title: Blood Sample from Individual 34

city: Madison

first: Hamid R.

middle: R

last: Eghbalnia

state: WI

address: 433 Babcock

institute: University of Wisconsin-Madison

description: id 34

data_processing:
Fastq data files containing 53-77 million single-end reads were trimmed and processed for data analysis.
Bowtie2 was used for alignments
Samtools was used to create necessary intermediate files
Cufflinks was used to obtain abundances
Standard normalization steps were performed using in-house tools as described in the manuscript
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreasheet containing normalized expression data for each sample

source_name: Blood

extract_protocol:
The RNA extracted from the 35 control samples passed quality control assessment prior to the addition of External RNA Controls Consortium ExFold RNA spike-in mixes (ERCC: Ambion, 4456739; Foster City CA) and removal of ribosomal and globin RNA from the samples (Illumina GZG1206; San Diego, CA).
The cDNA libraries were processed according to standardized Illumina protocols and sequenced on the Illumina HiSeq 2000 platform.

tag: sample type

value: Control


title: Blood Sample from Individual 31

status: Public on Mar 23 2021

type: SRA

country: USA

description: id 31

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: Blood Sample from Individual 27

description: id 27


title: Blood Sample from Individual 28

description: id 28


title: Blood Sample from Individual 33

description: id 33


title: Blood Sample from Individual 35

description: id 35


title: Blood Sample from Individual 32

description: id 32


title: Blood Sample from Individual 29

description: id 29


title: Blood Sample from Individual 26

description: id 26


title: nasal mucosa-control-rep2

type: RNA

city: nanchang

first: Jieqing

last: Yu

state: Jiangxi Province

address: No. 17, Yongwaizheng street

country: China

institute: The First Affiliated Hospital of Nanchang University

description: Gene expression in control nasal mucosa

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: nasal mucosa,control,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

tag: tissue

value: nasal mucosa


title: EOs_Gut_L_2

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Gene expression for intestine of gilthead sea bream fed 0.5% EOs diet pool 2

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to S. aurata array (ID 024502, Agilent) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: For microarray analysis, a percentile shift normalization was carried out and then data were filtered by expression (standard deviation) among groups. Then, gene-level analysis was conducted in order to obtain the median of signal intensities from spots within a probe set. Statistical test (t-test unpaired) was done with GeneSpring software GX 14.3 to obtain the differentially expressed genes (p-value < 0.05) between control and treatments.

organism: Sparus aurata

source_name: Intestine

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Gilthead sea bream (Sparus aurata) were obtained from an aquaculture company (Valencia, Spain) and transported to the on-grown facilities of IRTA in Sant Carles de La Ràpita (Tarragona, Spain).

extract_protocol: Total RNA was extracted from intestine using  the RNeasy® Mini Kit (Qiagen, Germany). Total RNA was eluted in a final volume of 35 μL nuclease-free water and treated with DNAse using the DNA-freeᵀᴹ DNA Removal Kit according to manufacturer’s instructions (Invitrogen, Thermo Fisher Scientific, Lithuania). Total RNA concentration and purity were quantified using a Nanodrop-2000® spectrophotometer (Thermo Scientific, USA) and stored at -80 °C until analysis. Prior to hybridization with microarrays, samples were diluted to 133.33 ng/µL concentration and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Spain). All the RNA analysed in this study were selected by the criteria of a RIN value > 8.5.

treatment_protocol: All animal experimental procedures were conducted in compliance with the experimental research protocol approved by the Committee of Ethics and Animal Experimentation of the Institut de Recerca i Tecnologia Agroalimentàries (IRTA) and in accordance with the Guidelines of the European Union Council (86/609/EU) for the use of laboratory animals. After transport, fish received three treatments with hydrogen peroxide and two treatments with formaldehyde (150 ppm, during one hour each) to treat injuries and avoid the presence of any parasite. After the on-growing period of 105 days, 150 fish (BW = 40.26 ± 0.14 g) were randomly distributed in six aerated 450 L square-shaped tanks with smoothed corners, using an IRTAmar® recirculation system (5-10 % water replacement per day) under natural photoperiod. Water temperature (21-28 °C), oxygen (6.8 ± 1.7 mg/L) and pH (7.5 ± 0.01) were daily controlled, whereas salinity (35‰)as well as ammonia (0.13 ± 0.1 mg NH4+ L−1) and nitrite (0.18 ± 0.1 mg NO2- L−1) levels were weekly monitored.The nutritional assay was carried out in triplicate tanks with an initial density of 2 kg/m3 (25 fish per tank). Fish were fed both diets two times per day at the daily rate of 3.0% of the stocked biomass, which approached apparent satiation.  At day 65 of feeding, four fish were randomly selected from each tank, euthanized with anaesthetic (MS-222, Sigma-Aldrich) and a section from the mid-anterior intestine was sampled and stored in RNAlater™, incubated overnight at 4 °C, and stored at -80 °C until analysed.

value: Intestine

tag: age

value: juveniles, 155 g

tag: diet

value: 0.5% inclusion of a microencapsulated additive composed of a blend of garlic, carvacrol, and thymol synthetic EOs


title: Control_Gut_1

description: Gene expression for control group pool 1

value: control


title: AHF219

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

description: Bacterial rRNA amplified and sequenced

data_processing:
During the read pre-processing step, sequencing adapters and PCR primers were first removed using the ILLUMINACLIP step in Trimmomatic(v0.35) run in paired-end mode.
Paired-end reads were then joined using FLASh (v1.2.11) with a maximum overlap of 250 bp, before quality trimming (qtrim = rl; trimq = 30) using BBDuk of BBTools (v35.85) and finally filtered for at least 50 bp using the MINLEN step in Trimmomatic run in single-end mode.
After preprocessing, 16S samples were mapped against the SILVA (v.123) database.
The pick_closed_reference_otus.py script in QIIME (v1.8.0), implementing the usearch (v7.0.1090) algorithm, was used for OTU picking, enabling reverse strand matching and requiring a minimum similarity of 99%.
Genome_build: NA
Supplementary_files_format_and_content: Operational taxonomic units (OTUs) occurring only once (singletons) were removed from the entire dataset. Samples with fewer than 500 reads were removed. Alpha- (Shannon and Chao1 indices) and beta-diversity analyses (Bray-Curtis and weighted UniFrac distances) were performed in QIIME(Caporaso et al., 2010) (v1.8.0) on OTU tables that had been rarefied to 1,000 reads per sample for 10 times.

organism: human gut metagenome

source_name: Human fetal tissues

extract_protocol:
DNA from fetal tissues was extracted according to the protocol as previously described(Rancati et al., 2008), except that the volume of Breaking Buffer and phenol/chloroform/IAA used was 400μL. Three consecutive phenol/chloroform/isoamylalcohol extractions were performed to reduce protein contamination. A final chloroform extraction was performed to remove phenol contamination, prior to ethanol precipitation. RNA contamination was removed by treating the gDNA samples with 70 ng/μl affinity-purified RNAse A (Ambion) for 1 h at +37 °C. Final yields were quantified with a ND- 1000 spectrophotometer (NanoDrop). Fetal microbiome reagent and environmental controls were concurrently performed during the DNA extraction process.
Genomic DNA isolated from fetal tissues and control samples were treated with McrBC restriction enzyme (New England BioLabs) according to manufacturer’s instructions, to remove host DNA and to enrich for microbial DNA. The treated DNA samples were purified using 0.8X ratio of AMPure XP beads (Beckman Coulter). The McrBC-treated, purified gDNA was quantified using Quant-iT TM Picogreen® dsDNA Assay kit (Invitrogen). For amplification of the 16S rRNA gene-variable regions three rounds of amplification were performed using 100ng of McrBC-treated gDNA with LongAmp Taq DNA polymerase (New England Biolabs) according to manufacturer’s instructions. The first step aimed at enriching microbial sequences was performed using primers that amplify V2-V6 regions (Table S3). PCR cycling parameters consisted of initial denaturation step for 30s at 94°C, followed by 12 cycles of 15s at 94°C, 30s at 45°C, and 1min at 65°C with a final extension for 10 min at 65°C. Subsequently a nested PCR was performed targeting V4-V5 regions using the enriched V2-V6 amplicon as template. PCR Cycling parameters for amplifying V4-V5 regions were similar to V2- V6 PCR cycling profile, except that the extension was for 30s at 65 °C. The final amplification step involved addition of barcodes for identifying, de-multiplexing individual samples and Illumina adapter sequences to the V4-V5 enriched product using communal primers. Communal PCR amplification consisted of initial denaturation step for 30 s at 94 °C, followed by 30 cycles of 15s at 94 °C, 30s at 45°C, and 1 min at 65°C with a final extension for 10 min at 65°C. Equimolar concentrations of the prepared libraries were pooled and electrophoresed using 1% agarose gel. Pooled amplicon libraries were gel-purified using the Qiaquick Gel Extraction Kit (Qiagen). Integrity of gel-purified libraries were validated using the High Sensitivity DNA kit (Agilent Technologies). The libraries were quantified using KAPA Library Quantification Kit (Kapa Biosystems) to ascertain the loading concentration and sequenced on a HiSeq 2500 System (Illumina) operated in Rapid Run Mode to generate 2 ×250 bp paired-end reads
16S rRNA sequencing on HiSeq 2500 System (Illumina)

value: Fetal gut, lungs, skin, thymus, spleen and placenta

tag: cell type

value: Bacterial


title: Blood Sample from Individual 30

description: id 30


title: Blood Sample from Individual 25

description: id 25


title: Control_Gut_3

description: Gene expression for control group pool 3


title: AHF218

description: Bacterial rRNA amplified and sequenced


title: nasal mucosa-non-ECRSwNP-rep2

description: Gene expression in non-ECRSwNP nasal mucosa

source_name: nasal mucosa,non-ECRSwNP,replicate 2


title: AHF217

description: Bacterial rRNA amplified and sequenced


title: EOs_Gut_L_1

description: Gene expression for intestine of gilthead sea bream fed 0.5% EOs diet pool 1


