninfected HL60 promyelocytic leukemia cell replicate 1

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

country: USA

institute: University of Maryland Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh37 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: H. sapiens (GRCh37)
Supplementary_files_format_and_content: tab-delimited text files include raw gene expression counts for each sample

organism: Homo sapiens

source_name: promyelocytic HL-60 cell line

growth_protocol: Promyelocytic HL-60 (ATCC CCL-240) cells were differentiated 5 days with 1 µM all-trans retinoic acid (ATRA) prior to infection. Cells were grown in a humidified incubator at 37°C with 5% CO2. Cell density was kept <10^6 cells/mL by diluting with fresh medium. Infection was established by inoculating low passage (<10 passages in vitro) A. phagocytophilum (Webster strain)-infected HL-60 cells into freshly prepared HL-60 cells to contain approximately 20% infected cells. After infection was established, the proportion of infected cells was adjusted to 10-20% with uninfected HL-60 cells and ATRA was added to the medium. After 5 days, triplicate cultures that contained >90% infected cells and triplicate uninfected cultures were harvested.

extract_protocol:
Total RNA was isolated from each sample using the Zymo Quick-RNA miniprep (Irvine, CA) kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HL-60 cells infected with or without A. phagocytophilum differentiated with ATRA 1 µM for 5 days

tag: cell line

value: ATRA-differentiated HL-60

tag: passages

value: less than 10

tag: infection status

value: Uninfected


title: Uninfected HL60 promyelocytic leukemia cell replicate 3


title: Uninfected HL60 promyelocytic leukemia cell replicate 2


title: Anaplasma phagocytophilum infection replicate 3

source_name: ATRA-differentiated HL-60 cells

value: A. phagocytophilum infected


title: Anaplasma phagocytophilum infection replicate 2


title: Anaplasma phagocytophilum infection replicate 1


title: DNA hydroxymethylation in iAsT cells

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

library_source: genomic

data_processing:
Raw data files had their adapters removed using trim_galore, quality trimming was also done, reads shorter than 20 bp were discarded
Pre-processed fastq files were aligned to human hg19 using bowtie1
Alignment files were analyzed and the count of reads with CCGG was calculated, this data is provided in bigbed files
Genome_build: hg19
Supplementary_files_format_and_content: bigbed, browser tracks that contain CCGG read counts

molecule: genomic DNA

source_name: Lung Epithelial

growth_protocol: Cell cultures were incubated at 37 degree with humidified air and 5% CO2. Cells were harvested after each treatment. Cells were grown ensuring that 95% of the cells were viable. Harvested cells were centrifuged for five minutes at 200 X g.

extract_protocol:
Genomic DNA was extracted using Qiagen Dneasykit according to manusfacturers instructions.
RRHP

treatment_protocol: Cells were treated with 0.5 uM Sodium Arsenite for 36 days until transformation

tag: treatment

value: Sodium Arsenite


title: DNA hydroxymethylation in NT cells


title: PC3 (OE Pbx4)-input

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.7.0) 'mem' algorithm.
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads after PCR duplicate removal to perform peak calling using MACS2 [q < 0.05]
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format for ucsc genome browser, including 10 columns: "chromosome" "start of region" "end of region" "region ID" "integer score for display" "." "fold-change" "-log10pvalue" "-log10qvalue", "relative summit position to peak start"

source_name: Prostate cancer line

extract_protocol:
Cells were fixed with 1% formaldehyde for 10mins at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Cells were washed with ice cold TBSE(20mM Tris-HCl, 150mM NaCl, 1mM EDTA) for three times. Chromatin were then extracted and sonicated to ~500bp. Input DNA was precleared with protein G Dynabeads (Life technologies), and followed by chromatin immunoprecipitation with Hoxc5 (HPA026794, Sigma) and PBX4 (HPA049859, Sigma) at 4°C overnight. ChIP beads were washed six times at room temperature.
At least 10ng ChIP DNA were used to prepare libraries with NEBNext ChIP-Seq library prep reagent set (New England Biolabs), and multiplexed (New England Biolabs).

value: Prostate cancer line PC-3

tag: genotype/variation

value: Pbx4 overexpression

tag: chip antibody


title: PC3 (OE Pbx4)-Pbx4


title: PC3 (Endogenous)-Hoxc5_rep2


title: PC3 (Endogenous)-input_rep2


title: Rpm1_day3_15h_2

description: Sample E

value: 4 week old plants


title: PC3 (Endogenous)-Hoxc5_rep1

description: Barcode: GATCAG


title: PC3 (Endogenous)-input_rep1

description: Barcode: CAGATC


title: PC3 (OE Hoxc5)-input

description: Barcode: ACTTGA

value: Hoxc5 overexpression


title: PC3 (OE Hoxc5)-Hoxc5

description: Barcode: CAGATC


title: Case_324

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description: RawCounts.csv

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed with adaptor sequence using cutadapt v1.2.1  and mapped to hg19 reference with corresponding RefGene GTF annotation using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 and TPM estimation using RSEM_1.2.7
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with counts and RPKM values of each sample

