title: Sample 3_L. lactis non-induced, acetaldehyde-induced replicate 3

city: Groningen

first: Jhonatan

middle: Alejandro

last: HernandezValdes

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: Biological replicate 3 of 3: Cy3 control, Cy5 induced

hyb_protocol: Hybridization to the probes spotted on the L. lactis MG1363 mixed amplicon and oligonucleotide DNA microarray slides, covering 2308 of the 2435 predicted ORF’s, was done using the Slidehyb 1 hybridization buffer (Ambion Biosystems, Foster City, CA, USA), during 16 h at 45 °C. After hybridization, slides were washed for 5 min in 2X SSC (150 mM NaCl and 15 mM trisodium citrate) with 0.5 % SDS, 2 times for 5 min in 1X SSC with 0.25 % SDS and 5 min in 1X SSC with 0.1 % SDS. All washing steps were performed at 30 °C with preheated buffers. The washing buffers were removed via centrifugation (Eppendorf 5810R, 2 min, 2000 rpm).

scan_protocol: The DNA microarray slides were scanned using a GenePix Autoloader 4200AL confocal laser scanner (Molecular Devices Corporation, Sunnyvale, CA, USA).

data_processing: The resulting images were analyzed using the ArrayPro Analyzer 4.5 software (Media Cybernetics, Silver Spring, MD, USA). Signal intensities were quantified for each spot on the DNA microarray slides after subtracting the background intensities, which were determined for each spot by reading the signals in the regions that separated diagonal spots.

organism: Lactococcus lactis

source_name: L. lactis control 30min

label_protocol: Incorporation of amino allyl-modified dUTPs during cDNA synthesis allowed Cy3/Cy5 labeling with the CyScribe Post labeling Kit (Amersham Biosciences, Piscataway, NJ, USA), according to the supplier’s instructions. All intermediate and final purifications of either labeled or unlabeled cDNA were performed with a NucleoSpin Extract II Kit (Clontech Laboratories, Mountain View, CA, USA), according to manufacturer’s instructions except when purifying unlabeled cDNA, where 80 % ethanol was used in a second washing step and 0.1 M sodium bicarbonate, pH 9.0, was used as the elution buffer.

growth_protocol: The bacterial strain Lactococcus lactis was grown as standing cultures at 30 °C in M17 broth (DifcoTM BD, NJ, USA) supplemented with glucose (GM17; Sigma-Aldrich, MO, USA) at a concentration of 0.5 % (w/v).

extract_protocol: For RNA isolation, 0.5 g of glass beads (~ 100 μm in diameter), 50 μL of 10% sodium dodecylsulfate (SDS; Sigma-Aldrich, MO, USA), 500 μL of premixed phenol:chloroform:isoamylalcohol (25:24:1) and 175 μL of macaloid suspension were added to the thawed cells in the screw cap tube. Cells were disrupted using 2 cycles of 45 s of bead beating with a 1 min interval on ice. The cell lysate was cleared by centrifugation in an Eppendorf 5417R centrifuge (Eppendorf AG, Hamburg, Germany) during 10 min centrifugation, speed 10000 rpm, at 4 °C. Next, the upper phase was extracted with 500 μL of chloroform: isoamylalcohol (24:1). The two phases were resolved by centrifugation (10 min, 10000 rpm, 4 °C) and total RNA was isolated from the aqueous phase using the High Pure RNA Isolation Kit (Roche Molecular Biochemicals, Mannheim, Germany), according the manufacturer’s instructions.

treatment_protocol: At exponential growth phase (OD600 = 0.4) acetaldehyde was added at a concentration of 0.7 M. After 30 min, the equivalent of 10 OD600 units of volume (volume in mL multiplied by OD600) was taken. Cells were collected by centrifugation in 50 mL Greiner tubes in an Eppendorf 5810R centrifuge (Eppendorf AG, Hamburg, Germany), during 10 min centrifugation, speed 10,000 rpm, at 4 °C.

tag: strain

value: control

tag: time

value: 30 min

source_name: L. lactis induced 30min

value: acetaldehyde


title: DNA_2N+_25_S73

status: Public on Mar 30 2020

type: SRA

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
library strategy: scWGS for CNV analysis
Adapter removal and removing reads shorter than 36bp using Bbduk
Reads aligned to refenrence genome mm9 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
The duplicate removed aligned reads were then assigned to variable length bins across the genome based on where they align in the genome
The average bin counts were calculated and used as the diploid 2N average. Bins with higher number are considered as amplified and those with lower are considered deleted. CNV profiles were generated using R.
Genome_build: mm9
Supplementary_files_format_and_content: Varbin files with bincounts for CNV analysis

molecule: genomic DNA

organism: Mus musculus

source_name: KPC1199EGFP Adherent cells at passage 9

growth_protocol: KPC1199-EGFP cells were thawed and passaged in DMEM supplemented with 10% Fetal Bovine Serum, 1% Pencillin/streptomycin

extract_protocol:
Adherent cells were trypsinzed, counted and resuspended in NST-DAPI buffer. Cells were sorted on flow cytometer based on the DNA content to obtain single nuclei for scWGS
Single cells isolated into 10x Lysis and Fragmentation Buffer were processed for genomic DNA amplification using SeqXE kit from Sigma Aldrich. Manufacturer's instructions very followed for gDNA amplification. Library preparation was done by end repair, adenylation, adapter ligation and PCR steps.

treatment_protocol: No treatment

tag: strain background

tag: cell line

tag: cell type

value: Pancreatic cancer tumor cell line

tag: labelling for flow

value: EGFP expression

tag: molecule subtype

value: genomic DNA in nuclei


title: methylation_55_Combined

type: genomic

city: Chicago

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

department: Human Genetics

institute: The University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard Illumina scanner settings

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5% in either African Americans or European Americans) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
normalized data file includes normalized (SWAN and background normalization) Average Beta
The raw data file "Unprocessed_Methylation_FinalGEO.csv" includes unmethylated and methylated signal intensities

organism: Homo sapiens

source_name: primary cultured airway smooth muscle cell

label_protocol: Standard Illumina protocol.

growth_protocol: ASMCs were cultured in 96-well Nusil coated plates in serum free media for 48 hours prior to cytokine exposure.

extract_protocol: Genomic DNA from IL-13, IL-17, IL-13+IL-17, or vehicle-exposed airway smooth muscle cells was extracted and purified using the AllPrep Kit from QIAgen according to standard instructions

treatment_protocol: ASMCs were exposed to IL-13 (10ng/mL), IL-17 (3ng/mL), IL-13+IL-17, or vehicle (10% FBS in PBS) for 24 hours prior to RNA and DNA extraction.

tag: donor

tag: treatment

value: Combined

tag: asthma

value: No

tag: age

tag: Sex

value: Female

tag: imputedsmoking

tag: race

value: EuropeanAmerican


title: methylation_55_IL-17

value: primary cultured airway smooth muscle cell


title: Sample 4_L. lactis acetaldehyde-induced, non-induced replicate 1

type: RNA

description: Biological replicate 1 of 3: Cy3 induced, Cy5 control

molecule: total RNA


title: DNA_2N+_24_S72


title: DNA_2N+_23_S71


title: ch12_Med14Nsmash_chipseq_SP1_APR60h_rep1

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)

source_name: CH12 B cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of -mercaptoethanol (Thermo Fisher Scientific). A 3xFlag and small molecule–assisted shutoff (SMASh) tag was introduced to the N-terminus of Med14 using CRISPR-Cas9 based knock-in via homologous recombination. Single cell clones were established and degradation of Med14 was assessed by western blotting for Med14 (Abcam) after treatment of cells with 3 M Asunaprevir (MCE).

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 3000 or Novaseq 6000 (Illumina).

tag: genotype

tag: tissue

value: lymphoma cell line

tag: chip antibody

value: Abcam, ab13370

tag: experimental type

value: ChIPseq


title: Sample 2_L. lactis non-induced, acetaldehyde-induced replicate 2

description: Biological replicate 2 of 3: Cy3 control, Cy5 induced

tag: strain

tag: time


title: Sample 6_L. lactis  diacetyl-induced, non-induced replicate 3

description: Biological replicate 3 of 3: Cy3 induced, Cy5 control

treatment_protocol: At exponential growth phase (OD600 = 0.4) diacetyl was added at a concentration of 5 mM. After 30 min, the equivalent of 10 OD600 units of volume (volume in mL multiplied by OD600) was taken. Cells were collected by centrifugation in 50 mL Greiner tubes in an Eppendorf 5810R centrifuge (Eppendorf AG, Hamburg, Germany), during 10 min centrifugation, speed 10,000 rpm, at 4 °C.

value: diacetyl

tag: treament


title: Sample 1_L. lactis non-induced, acetaldehyde-induced replicate 1

description: Biological replicate 1 of 3: Cy3 control, Cy5 induced


title: methylation_55_IL-13

tag: cell type


title: Sample 6_L. lactis acetaldehyde-induced, non-induced replicate 3


title: DNA_2N+_22_S70

tag: strain background

tag: cell line

tag: labelling for flow


title: Sample 4_L. lactis  diacetyl-induced, non-induced replicate 1

tag: treatment


title: DNA_2N+_21_S69

tag: molecule subtype


title: methylation_62_Vehicle

tag: donor

value: Vehicle

tag: asthma

tag: age

value: Male

value: Yes


title: Sample 5_L. lactis acetaldehyde-induced, non-induced replicate 2

description: Biological replicate 2 of 3: Cy3 induced, Cy5 control

value: 30 min

value: control


title: input_DNA_R1

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Basecalls were performed using CASAVA.
Quality of ChIP-seq libraries was assessed using FastQC (v0.9.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the identified 3’ adapters in the zebrafish ChIP libraries were removed using cutadapt v1.3 (Martin 2011) with the following specifications –O 5 –match-read-wildcards –m 50.
Reads were mapped to the danRer10 genome versions with Bowtie 2 version 2.2.5 (Langmead and Salzberg 2012) using –end-to-end –sensitive parameters. Alignment reports were converted to sorted BAM files using samtools version 1.1 (Li et al. 2009) to discard reads with mapping quality lower than 20.
Duplicated reads were removed using MarkDuplicates from Picard Tools (version 1.45, https://broadinstitute.github.io/picard/) with parameters: REMOVE_DUPLICATES = true OPTICAL_DUPLICATE_PIXEL_DISTANCE = 100. Next, reads from technical replicates were combined with samtools merge.
Peak calling was performed with MACS2 callpeak using the input libraries as control of the ChIP libraries and the following parameters: -g 9.9e8 –keep-dup all –bw [187|183] –call-summits. Pileup tracks were generated using MACS2 commands callpeak (--keep-dup all –B –model –extsize [187|183] –SPMR –g 9.9e8 or 2.3e9) and bdgcmp (-m subtract).
Pearson correlation between duplicates was calculated with deepTools version 3.0.1 (Ramírez et al. 2016) multiBigwigSummary (--binSize 10000) and plotCorrelation (--corMethod pearson –log1p --removeOutliers). As high correlation was observed, biological replicates were combined by first normalizing the signal for each replicate using MACS2 callpeak (-B –nomodel –extsize 185 –g 9.9e8 –keep-dup all) and bdgcmp (-m ppois). Replicates were then combined using the generated bedgraph files as input of cmbreps (-m fisher) and peaks identified with bdgpeakcall using the bedgraph file with the combined signal (-l 200 –g 100 –c 8). The final bedgraph file was converted to bigwig format with bedGraphToBigWig.
Genome_build: danRer10
Supplementary_files_format_and_content: bigwig file was generated using the final bedgraph file from MACS2 (score = –log10 (p-value))
Supplementary_files_format_and_content: bed file was generated using the final bedgraph file from MACS2, contains identified peaks in chromosomes

organism: Danio rerio

source_name: AB

growth_protocol: Zebrafish were maintained according to standard protocols (Westerfield, 2000) that follow the current Directive 2010/63/EU.