title: nasal mucosa-control-rep3

description: Gene expression in control nasal mucosa

source_name: nasal mucosa,control,replicate 3


title: Control_Gut_2

description: Gene expression for control group pool 2


title: nasal mucosa-ECRSwNP-rep3

description: Gene expression in ECRSwNP nasal mucosa

source_name: nasal mucosa,ECRSwNP,replicate3


title: nasal mucosa-non-ECRSwNP-rep1

source_name: nasal mucosa,non-ECRSwNP,replicate 1


title: nasal mucosa-control-rep1

description: Gene expression in control nasal mucosa

source_name: nasal mucosa,control,replicate 1


title: nasal mucosa-ECRSwNP-rep2

description: Gene expression in ECRSwNP nasal mucosa

source_name: nasal mucosa,ECRSwNP,replicate2


title: nasal mucosa-non-ECRSwNP-rep3

source_name: nasal mucosa,non-ECRSwNP,replicate 3


title: EOs_Gut_L_3

description: Gene expression for intestine of gilthead sea bream fed 0.5% EOs diet pool 3


title: Blood Sample from Individual 21

description: id 21


title: AHF216

description: Bacterial rRNA amplified and sequenced


title: AHF215

description: Bacterial rRNA amplified and sequenced


title: AHF213

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 22

description: id 22


title: AHF201

description: Bacterial rRNA amplified and sequenced


title: AHF202

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 16

description: id 16


title: Blood Sample from Individual 19

description: id 19


title: Blood Sample from Individual 17

description: id 17


title: Blood Sample from Individual 18

description: id 18


title: Blood Sample from Individual 15

description: id 15


title: AHF200

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 14

description: id 14


title: AHF199

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 20

description: id 20


title: Blood Sample from Individual 24

description: id 24


title: AHF214

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 13

description: id 13


title: AHF198

description: Bacterial rRNA amplified and sequenced


title: nasal mucosa-ECRSwNP-rep1

description: Gene expression in ECRSwNP nasal mucosa

source_name: nasal mucosa,ECRSwNP,replicate 1


title: AHF197

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 12

description: id 12


title: Blood Sample from Individual 23

description: id 23


title: Blood Sample from Individual 10

description: id 10


title: AHF212

description: Bacterial rRNA amplified and sequenced


title: AHF186

description: Bacterial rRNA amplified and sequenced


title: AHF196

description: Bacterial rRNA amplified and sequenced


title: AHF195

description: Bacterial rRNA amplified and sequenced


title: AHF185

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 9

description: id 9


title: Blood Sample from Individual 8

description: id 8


title: Blood Sample from Individual 6

description: id 6


title: Blood Sample from Individual 4

description: id 4


title: Blood Sample from Individual 7

description: id 7


title: AHF178

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 5

description: id 5


title: AHF181

description: Bacterial rRNA amplified and sequenced


title: AHF183

description: Bacterial rRNA amplified and sequenced


title: AHF182

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 2

description: id 2


title: AHF180

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 1

description: id 1


title: AHF179

description: Bacterial rRNA amplified and sequenced


title: AHF177

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 11

description: id 11


title: Organoid 13

city: Rotterdam

first: Jiang

last: Chang

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using tophat2 default setting
reads uniqely overlaped in coding region were collected by Htseq count
The raw count were normalized by TPM (transcripts per kilobase million), which is counts per length of transcript (kb) per million reads mapped.
Genome_build: hg38
Supplementary_files_format_and_content: A summary of raw read count matrix including all samples
Supplementary_files_format_and_content: A summary of normalziaed read count (TPM) matrix including all samples

source_name: Pancreas

growth_protocol: Pancreatic cells were mounted in matrigel (Corning, #356231) and were cultured in serum-free organoid growth media, composed of basic medium supplemented with: 1mM N-Acetyl L cysteine (Sigma, #A9165), 1mM Nicotinamide (Sigma, #N0630), 100 ng/ml mouse recombinant NOGGIN (Peprotec, #250-38), 500 ng/mL recombinant RSPONDIN (Peprotec, #120-38), 25% serum free WNT conditioned media (Mihara et al., 2016), 50 ng/mL mouse recombinant EGF (Gibco, #PMG8041), 100 ng/mL FGF10 ( Peprotec, #100-26), 10 nM Gastrin I (Sigma, #G9020), 500 nM A83-01 (Tocris, #2939), and 10 µM Y-27632 dihydrochloride (Tocris, #1254).

extract_protocol: Snap-frozen tumor tissues were carried on dry ice. Lysis buffer using AllPrep DNA/RNA mini kit (QIAGEN) was added to the samples according to manufacturer’s protocol; samples were processed as quickly as possible with homogenization using Ultra-Turrax T25 homogenizer (Janke & Kunkel).  Lysed and homogenized tissues were processed for DNA/RNA extraction using AllPrep DNA/RNA mini kit (QIAGEN) according to manufacturer’s instructions.    Organoids were extracted from matrigel domes using Cell Recovery Solution (Corning, #354253). Organoids were centrifuged and washed with PBS twice to discard remaining matrigel. DNA and RNA were extracted simultaneously using AllPrep DNA/RNA mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: 8 cycles of FOLFIRINOX

tag: treatment

value: FOLFIRINOX

tag: disease state

value: Stage I


title: Organoid 12


title: AHF176

description: Bacterial rRNA amplified and sequenced


title: AHF175

description: Bacterial rRNA amplified and sequenced


title: Organoid 11


title: AHF184

description: Bacterial rRNA amplified and sequenced


title: AHF174

description: Bacterial rRNA amplified and sequenced


title: AHF173

description: Bacterial rRNA amplified and sequenced


title: Blood Sample from Individual 3

description: id 3


title: Organoid 4

value: No therapy


title: Organoid 10


title: Organoid 5


title: AHF172

description: Bacterial rRNA amplified and sequenced


title: AHF171

description: Bacterial rRNA amplified and sequenced


title: Organoid 9


title: AHF170

description: Bacterial rRNA amplified and sequenced


title: AHF169

description: Bacterial rRNA amplified and sequenced


title: Organoid 3


title: Organoid 1


title: Organoid 2


title: Primary PDAC tissue 11


title: AHF168

description: Bacterial rRNA amplified and sequenced


title: Primary PDAC tissue 12


title: Primary PDAC tissue 13


title: AHF165

description: Bacterial rRNA amplified and sequenced


title: AHF167

description: Bacterial rRNA amplified and sequenced


title: AHF164

description: Bacterial rRNA amplified and sequenced


title: AHF166

description: Bacterial rRNA amplified and sequenced


title: Primary PDAC tissue 10


title: AHF163

description: Bacterial rRNA amplified and sequenced


title: AHF161

description: Bacterial rRNA amplified and sequenced


title: AHF162

description: Bacterial rRNA amplified and sequenced


title: Primary PDAC tissue 4


title: Primary PDAC tissue 5


title: Primary PDAC tissue 3


title: AHF160

description: Bacterial rRNA amplified and sequenced


title: Primary PDAC tissue 9


title: Primary PDAC tissue 2


title: AHF157

description: Bacterial rRNA amplified and sequenced


title: AHF158

description: Bacterial rRNA amplified and sequenced


title: AHF159

description: Bacterial rRNA amplified and sequenced


title: Primary PDAC tissue 1


title: AHF155

description: Bacterial rRNA amplified and sequenced


title: AHF152

description: Bacterial rRNA amplified and sequenced


title: MIT/ML324 03

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
Sample 9 (C03)
C.gene.count.matrix.annot

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using Bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Prostate stromal cell

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS. For mouse in vivo implantation, a total number of approximately 250,000 was reached and subject to in vitro combination with human prostate cancer cells (PC3, in a number of 1,000,000). After xenografting of cell mixtures to the hind flank of animals, the chemotherapeutic agent mitoxantrone (MIT) and/or ML324 was administered biweekly from the 3rd week post implantation.

extract_protocol:
Stromal cells were specifically isolated via laser capture microdissection (LCM) of histologically stained (hematoxylin) mouse tumor sections before lysed for RNA preparation. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total amplified RNA for the construction of sequencing libraries per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols. Three independent libraries were generated from 3 individual samples per treatment group.

treatment_protocol: Animals were treated by MIT (0.2 mg/kg) alone or MIT plus ML324 (4 mg/kg) (dissolved in 10% DMSO and supplemented with 40% PEG300/5% Tween-80/45% saline). Agents were delivered intraperitoneally (i.p.) once every 2 weeks starting from the beginning of the 3rd week, with a total number of 3 biweek cycles throughout the whole regimen (8-week regimen).

