title: 1001703001_C18

description: mRNA + vRNA


title: Serum cfRNA - 65yo male

status: Public on Feb 25 2020

type: SRA

city: Cincinnati

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

country: USA

institute: University of Cincinnati College of Medicine

description:
small non-coding RNA
M65_Serum_cfRNA

library_source: transcriptomic

data_processing:
Base calling software: bcl2fastq 2.19
Preprocessing: Demultiplexed samples were pre-processed with standard protocol following best practices (adaptor removal, quality accessing, removal of low quality reads)
Alignment: Reads were aligned to the reference human genome (GRCh38/hg38) using STAR aligner
Counts: Small ncRNA (miRNA, misc_RNA, scRNA, snRNA, snoRNA, sRNA, scaRNA) were quantified based on the M16 release of GENCODE via RNA-Seq by Expectation Maximization (RSEM) using the RSEM package.
Normalized abundance measures: RPKM
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: The processed data file is in Excel format and contains a table of normalized abundance (RPKM) data for small ncRNA transcripts (rows) by sample (columns)

molecule: total RNA

organism: Homo sapiens

source_name: Serum cell-free RNA

extract_protocol:
cfRNA was purified using the Direct-zol RNA micro prep kit (Zymo Research, Irvine, CA) according to the manufacturers suggested protocol for biological fluids
NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA) was used with ~5 ng of total RNA determined by Bioanalyzer RNA 6000 Pico Kit (Agilent, Santa Clara, CA) in a 5 µL solution as input, following the manufacturer’s suggested protocol excepting a modification of library size selection to increase small RNA detection sensitivity and specificity. After 15 cycles of PCR for indexing and library enrichment, an equal-volume of 10 ml PCR mix (library without size selection) per sample together with the same volume of the negative control were pooled, followed by DNA cleanup using DNA Clean & Concentrator (Zymo Research, Irvine, CA) and mixed with 135 and 319 bp custom-made ladders targeting the library 16 – 200 nt small RNA cDNA insert. Next, precise size selection of the 135-319 bp library via 2.75% agarose gel electrophoresis was performed, library concentration was measured by qPCR using the NEBNext Library Quant Kit (New England BioLabs) on a QuantStudio 5 Real-Time PCR System (Thermo Fisher Scientific).

tag: age (years)

tag: Sex

value: Male

tag: tissue

value: serum

tag: tissue compartment

value: cell free RNA


title: JurkatMK1000R

city: Aurora

first: Etienne

last: Danis

state: CO

institute: University of Colorado, Denver - Anschutz Medical Campus

description: Jurkat cells resistant to AZD1775 treated with AZD1775 (1000 nM)

data_processing:
Sequencing reads were trimmed using BBDuk from BBTools
Trimmed reads were aligned with STAR
Bam files were further filtered for uniquely mapped reads and 50M reads were randomly extracted from each bam file using samtools view
The matrix with the read counts for each transcript was generated using summarizeOverlaps() from the R package GenomicAlignments
Genome_build: hg38

source_name: Blood

extract_protocol:
Total RNA was extracted using a RNeasy kit (Qiagen Inc., Valencia, CA)
DNA libraries were constructed for each sample using the TruSeq Stranded RNA kit (Illumina Inc., San Diego, CA) according to the manufacturer’s protocol.

treatment_protocol: Cells were treated for 24 hours with control or with AZD1775 (MK-1775) at 1000 nM

tag: cell line

value: Jurkat cells

tag: phenotype

value: resistant to AZD1775

tag: treatment

value: treated with AZD1775 (1000 nM)


title: Jurkat_naive

description: Jurkat cells sensitive to AZD1775 treated with AZD1775 (1000 nM)

value: sensitive to AZD1775


title: C8_H011

type: RNA

city: Missouri City

first: Jun

last: Wang

address: 6770 Bertner Ave.

institute: Texas Heart Institute

description: RNA passed QC. NO genomic DNA was spoted.

hyb_protocol: Phalanx Method

scan_protocol: Phalanx Biotech mouse OneArray Microarray v2

data_processing: Agilent Extended Dynamic Range. Internally validated metrics for hybridization efficiency using control microarray probes

organism: Mus musculus

source_name: E11.5  embryonic heart, wild type

label_protocol: Cy-dye coupling to aa-dUTP, Internally validated thresholds for labeling efficiency measured with NanoDrop

extract_protocol: Trizol was used to purify total RNA from embryonic hearts, NanoDrop QC (260/230 > 1.5, 260/280 > 1.8)

value: embronic heart


title: 1001703001_C1

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

description: mRNA + vRNA

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

source_name: U87 cells

extract_protocol:
no extraction
viscRNA-Seq
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

treatment_protocol: Infection with VEEV TC-83

tag: moi

tag: hours post infection

tag: plate

tag: well


title: C8_H012


title: Serum cfRNA - 63yo female

description:
small non-coding RNA
D63_Serum_cfRNA

value: Female


title: Serum cfRNA - 39yo female

description:
small non-coding RNA
F39_Serum_cfRNA


title: 1001703001_C15

description: mRNA + vRNA


title: Reh_naive

description: REH cells sensitive to AZD1775 treated with AZD1775 (1000 nM)

value: REH cells


title: Serum cfRNA - 40yo male

description:
small non-coding RNA
M40_Serum_cfRNA


title: 1001703001_B9

description: mRNA + vRNA


title: M13MK1000R

description: Molm13 cells resistant to AZD1775 treated with AZD1775 (1000 nM)

value: Molm13 cells


title: 1001703001_B8

description: mRNA + vRNA


title: C7_H009


title: APC_CTRL_atacseq_REP2

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

library_source: genomic

data_processing:
Raw sequencing reads were filtered for low-quality after adapter removal and aligned on GRCh38 using Bowtie2  with default mapping parameters
PCR duplicates were removed using Picard. The mapped reads of all replicates were merged for each condition prior to peak calling. Peaks were called on each sample using MACS2 with “--nomodel --shift -100 --extsize 200”, to obtain a consensus peak set for each sample. The peak set was used to build a count matrix using the aligned reads for all samples and their replicates.
Differential peaks between sample groups were identified using edgeR. For this, the count matrix was filtered for peaks with low coverage across all samples based on minimum read count of 10 for each sample. The remaining counts were normalized using the total library size as well as edgeR’s TMM derived normalization factors.
Between two sample groups, only regions with a log fold change above > 0.5 and an FDR value < 0.05 were considered as differentially accessible for further analysis. The peaks were annotated using HOMER
Genome_build: GRCh38

molecule: genomic DNA

growth_protocol: Culture medium of Human Intestinal Organoids contained Advanced DMEM/F12 supplemented with 10 mM HEPES, 1x Glutamax, 1% Penicillin/Streptomycin, 1x N2, 1x B27, 1.25 mM N-acetylcysteine, 50% WNT3A-conditioned medium (CM), 20% RSPO1-CM 20%, 10% NOGGIN-CM (all CM produced in-house), 10 mM Nicotinamide, 50 ng/ml human EGF, 10 nM Gastrin, 0.5 µM TGFß type I receptor inhibitor A83-01 and 10 µM p38-inhibitor SB202190

extract_protocol:
Lysis buffer
For ATAC-Seq with hSI organoids, organoids were dissociated into single cells and 50,000 cells were lysed in 50 µl cold Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 500 g for 10 min at 4˚C, cells were resuspended in 1X transposition mix (Illumina; 25 µl Tagment DNA Buffer, 2.5 µl Tagment DNA Enzyme, 22.5 µl ddH2O) and incubated for 30 min at 37˚C on a shaker at 300 rpm. Immediately after the transposition reaction, DNA was purified using the QIAgen MinElute PCR Purification Kit according to the manufacturer’s instructions. Library was amplified with Nextera Sequencing primers in NEBNext Q5 Hot Start HiFi 2X PCR master mix for 5 cycles. To remove large DNA fragments, the PCR reaction was incubated with 0.55X AMPure XP beads (Beckman Coulter) and the unbound supernatant was subsequently purified with QIAgen MinElute coloumns. Again, DNA was amplified with Nextera Sequencing primers in NEBNext Q5 Hot Start HiFi 2X PCR master mix for 9 cycles. Finally, to remove primers and small DNA fragments, PCR reaction was bead-purified with 1.8X AMPure XP beads.

treatment_protocol: For TGF-pathway activation, organoids were cultured without A83-01 and in 10 ng/ml recombinant TGFB1

tag: cell type

value: organoids

value: Human small intestine

tag: genotype

value: APC-KO


title: APC_CTRL_atacseq_REP1


title: C7_H008


title: M13_naive

description: Molm13 cells sensitive to AZD1775 treated with AZD1775 (1000 nM)


title: Serum sEV - 65yo male

description:
small non-coding RNA
M65_Serum_sEV

source_name: Serum small extracellular vesicles

extract_protocol:
Total RNA was extracted from sEV isolates using the miRNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s suggested protocol
NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA) was used with ~5 ng of total RNA determined by Bioanalyzer RNA 6000 Pico Kit (Agilent, Santa Clara, CA) in a 5 µL solution as input, following the manufacturer’s suggested protocol excepting a modification of library size selection to increase small RNA detection sensitivity and specificity. After 15 cycles of PCR for indexing and library enrichment, an equal-volume of 10 ml PCR mix (library without size selection) per sample together with the same volume of the negative control were pooled, followed by DNA cleanup using DNA Clean & Concentrator (Zymo Research, Irvine, CA) and mixed with 135 and 319 bp custom-made ladders targeting the library 16 – 200 nt small RNA cDNA insert. Next, precise size selection of the 135-319 bp library via 2.75% agarose gel electrophoresis was performed, library concentration was measured by qPCR using the NEBNext Library Quant Kit (New England BioLabs) on a QuantStudio 5 Real-Time PCR System (Thermo Fisher Scientific).

