title: tumor_endometrial [GL4440E], Dataset A

description:
GL4440E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2865E], Dataset A

status: Public on Jan 08 2018

type: RNA

city: New York

first: Li-Xuan

last: Qin

state: New York

address: 485 Lexington Ave

department: Epidemiology and Biostatistics

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
JB2865E
microRNA expression of tumor tissue.
Total RNA or miRNA

hyb_protocol: Human miRNA microarrays (Agilent Technologies), containing 3,523 markers that represent 1,205 human and 142 human viral miRNAs, were used for miRNA expression profiling according to the manufacturer’s protocol.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner G2505C US83903565 using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters. Logged 2 transformation followed by median probe-set summarization was done in R-3.3.0 software.

molecule: total RNA

organism: Homo sapiens

source_name: endometrial tumor sample

label_protocol: For samples meeting the quality control standards, 200 ng of total RNA was labeled using the miRNA Complete Labeling and Hybridization Kit (Agilent). The manufacturer's instructions were followed.

extract_protocol: Sample preparation used strict quality control on the specimens. Freshly harvested tissue was snap frozen for eventual cryomold embedding and RNA extraction or microarray analysis. Before RNA extraction, a 5-um hematoxylin and eosin histologic section was cut from the top of the cryomold to assess for tumor content and percentage of necrosis. For any specimens with less than 60% tumor cell nuclei, we used macrodissection to obtain enriched areas so as to make the specimen usable for RNA extraction and as uniform as possible. All specimens had less than 20% necrosis. All pathology specimens used for molecular study were diagnosed by dedicated gynecologic pathologists to establish histologic cell type, grade of malignancy, and site of origin. RNA was extracted from 30 to 100 mg of macrodissected cryomold tissue using the Ambion mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Total RNA yield and quality were assessed using a NanoDrop spectrophotometer and an Agilent Bioanalyzer.

tag: disease state

value: endometrioid endometrial cancer

tag: tissue

value: tumor


title: tumor_ovarian [JB4453V], Dataset A

description:
JB4453V
microRNA expression of tumor tissue.
Total RNA or miRNA

source_name: ovarian tumor sample

value: advanced serous ovarian cancer


title: tumor_ovarian [JB3137V], Dataset A

description:
JB3137V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1996E], Dataset A

description:
JB1996E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2906E], Dataset A

description:
JB2906E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4899V], Dataset A

description:
JB4899V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4577V], Dataset A

description:
JB4577V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2669E], Dataset A

description:
JB2669E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2636E], Dataset A

description:
JB2636E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2851E], Dataset A

description:
JB2851E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL3907E], Dataset A

description:
GL3907E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: gsi_2

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description:
replicate 2
5056679033_G

hyb_protocol: An aliquot of cRNA was run in triplicate on a Nanodrop spectrophotometer to determine sample concentration and yield. Samples were normalised to 150ng/µl. An aliquot of normalised cRNA was run on an Agilent Bioanalyser RNA Nano capillary electrophoresis chip to determine quality.   750ng of labelled cRNA was hybridised to Illumina BeadArrays overnight following Illumina WGGX DirectHyb Assay Guide (11286331 RevA)

scan_protocol: BeadArrays were scanned using the AutoLoader and BeadArray scanner at default settings following the BeadArray Reader User Guide (11179510 RevB). Metric files produced automatically save P95 and P05 readings and .xml files save scanner settings.

data_processing: The data was log base 2 quantile normalised using the beadarray package in R

source_name: MCF-7 human cell lines

label_protocol: BeadArrays were washed and stained with streptavidin Cy3 following the Illumina WGGX DirectHyb Assay Guide (11286331 RevA)

growth_protocol: MCF-7 breast cancer cells were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted from treated MCF-7 breast cancer cells using the Qiagen miRNeasy kit according to the manufacturer's instructions.

treatment_protocol: EDTA treatment was performed at a final concentration of 10mM for 1 hour.  GSI treatment was with the compound MRK-003 at a dose of 10uM for four hours.  For the combination treatment arm, cells were treated with the GSI at 10uM for four hours, and EDTA at 10mM was added for the final hour.

tag: cell line

value: MCF-7 breast cancer cells

tag: agent

value: gsi


title: tumor_endometrial [GL4660E], Dataset A

description:
GL4660E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: control_3

description:
replicate 3
5056679033_L

value: control


title: edtagsi_1

description:
replicate 1
5056679033_J

value: edtagsi


title: tumor_endometrial [JB4870E], Dataset A

description:
JB4870E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: edta_2

description:
replicate 2
5056679033_K

value: edta


title: gsi_1

description:
replicate 1
5056679033_I


title: edtagsi_2

description:
replicate 2
5056679033_H


title: edta_1

description:
replicate 1
5056679033_E


title: tumor_ovarian [JB3905V], Dataset A

description:
JB3905V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: gsi_3

description:
replicate 3
5056679033_D


title: control_2

description:
replicate 2
5056679033_F


title: tumor_ovarian [JB5011V], Dataset A

description:
JB5011V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3172V], Dataset A

description:
JB3172V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB5143V], Dataset A

description:
JB5143V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: edtagsi_3

description:
replicate 3
5056679033_C


title: edta_3

description:
replicate 3
5056679033_B


title: control_1

description:
replicate 1
5056679033_A


title: R-7: Breast cancer_neo-adjuvant chemotherapy resistant_CAFs_patient7

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: This sample is isolated from breast cancer resistant to neo-adjuvant chemotherapy

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing:
Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.
High quality expression values will be selected for analysis(for example, where at least 6 out of 14 samples have values within cut-off, cut-off =50). Then differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups.

source_name: Cancer associated fibroblasts (CAFs) from neo-adjuvant chemotherapy resistant breast cancer

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Primary cancer associated fibroblasts (CAFs) and breast cancer cells were isolated from breast invasive ductal carcinoma samples obtained from vacuum-assisted biopsies or mastectomies

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: neo-adjuvant chemotherapy

value: resistant


title: R-5: Breast cancer_neo-adjuvant chemotherapy resistant_CAFs_patient5

value: Cancer associated fibroblasts (CAFs) from neo-adjuvant chemotherapy resistant breast cancer


title: S-1: Breast cancer_neo-adjuvant chemotherapy sensitive_CAFs_patient1

description: This sample is isolated from breast cancer sensitive to neo-adjuvant chemotherapy

source_name: Cancer associated fibroblasts (CAFs) from neo-adjuvant chemotherapy sensitive breast cancer

value: sensitive


title: R-6: Breast cancer_neo-adjuvant chemotherapy resistant_CAFs_patient6


title: S-4: Breast cancer_neo-adjuvant chemotherapy sensitive_CAFs_patient4

value: Cancer associated fibroblasts (CAFs) from neo-adjuvant chemotherapy sensitive breast cancer


title: S-7: Breast cancer_neo-adjuvant chemotherapy sensitive_CAFs_patient7


title: R-2: Breast cancer_neo-adjuvant chemotherapy resistant_CAFs_patient2


title: S-5: Breast cancer_neo-adjuvant chemotherapy sensitive_CAFs_patient5


title: R-1: Breast cancer_neo-adjuvant chemotherapy resistant_CAFs_patient1


title: S-2: Breast cancer_neo-adjuvant chemotherapy sensitive_CAFs_patient2


title: S-6: Breast cancer_neo-adjuvant chemotherapy sensitive_CAFs_patient6


title: R-3: Breast cancer_neo-adjuvant chemotherapy resistant_CAFs_patient3


title: R-4: Breast cancer_neo-adjuvant chemotherapy resistant_CAFs_patient4


title: Caki-1 Dasatinib 12h, biological rep3

city: Shanghai

first: Meiyu

last: Geng

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Material Medica

description: Renal cell carcinoma

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix)in Hybridization Oven 645 (Affymetrix)and Fluidics Station 450 (Affymetrix) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Affymetrix) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies).

label: biotin

source_name: Caki-1 treated with Dasatinib at 1uM for 12h

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Affymetrix) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells were routinely cultured in air incubator at 37°C with 5% CO2

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit (QIAGEN) and RNase-Free DNase Set (QIAGEN).

treatment_protocol: Cells were treated with DMSO or Dasatinib at 1uM for 6, 12 and 24 hours.

tag: treatment

value: Dasatinib at 1uM for 12h


title: 769-P Dasatinib 6h, biological rep3

description: Renal cell carcinoma

source_name: 769-P treated with Dasatinib at 1uM for 6h

value: Dasatinib at 1uM for 6h


title: Caki-1 Dasatinib 24h, biological rep1

description: Renal cell carcinoma

source_name: Caki-1 treated with Dasatinib at 1uM for 24h

value: Dasatinib at 1uM for 24h


title: 769-P control, biological rep1

description: Renal cell carcinoma

source_name: 769-P treated with DMSO

value: DMSO


title: 769-P Dasatinib 24h, biological rep3

description: Renal cell carcinoma

source_name: 769-P treated with Dasatinib at 1uM for 24h


title: 769-P Dasatinib 12h, biological rep2

description: Renal cell carcinoma

source_name: 769-P treated with Dasatinib at 1uM for 12h


title: 769-P Dasatinib 24h, biological rep1

description: Renal cell carcinoma


title: 769-P control, biological rep3

description: Renal cell carcinoma


title: Caki-1 Dasatinib 24h, biological rep3

description: Renal cell carcinoma


title: 769-P Dasatinib 6h, biological rep2

description: Renal cell carcinoma


title: 769-P Dasatinib 12h, biological rep1

description: Renal cell carcinoma


title: 769-P Dasatinib 12h, biological rep3

description: Renal cell carcinoma


title: 769-P Dasatinib 24h, biological rep2

description: Renal cell carcinoma


title: 769-P Dasatinib 6h, biological rep1

description: Renal cell carcinoma


title: Caki-1 Dasatinib 24h, biological rep2

description: Renal cell carcinoma


title: 8713.03

type: SRA

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.1)
Reads were mapped to the reference genome (bosTau7) using the software package Tophat (version: 2.0.13).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.2.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.2.1) was used for merging together each of the assemblies with the reference mouse annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Cow genome assembly: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files including locus, number of mapped reads, and gene name

organism: Bos taurus

source_name: Mammary gland

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration was determined on Qubit® 2.0 Fluorometer (ThermoFisher, Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, USA). Sequencing libraries were created from 500 ng samples and sequenced with Illumina’s NextSeq 500 at the University of Florida Biotechnology Center.

value: Mammary gland

tag: breed

value: Holstein

tag: subject id

value: HT

tag: time

value: Day 3


title: S-3: Breast cancer_neo-adjuvant chemotherapy sensitive_CAFs_patient3


title: 8713.25

value: Day 25


title: 8713.14

value: Day 14


title: Caki-1 Dasatinib 6h, biological rep2

description: Renal cell carcinoma

source_name: Caki-1 treated with Dasatinib at 1uM for 6h


title: 769-P control, biological rep2

description: Renal cell carcinoma


title: Caki-1 Dasatinib 12h, biological rep1

description: Renal cell carcinoma


title: Caki-1 Dasatinib 6h, biological rep1

description: Renal cell carcinoma


title: 8713.00

value: Day -3


title: Caki-1 Dasatinib 12h, biological rep2

description: Renal cell carcinoma


title: Caki-1 control, biological rep3

description: Renal cell carcinoma

source_name: Caki-1 treated with DMSO


title: 8686.00

value: CL


title: 8686.14


title: 8686.07

value: Day 7


title: Caki-1 Dasatinib 6h, biological rep3

description: Renal cell carcinoma


title: 8686.25


title: 8660.03


title: 8668.14


title: 8660.25


title: 8686.03


title: 8668.03


title: 8668.25


title: 8660.14


title: 8713.07


title: 8668.00


title: 8647.14


title: 8668.07


title: 8647.07


title: 8660.07


title: 8647.03


title: 8660.00


title: Caki-1 control, biological rep2

description: Renal cell carcinoma


title: Caki-1 control, biological rep1

description: Renal cell carcinoma


title: 8603.25


title: 8603.07


title: 8603.14


title: 8647.00


title: 8603.03


title: 8603.00


title: 8564.07


title: 8564.14


title: 8564.00


title: 8647.25


title: 8541.07


title: 8513.14


title: 8541.00


title: 8541.03


title: 8513.25


title: 8513.07


title: HFD-WT-2-4

city: New Haven

first: Xinshou

last: Ouyang

state: CT

address: 1 Gilbert street

department: Internal Medicine

institute: Yale University

hyb_protocol: Illumina Mouse Ref-8 v2.0 Expression BeadChips.

scan_protocol: Arrays were scanned.

data_processing:
We used the gcRMA normalization, which is one type of quantile normalization. When the normalization was done, every array was included. Then, the different biological replicates were merged into one group and we compared the gene expression profiles across different treatment groups to identify differentially expressed genes. The fold change between any given two groups was calculated in the following way. If the ratio of group1/group2 is larger than 1, the fold change will be group1/group2. If the ratio of group1/group2 is smaller than 1, the fold change will be – group2/group1. In this way, the sign of the fold change reflects whether the gene is up- or down-regulated in group1 compared to group2.
The gcRMA data for each sample is not available.

label: Biotin

organism: Mus musculus

source_name: Liver

label_protocol: This assay used biotin labeled RNA. Illumina Total Prep RNA Amplification Kit (AMIL1791).

extract_protocol: The total RNA was extracted from whole liver tissue using TRIZOL reagent (Invitrogen), and further cleaned up by RNeasy clean up kit (QIAGEN).

treatment_protocol: The C57BL/6 mice were on high-fat diet (HFD) with con-current treatment of digoxin (1mg/g, twice a week, I.P.).

tag: strain/background

value: Liver

tag: diet

value: HFD for 12 weeks

value: Vehicle control


title: 8513.03


title: 8314.14


title: 8314.25


title: 8541.14


title: 8513.00


title: 8314.07


title: HFD-DIG-1-6

value: Digoxin


title: 8314.03


title: HFD-WT-1-3


title: WT-LIVER-2

value: Normal chow


title: 8564.25


title: 8564.03


title: 8060.25


title: HFD-WT-3-5


title: 8541.25


title: 8060.00


title: HFD-DIG-3-8


title: HFD-DIG-2-7


title: 7965.14


title: Xal2

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

description: Xal.fpkm.xls

data_processing:
Illumina HiSeq 2000 software used for basecalling.
Clean reads were obtained by removing low quality sequences, reads containing adapter and reads containing ploy-N.
In the mapping process,  index of the C. sinensis genome (http://citrus.hzau.edu.cn/orange/index.php) was built using the software Bowtie aligner (Langmead and Salzberg, 2012)
The remaining reads were mapped to the C. sinensis genome using the software TopHat2 (Kim et al., 2013). HTSeq (Anders et al, 2014) was used to count the reads numbers mapped to each gene.
The gene expression level was calculated by RPKM (reads per kilobases per millionmapped reads) method (Trapnell et al., 2010). Differentially expressed genes (DEGs) analysis were performed using EdgeR (version 1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach (Benjamini and Hochberg et al,1995) DEGs were identified using a FDR (false discovery rate) ≤ 0.05 and an absolute value of the log2 ratio ≥1.
Supplementary_files_format_and_content: Excel files include FPKM values for each gene.

organism: Citrus sinensis

source_name: citrus leaves

extract_protocol:
Equal amounts of frozen leaves from five seedlings (one seedling per pot) were pooled as one biological replicate. There were two biological replicates for each treatment. Total RNA was independently extracted twice from ca. 100 - 200 mg frozen control and +Al leaves of C. sinensis and C. grandis seedlings using Recalcirtant Plant Total RNA Extraction Kit (Centrifugal column type, Bioteke Corporation, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: seedling

value: leaves

tag: treament

value: Aluminum for 18 weeks


title: Xal1

description: Xal.fpkm.xls


title: 7965.03

value: Mammary gland


title: WT-LIVER-1


title: Yal2

description: Yal.fpkm.xls

organism: Citrus maxima


title: 7965.25

value: Holstein


title: 8060.14


title: 8314.00

value: HT


title: DC

status: Public on Jan 07 2018

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

institute: Institute of Psychology

data_processing:
Low quality reads and unpaired reads was trimmed with Trimmomatic. Trimmed RNA raw reads were aligned  with TopHat 2.0.9.  Aligned bam files were assessed using cufflinks v.2.2.1(34) to generate a transcriptome assembly and to estimate the expression level (FPKM) of all detected genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
gene_expSC_DC.txt, where SC is control(q1)
gene_expSS_DS.txt, where SS is control(q1)
gene_expSS_SC.txt, where SS is control(q1)

source_name: DC, prefrontal cortex

extract_protocol:
Total RNA was extracted from the frozen tissues using the TIANamp DNA/RNA Isolation Kit (TIANGEN, Beijing, China), including additional treatment with RNase-free DNase I (Ambion, Guangzhou, China) for 30 minutes at 37°C to remove contaminating DNA.
1µg of RNA from a pool of 5 animals (200ng each) per experimental condition was used to generate an mRNA sequencing library using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, USA) following the manufacturer’s protocol. Briefly, polyA mRNA was purified and fragmented. Then, first and second strand cDNA synthesis was performed, ends were repaired and adenylated, adapters were ligated, and fragments were enriched with PCR amplification.
HiSEQ2K platform

treatment_protocol: Four treatment groups: (1) saline + saline (SS, n=10), (2) DDTC + saline (DS, n=10), (3) DDTC + cocaine (DC, n=10), and (4) saline + cocaine (SC, n=10). The treatment period was 8 days, days 1-3, baseline locomoter activity of every treatment group was assessed for 1 hour immediately following an intraperitoneal injection of saline. On days 4-8, groups (2) and (3) received an injection of saline or cocaine, respectively, 30 minutes after an injection of DDTC, while groups (1) and (4) also received an injection of saline or cocaine, respectively, but 30 minutes following an injection of saline.

value: DDTC + cocaine

value: prefrontal cortex


title: Yck1

description: Yck.fpkm.xls

value: control


title: DS

source_name: DS, prefrontal cortex

value: DDTC + saline


title: 7965.07

value: CL


title: Xck1

description: Xck.fpkm.xls


title: SS

source_name: SS, prefrontal cortex

value: saline + saline


title: 8060.03

value: Day 3


title: Yck2

description: Yck.fpkm.xls


title: 8060.07

value: Day 7


title: Yal1

description: Yal.fpkm.xls


title: 7965.00

value: Day -3


title: Ecad- 98

status: Public on Jan 06 2018

city: Cold Spring Harbor

first: Arnaud

last: Pommier

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor laboratory

data_processing:
Quality control performed with FastQC version 0.11.5
Reads alignement, mapping to the genome, data filtering, TPM calculation and PCA analysis was performed with AltAnalyze version 2.1.0 running the Kallisto algorithm
Pathway enrichment analysis was performed using Cytoscape version 3.5.1 with the ClueGO plugin version 2.0.0
Genome_build: EnsMart72, Mm (mm10)
Supplementary_files_format_and_content: TPM values for each sample

source_name: Pancreatic ductal adenocarcinoma cell line

growth_protocol: Cells were cultured in DMEM 10% FBS, passages 4 to 6 were used

extract_protocol:
PDA cells were adjusted to 200 cells/µL and applied to the Fluidigm C1 system for single-cell capture with a 10-17mm IFC. In the C1, whole-transcriptome amplification was performed with the Clontech SMARTer kit.
Illumina Nextera XT

treatment_protocol: Cells were trypsinized, stained with anti-Ecad antibody and sorted between positives and negatives on a FACSAria system

tag: strain

value: KPC

tag: Sex

value: male

tag: origin

value: liver metastasis

tag: cell type

value: Pancreatic ductal adenocarcinoma cells

tag: cell subpopulation

value: Ecad-


title: Ecad- 97


title: Ecad- 96


title: Ecad- 94


title: Ecad- 95


title: Ecad- 93


title: CS

source_name: CS, prefrontal cortex

value: saline + cocaine

tag: tissue


title: Ecad- 92


title: Ecad- 85


title: Ecad- 87


title: Ecad- 88


title: Ecad- 86


title: Ecad- 89


title: Ecad- 81


title: Spleen T regulatory cells #5

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Gene expression data from IL-2/IL-2ab complex enriched splenic derived Tregs

hyb_protocol: Samples were labled, hybridized, washed and stained according to manufacturer instructions.

scan_protocol: Arrays were scanned using the Affymerix Scanner 3000 7G

data_processing: Data were processed (corrections, normalization) using the Affymetrix Gene Expression Console, full signals and RMA normalization procedure.