value: Normal human prostate derived primary stromal cells

tag: passage

tag: agent

tag: name


title: MIT/ML324 02

description:
Sample 8 (C02)
C.gene.count.matrix.annot


title: AHF154

description: Bacterial rRNA amplified and sequenced


title: AHF151

description: Bacterial rRNA amplified and sequenced


title: MIT/ML324 01

description:
Sample 7 (C01)
C.gene.count.matrix.annot


title: AHF149

description: Bacterial rRNA amplified and sequenced


title: MIT 03

description:
Sample 6 (B03)
B.gene.count.matrix.annot

value: MIT


title: AHF150

description: Bacterial rRNA amplified and sequenced


title: AHF146

description: Bacterial rRNA amplified and sequenced


title: MIT 02

description:
Sample 5 (B02)
B.gene.count.matrix.annot


title: MIT 01

description:
Sample 4 (B01)
B.gene.count.matrix.annot


title: AHF147

description: Bacterial rRNA amplified and sequenced


title: AHF145

description: Bacterial rRNA amplified and sequenced


title: Vehicle 03

description:
Sample 3 (A03)
A.gene.count.matrix.annot

value: Vehicle


title: AHF144

description: Bacterial rRNA amplified and sequenced


title: AHF156

description: Bacterial rRNA amplified and sequenced


title: AHF143

description: Bacterial rRNA amplified and sequenced


title: AHF141

description: Bacterial rRNA amplified and sequenced


title: Vehicle 02

description:
Sample 2 (A02)
A.gene.count.matrix.annot


title: AHF148

description: Bacterial rRNA amplified and sequenced


title: AHF140

description: Bacterial rRNA amplified and sequenced


title: AHF139

description: Bacterial rRNA amplified and sequenced


title: Vehicle 01

description:
Sample 1 (A01)
A.gene.count.matrix.annot


title: AHF138

description: Bacterial rRNA amplified and sequenced


title: AHF137

description: Bacterial rRNA amplified and sequenced


title: AHF136

description: Bacterial rRNA amplified and sequenced


title: PXA2

city: Heidelberg

first: Christopher

last: Previti

state: Baden-Wuerttemberg

address: Im Neuenheimer Feld 280

department: Omics IT and Data Management Core Facility (W610)

country: Germany

institute: DKFZ (German Cancer Research Center)

hyb_protocol: Subsequent library preparation, hybridization, and quality control was conducted following the manufacturer’s guideline.

scan_protocol: Affymetrix

data_processing: Expression data were normalized using the MAS5.0 algorithm. Identification of significantly differentially expressed genes between subgroups (test: anova; correction for multiple testing: false discovery rate, transform: z-score) and unsupervised hierarchical clustering were performed within the R2: Genomics Analysis and Visualization Platform (http://r2.amc.nl).

label: biotin

source_name: Heidelberg

label_protocol: Tumor samples with sufficient high-quality RNA were analyzed on the Affymetrix GeneChip Human Genome U133 Plus (v.2.0) Array (Affymetrix, Santa Clara, USA) at the Microarray Department of the University of Amsterdam, the Netherlands or the Genomics ad Proteomics Core Facility of the German Cancer Research Center (DKFZ).

growth_protocol: Human tumor material.

extract_protocol: RNA extraction from fresh frozen tissue was performed using the Maxwell RSC simplyRNA Tissue Kit (Promega, Madison, WI, USA). RNA quality control and quantification were performed using the Agilent2100 Bionanalyzer (Agilent Technologies, Wilmington, USA). RNA samples with an integrity number (RIN) > 6.0 and no evidence of ribosomal degradation were further analyzed.

treatment_protocol: Not applicable.

tag: methylation subgroup

value: PXA


title: PXA6


title: PXA8


title: PXA7


title: PXA3


title: PXA5


title: PXA1


title: AHF135

description: Bacterial rRNA amplified and sequenced


title: MrgprdDTR_rep3, mast cells

city: Pittsburgh

first: Daniel

middle: H

last: Kaplan

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

data_processing:
RNA-sB68eq:  Paired-end reads were aligned using STAR aligner to mm9 genome assmebly. Cufflinks was used to measure transcripts abundance and report it as FPKM values.
Software used:  STAR aligner,  Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq data as cufflink reported FPKM values

organism: Mus musculus

source_name: MrgprdDTR

growth_protocol: peritoneal-derived mast cells (PCMC) were cultured for 48 hours with vehicle or NS102; or PCMC cultured for 6 hours in glutamate-free Tyrode’s buffer supplemented with vehicle or 4 mM glutamate.

extract_protocol:
The whole skin tissues or sorted mast cells were homogenized using a homogenizer, and mRNA was processed using the Qiagen RNeasy Kit following the manufacturer’s instructions.
Illumina single and paired end libraries, RNA-seq and DNA-seq
Adapter ligation to fragements followed by pcr amplification using indexed primers for Illumnia HiSeq-2500

treatment_protocol: MrgprdDTR mice and control MrgprdCre mice were treated with DT for 3-4 weeks. Ear of WT mice were treated with 50 mM β-ala or vehicle once daily for two days.

value: Mast Cells

tag: sample derived from

value: Epidermal

tag: strain

value: DT (IP) + Acetone:Olive oil (4:1)


title: MrgprdDTR_rep4, mast cells


title: MrgprdDTR_rep2, mast cells


title: AHF134

description: Bacterial rRNA amplified and sequenced


title: AHF142

description: Bacterial rRNA amplified and sequenced


title: MrgprdDTR_rep1, mast cells


title: AHF131

description: Bacterial rRNA amplified and sequenced


title: MYCN8

value: MYCN


title: PXA4


title: MYCN7


title: AHF132

description: Bacterial rRNA amplified and sequenced


title: MrgprdCre_rep4, mast cells

source_name: MrgprdCre

value: Acetone:Olive oil (4:1)


title: AHF130

description: Bacterial rRNA amplified and sequenced


title: AHF129

description: Bacterial rRNA amplified and sequenced


title: AHF128

description: Bacterial rRNA amplified and sequenced


title: MYCN5


title: AHF127

description: Bacterial rRNA amplified and sequenced


title: MrgprdCre_rep3, mast cells


title: MYCN6


title: MYCN4


title: MrgprdCre_rep2, mast cells


title: AHF133

description: Bacterial rRNA amplified and sequenced


title: MrgprdCre_rep1, mast cells


title: AHF124

description: Bacterial rRNA amplified and sequenced


title: AHF123

description: Bacterial rRNA amplified and sequenced


title: AHF122

description: Bacterial rRNA amplified and sequenced


title: AHF125

description: Bacterial rRNA amplified and sequenced


title: AHF118

description: Bacterial rRNA amplified and sequenced


title: AHF121

description: Bacterial rRNA amplified and sequenced


title: AHF120

description: Bacterial rRNA amplified and sequenced


title: AHF119

description: Bacterial rRNA amplified and sequenced


title: KP_CCB_rep1

city: Berlin

first: Michaela

last: Reissland

address: Ihnestr. 63

department: Genome Regulation

institute: Max Planck Institut for molecular genetics

data_processing:
Illumina’s FASTQ Generation software v1.0.0
Sequenced reads were mapped to mm10 using bowtie2 v2.4.1
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung tumor derived cell-line

extract_protocol:
WT lungs were removed, flash frozen in liquid nitrogen and RNA was harvested using ReliaPrepTM RNA Cell miniprep System Promega Kit. RNA from Cell-lines was isolated according to maufacturer`s instruction manual with ReliaPrepTM RNA Cell miniprep System Promega Kit. mRNA was purified with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: lung

tag: cell line

value: KPCrispr


title: KP_CCB_rep2


title: AHF117

description: Bacterial rRNA amplified and sequenced


title: AHF126

description: Bacterial rRNA amplified and sequenced


title: MYCN2


title: MYCN3


title: AHF116

description: Bacterial rRNA amplified and sequenced


title: AHF115

description: Bacterial rRNA amplified and sequenced


title: KP_CCA_rep2


title: AHF114

description: Bacterial rRNA amplified and sequenced


title: AHF112

description: Bacterial rRNA amplified and sequenced


title: KP_CCA_rep1


title: RTK2_1


title: AHF110

description: Bacterial rRNA amplified and sequenced


title: AHF111

description: Bacterial rRNA amplified and sequenced


title: RTK2_3


title: RTK2_2


title: MYCN1


title: RTK1_4


title: RTK1_5


title: KP_GemmB_rep3

value: KPGemm


title: KP_GemmB_rep2


title: RTK1_2


title: AHF108

description: Bacterial rRNA amplified and sequenced

value: Fetal gut, lungs, skin, thymus, spleen and placenta


title: KP_GemmB_rep1


title: KP_CCA_rep3


title: AHF113

description: Bacterial rRNA amplified and sequenced

value: Bacterial


title: AHF106

description: Bacterial rRNA amplified and sequenced


title: RTK1_1


title: AHF103

description: Bacterial rRNA amplified and sequenced


title: KP_GemmA_rep3


title: RTK1_3


title: AHF109

description: Bacterial rRNA amplified and sequenced


title: AHF101

description: Bacterial rRNA amplified and sequenced


title: AHF099

description: Bacterial rRNA amplified and sequenced


title: RIG25

tag: location

value: cerebellum

tag: primary malignancy

value: medulloblastoma (MB)


title: KP_GemmA_rep1


title: AHF105

description: Bacterial rRNA amplified and sequenced


title: AHF097

description: Bacterial rRNA amplified and sequenced


title: AHF100

description: Bacterial rRNA amplified and sequenced


title: KP_CCB_rep3


title: WT_rep3

source_name: Lung

value: WT


title: AHF104

description: Bacterial rRNA amplified and sequenced


title: WT_rep2


title: AHF094

description: Bacterial rRNA amplified and sequenced


title: RIG13

value: temporal


title: AHF095

description: Bacterial rRNA amplified and sequenced


title: AHF102

description: Bacterial rRNA amplified and sequenced


title: RIG15


title: WT_rep1


title: AHF093

description: Bacterial rRNA amplified and sequenced


title: AHF092

description: Bacterial rRNA amplified and sequenced


title: RIG11


title: AHF090

description: Bacterial rRNA amplified and sequenced


title: RIG24

value: frontal lobe


title: AHF091

description: Bacterial rRNA amplified and sequenced


title: KP_GemmA_rep2


title: AHF096

description: Bacterial rRNA amplified and sequenced


title: RIG08

value: parietal left

value: acute lymphoblastic leukemia (ALL)


title: AHF089

description: Bacterial rRNA amplified and sequenced


title: OSK-plus-Sall4-D7-rep2

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results.txt and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: OSK-plus-Sall4-D7_reprogramming cells