value: small extracellular vesicles


title: 1001703001_B7

description: mRNA + vRNA


title: RehMK1000R

description: REH cells resistant to AZD1775 treated with AZD1775 (1000 nM)


title: Serum sEV - 63yo female

description:
small non-coding RNA
F63_Serum_sEV


title: C7_H007


title: Urine sEV - 63yo female

description:
small non-coding RNA
F63_Urine_sEV

source_name: Urinary small extracellular vesicles

value: urine


title: 1001703001_B6

description: mRNA + vRNA


title: 1001703001_B4

description: mRNA + vRNA


title: 1001703001_B3

description: mRNA + vRNA


title: C8_H010


title: Urine sEV - 65yo male

description:
small non-coding RNA
M65_Urine_sEV


title: M5_H005

source_name: E11.5 embryonic heart, YY2-overexpression


title: M1_H003


title: Serum sEV - 39yo female

description:
small non-coding RNA
F39_Serum_sEV


title: M5_H004


title: Serum sEV - 40yo male

description:
small non-coding RNA
M40_Serum_sEV


title: Saliva sEV - 65yo male

description:
small non-coding RNA
M65_Saliva_sEV

source_name: Salivary small extracellular vesicles

value: saliva


title: M1_H001


title: Saliva sEV - 63yo female

description:
small non-coding RNA
F63_Saliva_sEV


title: 1001703001_B5

description: mRNA + vRNA


title: M1_H002


title: 1001703001_B22

description: mRNA + vRNA


title: Urine sEV - 40yo male

description:
small non-coding RNA
M40_Urine_sEV

value: Male


title: 1001703001_B20

description: mRNA + vRNA


title: Urine sEV - 39yo female

description:
small non-coding RNA
F39_Urine_sEV


title: 1001703001_B2

description: mRNA + vRNA


title: Saliva sEV - 39yo female

description:
small non-coding RNA
F39_Saliva_sEV


title: Saliva sEV - 40yo male

description:
small non-coding RNA
M40_Saliva_sEV


title: 1001703001_B19

description: mRNA + vRNA


title: 1001703001_B24

description: mRNA + vRNA


title: 1001703001_B18

description: mRNA + vRNA


title: 1001703001_B23

description: mRNA + vRNA


title: 1001703001_B17

description: mRNA + vRNA


title: N2_3 (WT_LPS)

city: Zunyi

first: HUIZI

last: CHEN

state: GuiZhou

address: Honghuagang District

department: Zunyi Medical University

country: China

institute: Zunyi Medical University

data_processing:
Reads were mapped to the mm8 genome with hissat2
The number of reads mapped to each Ensembl gene was counted HTSeq
Genome_build: mm8
Supplementary_files_format_and_content: Supplementary_files_format_and_content: txt, Reads count for each gene in each sample.

source_name: Macrophages

extract_protocol:
Total RNA of  macrophages (from WT or miR_7 deficiency mice) stimulated with 100 ng/mL LPS for 12 hrs or left unstimulated was purified using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone Marrow_Derived Macrophage

tag: age

value: 8-10 weeks

tag: strain

value: wild type

tag: stimulation

value: LPS


title: 1-NC

city: Guangzhou

first: Yiming

last: Zhang

address: No.253 Gongyedadao middle Road, Haizhu district

institute: Zhujiang Hospital

description: Gene expression data from normal LNCAP cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on PrimeView™ Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

source_name: Normal LNCAP cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: LNCAP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serumat 37°C with 5% CO2.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: LNCAP cells were treated with PC-3 exosomes while the control group was treated with PBS.

tag: agent

value: LNCAP


title: N2_5 (miR_7def)

value: miR_7 deficiency

value: unstimulated


title: N2_2 (WT)


title: 2-NC


title: 1001703001_B21

description: mRNA + vRNA


title: 1-EXO

description: Gene expression data from LNCAP cells treated with PC-3 exosomes

source_name: LNCAP cells treated with PC-3 exosomes

value: PC-3 exosomes


title: 1001703001_B16

description: mRNA + vRNA


title: 2-EXO


title: Line 16.7 vs WT7

city: Valencia

first: Eduardo

last: Bueso

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: IBMCP

country: Spain

institute: Universitat Politècnica de València

description: three independent replicates of wild type and two overexpressing subtilase4.13 lines were compared. We used seedlings of 10 days old.

hyb_protocol: Fragmented aa‐aRNA was used directly in the hybridization mix, which contains 50 μl deionized formamide (Sigma), 30 μl 20 × SSC, 5 μl 100 × Denhardt’s solution (Sigma) and 5 μl 10% SDS in a final volume of 100 μl. The hybridization mixture was denatured at 95°C for 5 min, spun briefly and applied by capillary between a pre‐treated slide (see above) and a 60 × 42 mm coverslip LifterSlip (Erie Scientific). Slides were incubated overnight at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, TeleChem). The next morning, slides were washed sequentially once in 1 × SSC 0.1% SDS 5 min at 30°C; once in 0.2 × SSC 0.1% SDS 5 min at 30°C; twice in 0.1 × SSC 2 min each at 30°C; and finally 0.01 × SSC 10 sec at 25°C. Slides were dried by centrifugation at 1500g for 1 min at room temperature.

scan_protocol: Hybridized microarray slides were scanned at 532 nm for Cy3 and 635 nm for Cy5, with a GenePix 4000B scanner (Axon Molecular Devices, http://www.moleculardevices.com), at 10 nm resolution and 100% laser power. Photomultiplier tube voltages were adjusted manually to equal the overall signal intensity for each channel, to increase the signal‐ to‐noise ratio, and to reduce the number of spots with saturated pixels.

data_processing: Spot intensities were quantified using genepix pro 6.0 microarray‐analysis software (Axon Molecular Devices). Data were normalized by mean global intensity and with lowess (locally weighted scatter plot) correction (Yang et al., 2001) with genepix pro 6.0 and acuity 4.0 software (Axon Molecular Devices), respectively.

organism: Arabidopsis thaliana

source_name: 10 days old seedling grown in MS plates in long days condition

label_protocol: Amplification reaction using the MessageAmp II aRNA Amplification kit (Ambion, http://www.ambion.com/), basically as described by the manufacturer. 5‐(3‐aminoallyl)‐UTP (aa‐UTP) (Ambion), was incorporated into the amplified RNA (aRNA) in the amplification reaction and at ratio 1:1 with UTP. After purification 7.5 μg of aminoallyl‐aRNA (aa‐aRNA) was used in a coupling eaction with either fluorescent Cy3 or Cy5 as reactive N‐hydroxyl succinimidal dyes (NHS‐dyes) (Amersham Pharmacia Biotech, http://www5.amershambiosciences.com/).

growth_protocol: mutant seedlings overexpressing subtilase4.13 and wild type seedlings were grown in MS medium during 10 days at 16 h light and 8 h darkness

extract_protocol: Total RNA isolation using QIAGEN Plant RNEasy kit with on column DNAse digestion.

treatment_protocol: no treatment was done

value: seedling

value: overexpressing subtilase4.13

tag: line id

value: Line 16.7

value: WT


title: 1001703001_B15

description: mRNA + vRNA


title: N2_6 (miR_7def_LPS)


title: M5_H006

value: embronic heart


title: 1001703001_B13

description: mRNA + vRNA


title: 1001703001_B11

description: mRNA + vRNA


title: 1001703001_B12

description: mRNA + vRNA


title: Line 5.4 vs WT4

value: Line 5.4


title: Line 5.7 vs WT 7

value: Line 5.7


title: 1001703001_B10

description: mRNA + vRNA


title: 1001703001_A9

description: mRNA + vRNA


title: 1001703001_B1

description: mRNA + vRNA


title: line 16.3 vs WT3

value: Line 16.3

value: WT 3


title: Swarna_Drought_Panicle-3

city: Los Banos

first: Jeshurun Asher

middle: Marayag

last: Tarun

state: Laguna

address: Pili Drive

department: Plant Breeding

country: Philippines

institute: International Rice Research Institute

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18). The BCL (base calls) binary is converted into FASTQ utilizing Illumina package bcl2fastq (v1.8.4).
The raw fasta reads were filtered using trimmomatic (RRID: SCR_011848; http://www.usadellab.org/cms/index.php?page=trimmomatic) with mostly default settings (ILLUMINACLIP:./TruSeq3-PE-2.fa:2:30:15 TRAILING:28 LEADING:28 MINLEN:30).
A transcriptome fasta file of the rice japonica genome fasta file and gff3 annotations downloaded from RGAP (MSUv.7) was made using the gffread function under Cufflinks (version 2.2.1) software.
Using the converted transcriptome fasta file, the Salmon software (version 0.7.2) indexed the transcriptome (Patro et al., 2017).
We then used Salmon to quantify transcript abundance in quassi-mapping mode directly using the indexed transcriptome, and the trimmed high-quality paired-end reads. The parameters -l A, -seqBias and -gcBias was provided to allow Salmon to automatically infer library type, to enable Salmon to learn and correct for sequence-specific and fragment-level GC content biases, respectively. Gene expression levels were then normalized using the transcripts per million mapped reads (TPM) method.
The estimated transcript abundance from Salmon was imported and aggregated to the gene level using the Bioconductor package tximport (version 1.2.0) (Soneson et al., 2016) complemented with the reader package (version 1.1.1) through R (version 3.3.3) software. Principal component analysis (PCA) was performed using ggplot2 (version 2.2.1) and gplots package (version 3.0.1) to determine relationships between samples.
DESeq2 software (version 1.14.1) was used in R to identify DEGs in pairwise comparisons (Love et al., 2014). Two series of differential expression (DE) analysis using the contrast argument was performed for the reference assembly approach in flag-leaf and panicle samples. Firstly, the contrasts of the condition effect for each genotype, i.e., IL_D vs IL_C, and SWA_D vs SWA_C. Secondly, the contrasts of the genotypic effect for each condition, i.e., IL_C vs SWA_C and IL_D vs SWA_D. Only genes that have at least ten reads total were used for DE analysis. The pre-filtered raw counts of the panicle datasets were used for the transformation on the log2 scale, which has been normalized concerning library size using vst function in the DESeq2 package. Differentially expressed genes (DEGs) were defined as those presenting an absolute fold change (FC) ≥2 and an adjusted P-value (FDR) ≤ 0.05 in any pairwise comparison.
Genome_build: Rice Genome Annotation version 7
Supplementary_files_format_and_content: csv file in matrix table of the aggregated raw gene counts and csv files (four pairwise comparisons) with genes that passed the adjusted p-value < 0.05 correction without the log2-fold change filtering:
Supplementary_files_format_and_content: Aggregated gene counts_panicle.csv: Raw gene counts of sequencing reads in csv format.
Supplementary_files_format_and_content: ILDroughtvsSwarnaDrought_panicle-gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.
Supplementary_files_format_and_content: ILControlvsSwarnaControl_panicle-gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.
Supplementary_files_format_and_content: SwarnaDroughtvsSwarnaControl_panicle-gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.
Supplementary_files_format_and_content: ILDroughtvsILControl_panicle-gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.