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA was extracted from MACS isolated liver and spleen Treg using Nucleospin Kit (Macherey Nagel, Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: Following  treatment with IL-2/IL-2Ab complex on three subsequent days and 3 days pause, Treg from spleens and livers of Foxp3-GFP mice were sorted with a FACS Aria II Cell Sorter (BD Biosciences) and microarray analysis was performed using Affymetrix Mouse Gene ST 2.0 arrays (Affymetrix).

value: Spleen

value: Treg

tag: genotype


title: Spleen T regulatory cells #6

source_name: IL-2/IL-2ab complex enriched splenic derived Tregs


title: Ecad- 84


title: Liver T regulatory cells #3

description: Gene expression data from IL-2/IL-2ab complex enriched liver derived Tregs

value: Liver


title: Ecad- 78


title: Ecad- 80


title: Liver T regulatory cells #2

source_name: IL-2/IL-2ab complex enriched liver derived Tregs


title: Ecad- 82


title: Spleen T regulatory cells #4


title: Ecad- 79


title: Ecad- 90


title: Ecad- 77


title: Ecad- 74


title: Ecad- 75


title: Ecad- 83


title: Ecad- 73


title: Ecad- 91


title: Ecad- 72


title: Ecad- 76


title: Ecad- 69


title: Ecad- 71


title: Ecad- 70


title: Ecad- 68


title: Ecad- 67


title: Ecad- 66


title: Ecad- 65


title: Ecad- 53


title: Ecad- 63


title: Ecad- 61


title: Ecad- 62


title: Ecad- 60


title: Ecad- 56


title: Liver T regulatory cells #7


title: Ecad- 58


title: Ecad- 46


title: Ecad- 51


title: Ecad- 59


title: Ecad- 57


title: Ecad- 52


title: Ecad- 45


title: Ecad- 48


title: Ecad- 50


title: Ecad- 64


title: Ecad- 44


title: Ecad- 55


title: Ecad- 42


title: Ecad- 40


title: Ecad- 39


title: Ecad- 41


title: Ecad- 38


title: Ecad- 47


title: Ecad- 49


title: Ecad- 54


title: Ecad- 43


title: Ecad- 37


title: Ecad- 33


title: Ecad- 29


title: Ecad- 36


title: Ecad- 27


title: Ecad- 31


title: Ecad- 35


title: Ecad- 32


title: Ecad- 18


title: Ecad- 28


title: Ecad- 26


title: Ecad- 19


title: Ecad- 25


title: Ecad- 22


title: Ecad- 23


title: Ecad- 17


title: Ecad- 34


title: Ecad- 30


title: Ecad- 9


title: Ecad- 24


title: Ecad- 15


title: Ecad- 13


title: Ecad- 14


title: Ecad- 12


title: Ecad- 16


title: Ecad- 6


title: Ecad- 5


title: Ecad- 10


title: Ecad- 4


title: Ecad- 11


title: Ecad- 8


title: Ecad- 2


title: Ecad+ 104

value: Ecad+


title: Ecad- 3


title: Ecad+ 103


title: Ecad- 20


title: Ecad- 7


title: Ecad- 21


title: Ecad+ 92


title: Ecad+ 95


title: Ecad+ 102


title: Ecad+ 100


title: Ecad+ 90


title: Ecad+ 99


title: Ecad+ 93


title: Ecad+ 94


title: Ecad+ 96


title: Ecad+ 101


title: Ecad+ 97


title: Ecad+ 91


title: Ecad+ 89


title: Ecad+ 98


title: Xck2

description: Xck.fpkm.xls

value: seedling

value: leaves

value: control


title: Ecad+ 88


title: Ecad+ 86


title: Ecad+ 85


title: Ecad+ 84


title: Ecad+ 87


title: Ecad+ 82


title: Ecad+ 83


title: Ecad- 1


title: Ecad+ 80


title: Ecad+ 81


title: Ecad+ 79


title: Ecad+ 76


title: Ecad+ 77


title: Ecad+ 75


title: Ecad+ 78


title: Ecad+ 73


title: Ecad+ 74


title: Ecad+ 72


title: Ecad+ 69


title: Ecad+ 70


title: Ecad+ 71


title: Ecad+ 68


title: Ecad+ 66


title: Ecad+ 65


title: Ecad+ 64


title: Ecad+ 58


title: Ecad+ 59


title: Ecad+ 63


title: Ecad+ 57


title: Ecad+ 62


title: Ecad+ 60


title: Ecad+ 56


title: Ecad+ 55


title: Ecad+ 53


title: Ecad+ 52


title: Ecad+ 54


title: Ecad+ 50


title: Ecad+ 67


title: Ecad+ 49


title: Ecad+ 48


title: Ecad+ 46


title: Ecad+ 45


title: Ecad+ 61


title: Ecad+ 41


title: Ecad+ 39


title: Ecad+ 43


title: Ecad+ 44


title: Ecad+ 47


title: Ecad+ 40


title: Ecad+ 36


title: Ecad+ 42


title: Ecad+ 35


title: Ecad+ 38


title: Ecad+ 37


title: Ecad+ 33


title: Ecad+ 29


title: Ecad+ 31


title: Ecad+ 28


title: Ecad+ 51


title: Ecad+ 27


title: Ecad+ 34


title: Ecad+ 32


title: Ecad+ 26


title: Ecad+ 25


title: Ecad+ 23


title: Ecad+ 22


title: Ecad+ 17


title: Ecad+ 21


title: Ecad+ 18


title: Ecad+ 19


title: Ecad+ 12


title: Ecad+ 20


title: Ecad+ 16


title: Ecad+ 13


title: Ecad+ 11


title: Ecad+ 14


title: Ecad+ 30


title: Ecad+ 10


title: Ecad+ 4


title: Ecad+ 6


title: Ecad+ 9


title: Ecad+ 7


title: Ecad+ 3


title: Ecad+ 1


title: Ecad+ 5


title: Ecad+ 2


title: Ecad+ 24


title: Ecad+ 15


title: Ecad+ 8


title: C57BL/6 Spleen infected with P.berghei treated with SALINE rep 1

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip mouse 2.0 ST arrays according to manufacturer's recommendations

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: Cel files representing individual samples were normalized using RMA normalization followed by median normalization.

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: C57BL/6 mice were were obtained from The Jackson Laboratories.

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: Mice were infected by injecting intraperitoneally 1x106 PbA or saline.  For treatment of mice in these studies which weighed approximately 20g, the stock rapamycin solution was diluted into a solution of 5% Poly(ethylene glycol) (Sigma)-400, 4% ethanol and 5% Tween 80 for a final concentration of rapamycin of 1 mg/ml or saline.

tag: infection

value: SALINE


title: C57BL/6 Spleen infected with P.berghei treated with RAPAMYCIN rep 2

value: RAPAMYCIN


title: C57BL/6 Spleen infected with Saline treated with SALINE rep 3

value: Saline


title: C57BL/6 Spleen infected with Saline treated with SALINE rep 1


title: C57BL/6 Spleen infected with P.berghei treated with SALINE rep 4


title: C57BL/6 Spleen infected with Saline treated with RAPAMYCIN rep 3


title: C57BL/6 right hemisphere infected with Saline treated with SALINE rep 3

value: right hemisphere


title: C57BL/6 Spleen infected with Saline treated with SALINE rep 2


title: C57BL/6 Spleen infected with Saline treated with RAPAMYCIN rep 1


title: C57BL/6 Spleen infected with Saline treated with SALINE rep 4


title: C57BL/6 right hemisphere infected with P.berghei treated with SALINE rep 4


title: C57BL/6 Spleen infected with Saline treated with RAPAMYCIN rep 2


title: C57BL/6 Spleen infected with P.berghei treated with RAPAMYCIN rep 3


title: C57BL/6 Spleen infected with Saline treated with RAPAMYCIN rep 4


title: C57BL/6 Spleen infected with P.berghei treated with RAPAMYCIN rep 4


title: C57BL/6 Spleen infected with P.berghei treated with SALINE rep 2


title: C57BL/6 right hemisphere infected with Saline treated with SALINE rep 2


title: C57BL/6 right hemisphere infected with Saline treated with RAPAMYCIN rep 2


title: C57BL/6 right hemisphere infected with Saline treated with RAPAMYCIN rep 4


title: C57BL/6 right hemisphere infected with P.berghei treated with RAPAMYCIN rep 3


title: C57BL/6 right hemisphere infected with Saline treated with SALINE rep 1


title: C57BL/6 right hemisphere infected with Saline treated with RAPAMYCIN rep 1


title: C57BL/6 right hemisphere infected with P.berghei treated with SALINE rep 1


title: C57BL/6 right hemisphere infected with P.berghei treated with RAPAMYCIN rep 4


title: C57BL/6 right hemisphere infected with P.berghei treated with SALINE rep 3


title: C57BL/6 right hemisphere infected with Saline treated with SALINE rep 4


title: C57BL/6 right hemisphere infected with P.berghei treated with SALINE rep 2


title: C57BL/6 Spleen infected with P.berghei treated with SALINE rep 3


title: C57BL/6 right hemisphere infected with Saline treated with RAPAMYCIN rep 3


title: C57BL/6 Spleen infected with P.berghei treated with RAPAMYCIN rep 1


title: C57BL/6 Olfactory bulb infected with P.berghei treated with SALINE rep 3

value: Olfactory bulb


title: C57BL/6 Olfactory bulb infected with Saline treated with RAPAMYCIN rep 3


title: C57BL/6 Olfactory bulb infected with P.berghei treated with RAPAMYCIN rep 2


title: C57BL/6 right hemisphere infected with P.berghei treated with RAPAMYCIN rep 2


title: C57BL/6 Olfactory bulb infected with Saline treated with RAPAMYCIN rep 2


title: C57BL/6 Olfactory bulb infected with Saline treated with SALINE rep 3


title: C57BL/6 Olfactory bulb infected with Saline treated with SALINE rep 1


title: C57BL/6 right hemisphere infected with P.berghei treated with RAPAMYCIN rep 1


title: C57BL/6 Olfactory bulb infected with P.berghei treated with RAPAMYCIN rep 3


title: C57BL/6 Olfactory bulb infected with P.berghei treated with RAPAMYCIN rep 1


title: C57BL/6 Olfactory bulb infected with Saline treated with RAPAMYCIN rep 4


title: C57BL/6 Olfactory bulb infected with Saline treated with SALINE rep 4


title: C57BL/6 Cerebellum infected with P.berghei treated with SALINE rep 4

value: Cerebellum


title: C57BL/6 Olfactory bulb infected with Saline treated with RAPAMYCIN rep 1


title: C57BL/6 Cerebellum infected with Saline treated with SALINE rep 3


title: C57BL/6 Olfactory bulb infected with Saline treated with SALINE rep 2


title: C57BL/6 Olfactory bulb infected with P.berghei treated with RAPAMYCIN rep 4


title: C57BL/6 Olfactory bulb infected with P.berghei treated with SALINE rep 2


title: C57BL/6 Cerebellum infected with P.berghei treated with SALINE rep 2


title: C57BL/6 Cerebellum infected with Saline treated with RAPAMYCIN rep 3


title: C57BL/6 Olfactory bulb infected with P.berghei treated with SALINE rep 4


title: C57BL/6 Cerebellum infected with Saline treated with SALINE rep 1


title: C57BL/6 Cerebellum infected with P.berghei treated with SALINE rep 1


title: C57BL/6 Olfactory bulb infected with P.berghei treated with SALINE rep 1


title: C57BL/6 Cerebellum infected with P.berghei treated with SALINE rep 3


title: C57BL/6 Cerebellum infected with Saline treated with SALINE rep 2


title: C57BL/6 Cerebellum infected with Saline treated with SALINE rep 4


title: C57BL/6 Cerebellum infected with Saline treated with RAPAMYCIN rep 2


title: C57BL/6 Cerebellum infected with Saline treated with RAPAMYCIN rep 4


title: C57BL/6 Cerebellum infected with Saline treated with RAPAMYCIN rep 1


title: C57BL/6 Cerebellum infected with P.berghei treated with RAPAMYCIN rep 3


title: C57BL/6 Cerebellum infected with P.berghei treated with RAPAMYCIN rep 1


title: C57BL/6 Cerebellum infected with P.berghei treated with RAPAMYCIN rep 4


title: Appressoria-24h-Biorep3, techrep1

status: Public on Jan 05 2018

city: College Station

first: Andrew

last: Tag

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

hyb_protocol: Agilent 60-mer oligo microarray processing protocol for cRNA targets.

scan_protocol: Scanned on an Affymetrix 428 array scanner. Images quantified using Axon GenePix software version 4.0.1.19

data_processing: Agilent GeneSpring version 7.3 software was used for background subtraction and LOWESS normalization.

organism: Pyricularia grisea

source_name: Delta bip1 24h appressoria on Teflon

label_protocol: Ambion AminoAllyl MessageAmp aRNA kit according to the manufacturer's recommendations.

extract_protocol: Hot acid phenol method (Ausubel, et al., 1994).

tag: genotype/variation

value: Delta bip1

value: Appressoria

source_name: P1.2 24h appressoria on Teflon


title: Appressoria-24h-Biorep1, techrep2s


title: Appressoria-24h-Biorep3, techrep2s


title: Appressoria-24h-Biorep2, techrep2s


title: Appressoria-24h-Biorep1, techrep2


title: C57BL/6 Cerebellum infected with P.berghei treated with RAPAMYCIN rep 2

tag: treatment


title: Appressoria-24h-Biorep3, techrep2


title: Appressoria-24h-Biorep2, techrep2


title: Appressoria-24h-Biorep2, techrep1s


title: Appressoria-24h-Biorep3, techrep1s


title: Appressoria-24h-Biorep1, techrep1s


title: Appressoria-24h-Biorep2, techrep1


title: Appressoria-24h-Biorep1, techrep1


title: Brain tumor; SAMPLE 188

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'

label: biotin/DNP

molecule: genomic DNA

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: brain tumor

tag: histology

value: Glioblastoma (WHO grade IV)

tag: age

tag: mgmtstatus

value: unmethylated

tag: os

tag: OS status

tag: pfs


title: Brain tumor; SAMPLE 180


title: Brain tumor; SAMPLE 178


title: Brain tumor; SAMPLE 189


title: Brain tumor; SAMPLE 177


title: Brain tumor; SAMPLE 186

value: Diffuse Astrocytoma (WHO grade II)


title: Brain tumor; SAMPLE 174


title: Brain tumor; SAMPLE 175


title: Brain tumor; SAMPLE 183

value: Ganglioneuroblastom


title: Brain tumor; SAMPLE 184


title: Brain tumor; SAMPLE 179

value: methylated


title: Brain tumor; SAMPLE 181


title: Brain tumor; SAMPLE 185

value: Pilocytic Astrocytoma (WHO grade I)


title: Brain tumor; SAMPLE 172


title: Brain tumor; SAMPLE 187


title: Brain tumor; SAMPLE 182


title: Brain tumor; SAMPLE 169


title: Brain tumor; SAMPLE 173


title: Brain tumor; SAMPLE 162


title: Brain tumor; SAMPLE 167


title: Brain tumor; SAMPLE 161


title: Brain tumor; SAMPLE 176


title: Brain tumor; SAMPLE 163


title: Brain tumor; SAMPLE 171


title: Brain tumor; SAMPLE 164


title: Brain tumor; SAMPLE 166


title: Brain tumor; SAMPLE 170


title: Brain tumor; SAMPLE 168


title: Brain tumor; SAMPLE 160


title: Brain tumor; SAMPLE 165


title: Brain tumor; SAMPLE 157

value: Gliosarcoma (WHO grade IV)


title: Brain tumor; SAMPLE 155


title: Brain tumor; SAMPLE 159


title: Brain tumor; SAMPLE 156


title: Brain tumor; SAMPLE 149


title: Brain tumor; SAMPLE 152


title: Brain tumor; SAMPLE 148


title: Brain tumor; SAMPLE 153


title: Brain tumor; SAMPLE 154


title: Brain tumor; SAMPLE 143


title: Brain tumor; SAMPLE 144


title: Brain tumor; SAMPLE 140


title: Brain tumor; SAMPLE 146


title: Brain tumor; SAMPLE 141


title: Brain tumor; SAMPLE 150


title: Brain tumor; SAMPLE 138


title: Brain tumor; SAMPLE 147


title: Brain tumor; SAMPLE 158


title: Brain tumor; SAMPLE 137


title: Brain tumor; SAMPLE 142

value: Diffuse astrocytoma (WHO grade II)


title: Brain tumor; SAMPLE 145


title: Brain tumor; SAMPLE 139


title: Brain tumor; SAMPLE 151


title: Brain tumor; SAMPLE 136


title: Brain tumor; SAMPLE 130


title: Brain tumor; SAMPLE 134


title: Brain tumor; SAMPLE 135


title: Brain tumor; SAMPLE 131


title: Brain tumor; SAMPLE 132


title: Brain tumor; SAMPLE 133

value: Anaplastic astrocytoma (WHO grade III)


title: Brain tumor; SAMPLE 127


title: Brain tumor; SAMPLE 129


title: Brain tumor; SAMPLE 123


title: Brain tumor; SAMPLE 122

value: Anaplastic Astrocytoma (WHO grade III)


title: Brain tumor; SAMPLE 120


title: Brain tumor; SAMPLE 112


title: Brain tumor; SAMPLE 124


title: Brain tumor; SAMPLE 121


title: Brain tumor; SAMPLE 114


title: Brain tumor; SAMPLE 116


title: Brain tumor; SAMPLE 111


title: Brain tumor; SAMPLE 99


title: Brain tumor; SAMPLE 117


title: Brain tumor; SAMPLE 128


title: Brain tumor; SAMPLE 103


title: Brain tumor; SAMPLE 101


title: Brain tumor; SAMPLE 107

value: Maligner glialer Tumor


title: Brain tumor; SAMPLE 100


title: Brain tumor; SAMPLE 105


title: Brain tumor; SAMPLE 102


title: Brain tumor; SAMPLE 96


title: Brain tumor; SAMPLE 98


title: Brain tumor; SAMPLE 104


title: Brain tumor; SAMPLE 119


title: Brain tumor; SAMPLE 113


title: Brain tumor; SAMPLE 110

value: Malignes Hirnstammgliom


title: Brain tumor; SAMPLE 108


title: Brain tumor; SAMPLE 95


title: Brain tumor; SAMPLE 94


title: Brain tumor; SAMPLE 97


title: Brain tumor; SAMPLE 93


title: Brain tumor; SAMPLE 92


title: Brain tumor; SAMPLE 109


title: Brain tumor; SAMPLE 90


title: Brain tumor; SAMPLE 89


title: Brain tumor; SAMPLE 91


title: Brain tumor; SAMPLE 86


title: Brain tumor; SAMPLE 83


title: Brain tumor; SAMPLE 87


title: Brain tumor; SAMPLE 71


title: Brain tumor; SAMPLE 70


title: Brain tumor; SAMPLE 79


title: Brain tumor; SAMPLE 73


title: Brain tumor; SAMPLE 69


title: Brain tumor; SAMPLE 76


title: Brain tumor; SAMPLE 75


title: Brain tumor; SAMPLE 88


title: Brain tumor; SAMPLE 72


title: Brain tumor; SAMPLE 81


title: Brain tumor; SAMPLE 84


title: Brain tumor; SAMPLE 85


title: Brain tumor; SAMPLE 65


title: Brain tumor; SAMPLE 74


title: Brain tumor; SAMPLE 77


title: Brain tumor; SAMPLE 78


title: Brain tumor; SAMPLE 68


title: Brain tumor; SAMPLE 66


title: Brain tumor; SAMPLE 64


title: Brain tumor; SAMPLE 67


title: Brain tumor; SAMPLE 62


title: Brain tumor; SAMPLE 80


title: Brain tumor; SAMPLE 63


title: Brain tumor; SAMPLE 59


title: Brain tumor; SAMPLE 60


title: Brain tumor; SAMPLE 52


title: Brain tumor; SAMPLE 56


title: Brain tumor; SAMPLE 57


title: ExVivoBlood_Normal Control_rep1_miRNA

first: cai

last: cheng

address: No. 355, Luding Road

department: Department of neonatology

institute: Shanghai Children’s Hospital, Shanghai Jiao Tong University

description:
NC
Gene expression in Normal Control human blood

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual. a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min.b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.
The data matrix contains normalized signal intensity and is available on the series record.