growth_protocol: MEFs infected with OKS+DsRed/Sall4/Cecr2 retrovirus for 48 hours and then change the medium to iCD1 and induction for 7 days

extract_protocol:
Total RNAs were prepared with TRIzol. VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme) was used for library constructions and sequencing done with NextSeq500 Mid output 150 cycles (FC-404-2001, Illumina) for RNA-seq.
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x C57BL/6J) crossed to 129S12/SvJaeJ female mice

tag: developmental stage/tissue

value: E13.5 mouse embryos

value: Primary mouse embryonic fibroblasts (MEFs)

tag: genotype/variation

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing

tag: passages

tag: day of reprogramming


title: AHF088

description: Bacterial rRNA amplified and sequenced

source_name: Human fetal tissues

tag: tissue

tag: cell type


title: AHF086

description: Bacterial rRNA amplified and sequenced


title: OSK-plus-Sall4-D5-rep2

source_name: OSK-plus-Sall4-D5_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: AHF085

description: Bacterial rRNA amplified and sequenced


title: OSK-plus-Sall4-D3-rep2

source_name: OSK-plus-Sall4-D3_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: AHF084

description: Bacterial rRNA amplified and sequenced


title: AHF082

description: Bacterial rRNA amplified and sequenced


title: AHF083

description: Bacterial rRNA amplified and sequenced


title: HEMnDP2 UVR1

city: Philadelphia

first: Sarah

last: Alp

address: 3307 N Broad Street

department: Fels Institute

institute: Temple University

description: UVR

data_processing:
Adapter sequences were removed using Trimgalore. Read quality was checked for each sample using FastQC. Reads were aligned to the hg19/GRCh37 genome build and counted using STAR. Raw count files were normalized and differential expression analysis was performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-deliminated text file. Raw counts for each ENSEMBL gene ID for each sample. Normalized abundace was calculated using DESeq2 for each ENSEMBL gene ID.

growth_protocol: HEMn-DP cells were cultured in Medium 254 (Gibco) supplemented with human melanocyte growth supplement (Gibco) and phorbol 12-myristate acetate (200nM).

extract_protocol:
Cells were pelleted and lysed in triozol and 1/5 volume of chloroform was added to each sample. Phase separation was performed by centrifugation. Supernatant was recovered and an equal volume of ethanol was added. This solution was added to the QIAGEN RNeasy mini Kit column (QIAGEN) and subsequent steps were performed according the the manufacturers protocol, including on column DNase digestion.
Libraries were constructed using 1ug of RNA with the NEBNext Ultra II RNA Library Prep kit (NEB) with Poly-A mRNA enrichment was performed using NEBNext Poly(A) enrichment (NEB) protocol according to the manufacturer's guidelines. Libraries were indexed with NEB NEXT i7 index primers (NEB). Libraries were pooled to 10 nM and spiked 10% with phiX. They were sequenced 75 bases single-end on Illumina HiSeq 2500.

treatment_protocol: Cells were plated in biological triplicate 2 days before UVR exposure.  Cells were at 80% confluence at time of treatment. Cells were washed with DPBS and covered with Saran wrap for UVR exposure.  Two TL-20 lamps emitting a broad spectrum waveband  (35% UVA and 65% UVB) were used.  Cells received a total dose of 175 J/m2 over 90 s at a rate of 1.94 W/m2. The majority of the cells survive this exposure.  Cells were cultured for one month after UVR treatment before detecting changes in DNA methylation.

value: melanocyte cell line


title: HEMnDP2 UVR3

description: UVR


title: HEMnDP2 UVR2

description: UVR


title: HEMnDP2 control3

description: Control


title: AHF080

description: Bacterial rRNA amplified and sequenced


title: HEMnDP2 control2

description: Control


title: OSK-plus-Sall4-D1-rep2

source_name: OSK-plus-Sall4-D1_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: OSK-plus-DR-D7-rep2

source_name: OSK-plus-DR-D7_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing


title: HEMnDP2 control1

description: Control


title: OSK-plus-Sall4-D0-rep2

source_name: OSK-plus-Sall4-D0_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then digested for sequencing


title: AHF076

description: Bacterial rRNA amplified and sequenced

value: Fetal gut, lungs, skin, thymus, spleen and placenta

value: Bacterial


title: OSK-plus-DR-D5-rep2

source_name: OSK-plus-DR-D5_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: AHF075

description: Bacterial rRNA amplified and sequenced


title: HEK293T-hACE2 + SARS-CoV-2-S pseudovirions

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: LIST file includes FPKM values for each Sample

source_name: human embryonic kidney cells

growth_protocol: HEK293T-hACE2 and Vero E6 cells were treated Mock or SARS-CoV-2-S pseudovirions and cultured in 10%FBS BMEM medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: HEK293T-hACE2 and Vero E6 cells were treated Mock or SARS-CoV-2-S pseudovirions for 48h.

value: renal epithelial cells

tag: treatment

value: SARS-CoV-2-S pseudovirions


title: RIG02

value: left parietal

tag: age


title: OSK-plus-DR-D3-rep2

source_name: OSK-plus-DR-D3_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: AHF074

description: Bacterial rRNA amplified and sequenced


title: OSK-plus-DR-D1-rep2

source_name: OSK-plus-DR-D1_reprogramming cells

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x C57BL/6J) crossed to 129S12/SvJaeJ female mice

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: HEK293T-hACE2 + Mock

value: mock


title: OSK-plus-DR-D0-rep2

source_name: OSK-plus-DR-D0_reprogramming cells

value: E13.5 mouse embryos

value: Primary mouse embryonic fibroblasts (MEFs)

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then digested for sequencing


title: con rep2

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

description:
processed data file: con_ICN_CTdel_2.GeneExpression.FPKM.txt
con_FPKM

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: UCSC_mm10
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample.

growth_protocol: Cells were cultured in Gibco RPMI 1640 containing 10% FBS and 2ng/mL mouse IL-3 at 37°C with 5% CO2 and were maintained between a density of 5 × 10^5 cells/ml and 2 × 10^6 cells/ml.

extract_protocol:
Tissue blocks were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

treatment_protocol: BaF3 cells were nucleofected with plasmids(pmax-Clover/pmax-Clover-ICN/pmax-Clover-CTdel) and cell sorting after 24 hours.

value: pro-B chronic lymphocytic leukemia (CLL) cell line

tag: transfected plasmid

value: pmax-Clover


title: AHF079

description: Bacterial rRNA amplified and sequenced


title: CTdel rep1

description:
processed data file: con_ICN_CTdel_1.GeneExpression.FPKM.txt
CTdel_FPKM

value: pmax-Clover-CTdel


title: ICN rep1

description:
processed data file: con_ICN_CTdel_1.GeneExpression.FPKM.txt
ICN_FPKM

value: pmax-Clover-ICN


title: con rep1

description:
processed data file: con_ICN_CTdel_1.GeneExpression.FPKM.txt
con_FPKM


title: AHF077

description: Bacterial rRNA amplified and sequenced

value: Fetal gut, lungs, skin, thymus, spleen and placenta


title: OSK-plus-Cecr2-D3-rep2

source_name: OSK-plus-Cecr2-D3_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: CTdel rep2

description:
processed data file: con_ICN_CTdel_2.GeneExpression.FPKM.txt
CTdel_FPKM


title: OSK-plus-Cecr2-D5-rep2

source_name: OSK-plus-Cecr2-D5_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: AHF078

description: Bacterial rRNA amplified and sequenced

value: Bacterial


title: OSK-plus-Cecr2-D7-rep2

source_name: OSK-plus-Cecr2-D7_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing


title: OSK-plus-Cecr2-D0-rep2

source_name: OSK-plus-Cecr2-D0_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then digested for sequencing


title: OSK-plus-Cecr2-D1-rep2

source_name: OSK-plus-Cecr2-D1_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: ICN rep2

description:
processed data file: con_ICN_CTdel_2.GeneExpression.FPKM.txt
ICN_FPKM


title: OSK-plus-Sall4-D7-rep1

source_name: OSK-plus-Sall4-D7_reprogramming cells

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x C57BL/6J) crossed to 129S12/SvJaeJ female mice

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing


title: nasal mucosa-control-rep3

description: Gene expression in control nasal mucosa

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

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

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: nasal mucosa,control,replicate 3

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

value: nasal mucosa


title: OSK-plus-Sall4-D1-rep1

value: E13.5 mouse embryos

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: OSK-plus-Sall4-D3-rep1

value: Primary mouse embryonic fibroblasts (MEFs)

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: OSK-plus-DR-D7-rep1

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing


title: nasal mucosa-non-ECRSwNP-rep3

description: Gene expression in non-ECRSwNP nasal mucosa

source_name: nasal mucosa,non-ECRSwNP,replicate 3


title: nasal mucosa-non-ECRSwNP-rep1

source_name: nasal mucosa,non-ECRSwNP,replicate 1


title: nasal mucosa-non-ECRSwNP-rep2

source_name: nasal mucosa,non-ECRSwNP,replicate 2


title: OSK-plus-Sall4-D0-rep1

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then digested for sequencing


title: nasal mucosa-control-rep2

description: Gene expression in control nasal mucosa

source_name: nasal mucosa,control,replicate 2


title: nasal mucosa-control-rep1

description: Gene expression in control nasal mucosa

source_name: nasal mucosa,control,replicate 1


title: nasal mucosa-ECRSwNP-rep1

description: Gene expression in ECRSwNP nasal mucosa

source_name: nasal mucosa,ECRSwNP,replicate 1


title: nasal mucosa-ECRSwNP-rep3

description: Gene expression in ECRSwNP nasal mucosa

source_name: nasal mucosa,ECRSwNP,replicate3


title: OSK-plus-DR-D5-rep1

source_name: OSK-plus-DR-D5_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: OSK-plus-DR-D3-rep1

source_name: OSK-plus-DR-D3_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: nasal mucosa-ECRSwNP-rep2

description: Gene expression in ECRSwNP nasal mucosa

source_name: nasal mucosa,ECRSwNP,replicate2


title: GIT1p.Hel2_IPed.memb.solubilized.rep1

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

country: Japan

institute: The University of Tokyo,

description:
Ribosome Profiling
Sample 23

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming and sorting by sample barcode with FastX-toolkit
Unique molecular identifer (UMI) triming with UMI-tools
rRNA alignment with bowtie2
Alignment with TopHat to Genome
Read quantitation using plastid
Genome_build: sacCer3
Supplementary_files_format_and_content: csv files for sample 1 ~ 8: relative ribosome occupancy and Hel2-enrichment score at given codon in transcripts; csv files for sample 9 ~24: reads counts and normalized reads count (RPKM) for individual CDS.