organism: Oryza sativa

source_name: panicle tissue

growth_protocol: A pot experiment was arranged in a randomized complete block design with two treatments (well-watered and 2-weeks drought-stressed), two genotypes, and six replications or pots in a greenhouse at the International Rice Research Institute (Los Banos, Philippines). For reproductive-stage drought stress (RDS), water was withheld at reproductive (R2) stage on discrete morphological criteria as described by Counce et al. (2000) until the soil moisture level progressively dropped to 75% field capacity (FC) and was maintained for nine days, whereas control plants were well-watered. After the 10th day, the FC was brought down and maintained at 50% for three more days. During the drought stress period, the pots were weighed daily, and the difference in weight on subsequent days was corrected by adding water to maintain the required FC. Panicle samples of well-watered and drought-stressed treatments were collected at the R3 stage on the 12th day of RDS and immediately flash-frozen in liquid nitrogen. Four independent biological replicates for each tissue sample were harvested.

extract_protocol:
Panicle tissue under control and drought-stress conditions were removed, flash frozen on dry liquid nitrogen, and total RNA was extracted using TRIzol reagent and isolated using the Qiagen RNeasy Plant Mini Kit (Qiagen, Limburg, Netherlands). The total RNA concentration was quantified using Nanodrop spectrophotometer (ND-1000; Nanodrop Technologies, Wilmington, DE), with absorbance at 260 nm. RNA purity and integrity were examined using an Agilent 2100 BioAnalyzer RNA 6000 Kit (Agilent Technologies). 2 ug of total RNA was submitted and Illumina library preparation and sequencing were completed following the standard protocols of Macrogen INC (Seoul, Korea).
RNA libraries were prepared for sequencing using standard Illumina protocols as per Macrogen Korea specifications.

value: Panicle

tag: developmental stage

value: Reproductive-stage

value: Swarna (recipient parent)

value: Drought-sensitive

value: Drought


title: Swarna_Drought_Panicle-6

tag: tissue


title: Swarna_Drought_Panicle-4


title: Swarna_Control_Panicle-5

value: Control


title: Swarna_Control_Panicle-3


title: 1001703001_A8

description: mRNA + vRNA


title: Swarna_Control_Panicle-2


title: 1001703001_A6

description: mRNA + vRNA


title: 1001703001_A7

description: mRNA + vRNA


title: 1001703001_A5

description: mRNA + vRNA


title: 1001703001_B14

description: mRNA + vRNA


title: line 5.3 vs WT3

value: Line 5.3


title: Swarna_Control_Panicle-1


title: Nil-95_Drought_Panicle-4

value: IL (introgression line)

value: Drought-tolerant


title: 1001703001_A3

description: mRNA + vRNA


title: Nil-95_Drought_Panicle-5


title: 1001703001_A23

description: mRNA + vRNA


title: 1001703001_A24

description: mRNA + vRNA


title: Nil-95_Drought_Panicle-3


title: Swarna_Drought_Panicle-2


title: Nil-95_Control_Panicle-6


title: 1001703001_A4

description: mRNA + vRNA


title: Nil-95_Control_Panicle-5


title: 1001703001_A21

description: mRNA + vRNA


title: 1001703001_A20

description: mRNA + vRNA


title: Nil-95_Control_Panicle-1


title: 1001703001_A2

description: mRNA + vRNA


title: 1001703001_A19

description: mRNA + vRNA


title: Nil-95_Drought_Panicle-2


title: 1001703001_A18

description: mRNA + vRNA


title: 1001703001_A17

description: mRNA + vRNA


title: LM6_CSF_before_rep1

city: Changchun

first: Guozi

last: Yang

state: Jilin

address: No.71 Xinmin Street

department: Radiation-Oncology

institute: The First Hospital of Jilin University

description: Cerebrospinal fluid before initial leptomeningeal metastasis-directed therapy

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 11.5 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cerebrospinal fluid

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: RNA was prepared using the QIAamp Circulating Nucleic Acid Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Cerebrospinal fluid

tag: gender

value: Female

tag: diagnosis

value: leptomeningeal metastasis with lung adenocarcinoma


title: 1001703001_A16

description: mRNA + vRNA


title: LM4_CSF_before_rep1


title: Nil-95_Control_Panicle-3

tag: phenotype


title: LM5_CSF_before_rep1

value: Male


title: LM4_CSF_after_rep1

description: Cerebrospinal fluid after initial leptomeningeal metastasis-directed therapy


title: LM3_CSF_after_rep1


title: Line 16.4 vs WT4

value: seedling

value: overexpressing subtilase4.13

value: Line 16.4

value: WT


title: 1001703001_A22

description: mRNA + vRNA


title: ESCs_cAMP treat with WT1 siRNA_rep1

city: Ube

first: Isao

last: Tamura

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

country: Japan

institute: Yamaguchi University Graduate School of Medicine

description: cAMP treatment with WT1 siRNA

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

source_name: cAMP-treated endometrial stromal cells with WT1 siRNA

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

growth_protocol: ESCs were incubated in Phenol Red-free DMEM containing glutamine, antibiotics, and 10% dextran-coated charcoal-stripped FBS at 37°C, 95% air and 5% CO2.

extract_protocol: Total RNA was isolated from the cultured cells with an RNeasy® Mini Kit.

treatment_protocol: ESCs were transfected with WT1 siRNA and then treated with or without dibutyryl cyclic adenosine monophosphate (cAMP), a decidualization stimulus, for 4 days to induce decidualization

value: human endometrium

value: female


title: ESCs_cAMP treat with control siRNA_rep1

description: cAMP treatment with control siRNA

source_name: cAMP-treated endometrial stromal cells with control siRNA


title: LM6_CSF_after_rep1


title: 1001703001_A14

description: mRNA + vRNA


title: LM5_CSF_after_rep1


title: 1009902915

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

data_processing:
Fastqs are aligned to Toxoplasma gondii GT1 references.
Gene counts are quantified using htseq-count (version 0.10.0) using default parameters. We used GT1 gff3 annotation files.
We filtered samples by read depth
Genome_build: Toxoplasma gondii GT1 (ToxoDB version 36)
Supplementary_files_format_and_content: h5ad (hdf5) contains gene expression matrix

molecule: polyA RNA

organism: Toxoplasma gondii RH

source_name: 10 T1/2 cells treated with parasite-free lysate and the drug cytochalasin D (CytD mock) 2 hpi

growth_protocol: 10 T1/2 host cells approximately 1 week from their date of thaw were: 1) seeded into 6-well tissue culture plates at a density of approximately 2.6 x 10^5 cells per well, 2) incubated for >2 hours at 37 degrees Celsius and 5% carbon dioxide in complete Dulbeco's Modified Eagle Medium (cDMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100 Âµg/ml streptomycin, and 3) serum starved by incubation in cDMEM containing 0.5% FBS (low serum DMEM), instead of 10% FBS, for 24 hours.

extract_protocol:
All cells were sorted directly into lysis buffer containing (per every 8 ml) 5.888 ml water, 160 ul recombinant RNase inhibitor (Takara Clonetech), 1.6 ml of 10 mM dNTP (Thermo Fisher), 160 ul of 100 M oligo-dT (iDT), 1:600,000 diluted ERCC spike-in RNA molecules (Thermo Fisher), and 32 ul of 10 % Triton X-100.
RNA was converted to cDNA using the SmartSeq2 protocol, with 19 rounds of pre-amplification PCR.  All samples were quantified using EvaGreen and diluted in EB buffer to obtain a final concentration of 0.4 - 0.8 ng/ul per sample. Library preparation continued using in-house Tn5 for tagmentation. For single cell libraries, custom barcoded indices were used for each cell, and for bulk libraries, Nextera XT indices were used for each sample.
Smart-seq2 single cell RNA-sequencing.

treatment_protocol: 10 T1/2 host cell monolayers prepared as described in the growth protocol were treated with either RH Toxofilin-HA-BLA TdTomato parasites at an MOI of 6 (Wt condition), RH dmyr1 mCherry Toxofilin-HA-BLA parasites at an MOI of 6 (Dmyr1 condition), RH Toxofilin-HA-BLA TdTomato parasites pre-treated with 1 ÂµM of the invasion inhibitor cytochalasin D (CytD condition), or parasite-free lysate from the feeder host cells that are normally mechanically disrupted to release the parasites used for infection (Mock condition).  Infections were allowed to proceed for 1, 2, or 3 hours.  In the last 30 minutes of infection, the FRET-based dye CCF2-AM was applied to each monolayer to distinguish cells injected with parasite ROP proteins from those not injected.  The host cells were then trypsinized to harvest them from the well bottoms, kept at 4 degrees Celsius to halt all biological processes in the cells, and treated with a viability stain and a second stain to identify extracellular parasites.  The cells were sorted into 384-well plates at 1 cell per well or into 96-well plates at 50-100 cells per well, based on their color profiles.  From monolayers infected with live parasites, cells uninfected with parasites but injected with parasite proteins (U-I cells), uninfected with parasites and uninjected with parasite proteins (U-U cells), and cells infected with parasites and injected with parasite proteins (I-I cells) were sorted (the cells also had to be alive based on the viabiity dye).  From monolayers treated with parasite-free lysate, live cells were sorted.