extract_protocol:
Biological replicates were prepared with 2,000 embryos each, collected from independent crosses of ctcf HA/wt fish. Embryos were dechorionated and homogenized in 1% formaldehyde to crosslink chromatin (Thermo Scientific, Prod # 28906) for 15 minutes at room temperature. The fixation reaction was quenched with 0.125 M glycine. Cells were collected and washed twice with ice-cold 1X PBS before snap freezing them with dry ice to store samples at -80°C. Samples were thawed and independent batches combined to get two biological replicates before cell lysis. Chromatin was sheared to 100-200 bp on a Covaris S220 sonicator in a waterbath maintained at 4°C using 4 cycles of 1 minute each with the following settings: duty factor 10, peak power 175, cycles/burst 200. After sonication, samples were centrifuged to remove debris and 50 μL of each replicate were kept to prepare input control libraries. ChIP was performed using ~7 μg of Anti-HA.11 epitope tag (BioLegend, Lot B222920) for each 50 μL of Dynabeads Protein A (Invitrogen, Lot 00355924). Samples were incubated with the antibody/magnetic bead mix overnight at 4°C. Magnetic beads were washed six times with ice-cold RIPA buffer before DNA elution. Reverse crosslinked eluates of ChIPed DNA and input controls were treated with 8 μL of RNase A (Thermo Scientific) and 4 μL of proteinase K (Roche). DNA was purified with phenol:chloroform and resuspended in 15 μL of 10 mM Tris-HCl pH 8.
Purified DNA was used to construct single-end (SR100) Illumina sequencing libraries with the TruSeq – ChIP-seq protocol. Libraries were sequenced in a HiSeq 2500 system.

tag: developmental stage

value: 24 hpf embryos

value: AB

value: ctcf{HPSH}


title: methylation_62_IL-13

tag: Sex

tag: imputedsmoking

tag: race


title: CTCF_ChIP-seq_R1

tag: genotype

tag: chip antibody

value: anti-HA.11 epitope tag (BioLegend, Clone 16B12, Lot B224726)


title: CTCF_ChIP-seq_R2

tag: strain


title: Sample 3_L. lactis non-induced, diacetyl-induced replicate 3

tag: time

tag: treament


title: Sample 5_L. lactis  diacetyl-induced, non-induced replicate 2


title: DNA_2N+_20_S68

tag: strain background

tag: cell type

value: Pancreatic cancer tumor cell line

value: EGFP expression

value: genomic DNA in nuclei


title: methylation_62_Combined

value: primary cultured airway smooth muscle cell

value: Combined

value: No

value: EuropeanAmerican


title: input_DNA_R2


title: DNA_2N+_2_S50

tag: cell line

tag: labelling for flow


title: methylation_62_IL-17

tag: treatment


title: DNA_2N+_19_S67

tag: molecule subtype


title: Sample 2_L. lactis non-induced, diacetyl-induced replicate 2

value: diacetyl


title: methylation_50_Combined

tag: donor

tag: asthma

value: Female

value: AfricanAmerican


title: DNA_2N+_18_S66


title: methylation_50_IL-17

tag: age

value: Yes


title: T4-3

city: Guiyang

first: LU

last: YUXI

address: Guizhou Academy of Agricultural Sciences

country: China

institute: Institute of Horticulture

library_source: transcriptomic

data_processing:
Illumina HiSeq 2000 software used for basecalling.
The reads with more than 10% unknown bases and those of low quality were removed from the raw sequencing data using the software Illumina GA Pipeline (v1.6).
The filtered reads were aligned to the cucumber Chinese long v2 genome using TopHat2 (http://tophat.cbcb.umd.edu/) software.
Use HTSeq 0.6.1p2 (http://www-huber.embl.de/users/anders/HTSeq) to compare the read count value of each gene as the original expression amount of the gene
perform expression level for mRNAs by calculating RPKM
Genome_build: Cucumis_sativus_v 20
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Cucumis sativus

source_name: Ovary tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA was isolated using TRIzol (Invitrogen), and DNase I (Fermentas) digestion was performed for 30 min at 25 oC to remove DNA, according to the manufacturer’s instructions. The integrity and quality of the total RNA were checked using a NanoDrop 1000 spectrophotometer and formaldehyde-agarose gel electrophoresis. RNA was used only when the OD260: OD280 ratio was above 1.8. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina HiSeqTM 2000 at the (Personal-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Ovary

value: the embryos were cultured for 30d


title: T5-3

value: the embryos were cultured for 60d


title: T5-2


title: methylation_50_IL-13

tag: Sex

tag: imputedsmoking


title: Sample 1_L. lactis non-induced, diacetyl-induced replicate 1

value: control

value: 30 min


title: T4-2


title: DNA_2N+_17_S65


title: methylation_50_Vehicle

value: Vehicle

tag: race


title: DNA_2N+_16_S64

value: Pancreatic cancer tumor cell line


title: methylation_32_Vehicle

value: Male


title: DNA_2N+_15_S63

value: EGFP expression

value: genomic DNA in nuclei


title: methylation_32_Combined

value: primary cultured airway smooth muscle cell

value: Combined


title: DNA_2N+_14_S62


title: T5-1


title: T3-2

value: the embryos were cultured for 20d


title: T3-3


title: T4-1


title: methylation_32_IL-17

value: EuropeanAmerican


title: DNA_2N+_13_S61


title: T3-1


title: DNA_2N+_12_S60


title: methylation_32_IL-13


title: DNA_2N+_11_S59


title: 1022_D1

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

description: RNA from whole blood

hyb_protocol: 5 micrograms of purified DNA were fragmented into 50-200 bp fragments and were 3-labeled using Encore Biotin Module kit (Nugen). The resulting target was mixed with standard hybridization controls and B2 oligonucleotides following recommendations of manufacturer. The hybridization cocktail was heat-denatured at 99°C for 2 minutes, incubated at 50°C for 5 minutes and centrifuged at 16,000 g for 5 minutes to pellet the residual salts. The HERV-V3 microarrays were prehybridized with 200 µL of hybridization buffer and placed under stirring (60 rpm) in an oven at 50°C for 10 minutes. The hybridization buffer was then replaced by the denatured hybridization cocktail. Hybridization was performed at 50°C for 18 hours in the oven under constant stirring (60 rpm). Washing and staining were carried out according to the protocol supplied by the manufacturer, using a fluidic station: GeneChip fluidic station 450 (Affymetrix).

scan_protocol: The arrays were finally scanned using a fluorometric scanner: GeneChip scanner 3000 7G (Affymetrix)

data_processing: CEL files were transformed into matrix, normalized, adjusted for background noise (RMA normalization) and probes were summarized into probesets  with command apt-probeset-summarize (V 1.18.0)  with rma option . Batch effects were removed using COMBAT. Probesets were filtered when log2 signal was under 5.5 in more than 68% of samples.

label: biotin

source_name: Whole blood

label_protocol: The cDNA synthesis and amplification steps were performed from 16 ng of RNA using the Ovation Pico WTA System V2 kit (Nugen). Briefly, cDNA synthesis was done using a mixture of random and polydT primers, followed by the synthesis of the complementary strand. The Single Primer Isothermal Amplification (SPIA) was then performed with hybrid DNA/RNA primers sensitive to RNAse-H digestion, in the presence of a DNA polymerase with strong strand displacement activity. The resulting amplified cDNA was purified using the QIAquick purification kit (Qiagen), from which, total DNA concentration was measured using the NanoDrop 1000 spectrophotometer (Thermo Scientific) and the product quality was checked on the Bioanalyser 2100 (Agilent).

extract_protocol: Total RNA was extracted from whole blood using PAXgene Blood RNA kit (PreAnalytix) according to the manufacturer’s instructions. No sample with RNA integrity number ≤ 6 (bad RNA quality) was present.

treatment_protocol: Peripheral whole blood from ICU patients or healthy volunteers was collected from ICU patients or healthy volunteers was collected in PAXgeneTM Blood RNA tubes (PreAnalytix). Samples were stabilized at least 4h at room temperature after collection and frozen at -80°C following the manufacturer’s guidelines. For ICU patients, blood was collected at D1, D3 and D6, after ICU admission.

value: Whole blood

value: Patient

tag: diagnosis

value: septic shock


title: 5169_D3

description: RNA from whole blood


title: T2-2

value: Ovary

value: the embryos were cultured for 10d


title: methylation_3_IL-17

value: No

value: Yes


title: 5169_D1

description: RNA from whole blood


title: methylation_3_IL-13


title: T2-1


title: DNA_2N+_1_S49


title: T1-3

value: the ovules were cultured for 2d


title: methylation_3_Combined


title: methylation_3_Vehicle

value: Vehicle


title: T1-2


title: DNA_2N_8_S08

value: Pancreatic cancer tumor cell line


title: 5169_D6

description: RNA from whole blood


title: 2093_D3

description: RNA from whole blood


title: DNA_2N+_10_S58


title: DNA_2N_9_S09


title: 1022_D6

description: RNA from whole blood


title: T2-3


title: methylation_75_IL-17

value: Male

value: AfricanAmerican


title: DNA_2N_7_S07

value: EGFP expression

value: genomic DNA in nuclei


title: methylation_75_IL-13

value: primary cultured airway smooth muscle cell


title: methylation_75_Vehicle


title: DNA_2N_6_S06


title: 2093_D6

description: RNA from whole blood


title: 4112_D6

description: RNA from whole blood


title: 2093_D1

description: RNA from whole blood


title: T0-3

value: fresh unpollinated ovaries


title: methylation_75_Combined

value: Combined


title: DNA_2N_5_S05


title: T1-1


title: T0-2


title: 4112_D3

description: RNA from whole blood

value: Whole blood


title: 2202_D6

description: RNA from whole blood

value: Patient


title: methylation_74_IL-17

value: Female

value: EuropeanAmerican


title: T0-1

value: Ovary


title: methylation_74_IL-13

value: No


title: DNA_2N_46_S47


title: methylation_74_Vehicle

value: Yes


title: DNA_2N_45_S46


title: 4112_D1

description: RNA from whole blood

value: septic shock


title: DNA_2N_47_S48


title: methylation_71_IL-17


title: DNA_2N_44_S45


title: methylation_74_Combined


title: DNA_2N_43_S44


title: 2202_D3

description: RNA from whole blood


title: DNA_2N_42_S43


title: 2202_D1

description: RNA from whole blood


title: methylation_71_IL-13


title: methylation_71_Vehicle

value: Vehicle


title: DNA_2N_41_S42

value: Pancreatic cancer tumor cell line


title: SS64 miR-214 4

city: Tokyo

first: Takuro

last: Nakamura

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

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mouse synovial sarcoma cell introduced with miR-214

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse synovial sarcoma cell #64 introduced with miR-214