organism: Saccharomyces cerevisiae

growth_protocol:
cultured until OD600nm = 0.5 ~ 0.6 in YPD medium at 30 ºC
The cells were grown until OD600nm = 0.5 ~ 0.6 at 30 ºC in YPD medium

extract_protocol:
RNase I footprinting, RNA extraction
Total RNA was extracted by TRIzol reagent
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129 .

treatment_protocol: Membrane fraction was solubized or not solubized by 1 %  TritonX-100. SRP72 expression is regulated by SRP72 promoter or GIT1 promoter.

value: 1% TritonX-100 Hel2-IP GIT1 promoter

tag: genetic background

value: MATa ade2 his3 leu2 trp1 ura3 can1 HEL2-FTP::natNT2 srp72::HISMX6 pRS415-GIT1p-SRP72-V5

value: HEL2-FTP GIT1p-SRP72-V5

tag: extracted molecule

value: total RNA


title: GIT1p.Hel2_IPed.cytosolic.rep2

description:
Ribosome Profiling
Sample 20

value: Hel2-IP GIT1 promoter


title: GIT1p.Input.cytosolic.rep1

description:
Ribosome Profiling
Sample 17

value: GIT1 promoter


title: OSK-plus-DR-D1-rep1

source_name: OSK-plus-DR-D1_reprogramming cells

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x C57BL/6J) crossed to 129S12/SvJaeJ female mice

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: GIT1p.Input.cytosolic.rep2

description:
Ribosome Profiling
Sample 18


title: GIT1p.Hel2_IPed.cytosolic.rep1

description:
Ribosome Profiling
Sample 19


title: GIT1p.Input.memb.solubilized.rep1

description:
Ribosome Profiling
Sample 21

value: 1% TritonX-100 GIT1 promoter


title: OSK-plus-DR-D0-rep1

source_name: OSK-plus-DR-D0_reprogramming cells

value: E13.5 mouse embryos

value: infected with Oct4, Klf4, Sox2 and DsRed retrovirus for 48 hrs and then digested for sequencing


title: OSK-plus-Cecr2-D7-rep1

source_name: OSK-plus-Cecr2-D7_reprogramming cells

value: Primary mouse embryonic fibroblasts (MEFs)

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing


title: OSK-plus-Cecr2-D5-rep1

source_name: OSK-plus-Cecr2-D5_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: SRP72p.Hel2_IPed.memb.solubilized.rep2

description:
Ribosome Profiling
Sample 16

value: 1% TritonX-100 Hel2-IP　SRP72 promoter

value: MATa ade2 his3 leu2 trp1 ura3 can1 HEL2-FTP::natNT2 srp72::HISMX6 pRS415-SRP72p-SRP72-V5

value: HEL2-FTP SRP72p-SRP72-V5


title: OSK-plus-Sall4-D5-rep1

source_name: OSK-plus-Sall4-D5_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: OSK-plus-Cecr2-D3-rep1

source_name: OSK-plus-Cecr2-D3_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: GIT1p.Hel2_IPed.memb.solubilized.rep2

description:
Ribosome Profiling
Sample 24

value: 1% TritonX-100 Hel2-IP GIT1 promoter

value: MATa ade2 his3 leu2 trp1 ura3 can1 HEL2-FTP::natNT2 srp72::HISMX6 pRS415-GIT1p-SRP72-V5

value: HEL2-FTP GIT1p-SRP72-V5


title: SRP72p.Input.memb.solubilized.rep2

description:
Ribosome Profiling
Sample 14

value: 1% TritonX-100　SRP72 promoter

value: total RNA


title: OSK-plus-Cecr2-D0-rep1

source_name: OSK-plus-Cecr2-D0_reprogramming cells

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x C57BL/6J) crossed to 129S12/SvJaeJ female mice

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then digested for sequencing


title: GIT1p.Input.memb.solubilized.rep2

description:
Ribosome Profiling
Sample 22

value: 1% TritonX-100 GIT1 promoter


title: SRP72p.Hel2_IPed.cytosolic.rep2

description:
Ribosome Profiling
Sample 12

value: Hel2-IP SRP72 promoter


title: OSK-plus-Sall4-D7_ATAC-seq

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: bed file were generated with genomeCoverageBed and bedGraphToBigbed. Scores represent the number of fragments overlapping each genomic position.

molecule: genomic DNA

source_name: reprogramming cells

growth_protocol: Mouse ESCs an iPSCs were cultured feeders-free with N2B27-2i medium (50% (v/v) DMEM (Hyclone), 50% (v/v) knock out DMEM (Gibco), N2 (Gibco), B27 (Gibco), 1mM sodium pyruvate (Gibco), 1mM non-essential amino acids (Gibco), 1 × GlutaMAX (Gibco), 0.1 mM 2 mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (LIF) (Millipore), and the 2i inhibitors, 3 μM CHIR99021 (Sigma), and 1 μM PD0325901 (Sigma).  MEFs infected with 7 factors or single factor dropout retrovirus for 48 hours and then change the medium to iCD1  and induction for 7 days

extract_protocol:
For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

value: E13.5 mouse embryos

value: Primary mouse embryonic fibroblasts (MEFs)

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing


title: OSK-plus-Cecr2-D1-rep1

source_name: OSK-plus-Cecr2-D1_reprogramming cells

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: KO-IR-B

city: Haifa

first: Feras

last: Machour

address: Technion City

country: Israel

institute: Technion

data_processing:
STAR aligner was used to map reads
DESeq2 was used for differential gene expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Excel table containing differential gene expression analysis using DESeq2 comparing control vs KO cells before and after IR.

source_name: MCF10A-Hras cell line

growth_protocol: MCF10A-Hras cells are grown in DMEM-F12 medium supplemented with 5% horse serum (Invitrogen), 20 ng/ml EGF (Peprotech), 0.5 mg/ml hydrocortisone (Sigma H-0888), 100 ng/ml cholera toxin (Sigma C-8052), and 10 μg/ml insulin (Sigma I-1882).

extract_protocol:
total RNA was extracted using TRIzol reagent
RNA sequencing libraries were prepared using TruSeq mRNA library preparation kit
Sequencing was performed on a HiSeq 2500 sequencer with V4 sequencing chemistry to obtain 150bp paired-end reads

treatment_protocol: Cells were exposed to 5Gy ionizing radiation from an X-ray machine (CellRad) and allowed to recover for 12hrs before RNA extraction.

value: 12hrs IR


title: SRP72p.Hel2_IPed.cytosolic.rep1

description:
Ribosome Profiling
Sample 11

value: MATa ade2 his3 leu2 trp1 ura3 can1 HEL2-FTP::natNT2 srp72::HISMX6 pRS415-SRP72p-SRP72-V5

value: HEL2-FTP SRP72p-SRP72-V5


title: OSK-plus-Sall4-D5_ATAC-seq

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: SRP72p.Input.cytosolic.rep2

description:
Ribosome Profiling
Sample 10

value: SRP72 promoter


title: SRP72p.Input.cytosolic.rep1

description:
Ribosome Profiling
Sample 9


title: OSK-plus-Sall4-D1_ATAC-seq

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: SRP72p.Hel2_IPed.memb.solubilized.rep1

description:
Ribosome Profiling
Sample 15

value: 1% TritonX-100 Hel2-IP　SRP72 promoter


title: KO-IR-A


title: OSK-plus-Sall4-D3_ATAC-seq

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: KO-UT-A

value: untreated


title: OSK-plus-Sall4-D0_ATAC-seq

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x C57BL/6J) crossed to 129S12/SvJaeJ female mice

value: infected with Oct4, Klf4, Sox2 and Sall4 retrovirus for 48 hrs and then digested for sequencing


title: Hel2_IPed.memb.solubilized.rep2

description:
Ribosome Profiling
Sample 8

value: 1% TritonX-100 Hel2-IP

value: MATa ade2 his3 leu2 trp1 ura3 can1 HEL2-FTP::natNT2

value: total RNA


title: SRP72p.Input.memb.solubilized.rep1

description:
Ribosome Profiling
Sample 13

value: 1% TritonX-100　SRP72 promoter


title: Hel2_IPed.memb.solubilized.rep1

description:
Ribosome Profiling
Sample 7


title: OSK-plus-Cecr2-D7_ATAC-seq

value: E13.5 mouse embryos

value: Primary mouse embryonic fibroblasts (MEFs)

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 168 hrs before digested for sequencing


title: drought day3 shoot replicate 6

city: Tsukuba

first: Yoshiki

last: Habu

state: Ibaraki

address: Kannondai 2-1-2

department: Institute of Agrobiological Sciences

institute: National Agriculture and Food Research Organization

description: Biological replicate 3 of 4. Drought seedling shoot, harvested after 3 days.

hyb_protocol: Agilent protocol G4140-90050. 825 ng of each Cy-3- and Cy-5-labeled cRNAs were used for hybridization.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Oryza sativa

source_name: rice seedling shoot drought day 3

label_protocol: 400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).