tag: host cells

value: 10T 1/2 tissue culture

value: RH


title: ESCs_no treat with control siRNA_rep1

description: no treatment with control siRNA

source_name: non treated-endometrial stromal cells with control siRNA


title: SNAIL knockdown, rep2

city: kyoto

first: Ru

last: chen

address: kawahara-cho 53, shogoin, sakyo-ku

institute: kyoto university

description: Gene expression data from HGC27 cell line with SNAIL knockdown using shRNA-B

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools(APT).  We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis

label_protocol: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol  (GeneChip Whole Transcript PLUS reagent Kit).  cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.   The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Cells were cultured in DMEM (Nacalai Tesque, Japan) supplemented with 10% fetal bovine serum (HyClone Defined Fetal Bovine Serum (FBS), USA) and penicillin-streptomycin mixed solution (10,000u/ml, Nacalai Tesque, Japan).

extract_protocol: For RNA extraction from each cell line, NucleoSpin RNA Plus (Takarabio, Japan) was used following the manufacturer’s instructions.

treatment_protocol: For shRNA knockdown, HGC27 cells were seeded onto 6-well plates and infected with optimal virus concentrations supplemented with 6 µg/mL Polybrene (Sigma, St. Louis, MO, USA), then incubated for 12 hours before replacing with fresh medium. Cells were then selected by puromycin (INVIVOGEN, Japan) at the concentration of 1.8 µg/ml for 2 weeks.

tag: disease

value: gastric cancer

tag: organism part

value: stomach

value: gastric cancer cell

tag: cell lines

tag: treatment

value: SNAIL1B knockdown


title: T24 HR RNA

city: Hsinchu

first: Ming-Han

last: Kuo

address: No. 101, Section 2, Kuang-Fu Road, Hsinchu, Taiwan 30013, R.O.C.

country: Taiwan

institute: National Tsing Hua University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by G2505C  scanner (Dye channel: R ; Scan resolution : 10 um; Tiff: 16-bit; Red PMT gain: 100%; XDR: 100 10) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: urinary bladder transitional cell carcinoma

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

value: T24 cells transduced with lentiviral particles encoding HR'-puro control  (Ctrl).


title: LM3_CSF_before_rep1

value: Cerebrospinal fluid


title: 1001703001_A13

description: mRNA + vRNA

tag: moi

tag: hours post infection

tag: plate

tag: well


title: LM2_CSF_after_rep1

tag: age


title: T24 S2 RNA

value: T24 cells transduced with lentiviral particles encoding HR'-SOX2 (SOX2).


title: 1001703001_A15

description: mRNA + vRNA


title: hstp4_4_5

city: Bar Harbor

first: Abigail

last: Tadenev

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Filtering of reads was perfomed using NGSQCToolkit/2.3 and custom perls scripts
Read alignment was done using bowtie2/2.2.0
Read count estimations were performed using rsem/1.2.12
Genome_build: We used the Mus musculus GRCm38v74 genome for this work
Supplementary_files_format_and_content: Read counts matrix from rsem

source_name: Brain

extract_protocol:
Whole brains were isolated, cut into 8-10 pieces, and immersed overnight in RNALater at 4°C, at which point they were transferred to -80°C for storage until being processed. Frozen brain tissues were homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). Total RNA was isolated by the Genome Technologies core facility at The Jackson Laboratory using the TRIzol Plus RNA Purification Kit (ThermoFisher Scientific), according to manufacturers’ protocols, including an optional DNase digest step. Sample concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Nano LabChip assay (Agilent Technologies).
Poly(A) RNA-seq libraries were constructed by the Genome Technologies core facility at The Jackson Laboratory using the TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were checked for quality and concentration using the DNA 1000 LabChip assay (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturers’ instructions. Libraries were pooled and sequenced 100 bp paired-end on the HiSeq 2500 (Illumina) using TruSeq SBS Kit v3-HS (Illumina).

tag: background strain

tag: genotype

value: brain

value: 6 weeks


title: HGC27 control, rep2

description: Gene expression data from HGC27 cell line with empty vector introduction

tag: cell type

value: vector


title: 1009902913

source_name: 10 T1/2 cells treated with parasite-free lysate (mock) 2 hpi

tag: strain


title: SNAIL knockdown, rep1

description: Gene expression data from HGC27 cell line with SNAIL knockdown using shRNA-A

value: SNAIL1A knockdown


title: HGC27 control, rep1

description: Gene expression data from HGC27 cell line

source_name: HGC27 cell line


title: LM2_CSF_before_rep1

tag: tissue

tag: gender

value: Male

value: leptomeningeal metastasis with lung adenocarcinoma


title: 1001703001_A12

description: mRNA + vRNA

source_name: U87 cells


title: 26191_3


title: 1009902905

source_name: 10 T1/2 cells sorted from monolayer infected with wild type Toxoplasma parasites treated with the drug cytochalasin D (CytD U-U, CytD U-I, and CytD I-I cells) 2 hpi


title: 1001703001_A11

description: mRNA + vRNA


title: LM1_CSF_after_rep1

value: Female

tag: diagnosis


title: hstp4_5_4


title: 1001703001_A10

description: mRNA + vRNA


title: LM1_CSF_before_rep1


title: 26191_2


title: 26191_1


title: 1009902902

source_name: 10 T1/2 cells sorted from monolayer infected with wild type Toxoplasma parasites (Wt U-U, Wt U-I, and Wt I-I cells) 2 hpi

tag: host cells


title: hstp4_4_3


title: 1009902911

source_name: 10 T1/2 cells sorted from monolayer infected with Dmyr1 mutant Toxoplasma parasites (Dmyr1 U-U, Dmyr1 U-I, and Dmyr1 I-I cells) 2 hpi


title: 1001703001_A1

description: mRNA + vRNA


title: 25973_3


title: 25973_2


title: 1009902204

source_name: 10 T1/2 cells injected (but not infected) with wild type Toxoplasma (Wt U-I) 1 hpi


title: NC5_CSF_rep1

description: Cerebrospinal fluid at the time of lumbar anesthesia prior to the necessary surgery

value: caesarean sections


title: NC4_CSF_rep1

value: appendicitis


title: WT_24h_rep3

data_processing:
Reads were quality-checked with FastQC. Sequencing adapters were removed with Trimmomatic and reads were hard-trimmed by 5 bases at the 3’-end (Bolger et al., 2014)
Successively, reads at least 20 bases long, and with an overall average phred quality score greater than 10 were aligned to the reference genome and transcriptome of Homo Sapiens (FASTA and GTF files, respectively, downloaded from GRCh38) with STAR v2.5.1  with default settings for single end reads (Dobin et al., 2013)
Distribution of the reads across genomic isoform expression was quantified using the R package GenomicRanges  from Bioconductor Version 3.0 (Lawrence et al., 2013). Differentially expressed genes (DE) were identified using the R package edgeR  from Bioconductor Version 3.0 (Robinson et al., 2010).
A gene is marked as DE if it possesses the following characteristics: 1) at least 10 counts in at least half of the samples in one group, 2) p < 0.05. and 3) log2 ratio >= 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: WT_24h_human intestinal organoids

extract_protocol:
Qiagen RNEasy
For RNA extraction, 8 x 20 µl Matrigel droplets with organoids were harvested and organoid pellets were lysed in RLT buffer. RNA was isolated using the RNeasy Kit (Qiagen) according to the manufacturer’s instructions. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies) and a Bioanalyzer 2100 (Agilent). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq RNA Sample Prep Kit v2 (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly-A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences). The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq PE Cluster Kit HS4000 or TruSeq SR Cluster Kit HS4000 (Illumina) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq2000 single end 100 bp using the TruSeq SBS Kit HS4000 (Illumina, Inc, California, USA).

value: organoids

value: Human small intestine

value: WT


title: APC_0min_cutnrun

data_processing:
library strategy: CUT&RUN
Quality control of fastq files was done using FastQC before analysis was started. After adapter and PCR duplicate removal reads were mapped to the human genome (GRCh38) using Bowtie2 with options “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Differential peaks in SMAD3 binding (Treated vs. Untreated) were called using MACS2, applying the following parameters: “--nomodal --extsize 160”
Profiles were displayed using IGV version 2.5.3. The peaks were annotated using HOMER.

source_name: Human Intestinal Organoids

extract_protocol:
MNAse digest
200.000 single cells were harvested from human small intestinal organoids. After two washes, cells were bound to 10 µl of Concanavalin A-coated beads (Bangs Laboratories, cat. no. BP531), diluted in 1ml of binding buffer and rotated 10 min at RT. Cells were cleared on a magnetic rack and beads were resuspended in 50 µl antibody solution. The antibody anti-SMAD3 (1:50, abcam28379; RRID: AB_2192903) was used, and incubated on a rotator overnight at 4˚C. Beads were cleared on a magnetic rack and washed in digitonin buffer before resuspension in 50 µl of digitonin buffer with 700 ng/µl pA-MNase, in order to bind the fusion protein to the antibody. After 1h rotating at 4˚C, beads were cleared on a magnetic rack and washed twice. To activate MNase activity, beads were resuspended in 150 µl digitonin buffer and chilled down to 0˚C before 3 µl of 100 mM CaCl2 were added for 30 min at 0˚C. Reaction was stopped by adding 150 µl of 2X Stop buffer and tubes were incubated for 10 min at 37˚C to release chromatin. After centrifugation for 5 min at 4˚C at 16 000g, tubes were placed on a magnetic rack in order to remove beads. The supernatant was collected and purified using the NucleoSpin PCR clean up kit. DNA was stored at -20˚C before Illumina library preparation.