source_name: blood

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ptsd

value: Current

tag: replicates


title: Case_323

description: RawCounts.csv

value: Never


title: Case_319

description: RawCounts.csv


title: Case_321

description: RawCounts.csv

value: Past


title: Case_316

description: RawCounts.csv


title: Case_318

description: RawCounts.csv


title: Case_317

description: RawCounts.csv


title: Case_309

description: RawCounts.csv


title: Case_308

description: RawCounts.csv


title: Case_312

description: RawCounts.csv


title: Case_310

description: RawCounts.csv


title: Case_314

description: RawCounts.csv


title: Case_313

description: RawCounts.csv


title: Case_305

description: RawCounts.csv


title: Case_311

description: RawCounts.csv


title: Case_306

description: RawCounts.csv


title: Case_307

description: RawCounts.csv


title: Case_304

description: RawCounts.csv


title: Case_301

description: RawCounts.csv


title: Case_299

description: RawCounts.csv


title: Case_302

description: RawCounts.csv


title: Case_320

description: RawCounts.csv


title: Case_300

description: RawCounts.csv


title: Case_298

description: RawCounts.csv


title: Case_322

description: RawCounts.csv


title: Case_303

description: RawCounts.csv


title: Case_296

description: RawCounts.csv


title: Case_293

description: RawCounts.csv


title: Case_295

description: RawCounts.csv


title: Case_291

description: RawCounts.csv


title: Case_294

description: RawCounts.csv


title: Case_315

description: RawCounts.csv


title: Case_290

description: RawCounts.csv


title: Case_297

description: RawCounts.csv


title: Case_292

description: RawCounts.csv


title: Case_287

description: RawCounts.csv


title: Case_282

description: RawCounts.csv


title: Case_289

description: RawCounts.csv


title: Case_280

description: RawCounts.csv


title: Case_281

description: RawCounts.csv


title: Case_283

description: RawCounts.csv


title: Case_285

description: RawCounts.csv


title: Case_284

description: RawCounts.csv


title: Case_279

description: RawCounts.csv


title: Case_286

description: RawCounts.csv


title: Case_288

description: RawCounts.csv


title: Case_278

description: RawCounts.csv


title: Case_275

description: RawCounts.csv


title: Case_273

description: RawCounts.csv


title: Case_276

description: RawCounts.csv


title: Case_270

description: RawCounts.csv


title: Case_269

description: RawCounts.csv


title: Case_274

description: RawCounts.csv


title: Case_272

description: RawCounts.csv


title: Case_268

description: RawCounts.csv


title: Case_271

description: RawCounts.csv


title: Case_265

description: RawCounts.csv


title: Case_264

description: RawCounts.csv


title: Case_266

description: RawCounts.csv


title: Case_263

description: RawCounts.csv


title: Case_262

description: RawCounts.csv


title: Case_261

description: RawCounts.csv


title: Case_260

description: RawCounts.csv


title: Case_259

description: RawCounts.csv


title: Case_257

description: RawCounts.csv


title: Case_256

description: RawCounts.csv


title: Case_255

description: RawCounts.csv


title: Case_254

description: RawCounts.csv


title: Case_277

description: RawCounts.csv


title: Case_251

description: RawCounts.csv


title: Case_267

description: RawCounts.csv


title: Case_253

description: RawCounts.csv


title: Case_252

description: RawCounts.csv


title: Case_250

description: RawCounts.csv


title: Case_249

description: RawCounts.csv


title: Case_248

description: RawCounts.csv


title: Case_243

description: RawCounts.csv


title: Case_247

description: RawCounts.csv


title: Case_242

description: RawCounts.csv


title: Case_241

description: RawCounts.csv


title: Case_240

description: RawCounts.csv


title: Case_239

description: RawCounts.csv


title: Case_245

description: RawCounts.csv


title: Case_236

description: RawCounts.csv


title: Case_237

description: RawCounts.csv


title: Case_238

description: RawCounts.csv


title: Case_232

description: RawCounts.csv


title: Case_235

description: RawCounts.csv


title: Case_233

description: RawCounts.csv


title: Case_234

description: RawCounts.csv


title: Case_231

description: RawCounts.csv


title: Case_229

description: RawCounts.csv


title: Case_230

description: RawCounts.csv


title: Case_227

description: RawCounts.csv


title: Case_246

description: RawCounts.csv


title: Case_244

description: RawCounts.csv


title: Case_226

description: RawCounts.csv


title: Case_258

description: RawCounts.csv


title: Case_225

description: RawCounts.csv


title: Case_224

description: RawCounts.csv


title: Case_223

description: RawCounts.csv


title: Case_222

description: RawCounts.csv


title: Case_220

description: RawCounts.csv


title: Case_221

description: RawCounts.csv


title: Case_217

description: RawCounts.csv


title: Case_219

description: RawCounts.csv


title: Case_216

description: RawCounts.csv


title: Case_215

description: RawCounts.csv


title: Case_218

description: RawCounts.csv


title: Case_211

description: RawCounts.csv


title: Case_214

description: RawCounts.csv


title: Case_204

description: RawCounts.csv


title: Case_213

description: RawCounts.csv


title: Case_209

description: RawCounts.csv


title: Case_210

description: RawCounts.csv


title: Case_205

description: RawCounts.csv


title: Case_202

description: RawCounts.csv


title: Case_201

description: RawCounts.csv


title: Case_207

description: RawCounts.csv


title: Case_200

description: RawCounts.csv


title: Case_199

description: RawCounts.csv


title: Case_195

description: RawCounts.csv


title: Case_196

description: RawCounts.csv


title: Case_192

description: RawCounts.csv


title: Case_197

description: RawCounts.csv


title: Case_193

description: RawCounts.csv


title: Case_206

description: RawCounts.csv


title: Case_198

description: RawCounts.csv


title: Case_188

description: RawCounts.csv


title: Case_191

description: RawCounts.csv


title: Case_187

description: RawCounts.csv


title: Case_190

description: RawCounts.csv


title: Case_186

description: RawCounts.csv


title: Case_194

description: RawCounts.csv


title: Case_212

description: RawCounts.csv


title: Case_208

description: RawCounts.csv


title: Case_181

description: RawCounts.csv


title: Case_183

description: RawCounts.csv


title: Case_184

description: RawCounts.csv


title: Case_178

description: RawCounts.csv


title: Case_185

description: RawCounts.csv


title: Case_182

description: RawCounts.csv


title: Case_176

description: RawCounts.csv


title: Case_180

description: RawCounts.csv


title: Case_170

description: RawCounts.csv


title: Case_172

description: RawCounts.csv


title: Case_203

description: RawCounts.csv


title: Case_175

description: RawCounts.csv


title: Case_171

description: RawCounts.csv


title: Case_165

description: RawCounts.csv


title: Case_167

description: RawCounts.csv


title: Case_168

description: RawCounts.csv


title: Case_164

description: RawCounts.csv


title: Case_173

description: RawCounts.csv


title: Case_163

description: RawCounts.csv


title: Case_189

description: RawCounts.csv


title: Case_169

description: RawCounts.csv


title: Case_166

description: RawCounts.csv


title: Case_179

description: RawCounts.csv


title: Case_158

description: RawCounts.csv


title: Case_160

description: RawCounts.csv


title: Case_154

description: RawCounts.csv


title: Case_159

description: RawCounts.csv


title: Case_152

description: RawCounts.csv


title: Wild-type_SK36_Rep3

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

description: replicate 3

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intesity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using Rockhopper v. 2.03
Analyses were run on default parameter settings with verbose output adjusted for reads to the reverse complement in order to obtain expression data. Significance was represented by a q-value ≤ 0.01 adjusted for a false discovery rate of 1%.
Genome_build: Streptococcus sanguinis reference genome
Supplementary_files_format_and_content: tab-delimited text file includes transcription and translation start/stop site, strand direction, gene name and ID, gene product, raw and normalized counts for each replicate, Reads Per Kilobase of exon per Megabase of library size (RPKM), expression, p-value and Rockhopper's adjusted q-value for the mutant expression vs. the wild-type SK36 expression

organism: Streptococcus sanguinis SK36

source_name: Wild-type SK36

growth_protocol: Cells were incubated at 37°C under anaerobic conditions in brain-heart infusion media and harvested at late-log phase. The ciaR mutant and complementary strain were supplemented with kanamycin (500 µg/ml) for selection of the antibiotic resistance cassette.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacterer's protocol. Illlumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligs for Illumina - Index Primers 2, 11, 12, 13, 15, 16, 18, 20, 21, 22). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