growth_protocol: Rice seedlings were grown on soil in prastic pot (6 cm x 6 cm x 6 cm) at 30C under 14 hours light/10 hours dark light cycle for 2 weeks.

extract_protocol: Total RNA samples were prepared with RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: Two-weeks old seedlins were subjeted to drought or control condition. Plants were grown for further 3 days.

value: shoot

value: drought day 3

tag: cultivar

value: Nipponbare

value: 2 weeks

source_name: rice reference seedling shoot well-watered day 3

value: well-watered day 3


title: Input.memb.solubilized.rep2

description:
Ribosome Profiling
Sample 6

value: 1% TritonX-100


title: WT-IR-A

value: WT (control)

value: 12hrs IR


title: OSK-plus-Cecr2-D5_ATAC-seq

tag: strain

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x C57BL/6J) crossed to 129S12/SvJaeJ female mice

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 120 hrs before digested for sequencing


title: drought day3 shoot replicate 7

description: Biological replicate 4 of 4. Drought seedling shoot, harvested after 3 days.


title: KO-UT-B

tag: genotype

value: untreated


title: drought day3 shoot replicate 5

description: Biological replicate 2 of 4. Drought seedling shoot, harvested after 3 days.


title: drought day3 shoot replicate 3

description: Biological replicate 1 of 4. Drought seedling shoot, harvested after 3 days.


title: control day3 shoot replicate 5

description: Biological replicate 4 of 4 Control seedling shoot, harvested after 3 days.

source_name: rice seedling shoot well-watered day 3


title: WT-UT-B


title: Input.memb.solubilized.rep1

description:
Ribosome Profiling
Sample 5

value: MATa ade2 his3 leu2 trp1 ura3 can1 HEL2-FTP::natNT2

tag: cell line


title: WT-UT-A


title: Hel2_IPed.cytosolic.rep2

description:
Ribosome Profiling
Sample 4

value: total RNA


title: OSK-plus-Cecr2-D3_ATAC-seq

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 72 hrs before digested for sequencing


title: OSK-plus-Cecr2-D1_ATAC-seq

value: E13.5 mouse embryos

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then induced in iCD1 medium for 24 hrs before digested for sequencing


title: WT-IR-B


title: control day3 shoot replicate 1

description: Biological replicate 1 of 4. Control seedling shoot, harvested after 3 days.


title: Hel2_IPed.cytosolic.rep1

description:
Ribosome Profiling
Sample 3


title: potassium acetate day4 root replicate 3

description: Biological replicate 3 of 3. Potassium acetate-treated seedling root, harvested after 4 days.

source_name: potassium acetate-treated rice seedling root day 4

treatment_protocol: Pots containing two-weeks old seedlins were drained and soaked in 30 mM acetic acid, potassium acetate, or control water. Plants were grown for further 2 or 4 days.

value: root

value: potassium acetate-treated day 4

source_name: rice reference control non-treated seedling root


title: potassium acetate day4 root replicate 2

description: Biological replicate 2 of 3. Potassium acetate-treated seedling root, harvested after 4 days.


title: OSK-plus-Cecr2-D0_ATAC-seq

value: Primary mouse embryonic fibroblasts (MEFs)

value: infected with Oct4, Klf4, Sox2 and Cecr2 retrovirus for 48 hrs and then digested for sequencing


title: control day3 shoot replicate 3

description: Biological replicate 3 of 4. Control seedling shoot, harvested after 3 days.

value: shoot

value: Nipponbare

value: 2 weeks


title: Input.cytosolic.rep2

description:
Ribosome Profiling
Sample 2


title: control day3 shoot replicate 2

description: Biological replicate 2 of 4. Control seedling shoot, harvested after 3 days.

value: well-watered day 3


title: Input.cytosolic.rep1

description:
Ribosome Profiling
Sample 1


title: LC-DTA Croton oil rep4

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

data_processing:
Adapter sequences were trimmed from raw sequencing reads using Cutadapt (Martin, 2011).
Trimmed reads were mapped to the mm10 mouse genome with HISAT2 (Kim et al., 2015).
Gene expression values (Transcripts per Million; TPM) were calculated following assignment to genomic features with Subread featurecounts (Liao et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: whole ear tissue

extract_protocol:
Qiagen RNeasy Kit
Illumina Truseq Stranded mRNA Library Prep kit

treatment_protocol: paint 20ul vehicle (aceton:olive oil = 4:1) or 1% croton oil in vehicle on ear (two sides) for 6 hours

value: Croton Oil

value: DTA

tag: sample type

value: mRNAseq


title: LC-DTA Croton oil rep3


title: LC-DTA Croton oil rep2


title: acetic acid day4 root replicate 4

description: Biological replicate 3 of 3. Acetic acid-treated seedling root, harvested after 4 days.

source_name: acetic acid-treated rice seedling root day 4

value: acetic acid-treated day 4

value: untreated


title: potassium acetate day4 root replicate 1

description: Biological replicate 1 of 3. Potassium acetate-treated seedling root, harvested after 4 days.


title: acetic acid day4 root replicate 1

description: Biological replicate 1 of 3. Acetic acid-treated seedling root, harvested after 4 days.


title: LC-DTA Croton oil rep1


title: LC-DTA Control rep3

value: vehicle


title: LC-DTA Control rep2


title: FFPE from progressive MIBC (B1868)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Bioconductor (v2.5) Lumi package.

source_name: Bladder, FFPE

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: RNA were extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol

tag: disease state

value: progressive MIBC

value: Bladder, FFPE


title: FFPE from progressive MIBC (B1866)


title: T4

city: 常州市

first: Yin

last: Zhang

state: 江苏省

address: No.185 Juqianjie Road, Changzhou, Jiangsu, China

institute: Changzhou First People's Hospital

description: Gene expression of submocal tissue, 7 days after ESD procedure

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test.

label_protocol: Total RNA was dephosphorylated, ligated with pCpCy3 and then hybridized to the microarray samples, which were then washed. Using an Agilent Scanner G2505C (Agilent Technologies, Inc.), the array was analyzed.

extract_protocol: Total RNA was isolated from the tissue by using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.). The concentration and purity of total RNA were determined using Nanodrop NC2000 spectrophotometer (Thermo Fisher Scientific, Inc.). RNA integrity was accessed by agarose gel electrophoresis. The microarray with the Agilent Human miRNA Microarray kit, Release 21.0, 8 x 60K (design ID: 070156) and data analysis of the 10 samples from esophageal submucosal tissues were performed by OE Biotechnology Co., Ltd.

treatment_protocol: In the normal esophageal (NE) group, the remaining submucosal tissue at the edge of the lesion immediately after the ESD procedure was collected. In the post-operative esophageal (PE) group, the tissue was collected at the edge of the lesion 7 days after ESD. For each group, a total of five cases were enrolled in the study.

value: esophageal submucal tissue

tag: gender

value: female


title: T3

source_name: submocal tissue, 7 days after ESD procedure


title: T5


title: acetic acid day4 root replicate 3

description: Biological replicate 2 of 3. Acetic acid-treated seedling root, harvested after 4 days.

value: root


title: control day4 root replicate 2

description: Biological replicate 2 of 3. Control seedling root, harvested after 4 days.

source_name: rice mock-treated seedling root day 4

value: mock-treated day 4


title: T2

value: male


title: control day4 root replicate 3

description: Biological replicate 3 of 3. Control seedling root, harvested after 4 days.


title: FFPE from progressive MIBC (B1850)


title: potassium acetate day2 root replicate 4

description: Biological replicate 3 of 3. Potassium acetate-treated seedling root, harvested after 2 days.

source_name: potassium acetate-treated rice seedling root day 2

value: potassium acetate-treated day 2


title: control day4 root replicate 1

description: Biological replicate 1 of 3. Control seedling root, harvested after 4 days.

value: Nipponbare


title: LC-DTA Control rep1


title: potassium acetate day2 root replicate 2

description: Biological replicate 2 of 3. Potassium acetate-treated seedling root, harvested after 2 days.

value: 2 weeks


title: LC-DTR Croton oil rep4

value: DTR


title: T1


title: FFPE from progressive MIBC (B1852)


title: FFPE from progressive MIBC (B1848)


title: C5

description: Gene expression of submocal tissue, immediately after ESD procedure


title: FFPE from progressive MIBC (B1846)


title: FFPE from de novo MIBC (B1830)

value: de novo MIBC


title: FFPE from progressive MIBC (B1691)


title: acetic acid day2 root replicate 3

description: Biological replicate 3 of 3. Acetic acid-treated seedling root, harvested after 2 days.

source_name: acetic acid-treated rice seedling root day2

value: acetic acid-treated day 2


title: LC-DTR Croton oil rep3

value: Croton Oil

value: mRNAseq


title: FFPE from de novo MIBC (B1776)


title: C4

source_name: submocal tissue, immediately after ESD procedure


title: acetic acid day2 root replicate 2

description: Biological replicate 2 of 3. Acetic acid-treated seedling root, harvested after 2 days.

value: untreated


title: LC-DTR Croton oil rep2


title: acetic acid day2 root replicate 1

description: Biological replicate 1 of 3. Acetic acid-treated seedling root, harvested after 2 days.


title: LC-DTR Croton oil rep1


title: potassium acetate day2 root replicate 1

description: Biological replicate 1 of 3. Potassium acetate-treated seedling root, harvested after 2 days.


title: LC-DTR Control rep3

value: vehicle


title: C3


title: C1


title: C2


title: FFPE from progressive MIBC (B1684b)

value: progressive MIBC


title: FFPE from progressive MIBC (B1683b)

value: Bladder, FFPE


title: LC-DTR Control rep1


title: LC-DTR Control rep2


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pJM963 replicate 3

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

data_processing:
Library strategy: HydEn-seq
All reads were trimmed for quality and adaptor sequence with cutadapt 1.2.1 (-m 15 -q 10–match-read-wildcards). Pairs with one or both reads shorter than 15 nt were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligonucleotides used in the preparation of these libraries using Bowtie 0.12.8 (DOI: 10.1186/gb-2009-10-3-r25) and the flags -m1 -v2. All pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the sacCer3 S. cerevisiae UCSC reference genome (-m1 -v2 -X10000–best). Single-end alignments were then performed with mate 1 of all unaligned pairs with the flags -m1 -v2.
Genome_build: Escherichia_coli_K_12_DH10B_NCBI_2008-03-17
Supplementary_files_format_and_content: bed: tab-separated bedgraph file format. Column one holds the chromosome name, column two and three hold the nucleotide position, column four holds the read count.

organism: Escherichia coli

source_name: culture

growth_protocol: Cells were streaked out from frozen stocks on LB agar plates containing kanamycin (50μg/ml), spectinomycin (25μg/ml), and zeocin (25μg/ml). 4-6 colonies were diluted in 2-3 ml LB media containing antibiotics and incubated at 37°C overnight. The overnight culture was then diluted 1:X into 25 ml LB media containing antibiotics. Where noted, ciprofloxacin was added to the media to a final concentration of 30 ng/ml. Cells were grown 2-3 hours to reach exponential growth (OD600=0.4-0.6) and then centrifuged to harvest the cell pellet. The saved pellet was used for DNA extraction. For spot survival assays, the bacterial cells were cultured overnight in LB medium containing kanamycin (50μg/ml), spectinomycin (25μg/ml), and zeocin (25μg/ml).  For all strains, a series of serial dilutions were prepared. Then, 10 µl of the suspension was spotted on LB agar plates with overnight incubation at 37°C. For ciprofloxacin experiments, the plates contained 30 ng/ml ciprofloxacin.

extract_protocol:
DNA was extracted using MasterPure™ Complete DNA and RNA Purification Kit (Lucigen, Epicentre, MC85200) and its concentration was measured using Qubit® dsDNA BR Assay Kit (Life technologies, molecular probes, Q32853).
1 µg extracted DNA was mixed with 0.3 M KOH and incubated at 55°C for 2 hours. After ethanol precipitation, the pellet was dissolved in 20 µl elution buffer (Qiagen, 1014609). DNA was denatured by 3 min incubation at 85°C. In the phosphorylation step, 5'-OH end generated after KOH hydrolysis at the ribonucleotide site was phosphorylated using a mix of 10 U 3'-phosphatase minus T4 polynucleotide kinase (BioLabs, M0236L), 2.5 µl of 10X reaction buffer (BioLabs, B0201S), and 2.5 µl of 10 mM adenosine 5'-triphosphate (BioLabs, P0756S) in a total volume of 25 µl. After 30 min incubation at 37°C, the reaction was stopped by 20 min incubation at 65°C. The samples were bead-washed using CleanPCR kit (GC biotech, CPCR-0050). In the ligation step, ARC140 adaptor was ligated to the 5'-OP. Denatured DNA was ligated using a mix of 10 U T4 RNA Ligase 1 (ssRNA Ligase) (BioLabs, M0204S), 5 µl of 10X reaction buffer (BioLabs, B0216S), 0.5 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 25 µl PEG8000(50%), 5 µl of 10 mM [Co(NH3)6]Cl3, and 0.5 µl of 100 µM oligo ARC140 in a total volume of 50 µl. After overnight incubation at the room temperature, the samples were twice beads-washed and dissolved in 14 µl elution buffer. In second strand synthesis step, denatured DNA was polymerized at the room temperature for 5 min using a mix of 4 U T7 DNA polymerase (unmodified) (BioLabs, M0274L), 2 µl of 10X reaction buffer (BioLabs, B0274A), 2 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 0.8 µl of BSA (1 mg/ml) (BioLabs, B9000S), and a heterodimer oligo, ARC76/77 in a total volume of 20 µl. After beads-wash and elution, the libraries were amplified by PCR reactions using KAPA HiFi hotstart readymix (2X) kit (KAPA biosystems, KK2602, 07958935001) with PCR parameters as follows: 95 °C for 45 s, followed by 18 cycles at 95 °C for 15 s, 65 °C for 30 s, and 72 °C for 30 s. The amplified libraries were beads-washed and eluted in 20 µl TE. The library concentration was measured using Qubit® dsDNA HS Assay Kit (Life technologies, molecular probes, Q32854). The library quality was checked by the Agilent 2100 bioanalyzer system (Agilent Technologies). Illumina NextSeq 500 system was used for paired-end sequencing.


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pJM963 replicate 4


title: FFPE from progressive MIBC (B1682b)


title: control day2 root replicate 2

description: Biological replicate 2 of 3. Control seedling root, harvested after 2 days.

source_name: rice mock-treated seedling root day 2

value: mock-treated day 2


title: control day2 root replicate 3

description: Biological replicate 3 of 3. Control seedling root, harvested after 2 days.


title: potassium acetate day4 shoot replicate 3

description: Biological replicate 3 of 3. Potassium acetate-treated seedling shoot, harvested after 4 days.

source_name: potassium acetate-treated rice seedling shoot day 4

value: shoot

value: potassium acetate-treated day 4

source_name: rice reference non-treated seedling shoot


title: iKO3

city: Hong Kong

first: Shaopu

last: Zhou

address: Room 6202D, Academic Building, HKUST, Clear Water Bay

department: Life Science

institute: HKUST

data_processing:
fastq files were generated on basespace
Low quality reads and adaptor sequences were trimmed from the raw reads file using Trim Galore.
Trimmed sequencing reads were mapped to the mouse mm10 genome assembly using the STAR RNA-seq aligner
Gene count table was generated using featureCounts from Subread package with following parameters: -p -t exon  -g gene_id
Differential analysis was done using DEseq2 package in R.
Genome_build: mm10 (Mus musculus)
Supplementary_files_format_and_content: tab-delimited text file containing raw counts for each sample
Supplementary_files_format_and_content: tab-delimited text file containing fpkm values for each sample

source_name: MuSC

extract_protocol:
RNA extraction was done with NucleoSpin® RNA XS kit from Macherey-Nagel
cDNA reverse transcription was done according to Smart-Seq2 protocol. Amplifed cDNAs were then sonicated using a Covaris ultrasonicator.The NuGEN Ovation Ultrallow System V2 was used for adaptor ligation and amplification of sequencing library.

treatment_protocol: Lower hindlimb muscles were injured with 30μl cardiotoxin (CTX). 24 hours later, YFP positive muscle stem cells were sorted by flow cytometry and subjected to RNA isolation.


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pJM963 replicate 2


title: control day2 root replicate 1

description: Biological replicate 1 of 3. Control seedling root, harvested after 2 days.

value: root


title: FFPE from progressive MIBC (B668)


title: FFPE from progressive MIBC (B336)


title: potassium acetate day4 shoot replicate 2

description: Biological replicate 2 of 3. Potassium acetate-treated seedling shoot, harvested after 4 days.


title: iKO2


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pRW134 replicate 4


title: FFPE from progressive MIBC (B155)


title: iKO1


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pRW134 replicate 3


title: acetic acid day4 shoot replicate 4

description: Biological replicate 3 of 3. Acetic acid-treated seedling shoot, harvested after 4 days.

source_name: acetic acid-treated rice seedling shoot day 4

value: acetic acid-treated day 4


title: potassium acetate day4 shoot replicate 1

description: Biological replicate 1 of 3. Potassium acetate-treated seedling shoot, harvested after 4 days.


title: FFPE from de novo MIBC (B1196)


title: Ctrl3


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pRW134 replicate 2


title: Ctrl2


title: FFPE from progressive MIBC (B1681b)


title: acetic acid day4 shoot replicate 2

description: Biological replicate 1 of 3. Acetic acid-treated seedling shoot, harvested after 4 days.


title: FFPE from de novo MIBC (B1197)


title: FFPE from de novo MIBC (B1193)


title: FFPE from de novo MIBC (B1218)


title: control day4 shoot replicate 3

description: Biological replicate 3 of 3. Control seedling shoot, harvested after 4 days.

source_name: rice mock-treated seedling shoot day 4

value: mock-treated day 4


title: acetic acid day4 shoot replicate 3

description: Biological replicate 2 of 3. Acetic acid-treated seedling shoot, harvested after 4 days.

value: Nipponbare


title: Ctrl1


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782 ::kan with pJM963 replicate 3


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782 ::kan with pJM963 replicate 2


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pRW134 - replicate 4


title: CL_48

first: Camila

last: Farias Amorim

state: United States

address: 380 S University Ave

department: Pathobiology

institute: University of Pennsylvania

description: cutaneous

data_processing:
Raw reads from fastq files were mapped to the human reference transcriptome (Ensembl; Homo sapiens version 86) using Kallisto, version 0.44.0
All subsequent analyses were carried out using the statistical computing environment, R version 3.5.1 in RStudio version 1.1.456 and Bioconductor, version 3.8
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Data was normalized using the TMM method in EdgeR
Normalized data was variance stabilized using the VOOM function in limma
Differentially expressed genes (FC>2 and FDR<.01) were identified on filtered-normalized, not batch-corrected gene expression matrix by linear modeling and Bayesian statistics using the Limma package, using the batch as factor for interception.
Genome_build: Ensembl; Homo sapiens version 86, GRCh38 Release 97
Supplementary_files_format_and_content: raw data file format and content: Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary_files_format_and_content: normalized data file format and content: Tab-delimited text filtered normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method) and batch correction with Combat() function from the sva R package
Supplementary_files_format_and_content: study design: Comma-separated values file with study design including healthy subjects and cutaneous leishmaniasis patients clinical metadata

source_name: cutaneous

growth_protocol: Before treatment, 3 ml of peripheral blood was collected from CL patients and 14 endemic non-L. braziliensis infected controls (healthy subjects, HS) in Corte de Pedra, Bahia, Brazil, and were stored in Tempus Tubes (Applied Biosystems) at -20oC

extract_protocol:
Frozen blood samples were shipped to the University of Pennsylvania, where RNA extraction, cDNA library preparation, and RNA sequencing were performed.  RNA was extracted using the Tempus Spin RNA Isolation Reagent Kit (Applied Biosystems)
Whole-transcriptome sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina) and sequenced on an Illumina NextSeq 500 to produce 75 bp paired-end reads
RNA quality and quantification were assessed using a Tapestation 4200 (Agilent) and Qubit 3 (Invitrogen)

tag: Sex

value: M

value: Cure

value: neg

value: no

tag: dth


title: CL_49

description: cutaneous

value: F


title: CL_50

description: cutaneous

value: Failure

value: yes

value: cutaneous


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782 ::kan with pJM963 replicate 4


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pRW134 - replicate 3


title: control day4 shoot replicate 2

description: Biological replicate 2 of 3. Control seedling shoot, harvested after 4 days.

value: 2 weeks

value: untreated


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pRW134 - replicate 2


title: FFPE from de novo MIBC (B643)

value: de novo MIBC

value: Bladder, FFPE


title: FFPE from de novo MIBC (B897)


title: CL_46

description: cutaneous


title: B18_219

city: Irvine

first: Zeba

middle: A

last: Wunderlich

state: CA

address: 4432 Natural Science II

department: Developmental and Cell Bio

institute: University of California Irvine

data_processing:
trimming and filtering: trimmomatic 0.35 with the following settings ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:6 SLIDINGWINDOW:4:15 MINLEN:30
Pseudoaligning and quantifying: Reads were Pseudo aligned tp the Iso1 DM6 transcriptome  using Salmon Aligner 0.12.0 using the quant functionality to generate Count data with the settings:  -l A --validateMappings
Assigning alleles
Aligning and quantifying allelic reads :Alleleic Reads were Pseudo aligned to either the A4 or the B6 transcriptome using Salmon Aligner 0.12.0 using the quant functionality to generate count data , with the settings:  -l A --validateMappings
Gene Summaries: Transcript level count  data was summarized to gene-level In R, using Tximport 1.12.3. These count data for all samples alligned to ISO-1, and parsed allelic reads aligned  to either A4 or B6, and  unparsed Reads aligned to either A4 or B6 where combined into a single DataMatrix in R.
Genome_build: dm6, Dmel_A4_1.0, ASM339711v2
Supplementary_files_format_and_content: Count matrix with rows of gene names and columns of samples either aligned to Iso 1, or allele-called reads alligned to the appropriate Genome with "g1" designating A4 alignment and "g2" representing B6, sample names with neither the "iso1", "g1" or "g2" indicators are unparsed homozygous samples aligned to thier corresponding genome (see meta data)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: 25˚C on standard yeast-cornmeal fly food

extract_protocol:
Samples where brought to room temperature for 5 minutes and then homogenized, centrifuged for 10 minutes at 4˚C and supernatant mixed with equal parts 100% ethanol. mRNA was then purified from Trizol reagent using Zymo dirct-zol RNA extraction protocol.
Libraries where prepared using the modified SmartSeq2 protocol outlined in "Adapting trhe SmartSeq2 Protocol for Robust Single Worm RNA-seq". Libraries were then barcoded using Illumina/Nextera i5 common adapterand i7 index adapters

treatment_protocol: Microinjection of ~10000 CFUs of bacteria. dissection of fat body 3 hours post infection, (with three fat bodies collected per sample) and store in trizol and stored at -80˚C for extraction

value: Serratia marcescens infection

tag: paternal genotype

tag: maternal genotype

tag: extraction batch

tag: generation


title: B19_083

tag: treatment


title: Weedy_2011_Rep2

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

description: Read 2 file for this sample was corrupt and could not be uploaded to SRA.

data_processing:
Raw sequence reads were checked for quality using the FastQC0.10.0 program and quality trimmed using the Sickle-quality-base-triming program in the iPlant discovery environment with the parameters minimum quality = 20 and minimum number of bases = 70.
The Tuxedo Suite (Tophat 1.0, Cufflinks 1.0 and Cuffdiff 1.0 for Single End reads) were used to map the quality trimmed sequences to the Glycine Max genome (Phytozome 9.0) in the iPlant archive (for only the first paired end reads since the quality of the second end was significantly less good).
The resulting FPKM values from the Cufflinks output files (genes.fpkm_tracking) were placed in a single file and those that matched known soybean gene models were kept.
FPKM values were log transformed (for use in follow-on programs to assess biological relevance).
Genome_build: Glycine Max genome (Phytozome 9.0)
Supplementary_files_format_and_content: Data table containing gene model, Protien name as indicated by most similar arabidopsis annotation, Most similar arabidopsis gene model name based on Phytozome 9.0 gene model annotation, Log2 transformed FPKM (fragments per kilobase per million reads) vales for indicated library, Average log ratio of the expression (weedy minus control) for the indicated year, P value as generated by CuffDiff program for weedy verses control from the two samples collected from indicated year Q value as generated by CuffDiff program for weedy verses control from the two samples collected from indicated year, and Functional annotation assigned to the gene model based on the Phytozome 9.0 database.

organism: Glycine max

source_name: Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot

growth_protocol: Soybean were grown to the V3 stage in field conditions near Brookings SDl. Soil consistes of loess over glacial outwash, and the soil series is Brandt silty clay loam.

extract_protocol:
RNA extraction was performed by grinding approximately 0.1 grams of frozen tissue in liquid nitrogen to a fine powder, and adding 1 ml Trizol reagent (Ambion/Life Technologies). Chloroform:Isoamyl (24:1) was added to the Trizol/tissue mixture, centrifuged, and RNA was extracted from the resulting supernatant using an RNeasy Plant Mini kit (Qiagen). Quality control was assessed using a nanodrop bioanalyzer on the RNA setting.
cDNA libraries were created following the Illumina TruSeq RNA Sample Preparation kit (Illumina). In short, 4000 ng of RNA was purified and fragmented into mRNA, followed by first and second strand cDNA synthesis. End repair and adenylation of 3’ ends preceded adapter ligation and PCR amplification. Library quality was assessed using an Agilent Bioanalyzer, and quantified for pooling by qRT-PCR using the PhiX Control Kit v2 according to manufacturer specifications. Libraries were paired-end sequenced on an Illumina HiSeq2000.

treatment_protocol: plants were either grown with various weeds (see "Weedy" treatment conditions in metaflie) or under weed free conditions (see "Control" conditions in metafile)

value: "Weedy" with weeds being naturally occurring velvetleaf and weedy common sunflower (Helianthus annuus) at denisties of about 160 m-2

tag: cummulative precipitation at sampling

tag: temperature at sampling

tag: r1.fastq spacing

value: R1.fastq (18 cm)

tag: sampling date


title: FFPE from de novo MIBC (B1192)

tag: tissue


title: B18_210


title: Weedy_2011_Rep1

tag: cultivar

value: R1.fastq (76 cm)


title: potassium acetate day2 shoot replicate 2

description: Biological replicate 2 of 3. Potassium acetate-treated seedling shoot, harvested after 2 days.

source_name: potassium acetate-treated rice seedling shoot day 2

value: shoot

value: potassium acetate-treated day 2

value: Nipponbare

tag: age


title: FFPE from de novo MIBC (B1216)

source_name: Bladder, FFPE


title: control day4 shoot replicate 1

description: Biological replicate 1 of 3. Control seedling shoot, harvested after 4 days.

value: mock-treated day 4


title: potassium acetate day2 shoot replicate 1

description: Biological replicate 1 of 3. Potassium acetate-treated seedling shoot, harvested after 2 days.


title: FFPE from de novo MIBC (B1202)


title: FFPE from de novo MIBC (B778)


title: Weedy_2010_Rep2

value: "Weedy" with weeds being flax at denisties of about 600 m-2


title: B18_204


title: B19_074


title: potassium acetate day2 shoot replicate 3

description: Biological replicate 3 of 3. Potassium acetate-treated seedling shoot, harvested after 2 days.


title: acetic acid day2 shoot replicate 4

description: Biological replicate 3 of 3. Acetic acid-treated seedling shoot, harvested after 2 days.

source_name: acetic acid-treated rice seedling shoot day 2

value: acetic acid-treated day 2


title: Weedy_2010_Rep1


title: CL_45

description: cutaneous

value: F

value: Failure

value: neg

value: no


title: CL_44

description: cutaneous


title: CL_43

description: cutaneous

value: Cure


title: acetic acid day2 shoot replicate 2

description: Biological replicate 2 of 3. Acetic acid-treated seedling shoot, harvested after 2 days.

value: 2 weeks

value: untreated


title: Weedy_2009_Rep1

value: "Weedy" with weeds being a natural population of velvetleaf and buckwheat at denisties of about 48 m-2


title: CL_42

description: cutaneous


title: acetic acid day2 shoot replicate 1

description: Biological replicate 1 of 3. Acetic acid-treated seedling shoot, harvested after 2 days.


title: CL_41

description: cutaneous


title: B18_228

value: Serratia marcescens infection


title: Weedy_2008_Rep1

value: "Weedy" with weeds being a natural population of velvetleaf and buckwheat at denisties of about 300 m-2


title: B18_202


title: control_2011_Rep2

value: "Control" with weeds controlled by application of Roundup Weather Max (glyphosate), Dual II Magnum (s-metolachlor), Poast (sethoxydim), and Pursuit (imazethapyr) were used at suggested rates and times.

value: R1.fastq (18 cm)