source_name: Peripheral Blood, Normal Control, replicate 1

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps: a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: A total of 20 premature infants with BPD according to the National Institute of Child Health and Human Development (NICHD) guidelines and 20 non-BPD age-matched controls were enrolled from clinic at department of neonatology in Shanghai Children Hospital.

value: whole blood

tag: gestational age

value: 28 weeks

tag: diagnosis

value: normal


title: Brain tumor; SAMPLE 55


title: Brain tumor; SAMPLE 44


title: Brain tumor; SAMPLE 58


title: ExVivoBlood_Normal_rep6_miRNA

description:
N6
Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 6


title: Brain tumor; SAMPLE 49


title: Brain tumor; SAMPLE 82


title: Brain tumor; SAMPLE 61


title: Brain tumor; SAMPLE 54


title: Brain tumor; SAMPLE 38


title: Brain tumor; SAMPLE 39


title: Brain tumor; SAMPLE 53


title: Brain tumor; SAMPLE 42


title: 8465N

city: Tucson

first: Adam

middle: David

last: Grant

state: Arizona

address: 3760 E. Felix Blvd

department: Cancer Biology

institute: University of Arizona

data_processing:
RNA-sequencing was performed using Thermofisher’s SOLiD platform
RNA reads were aligned using ThermoFisher’s LifeScope Genomic Analysis software v.2.5.1
Counts were generated from aligned BAM files using HTSeq.
Counts were log-normalized using the edgeR R package.
Genes that had a TMM value less than 0 across all samples were discarded from the study
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file (gene sample expression matrix) includes gene TMM normalized values for each Sample

source_name: Breast Tissue

growth_protocol: Excess tissue from TNBC surgical resections was collected under an IRB approved protocol.

extract_protocol:
Total RNA was prepared from frozen tissue
Solid Total RNA sequencing kit

tag: disease state

value: TNBC

tag: rb status

value: pos

value: Breast (normal)

tag: grade


title: Brain tumor; SAMPLE 47

value: brain tumor

value: Glioblastoma (WHO grade IV)


title: Brain tumor; SAMPLE 45


title: 8465T

source_name: Triple Negative Breast Cancer

value: Breast (TNBC)


title: Brain tumor; SAMPLE 40

value: unmethylated


title: ExVivoBlood_Normal_rep4_miRNA

description:
N4
Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 4


title: Brain tumor; SAMPLE 41


title: 6169T


title: ExVivoBlood_Normal_rep2_miRNA

description:
N2
Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 2


title: 4334T

value: neg


title: ExVivoBlood_BPD_rep5_miRNA

description:
B5
Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 5

value: Bronchopulmonary dysplasia (BPD)


title: Brain tumor; SAMPLE 37

value: methylated


title: ExVivoBlood_BPD_rep4_miRNA

description:
B4
Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 4


title: Brain tumor; SAMPLE 48


title: 4334N


title: Brain tumor; SAMPLE 35


title: Brain tumor; SAMPLE 32


title: ExVivoBlood_BPD_rep3_miRNA

description:
B3
Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 3


title: Brain tumor; SAMPLE 36


title: Brain tumor; SAMPLE 33

value: Anaplastic astrocytoma (WHO grade III)


title: Brain tumor; SAMPLE 31


title: 2749T


title: 25511T


title: ExVivoBlood_BPD_rep2_miRNA

description:
B2
Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 2


title: Brain tumor; SAMPLE 34


title: Brain tumor; SAMPLE 28


title: 25511N


title: Brain tumor; SAMPLE 30


title: ExVivoBlood_BPD_rep1_miRNA

description:
B1
Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 1


title: ExVivoBlood_Normal_rep5_miRNA

description:
N5
Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 5


title: 24934T


title: Brain tumor; SAMPLE 46

value: Gliosarcoma (WHO grade IV)


title: arp6;brm Mnase-seq - rep2

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

institute: Emory University

description:
Nucleosomal DNA
processed data: arp6brm_30M.nucleosomes.bw
processed data: data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls

library_source: genomic

data_processing:
ChIP-seq workflow:
Reads were mapped to the TAIR10 A. thaliana reference genome with Bowtie2, using default parameters.
Reads were processed and quality filtered with the –q 2 option using SAMtools software.
H2A.Z peaks were called with Homer findpeaks software, using options “style histone” and “–region”.
RNA-seq workflow:
Sequencing reads were mapped to the TAIR10 Arabidopsis thaliana reference genome using Tophat2 (using the second strand option) and the accepted hits file was name-sorted and indexed using SAMtools.
Read counts were quantified for each exon using htseq-counts with name order and strict intersection options.
Differential expression was calculated using edgeR software.
MNase-seq workflow:
Sequence reads were mapped to the TAIR10 Arabidopsis thaliana reference genome using Bowtie2 and were then further sorted and indexed using SAMtools.
We filtered using the SAMtools view command with the –q 2 option to filter for quality and option –f 0x02 to filter for properly paired reads.
Libraries were subsampled using SAMtools –s parameter to normalize all to the same number of reads (30.46 M reads).
Mapped reads from both biological replicates for each of the four genotypes were analyzed using the DANPOS2 dpos program to generate nucleosome peak files and nucleosome occupancy wiq files.
DANPOS2 generated wig files were converted to the bigwigwig format with wig2bigwig command (UCSC).
arp6 deletion mapping workflow:
Sequenced reads were mapped using BWA mem software, indexed and quality sorted (-s option) using SAMtools, and randomly subsetted using a python script, leaving 61.5 M mapped reads.
Deletions were called in the arp6 mutant using CNVnator (v0.3.3) software using bin sizes of 100 bp.
Genome_build: TAIR10
Supplementary_files_format_and_content: WT1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the WT replicate 1 sample.
Supplementary_files_format_and_content: WT2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the WT replicate 2 sample.
Supplementary_files_format_and_content: A1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the arp6 replicate 1 sample.
Supplementary_files_format_and_content: A2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the arp6 replicate 2 sample.
Supplementary_files_format_and_content: B1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the brm replicate 1 sample.
Supplementary_files_format_and_content: B2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the brm replicate 2 sample.
Supplementary_files_format_and_content: WT_vs_arp6.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two arp6 mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_vs_brm.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two brm mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_vs_arp6brm.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two arp6;brm mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from WT plants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from arp6 mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: brm_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from brm mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6brm_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from arp6;brm mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between arp6 mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between brm mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between arp6;brm mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6_CNVnator_deletions.bed: Bed file containing the coordinates for large (>200bp) deletions in arp6 genotype relative to the TAIR10 reference genome generated by the CNVnator software.

organism: Arabidopsis thaliana

source_name: 4-5 leaf developmentally-staged shoot tissue

growth_protocol: Arabidopsis seedlings were grown on soil in 16 hours light/ 8 hours dark conditions.

extract_protocol:
Native chromatin from purified nuclei was digested with MNase. After lysing nuclei with 1% SDS, nucleosome associated DNA was purified using the MinElute kit (Qiagen), after RNase A and Proteinase K treatments. Fragments were size selected for those >400 bp using SeraPure magnetic beads.
Libraries were prepared with the ThruPLEX DNA-Seq kit (Rubicon Genomics) using 25 ng of MNase-digested DNA. Libraries were sequenced on a an Illumina NextSeq500 with 76 bp paired-end reads.

value: 4-5 leaf developmentally-staged shoot


title: 1836T


title: ExVivoBlood_Normal_rep3_miRNA

description:
N3
Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 3


title: arp6;brm Mnase-seq - rep1


title: 1836N


title: 15443T


title: brm Mnase-seq - rep1

description:
Nucleosomal DNA
processed data: brm_30M.nucleosomes.bw
processed data: data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls

value: brm


title: arp6 Mnase-seq - rep2

description:
Nucleosomal DNA
processed data: arp6_30M.nucleosomes.bw
processed data: data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls


title: Brain tumor; SAMPLE 23


title: Brain tumor; SAMPLE 25


title: Brain tumor; SAMPLE 21


title: Brain tumor; SAMPLE 27


title: 15443N


title: Brain tumor; SAMPLE 20


title: arp6 Mnase-seq - rep1


title: Brain tumor; SAMPLE 18


title: WT Mnase-seq - rep2

description:
Nucleosomal DNA
processed data: WT_30M.nucleosomes.bw
processed data: data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls
processed data: data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls
processed data: data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls

value: WT


title: Brain tumor; SAMPLE 19


title: STEC EC472 after 3 hrs incubation in fresh medium, replicate 2 [FRESH]

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description:
Gene expression from STEC EC472 after 3 hrs incubation in fresh medium, replicate 2
EC472F#14

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was hybridized to Agilent-020097 Escherichia coli Gene Expression Microarray (G4813A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 020097_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities but not included the normalization process.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Escherichia coli

source_name: STEC EC472/01, fresh medium

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 5 ug RNA using the Two-color microarray-based brokaryote analysis (Fairplay III labeling, versin APRIL/2009) modified for one color (Cy-3), followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: STEC strains were lysate using lysozyme (1 mg/mL) and proteinase K (2 mg/mL) and incubated for 10 min at 20°C. Total RNA was obtained using the RNeasy Mini Kit (Qiagen cat no. 74104, Valencia, CA) according to the manufacturer's instructions. The purity and quantification for all RNA samples were done using the NanoVue spectrophotometer and the RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA). All samples that present RIN > 7.0 were stored at -80°C until used in hybridization experiments.

treatment_protocol: The fresh medium (F) was the DMEM medium containing 10% FBS without antibiotics. 400 µL of STEC culture were inoculated in 4 mL of F medium and incubated for 3 hrs at 37°C. After this period the bacteria were recovered by centrifugation for 10 min at 5000 xg and the pellet was ressuspended in 600 µL of RNAprotect Bacteria Reagent (Qiagen cat. no. 76506, Valencia, CA) for RNA extraction.

tag: strain

value: EC472/01 (isolated from cattle)

tag: e.coli culture protocol

value: fresh medium


title: STEC EC472 after 3 hrs incubation in fresh medium, replicate 4 [FRESH]

description:
Gene expression from STEC EC472 after 3 hrs incubation in fresh medium, replicate 4
EC472F#16


title: STEC EC472 after 3 hrs incubation in fresh medium, replicate 3 [FRESH]

description:
Gene expression from STEC EC472 after 3 hrs incubation in fresh medium, replicate 3
EC472F#15


title: STEC EC472 after 3 hrs incubation in fresh medium, replicate 1 [FRESH]

description:
Gene expression from STEC EC472 after 3 hrs incubation in fresh medium, replicate 1
EC472F#13


title: Brain tumor; SAMPLE 9

tag: tissue


title: STEC EH41 after 3 hrs incubation in fresh medium, replicate 4 [FRESH]

description:
Gene expression from STEC EH41 after 3 hrs incubation in fresh medium, replicate 4
EH41F#8

source_name: STEC EH41, fresh medium

value: EH41 (isolated from patient with HUS)


title: Brain tumor; SAMPLE 10

source_name: brain tumor


title: 3B M3

city: GUANGZHOU

first: LIANG

middle: JIAN

last: KAI

state: GUANGDONG

address: NO.74 ZHONGSHAN NO.2 ROAD YUEXIU DISTRICT

department: PHARMACOLOGY

institute: SUN YAT-SEN UNIVERSITY

description: Gene expression data from normal human thalamencephalon

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 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.

source_name: Infected Hep3B cells

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

growth_protocol: DMEM added with 10%FBS

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: Mock infected or infected with M1 virus

tag: cell line

tag: cell type

value: liver cancer cell line

tag: infected with

value: M1 virus


title: arp6;brm RNA-seq - rep1

description: processed data: WT_vs_arp6brm.edgeR.txt

extract_protocol:
RNA was isolated from nuclei using the Spectrum Plant Total RNA kit (Sigma).
Libraries were prepared using the Ovation RNA-seq for Model Organisms kit (NuGEN), inputting 100 ng of RNA from each sample. Libraries were sequenced with the Illumina NextSeq generating paired-end 36-nt sequence reads.

tag: genotype/variation


title: Brain tumor; SAMPLE 24

description: Methylation data from brain tumor sample.

value: brain tumor

tag: histology

tag: age


title: Brain tumor; SAMPLE 14

value: Glioblastoma (WHO grade IV)

tag: mgmtstatus

tag: os


title: Brain tumor; SAMPLE 12

tag: OS status

tag: pfs


title: 3B M2


title: Brain tumor; SAMPLE 6


title: Brain tumor; SAMPLE 15


title: STEC EH41 after 3 hrs incubation in fresh medium, replicate 3 [FRESH]

description:
Gene expression from STEC EH41 after 3 hrs incubation in fresh medium, replicate 3
EH41F#7


title: 3B M1


title: brm RNA-seq - rep3

description: processed data: WT_vs_brm.edgeR.txt


title: Brain tumor; SAMPLE 26


title: Brain tumor; SAMPLE 16


title: brm RNA-seq - rep2

description: processed data: WT_vs_brm.edgeR.txt


title: Brain tumor; SAMPLE 11


title: Brain tumor; SAMPLE 7


title: STEC EH41 after 3 hrs incubation in fresh medium, replicate 1 [FRESH]

description:
Gene expression from STEC EH41 after 3 hrs incubation in fresh medium, replicate 1
EH41F#5


title: STEC EH41 after 3 hrs incubation in fresh medium, replicate 2 [FRESH]

description:
Gene expression from STEC EH41 after 3 hrs incubation in fresh medium, replicate 2
EH41F#6


title: brm RNA-seq - rep1

description: processed data: WT_vs_brm.edgeR.txt


title: Brain tumor; SAMPLE 51


title: 3B CTL3

source_name: Hep3B cells

value: mock (control)


title: 3B CTL2


title: Brain tumor; SAMPLE 4

value: unmethylated


title: STEC EC472 after 3 hrs incubation in conditioned medium, replicate 4 [COND]

description:
Gene expression from STEC EC472 after 3 hrs incubation in conditioned medium, replicate 4
EC472C#12

source_name: STEC EC472/01, conditioned medium

treatment_protocol: The conditioned medium (C) was the DMEM medium containing 10% FBS without antibiotics recovered after 24 hrs incubation with differentiated Caco-2 cells. 400 µL of STEC culture were inoculated in 4 mL of C medium and incubated for 3 hrs at 37°C. After this period the bacteria were recovered by centrifugation for 10 min at 5000 xg and the pellet was ressuspended in 600 µL of RNAprotect Bacteria Reagent (Qiagen cat. no. 76506, Valencia, CA) for RNA extraction.

value: conditioned Caco-2 cell medium


title: GAS 5448 WT vs pepO, rep3

city: St Lucia

first: Stephan

last: Brouwer

state: QLD

address: Cooper Road, Building 76, Rm 151

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

description: Biological replicate 3 of 3

hyb_protocol: 200 pmol each of Cy-dye (WT cDNA (Cy5) and pepO mutant cDNA (Cy3)) were combined in 200 µl hybridization buffer, denatured and hybridized to the array at 42˚C for at least 16 h, followed by subsequent washes

scan_protocol: Scanned on a GenePix 4000B scanner. Images were quantified using GenePixPro 4.0 software.

data_processing: Global normalization after removing genes not present in GAS M1T1 5448

organism: Streptococcus pyogenes

source_name: GAS M1T1 wild-type strain

label_protocol: Labeled cDNA was generated from 10 µg of total RNA using the Fairplay III microarray labelling kit (Agilent Technologies, Stratagene) using random primers

growth_protocol: M1T1 GAS 5448 strains grown in THY to mid-logarithmic growth phase (A600 ~ 0.8)

extract_protocol: Total RNA was extracted using the RNeasy minikit (Qiagen) according to the manufacturer's protocol

source_name: GAS M1T1 pepO mutant strain


title: arp6 RNA-seq - rep3

description: processed data: WT_vs_arp6.edgeR.txt


title: Brain tumor; SAMPLE 8


title: Brain tumor; SAMPLE 5


title: GAS 5448 WT vs pepO, rep2

description: Biological replicate 2 of 3


title: Brain tumor; SAMPLE 3


title: GAS 5448 WT vs pepO, rep1

description: Biological replicate 1 of 3


title: arp6 RNA-seq - rep2

description: processed data: WT_vs_arp6.edgeR.txt


title: 3B CTL1


title: STEC EC472 after 3 hrs incubation in conditioned medium, replicate 3 [COND]

description:
Gene expression from STEC EC472 after 3 hrs incubation in conditioned medium, replicate 3
EC472C#11


title: Brain tumor; SAMPLE 17


title: arp6;brm RNA-seq - rep3

description: processed data: WT_vs_arp6brm.edgeR.txt


title: arp6 RNA-seq - rep1

description: processed data: WT_vs_arp6.edgeR.txt


title: Brain tumor; SAMPLE 29


title: WT RNA-seq - rep3

description:
processed data: WT_vs_arp6.edgeR.txt
processed data: WT_vs_brm.edgeR.txt
processed data: WT_vs_arp6brm.edgeR.txt


title: brm Mnase-seq - rep2


title: STEC EC472 after 3 hrs incubation in conditioned medium, replicate 1 [COND]

description:
Gene expression from STEC EC472 after 3 hrs incubation in conditioned medium, replicate 1
EC472C#9


title: STEC EC472 after 3 hrs incubation in conditioned medium, replicate 2 [COND]

description:
Gene expression from STEC EC472 after 3 hrs incubation in conditioned medium, replicate 2
EC472C#10


title: STEC EH41 after 3 hrs incubation in conditioned medium, replicate 4 [COND]

description:
Gene expression from STEC EH41 after 3 hrs incubation in conditioned medium, replicate 4
EH41C#4

source_name: STEC EH41, conditioned medium


title: Brain tumor; SAMPLE 2


title: brm H2A.Z ChIP - rep2

description:
IP DNA
processed data: B2_Z_histone.bed

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with an H2A.Z antibody described previously (Deal et al. (2007) Plant Cell 19(1):74-83). DNA collected from the IP and input material was purified using 1.8x volume of SPRI beads (Beckman Coulter).
Libraries were prepared from 1 ng of DNA per sample with the Accel NGS 2S Plus DNA Library kit (Swift Biosciences) and sequenced on an Illumina NextSeq500 using 76 nt single-end reads.

tag: chip antibody


title: brm H2A.Z ChIP - rep1

description:
IP DNA
processed data: B1_Z_histone.bed


title: ExVivoBlood_Normal Control_rep1_mRNA

description: Gene expression in Normal Control human blood

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.

scan_protocol: 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).

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, genes that at least 1 out of 11 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: Peripheral Blood, Normal Control, replicate 1

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated from patient blood samples (BPD children and controls) using TRIzol reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions. RNA was quantified using NanoDrop ND-2000 Spectrophotometer (NanoDrop Wilmington DE

value: whole blood

tag: gestational age

value: 28 weeks

tag: diagnosis

value: normal


title: WT RNA-seq - rep2


title: ExVivoBlood_Normal_rep6_mRNA

description: Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 6


title: arp6;brm RNA-seq - rep2

description: processed data: WT_vs_arp6brm.edgeR.txt


title: brm input - rep2


title: STEC EH41 after 3 hrs incubation in conditioned medium, replicate 3 [COND]

description:
Gene expression from STEC EH41 after 3 hrs incubation in conditioned medium, replicate 3
EH41C#3


title: arp6 input - rep2


title: STEC EH41 after 3 hrs incubation in conditioned medium, replicate 1 [COND]

description:
Gene expression from STEC EH41 after 3 hrs incubation in conditioned medium, replicate 1
EH41C#1


title: ExVivoBlood_Normal_rep5_mRNA

description: Gene expression in Normal human blood


title: ExVivoBlood_Normal_rep2_mRNA

description: Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 2


title: brm input - rep1


title: WT RNA-seq - rep1


title: arp6 input - rep1


title: ExVivoBlood_BPD_rep4_mRNA

description: Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 4

value: Bronchopulmonary dysplasia (BPD)


title: ExVivoBlood_BPD_rep5_mRNA

description: Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 5


title: arp6 H2A.Z ChIP - rep2

description:
IP DNA
processed data: A2_Z_histone.bed

value: 4-5 leaf developmentally-staged shoot


title: ExVivoBlood_BPD_rep3_mRNA

description: Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 3


title: ExVivoBlood_Normal_rep3_mRNA

description: Gene expression in Normal human blood


title: ExVivoBlood_Normal_rep4_mRNA

description: Gene expression in Normal human blood

source_name: Peripheral Blood, Normal, replicate 4


title: arp6 H2A.Z ChIP - rep1

description:
IP DNA
processed data: A1_Z_histone.bed

source_name: 4-5 leaf developmentally-staged shoot tissue


title: Brain tumor; SAMPLE 22


title: STEC EH41 after 3 hrs incubation in conditioned medium, replicate 2 [COND]

description:
Gene expression from STEC EH41 after 3 hrs incubation in conditioned medium, replicate 2
EH41C#2


title: WT H2A.Z ChIP - rep2

description:
IP DNA
processed data: WT2_Z_histone.bed


title: ExVivoBlood_BPD_rep2_mRNA

description: Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 2


title: WT H2A.Z ChIP - rep1

description:
IP DNA
processed data: WT1_Z_histone.bed


title: WT Input - rep1


title: WT Input - rep2


title: arp6 genomic DNA

description: processed data: arp6_CNVnator_deletions.bed

data_processing:
Library strategy: DNA-seq
ChIP-seq workflow:
Reads were mapped to the TAIR10 A. thaliana reference genome with Bowtie2, using default parameters.
Reads were processed and quality filtered with the –q 2 option using SAMtools software.
H2A.Z peaks were called with Homer findpeaks software, using options “style histone” and “–region”.
RNA-seq workflow:
Sequencing reads were mapped to the TAIR10 Arabidopsis thaliana reference genome using Tophat2 (using the second strand option) and the accepted hits file was name-sorted and indexed using SAMtools.
Read counts were quantified for each exon using htseq-counts with name order and strict intersection options.
Differential expression was calculated using edgeR software.
MNase-seq workflow:
Sequence reads were mapped to the TAIR10 Arabidopsis thaliana reference genome using Bowtie2 and were then further sorted and indexed using SAMtools.
We filtered using the SAMtools view command with the –q 2 option to filter for quality and option –f 0x02 to filter for properly paired reads.
Libraries were subsampled using SAMtools –s parameter to normalize all to the same number of reads (30.46 M reads).
Mapped reads from both biological replicates for each of the four genotypes were analyzed using the DANPOS2 dpos program to generate nucleosome peak files and nucleosome occupancy wiq files.
DANPOS2 generated wig files were converted to the bigwigwig format with wig2bigwig command (UCSC).
arp6 deletion mapping workflow:
Sequenced reads were mapped using BWA mem software, indexed and quality sorted (-s option) using SAMtools, and randomly subsetted using a python script, leaving 61.5 M mapped reads.
Deletions were called in the arp6 mutant using CNVnator (v0.3.3) software using bin sizes of 100 bp.
Genome_build: TAIR10
Supplementary_files_format_and_content: WT1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the WT replicate 1 sample.
Supplementary_files_format_and_content: WT2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the WT replicate 2 sample.
Supplementary_files_format_and_content: A1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the arp6 replicate 1 sample.
Supplementary_files_format_and_content: A2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the arp6 replicate 2 sample.
Supplementary_files_format_and_content: B1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the brm replicate 1 sample.
Supplementary_files_format_and_content: B2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the brm replicate 2 sample.
Supplementary_files_format_and_content: WT_vs_arp6.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two arp6 mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_vs_brm.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two brm mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_vs_arp6brm.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two arp6;brm mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from WT plants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from arp6 mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: brm_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from brm mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6brm_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from arp6;brm mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between arp6 mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between brm mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between arp6;brm mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6_CNVnator_deletions.bed: Bed file containing the coordinates for large (>200bp) deletions in arp6 genotype relative to the TAIR10 reference genome generated by the CNVnator software.

source_name: Mature rosette leaves

extract_protocol:
Genomic DNA was isolated from mature rosette leaves from 50 pooled arp6 mutants using phenol:chloroform extraction followed by ethanol precipitation. DNA was sonicated before library preparation.
The NEXTflex Rapid DNA-seq Kit (option 2) (Bioo Scientific) was used to prepare libraries.

value: Mature rosette leaves


title: 06_cit500-3-liq

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

description: Raised on NGM  for 48 hours (L1 to L4 stage), then exposed 24 hours in 50% M9 supplemented with 500 µg/ml C-SPIONs

hyb_protocol: 5 μg of Biotin labeled cDNA was fragmented and hybridized to the Affymetrix C. elegans Gene 1.0 ST arrays as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing: To summarize the probe level data in the Affymetrix GeneChip® arrays, CEL files of C.elegans pOPC7 control condition was imported into the Affymetrix Expression ConsoleTM software for the quality control, data normalization and fold change algorithm. RMA normalization was carried out in Expression COnsole. Exported excel file with all genes and their exposure/control fold changes are listed.

organism: Caenorhabditis elegans

source_name: C.elegans L4_C-SPIONs3

label_protocol: 200 ng of total RNA was subjected to cDNA conversion and amplification using NuGEN Ovation Pico WTA V2 kit, to produce biotin-labelled cDNA.

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grown to L4 stage.

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

treatment_protocol: L4 stage animals were exposed 24 hours at 20 ºC in 50% M9 buffer (unexposed) or in 50% M9 supplemented with 500 µg/ml C-SPIONs (exposed).

value: stage L4 hermaphrodite


title: 01_ctrl-1-liq

description: Raised on NGM  for 48 hours (L1 to L4 stage), then exposed 24 hours in 50% M9

source_name: C.elegans L4_control1


title: 05_cit500-2-liq

source_name: C.elegans L4_C-SPIONs2


title: 03_ctrl-3-liq

source_name: C.elegans L4_control2


title: 02_ctrl-2-liq


title: 04_cit500-1-liq

source_name: C.elegans L4_C-SPIONs1


title: C.elegans L4_BSA-SPIONs_rep2

description: Raised on NGM  for 48 hours (L1 to L4 stage), then exposed 24 hours in 50% M9 supplemented with 500 µg/ml BSA-SPIONs

source_name: C.elegans L4_BSA-SPIONs2

treatment_protocol: L4 stage animals were exposed 24 hours at 20 ºC in 50% M9 buffer (unexposed) or in 50% M9 supplemented with 500 µg/ml BSA-SPIONs (exposed).


title: C.elegans L4_control_rep3


title: ORS285_AI_14dpi_WT_3

city: Gif sur Yvette

first: Florian

last: Lamouche

address: 1, Avenue de la Terrasse

department: Institute of Integrative Biology of the Cell (I2BC)

country: France

institute: Centre national de la Recherche Scientifique (CNRS)

data_processing:
CLC Workbench 10 software (CLC bio, Aarhus, Denmark) was used for trimming, sizing, and mapping the reads on the reference genome of Bradyrhizobium sp. ORS285 strain. Only unique gene reads mapping on 80% of their length and displaying a 90% identity have been conserved.
Genome_build: NZ_LT859959
Supplementary_files_format_and_content: tab-delimited text files including the raw counts of sequencing reads for each sample. Each sheet contains Gene Name/Region/Gene length/Unique gene reads/Total gene reads columns.

organism: Bradyrhizobium sp. ORS 285

source_name: From A. indica nodule tissues at 14 days post inoculation

growth_protocol: Bacterial culture was grown in YM rich medium. Bacteroid were obtained from nodulated plants. Aeschynomene spp. seeds were scarified and surface-sterilized using pure sulfuric acid and calcium hypochlorite, germinated in Khalys agar plates and transferred in transparent, light permissive test tubes filled with BNM medium (Erhardt et al., 1992).

extract_protocol:
Nodules were harvested at 14 days post inoculation (dpi), frozen in liquid N2 and kept at -80°C until RNA extraction. For transcriptomic analysis, total nodule RNA was extracted as previously described in Mergaert et al., 20036, and submitted to plant and bacterial rRNA and eukaryotic mRNA depletion using RiboZero kits for plants and for Gram-negative bacteria (Epicentre, Madison, USA). Total RNA of free-living cells were extracted from bacterial pellets obtained from cultures grown in YM medium at OD600= 0.5 using hot phenol and hot SDS method according to Chapelle et al. (2015).
Oriented libraries of bacterial mRNA were produced using the SOLiD total RNA-seq kit and sequenced on a SOLiD 5500XL (50bp per read).

treatment_protocol: Five days after transfer, plants were inoculated with 2mL of bacterial suspension at OD600=0.1, according to Guefrachi et al., 2015. Mock inoculations were performed when necessary using 2 mL sterile BNM medium. Plants were grown at 28°C, 80% humidity and under a 16/8 hour of light/dark photoperiod.

tag: condition

value: A. indica nodule Spherical bacteroids

tag: genotype

value: Wild type


title: C.elegans L4_control_rep1


title: C.elegans L4_control_rep2


title: Postia placenta 30-35 mm_rep3

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

description:
Temporal seperation of brown rot was sptially acomplished by wafer design
UMN_augustus_PplATCC44394.aa
UMN_augustus_PplATCC44394.gtf
Dataset_1_All_genes_expression_profiles_during_wood_decay_in_brown_and_white_rot_fungi.xlsx

data_processing:
Raw RNA-seq reads were trimmed for Truseq2 adapters and for low-quality sequence with Trimmomatic (v0.33) and quality control was integrated using FastQC (v0.11.5). Remaining reads were mapped to the respective reference genome using Genomic Short-read Nucleotide Alignment Program (GSNAP) (Wu and Nacu, 2010). Beaker (v1.8) was used to annotate the genome by incorporating the above RNA-seq mapping data. These newly annotated genomes (AA files and GTF files) were compared with JGI’s (Joint Genome Institute, http://jgi.doe.gov/) genome annotation by testing the location of RNA-seq reads relative to exons, and this generated significantly improved annotations for all four fungi. The aligned read counts were computed using the “featureCounts” function of the Rsubread package (v1.22.2), and normalized as Reads Per Kilobase of transcript per Million mapped reads (RPKM) as gene expression level. The test of differential expression was made using edgeR's (v3.14) “glmQLFit” routine on the design matrix. The profiling data for whole-genome transcripts and DEGs are available in Dataset 1 (Excel file).
Genome_build: Postia placenta MAD-698-R-SB12 v1.0, Gloeophyllum trabeum v1.0, Trametes versicolor v1.0 and Pleurotus ostreatus PC15 v2.0 from JGI (https://genome.jgi.doe.gov/programs/fungi/index.jsf)
Supplementary_files_format_and_content: AA files include amino acid sequences; GTF files include genome annotations; Excel file (.xlsx) includes pairwise comparison and RPKM levels.

organism: Rhodonia placenta

source_name: brown rot decayed wood

growth_protocol: Directional growth of fungi on wood wafers was used to segregate fungal wood decay stages (space-for-time) in modified ASTM soil-block microcosms, described in detail, previously (Zhang et al., 2016). Sterilized wood wafers (length × width × thickness = 60 × 25 × 2.5 mm) cut from aspen (Populus sp.) lumber were propped in microcosms with the 25-mm edge resting on the soil surface, colonized from the base by one of four test fungi. Soil medium was a 1:1:1 mixture of soil, peat, and vermiculite hydrated to 40–45% (wt/vol) moisture content. Two brown rot fungi Postia placenta ATCC 44394 and Gloeophyllum trabeum ATCC 11539 and two white rot fungi Trametes versicolor A1-ATF (Minnesota Forest Pathology culture collection, University of Minnesota, USA) and Pleurotus ostreatus ATCC 32237 were maintained on 1.5% (wt/vol) malt extract agar prior to inoculating microcosms. Wafers were harvested when fungi had progressed 50 mm up the length of a wafer. By defining the visible hyphal front as a benchmark (0 mm), four 5-mm sections (5 x 25 x 2.5 mm) were extracted, one from 5 mm above the hyphal front (no fungus), one that included the hyphal front (0-5 mm), and two from further behind the hyphal front (15-20, 30-35 mm).

extract_protocol:
Total fungal RNA was extracted from fresh wood sections with TRIzol (Life Technologies) and cleaned up with a Qiagen RNeasy Mini Kit (Qiagen, Inc.) prior to RNA sequencing or quantitative RT-PCR (qRT-PCR), a method validated in Zhang et al. (2016).
For RNA sequencing, TruSeq RNA v2 libraries were prepared and sequenced on a HiSeq 2500 System (Illumina Inc., San Diego, CA) by using the standard protocols from Illumina.

tag: strain

tag: wafer locus

tag: decay stage

value: late decay


title: Postia placenta 30-35 mm_rep2


title: ExVivoBlood_BPD_rep1_mRNA

city: Shanghai

description: Gene expression in BPD human blood

source_name: Peripheral Blood, BPD, replicate 1

tag: tissue


title: ORS285_AI_14dpi_WT_2


title: C.elegans L4_BSA-SPIONs_rep3

source_name: C.elegans L4_BSA-SPIONs3


title: Postia placenta 30-35 mm_rep1


title: Postia placenta 15-20 mm_rep3

value: middle late decay


title: C.elegans L4_BSA-SPIONs_rep1

source_name: C.elegans L4_BSA-SPIONs1


title: ORS285_AI_14dpi_WT_1


title: Caco without interaction - control, replicate 2 [EC472]

description:
Gene expression from Caco-2 after 3 hrs without interaction as a control, replicate 2
Caco-CT#26

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D__F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities but not included the normalization process.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Caco-2 cell, control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Total RNA was extracted from cells after lysing with RLT buffer and the RNeasy Mini Kit (Qiagen cat no. 74104, Valencia, CA) according to the manufacturer's instructions. The purity and quantification for all RNA samples were done using the NanoVue spectrophotometer and the RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA). All samples that present RIN > 8.0 were stored at -80°C until used in hybridization experiments.

treatment_protocol: The Caco-2 intestinal cells were maintained in DMEM medium with 10% fetal bovine serum (complete medium) and penicillin-streptomycin in a 5% CO2 incubator at 37°C until cells differentiate in enterocyte-like. Prior to interaction assays Caco-2 cells were washed and incubated with complete medium. After 24 hrs 1/10 volume of bacterial culture were placed on a Caco-2 monolayer and incubated in a 5% CO2 at 37°C for 3 hrs.  After this period Caco-2 cells infected and uninfected (control) were washed 3 times with phosphate buffered saline (PBS) and the cells were recovered with 5 mL of PBS by pipetting. The cells were then centrifuged for 5 min at 5000 xg and the pellet was ressuspended in 600 µL of RNAlater Reagent (Qiagen cat. no. 76154, Valencia, CA) for RNA extraction.

tag: cell line

value: intestinal cell line Caco-2

tag: stress

value: control (without interaction)


title: Caco without interaction - control, replicate 4 [EH41]

description:
Gene expression from Caco-2 after 3 hrs without interaction as a control, replicate 4
Caco-CT#28


title: Caco after 3 hrs interaction with STEC EC472, replicate 3 [EC472]

description:
Gene expression from Caco-2 after 3 hrs of interaction with STEC strain EC472, replicate 3
Caco-EC472#37

source_name: Caco-2 cell, STEC interaction

value: interaction with STEC strain EC472


title: Caco after 3 hrs interaction with STEC EC472, replicate 1 [EC472]

description:
Gene expression from Caco-2 after 3 hrs of interaction with STEC strain EC472, replicate 1
Caco-EC472#35


title: Caco after 3 hrs interaction with STEC EC472, replicate 2 [EC472]

description:
Gene expression from Caco-2 after 3 hrs of interaction with STEC strain EC472, replicate 2
Caco-EC472#36


title: Caco without interaction - control, replicate 1 [EC472]

description:
Gene expression from Caco-2 after 3 hrs without interaction as a control, replicate 1
Caco-CT#25


title: Caco without interaction - control, replicate 4 [EC472]


title: Caco without interaction - control, replicate 1 [EH41]


title: Caco without interaction - control, replicate 3 [EH41]

description:
Gene expression from Caco-2 after 3 hrs without interaction as a control, replicate 3
Caco-CT#27


title: Caco after 3 hrs interaction with STEC EH41, replicate 4 [EH41]

description:
Gene expression form Caco-2 after 3 hrs of interaction with STEC strain EH41, replicate 4
Caco-EH41#40

value: interaction with STEC strain EH41


title: WT Mnase-seq - rep1

description:
Nucleosomal DNA
processed data: WT_30M.nucleosomes.bw
processed data: data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls
processed data: data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls
processed data: data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls

tag: genotype/variation

value: WT


title: Postia placenta 15-20 mm_rep1


title: ORS285_AA_14dpi_WT_2

source_name: From A. afraspera nodule tissues at 14 days post inoculation

value: A. afraspera nodule Elongated bacteroids


title: ORS285_AA_14dpi_WT_3


title: ORS285_YM_WT_2

source_name: Culture in rich medium

value: YM culture


title: ORS285_AA_14dpi_WT_1


title: ORS285_YM_WT_3


title: H3.3-addback

city: Harbin

first: Xiaolei

last: Zhang

address: No.59 Mucai street

institute: Northeast Agricultural University

data_processing:
RNA-seq reads were aligned to the mouse genome (mm10) using TopHat
Expression levels were obtained using CuffLinks, using upper-quartile and GC-normalization
Pathway analysis was performed using mouse Gene Ontology pathways
Genome_build: mm10
Supplementary_files_format_and_content: Expression levels were obtained using CuffLinks

source_name: embryo

extract_protocol:
Five to ten embryos were transferred into a PCR tube with 100 µl lysate buffer by mouth pipette and RNA was prepared using Arcturus PicoPure kit (Life technologies, KIT0204)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR


title: Postia placenta 15-20 mm_rep2


title: WT


title: ORS285_YM_WT_1


title: H3.3KD


title: Gloeophyllum trabeum 30-35 mm_rep3

description:
Temporal seperation of brown rot was sptially acomplished by wafer design
UMN_augustus_GtrATCC11539.aa
UMN_augustus_GtrATCC11539.gtf
Dataset_1_All_genes_expression_profiles_during_wood_decay_in_brown_and_white_rot_fungi.xlsx

organism: Gloeophyllum trabeum


title: Trametes versicolor  30-35 mm_rep2

description:
Temporal seperation of white rot was sptially acomplished by wafer design
UMN_augustus_TveA1_ATF.aa
UMN_augustus_TveA1_ATF.gtf
Dataset_1_All_genes_expression_profiles_during_wood_decay_in_brown_and_white_rot_fungi.xlsx

organism: Trametes versicolor

source_name: white rot decayed wood

value: UMN A1-ATF


title: Caco without interaction - control, replicate 2 [EH41]


title: Pleurotus ostreatus 30-35 mm_rep3

description:
Temporal seperation of white rot was sptially acomplished by wafer design
UMN_augustus_PosATCC32237.aa
UMN_augustus_PosATCC32237.gtf
Dataset_1_All_genes_expression_profiles_during_wood_decay_in_brown_and_white_rot_fungi.xlsx

organism: Pleurotus ostreatus


title: Trametes versicolor  30-35 mm_rep1


title: Trametes versicolor  30-35 mm_rep3


title: Pleurotus ostreatus 30-35 mm_rep1


title: Pleurotus ostreatus 30-35 mm_rep2


title: Gloeophyllum trabeum 30-35 mm_rep2


title: Caco after 3 hrs interaction with STEC EC472, replicate 4 [EC472]

description:
Gene expression from Caco-2 after 3 hrs of interaction with STEC strain EC472, replicate 4
Caco-EC472#41


title: Caco after 3 hrs interaction with STEC EH41, replicate 2 [EH41]

description:
Gene expression form Caco-2 after 3 hrs of interaction with STEC strain EH41, replicate 2
Caco-EH41#38


title: Pleurotus ostreatus 15-20 mm_rep3


title: Trametes versicolor  15-20 mm_rep2


title: Gloeophyllum trabeum 15-20 mm_rep3


title: Gloeophyllum trabeum 30-35 mm_rep1


title: Trametes versicolor  15-20 mm_rep3


title: Caco after 3 hrs interaction with STEC EH41, replicate 3 [EH41]

description:
Gene expression form Caco-2 after 3 hrs of interaction with STEC strain EH41, replicate 3
Caco-EH41#39


title: Caco after 3 hrs interaction with STEC EH41, replicate 1 [EH41]

description:
Gene expression form Caco-2 after 3 hrs of interaction with STEC strain EH41, replicate 1
Caco-EH41#32


title: Gloeophyllum trabeum 15-20 mm_rep2


title: Trametes versicolor  0-5 mm_rep2

value: early decay


title: Pleurotus ostreatus 0-5 mm_rep3


title: Pleurotus ostreatus 15-20 mm_rep1


title: Gloeophyllum trabeum 15-20 mm_rep1


title: Pleurotus ostreatus 15-20 mm_rep2


title: Trametes versicolor  0-5 mm_rep3


title: Pleurotus ostreatus 0-5 mm_rep2


title: Trametes versicolor  0-5 mm_rep1


title: Pleurotus ostreatus 0-5 mm_rep1


title: Trametes versicolor  15-20 mm_rep1