value: APC-KO


title: 25973_1


title: NC3_CSF_rep1


title: 1009902406

source_name: 10 T1/2 cells injected (but not infected) by wild type Toxoplasma treated with cytochalasin D (CytD U-I) 3 hpi

value: 10T 1/2 tissue culture

value: RH


title: APC_30min_cutnrun


title: NC1_CSF_rep1

source_name: Cerebrospinal fluid

value: Cerebrospinal fluid


title: 1094

value: wt


title: NC2_CSF_rep1


title: WT_24h_rep1


title: LM10_CSF_rep1


title: 1009902403

source_name: 10 T1/2 cells injected (but not infected) by wild type Toxoplasma (Wt U-I) 3 hpi


title: 1009902409

source_name: 10 T1/2 cells injectd (but not infected) by dmyr1 mutant Toxoplasma gondii (Dmyr1 U-I) 3 hpi


title: 1009902402

source_name: 10 T1/2 cells infected with wild type Toxoplasma (Wt I-I) 3 hpi


title: BM5_CSF_rep1

description: Cerebrospinal fluid at diagnostic lumbar puncture

value: Brain metastasis with lung adenocarcinoma


title: 1093

value: brain

value: 6 weeks


title: 1009902207

source_name: 10 T1/2 cells injected (but not infected) with dmyr1 mutant Toxoplasma (Dmyr1 U-I) 1 hpi


title: LM9_CSF_rep1


title: SAM24339045 PS2APP

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
Supplementary_files_format_and_content: nRPKM

source_name: RNA from sorted cells

extract_protocol: Frozen tissue was dissociated on ice as described in manuscript, RNA was extracted from CD11b+ myeloid cells.

tag: Sex


title: SAM24339042 PS2APP


title: 25926_5

source_name: Brain


title: 1009902203

source_name: 10 T1/2 cells infected with wild type Toxoplasma (Wt I-I) 1 hpi


title: 1009902408

source_name: 10 T1/2 cells infected with dmyr1 mutant Toxoplasma (Dmyr1 I-I) 3 hpi


title: SAM24339055 PS2APP;Trem2KO


title: LM8_CSF_rep1


title: 1009902206

source_name: 10 T1/2 cells infected with dmyr1 mutant Toxoplasma (Dmyr1 I-I) 1 hpi


title: WT_0h_rep2

source_name: WT_0h_human intestinal organoids


title: WT_0h_rep1


title: SMARCA4_30min_cutnrun

data_processing:
library strategy: CUT&RUN
Quality control of fastq files was done using FastQC before analysis was started. After adapter and PCR duplicate removal reads were mapped to the human genome (GRCh38) using Bowtie2 with options “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Differential peaks in SMAD3 binding (Treated vs. Untreated) were called using MACS2, applying the following parameters: “--nomodal --extsize 160”
Profiles were displayed using IGV version 2.5.3. The peaks were annotated using HOMER.
Genome_build: GRCh38

value: APC-KO, SMARCA4-KO

value: 10 ng/ml recombinant TGFB1


title: WT_24h_rep2


title: 1009902405

source_name: 10 T1/2 cells infected by wild type Toxoplasma treated with cytochalasin D (CytD I-I) 3 hpi


title: SAM24339051 PS2APP;Trem2KO

value: Male


title: SAM24339044 PS2APP

value: Female


title: SMARCA4_0h_cutnrun


title: WT_0h_rep3


title: ARID1A_30min_cutnrun

value: APC-KO, ARID1A-KO


title: SAM24339053 PS2APP;Trem2KO


title: 1009902411

source_name: 10 T1/2 cells exposed to parasite-free lysate treated with cytochalasin D (cytD mock) 3 hpi


title: 1009902410

source_name: 10 T1/2 cells exposed to parasite-free lysate (mock-infected) 3 hpi


title: SAM24339052 PS2APP;Trem2KO


title: BM4_CSF_rep1


title: 1009902208

source_name: 10 T1/2 cells exposed to parasite-free lysate (mock-infected) 1 hpi


title: LM7_CSF_rep1

value: leptomeningeal metastasis with lung adenocarcinoma


title: LM6_CSF_rep1


title: SAM24339041 PS2APP


title: human chondrocyte_dedifferentiated_passage 5 generation_rep 3_B3

first: Lin

last: Chen

address: 126 xinmin

department: Basic Medical College

institute: Jiin University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Arraystar Human LncRNA Microarray V4.0 is designed for the global profiling of human LncRNAs and protein-coding transcripts, which is updated from the previous Microarray V3.0. About 40,173 LncRNAs and 20,730 coding transcripts can be detected by our third-generation LncRNA microarray.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer (Additional fees apply).The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

growth_protocol: Human hyaline chondrocytes were isolated from donors after death or trauma (n = 3; age = 39, 55, 67 years; 2 male and 1 female). All tissues were examined by safranin O staining and graded according to a modified Mankin scale. The tissues that scored less than 2 were considered as normal hyaline cartilage. All three patients or their families included in the study signed informed consent for voluntary donation of living tissue for scientific research. This study was approved by the Clinical Ethics Committee of China-Japan Union Hospital of Jilin University.

extract_protocol: TRIzol Reagent (Invitrogen) was used to extract total RNA as per the manufacturer’s instructions. NanoDrop ND-1000 was used to determine the content and quality of extracted RNA. The total RNA was stored at -80°C for microarray analysis

treatment_protocol: First, the obtained cartilage tissues were cut into small pieces and incubated overnight at 37°C, 5% CO2 in Dulbecco’s modified Eagle medium (DMEM; HyClone) containing 1 mg/mL type II collagenase (Sigma Aldrich). Primary chondrocytes were cultured in DMEM supplemented with 10% fetal bovine serum (FBS; TransGen Biotech Co. Ltd., Beijing, China) and 1% penicillin-streptomycin (Invitrogen) at a density of 25,000 cells/cm2 [13]. The culture medium was changed every two days. When more than 80% chondrocytes fused, they were digested with 0.25% trypsin-EDTA (Gibco) to passage culture until P5, and the P1 and P5 chondrocytes were selected for the next experiments.

value: male

value: Knee joint; cartilage

value: human chondrocyte

tag: cell subtype

value: dedifferentiated_passage 5


title: 1009902201

source_name: 10 T1/2 cells exposed to but not infected with wild type Toxoplasma (Wt U-U cells) 1 hpi

value: 10T 1/2 tissue culture


title: human chondrocyte_dedifferentiated_passage 5 generation_rep 2_B2

value: female


title: SAM24339047 PS2APP


title: 1009902205

source_name: 10 T1/2 cells exposed to but not infected with dmyr1 mutant Toxoplasma (Dmyr1 U-U cells) 1 hpi

value: RH


title: LM5_CSF_rep1

source_name: Cerebrospinal fluid

value: Cerebrospinal fluid


title: SAM24339049 PS2APP;Trem2KO


title: human chondrocyte_differentiated_passage 1 generation_rep 3_A3

value: differentiated_passage 1


title: 1009902404

source_name: 10 T1/2 cells exposed to but not infected by wild type Toxoplasma treated with cytochalasin D (CytD U-U) 3 hpi


title: BM1_CSF_rep1

value: Brain metastasis with lung adenocarcinoma


title: human chondrocyte_differentiated_passage 1 generation_rep 2_A2


title: SAM24339043 PS2APP


title: SAM24339040 PS2APP


title: 1009902401

source_name: 10 T1/2 cells exposed to but not infected by wild type Toxoplasma (Wt U-U) 3 hpi


title: human chondrocyte_differentiated_passage 1 generation_rep 1_A1


title: LM3_CSF_rep1


title: LM4_CSF_rep1


title: ARID1A_0min_cutnrun

source_name: Human Intestinal Organoids

value: organoids

value: Human small intestine


title: 1009902407

source_name: 10 T1/2 cells exposed to but not infected by dmyr1 mutant Toxoplasma (Dmyr1 U-U) 3 hpi


title: SAM24339054 PS2APP;Trem2KO

source_name: RNA from sorted cells


title: BM3_CSF_rep1


title: LM2_CSF_rep1


title: BM2_CSF_rep1


title: human chondrocyte_dedifferentiated_passage 5 generation_rep 1_B1


title: LM1_CSF_rep1


title: siYT_D

status: Public on Feb 24 2020

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

data_processing:
Reads were trimmed using Cutadapt 1.18 for adapters and low-quality bases
alignment to the human reference genome, hg19, was performed using STAR 2.6.1.
Gene counts were calculated using Quantify to annotation model with Ensembl Transcripts release 75 (Partek E/M, PartekFlow 8.0.19.0819)
counts were filtered to exclude genes with maximum <= 5.0 with Partek Flow 8.0.19.0819
Counts were added +1 and gene expression was normalized to TMM and TPM using PartekFlow 8.0.19.0819
TMM values were used for differential analysis to identify genes that are differentially expressed using the GSA function in PartekFlow 8.0.19.0819 with q value calculation, by comparing the siYT samples to siCon samples.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files includes TMM values and GSA analysis for all samples

source_name: N/TERT2G keratinocytes

growth_protocol: Cells were cultured at 37°C in the presence of 5% CO2 and cultured in EPILIFE medium (Life Technologies) with Human Keratinocyte Growth Supplement (HKGS, Life Technologies).