tag: strain

tag: growth phase

value: late-log

tag: genotype


title: Case_156

description: RawCounts.csv


title: Case_150

description: RawCounts.csv


title: Case_162

description: RawCounts.csv


title: Case_174

description: RawCounts.csv


title: Case_177

description: RawCounts.csv


title: Case_149

description: RawCounts.csv


title: Case_143

description: RawCounts.csv


title: Case_145

description: RawCounts.csv


title: Case_142

description: RawCounts.csv


title: Case_153

description: RawCounts.csv


title: Case_141

description: RawCounts.csv


title: Case_147

description: RawCounts.csv


title: Case_155

description: RawCounts.csv


title: Case_148

description: RawCounts.csv


title: Case_146

description: RawCounts.csv


title: Case_144

description: RawCounts.csv


title: Case_135

description: RawCounts.csv


title: Case_157

description: RawCounts.csv


title: Case_137

description: RawCounts.csv


title: Case_161

description: RawCounts.csv


title: Case_136

description: RawCounts.csv


title: Case_132

description: RawCounts.csv


title: Case_134

description: RawCounts.csv


title: Case_130

description: RawCounts.csv


title: Case_151

description: RawCounts.csv


title: Case_138

description: RawCounts.csv


title: Case_133

description: RawCounts.csv


title: Case_127

description: RawCounts.csv


title: Case_128

description: RawCounts.csv


title: Case_124

description: RawCounts.csv


title: Case_122

description: RawCounts.csv


title: Case_123

description: RawCounts.csv


title: Case_139

description: RawCounts.csv


title: Case_228

description: RawCounts.csv


title: Case_126

description: RawCounts.csv


title: Case_140

description: RawCounts.csv


title: Case_121

description: RawCounts.csv


title: Case_120

description: RawCounts.csv


title: Case_129

description: RawCounts.csv


title: Case_119

description: RawCounts.csv


title: Case_114

description: RawCounts.csv


title: Case_118

description: RawCounts.csv


title: Case_115

description: RawCounts.csv


title: Case_113

description: RawCounts.csv


title: Case_116

description: RawCounts.csv


title: Case_131

description: RawCounts.csv


title: Case_103

description: RawCounts.csv


title: Case_111

description: RawCounts.csv


title: Case_112

description: RawCounts.csv


title: Case_101

description: RawCounts.csv


title: Case_107

description: RawCounts.csv


title: Case_106

description: RawCounts.csv


title: Case_98

description: RawCounts.csv


title: Case_117

description: RawCounts.csv


title: Case_105

description: RawCounts.csv


title: Case_104

description: RawCounts.csv


title: Case_125

description: RawCounts.csv


title: Case_102

description: RawCounts.csv


title: Case_95

description: RawCounts.csv


title: Case_108

description: RawCounts.csv


title: Case_99

description: RawCounts.csv


title: Case_91

description: RawCounts.csv


title: Case_85

description: RawCounts.csv


title: Case_96

description: RawCounts.csv


title: Case_90

description: RawCounts.csv


title: Case_100

description: RawCounts.csv


title: Case_92

description: RawCounts.csv


title: Case_110

description: RawCounts.csv


title: Case_84

description: RawCounts.csv


title: Case_94

description: RawCounts.csv


title: Case_81

description: RawCounts.csv


title: Case_109

description: RawCounts.csv


title: Case_77

description: RawCounts.csv


title: Case_87

description: RawCounts.csv


title: Case_97

description: RawCounts.csv


title: Case_82

description: RawCounts.csv


title: Case_89

description: RawCounts.csv


title: Case_78

description: RawCounts.csv


title: Case_75

description: RawCounts.csv


title: Case_88

description: RawCounts.csv


title: Case_74

description: RawCounts.csv


title: Case_83

description: RawCounts.csv


title: Case_72

description: RawCounts.csv


title: Case_93

description: RawCounts.csv


title: Case_86

description: RawCounts.csv


title: Case_80

description: RawCounts.csv


title: Case_76

description: RawCounts.csv


title: Case_71

description: RawCounts.csv


title: Case_73

description: RawCounts.csv


title: Case_70

description: RawCounts.csv


title: Case_69

description: RawCounts.csv


title: Case_79

description: RawCounts.csv


title: Case_68

description: RawCounts.csv


title: Case_66

description: RawCounts.csv


title: Case_67

description: RawCounts.csv


title: Case_65

description: RawCounts.csv


title: Case_64

description: RawCounts.csv


title: Case_62

description: RawCounts.csv


title: Case_61

description: RawCounts.csv


title: Case_63

description: RawCounts.csv


title: Case_60

description: RawCounts.csv


title: Case_59

description: RawCounts.csv


title: Case_55

description: RawCounts.csv


title: Case_54

description: RawCounts.csv


title: Case_58

description: RawCounts.csv


title: Case_56

description: RawCounts.csv


title: Case_57

description: RawCounts.csv


title: Case_52

description: RawCounts.csv


title: Case_50

description: RawCounts.csv


title: Case_53

description: RawCounts.csv


title: Case_48

description: RawCounts.csv


title: Case_51

description: RawCounts.csv


title: Case_45

description: RawCounts.csv


title: Case_47

description: RawCounts.csv


title: Case_46

description: RawCounts.csv


title: Case_49

description: RawCounts.csv


title: Case_43

description: RawCounts.csv


title: Case_39

description: RawCounts.csv


title: Case_42

description: RawCounts.csv


title: Case_40

description: RawCounts.csv


title: Case_41

description: RawCounts.csv


title: Case_38

description: RawCounts.csv


title: Case_37

description: RawCounts.csv


title: Case_36

description: RawCounts.csv


title: Case_33

description: RawCounts.csv


title: Case_35

description: RawCounts.csv


title: Case_34

description: RawCounts.csv


title: Case_24

description: RawCounts.csv


title: Case_29

description: RawCounts.csv


title: Case_28

description: RawCounts.csv


title: Case_32

description: RawCounts.csv


title: Case_31

description: RawCounts.csv


title: Case_22

description: RawCounts.csv


title: Case_44

description: RawCounts.csv


title: Case_17

description: RawCounts.csv


title: Case_18

description: RawCounts.csv


title: Case_20

description: RawCounts.csv


title: Case_21

description: RawCounts.csv


title: Case_26

description: RawCounts.csv


title: Case_19

description: RawCounts.csv


title: Case_27

description: RawCounts.csv


title: Case_15

description: RawCounts.csv


title: Case_25

description: RawCounts.csv


title: Case_13

description: RawCounts.csv


title: Case_11

description: RawCounts.csv


title: Case_14

description: RawCounts.csv


title: Case_12

description: RawCounts.csv


title: Case_30

description: RawCounts.csv


title: Case_9

description: RawCounts.csv


title: Case_8

description: RawCounts.csv


title: Case_7

description: RawCounts.csv


title: Case_6

description: RawCounts.csv


title: Case_4

description: RawCounts.csv


title: Case_5

description: RawCounts.csv


title: Case_2

description: RawCounts.csv


title: Case_3

description: RawCounts.csv


title: Case_1

description: RawCounts.csv


title: Case_16

description: RawCounts.csv


title: Case_10

description: RawCounts.csv


title: ADcoN3

city: New York

first: Zhidong

last: Tu

state: New York

address: 1 Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Quality control on RNA-seq data: We filtered  ribosomal RNAs (rRNAs) using SortMeRNA and trimmed Illumina adaptors using Trimmomatic following the exact protocol provided by Epigenesys.
Alignment of pair-ended RNA reads:The short reads were mapped to the reference genome (Hg38) by STAR 2-pass with annotation GENCODE V21 and only the uniquely mapped reads were kept. The resulted SAM files were put through the usual Picard processing steps: fixing mate, adding read group information, sorting, marking duplicates, and indexing. GATK tool SplitNCigarReads was used to split the reads into exon segments and hard-clip any sequences overhanging into the intronic regions, and GATK tools ReassignOneMappingQuality was used to reassign mapping qualities. In addition, a base call recalibration was done by using GATK tool BaseRecalibrator against SNP data downloaded from 1000 genome project (version All_20160527).  Samtools mpileup was used to retrieve the base profile mapped at each locus.
Gene expression: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
SNV call on cell pellets: We applied the GATK pipeline to call single nucleotide variants (SNV) on all samples. The SNPs being called with read depth greater than or equal to 10 and passing the filtering criteria, i.e., (1) filtering clusters of at least 3 SNPs that are within a window of 35 bases and (2) filtering based on Fisher Strand values (FS > 30.0), and (3) filtering the “LowQual” variant with quality score less than 30 for each sample.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files

source_name: human differentiated adipocyte cell

extract_protocol:
Exosomes were isolated using sequential centrifugation essentially as described by Thery et al. Total RNA from cell pellets and exosomes was extracted using the miRNeasy kit (Qiagen) and RNA was eluted into RNAse free water.  Total RNA from exosomes given the low yield was subject to a separate amplification protocol
Exosomal RNA samples were subject to first strand cDNA synthesis using the Clontech Smart-Seq v4 Ultra Low Input kit procedure
cDNA library was prepared cellular RNA using a non-strand specific protocol with ribozero depletion of rRNA. Sequencing was paired-end at a length of 100nt. DNA was extracted from pellets collected from cells cultured alone using QiaAmp DNA blood mini kit (Qiagen). DNA from each condition was genotyped by the Illumina HumanOmni2.5Exome-8 BeadChip.


title: ADcoN2


title: ADaloneN1


title: ADaloneN2


title: MOaloneN2

source_name: human differentiated macrophage cell


title: MOaloneN1


title: MOcoN2


title: MOcoN1


title: MOexosome

source_name: extracellular vesicles


title: ADMOexosome


title: MOcoN3


title: + C4_X

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

data_processing:
reads were mapped to hg19 using TopHat v2.1.0 with the following parameters: -g 1 -N 1 --no-novel-juncs --realign-edit-dist 2
mapped fragments were counted over the UCSC provided gene annotation in the union mode using the R package GenomicAlignments
abundance measurments were further normalized by the standard procedure of the DESeq2 Bioconductor R package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file contains DESeq2 normalized abundance measurments

source_name: Flp-In T-REx 293_+ C4

extract_protocol:
The RNA isolation procedure was performed with the NucleoSpin RNA Kit according to the manufacturer’s instructions.
Library preparation, comprising rRNA depletion, polyA enrichment, fragmentation to ~270 nucleotide length and reverse transcription to cDNA, using random hexamer primers and adapter ligation, was accomplished with the TruSeq RNA Sample Preparation Kit v2 according to the manufacturer’s protocol by EMBL GeneCore facility in Heidelberg (Dr. Vladimir Benes).

treatment_protocol: Total RNA was prepared from 24 hours induced (1 ng/µl Dox) and non-induced Flp-In™ T-REx™ 293 cells (2 million cells per sample were seeded one day before induction). 2 biological replicates were performed (named _A and _X).

tag: cell line background

value: Hek 293

value: FLP-In T-REx 293 cells

tag: induction

value: induction (with doxycyline) of human CHD4-(C)GFP


title: - C4_X

source_name: Flp-In T-REx 293_- C4

value: no induction of human CHD4-(C)GFP


title: + C3_X

source_name: Flp-In T-REx 293_+ C3

value: induction (with doxyxycline) of CHD3-(C)GFP


title: + GFP_X

source_name: Flp-In T-REx 293_+ GFP

value: induction (with doxycyline) of GFP


title: - GFP_X

source_name: Flp-In T-REx 293_- GFP

value: no induction of GFP


title: - C3_X

source_name: Flp-In T-REx 293_- C3

value: no induction of human CHD3-(C)GFP


title: - C4_A


title: + C4_A


title: + C3_A


title: - C3_A


title: - GFP_A


title: + GFP_A


title: ADcoN1


title: 360_75

city: Edmonton

first: Ke

last: Zhao

country: Canada

institute: University of Alberta

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
RNA-seq reads were aligned to the bovine genome (UMD 3.1) using Tophat 2.0.10 with default parameters. The number of reads mapped to each gene was counted by htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) based on the annotation from the ENSEMBL (http://uswest.ensembl.org/) bovine gene annotation software (v75.30).
The expression levels of mRNA in each library was calculated by normalizing reads to reads per million (RPM) by the following formula: RPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: bovine genome (UMD 3.1)
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

organism: Bos taurus

extract_protocol:
Ruminal papillae samples were ground while immersed in liquid nitrogen using a frozen mortar and pestle prior to RNA extraction. Total RNA was extracted from 50 mg of papillae powder using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All the heifers were assigned to a rapid grain transition treatment (n = 15) throughout a 29-d experiment period. Briefly, heifers were initially fed a diet containing 3% grain (days 1 to 4) and transitioned to a final diet containing 92% grain using the following intermediate diets: 40% grain (days 5 to 8), 60% grain (days 9 to 12), 75% grain (days 13 to 16), 85% grain (days 17 to 20), and 92% grain (days 21 to 29).

tag: animal id

tag: animal status

value: heathy beef heifers

tag: exposed to

value: rapid grain transition treatment

tag: tissue

value: rumen papillae


title: 360_3


title: 360_92


title: YY2-HeLa

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

description: YY2 ChIP-seq in HeLa cells

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg18 genome assembly using Bowtie version 2.2.1.
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.

source_name: HeLa cells stably expressing HA-tagged YY2

growth_protocol: HeLa cells were cultured inMEM alpha medium supplemented with 10% FBS.

extract_protocol:
For ChIP-seq, fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen).
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: Cells grown to ~90% confluent were fixed directly with 1% formaldehyde.

tag: cell line

value: HeLa

value: anti-HA antibody (ab9110)


title: 286_92


title: 286_75


title: 286_3


title: 352_92


title: 178_3


title: 352_3


title: 262_75


title: 352_75


title: 178_75


title: Case_23

description: RawCounts.csv


title: 262_92


title: 178_92


title: 258_75


title: 258_92


title: 262_3


title: 362_92


title: 362_75


title: 246_92


title: 246_75


title: 362_3


title: 294_92


title: 246_3


title: 294_75


title: 294_3


title: 172_92


title: 182_92


title: 172_3


title: 182_3


title: 182_75


title: 258_3


title: 170_3


title: 170_92


title: X1210GNC2_drug_rep2

city: changchun

first: fanhui

last: meng

address: xinminstreet

institute: The First Hospital of Jilin University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the Caenorhabditis_elegans_WBcel235 using Tophat version 2.1.0
Gene abundance measurements were generationed and normalized  using Cufflink version 2.1.1.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed using cuffdiff.
Genome_build: Caenorhabditis_elegans_WBcel235
Supplementary_files_format_and_content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

organism: Caenorhabditis elegans

growth_protocol: 3.94 mg/mL GNC or a vehicle control (H2O) treating the worms, and E. coli OP50 were added as a food source.