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The tumor was grown subcutaneously in Ba/b/c nude mice. The mesenchymal cells were grown in Iscove's modified DMEM supplemented with 15% FBS. Mouse synovial sarcoma cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: The mesenchymal cells were transduced with pMYs-SS18-SSX1 or pMYs-IRES-GFP retroviruses by spinofection. Mouse synovial sarcoma cells were transfected with miR-214.

tag: tissue/cell type

value: synovial sarcoma

tag: genotype/variation

value: introduced with miR-214


title: 4176_D3

description: RNA from whole blood


title: SS64 NC 4

description: Gene expression data from mouse synovial sarcoma cell

source_name: mouse synovial sarcoma cell #64


title: SS64 miR-214 3


title: SS64 miR-214 1


title: 4176_D1

description: RNA from whole blood


title: SS64 miR-214 2


title: 2208_D6

description: RNA from whole blood


title: DNA_2N_40_S41

value: EGFP expression


title: 4176_D6

description: RNA from whole blood


title: SS64 NC 3


title: methylation_71_Combined

value: AfricanAmerican


title: SS64 NC 2


title: methylation_30_Combined

value: primary cultured airway smooth muscle cell

value: Male


title: 2237_D6

description: RNA from whole blood


title: 2208_D3

description: RNA from whole blood


title: 2237_D1

description: RNA from whole blood


title: 2208_D1

description: RNA from whole blood


title: DNA_2N_4_S04

value: genomic DNA in nuclei


title: methylation_30_Vehicle


title: DNA_2N_37_S38


title: SS40 miR-214 4

source_name: mouse synovial sarcoma cell #40 introduced with miR-214


title: DNA_2N_39_S40


title: 2237_D3

description: RNA from whole blood

value: Whole blood


title: 2017_D6

description: RNA from whole blood

value: Patient


title: methylation_30_IL-17


title: DNA_2N_38_S39


title: DNA_2N_35_S35


title: methylation_30_IL-13


title: SS64 NC 1


title: methylation_7_Combined

value: Combined

value: Female


title: methylation_7_IL-17

value: EuropeanAmerican


title: DNA_2N_36_S36


title: methylation_7_IL-13

value: No


title: DNA_2N_33_S33


title: SS40 miR-214 1


title: SS40 miR-214 3


title: SS40 NC 4

source_name: mouse synovial sarcoma cell #40


title: SS40 NC 2


title: 2017_D3

description: RNA from whole blood


title: 2017_D1

description: RNA from whole blood


title: methylation_7_Vehicle

value: Yes


title: DNA_2N_32_S32


title: methylation_73_IL-17


title: SS40 miR-214 2


title: 5236_D1

description: RNA from whole blood

value: septic shock


title: 4095_D6

description: RNA from whole blood


title: methylation_73_Vehicle

value: Vehicle


title: SS40 NC 3


title: DNA_2N_31_S31

value: Pancreatic cancer tumor cell line


title: SS40 NC 1

value: synovial sarcoma


title: methylation_73_IL-13


title: DNA_2N_3_S03


title: DNA_2N_30_S30


title: 4095_D1

description: RNA from whole blood


title: 5161_D3

description: RNA from whole blood


title: methylation_73_Combined


title: 5161_D6

description: RNA from whole blood


title: 5161_D1

description: RNA from whole blood


title: 4095_D3

description: RNA from whole blood


title: methylation_46_Combined


title: DNA_2N_29_S29


title: DNA_2N_28_S28


title: SS214 9

description: Gene expression data from mouse synovial sarcoma overexpressing miR-214

source_name: mouse synovial sarcoma expressing miR-214

value: expressing miR-214


title: DNA_2N_27_S27

value: EGFP expression


title: SS214 8


title: 2107_D6

description: RNA from whole blood


title: methylation_46_IL-13

value: AfricanAmerican


title: methylation_46_IL-17

value: primary cultured airway smooth muscle cell


title: methylation_46_Vehicle

value: Male


title: DNA_2N_26_S26

value: genomic DNA in nuclei


title: DNA_2N_25_S25


title: methylation_35_Vehicle


title: DNA_2N_24_S24


title: 5236_D3

description: RNA from whole blood

value: Whole blood


title: SS214 7


title: methylation_35_Combined


title: DNA_2N_23_S23


title: SS214 4


title: SS214 6


title: SS214 2


title: SS214 16


title: DNA_2N_22_S22


title: 2107_D3

description: RNA from whole blood

value: Patient


title: SS214 3


title: SS214 15


title: methylation_35_IL-13


title: SS214 5


title: methylation_35_IL-17


title: 2107_D1

description: RNA from whole blood


title: 2182_D6

description: RNA from whole blood


title: DNA_2N_21_S21


title: methylation_29_IL-17


title: methylation_29_IL-13


title: 2170_D1

description: RNA from whole blood


title: DNA_2N_20_S20


title: 2182_D1

description: RNA from whole blood


title: methylation_29_Vehicle


title: DNA_2N_2_S02


title: T6

city: Jongno-gu

first: Sun-Wha

last: Im

state: Seoul

address: 103, Daehak-ro

department: Genomic Medicine Institute, Medical Research Center

country: South Korea

institute: Seoul National University

data_processing:
For expression analysis, we used RSEM (v1.2.31) to calculate the read counting and Fragments Per Kilobase Million (FPKM) values for the Ensemble gene set.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all Samples

source_name: bladder cancer tumor

extract_protocol:
RNA was extracted from tumor FFPE tissue using the Trizol method.
By using the Illumina TruSeq RNA Access Library Preparation Kit, RNA sequencing library was constructed for RNA samples with DV200 values of >30%.

tag: tumor (pt) stage

value: Ta

tag: tumor grade

value: PUNLMP

tag: sex of patient

tag: age of patient at diagnosis


title: 2182_D3

description: RNA from whole blood


title: DNA_2N_19_S19

tag: strain background

tag: cell line

tag: cell type

tag: labelling for flow


title: 2170_D6

description: RNA from whole blood


title: SS214 14


title: SS214 13


title: 2170_D3

description: RNA from whole blood


title: Normal tissue mix 3

description: Gene expression data from mouse normal tissues

source_name: mouse normal tissue mix

value: mixture of mouse normal tissues


title: 6013_D6

description: RNA from whole blood


title: 6013_D3

description: RNA from whole blood


title: methylation_65_IL-13

tag: donor

tag: treatment

tag: asthma

value: EuropeanAmerican


title: DNA_2N_18_S18

tag: molecule subtype


title: 6013_D1

description: RNA from whole blood

tag: tissue


title: Normal tissue mix 4


title: methylation_65_IL-17

value: Yes

tag: age

tag: Sex

tag: imputedsmoking

tag: race


title: methylation_68_IL-17

value: No

value: Female


title: methylation_65_Combined

value: Combined


title: DNA_2N_14_S14

value: Pancreatic cancer tumor cell line


title: methylation_65_Vehicle

value: Vehicle


title: DNA_2N_16_S16

value: EGFP expression


title: 1014_D6

description: RNA from whole blood

tag: diagnosis

value: septic shock


title: methylation_29_Combined

value: primary cultured airway smooth muscle cell

value: AfricanAmerican


title: Normal tissue mix 2

tag: tissue/cell type


title: DNA_2N_17_S17

value: genomic DNA in nuclei


title: DNA_2N_15_S15


title: 1014_D3

description: RNA from whole blood

value: Whole blood


title: SS 5

description: Gene expression data from mouse synovial sarcoma

source_name: mouse synovial sarcoma

value: synovial sarcoma


title: Normal tissue mix 1


title: SS 33


title: SS214 1

tag: genotype/variation

value: expressing miR-214


title: DNA_2N_13_S13


title: SS 30


title: DNA_2N_34_S34


title: methylation_68_IL-13


title: 1014_D1

description: RNA from whole blood

value: Patient


title: DNA_2N_12_S12


title: 4125_D6

description: RNA from whole blood


title: 4125_D1

description: RNA from whole blood


title: methylation_68_Vehicle


title: SS 29


title: 4125_D3

description: RNA from whole blood


title: DNA_2N_11_S11


title: methylation_68_Combined


title: DNA_2N_10_S10


title: methylation_38_IL-13


title: 4020_D6

description: RNA from whole blood


title: DNA_2N_1_S01


title: SS 28


title: methylation_38_Vehicle


title: methylation_38_Combined


title: 4020_D3

description: RNA from whole blood


title: DNA_2N_Bulk_S37


title: methylation_4_Combined


title: methylation_4_IL-17


title: methylation_4_IL-13


title: methylation_4_Vehicle


title: methylation_38_IL-17


title: SS 24


title: methylation_37_IL-13

value: Male


title: SS 23


title: methylation_37_Vehicle

value: EuropeanAmerican


title: 4020_D1

description: RNA from whole blood


title: SS 27


title: methylation_37_Combined

value: Yes


title: eMC SS18-SSX1 4

description: Gene expression data from mesenchymal cells 48 h after retroviral transduction

source_name: eMCs transduced with SS18-SSX1 retrovirus

value: primary mesenchymal cell


title: SS 20


title: SS 22


title: 2251_D6

description: RNA from whole blood


title: 2251_D3

description: RNA from whole blood


title: eMC SS18-SSX1 3

value: eMCs transduced with SS18-SSX1 retrovirus


title: SS 19


title: SS 18


title: eMC SS18-SSX1 1


title: eMC SS18-SSX1 2


title: methylation_37_IL-17

value: No


title: methylation_53_Vehicle


title: eMC empty retrovirus 4

source_name: eMCs transduced with empty retrovirus

value: eMCs transduced with empty retrovirus


title: methylation_53_Combined

value: Combined


title: methylation_53_IL-17


title: 2240_D3

description: RNA from whole blood


title: 2251_D1

description: RNA from whole blood


title: 2240_D1

description: RNA from whole blood


title: 5123_D6

description: RNA from whole blood


title: 5240_D6

description: RNA from whole blood


title: 2240_D6

description: RNA from whole blood


title: 5240_D3

description: RNA from whole blood


title: 5240_D1

description: RNA from whole blood


title: 5123_D3

description: RNA from whole blood


title: eMC empty retrovirus 3


title: eMC empty retrovirus 1


title: methylation_53_IL-13


title: methylation_25_Vehicle

value: Vehicle


title: eMC empty retrovirus 2


title: 61_IL13

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scan protocol.

data_processing: All samples had RIN scores >9.6 The probe level raw intensity values across arrays were normalized using quantile normalization and background corrected normalized expression values were obtained for each probe using the R package lumi. Probes that were indistinguishable from background intensity (P<0.01), contained more than one HapMap SNP, or mapped to multiple locations in the genome were excluded. When multiple probes mapped to the same gene, the median probe expression value was used for that gene.

label_protocol: not provided

extract_protocol: RNA for gene expression studies were isolated from cell lysates using the QIAgen AllPrep Kit.

treatment_protocol: ASMCs were exposed to IL-13 (10ng/mL), IL-17 (3 ng/mL), IL-13+IL-17, or vehicle (10% FBS in PBS) for 24 hours prior to RNA and DNA extraction.


title: 4004_D6

description: RNA from whole blood

value: septic shock


title: 61_Combined

value: primary cultured airway smooth muscle cell


title: 61_Vehicle


title: 5123_D1

description: RNA from whole blood


title: methylation_25_Combined

value: AfricanAmerican


title: 61_IL17


title: methylation_25_IL-13


title: methylation_64_IL-13

value: Female


title: 58_Combined


title: methylation_64_Vehicle


title: methylation_64_Combined


title: methylation_64_IL-17


title: methylation_56_Vehicle


title: 58_IL17


title: methylation_56_Combined


title: 58_IL13


title: 2175_D3

description: RNA from whole blood

value: Whole blood


title: 58_Vehicle


title: 2175_D6

description: RNA from whole blood


title: methylation_56_IL-17


title: 37_IL13


title: 2175_D1

description: RNA from whole blood


title: 4249_D6

description: RNA from whole blood


title: 37_Combined


title: 4004_D1

description: RNA from whole blood


title: 37_Vehicle


title: methylation_56_IL-13


title: methylation_41_IL-17


title: 14_IL13


title: 37_IL17


title: methylation_41_IL-13


title: 1174_D3

description: RNA from whole blood


title: 14_Vehicle


title: 4249_D3

description: RNA from whole blood


title: 1174_D1

description: RNA from whole blood


title: 1174_D6

description: RNA from whole blood


title: methylation_41_Vehicle


title: 4267_D6

description: RNA from whole blood


title: 4267_D3

description: RNA from whole blood


title: 1017_D6

description: RNA from whole blood


title: 4267_D1

description: RNA from whole blood


title: methylation_13_Vehicle


title: methylation_13_IL-13


title: 14_IL17


title: 21_IL17


title: methylation_41_Combined


title: 14_Combined


title: 1017_D3

description: RNA from whole blood


title: 1017_D1

description: RNA from whole blood


title: 21_Vehicle


title: 21_IL13


title: methylation_43_IL-17


title: 4004_D3

description: RNA from whole blood


title: 21_Combined


title: methylation_13_Combined


title: 7_IL17


title: 2048_D6

description: RNA from whole blood


title: 2048_D3

description: RNA from whole blood


title: methylation_13_IL-17


title: 7_Combined


title: methylation_43_IL-13


title: 1102_D6

description: RNA from whole blood


title: 7_IL13


title: methylation_43_Vehicle


title: 2048_D1

description: RNA from whole blood


title: 4226_D6

description: RNA from whole blood


title: 1102_D1

description: RNA from whole blood


title: methylation_43_Combined


title: methylation_6_Combined


title: methylation_6_IL-17


title: methylation_6_IL-13


title: methylation_25_IL-17


title: methylation_6_Vehicle


title: 62_IL13


title: 62_Vehicle


title: 7_Vehicle


title: 4226_D3

description: RNA from whole blood


title: methylation_27_IL-17


title: 62_Combined


title: 4226_D1

description: RNA from whole blood


title: 64_IL13


title: 62_IL17


title: 1102_D3

description: RNA from whole blood


title: 64_Combined


title: 64_Vehicle


title: methylation_27_IL-13


title: 1036_D6

description: RNA from whole blood


title: methylation_27_Vehicle


title: methylation_27_Combined


title: methylation_36_Combined


title: methylation_36_Vehicle


title: methylation_36_IL-13


title: methylation_36_IL-17


title: 4249_D1

description: RNA from whole blood


title: 1036_D1

description: RNA from whole blood


title: 64_IL17


title: 5116_D3

description: RNA from whole blood


title: 72_Combined


title: 5116_D6

description: RNA from whole blood


title: 1036_D3

description: RNA from whole blood


title: methylation_72_IL-17


title: 72_IL17


title: 72_Vehicle


title: 5116_D1

description: RNA from whole blood


title: 3006_D3

description: RNA from whole blood


title: 11_IL13


title: 72_IL13


title: 5_Combined


title: 11_IL17


title: 3006_D6

description: RNA from whole blood


title: 11_Vehicle


title: 2039_D1

description: RNA from whole blood


title: 2039_D6

description: RNA from whole blood


title: 3006_D1

description: RNA from whole blood


title: methylation_72_Combined


title: methylation_72_IL-13


title: methylation_72_Vehicle


title: methylation_49_Combined


title: methylation_49_IL-17


title: 2019_D3

description: RNA from whole blood


title: methylation_49_Vehicle


title: methylation_11_Combined


title: methylation_11_IL-17


title: methylation_49_IL-13


title: 2039_D3

description: RNA from whole blood


title: 2019_D6

description: RNA from whole blood


title: 2019_D1

description: RNA from whole blood


title: 40_IL13


title: 5_IL17


title: 5_Vehicle


title: 5_IL13


title: 40_Vehicle


title: 40_IL17


title: methylation_11_Vehicle


title: 6001_D3

description: RNA from whole blood


title: 6001_D6

description: RNA from whole blood


title: 6001_D1

description: RNA from whole blood


title: 5018_D6

description: RNA from whole blood


title: methylation_11_IL-13


title: 11_Combined


title: 73_Vehicle


title: 73_IL17


title: 73_IL13


title: methylation_18_IL-17


title: methylation_18_IL-13


title: 4242_D1

description: RNA from whole blood


title: 40_Combined


title: methylation_18_Vehicle


title: methylation_18_Combined


title: 5018_D3

description: RNA from whole blood


title: 4242_D3

description: RNA from whole blood


title: 5018_D1

description: RNA from whole blood


title: 1173_D6

description: RNA from whole blood


title: 55_Vehicle


title: methylation_31_Vehicle


title: methylation_31_Combined


title: methylation_31_IL-17


title: 73_Combined


title: methylation_31_IL-13


title: 4242_D6

description: RNA from whole blood


title: 55_IL17


title: 55_Combined


title: methylation_57_Vehicle


title: 1173_D3

description: RNA from whole blood


title: 35_IL13


title: 55_IL13


title: 35_Combined


title: methylation_57_Combined


title: 35_Vehicle


title: methylation_57_IL-17


title: 1130_D1

description: RNA from whole blood


title: 4083_D6

description: RNA from whole blood


title: 1173_D1

description: RNA from whole blood


title: 1130_D3

description: RNA from whole blood


title: 1130_D6

description: RNA from whole blood


title: 35_IL17


title: methylation_48_IL-17


title: methylation_48_IL-13


title: 22_IL17


title: 22_Vehicle


title: 22_Combined


title: methylation_48_Combined


title: 4083_D3

description: RNA from whole blood


title: 4083_D1

description: RNA from whole blood


title: 5220_D6

description: RNA from whole blood


title: methylation_48_Vehicle


title: methylation_21_IL-17


title: methylation_21_IL-13


title: 22_IL13


title: 74_IL17


title: 5220_D1

description: RNA from whole blood


title: 4007_D3

description: RNA from whole blood


title: methylation_21_Vehicle


title: 74_Combined


title: methylation_21_Combined


title: 4007_D6

description: RNA from whole blood


title: 74_IL13


title: 74_Vehicle


title: 54_Vehicle


title: 4007_D1

description: RNA from whole blood


title: 2160_D1

description: RNA from whole blood


title: 2160_D3

description: RNA from whole blood


title: 2145_D6

description: RNA from whole blood


title: methylation_40_IL-17


title: methylation_40_IL-13


title: methylation_40_Vehicle


title: 39_IL13


title: 54_IL17


title: 4044_D3

description: RNA from whole blood


title: 54_IL13


title: 54_Combined


title: methylation_40_Combined


title: 39_Vehicle


title: 2145_D1

description: RNA from whole blood


title: 5220_D3

description: RNA from whole blood


title: 4044_D6

description: RNA from whole blood


title: methylation_70_IL-13


title: methylation_57_IL-13


title: methylation_70_Vehicle


title: 2145_D3

description: RNA from whole blood


title: 5119_D6

description: RNA from whole blood


title: methylation_70_IL-17


title: methylation_17_IL-13


title: methylation_17_Vehicle


title: 46_Combined


title: 46_IL17


title: methylation_70_Combined


title: 39_Combined


title: 39_IL17


title: 4044_D1

description: RNA from whole blood


title: methylation_17_IL-17


title: methylation_17_Combined


title: 46_Vehicle


title: 46_IL13


title: 5119_D1

description: RNA from whole blood


title: 3_IL17


title: methylation_12_Combined


title: methylation_12_IL-17


title: 6054_D3

description: RNA from whole blood


title: 5119_D3

description: RNA from whole blood


title: methylation_12_IL-13


title: methylation_12_Vehicle


title: methylation_59_Vehicle


title: methylation_59_Combined


title: 1152_D6

description: RNA from whole blood


title: 1152_D3

description: RNA from whole blood


title: 3_IL13


title: methylation_59_IL-17


title: 6054_D1

description: RNA from whole blood


title: 1048_D6

description: RNA from whole blood


title: 3_Combined


title: 6054_D6

description: RNA from whole blood


title: 3_Vehicle


title: 23_Combined


title: 23_Vehicle


title: 23_IL17


title: 41_IL17


title: methylation_59_IL-13


title: 23_IL13


title: 1048_D1

description: RNA from whole blood


title: methylation_22_IL-13


title: 3002_D3

description: RNA from whole blood


title: 5070_D1

description: RNA from whole blood


title: 5070_D3

description: RNA from whole blood


title: methylation_67_IL-13


title: methylation_67_Vehicle


title: 41_Vehicle


title: 5070_D6

description: RNA from whole blood


title: 1048_D3

description: RNA from whole blood


title: methylation_22_Combined


title: methylation_22_Vehicle


title: 41_Combined


title: 3002_D1

description: RNA from whole blood


title: 20_Combined


title: 41_IL13


title: 20_Vehicle


title: methylation_67_Combined


title: 2220_D6

description: RNA from whole blood


title: 75_IL17


title: 2220_D3

description: RNA from whole blood


title: 3002_D6

description: RNA from whole blood


title: 20_IL17


title: methylation_67_IL-17


title: 2220_D1

description: RNA from whole blood


title: Original

city: Shanghai

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

description: all.counts.exp.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
MapSplice mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: NU-DUL-1-ORI cells

growth_protocol: NU-DUL-1 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NU-DUL-1-R cells were treated with 32 mg/mL Rituximab and 20% NHS every 21 days to maintain resistance. NU-DUL-1-CHO cells were treated with 2mg/mL 4-HC, 25 ng/mL Doxorubicin and 0.7 ng/mL Vincristine every 21 days. NU-DUL-1-RCHO cells  were treated with 2mg/mL 4-HC, 25 ng/mL Doxorubicin and 0.7 ng/mL Vincristine following 32 mg/mL Rituximab and 20% NHS treatment every 21 days.

value: Diffuse large B-cell lymphoma

tag: genotype

value: ABC subtype

value: original


title: 5238_D3

description: RNA from whole blood

value: Patient


title: methylation_45_Combined

value: Male


title: 5238_D6

description: RNA from whole blood


title: R+

description: all.counts.exp.txt

source_name: NU-DUL-1-R cells

value: 32 mg/mL Rituximab and 20% NHS every 21 days


title: 5238_D1

description: RNA from whole blood


title: methylation_45_IL-13

source_name: primary cultured airway smooth muscle cell

value: Yes


title: R-CHOP

description: all.counts.exp.txt

source_name: NU-DUL-1-RCHO cells

value: 2mg/mL 4-HC, 25 ng/mL Doxorubicin and 0.7 ng/mL Vincristine following 32 mg/mL Rituximab and 20% NHS treatment


title: methylation_45_IL-17


title: methylation_22_IL-17

value: EuropeanAmerican


title: CHOP

description: all.counts.exp.txt

source_name: NU-DUL-1-CHO cells

value: 2mg/mL 4-HC, 25 ng/mL Doxorubicin and 0.7 ng/mL Vincristine


title: 5138_D6

description: RNA from whole blood


title: methylation_45_Vehicle


title: LY8&D&C

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
MapSplice mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: LY8-RCHO cells

growth_protocol: OCI-LY8 cells were maintained in Iscove's modified Dulbecco's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

treatment_protocol: LY8-R cells were treated with 32 mg/mL Rituximab and 20% NHS every 21 days to maintain resistance. LY8-CHO cells were treated with 2mg/mL 4-HC, 125 ng/mL Doxorubicin and 3.5 ng/mL Vincristine every 21 days. LY8-RCHO cells  were treated with 2mg/mL 4-HC, 125 ng/mL Doxorubicin and 3.5 ng/mL Vincristine following 32 mg/mL Rituximab and 20% NHS treatment every 21 days.

value: GCB subtype


title: 75_IL13

value: No


title: LY8-D

source_name: LY8-R cells

value: 32 mg/mL Rituximab and 20% NHS


title: methylation_23_IL-17

value: primary cultured airway smooth muscle cell


title: 5138_D3

description: RNA from whole blood

source_name: Whole blood

value: septic shock


title: 75_Vehicle

value: Vehicle

value: AfricanAmerican


title: LY8-C

source_name: LY8-CHO cells

value: Diffuse large B-cell lymphoma

value: 2mg/mL 4-HC, 125 ng/mL Doxorubicin and 3.5 ng/mL Vincristine


title: LY8

source_name: LY8-ORI cells

value: Original


title: 75_Combined

value: Combined


title: 43_IL13

value: Male


title: 43_IL17


title: methylation_23_Vehicle

value: Female


title: 50_Combined


title: 43_Vehicle


title: methylation_23_IL-13

value: Yes


title: methylation_23_Combined


title: 20_IL13


title: 43_Combined


title: 5175_D3

description: RNA from whole blood

value: Whole blood

value: Patient


title: 3016_D6

description: RNA from whole blood


title: 3016_D3

description: RNA from whole blood


title: 5138_D1

description: RNA from whole blood


title: methylation_2_IL-17

value: EuropeanAmerican


title: KO C 2 hour stim

city: San Francisco

first: Julie

last: Zikherman

state: CA

address: 513 Parnassus Ave, HSW1201a

institute: University of California San Francisco

data_processing:
Samples were analysed using Q2 solutions in-house RNAv9.1 pipeline. In brief:
Low quality reads, bases homopolymers and adapter sequences were removed using fastq-mcf4
Samples were aligned to the mouse genome as defined by UCSC using STAR software version 2.4.
Genes were quantified using RSEM version 1.2.14.
Gene definition for this pipeline consists of 31,252 genes and 61,025 isoforms.
Genome_build: mm10
Supplementary_files_format_and_content: tab-deliminated text file includes FPKM values for each sample

source_name: Spleen and lymph node

extract_protocol:
Cells were flash frozen and sent to Q2 solutions for further analysis.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103)

treatment_protocol: Spleens and Lymph nodes were harvested, and B cells were sorted via MACs negative selection. Cells were stimulated for 2 hours with 10 μg/mL anti-IgM.

tag: strain

tag: agent

value: 10 microg/mL anti-IgM

tag: time point

value: 2 hour

value: 10 weeks


title: KO D 2 hour stim


title: 50_IL17

tag: cell type

value: primary cultured airway smooth muscle cell

value: No


title: 50_IL13

tag: donor


title: 5175_D1

description: RNA from whole blood

value: septic shock


title: 1141_D6

description: RNA from whole blood


title: methylation_2_Combined

tag: treatment


title: 5175_D6

description: RNA from whole blood


title: KO B 2 hour stim


title: KO A 2 hour stim


title: methylation_2_IL-13

tag: asthma


title: 1141_D3

description: RNA from whole blood


title: 1152_D1

description: RNA from whole blood


title: WT D 2 hour stim


title: WT C 2 hour stim


title: methylation_69_IL-13


title: WT B 2 hour stim


title: methylation_69_IL-17


title: methylation_2_Vehicle

value: Vehicle


title: 4191_D3

description: RNA from whole blood


title: methylation_69_Vehicle


title: 50_Vehicle

value: AfricanAmerican


title: 29_IL17


title: methylation_69_Combined


title: 29_Vehicle


title: 29_IL13


title: 1141_D1

description: RNA from whole blood


title: 29_Combined


title: 15_IL13


title: methylation_52_Vehicle


title: 4191_D6

description: RNA from whole blood


title: 15_Vehicle


title: 15_Combined


title: Retina_P17

city: Wenzhou

first: Zai-Long

last: Chi

state: Zhejiang

address: 270 Xueyuan Road

department: School of Opthalmology & Optometry

institute: Wenzhou Medical University

data_processing:
The raw reads were processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads.
Mapping reads were obtained by mapping clean reads to the mouse reference genome mm10 by BWA.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA.
The miRNA expression were calculated by RPM (Reads Per Million) values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include both count and RPM values

source_name: Retina

extract_protocol:
After the mice were euthanized, the retinas were isolated from the dissected eye and moved into the RNA-Solv Reagent (Omega Bio-tek, Norcross, GA, USA). Retinas from 5 eyes were pooled as one sample. T10 basic S25 ULTRA-TURRAX Disperser (IKA, Guangzhou, China) was used to homogenize retinas. Total RNA was extracted by miRNA Kit (200) (Omega Bio-tek) according to the manufacturer’s instructions. The quantity and integrity of RNA yield was assessed by using the Qubit®2.0 (Life Technologies, USA) and Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
The total RNA (1 μg) of each samples were used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’s instructions.

value: retina

tag: developmental stage

value: postnatal day 17


title: methylation_52_Combined

value: Combined


title: 4113_D6

description: RNA from whole blood

tag: tissue


title: 53_Vehicle

value: Male

tag: age


title: 4113_D1

description: RNA from whole blood


title: 15_IL17

tag: Sex


title: methylation_52_IL-17

tag: imputedsmoking


title: 4191_D1

description: RNA from whole blood


title: 5255_D3

description: RNA from whole blood


title: 4113_D3

description: RNA from whole blood


title: Retina_P7

value: postnatal day 7


title: WT A no stim


title: Retina_P1

value: postnatal day 1


title: methylation_52_IL-13

value: Yes

tag: race


title: KO A no stim


title: 5255_D6

description: RNA from whole blood

value: Whole blood

value: Patient

tag: diagnosis


title: methylation_58_Vehicle

value: EuropeanAmerican


title: WT A 2 hour stim

value: 10 microg/mL anti-IgM

value: 2 hour


title: WT HFCF 3-months 2

city: kansas city

first: Yuxia

last: Zhang

state: KS

address: 3901 Rainbow Blvd, Hemenway 4001

department: Pharmacology, Toxicology, and Therapeutics

institute: University of Kansas Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm10 whole genome using CLCBio Genomics Workbench 11 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Zymogen Research Direct-zol RNA Miniprep Plus (Cat#R2072) was used. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep Set for Illumina

value: Liver

value: 6 months

tag: diet

value: fed HFCF diet for 3 months

tag: gender

value: male


title: WT HFCF 3-months 3


title: WT HFCF 3-months 1


title: 53_Combined

value: primary cultured airway smooth muscle cell

value: No


title: WT Chow 3-months 3

value: fed normal chow diet for 3 months


title: methylation_58_IL-13


title: WT Chow 3-months 2


title: methylation_44_IL-17

value: Female


title: 5255_D1

description: RNA from whole blood

value: septic shock


title: 5252_D3

description: RNA from whole blood


title: 5252_D6

description: RNA from whole blood


title: 53_IL17

value: Male


title: methylation_44_IL-13


title: 53_IL13


title: WT Chow 3-months 1


title: methylation_44_Vehicle

value: Vehicle


title: WT HFCF 1-month 3

value: 3 months

value: fed HFCF diet for 1 month


title: methylation_58_IL-17

value: Yes


title: 24_IL17

value: EuropeanAmerican


title: 24_Vehicle


title: 31_Vehicle


title: 24_IL13


title: 24_Combined

value: Combined


title: 5252_D1

description: RNA from whole blood

value: Whole blood

value: Patient


title: 5052_D3

description: RNA from whole blood


title: 5052_D6

description: RNA from whole blood


title: methylation_44_Combined


title: methylation_58_Combined


title: 31_Combined


title: methylation_8_Combined


title: WT HFCF 1-month 1

value: Liver


title: 1179_D3

description: RNA from whole blood


title: WT Chow 1-month 3

value: fed normal chow diet for 1 month


title: 31_IL17


title: methylation_8_IL-17


title: 1179_D6

description: RNA from whole blood


title: WT Chow 1-month 2

value: male


title: 5052_D1

description: RNA from whole blood


title: methylation_8_IL-13

value: primary cultured airway smooth muscle cell


title: 1179_D1

description: RNA from whole blood


title: WT HFCF 1-month 2


title: WT Chow 1-month 1


title: 2031_D6

description: RNA from whole blood


title: methylation_8_Vehicle

value: No


title: 2031_D1

description: RNA from whole blood


title: methylation_5_Combined


title: methylation_5_IL-17


title: 31_IL13


title: 57_Vehicle


title: 57_Combined


title: 57_IL13


title: methylation_5_IL-13


title: 57_IL17


title: methylation_5_Vehicle


title: 47_Combined


title: 1099_D3

description: RNA from whole blood


title: 1099_D6

description: RNA from whole blood


title: BCU--021 liver5Cs

city: Darlinghurst

first: Saskia

last: Reibe

state: NSW

address: 384 Victoria Street

department: Diabetes & Metabolism

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Quality Control: FastQC
Data trimming: Trim galore
Alignment: STAR aligner
counts: RSEM
Differential expression: Deseq2
Genome_build: Mus_musculus.GRCm38.83

source_name: liver tissue

growth_protocol: tissue harvested

extract_protocol:
RNA isolation NucleoSpin (Macherey-Nagel)
Illumina Truseq mRNA kit

value: DEN-treated

value: cornstarch diet

value: 5 month


title: methylation_66_IL-13

value: Male


title: 1099_D1

description: RNA from whole blood

value: septic shock


title: methylation_66_Vehicle

value: Vehicle


title: methylation_66_Combined


title: BCU--019 liver5Cs


title: methylation_66_IL-17


title: 47_IL17

value: Female


title: BCU--016 liver5Hfr

value: high-fructose diet


title: 47_IL13

value: EuropeanAmerican


title: 47_Vehicle


title: 2189_D6

description: RNA from whole blood


title: 6019_D6

description: RNA from whole blood


title: 2_Combined

value: Combined


title: 2189_D3

description: RNA from whole blood

value: Whole blood


title: methylation_28_IL-17


title: 2189_D1

description: RNA from whole blood

value: Patient


title: 2_IL13


title: BCU--020 liver5Cs


title: BCU--018 liver5Hfr


title: BCU--014 tum9Cs

source_name: tumour tissue (liver)