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
TruSeq mRNA Prep Kit RS-122-2101

treatment_protocol: Cells were transfected with the corresponding siRNAs one day after plating and were harvested 48hs after transfection. siRNAs were siGENOME SMARTpool from Dharmacon/Horizon, siYAP (M-012200-00-0005), siWWTR1(TAZ) (M-016083-00-0005) and non-targeting control siRNA (D-001206-13). siRNA was transfected at a concentration of 8 pmol cm-2 using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions.

tag: cell line

value: N/TERT2G keratinocytes

value: pooled siRNAs targeting YAP1 and TAZ (WWTR1)


title: siYT_C

tag: treatment


title: patient_AYL050

city: Oxford

first: Cristina

last: Di Genua

address: Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
RNA-Seq:Short reads were aligned to the human genome (GRCh37 assembly (hg19)) and mouse (mm10) using the Cell Rager software.
Read Count : Matrices of read counts were obtained based on the Cell Ranger software
Genome_build: GRCh37 assembly (hg19)
Genome_build: Mouse (mm10)
Supplementary_files_format_and_content: Cell Ranger Market Exchange Format (MEX)

source_name: Bone marrow

extract_protocol:
cDNA was generated according to the single-cell 10x genomics protocol
Illumina sequencing libraries were constructed according to manufacturer's protocol.

treatment_protocol: Cells were isolated by FACS.

value: Bone marrow

tag: phenotype


title: patient_OX1164


title: siYT_B


title: siYT_A


title: YC1_control

city: Taipei city

first: Li-Hang

last: Hsu

state: Taiwan (R.O.C)

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

department: Plant Pathology and Microbiology

institute: National Taiwan University

data_processing:
RNA-seq reads were processed using "Trinity v2.3.2".
Read quality was evaluated using "MultiQC v1.2".
The alignment and the read count quantification were performed with "bowtie2 v2.3.2" and "RSEM v1.2.31" respectively, and the alignment QC report was evaluated using "Qualimap v2".
The gene expression level is calculated by using FPKM method.
Genome_build: C. albicans SC5314, ASM18296v3
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM, BLASTP, BLASTX, and annotation

organism: Candida albicans

source_name: C. albicans cells

growth_protocol: C. albicans cells were grown overnight at 30°C, washed twice with sterile ddH2O, diluted to 0.25 OD600/mL in 5 mL YPD broth, and then incubated at 30°C for 3 h with shaking at 200 rpm.

extract_protocol:
Cells were centrifuged at 4°C for 10 min at 3,250 rpm, and washed with ice-cold ddH2O to discard medium. Total RNA was extracted using TRIzol reagent (Invitrogen, USA). Collected cells were freeze in liquid N2, and vortexed with beads. After adding 1 mL TRIzol, cultures were centrifuged at 4°C /12,000g for 10 min, and the supernatant was transferred to a new tube. After 5 min incubation at room temperature, 200 μL of chloroform was added and mixed thoroughly, and tubes were incubated at room temperature for 3 min, centrifuged at 4°C/12,000g for 15 min, and supernatant was transferred to a new tube. Tubes were added 500 μL of isopropanol, incubated at room temperature for 10 min, centrifuged at 4°C/12,000g for 10 min, and the supernatant was discarded. Pellet containing RNA was washed twice with 75% ethanol and resuspend with RNase free water.
The mRNA was enriched with oligo(dT) magnetic beads and shortened into approximately 200-base fragments in fragmentation buffer. The first strand of cDNA was synthesized by the use of a random hexamer, buffer, dNTPs, and RNase H, and the second by the use of DNA polymerase I. The double strand cDNAs were purified with magnetic beads. After end preparation and 3’ end single nucleotide adenine addition were performed, sequencing adaptors were ligated to the fragments, and amplified by PCR. An Aglient 2100 bioanalyzer and ABI StepOnePlus real-time PCR system were used to qualify and quantify the sample library, and the library products were sequenced via an illumina HiSeq 2000 instrument.

treatment_protocol: To the expeiment group, PMT12-BF4 was added into YPD broth at a final concentration of 1 μg/mL during the 3 h incubation, while the comtrol group was untreated.

value: wild type

tag: agent


title: siCON_A

description: siControl

value: non-targeting control siRNA


title: siKLF4_1

description:
siKLF4_TMM.xlsx
siKLF4_GSA.xlsx

data_processing:
Reads were trimmed using Cutadapt 1.18 for adapters and low-quality bases
alignment to the human reference genome, hg19, was performed using STAR 2.6.1.
Gene counts where calculated using Quantify to annotation model with Ensembl Transcripts release 75 (Partek E/M, PartekFlow 8.0.19.0819)
counts where filtered to exclude genes with maximum <= 5.0 with Partek Flow 8.0.19.0819
Counts where added +1 and gene expression was normalized to TMM and TPM using PartekFlow 8.0.19.0819
TMM values where used for differential analysis to identify genes that are differentially expressed using the GSA function in PartekFlow 8.0.19.0819 with q value calculation, by comparing the siYT samples to siCon samples.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files includes TMM values and GSA analysis for all samples

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
TruSeq Stranded mRNA Library Prep

treatment_protocol: Cells were transfected with the corresponding siRNAs one day after plating and were harvested 48hs after transfection. siRNAs were siGENOME SMARTpool from Dharmacon/Horizon siKLF4 (M-005089-03-0010) or non-targeting control siRNA (D-001206-13). siRNA was transfected at a concentration of 8 pmol cm-2 using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions.

value: cell line

tag: tranduction


title: 48H_TEADi_3

description: 48hs TEADi

data_processing:
Reads were trimmed using Trimmomatic 0.36 for adapters and low-quality bases
alignment to the human reference genome, hg19, was performed using STAR 2.5.1.
Gene counts where calculated using Quantify to annotation model with Ensembl Transcripts release 75 (Partek E/M, PartekFlow 8.0.19.0819)
counts where filtered to keep genes with maximum <= 8.0 with Partek Flow 8.0.19.0819
Counts where added +1 and gene expression was normalized to TMM and TPM using PartekFlow 8.0.19.0819
TMM values where used for differential analysis to identify genes that are differentially expressed using the GSA function in PartekFlow 8.0.19.0819 with q value calculation, by comparing the TEADi expressing cells vs GFP expressing cells at each timepoint.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes TMM values, TPM values and GSA analysis for all samples

treatment_protocol: Cells were transduced one day after plating with a multiplicity of infection (MOI) of 25 with adeno-GFP (control) or adeno-TEADi for the indicated times

value: keratinocytes cell line

tag: transduction

value: 48H TEADi


title: siKLF4_4

description:
siKLF4_TMM.xlsx
siKLF4_GSA.xlsx


title: siCON_3

description:
siKLF4_TMM.xlsx
siKLF4_GSA.xlsx

value: siControl


title: 48H_GFP_1

description: 48hs control

value: 48H GFP


title: 48H_TEADi_1

description: 48hs TEADi


title: 48H_TEADi_2

description: 48hs TEADi


title: siKLF4_2

description:
siKLF4_TMM.xlsx
siKLF4_GSA.xlsx


title: siKLF4_3

description:
siKLF4_TMM.xlsx
siKLF4_GSA.xlsx


title: 48H_GFP_3

description: 48hs control


title: siCON_2

description:
siKLF4_TMM.xlsx
siKLF4_GSA.xlsx


title: siCON_B

description: siControl


title: 48H_GFP_2

description: 48hs control


title: siCON_1

description:
siKLF4_TMM.xlsx
siKLF4_GSA.xlsx


title: 24H_TEADi_3

description: 24hs TEADi

value: 24H TEADi


title: 24H_TEADi_1

description: 24hs TEADi


title: 24H_TEADi_2

description: 24hs TEADi


title: 24H_GFP_3

description: 24hs control

value: 24H GFP


title: siCON_C

description: siControl


title: YC1_PMT12-BF4


title: 24H_GFP_2

description: 24hs control


title: 24H_GFP_1

description: 24hs control


title: 12H_TEADi_3

description: 12hs TEADi

value: 12H TEADi


title: 12H_TEADi_1

description: 12hs TEADi


title: 12H_GFP_2

description: 12hs control

value: 12H GFP


title: 12H_GFP_1

description: 12hs control


title: 12H_GFP_3

description: 12hs control


title: 12H_TEADi_2

description: 12hs TEADi


title: Low_Metastasis_S26

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US) at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Cat#G2565BA，Agilent technologies, Santa Clara, CA, US) with Scan resolution of 5um and PMT  to 100%.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

source_name: NPC Cell Line, Low Metastasis Potential

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Human nasopharyngeal carcinoma cell lines (S18 and S26) were cultured in DMEM (Invitrogen, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Grand Island, NY, USA). These cell lines were incubated in a humidified chamber with 5% CO2 at 37°C.

extract_protocol: TRIzol reagent (Invitrogen) was used to extract total RNA from nasopharyngeal carcinoma cell lines.

value: nasopharyngeal carcinoma


title: Ecc15 4hour challenge Rep #1

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
Drosophilia midgut 4 hours following Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
E4R1_MG_S54_L007_R1_001

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9 and dm3 for mouse and fruit fly small RNA-seq, mm10 for mouse RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.

organism: Drosophila melanogaster

source_name: Midgut

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: Midgut


title: Un-challenged midgut Rep #3

description:
Drosophilia midgut with no Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
B5R3_MG_S55_L007_R1_001


title: Soleus muscle from Dnm2 +/K562E mouse 1

first: Jorge

middle: A.