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (TaKaRa, China) according to the manufacturer’s instructions. RNA was further purified with an RNAClean XP Kit (Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and an RNase-Free DNase Set (QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Synchronized worms were cultured in S-complete liquid medium

tag: age

value: 22 days


title: X1210H2O2_control_rep2


title: 192_3


title: 192_75


title: 314_75


title: X1210H2O1_control_rep1


title: 236_92


title: 314_92


title: 170_75


title: X1210GNC1_drug_rep1


title: IM rep2

city: Shanghai

first: zhang

middle: ying

last: ying

state: Shanghai

address: Beidi Road No.2901

department: Institute of Animal Husbandry & Veterinary Science

institute: Shanghai Academy of Agricultural Sciences

description: 1 heads Chinese Qinchuan male cattle weaned at 3 mo

data_processing:
RNA-seq: Reads filtering under criteria removing reads with 20% of the base quality lower than 13
RNA-seq: Mapsplice v2.1.8 mapping to reference genome
RNA-seq: count counting
miRNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
miRNA-seq: Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Bos taurus miRNA database and GRCH37.p13 genome.
miRNA-seq: count counting
Genome_build: Btau_4.6.1_NCBI_year_2011
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Intramuscular fat

growth_protocol: Bulls were weaned at 3 mo of age and fed a diet with 3: 7 concentrate-to-forage ratios until 6 mo of age. The CM group was castrated at 6 months by surgical method after administering local anesthetic. After 6 mo of age, two groups were fed with concentrates 14% crude protein (CP) and 70% total digestible nutrient (TDN) until 12 mo of age, 12% CP and 71% TDN until 18 mo of age, 10% CP and 72% TDN to 24 mo of age.

extract_protocol:
RNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
miRNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA-seq: Ion  Proton Sequencing Protocol
miRNA-seq: Hiseq Sequencing Protocol

treatment_protocol: Six bulls were divided into two groups (IM and CM) which were weaned at 3 mo of age. The CM group was castrated at 6 months by surgical method after administering local anesthetic. The animals were slaughtered at 24 months and the IMF tissues were dissected quickly from the sternomandibularis muscle of CM and IM, and then snap frozen in liquid nitrogen promptly for further analysis.

value: Intramuscular fat dissected from sternomandibularis muscle

value: 24 mo

tag: breed

value: Chinese Qinchuan

value: intact


title: CM rep2

description: 1 heads Chinese Qinchuan male cattle weaned at 3 mo and castrated at 6 mo

tag: treatment

value: castrated


title: CM rep1


title: IM rep1


title: SOD1 rep5

city: Strasbourg

first: Alexandre

last: Henriques

address: At U1118, 11 rue Humann

country: France

institute: Spedding Research Solutions, SAS

data_processing:
Libraries of template molecules suitable for high throughput DNA sequencing were created and reads were mapped onto mm10 assembly of mouse genome using Tophat v2.0.14.
Quantification of gene expression was performed using HTSeq v0.6.1 and Ensembl release 81 database.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: Lumbar spinal cord

extract_protocol: RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: Total RNA was extracted from fresh forzen spinal cord using Trizol reagent.

tag: background strain

value: FVB

value: Lumbar spinal cord

value: post natal day 95


title: SOD1 rep4


title: 192_92


title: 172_75


title: 236_3


title: SOD1 rep2


title: SOD1 rep3


title: SOD1 rep1


title: WT rep5

value: wild type


title: WT rep4


title: WT rep3


title: WT rep1


title: 236_75


title: WT rep2


title: 314_3


title: IM

description: 3 heads Chinese Qinchuan male cattle weaned at 3 mo


title: CM

description: 3 heads Chinese Qinchuan male cattle weaned at 3 mo and castrated at 6 mo


title: 160OE14heat

city: Taipei

first: Jeng-Shane

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

country: Taiwan

institute: National Taiwan University

data_processing:
Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate 20M (million reads or Gb) per sample.
Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation.
For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: TAIR10
Supplementary_files_format_and_content: Gene_160_arf file includes FPKM values for each Sample

source_name: Seedlings_miR160 overexpression_heat

growth_protocol: Arabidopsis thaliana (Col-0) was grown in a controlled environment at 22°C under 16 h light/8 h dark with cool fluorescent light at 100 μmolm-2 s-1.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
Library construction of all samples were used by Agilent's SureSelect Strand Specific RNA Library Preparation Kit

treatment_protocol: The 7-day-old seedlings were treated with heat stress at 44oC for  30 min.

value: miR160 ovexpression transgenic

tag: background cultivar

value: seedling

value: 7 days


title: ARF16control

value: arf16 T-DNA insertion mutant


title: WT7Heat

value: Wild-type


title: ARF17Heat

value: arf17 T-DNA insertion mutant


title: ARF10control

value: arf10 T-DNA insertion mutant


title: ARF16Heat


title: ARF17control


title: dcmu_30um_27_b

city: Cambridge

first: Patrick

middle: James

last: Dickinson

address: The Sainsbury Laboratory , Bateman Street

department: Sainsbury Laboratory University of Cambridge

institute: University of Cambridge

description: grep

data_processing:
The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads, FPKM and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed.
Genome_build: TAIR10

source_name: Col0 WT seedlings grown in liquid media

extract_protocol:
Total RNA was isolated from a pool og 25 seedlings using the MagMAX-96 Total RNA Isolation kit (Ambion, AM1830), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed using 1 ug of total RNA using the TruSeq Stranded mRNA library preparation kit and TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2101 and RS-122-2001), following manufacturer’s instruction. The libraries were sequenced on a HiSeq2000 using paired-end sequencing of 100 bp in length at Max Planck Institute (MPI) Tubingen and the Beijing Genomics Institute (BGI) sequencing centres.

value: seedlings

tag: ecotype

tag: growth conditions

value: 27°C, short days, 170 umol light, grown in liquid media, treated with chemical at ZT-1.

tag: timepoint sampled

tag: replicate


title: dbmib_50um_22_b

tag: genotype

value: 22°C, short days, 170 umol light, grown in liquid media, treated with chemical at ZT-1.


title: col_27_b

value: 27°C, short days, 170 umol light, grown in liquid media.


title: 160OE14control

source_name: Seedlings_miR160 overexpression_control


title: ARF10Heat


title: dcmu_30um_22_b


title: etoh_22_b


title: dbmib_50um_27_b


title: dcmu_30um_27


title: etoh_27_b


title: dbmib_50um_27


title: etoh_27


title: col_27


title: dbmib_50um_22


title: etoh_22


title: ss3_4_pgm_17_2_b

source_name: Col0 ss3/ss4/pgm seedlings

value: 17°C, short days (8 h light, 16 h dark), 170 umol light.


title: dcmu_30um_22


title: col_22

value: 22°C, short days, 170 umol light, grown in liquid media.


title: ss3_4_pgm_17_0_b


title: ss3_4_17_0_b

source_name: Col0 ss3/ss4 seedlings


title: WT7control


title: ss3_4_17_2_b


title: pgm_17_2_b

source_name: Col0 pgm seedlings

value: pgm


title: pgm_17_0_b


title: ss3_4_pgm_17_2


title: ss3_4_17_2


title: ss3_4_17_0


title: col_22_b


title: ss4_17_16_b

source_name: Col0 ss4-1 seedlings


title: ss3_4_pgm_17_0


title: pgm_17_2


title: ss4_17_2_b


title: ss4_17_12_b


title: ss4_17_4_b


title: ss4_17_1_b


title: ss4_17_0_b


title: ss4_17_minus4_b


title: ss4_17_8_b


title: ss4_17_12


title: ss4_17_4


title: ss4_17_2


title: ss4_17_8


title: ss4_17_16


title: ss4_17_1


title: ss4_17_minus4


title: col_17_16_b

source_name: Col0 WT seedlings


title: col_17_12_b


title: ss4_17_0


title: col_17_8_b


title: col_17_4_b


title: col_17_0_b


title: col_17_1_b


title: col_17_16


title: pgm_17_0


title: col_17_minus4_b


title: col_17_4


title: col_17_8


title: col_17_0


title: col_17_2_b


title: col_17_12


title: col_17_1


title: RWPE1 ERG-S96E_RNA-seq_replicate 2

city: Bloomington

first: Vivekananda

last: Kedage

state: IN

address: 1001 E. third Street

institute: Indiana University

description: polyA selected RNA

data_processing:
Casava1.8.2 software was used for basecalling
Differential gene expression analysis was carried out with Tuxedo Suite RNA sequencing pipeline (Trapnell et al., Nature Protocol 2012). Sequence reads obtained from illumina sequencer was mapped to the human genome (hg19, UCSC) using Bowtie2. Differential gene expression was determined using Cuffdiff.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: Tab delimited text file of differential gene expression analysis. Output from CuffDiff

source_name: RWPE1 cell line

growth_protocol: RWPE1 cells were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract,  human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)

extract_protocol:
Total RNA from three biological replicates of RWPE1 cells expressing either empty vector, ERG-WT, ERG-S96A and ERG-S96E was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol. Total RNA was DNase treated with RNase-Free DNase set (Qiagen) according to manufacturer’s protocol.
polyA containing RNA was purified using oligo(dT) beads (Invitrogen). cDNAs of polyA selected RNA was generated with SuperScript III reverse transcriptase enzyme using random hexamers (Invitrogen). Second strand synthesis from cDNAs was carried out with E. coli DNA ligase and E. coli DNA polymerase I (New England BioLabs). The double-stranded cDNAs were sheared to ~150 nucleotide fragments using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis.Sheared DNA was end-repaired and ligated to indexing primers provided in Truseq sample preparation kit (Illumina). DNA libraries were pooled and sequenced in Illumina NextSeq 500 according to manufacturers protocol.


title: 2149

city: Philadelphia

first: William

middle: A.

last: Beltran

state: PA

address: 3900 Delancey Street, Ryan VHUP 2050

department: Clinical Studies

institute: University of Pennsylvania

data_processing:
Sequence data was recorded in FASTQ files
Reads with a poor quality run value ≥ 5 were eliminated.
Ribosomal repeats were removed by discarding any reads aligning to a generic set of ribosomal repeat sequences from humans.
RNA-seq Unified Mapper (RUM) was used to align reads to known transcripts in RefSeq, UCSC known genes and ENSEMBL transcripts, and to the dog genome. Unique alignments to refseq were extracted from the RUM output.
Differential gene expression analysis was performed using Edge-R package from R/Bioconductor. The p-values were corrected for multiple testing using the Benjamini and Hochberg mode to compute false discovery rate.
Genome_build: Canis_familiaris.CanFam3.1.dna_sm.toplevel.fa
Supplementary_files_format_and_content: Excel files contain log2 transcripts per million (TPM) values summarized to gene level.

organism: Canis lupus familiaris

source_name: RCD1 neuroretina

extract_protocol:
Beadbug homogenizer was use for homogenization of frozen neuroretina and standard Trizol extraction protocol was used for preparing total RNA.
cDNA library was prepared using Illumina Truseq mRNA library prep kit v2

treatment_protocol: Dogs were housed under standard kennel conditions. Dogs were euthanized at the appropriate age, enucleated, the neuroretina was dissected and stored immediately at -80⁰C.

tag: genotype/variation

value: 22 weeks

tag: Sex

value: female

value: neuroretina

tag: photorecptors remaining

value: < 50% of normal


title: CEACIV

source_name: Normal neuroretina

value: normal/control

value: 24 weeks

value: Normal (100%)


title: 2150


title: 2151


title: Z478

source_name: XLPRA2 neuroretina

value: 41 weeks


title: RWPE1 ERG-S96E_RNA-seq_replicate 1

description: polyA selected RNA


title: RWPE1_INPUT_2

data_processing:
Casava1.8.2 software was used for basecalling
Reads were aligned to Homo Sapien Genome (UCSC Hg19) uisng Bowtie2 (v0.12.8)
Peaks were called using Useq program (v8.4.0)
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab delimited text files with chromosome:start-end

growth_protocol: RWPE1 cells stably expressing either vector, wild-type (WT) or point mutants (S96A or S96E) of ERG were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract,  human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)

extract_protocol:
ChIP DNA was extracted as described in Hollenhorst et al., Genes and Dev. 2011
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol. ChIP DNA's were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

tag: chip antibody


title: CEACID


title: Z480


title: ERG-ChIP_RWPE1-ERG(S96E)

value: expressing point-mutant (S96E) of ERG

value: Anti-ERG Clone 9FY (Biocare, Catalog# CM421 C, Lot #021715)


title: Z479


title: RWPE1 ERG-S96E_RNA-seq_replicate 3

description: polyA selected RNA


title: col_17_2

value: seedlings

value: wild type


title: RWPE1 ERG-S96A_RNA-seq_replicate 2

source_name: RWPE1_expressing point-mutant (S96A) of ERG

extract_protocol:
Total RNA from three biological replicates of RWPE1 cells expressing ERG-S96A was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol. Total RNA was DNase treated with RNase-Free DNase set (Qiagen) according to manufacturer’s protocol.
polyA containing RNA was purified using oligo(dT) beads (Invitrogen). cDNAs of polyA selected RNA was generated with SuperScript III reverse transcriptase enzyme using random hexamers (Invitrogen). Second strand synthesis from cDNAs was carried out with E. coli DNA ligase and E. coli DNA polymerase I (New England BioLabs). The double-stranded cDNAs were sheared to ~150 nucleotide fragments using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis.Sheared DNA was end-repaired and ligated to indexing primers provided in Truseq sample preparation kit (Illumina). DNA libraries were pooled and sequenced in Illumina NextSeq 500 according to manufacturers protocol.

value: expressing point-mutant (S96A) of ERG


title: RWPE1 ERG-WT_RNA-seq_replicate 3

description: This is duplicated sample record of GSM2154815 for the convenient retrieval of the complete raw data from SRA

source_name: RWPE1_expressing WT ERG

value: expressing WT ERG


title: RWPE1 ERG-S96A_RNA-seq_replicate 3


title: RWPE1 ERG-S96A_RNA-seq_replicate 1


title: RWPE1 ERG-WT_RNA-seq_replicate 2

description: This is duplicated sample record of GSM2154814 for the convenient retrieval of the complete raw data from SRA


title: col_17_minus4

value: 17°C, short days (8 h light, 16 h dark), 170 umol light.


title: EZH2-ChIP_RWPE1-ERG(S96E)

value: Anti-EZH2 (Cell Signaling, Catalog # 5246, Lot #7)


title: control5

city: nanjing

first: gu

last: qihui

address: zhongyang road

institute: Nanjing Stomatological Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: rno6
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Rattus norvegicus

source_name: tooth movement with corticision

extract_protocol:
Total RNA was isolated from alveolar tissues using the TRIzol reagent (Invitrogen, San Giego, CA) according to the manufacturer’s instructions
The complementary DNA (cDNA) libraries for the single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions

value: alveolar tissue


title: control6


title: RWPE1_INPUT.fastq.gz


title: CEACMI


title: RWPE1 ERG-WT_RNA-seq_replicate 1

description: This is duplicated sample record of GSM2154813 for the convenient retrieval of the complete raw data from SRA


title: EZH2-ChIP_RWPE1-ERG(S96A).fastq.gz


title: FLU.H.2014.01.54FUR0091.0d.RNA.Access_S20

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
General quality control of the raw reads was performed using FastQC.
Ribosomal RNA reads were removed via mapping by Bowtie (v2.1.0) (Langmead and Salzberg, 2012) using an index of human, mouse, and rat rRNA sequences
For each sample about 90% of remaining reads were mapped against the human reference genome (hg19, build GRCh37, from the UCSC genome browser using STAR (v2.4.0h1) (Dobin et al., 2013).
Quantitative gene counts were produced utilizing the human annotation associated with the genome using the python package HT-Seq (Anders, Pyl, and Huber, 2015).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of gene abundance

source_name: Nasal Swab

extract_protocol:
Nasal swabs were collected from individuals (n=3) confirmed to be infected with H3N2 viruses.  Swabs were taken on the day of diagnosis (d0) as well as 3 and 7 days post-diagnosis.Total RNA was extracted from nasal swabs suspended in RLT buffer using the Qiagen miRNeasy Micro Kit (Qiagen, Valencia, CA).
Libraries for RNA sequencing were constructed using TruSeq RNA Access kit (Illumina).

value: nasal epithelial cells

tag: infection


title: FLU.H.2014.01.54FUR0065.7d

tag: tissue


title: ERG-ChIP_RWPE1-ERG(S96A).fastq.gz

tag: cell line


title: FLU.H.2014.01.54FUR0056.0d.RNA.Access_S18


title: case5

source_name: tooth movement without corticision


title: RWPE1 empty vector_RNA-seq_replicate 1

description: This is duplicated sample record of GSM2154810 for the convenient retrieval of the complete raw data from SRA

source_name: RWPE1_expressing empty vector

value: expressing empty vector


title: FLU.H.2014.01.54FUR0065.3d


title: EZH2-ChIP_RWPE1-Vector.fastq.gz


title: FLU.H.2014.01.54FUR0056.7d.RNA.Access_S23


title: case9


title: NL7 SSEA4neg

city: Los Angeles

first: David

last: Habiel

state: CA

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

description: NL7 SSEA4 neg_FPKM

data_processing:
Raw reads in FASTQ format were aligned to the UCSC human reference genome (hg19) using TOPHAT.
Gene expression was calculated using a gene transfer file (GTF) from UCSC genes
Normalized read quantification as FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was calculated with Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Rejected donor Lung Explants_SSEA4-

extract_protocol:
SSEA4+ and SSEA4- cells were sorted from normal or IPF lung fibroblast cultures (passages 4-8) using a BD FACS ARIA III cell sorter. RNA was then extracted using miRNeasy micro kit (qiagen) and a minimum of 700 ng of total RNA was utilized for sequencing analysis.
A minimum of 700 ng of total RNA was used in “Dynabeads® mRNA DIRECT™ Micro Purification Kit” (Ambion).  The libraries were prepared using the Ion Total RNA-Seq Kit v2 (Life Technologies).  Samples were then loaded into an Ion Torrent for amplification onto Ion Sphere Particles using Ion PI™ Template OT2 200 Kit v3 (Life Technologies), sequencing chemistry, Ion PI™ Sequencing 200 Kit v3 (Life Technologies) and sequencing Chip, Ion PI™ Chip Kit v2 (Life Technologies).  Samples were sequenced to at least 10 million reads.  Raw reads in FASTQ format were aligned to the UCSC human reference genome (hg19) using TOPHAT.  Gene expression was calculated using a gene transfer file (GTF) from UCSC genes and normalized read quantification as FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) calculated with Cufflinks.

tag: subject status

value: normal donor

value: lung

tag: progression

tag: cell type

value: lung fibroblast cultures (passages 4-8)

tag: facs-sorted population


title: control10


title: RWPE1 empty vector_RNA-seq_replicate 3

description: This is duplicated sample record of GSM2154812 for the convenient retrieval of the complete raw data from SRA


title: RWPE1 empty vector_RNA-seq_replicate 2

description: This is duplicated sample record of GSM2154811 for the convenient retrieval of the complete raw data from SRA


title: S76A SSEA4neg

description: S76A SSEA4 neg_FPKM

source_name: IPF Lung Biopsy_SSEA4-

value: Idiopathic Pulmonary Fibrosis (IPF)

value: Slow


title: NL4 SSEA4neg

description: NL4 SSEA4 neg_FPKM


title: S109 SSEA4neg

description: S109 SSEA4 neg_FPKM


title: case6


title: EZH2-ChIP_RWPE1-ERG(WT).fastq.gz

value: expressing wild type ERG


title: FLU.H.2014.01.54FUR0091.7d.RNA.Access_S25


title: NL16 SSEA4neg

description: NL16 SSEA4 neg_FPKM


title: S180 SSEA4neg

description: S180 SSEA4 neg_FPKM

value: Rapid


title: S56 SSEA4neg

description: S56 SSEA4 neg_FPKM


title: SAM24286377 PANC-1 control

city: South San Francisco

first: Suchit

last: Jhunjhunwala

address: 1 DNA Way, MS-444A

institute: Genentech

description: SAM24286377 PANC-1

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: PANC-1 cells

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

tag: sirna

value: control


title: SAM24286379 PANC-1 control

description: SAM24286379 PANC-1


title: S69 SSEA4neg

description: S69 SSEA4 neg_FPKM


title: SAM24286382 PANC-1 SUV420H2 knockdown

description: SAM24286382 PANC-1

value: SUV420H2 knockdown


title: S148 SSEA4neg

description: S148 SSEA4 neg_FPKM


title: SAM24286380 PANC-1 SUV420H2 knockdown

description: SAM24286380 PANC-1


title: NL16 SSEA4pos

description: NL16 SSEA4pos_FPKM

source_name: Rejected donor Lung Explants_SSEA4+


title: D6

city: Beijing

first: Xiangyang

last: Miao

state: Beijing

address: 2 Yuanmingyuan West Road,Nongda South, Haidian

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
mapping to reference genome using Tophat
count counting
Genome_build: Oar_v3.1

organism: Ovis aries

source_name: Ovaries

growth_protocol: 3 Dorset sheep (Dorset), 3 Small Tail Han FecB+FecB+ sheep (Han++) and 3 Small Tail Han FecBBFecBB sheep (Han BB) were used for the experiments.

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

treatment_protocol: Whole ovaries with ovulation points were excised and the samples were collected.

tag: breed

value: Dorset sheep

value: ovary

value: wild type


title: SAM24286381 PANC-1 SUV420H2 knockdown

description: SAM24286381 PANC-1


title: 159_GTCCGC

first: Galyna

last: Bondar

address: 10833 Le Conte Ave, CHS 32-164

department: Medicine-Cardiology

institute: UCLA

data_processing:
Single end sequencing runs was performed to align the cDNA sequences to the reference genome.
FASTQ files were generated and transferred to the AdHF Research Data Center.
Avadis NGS 1.5 was used to align raw RNA-Seq FASTQ reads to the reference genome.
RNA extraction, quantification and quality assessment was performed.
Total mRNA was amplified and sequenced on the whole-genome Illumina HiSeq 2500.
Data subjected to DeSeq normalization using NGS Strand/Avadis.
Batch effects were removed using the ‘ComBat’ algorithm in R program.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Excel file of normalized data including gene ID and normalized values.

source_name: RNA from blood, time point, 1 day before MCS surgery

extract_protocol:
Samples were collected on day one before mechanical circulatory support surgery. Eight ml of blood was drawn into a CPT tube (Becton Dickinson, Franklin Lakes, NJ). Peripheral Blood Mononuclear cells (PBMC) from each sample were purified within 2h of phlebotomy. The collected blood was mixed and centrifuged at room temperature (22⁰C) for 20min at 3000 RPM. The cell layer was collected, transferred to 15ml conical tubes and centrifuged for 20min at 1135 RPM at 4°C. The supernatant was aspirated and discharged. The cell pellet was resuspend in cold Phosphate Buffer Saline (Sigma-Aldrich, St. Louis, MO), transferred into an eppendorf tube and centrifuged for 20min at 5.6 RPM at 4°C. The supernatant was discharged. The pellet was resuspended in 0.5 ml RNA Protect Cell Reagent (Qiagen, Valencia, CA) and frozen at -80°C. The RNA was isolated from the PBMC using RNeasy Mini Kit (Qiagen, Valencia, CA).  The quality of the total RNA was assessed using NanoDrop® ND-8000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)  concentration above 50 ng/µl., purity - 260/280 ~ 2.0., integrity - RIN > 9.0 and average > 9.5.
mRNA library was prepared with Illumina TruSeq RNA kit according to the manufacturer’s instructions (Illumina, San Diego, CA). Library construction consists of random fragmentation of the polyA mRNA, followed by cDNA production using random polymers. The cDNA libraries were quantitated using Qubit and size distribution was checked on Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: age

tag: gender

value: Male

tag: underlying disease

value: NICM

tag: mcs type

value: HVAD

tag: tp1 intermacs

tag: tp 1 sofa

tag: tp 1 meldxi

tag: tp 5 sofa

tag: tp 5 meld-xi

tag: group

tag: outcome after 1 year

value: Dead

tag: echo

value: normal/mildly reduced right ventricular function

tag: tp 1 inotropes

value: 2 inotropes

tag: cpb time

value: no major bleeding

tag: blood transfusions

tag: Cause of death

value: Sepsis

value: blood

value: peripheral blood mononuclear cell


title: 183_CCGTCC

value: ICM

value: HMII

value: 1 inotrope

value: major bleeding

value: MOD

tag: tissue

tag: cell type


title: S170 SSEA4pos

description: S170 SSEA4pos_FPKM

source_name: IPF Lung Biopsy_SSEA4+

tag: subject status

value: Idiopathic Pulmonary Fibrosis (IPF)

value: lung

tag: progression

value: Slow

value: lung fibroblast cultures (passages 4-8)

tag: facs-sorted population


title: 139_AGTTCC

tag: age

tag: gender

value: Male

tag: underlying disease

value: NICM

tag: mcs type

tag: tp1 intermacs

value: Alive

value: ≥3 inotropes or MCS


title: D5

tag: breed

value: Dorset sheep

value: ovary

tag: genotype

value: wild type


title: S99 SSEA4neg

description: S99 SSEA4 neg_FPKM

value: Rapid


title: W8

value: Small Tail Han sheep

value: FecB+ FecB+


title: D4


title: S109 SSEA4pos

description: S109 SSEA4pos_FPKM


title: 115_GTGAAA

value: ICM

value: ECMO

tag: tp 1 sofa

tag: tp 1 meldxi

tag: group

tag: outcome after 1 year

value: Dead

tag: echo

value: moderately/severely reduced right ventricular function

value: 2 inotropes

value: no major bleeding

value: blood

value: peripheral blood mononuclear cell


title: S161 SSEA4pos

description: S161 SSEA4pos_FPKM

value: Idiopathic Pulmonary Fibrosis (IPF)

tag: tissue

value: lung

value: Slow

value: lung fibroblast cultures (passages 4-8)


title: S48 SSEA4neg

description: S48 SSEA4 neg_FPKM

tag: cell type


title: SAM24286378 PANC-1 control

description: SAM24286378 PANC-1

tag: sirna

value: control

tag: cell line


title: S99 SSEA4pos

description: S99 SSEA4pos_FPKM

tag: subject status

tag: progression

tag: facs-sorted population


title: W7

value: ovary


title: 167_AGTCAA

tag: age

tag: gender

value: Male

tag: underlying disease

value: NICM

value: TAH

tag: tp 5 sofa

tag: tp 5 meld-xi

tag: tp 1 inotropes

value: 0 inotrope

tag: cpb time

value: major bleeding

tag: blood transfusions

tag: Cause of death

value: MOD


title: S69 SSEA4pos

description: S69 SSEA4pos_FPKM

value: Rapid


title: S56 SSEA4pos

description: S56 SSEA4pos_FPKM


title: 86_GTCCGC

value: NCIM

tag: mcs type

value: HMII

tag: tp1 intermacs

tag: tp 1 sofa

tag: tp 1 meldxi

tag: group

tag: outcome after 1 year

value: Alive

tag: echo

value: moderately/severely reduced right ventricular function


title: W4

tag: breed

value: Small Tail Han sheep

tag: tissue

tag: genotype

value: FecBBFecBB


title: S76A SSEA4pos

description: S76A SSEA4pos_FPKM

tag: subject status

value: Idiopathic Pulmonary Fibrosis (IPF)

value: lung

tag: progression

value: Slow

tag: cell type

tag: facs-sorted population


title: 90_CGATGT

tag: age

tag: gender

tag: underlying disease

value: ICM

value: HMII/CMAG-RVAD

tag: tp 5 sofa

tag: tp 5 meld-xi

value: Dead

tag: tp 1 inotropes

tag: cpb time

value: blood

value: peripheral blood mononuclear cell


title: W6

value: ovary

value: FecB+ FecB+


title: S48 SSEA4pos

description: S48 SSEA4pos_FPKM

value: Rapid

value: lung fibroblast cultures (passages 4-8)


title: 56_ACTGAT

value: Male

tag: mcs type

value: HMII

tag: tp1 intermacs

tag: tp 1 sofa

tag: tp 1 meldxi

tag: group

value: 0 inotrope

value: no major bleeding

tag: blood transfusions

value: major bleeding

tag: Cause of death


title: NL4 SSEA4pos

description: NL4 SSEA4pos_FPKM

tag: subject status

value: normal donor

tag: tissue

tag: progression


title: W1

tag: breed

value: Small Tail Han sheep

tag: genotype

value: FecBBFecBB


title: 131_TTAGGC

tag: age

tag: gender

tag: underlying disease

value: ICM

tag: outcome after 1 year

tag: echo

value: normal/mildly reduced right ventricular function

value: 2 inotropes

value: MOD

tag: cell type


title: 100_GTCCGC

tag: mcs type

value: CMAG-LVAD

tag: tp1 intermacs

tag: tp 5 sofa

tag: tp 5 meld-xi

value: Dead

tag: tp 1 inotropes

value: 1 inotrope

tag: cpb time

value: blood

value: peripheral blood mononuclear cell


title: Dorset

data_processing:
Illumina Casava1.7 software used for basecalling.
MeDIP-seq reads were aligned to the Oar_v3.1 genome assembly using SOAP version 2.21 with the following setting: -s 34 -p 4 -v 2 -m 100 -x 500
convert sop files to bed files
peaks were called using MACS version 1.4.0 with the following setting: --tsize 49 --bw 200 --gsize 2600000000 --pvalue 1e-5 --wig --wigextend 300 --space 50  --mfold 10,30
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: wig files were generated using MACS_1.4.0

extract_protocol:
A phenol-chloroform extraction method
Genomic DNA mixtures were sonicated to gain fragments in the range 100–500 bp, and dAs were added to the 3’ ends of the DNA fragments. The adaptors were then ligated to the two ends of each fragment with paired-end DNA sample prep kit (Illumina) according to the manufacturer’s protocol. The double-stranded DNA was denatured to single strands, and then the anti-5-methylcytosine mouse monoclonal antibody (Calbiochem) was used to immunoprecipitate the DNA fragments containing regions of methylated cytosines with magnetic methylated DNA immunoprecipitation kit (Diagenode). The precipitated DNA fragments were then amplified by PCR and separated by agarose gel electrophoresis. The 200–300 bp fragments were excised and extracted using a gel extraction kit (28706; Qiagen). The selected DNA fragments were quantified using an Agilent 2100 Analyzer. The quantified library was sequenced in an Illumina HiSeq 2000 at the BGI (Shenzhen, China).
Libraries were prepared for sequencing using standard Illumina protocols

tag: sheep type

value: Dorset sheep

value: ovary

value: wild type


title: 41_ACTGAT

value: Male

value: HMII

tag: tp 1 sofa

tag: tp 1 meldxi

tag: group

value: moderately/severely reduced right ventricular function

value: ≥3 inotropes or MCS

value: no major bleeding

tag: blood transfusions

tag: Cause of death

tag: tissue


title: 6_GGCTAC

tag: age

tag: gender

tag: underlying disease

value: NICM

value: HMII/CMAG-RVAD

value: major bleeding


title: Han++

value: Small Tail Han sheep

tag: genotype

value: FecB+ FecB+


title: 163_ACAGTG

value: ICM

tag: mcs type

tag: outcome after 1 year

value: Dead

tag: echo

value: 2 inotropes

value: GI hemorrhage

tag: cell type


title: 149_CGATGT

value: Female

tag: tp1 intermacs

tag: tp 5 sofa

tag: tp 5 meld-xi

value: Alive

tag: tp 1 inotropes

value: 0 inotrope

value: blood

value: peripheral blood mononuclear cell


title: B15_CONT

city: Jerusalem

first: Raz

last: Yirmiya

address: Mount Scopus

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 40 nucleotides were discarded (cutadapt option –m 40).
Reads that had either a percentage of Adenine bases above 50% or a percentage of Thymine bases above 50% were discarded using a custom script.
TopHat (v2.0.10) was used to align the reads to the mouse genome (mm10)
Counting reads on mm10 refseq genes was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: olfactory bulb

extract_protocol:
RNA was extracted using PerfectPure RNA Tissue Kit, 5 PRIME
Inhouse poly A based RNA seq

treatment_protocol: Mice received PLX5622 diet or control diet for 25 days before they were sacrificed and the olfactory bulbs were removed and flash frozen in liquid nitrogen for later processing

tag: strain

value: olfactory bulb

tag: diet

value: Control diet


title: B16_CONT


title: 122_CAGATC

value: Male

value: ChemoCM

value: HMII

tag: tp 1 sofa

tag: tp 1 meldxi

tag: group

value: normal/mildly reduced right ventricular function

value: ≥3 inotropes or MCS

tag: cpb time

value: no major bleeding

tag: blood transfusions


title: RIL387_3

city: Cape Town

first: Shane

last: Murray

address: University Avenue North

department: Dept of Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

description: A leaf from three plants in field block 3 with a 1.5 (resistant) Cercospora zeina score  were pooled at harvest

data_processing:
Illumina Casava1.5 software used for basecalling.
Read quality was evaluated by the fastQC application v0.11.2.  Illumina 1.5 encoded quality scores (Q) were converted to Sanger scale (phred) using FASTQ Groomer Galaxy v1.0.4
Sequence reads for each biological replicate were mapped to v2 of the Maize B73 reference genome (5b.60) using TopHat v2.0.9.  Intron length was specified as between 5 to 60,000 bp, mean inner distance between mate pairs defined as 100 bp and up to two mismatches allowed per 25 bp kmer.
Cufflinks v2.0.2 was used to calculate transcript abundance which is reported as fragments per kilobase pair of exon model per million fragments mapped (FPKM).  The maximum intron length was specified as 60,000 bp.    In order to improve calculation of differential expression for less abundant genes and transcripts, quartile normalization was applied.
Six assemblies consisting of three resistant and three susceptible biological replicate samples were generated by Cufflinks.  The assemblies were merged with the reference annotation (Zea mays B73 reference v2 5b.60 filtered gene set) into a single .gtf file using Cuffmerge.
Differential expression analysis was conducted in CuffDiff (Cufflinks v2.0.2) using the merged files.  The False Discovery Rate (FDR) adjustment of the associated p values was set to a maximum of 0.05
Genome_build: Maize B73 reference genome (5b.60)v2
Supplementary_files_format_and_content: A tab delimited text file for each sample including FPKM vlaues for each gene

organism: Zea mays

source_name: Cercospora zeina-resistant line (RIL387)

growth_protocol: Plants were grown in rows in a randomised design in three replicate blocks at Baynesfield Experimental Station, Kwazulu-Natal, South Africa

extract_protocol:
A single leaf extract from three plants per biological replicate (field block) were combined.  The leaf extract consisted of a 12cm2 section of a single leaf displaying grey leafspot symptoms.  RNA was extracted from pooled leaves in each biological rep using  Qiazol and total RNA was purified using the RNeasy Mini kit (Qiagen).
Total RNA (1ug per sample) was used to prepare 50 bp short-insert libraries using the Illumina TruSeq RNA Sample Prep Kit and sequencing was performed on an Illumina HiSeq™ 2000 system at BGI.

treatment_protocol: Natural field infection with Cercospora zeina took place (plants were not sprayed with fungicide)

tag: genotype/variation

value: Recombinant Inbred Line 387  from CML444 X SC Malawi (F7:S6)

tag: c. zeina suceptibility

value: 1.5 (resistant) C. zeina score

tag: developmental stage

value: R5-early dent stage

tag: tissue

value: leaf

tag: pathogen


title: RIL387_2

description: A leaf from three plants in field block 2 with a 1.5 (resistant) Cercospora zeina score  were pooled at harvest

value: Natural field infection with Cercospora zeina


title: B14_CONT


title: HanBB

tag: sheep type

value: Small Tail Han sheep

value: ovary

tag: genotype

value: FecBBFecBB


title: 118_CGATGT

tag: age

tag: gender

tag: underlying disease

value: NICM

tag: mcs type

value: PVAD BVAD

tag: tp1 intermacs

tag: tp 5 sofa

tag: outcome after 1 year

value: Alive

tag: echo

value: moderately/severely reduced right ventricular function

value: 2 inotropes

value: major bleeding

tag: Cause of death

value: blood

tag: cell type

value: peripheral blood mononuclear cell


title: B4_PLX

tag: strain

value: olfactory bulb

tag: diet

value: PLX5622 diet (inducing a near-complete microglia depletion)


title: B5_PLX


title: RIL165_3

description: A leaf from three plants in field block 3 with a 7.5 (susceptible) Cercospora zeina score  were pooled at harvest

source_name: Cercospora zeina susceptible line (RIL165)

tag: genotype/variation

value: Recombinant Inbred Line 165  from CML444 X SC Malawi (F7:S6)

tag: c. zeina suceptibility

value: 7.5 (susceptible) C. zeina score

tag: developmental stage


title: RIL165_2

description: A leaf from three plants in field block 2 with a 7.5 (susceptible)  Cercospora zeina score were pooled at harvest

value: R5-early dent stage

tag: tissue

value: leaf

tag: pathogen


title: 95_CTTGTA

tag: age

value: Female

value: HVAD

tag: tp 1 sofa

tag: tp 1 meldxi

tag: tp 5 meld-xi

tag: group

tag: tp 1 inotropes

tag: cpb time

value: no major bleeding

tag: blood transfusions


title: 105_TGACCA

tag: gender

tag: underlying disease

value: NICM

tag: mcs type

tag: tp1 intermacs

tag: tp 5 sofa

tag: outcome after 1 year

value: Dead

tag: echo

value: 0 inotrope

tag: Cause of death

value: MOD


title: W2

tag: breed

value: Small Tail Han sheep

tag: tissue

value: ovary

tag: genotype

value: FecBBFecBB


title: RIL387_1

description: A leaf from three plants in field block 1 with a 1.5 (resistant) Cercospora zeina score  were pooled at harvest

tag: genotype/variation

value: Recombinant Inbred Line 387  from CML444 X SC Malawi (F7:S6)

tag: c. zeina suceptibility

value: 1.5 (resistant) C. zeina score

tag: developmental stage

tag: pathogen

value: Natural field infection with Cercospora zeina


title: RIL165_1

description: A leaf from three plants in field block 1 with a 7.5 (susceptible) Cercospora zeina score were pooled at harvest

value: Recombinant Inbred Line 165  from CML444 X SC Malawi (F7:S6)


title: 110_AGTCAA

tag: age

value: Male

value: TAH

tag: tp 1 sofa

tag: tp 1 meldxi

tag: tp 5 meld-xi

tag: group

value: Alive

value: moderately/severely reduced right ventricular function

tag: tp 1 inotropes

value: 2 inotropes

tag: cpb time

value: major bleeding

value: blood

tag: cell type

value: peripheral blood mononuclear cell


title: B3_PLX

tag: strain

value: olfactory bulb

tag: diet

value: PLX5622 diet (inducing a near-complete microglia depletion)


title: 81_CTTGTA

tag: gender

tag: underlying disease

value: NICM

tag: mcs type

value: HMII

tag: tp1 intermacs

tag: tp 5 sofa

tag: outcome after 1 year

tag: echo

value: ≥3 inotropes or MCS

value: no major bleeding

tag: blood transfusions

tag: Cause of death


title: KO_Th1

city: Seoul

first: Do-Hyun

last: Kim

address: 222 Wangsimni-ro

country: South Korea

institute: Hanyang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: mouse naive CD4 T cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SENSE mRNA-Seq Library Prep Kit  (Cat#001.96) standard protocols.

tag: strain background

tag: genotype/variation

value: in vitro skewed Th1 cell


title: 51_GGCTAC

tag: age

value: Female

value: PPCM

tag: tp 1 sofa

tag: tp 1 meldxi

tag: tp 5 meld-xi

tag: group

value: 1 inotrope

tag: tissue


title: WT_Th1

tag: cell type


title: 46_ATCACG

tag: gender

value: Male

tag: underlying disease

value: normal/mildly reduced right ventricular function

tag: tp 1 inotropes

tag: cpb time


title: 238_AGTCAA

tag: mcs type

value: HMII/CMAG-RVAD

tag: tp1 intermacs

tag: tp 5 sofa

tag: outcome after 1 year

value: Alive

value: moderately/severely reduced right ventricular function

value: 0 inotrope


title: 36_GGCTAC

value: ICM

tag: echo

tag: blood transfusions

tag: Cause of death

value: blood

value: peripheral blood mononuclear cell


title: 33KO Rep 2

city: New Haven

first: Nathan

middle: L

last: Price

state: CT

address: 10 Amistad St Rm 320

department: CMED

institute: Yale University

data_processing:
Base calling was done on Illumina HiSeq 2500 platform.
Reads were trimmed for quality using customs Perl scripts.
Alignment was carried out using TopHat2 with default parameters.
Transcript estimation and differential gene-expression was carried out using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Peritoneal Macrophage

extract_protocol:
Thioglycolate elicited peritoneal macrophages from WT and miR-33-/- mice were harvested by peritoneal lavage.  Cells were then plated for 2hr, then washed to remove non-adherant cells.  Macrophages were then scraped, pelleted and frozen at -80◦C.
Total RNA from WT and miR-33-/- thioglycollate-elicited peritoneal macrophages was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). The purity and integrity of total RNA sample was verified using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries from WT BMDMs were performed TrueSeq Small RNA Library preparation (Illumina) and were sequenced for 45 cycles on Illumina HiSeq 2000 platformm (1 x 75bp read length). The reads obtained from the sequencer are trimmed for quality using in-house developed scripts.  The trimmed reads are aligned to the reference genome using TopHat2.  The transcript abundances and differences calculated using cuffdiff.  The results were plotted using R and cummeRbund using in-house developed scripts.

tag: strain

value: Peritoneal Macrophage

tag: age

value: 5 month

tag: genotype


title: 33KO Rep 1


title: 33KO Rep 3


title: WT Rep 3

value: Wildtype


title: WT Rep 2


title: 25_GTTTCG

value: HMII

tag: tp 1 sofa

tag: tp 1 meldxi

tag: tp 5 meld-xi

tag: group

value: ≥3 inotropes or MCS

value: no major bleeding


title: Hela_LSD1_KO_RNA-Seq

city: Ganzhou

first: Wenjuan

last: Zhang

address: No. 23, Qingnian Road

institute: Gannan Medical University

data_processing:
For computational analysis of RNA-seq data, sequencing reads were aligned to hg19 human genome using the “Tuxedo suite”: Bowtie2-Tophat
EdgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) was used to compute the differential expressed genes (P<0.001, dispersion 0.001).
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
The HOMER suite (Hypergeometric Optimization of Motif EnRichment) was used to generate the input of EdgeR and calling EdgeR

source_name: HeLa

growth_protocol: HeLa cells were cultured in MEM alpha medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated from HeLa cells using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L).

treatment_protocol: Cells grown to ~90% confluent were used for RNA-seq.

tag: cell line

value: Hela

tag: tag


title: Hela_SET9_KO_RNA-Seq


title: Hela_YY2_KO_RNA-Seq


title: WT Rep 1

tag: tissue


title: 21_GATCAG

tag: gender

value: Female

tag: underlying disease

value: NICM

tag: mcs type

tag: tp 1 inotropes

value: 2 inotropes

tag: cpb time

tag: cell type


title: 16_ACTGAT

value: PPCM

value: HMII/CMAG-RVAD

tag: tp1 intermacs

tag: tp 5 sofa

tag: outcome after 1 year

tag: echo

tag: blood transfusions

tag: Cause of death


title: LDLRKO Rep 1

tag: strain

tag: age

tag: genotype

value: LDLR-/-


title: MDA-MB-231_shikonin 0 μM

city: Kaohsiung

first: CHIA-YANG

last: LI

address: 100,Shih-Chuan 1st Road

department: Graduate Institute of Medicine

institute: Kaohsiung Medical University

data_processing:
The reads were aligned with TopHat 2.0.13 to GRCh38 with default parameters,
using Ensembl v79 annotations. Transcript abundance was measured in fragments
per kb of exon per million fragments mapped (FPKM).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

growth_protocol: MCF-7 and MDA-MB-231 cells were maintained in DMEM supplemented with 10% heat-inactivated FBS and 100 μg/mL of penicillin-streptomycin, and SK-BR-3 cells were maintained in DMEM/F12 supplemented with 10% heat-inactivated FBS and 100 μg/mL of penicillin-streptomycin.

extract_protocol:
Total RNA was extracted with TRIzol reagent following the recommendations of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF-7, SK-BR-3 and MDA-MB-231 cells were treated with 10 μΜ shikonin for 6 hr.

tag: cell line

tag: treatment

value: shikonin 0 μM


title: LDLRKO Rep 2

tag: tissue


title: MDA-MB-231_shikonin 10 μM

value: shikonin 10 μM


title: SK-BR-3_shikonin 10 μM


title: DKO Rep 3


title: DKO Rep 1


title: SK-BR-3_shikonin 0 μM


title: DKO Rep 2


title: MCF-7_shikonin 10 μM


title: MCF-7_shikonin 0 μM


title: 31_ATCACG

tag: gender

value: Male

tag: underlying disease

tag: tp 1 sofa

tag: tp 1 meldxi

tag: tp 5 meld-xi

tag: group

value: Alive

value: moderately/severely reduced right ventricular function

value: major bleeding

value: blood