value: 9 month


title: 6019_D1

description: RNA from whole blood


title: 6019_D3

description: RNA from whole blood


title: 1081_D3

description: RNA from whole blood


title: 1081_D6

description: RNA from whole blood


title: 1081_D1

description: RNA from whole blood


title: methylation_28_IL-13


title: BCU--013 tum9Cs


title: BCU--012 tum9Hfr


title: methylation_28_Combined


title: methylation_28_Vehicle


title: 2_Vehicle


title: 4238_D6

description: RNA from whole blood


title: methylation_54_Combined

value: Yes


title: methylation_54_Vehicle


title: BCU--011 tum9Hfr


title: 33_Vehicle


title: 33_Combined


title: 33_IL17


title: methylation_54_IL-13


title: methylation_54_IL-17


title: 4238_D3

description: RNA from whole blood


title: BCU--008 liver9Cs


title: methylation_16_IL-13

value: AfricanAmerican


title: BCU--010 tum9Hfr


title: 36_Vehicle

value: primary cultured airway smooth muscle cell


title: 36_IL13

value: No


title: BCU--007 liver9Cs

value: DEN-treated


title: 36_Combined


title: 2134_D6

description: RNA from whole blood


title: BCU--006 liver9Hfr


title: 33_IL13


title: methylation_16_Vehicle


title: 36_IL17


title: 4238_D1

description: RNA from whole blood


title: 2134_D3

description: RNA from whole blood


title: BCU--005 liver9Hfr


title: 2134_D1

description: RNA from whole blood


title: 5232_D6

description: RNA from whole blood


title: 5232_D3

description: RNA from whole blood


title: BCU--004 liver9Hfr


title: methylation_16_IL-17


title: 8_Combined


title: 2_IL17


title: 8_IL17


title: methylation_16_Combined


title: 2226_D6

description: RNA from whole blood


title: 5232_D1

description: RNA from whole blood


title: humgraft_rat45_1b_FACS

city: Lund

first: Johan

last: Jakobsson

address: Solvegatan 17

country: Sweden

institute: Lund University

data_processing:
Raw basecalls were converted to Fastq using mkfastq program provided by 10X Genomics.
Reads were aligned to human genome GRCh38 assembly and matrix files for all the samples were obtained using cellranger counts version 3 pipeline provided by 10X Genomics..
Genome_build: GRCh38

molecule: polyA RNA

extract_protocol:
Grafted human ventral midbrain and grafted VM-patterned hESCs cells were dissected from rat striatum and dissociated into a single cell suspension using the papain kit
single-cell suspensions were loaded onto 10x Genomics Single Cell 3′ Chips along with the reverse transcription (RT) mastermix per the manufacturer’s protocol for the Chromium Single Cell 3′ Library to generate single-cell gel beads in emulsion (GEMs). cDNA amplification was done as per the guidelines from 10X Genomics. Sequencing libraries were generated with unique sample indices (SI) for each sample with the following specifications Read1 28 cycles, Read2 98 cycles, Index1 8 cycles.
Libraries for samples were multiplexed and sequenced on an Illumina NextSeq 500 machine using a 150-cycle NextSeq 500/550 High Output Reagent Kit v2.

tag: treated/control

value: FACS sorted


title: 8_IL13


title: 70_IL17


title: 8_Vehicle


title: 70_Combined


title: 70_IL13


title: 2226_D3

description: RNA from whole blood


title: 70_Vehicle


title: 52_Vehicle


title: humgraft_rat45_1a_FACS


title: 2096_D3

description: RNA from whole blood


title: 2096_D6

description: RNA from whole blood


title: 2_humgraft_rat39_3c

value: NOT FACS sorted


title: 4_humgraft_rat39_3b


title: 2096_D1

description: RNA from whole blood


title: 2226_D1

description: RNA from whole blood


title: 2111_D6

description: RNA from whole blood


title: 52_Combined

value: Male


title: 1_humgraft_rat39_3a

data_processing:
Raw basecalls were converted to Fastq using mkfastq program provided by 10X Genomics.
Reads were aligned to human genome GRCh38 assembly and matrix files for all the samples were obtained using cellranger counts version 3 pipeline provided by 10X Genomics. Sample Rat39_3a from Not FACS sorting was split into half (Rat39_3a and Rat39_3c) prior to cDNA amplification and was sequenced on separate lanes. Counts matrices obtained from these two samples were merged (rat39-3ac) during the downstream analysis.
Genome_build: GRCh38


title: 4307_D3

description: RNA from whole blood

value: septic shock


title: 52_IL17


title: 3_humgraft_rat11_2b


title: 52_IL13


title: 2111_D1

description: RNA from whole blood


title: 2111_D3

description: RNA from whole blood


title: 17_IL13


title: BCU--009 liver9Cs

value: cornstarch diet


title: 2_humgraft_rat11_2a


title: 17_Vehicle

value: Vehicle

value: Female


title: 17_Combined


title: 4307_D6

description: RNA from whole blood


title: E315A-RNA-3_clean

description:
315A-RNA-3_S15
Bulk RNA sequencing of RNA extracted from 315A cells.

data_processing:
Adapter removal and removing reads shorter than 36bp using Bbduk
Align reads to reference genome hg19 using Kallisto and obtain read count tables
Genome_build: hg19
Supplementary_files_format_and_content: read count table

source_name: 315A Diploid lymphoblastoid cell line

growth_protocol: Cells were cultured in respective media at 37C, 5% CO2

extract_protocol:
Cells were trypsinized and spun down to get a pellet. The cells were processed using Qiagen Rneasy kit. RNA was qunatified and then a reverse transcription step was done using Oligo dT primer and Clontech Reverse Transcriptase to generate cDNA. 2ug of cDNA was used for library preparation
2ug of cDNA was fragemented to 400bp using Covaris somicator. Following this, libraries for sequencing were prepared by subjecting the resulting DNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

tag: cell line

value: 315A Diploid lymphoblastoid cell line

tag: cell line source

value: Lymphoblastoid

value: Suspension cell line

tag: culture condition

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: 1_humgraft_rat11_1a


title: 17_IL17

tag: cell type


title: 5153_D1

description: RNA from whole blood

value: Whole blood

value: Patient


title: 4307_D1

description: RNA from whole blood


title: 16_IL13

tag: donor

value: Yes

value: AfricanAmerican


title: 5153_D3

description: RNA from whole blood


title: 2056_D6

description: RNA from whole blood


title: 5153_D6

description: RNA from whole blood


title: E315A-RNA-1_clean

description:
315A-RNA-1_S13
Bulk RNA sequencing of RNA extracted from 315A cells.


title: 16_Vehicle

value: primary cultured airway smooth muscle cell

tag: treatment


title: E315A-RNA-2_clean

description:
315A-RNA-2_S14
Bulk RNA sequencing of RNA extracted from 315A cells.


title: 2061_D6

description: RNA from whole blood


title: 2056_D3

description: RNA from whole blood


title: gDNA_organoid_Colorectal_Cancer [PDM-8]

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol. Normalization using ssNoob preprocessing method.

label: Cy5 and Cy3

source_name: HCM-CSHL-0064-C18 (ATCC PDM-8): Organoid cells from Colorectal Cancer

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA from ATCC

tag: patient id

tag: age at acquisition

value: Organoid cells

value: Colorectal cancer

tag: disease

value: primary adenocarcinoma

value: sigmoid colon

tag: primary site

value: colon


title: SKBR3-RNA-2_clean

description:
SKBR3-RNA-2_S23
Bulk RNA sequencing of RNA extracted from SKBR3 cells.

source_name: SKBR3 Her2 overexpresson breast cancer cell line

value: Breast

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 2056_D1

description: RNA from whole blood

tag: tissue

value: septic shock


title: 16_IL17

tag: Sex

value: Male

tag: age

tag: asthma


title: 18_IL13

value: Female

value: No

tag: race


title: gDNA_organoid_Colorectal_Cancer [PDM-7]

source_name: HCM-CSHL-0063-C18 (ATCC PDM-7): Organoid cells from Colorectal Cancer

tag: gender

tag: diagnosis


title: 16_Combined

source_name: primary cultured airway smooth muscle cell

value: Combined


title: gDNA_organoid_Esophageal_Cancer [PDM-71]

source_name: HCM-SANG-0295-C15 (ATCC PDM-71): Organoid cells from Esophagus Cancer

value: Esophageal cancer

value: adenocarcinoma

value: esophagus


title: 2061_D3

description: RNA from whole blood

value: Whole blood

value: Patient


title: SKBR3-RNA-1_clean

description:
SKBR3-RNA-1_S22
Bulk RNA sequencing of RNA extracted from SKBR3 cells.

tag: cell line

value: SKBR3 Her2 overexpresson breast cancer cell line


title: BT549-RNA-3_clean

description:
BT549-RNA-3_S21
Bulk RNA sequencing of RNA extracted from BT549 cells.

source_name: BT549 Triple negative breast cancer cell line

tag: cell line source

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: 18_Combined

value: primary cultured airway smooth muscle cell

value: AfricanAmerican


title: gDNA_organoid_Esophageal_Cancer [PDM-67]

source_name: HCM-SANG-0291-C15 (ATCC PDM-67): Organoid cells from Esophagus Cancer

value: Organoid cells


title: gDNA_organoid_Colorectal_Cancer [PDM-9]

source_name: HCM-CSHL-0065-C20 (ATCC PDM-9): Organoid cells from Colorectal Cancer

value: Colorectal cancer

value: metastatic adenocarcinoma

value: liver

value: colon


title: 18_IL17

value: Female


title: BT549-RNA-2_clean

description:
BT549-RNA-2_S20
Bulk RNA sequencing of RNA extracted from BT549 cells.

value: BT549 Triple negative breast cancer cell line

value: Breast

value: Adherent cell line

tag: culture condition


title: gDNA_organoid_Colorectal_Cancer [PDM-6]

source_name: HCM-CSHL-0062-C18 (ATCC PDM-6): Organoid cells from Colorectal Cancer

tag: cell type

value: primary adenocarcinoma

value: rectosigmoid junction

value: rectum


title: SKBR3-RNA-3_clean

description:
SKBR3-RNA-3_S24
Bulk RNA sequencing of RNA extracted from SKBR3 cells.

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: BT549-RNA-1_clean

description:
BT549-RNA-1_S19
Bulk RNA sequencing of RNA extracted from BT549 cells.


title: gDNA_organoid_Esophageal_Cancer [PDM-66]

source_name: HCM-SANG-0290-C15 (ATCC PDM-66): Organoid cells from Esophagus Cancer

value: Male

value: Esophageal cancer

value: adenocarcinoma

value: esophagus


title: 38_IL13

value: primary cultured airway smooth muscle cell

tag: donor

value: Yes

value: AfricanAmerican


title: 2061_D1

description: RNA from whole blood

source_name: Whole blood

value: Whole blood

value: Patient

value: septic shock


title: 18_Vehicle

tag: treatment

value: Vehicle

value: Female

value: No


title: A375-RNA-3_clean

description:
A375-RNA-3_S18
Bulk RNA sequencing of RNA extracted from A375 cells.

source_name: A375 Melanoma cancer cell line

value: A375 Melanoma cancer cell line

value: Skin

value: Adherent cell line


title: 2118_D6

description: RNA from whole blood


title: gDNA_organoid_Colorectal_Cancer [PDM-43]

source_name: HCM-SANG-0266-C20 (ATCC PDM-43): Organoid cells from Colorectal Cancer

tag: patient id

value: Organoid cells

value: Colorectal cancer

value: rectum


title: gDNA_organoid_Colorectal_Cancer [PDM-47]

source_name: HCM-SANG-0270-C20 (ATCC PDM-47): Organoid cells from Colorectal Cancer

tag: age at acquisition

value: primary adenocarcinoma


title: gDNA_organoid_Pancreatic_Cancer [PDM-90]

source_name: HCM-SANG-0315-C25 (ATCC PDM-90): Organoid cells from Pancreatic Cancer

value: Pancreatic cancer

tag: disease

value: malignant neoplasm of pancreas

value: pancreas


title: gDNA_organoid_Colorectal_Cancer [PDM-5]

source_name: HCM-CSHL-0061-C18 (ATCC PDM-5): Organoid cells from Colorectal Cancer

value: sigmoid colon

tag: primary site

value: colon


title: gDNA_organoid_Colorectal_Cancer [PDM-46]

source_name: HCM-SANG-0269-C18 (ATCC PDM-46): Organoid cells from Colorectal Cancer

value: Male

value: malignant neoplasm of colon

tag: tissue


title: 2118_D1

description: RNA from whole blood

value: Whole blood

value: Patient

value: septic shock


title: gDNA_organoid_Colorectal_Cancer [PDM-44]

source_name: HCM-SANG-0267-D12 (ATCC PDM-44): Organoid cells from Colorectal Cancer

value: adenoma


title: A375-RNA-2_clean

description:
A375-RNA-2_S17
Bulk RNA sequencing of RNA extracted from A375 cells.

value: A375 Melanoma cancer cell line

value: Skin

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 38_IL17

value: primary cultured airway smooth muscle cell

tag: Sex

value: Female

value: Yes

value: AfricanAmerican


title: gDNA_organoid_Pancreatic_Cancer [PDM-40]

source_name: HCM-CSHL-0093-C25 (ATCC PDM-40): Organoid cells from Pancreatic Cancer

value: Organoid cells

value: Pancreatic cancer

value: adenocarcinoma


title: 2118_D3

description: RNA from whole blood


title: 315A_DNA

description:
315A_DNA_S24
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

data_processing:
library strategy: GTO sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Map reads to hg19 genome using STAR aligner
Separate aligned reads into exonic and allnonexonic
Realign exonic reads to reference genome hg19 using Kallisto and obtain read count tables
Realign allnonexonic reads to refenrence genome hg19 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
Genome_build: hg19
Supplementary_files_format_and_content: read count tables for RNAseq section of data, Varbin files with bincounts for DNAseq section

source_name: 315A_Diploid lymphoblastoid cell line

extract_protocol:
Cells were trypsinized, diluted to 1000cells/ml and handpicked as single cells in 10x Lysis buffer
Single cells isolated into 10x Lysis Buffer with Rnase inhibitor were processed for mRNA transcription for first strand synthesis and cDNA amplification following SMART-Seq2 protocol. Samples were then treated ionically to fragment gDNA and cDNA to 400-700bp fragments. Later gDNA was amplified using SeqXE kit from Sigma Aldirch using manufacturer instructions. Libraries were made by end repair, Adenylation, Adapter ligation and PCR steps.

value: 315A_Diploid lymphoblastoid cell line

value: Lymphoblastoid

tag: culture type

value: Suspension cell line

tag: media

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin

tag: molecule type

value: genomic DNA and mRNA


title: 38_Combined

source_name: primary cultured airway smooth muscle cell

value: Combined

tag: age

tag: asthma

tag: race


title: 4037_D1

description: RNA from whole blood

value: Whole blood

value: Patient

tag: diagnosis

value: septic shock


title: 4037_D3

description: RNA from whole blood


title: 12_Combined

value: Male

value: No

value: EuropeanAmerican


title: 315A_Cy13_S23

description:
315A_Cy13_S23
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

tag: cell line

tag: cell line source


title: gDNA_organoid_Pancreatic_Cancer [PDM-41]

source_name: HCM-CSHL-0094-C25 (ATCC PDM-41): Organoid cells from Pancreatic Cancer

tag: gender

value: Female

tag: cell type

value: pancreas


title: gDNA_organoid_Colorectal_Cancer [PDM-4]

source_name: HCM-CSHL-0060-C18 (ATCC PDM-4): Organoid cells from Colorectal Cancer

tag: patient id

value: Organoid cells

value: Colorectal cancer

value: primary adenocarcinoma

value: sigmoid colon

value: colon


title: 4010_D6

description: RNA from whole blood


title: 315A_Cy13_S22

description:
315A_Cy13_S22
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

value: 315A_Diploid lymphoblastoid cell line

value: Lymphoblastoid

value: Suspension cell line


title: gDNA_organoid_Pancreatic_Cancer [PDM-38]

source_name: HCM-CSHL-0091-C25 (ATCC PDM-38): Organoid cells from Pancreatic Cancer

tag: age at acquisition

value: Pancreatic cancer

value: adenocarcinoma


title: 1138_D6

description: RNA from whole blood

value: Whole blood

value: Patient


title: 4037_D6

description: RNA from whole blood

value: septic shock


title: 12_IL13

value: primary cultured airway smooth muscle cell

tag: donor

tag: treatment

value: Male

value: No


title: 315A_Cy13_S20

description:
315A_Cy13_S20
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin

value: genomic DNA and mRNA


title: 12_IL17

value: EuropeanAmerican


title: 315A_Cy13_S19

description:
315A_Cy13_S19
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt


title: 4010_D3

description: RNA from whole blood

tag: tissue


title: 4010_D1

description: RNA from whole blood


title: gDNA_organoid_Lung_Cancer [PDM-3]

source_name: HCM-CSHL-0058-C34 (ATCC PDM-3): Organoid cells from Lung Cancer

value: Organoid cells

value: Lung cancer

tag: disease

value: primary adenocarcinoma

value: lung

tag: primary site

value: bronchus and lung


title: 27_IL13

tag: Sex


title: A375-RNA-1_clean

description:
A375-RNA-1_S16
Bulk RNA sequencing of RNA extracted from A375 cells.

value: A375 Melanoma cancer cell line

value: Skin

value: Adherent cell line

tag: culture condition

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 315A_Cy13_S18

description:
315A_Cy13_S18
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

value: 315A_Diploid lymphoblastoid cell line

value: Lymphoblastoid

tag: culture type

value: Suspension cell line

tag: media

tag: molecule type


title: gDNA_organoid_Pancreatic_Cancer [PDM-39]

source_name: HCM-CSHL-0092-C25 (ATCC PDM-39): Organoid cells from Pancreatic Cancer

value: Male

tag: diagnosis

value: Pancreatic cancer

value: adenocarcinoma

value: pancreas


title: 315A_Cy13_S21

description:
315A_Cy13_S21
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

tag: cell line

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin

value: genomic DNA and mRNA


title: 315A_Cy13_S17

description:
315A_Cy13_S17
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

tag: cell line source


title: 1138_D3

description: RNA from whole blood

value: Whole blood

value: Patient

value: septic shock


title: gDNA_organoid_Pancreatic_Cancer [PDM-36]

source_name: HCM-CSHL-0089-C25 (ATCC PDM-36): Organoid cells from Pancreatic Cancer

tag: gender

value: Organoid cells


title: SKBR3_Cy0_S94

description:
SKBR3_0cycles_S94_S94
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

source_name: SKBR3_Her2 overexpresson breast cancer cell line

value: Breast


title: 1138_D1

description: RNA from whole blood

source_name: Whole blood


title: 27_Vehicle

tag: cell type

value: primary cultured airway smooth muscle cell

value: Vehicle

tag: age

tag: asthma

value: No

tag: race

value: EuropeanAmerican


title: 6044_D3

description: RNA from whole blood


title: SKBR3_Cy0_S95

description:
SKBR3_0cycles_S95_S95
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 6044_D6

description: RNA from whole blood


title: gDNA_organoid_Stomach_Cancer [PDM-146]

source_name: HCM-BROD-0208-C16 (ATCC PDM-146): Organoid cells from Stomach Cancer

tag: patient id

value: Male

tag: age at acquisition

value: Stomach cancer

value: malignant neoplasm of stomach

value: stomach


title: 48_Vehicle

tag: donor

tag: treatment

value: Female

value: Yes


title: SKBR3_Cy0_S92

description:
SKBR3_0cycles_S92_S92
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: genomic DNA and mRNA


title: 27_Combined

value: Combined

tag: Sex


title: 48_Combined


title: 6044_D1

description: RNA from whole blood

tag: tissue

value: Whole blood

value: Patient

value: septic shock


title: SKBR3_Cy0_S93

description:
SKBR3_0cycles_S93_S93
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast

tag: culture type


title: 48_IL17

value: primary cultured airway smooth muscle cell


title: SKBR3_Cy0_S91

description:
SKBR3_0cycles_S91_S91
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: media


title: 27_IL17

value: No

value: EuropeanAmerican


title: gDNA_organoid_Colorectal_Cancer [PDM-2]

source_name: HCM-CSHL-0057-C18 (ATCC PDM-2): Organoid cells from Colorectal Cancer

value: Organoid cells

value: Colorectal cancer

tag: disease

value: primary adenocarcinoma

value: sigmoid colon

tag: primary site

value: colon


title: SKBR3_Cy0_S90

description:
SKBR3_0cycles_S90_S90
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: cell line

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin

tag: molecule type


title: 48_IL13

value: Female

value: Yes


title: SKBR3_Cy0_S89

description:
SKBR3_0cycles_S89_S89
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: cell line source

value: genomic DNA and mRNA


title: 19_IL17

tag: cell type

value: Male


title: 19_IL13

tag: age


title: 4011_D6

description: RNA from whole blood

value: Whole blood

value: Patient

tag: diagnosis

value: septic shock


title: 4011_D1

description: RNA from whole blood


title: 4011_D3

description: RNA from whole blood


title: SKBR3_Cy0_S88

description:
SKBR3_0cycles_S88_S88
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast


title: gDNA_organoid_Esophageal_Cancer [PDM-120]

source_name: HCM-BROD-0100-C15 (ATCC PDM-120): Organoid cells from Esophageal Cancer

tag: gender

value: Esophageal cancer

value: malignant neoplasm of esophagus

value: esophagus


title: SKBR3_Cy0_S87

description:
SKBR3_0cycles_S87_S87
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S86

description:
SKBR3_0cycles_S86_S86
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S85

description:
SKBR3_0cycles_S85_S85
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 19_Vehicle

value: primary cultured airway smooth muscle cell

value: Vehicle

tag: asthma

tag: race

value: EuropeanAmerican


title: 30_Vehicle

tag: donor

value: No


title: 5259_D6

description: RNA from whole blood


title: 5259_D3

description: RNA from whole blood


title: SKBR3_Cy0_S83

description:
SKBR3_0cycles_S83_S83
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line


title: SKBR3_Cy0_S82

description:
SKBR3_0cycles_S82_S82
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 30_Combined

tag: treatment

value: Combined


title: 30_IL17

tag: Sex


title: 5259_D1

description: RNA from whole blood

tag: tissue


title: 30_IL13


title: 19_Combined

value: Yes


title: gDNA_organoid_Pancreatic_Cancer [PDM-37]

source_name: HCM-CSHL-0090-C25 (ATCC PDM-37): Organoid cells from Pancreatic Cancer

tag: patient id

value: Female

tag: age at acquisition

value: Organoid cells

value: Pancreatic cancer

value: malignant neoplasm of pancreas

value: pancreas


title: SKBR3_Cy0_S81

description:
SKBR3_0cycles_S81_S81
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast

tag: culture type

tag: media

value: genomic DNA and mRNA


title: 3037_D3

description: RNA from whole blood

value: Whole blood

value: Patient

value: septic shock


title: 32_Combined

value: primary cultured airway smooth muscle cell

value: Male

value: EuropeanAmerican


title: 32_Vehicle

value: Vehicle


title: 12_Vehicle

value: No


title: SKBR3_Cy0_S80

description:
SKBR3_0cycles_S80_S80
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: cell line

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 32_IL17

value: Yes


title: 3037_D6

description: RNA from whole blood


title: 2092_D6

description: RNA from whole blood


title: SKBR3_Cy0_S79

description:
SKBR3_0cycles_S79_S79
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: molecule type


title: 1035_D3

description: RNA from whole blood


title: SKBR3_Cy0_S77

description:
SKBR3_0cycles_S77_S77
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: cell line source


title: 3037_D1

description: RNA from whole blood


title: SKBR3_Cy0_S76

description:
SKBR3_0cycles_S76_S76
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 1035_D6

description: RNA from whole blood


title: 2092_D3

description: RNA from whole blood


title: SKBR3_Cy0_S75

description:
SKBR3_0cycles_S75_S75
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 1035_D1

description: RNA from whole blood


title: gDNA_organoid_Stomach_Cancer [PDM-135]

source_name: HCM-BROD-0115-C16 (ATCC PDM-135): Organoid cells from Stomach Cancer

tag: cell type

value: Organoid cells

value: Stomach cancer

tag: disease

value: adenocarcinoma

value: stomach

tag: primary site


title: 38_Vehicle

value: Female

tag: age

value: AfricanAmerican


title: 32_IL13

tag: asthma


title: 6_IL13

tag: race


title: HC3

city: Nanjing

first: Feng-Jie

last: Jin

address: 159 Longpan Road

institute: Nanjing Forestry University

description: Geochip data from triplicate field plots for HC treatment

hyb_protocol: Hybridization was performed with a GeoChip 5.0 array chip on a hybridization station (MAUI, BioMicro Systems, Salt Lake City, UT, USA)  at 42°C for 16 hours.

scan_protocol: Scanning was performed with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Madison, WI, USA),  following their standard operating protocol.

data_processing:
The raw microarray data was processed by GeoChip Microarray Data Manager pipeline (http://ieg.ou.edu/microarray/) as previously described
GeoChip-normalized, averaged gene-level signal intensity

organism: uncultured soil microorganism

source_name: Soil sample

label_protocol: Purified DNA was labeled with the fluorescent dye Cy-3 (GE Healthcare, Little Chalfont, UK) using random primers, and the Klenow fragment of DNA polymerase I

growth_protocol: Genomic DNAs were extracted directly from soil samples

extract_protocol: Genomic DNAs were extracted from the soil samples, using the FastDNA Spin Kit for Soil (MP bio., US), according to the manufacturer’s protocol.

treatment_protocol: We applied five treatments:(1) control (CC), (2) biogas slurry applied at the rate of 250 m3 ha-1 (MC), (3) biogas slurry at the rate of 250 m3 ha-1) combined with biochar at the rate of 80 t ha-1 (MM) , (4) biogas slurry at the rate of 375 m3 ha-1 (HC), and (5) biogas slurry at the rate of 375 m3 ha-1 combined with biochar at the rate of 120 t ha-1 (HH).

value: Biogas slurry (375 m3 ha-1)


title: HH2

description: Geochip data from triplicate field plots for HH treatment

value: Biogas slurry (375 m3 ha-1) + Biochar (120 t ha-1)


title: HH3


title: HH1


title: 6_IL17

value: primary cultured airway smooth muscle cell

tag: donor


title: SKBR3_Cy13_DNA

description:
SKBR3_DNA_S35
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast

value: genomic DNA and mRNA


title: SKBR3_Cy0_S74

description:
SKBR3_0cycles_S74_S74
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy7_S43

description:
SKBR3_Cy7_S43_S43
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 2092_D1

description: RNA from whole blood

value: Whole blood

value: Patient

tag: diagnosis

value: septic shock


title: 6_Vehicle

tag: treatment

value: Vehicle

tag: Sex

value: No

value: EuropeanAmerican


title: 6_Combined

value: Combined


title: 28_Vehicle


title: SKBR3_Cy0_S73

description:
SKBR3_0cycles_S73_S73
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: HC1


title: 28_Combined

value: Female


title: MM3

description: Geochip data from triplicate field plots for MM treatment

value: Biogas slurry (250 m3 ha-1) + Biochar (80 t ha-1)


title: HC2

value: Biogas slurry (375 m3 ha-1)


title: 4003_D6

description: RNA from whole blood

tag: tissue


title: SKBR3_C1_Cy7_S40

description:
SKBR3_Cy7_S40_S40
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: MM2


title: SKBR3_C1_Cy7_S39

description:
SKBR3_Cy7_S39_S39
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 5262_D3

description: RNA from whole blood


title: 28_IL17


title: 4003_D1

description: RNA from whole blood


title: 4003_D3

description: RNA from whole blood


title: 28_IL13


title: MM1


title: SKBR3_C1_Cy7_S38

description:
SKBR3_Cy7_S38_S38
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy7_S41

description:
SKBR3_Cy7_S41_S41
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 5262_D1

description: RNA from whole blood


title: 1_IL17

value: Male


title: 1_IL13

value: primary cultured airway smooth muscle cell


title: 1_Combined


title: 4190_D6

description: RNA from whole blood


title: 1_Vehicle


title: 2206_D6

description: RNA from whole blood


title: MC3

description: Geochip data from triplicate field plots for MC treatment

value: Biogas slurry treatment (250 m3 ha-1)


title: SKBR3_C1_Cy17_S17

description:
SKBR3_Cy17_S17_S57
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast

value: genomic DNA and mRNA


title: MC1


title: SKBR3_C1_Cy17_S15

description:
SKBR3_Cy17_S15_S55
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy17_S14

description:
SKBR3_Cy17_S14_S54
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 2206_D3

description: RNA from whole blood

value: Whole blood

value: Patient


title: 2206_D1

description: RNA from whole blood

value: septic shock


title: CC3

description: Geochip data from triplicate field plots for control

value: Control; no treatment


title: 56_Vehicle

value: Vehicle

value: No

value: EuropeanAmerican


title: 4190_D3

description: RNA from whole blood


title: 4190_D1

description: RNA from whole blood


title: 56_Combined

value: Combined


title: SKBR3_C1_Cy7_S37

description:
SKBR3_Cy7_S37_S37
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 4107_D6

description: RNA from whole blood


title: CC1


title: SKBR3_C1_Cy17_S12

description:
SKBR3_Cy17_S12_S52
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy17_S11

description:
SKBR3_Cy17_S11_S51
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 56_IL17


title: CC2


title: TPTD rep8

city: Shizuoka

first: Tomoya

last: Tanaka

address: 632-1 Mifuku, Izunokuni

institute: Asahi Kasei Pharma

data_processing:
Sequencing was performed in the paired-end (100 x 2) mode on the HiSeq 2500 (Illumina) using a TruSeq SBS Kit v4-HS (Illumina).
Base call files for each cycle of sequencing were generated by the Real Time Analysis software program v1.18.64 (Illumina) and analyzed primarily and de-multiplexed into a FASTQ file using bcl2fastq v1.8.4 (Illumina).
Sequenced reads data were mapped onto the rn6 using the TopHat software program v2.0.14.
Fragments per kilobase per million (FPKM) values were computed by the Genedata Expressionist software program v9.1.4a (Genedata).
Genome_build: rn6
Supplementary_files_format_and_content: Excel (xlsx) file includes FPKM values and counts for each sample

organism: Rattus norvegicus

source_name: Dorsal root ganglia

extract_protocol:
The tissue samples were then immersed in RNAlater (Thermo Fisher Scientific) and stored at -80 °C until use. Total RNA was isolated using an RNeasy lipid-tissue mini kit with DNase I (QIAGEN). Sequence libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague-Dawley

value: dorsal root ganglia (L4-5)

value: 20 weeks old

tag: surgery

value: Ovariectomy

value: Teriparatide


title: 68_IL17

value: primary cultured airway smooth muscle cell

value: Female

value: AfricanAmerican


title: SKBR3_C1_Cy15_S60

city: New York

first: Yu-Jui

last: Ho

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description:
SKBR3_Cy15_S60_S60
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast

tag: culture type

tag: media

value: genomic DNA and mRNA


title: 56_IL13

city: Chicago

first: Emma

last: Thompson

address: 920 E 58th St, CLSC Rm 501

institute: The University of Chicago

value: Male


title: 68_IL13

value: No


title: 4107_D3

description: RNA from whole blood

data_processing: CEL files were transformed into matrix, normalized, adjusted for background noise (RMA normalization) and probes were summarized into probesets  with command apt-probeset-summarize (V 1.18.0)  with rma option . Batch effects were removed using COMBAT. Probesets were filtered when log2 signal was under 5.5 in more than 68% of samples.

value: Whole blood

value: Patient

value: septic shock


title: 4107_D1

description: RNA from whole blood


title: 68_Combined

value: Combined


title: 68_Vehicle

value: Vehicle


title: SKBR3_C1_Cy15_S58

description:
SKBR3_Cy15_S58_S58
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: cell line

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin

tag: molecule type


title: 59_Vehicle

tag: cell type


title: 1113_D6

description: RNA from whole blood


title: TPTD rep5

value: Sprague-Dawley

value: dorsal root ganglia (L4-5)

value: 20 weeks old

value: Ovariectomy


title: 1113_D3

description: RNA from whole blood


title: 1113_D1

description: RNA from whole blood


title: 5262_D6

description: RNA from whole blood


title: 1034_D6

description: RNA from whole blood


title: TPTD rep7

value: Teriparatide


title: SKBR3_C1_Cy15_S56

description:
SKBR3_Cy15_S56_S56
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

tag: cell line source

value: Breast


title: TPTD rep4


title: SKBR3_C1_Cy15_S59

description:
SKBR3_Cy15_S59_S59
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: genomic DNA and mRNA


title: TPTD rep6


title: SKBR3_C1_Cy15_S53

description:
SKBR3_Cy15_S53_S53
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 59_Combined

value: primary cultured airway smooth muscle cell

value: Female

value: AfricanAmerican


title: TPTD rep3


title: SKBR3_C1_Cy15_S52

description:
SKBR3_Cy15_S52_S52
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 4204_D6

description: RNA from whole blood

value: Whole blood

value: Patient


title: 4204_D3

description: RNA from whole blood

value: septic shock


title: 1034_D3

description: RNA from whole blood


title: SKBR3_C1_Cy13_S56

description:
SKBR3_Cy13_S56_S56
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 59_IL17

value: No


title: TPTD rep2


title: TPTD rep1


title: 1034_D1

description: RNA from whole blood


title: OVX rep8

value: Vehicle


title: SKBR3_C1_Cy13_S55

description:
SKBR3_Cy13_S53_S53
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line

value: Adherent cell line


title: OVX rep7

value: Sprague-Dawley