last: Pereira

address: Otto-Stern-Weg 7

department: Dep. of Biology

institute: ETH Zurich

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Trimmomatic (Version 0.33).
The read alignment was done with STAR (v2.5.1b). As reference we used the Ensembl genome build GRCm38.p5 with the gene annotations downloaded on 2015-06-25 from Ensembl (release 80.)
The STAR alignment options were "--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50".
Gene expression values were computed with the function featureCounts from the R package Rsubread (v1.22.3). The options for featureCounts were: - min mapping quality 10 - min feature overlap 10bp - count multi-mapping reads - count only primary alignments - count reads also if they overlap multiple genes.
To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package EdgeR (R version: 3.3.2, EdgeR version: 3.14.0 ) [EdgeR]. The differential expression was assessed using an exact test adapted for over-dispersed data. Genes showing altered expression with adjusted (Benjamini and Hochberg method) p-value < 0.05 were considered differentially expressed.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited txt-file including Raw Gene Counts from FeatureCount Function of Rsubreads

source_name: Soleus muscle from Dnm2 +/K562E mouse

extract_protocol:
Immediately after dissection of peripheral nerves, the perineurium with overlaying epineurium was removed as much as possible, and then the tissues were snap-frozen in liquid nitrogen. Soleus muscle were snap frozen in liquid nitrogen immediately after extraction. Each tissue was mechanically grinded while frozen using an RNAse free pestle to produce smaller chunks and frozen tissue powder. RNA extraction was performed using Qiazol (Qiagen) as per manufacturer's instructions.
RNA libraries were prepared for sequencing using Illumina's TruSeq Stranded Total RNA

tag: strain background

tag: genotype/variation

tag: age

value: 2 months

value: Soleus muscle


title: Un-challenged midgut Rep #2

description:
Drosophilia midgut with no Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
B5R2_MG_S29_L005_R1_001


title: Soleus muscle from Dnm2 +/K562E mouse 3


title: Soleus muscle from control mouse 3

source_name: Soleus muscle from control mouse


title: High_Metastasis_S18

source_name: NPC Cell Line, High Metastasis Potential

tag: cell type


title: Soleus muscle from control mouse 2


title: Ecc15 4hour challenge Rep #3

description:
Drosophilia midgut 4 hours following Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
E4R3_MG_S56_L007_R1_001


title: Un-challenged midgut Rep #1

description:
Drosophilia midgut with no Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
B5R1_MG_S40_L006_R1_001


title: Ecc15 12hour challenge Rep #2

description:
Drosophilia midgut 12 hours following Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
E12R2_MG_S51_L007_R1_001


title: Ecc15 12hour challenge Rep #3

description:
Drosophilia midgut 12 hours following Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
E12R3_MG_S43_L006_R1_001


title: Soleus muscle from Dnm2 +/K562E mouse 2


title: Soleus muscle from Dnm2 +/K562E mouse 4


title: Ecc15 12hour challenge Rep #1

description:
Drosophilia midgut 12 hours following Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
E12R1_MG_S39_L006_R1_001


title: Soleus muscle from control mouse 4


title: pregnant embryo mRNA rep 4

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

data_processing:
Reads were trimmed using cutadapt version 1.11 to remove the Illumina adaptor sequence.
The trimmed reads were mapped against the equine EquCab 2.80 reference genome using CLC genomics workbench version 9.0.1 (CLC).
Count tables were made by counting the reads that mapped against the genes defined by the Ensembl EquCab 2.80 Gene transfer format file and exported from CLC.
Genome_build: EquCab 2.80
Supplementary_files_format_and_content: comma separated values files including Gene counts and Gene ID

organism: Equus caballus

source_name: embryo

growth_protocol: Samples were collected from cycling or pregnant mares 13 days after ovulation

extract_protocol:
For RNA extraction from the B and the E tissue samples, the RNeasy Mini Kit (Qiagen) was combined with the RNeasy MinElute Cleanup Kit (Qiagen) in order to extract both small RNAs and larger RNAs (>200 nt) separately from the same tissue sample for mRNA- and miRNA-Sequencing respectively.
1 µg of RNA was used to perform an Illumina sequencing library preparation using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. During library preparation, 12 PCR cycles were used.

treatment_protocol: cyclic mares: no treatment, pregnant mares: inseminated and confirmed to be pregnant

value: embryo

tag: Stage

value: pregnant


title: pregnant embryo mRNA rep 5

tag: tissue


title: Soleus muscle from control mouse 1

city: Zurich


title: pregnant uterus mRNA rep 4

source_name: uterus

value: uterus


title: pregnant embryo mRNA rep 3


title: pregnant uterus mRNA rep 5


title: pregnant uterus mRNA rep 3


title: pregnant embryo mRNA rep 1


title: cyclic uterus mRNA rep 4

value: cyclic


title: pregnant uterus mRNA rep 2


title: pregnant embryo mRNA rep 2


title: pregnant uterus mRNA rep 1


title: cyclic uterus mRNA rep 3


title: cyclic uterus mRNA rep 1


title: cyclic uterus mRNA rep 2


title: WT_4wk_repB

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

country: Italy

institute: Humanitas Research Hospital

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR v2.5 (PMID: 23104886)
Transcript abundance was obtained using the internally  developed RNA read counter of STAR v2.5 (PMID: 23104886)
Differentially expressed genes were identified using R and edgeR (PMID: 19910308)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig were generated using the bam2wig.py module in RSeQC v2.6.4 (PMID: 22743226)

source_name: myocytes

extract_protocol:
Total RNA was isolated using PureZolTM RNA Isolation Reagent (BioRad Laboratories) and treated with DNase according to the manufacture’s protocol.
Total RNA quality was evaluated using the Agilent Bioanalyzer and the RNA 6000 Nano kit. Only samples with a RIN score ≥ 8 were processed further. RNA-seq libraries were generated from 1 µg of RNA using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero ribosomal RNA reduction chemistry (Illumina). Electrophoresis of the libraries on a Bioanalyzer 2100 instrument showed highest peaks at 230-270 bp. Paired-end multiplexed sequencing of libraries (four per flow cell lane) to generate reads of 100 bp was performed on a HiSeq 1000 instrument with TruSeq SBS and PE Cluster v3 Kits (Illumina). 70-100 million reads were obtained for all samples.
Paired end sequence reads (100-bp in length) were generated on an Illumina HiSeq 1000 (Sample 1 to 8)

tag: strain

value: Tibialis anterior muscle

tag: genotype

value: control


title: MKO_4wk_repA

value: MYPN Knockout


title: MKO_4wk_repB


title: WT_4wk_repA


title: MKO_2wk_repA


title: WT_2wk_repB


title: WT_2wk_repA


title: Ecc15 4hour challenge Rep #2

description:
Drosophilia midgut 4 hours following Ecc15 infection
drosophilia_infection_RPMMM_mirs_over_50.csv
E4R2_MG_S30_L005_R1_001


title: TT13-9653-AN13-0022 [US-1420994]

city: West Point

first: Alexei

last: Podtelezhnikov

state: PA

address: 770 Sumneytown Pike

department: Non-clinical Drug Safety

institute: Merck & Co., Inc.

description:
US-1420994
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

data_processing:
Genome alignment and gene quantitation was performed using OmicSoft Array Studio
Cleaned reads were aligned to the Rnor_6.0 genome reference using the OmicSoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RNA-Seq by expectation maximization algorithm as implemented in OmicSoft Array Studio and using Ensembl.R94 gene models
FPKM normalization was applied to RNA-Seq counts followed by log-transformation with smoothing, i.e., log10(FPKM+0.01)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Count, FPKM

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was purified from frozen liver samples using the MagMAX™ Express Magnetic Particle Processor (Applied Biosystems, # 4400074)
Total RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA HT Sample Preparation Kit (Illumina, #RS-122-2103)

tag: study

value: Han Wistar

value: M

value: 0.4percent (w/v) Hydroxypropyl Methylcellulose in Deionized Water

value: phenobarbital

tag: dose(mkd)

tag: days of administration

tag: rin


title: TT13-9653-AN13-0030 [US-1420957]

description:
US-1420957
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: Sex

tag: treatment


title: TT05-0106-AN05-9342 [US-1468400]

description:
US-1468400
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

tag: agent

value: 0.5percent (w/v) Methylcellulose in Deionized Water

value: -control-


title: TT13-9653-AN13-0024 [US-1420988]

description:
US-1420988
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-9653-AN13-0008 [US-1421051]

description:
US-1421051
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-9653-AN13-0028 [US-1420964]

description:
US-1420964
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8391 [US-1421141]

description:
US-1421141
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.4percent HPMC/ 5percent Polysorbate 80/ 20percent PEG 400


title: TT13-9653-AN13-0026 [US-1421063]

description:
US-1421063
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8390 [US-1421131]

description:
US-1421131
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-9653-AN13-0006 [US-1421065]

description:
US-1421065
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8389 [US-1421118]

description:
US-1421118
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT05-0106-AN05-9358 [US-1468425]

description:
US-1468425
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-9653-AN13-0010 [US-1420995]

description:
US-1420995
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8392 [US-1421227]

description:
US-1421227
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT05-0106-AN05-9340 [US-1468429]

description:
US-1468429
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-9653-AN13-0004 [US-1420993]

description:
US-1420993
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT05-0106-AN05-9354 [US-1468457]

description:
US-1468457
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MKO_2wk_repB


title: TT05-0106-AN05-9344 [US-1468403]

description:
US-1468403
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-3538-AN11-8280 [US-1421008]

description:
US-1421008
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8383 [US-1420998]

description:
US-1420998
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-9653-AN13-0002 [US-1420986]

description:
US-1420986
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-3538-AN11-8278 [US-1421138]

description:
US-1421138
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-3538-AN11-8277 [US-1421021]

description:
US-1421021
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-3538-AN11-8279 [US-1421025]

description:
US-1421025
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-3538-AN11-8263 [US-1421100]

description:
US-1421100
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-3538-AN11-8261 [US-1421128]

description:
US-1421128
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2581-AN13-0038 [US-1466388]

description:
US-1466388
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: zolpidem


title: TT13-2581-AN13-0036 [US-1466387]

description:
US-1466387
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2581-AN13-0008 [US-1466383]

description:
US-1466383
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2581-AN13-0004 [US-1466380]

description:
US-1466380
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2581-AN13-0002 [US-1466379]

description:
US-1466379
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2564-AN13-0014 [US-1466377]

description:
US-1466377
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Cmpd Z


title: TT11-3538-AN11-8264 [US-1421121]

description:
US-1421121
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-3538-AN11-8262 [US-1421113]

description:
US-1421113
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2564-AN13-0016 [US-1466378]

description:
US-1466378
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8382 [US-1421122]

description:
US-1421122
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2559-AN13-0024 [US-1466416]

description:
US-1466416
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 4percent Poloxamer 407 / 16percent Sucrose in Sterile water

value: troglitazone


title: TT13-2559-AN13-0004 [US-1466405]

description:
US-1466405
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2559-AN13-0020 [US-1466412]

description:
US-1466412
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2564-AN13-0008 [US-1466373]

description:
US-1466373
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8384 [US-1421017]

description:
US-1421017
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-3553-AN13-8381 [US-1421003]

description:
US-1421003
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2559-AN13-0008 [US-1466409]

description:
US-1466409
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2564-AN13-0010 [US-1466374]

description:
US-1466374
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2564-AN13-0006 [US-1466372]

description:
US-1466372
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2564-AN13-0002 [US-1466368]

description:
US-1466368
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2564-AN13-0004 [US-1466369]

description:
US-1466369
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2559-AN13-0006 [US-1466407]

description:
US-1466407
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2559-AN13-0022 [US-1466413]

description:
US-1466413
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2558-AN13-0032 [US-1466400]

description:
US-1466400
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sterile Water pH adjusted to ~ 3.0 using HCl

value: ximelagatran


title: TT13-2558-AN13-0030 [US-1466398]

description:
US-1466398
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2558-AN13-0026 [US-1466396]

description:
US-1466396
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2558-AN13-0028 [US-1466397]

description:
US-1466397
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2558-AN13-0008 [US-1466395]

description:
US-1466395
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2558-AN13-0004 [US-1466393]

description:
US-1466393
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2558-AN13-0006 [US-1466394]

description:
US-1466394
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2558-AN13-0002 [US-1466392]

description:
US-1466392
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2533-AN13-0062 [US-1466355]

description:
US-1466355
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: mibefradil


title: TT13-2564-AN13-0012 [US-1466376]

description:
US-1466376
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2533-AN13-0064 [US-1466356]

description:
US-1466356
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2559-AN13-0002 [US-1466402]

description:
US-1466402
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2533-AN13-0060 [US-1466354]

description:
US-1466354
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2559-AN13-0018 [US-1466411]

description:
US-1466411
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2533-AN13-0016 [US-1466353]

description:
US-1466353
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2533-AN13-0012 [US-1466351]

description:
US-1466351
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2533-AN13-0014 [US-1466352]

description:
US-1466352
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2533-AN13-0010 [US-1466350]

description:
US-1466350
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2521-AN13-0064 [US-1466367]

description:
US-1466367
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 60percent (w/w) Polyethylene Glycol 400 in 0.9percent (w/v) Sodium Chloride for Injection

value: alpidem


title: TT13-2521-AN13-0062 [US-1466366]

description:
US-1466366
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar


title: TT13-1502-AN13-0064 [US-1466349]

description:
US-1466349
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M

value: captopril


title: TT13-2521-AN13-0058 [US-1466363]

description:
US-1466363
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2521-AN13-0010 [US-1466358]

description:
US-1466358
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-1502-AN13-0062 [US-1466348]

description:
US-1466348
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2521-AN13-0012 [US-1466359]

description:
US-1466359
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-1502-AN13-0060 [US-1466347]

description:
US-1466347
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-1502-AN13-0012 [US-1466343]

description:
US-1466343
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-1502-AN13-0058 [US-1466346]

description:
US-1466346
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0080 [US-1470878]

description:
US-1470878
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: loracarbef


title: TT13-1502-AN13-0010 [US-1466440]

description:
US-1466440
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-1502-AN13-0016 [US-1466345]

description:
US-1466345
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0078 [US-1470887]

description:
US-1470887
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0014 [US-1472151]

description:
US-1472151
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0016 [US-1470891]

description:
US-1470891
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0010 [US-1470956]

description:
US-1470956
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2521-AN13-0060 [US-1466365]

description:
US-1466365
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0012 [US-1472140]

description:
US-1472140
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0076 [US-1470954]

description:
US-1470954
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9750-AN12-0064 [US-1420869]

description:
US-1420869
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Polysorbate 80/Deionized Water (10:90 w/w)

value: oxandrolone


title: TT13-2521-AN13-0014 [US-1466360]

description:
US-1466360
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT12-9750-AN12-0062 [US-1420910]

description:
US-1420910
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2521-AN13-0016 [US-1466361]

description:
US-1466361
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9750-AN12-0016 [US-1420938]

description:
US-1420938
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9750-AN12-0014 [US-1420800]

description:
US-1420800
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9750-AN12-0060 [US-1420875]

description:
US-1420875
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9750-AN12-0058 [US-1420924]

description:
US-1420924
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9751-AN12-0074 [US-1470912]

description:
US-1470912
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT12-9732-AN12-0048 [US-1421069]

description:
US-1421069
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: tetracycline


title: TT12-9732-AN12-0046 [US-1420954]

description:
US-1420954
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9732-AN12-0016 [US-1420991]

description:
US-1420991
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9732-AN12-0012 [US-1421049]

description:
US-1421049
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0080 [US-1470907]

description:
US-1470907
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 100percent PEG 400

value: lopinavir


title: TT12-9732-AN12-0014 [US-1421078]

description:
US-1421078
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0078 [US-1470931]

description:
US-1470931
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0074 [US-1470880]

description:
US-1470880
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0046 [US-1472126]

description:
US-1472126
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: chlormezanone


title: TT12-9731-AN12-0042 [US-1472134]

description:
US-1472134
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0048 [US-1472150]

description:
US-1472150
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0076 [US-1470930]

description:
US-1470930
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0016 [US-1472160]

description:
US-1472160
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9750-AN12-0012 [US-1420912]

description:
US-1420912
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0014 [US-1472169]

description:
US-1472169
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9732-AN12-0042 [US-1421088]

description:
US-1421088
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0016 [US-1470920]

description:
US-1470920
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0010 [US-1470915]

description:
US-1470915
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0012 [US-1470962]

description:
US-1470962
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0012 [US-1472143]

description:
US-1472143
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0010 [US-1472157]

description:
US-1472157
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9732-AN12-0044 [US-1421066]

description:
US-1421066
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9716-AN12-0046 [US-1472168]

description:
US-1472168
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 2percent carboxymethylcellulose

value: amprenavir


title: TT12-9716-AN12-0048 [US-1472174]

description:
US-1472174
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9732-AN12-0010 [US-1421071]

description:
US-1421071
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9716-AN12-0042 [US-1472119]

description:
US-1472119
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9716-AN12-0016 [US-1472163]

description:
US-1472163
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9716-AN12-0010 [US-1472117]

description:
US-1472117
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9716-AN12-0014 [US-1472161]

description:
US-1472161
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0044 [US-1472133]

description:
US-1472133
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9716-AN12-0012 [US-1472096]

description:
US-1472096
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9731-AN12-0014 [US-1470929]

description:
US-1470929
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9700-AN12-0016 [US-1420940]

description:
US-1420940
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9700-AN12-0076 [US-1420904]

description:
US-1420904
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: panadiplon


title: TT12-9700-AN12-0078 [US-1420844]

description:
US-1420844
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9700-AN12-0074 [US-1420865]

description:
US-1420865
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9700-AN12-0080 [US-1420909]

description:
US-1420909
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9716-AN12-0044 [US-1472170]

description:
US-1472170
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9700-AN12-0014 [US-1420859]

description:
US-1420859
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9700-AN12-0012 [US-1420855]

description:
US-1420855
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9700-AN12-0010 [US-1420889]

description:
US-1420889
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9750-AN12-0010 [US-1420934]

description:
US-1420934
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0048 [US-1472181]

description:
US-1472181
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: chloramphenicol


title: TT12-9695-AN12-0108 [US-1470649]

description:
US-1470649
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: trovafloxacin


title: TT12-9695-AN12-0110 [US-1470597]

description:
US-1470597
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar


title: TT12-9695-AN12-0044 [US-1472127]

description:
US-1472127
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: TT12-9695-AN12-0046 [US-1472156]

description:
US-1472156
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0106 [US-1470719]

description:
US-1470719
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0112 [US-1470595]

description:
US-1470595
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0016 [US-1470712]

description:
US-1470712
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0016 [US-1472154]

description:
US-1472154
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0014 [US-1472188]

description:
US-1472188
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0014 [US-1470651]

description:
US-1470651
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0010 [US-1470763]

description:
US-1470763
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0012 [US-1472120]

description:
US-1472120
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0010 [US-1472172]

description:
US-1472172
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0096 [US-1470598]

description:
US-1470598
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: zimelidine


title: TT12-9690-AN12-0092 [US-1470768]

description:
US-1470768
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0090 [US-1470641]

description:
US-1470641
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0046 [US-1470593]

description:
US-1470593
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: nifedipine


title: TT12-9690-AN12-0094 [US-1470636]

description:
US-1470636
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0048 [US-1470773]

description:
US-1470773
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0044 [US-1470711]

description:
US-1470711
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0042 [US-1472179]

description:
US-1472179
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0016 [US-1470715]

description:
US-1470715
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0042 [US-1470590]

description:
US-1470590
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0014 [US-1470645]

description:
US-1470645
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0016 [US-1470634]

description:
US-1470634
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0012 [US-1470708]

description:
US-1470708
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0014 [US-1470591]

description:
US-1470591
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9664-AN12-0044 [US-1420905]

description:
US-1420905
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: methimazole


title: TT12-9690-AN12-0010 [US-1470723]

description:
US-1470723
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0010 [US-1470713]

description:
US-1470713
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9664-AN12-0042 [US-1420919]

description:
US-1420919
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9664-AN12-0046 [US-1420907]

description:
US-1420907
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9690-AN12-0012 [US-1470584]

description:
US-1470584
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9695-AN12-0012 [US-1470596]

description:
US-1470596
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9664-AN12-0014 [US-1420872]

description:
US-1420872
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9664-AN12-0016 [US-1420937]

description:
US-1420937
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-1502-AN13-0014 [US-1466344]

description:
US-1466344
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9664-AN12-0012 [US-1420917]

description:
US-1420917
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9664-AN12-0010 [US-1420908]

description:
US-1420908
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9649-AN12-0076 [US-1470702]

description:
US-1470702
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9649-AN12-0078 [US-1470701]

description:
US-1470701
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9649-AN12-0014 [US-1470583]

description:
US-1470583
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9649-AN12-0074 [US-1470757]

description:
US-1470757
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9649-AN12-0012 [US-1470745]

description:
US-1470745
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz