title: RNA-Seq of chicken hypothalamus 6 with low egg production

city: XICHANG

first: Binlong

last: chen

state: SICHUAN

address: XUEFU ROAD NO. 1, ANNING TOWN

institute: XiChang University

data_processing:
The raw data generated after removing the low quality adaptors whose quality value is less than 20, poly (A) adaptors and N adaptors. The clean data were assembled with the Trinity program.
FPKM method (FragmentsPer Kilobaseof exon per Million Fragments mapped) was conducted to calculate the expression levels of differentially expressed genes.
Functional annotation was performed by Gene Ontology terms (GO:http://www.geneontology.org/), The KEEG pathways annotation was performed against Kyoto Encyclopedia of Genes and Genomes database (http://www.genome.jp/kegg/).

organism: Gallus gallus

source_name: hypothalamus

growth_protocol: Water and feed were provided ad libitum.

extract_protocol:
RNeasy Mini Kit (Qiagen, Hilden, Netherlands) was used to isolate the total RNA, all the processes followed the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: A total of 856 Chinese Luhua chicken was raised in poultry breeding farm of Sichuan Agricultural University, the highest two hundred and the lowest two hundred chicken egg production were considered as high egg production (HEP) and low egg production (LEP) according to the total egg number at 300 days of age, respectively

tag: group

value: low egg production group

tag: Sex

value: day 300

value: hypothalamus


title: RNA-Seq of chicken pituitary gland 6 with low egg production

status: Public on Dec 07 2019

type: SRA

country: China

description: B7_pituitary gland

library_source: transcriptomic

molecule: total RNA

source_name: pituitary gland

value: Female

tag: age

tag: tissue

value: pituitary gland


title: HEART_REP1

city: medellin

first: Jean

middle: Paul

last: Delgado

state: antioquia

department: Biology

country: Colombia

institute: University of Atioquia

data_processing:
Sequenced reads were assembly using Trinity V 2.0.6 software pipeline, and default Trimmomatic parameters to remove sequence adapters and low quality reads (Phred score < 5), The reference transcriptome was assembled from all RNA samples and all contigs with length ≥ 200 nucleotides.
Sequence reads generated from limb tissue samples were aligned to the reference transcriptome using Bowtie2 (Langmead & Salzberg 2012) and RSEM (RNA-Seq by Expectation Maximization) was used to obtain estimates of transcript abundance for all transcripts (Li & Dewey 2011). Expression levels were calculated as transcripts per million (TPM) and Fragments Per Kilobase Million (FPKM)
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample
Supplementary_files_format_and_content: reference transcriptome in fasta format

organism: Bolitoglossa vallecula

source_name: HEART

extract_protocol:
Total RNA from tissues were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of mRNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEART

tag: developmental stage

value: Adult


title: RNA-Seq of chicken hypothalamus 5 with low egg production


title: EM_middle_female_R1

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

description:
Exemastane2 female rep1
D2_4F_oA

data_processing:
High-throughput sequencing raw image data files were converted to reads using CASAVA Base Calling (bcf2fastq) analysis.
We used FastQC (0.11.8) to evaluate the raw reads quality. Sequencing report tool was MultiQC (0.9).
Reads were mapped to the corresponding reference genomes (Ensembl v93) by Hisat2 (2.0.5) with parameters “--dta -x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation in GTF format (Ensembl v93)
The output of Hisat2 were converted to BAM format and sorted by Samtools (1.5) and Samtools rmdup was used for removing PCR duplicates.
HTSeq (0.9.1) was used for counting reads with parameters “-t exon –i gene_id -r pos -s reverse”.
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw_readcounts file contains matrix with not normalized (raw) read counts for 16 samples. Column names in the file correspong to sample names in the Samples table, row names correspond to Ensembl gene ID, each cell is a number of reads for the gene in the row and the sample in the column.
Supplementary_files_format_and_content: Normalized_readcounts contains matrix with normalized read counts for 16 samples. Column names in the file correspong to sample names in the Samples table, row names correspond to Ensembl gene ID, each cell is a number of reads for the gene in the row and the sample in the column.

organism: Danio rerio

source_name: 100ug/L exmestane female gonad replicates1

growth_protocol: The zebrafish (AB strain) were maintained at 28.5°C in the recirculation systems with a light:dark cycle of 14 hr:10 hr according to the zebrafish book (Westerfield, M. 2000, https://zfin.org/zf_info/zfbook/zfbk.html ). The fish were fed twice daily with fish food (Zeigler AP100) for three months. The samples were obtained with the approval from National Research Council (NRC), strictly following the guidelines set for the usage of animals by this committee.

extract_protocol:
Total RNA were extracted using Trizol method. We added 1 ml Trizol (invitrogen) to the sample (4-7 million cells) stored at -80 °C and homogenized the sample by pipette. Then, 200 ul Chloroform was added to the homogenate and the sample was vigorously shaked by hand for 15 seconds until the phase separation disappeared. After standing at room temperature for 2-3 minutes, the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The colorless supernatant was transferred to another new centrifuge tube, mixed with equal volume of isopropanol thoroughly, kept standing at -20°C for 10 minutes, and then centrifuged at 12,000 g for 10 minutes at 4°C to pellet the RNA. The supernatant was carefully removed, and the pellet was gently washed with 1 ml fresh 75% ethanol for 2-3 times, dried for 2 to 3 minutes at room temperature and dissolved in 50 ul RNase-free water.
Stranded PolyA+ RNA libraries were prepared at BGI with in-house kits. The quality of the libraries were assessed by checking the distribution of the fragment size using the Agilent 2100 bioanalyzer, and the quantity of the libraries were measured using real-time quantitative PCR (TaqMan Probe). The qualified libraries were amplified on cBot to generate clusters on the flowcell, and then sequenced on the Illumina HiSeq XTen System.

treatment_protocol: Zebrafish with four treatments, including Exemestane (50ug/L), Exemestane (100ug/L), Exemestane (200ug/L) and control, were maintained in four tanks of separated recirculation systems. Each tank contained 3 males and 3 females. Exemestane (Lot#:C10070672, MACKLIN) was dissolved in Dimethyl sulfoxide (Sinopharm Chemical Reagent Co., Ltd.) before use. Drug was dissolved in system water and the water was changed every day to ensure the effective concentration of Exemestane. After 32 days drug treatment, zebrafish gonads were dissected and preserved in liquid nitrogen.

value: Gonad

tag: strain

value: AB

tag: gender

tag: drug concentration

tag: treatment

value: Exemastane

value: 4 month

tag: library type

value: fr-firststrand (dUTP)


title: T2

city: harbin

first: chunhua

last: wang

state: Heilongjaing

address: Mucai Street 59

department: Horticulture

institute: Notheast Agriculture Unversity

data_processing:
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the Cucumber v2.0 genome by tophat2. Aligned reads with more than one genome location were discarded due to their ambiguous location.
http://cmb.bnu.edu.cn/Cucumis_sativus_v20/.  Download Cucumis_sativus_v20-Cucumber_v2.cds.fasta file. For example, to verify the Csa1G014390 gene,  change the G into M, query this gene. (G is representative of the gene, M represents the mRNA, you download the CDS sequence, so it is M, not G. When we analyze sequence data, download the genome sequence, so expressed gene_value is G.)
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
After getting the Expression level of all genes in all samples, differentially expressed genes were analyzed by using edgeR(Robinson et al., 2010), one of R packages. 0.01 p-value and 2 fold change were set as the threshold to define DEGs.
Genome_build: C.sativus V2.0
Supplementary_files_format_and_content: tab-delimited MS Excel file including RPKM values for each Sample

organism: Cucumis sativus

source_name: fruit

extract_protocol:
Total RNA was extracted from tissue or cell samples by using TRIzol Reagent (Ambion) following the manufacturer’s instructions. RQ1 DNase (promega) was added to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were ion fragmented at 95 ℃ followed by end repair and 5' adaptor ligation. Then mRNA reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified. And products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing. Illumina HiSeq 2000 platform was used to generating paired-end reads. Illumina GAIIx platform was used to generating single-end reads.

value: Dorsal side of fruit

value: 2 days after anthesis


title: RNA-Seq of chicken ovary 6 with low egg production

source_name: ovary

value: ovary


title: RNA-Seq of chicken pituitary gland 5 with low egg production

description: B5_pituitary gland


title: EM_middle_male_R2

description:
Exemastane2 male rep2
D2_2M_tA

source_name: 100ug/L exmestane male gonad replicates2

value: Male


title: RNA-Seq of chicken ovary 5 with low egg production


title: RNA-Seq of chicken hypothalamus 4 with low egg production


title: A2

value: Ventral side of fruit


title: EM_low_female_R2

description:
Exemastane1 female rep2
D1_5F_oA

source_name: 50ug/L exmestane female gonad replicates2


title: EM_middle_male_R1

description:
Exemastane2 male rep1
D2_1M_tA

source_name: 100ug/L exmestane male gonad replicates1


title: RNA-Seq of chicken pituitary gland 4 with low egg production

description: B4_pituitary gland

value: low egg production group


title: RNA-Seq of chicken hypothalamus 3 with high egg production

value: high egg production group

value: day 300


title: RNA-Seq of chicken ovary 4 with low egg production

value: Female


title: RNA-Seq of chicken ovary 3 with high egg production


title: EM_low_female_R1

description:
Exemastane1 female rep1
D1_4F_oA

source_name: 50ug/L exmestane female gonad replicates1


title: RNA-Seq of chicken pituitary gland 2 with high egg production

description: A3_pituitary gland

value: pituitary gland


title: EM_low_male_R2

description:
Exemastane1 male rep2
D1_2M_tA

source_name: 50ug/L exmestane male gonad replicates2


title: RNA-Seq of chicken hypothalamus 1 with high egg production

value: hypothalamus


title: RNA-Seq of chicken pituitary gland 3 with high egg production

description: A9_pituitary gland


title: mutant 30C

city: Birmingham

first: Maria

last: Makarova

address: Egbaston 32

country: United Kingdom

institute: University of Birmingham

data_processing:
We used galaxy pipeline to process RNA seq data (Galaxy Version 2.1.1)
FASTGroomer to sanger format the data files (four raw data files -sample1, 2, 3 and 4)
Tophat to map reads against reference genome (reference genome was uploaded from https://fungi.ensembl.org/info/website/ftp/index.html). Processing included all four sample files.
Cuffdiff to find significant changes in gene expression levels between wild type cells and mutant cells with the replaced fas complex. GTF file was downloaded from https://fungi.ensembl.org/info/website/ftp/index.html. For two temperature conditions two comparative cuffdiff files were generated

organism: Schizosaccharomyces pombe

source_name: exponential growth in YES media

growth_protocol: cells were grown in rich medium YES

extract_protocol:
Qiagen kit
KAPA mRNA polyA HyperPrep  HiSeq 4000 75bp SR

treatment_protocol: cells were grown at two different temperature 24C and 30C

tag: growth

value: grown at 30C

tag: genotype/variation

value: mutant cells with the replaced fatty acid synthase complex from Schizosaccharomyces japonicus


title: wt 24C

value: grown at 24C

value: wild type cells


title: mutant 24C


title: wt 30C


title: RNA-Seq of chicken pituitary gland 1 with high egg production

description: A2_pituitary gland


title: RNA-Seq of chicken ovary 1 with high egg production


title: HCV_15

status: Public on Dec 06 2019

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: small RNAsequencing analysis

data_processing:
BCL basecall files were converted to FASTQ per sample using CASAVA v1.8.2 (Illumina) with default parameters to generate demultiplexed per sample fastq raw sequencing data files.
Per sample read quality was assessed using FastQC.
Trimming, quality filtering, mapping and raw read counting data processing steps were performed with mirPRo software (Shi J, et al, Sci Rep, 5:14617, 2015), which uses Novoalign (Li, H. & Homer, N. Brief. Bioinform. 11, 473–483, 2010) to map the reads.
Statistically significant differences in miRNA expression were determined both by DESeq2 (Love, 2014) with multiple testing adjustment. A dataset consistency step was perfomed by principal components analysis (PCA) to detect outliers. Data were renormalized after outlier removal prior to the final analysis.
Genome_build: Reads were mapped to GRCh38.87  and annotated with miRBase 21 mature database.
Supplementary_files_format_and_content: Processed miRNA expression profiling data table is provided as a supplementary file in excel workbook (.xlsx) format. It includes a single worksheet. This contains DESeq2 outputs. Column headers: FC or FoldChange (fold changes), pvalue (nominal p value), padj (adjusted pvalue by default Benjamini and Hochberg method) for all 7 comparisons presented in the publication, followed by baseMean (average normalized counts), and normalized counts for all samples.

organism: Homo sapiens

source_name: plasma

extract_protocol:
Blood samples were collected in EDTA tubes, then, plasma samples were obtained by a single centrifugation (1000g, 15min. at room temperature). For RNA extraction from 200ul of plasma, miRCURY RNA insolation kit-Biofluids (#300112) was used following manufacturer indications with modifications that included using glycogen as carrier and a 1:50 dilution of spike in RNA.
Barcoded sequencing libraries were prepared using the TruSeq SmallRNA library kit (Illumina) with slight modifications from the default recommendations (Part # 15004197 Rev. F, February 2014). Modifications included using all RNA extracted from 200 ul of plasma, in the subnanogram range, and increasing the number of cycles in the final PCR reaction (from 12 to 15).
Libraries were quality assessed with Bioanalyzer DNA 1000 assays (Agilent). Bioanalyzer concentration estimates were used to generate an equimolar library mix. The library pool was automatically size selected (135-160bp) using 3% agarose dye free cassettes with 3% DF marker F on a Pippin Prep system with software v.6.0 (Sage Science). QIAquick (Qiagen) column purifications were performed prior and after to size selection. The library pool was quantifiedby PCR with theKAPA Library Quantification Kit following manufacturer’s instructions (Roche). The library pool was run on 4 lanes of 1x50 bp sequencing was performed on HiSeq2500 platform (Illumina) using adapted protocols for TruSeq SR cluster kit v3 (Part#15023335) following cBot™ (Part#15006165) and HiSeq2500 System (Part#15035786) user guidelines. Raw data were analysed by Real Time Analysis software v. 1.17.21.3 and Sequence Analysis Viewer software v. 1.8.20 (Illumina.).

tag: individual unique id

tag: clinical grouping

value: HCV mono-infected

tag: hcv infection status

value: HCV positive

tag: virus

value: HIV negative

value: female

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: library batch

tag: size selection and sequencing pool

tag: inclusion in final analysis

value: included


title: HCV_14

description: small RNAsequencing analysis


title: HCV_16

description: small RNAsequencing analysis


title: HCV_13

description: small RNAsequencing analysis

value: male


title: HCV_11

description: small RNAsequencing analysis


title: HCV_9

description: small RNAsequencing analysis


title: HCV_12

description: small RNAsequencing analysis


title: HCV_10

description: small RNAsequencing analysis


title: HCV_8

description: small RNAsequencing analysis


title: HCV_7

description: small RNAsequencing analysis


title: HCV_5

description: small RNAsequencing analysis


title: HCV_6

description: small RNAsequencing analysis


title: HCV_2

description: small RNAsequencing analysis


title: HCV_1

description: small RNAsequencing analysis


title: HCV_4

description: small RNAsequencing analysis


title: HIV_ALT_norm_22

description: small RNAsequencing analysis

value: HIV mono-infected, normal ALT

value: HCV negative

value: HIV positive


title: HIV_ALT_norm_20

description: small RNAsequencing analysis


title: HIV_ALT_norm_21

description: small RNAsequencing analysis


title: EM_low_male_R1

description:
Exemastane1 male rep1
D1_1M_tA

source_name: 50ug/L exmestane male gonad replicates1

tag: tissue

value: Gonad

value: AB

value: Male

value: Exemastane

tag: age

value: 4 month

value: fr-firststrand (dUTP)


title: HIV_ALT_norm_19

description: small RNAsequencing analysis

tag: gender


title: HCV_17

description: small RNAsequencing analysis


title: HIV_ALT_norm_18

description: small RNAsequencing analysis


title: HIV_ALT_norm_15

description: small RNAsequencing analysis


title: HIV_ALT_norm_16

description: small RNAsequencing analysis


title: HIV_ALT_norm_10

description: small RNAsequencing analysis


title: HIV_ALT_norm_8

description: small RNAsequencing analysis


title: HIV_ALT_norm_12

description: small RNAsequencing analysis


title: HIV_ALT_norm_4

description: small RNAsequencing analysis


title: HIV_ALT_norm_9

description: small RNAsequencing analysis


title: HIV_ALT_norm_5

description: small RNAsequencing analysis


title: HIV_ALT_norm_11

description: small RNAsequencing analysis


title: HIV_ALT_norm_7

description: small RNAsequencing analysis


title: HIV_ALT_norm_3

description: small RNAsequencing analysis


title: HIV_ALT_norm_2

description: small RNAsequencing analysis


title: HCV_3

description: small RNAsequencing analysis


title: HIV_NH_11

description: small RNAsequencing analysis

value: HIV mono-infected, nodular hyperplasia


title: HIV_NH_10

description: small RNAsequencing analysis


title: HIV_NH_9

description: small RNAsequencing analysis


title: HIV_ALT_norm_1

description: small RNAsequencing analysis


title: HIV_NH_8

description: small RNAsequencing analysis


title: HIV_NH_6

description: small RNAsequencing analysis


title: HIV_ALT_norm_17

description: small RNAsequencing analysis


title: HIV_NH_5

description: small RNAsequencing analysis


title: HIV_NH_4

description: small RNAsequencing analysis


title: HIV_ALT_norm_14

description: small RNAsequencing analysis


title: HIV_ALT_norm_13

description: small RNAsequencing analysis


title: HIV_ALT_high_19

description: small RNAsequencing analysis

value: HIV mono-infected, elevated ALT


title: HIV_NH_3

description: small RNAsequencing analysis


title: HIV_NH_1

description: small RNAsequencing analysis


title: HIV_NH_2

description: small RNAsequencing analysis


title: HIV_ALT_high_20

description: small RNAsequencing analysis


title: HIV_ALT_norm_6

description: small RNAsequencing analysis


title: HIV_ALT_high_18

description: small RNAsequencing analysis


title: HIV_ALT_high_17

description: small RNAsequencing analysis


title: HIV_ALT_high_16

description: small RNAsequencing analysis


title: HIV_ALT_high_15

description: small RNAsequencing analysis


title: HIV_ALT_high_14

description: small RNAsequencing analysis


title: HIV_ALT_high_12

description: small RNAsequencing analysis


title: HIV_ALT_high_11

description: small RNAsequencing analysis


title: HIV_NH_7

description: small RNAsequencing analysis


title: HIV_ALT_high_9

description: small RNAsequencing analysis


title: HIV_ALT_high_7

description: small RNAsequencing analysis


title: HIV_ALT_high_5

description: small RNAsequencing analysis


title: HIV_ALT_high_10

description: small RNAsequencing analysis


title: HIV_ALT_high_8

description: small RNAsequencing analysis


title: HIV_ALT_high_6

description: small RNAsequencing analysis


title: HIV_ALT_high_4

description: small RNAsequencing analysis


title: HIV_ALT_high_3

description: small RNAsequencing analysis


title: HIV_ALT_high_1

description: small RNAsequencing analysis


title: 66277_MDABrM_BLZ

city: Lausanne

first: Florian

last: Klemm

state: Vaud

address: Ch. des Boveresses 155

department: DOF

country: Switzerland

institute: University of Lausanne, Ludwig Center for Cancer Research

data_processing:
Basecalls were performed using CASAVA version 1.8
Reads were adapter trimmed and quality clipped using trim_galore (v0.4.3) in paired mode.
Trimmed reads were mapped to a concatenated mouse (mm10) and human genome (hg38) using the STAR aligner v2.5.2b with default parameters.
Uniquely mapped reads were quantified per gene using the default STAR parameters (equal to htseq-count default settings). Within each sample only species-specific read counts were retained for further analysis.
Gene counts were normalized and analyzed for differential expression with DESeq2 (v1.22) in R (v3.5).
Genome_build: hg38 & mm10
Supplementary_files_format_and_content: Separate tab-delimited text files contain raw counts for all tumor cell or microglia and monocyte-derived macrophage samples.

source_name: MDA BrM

growth_protocol: For brain metastasis (BrM) generation in xenografted mice, 1x10e4 MDA-BrM cells were inoculated into the left cardiac ventricle of 6-8 week old female Athymic/nude mice. Tumor progression was monitored by weekly bioluminescence imaging (BLI). For BLI measurement, mice were injected with 150 ul of luciferin subcutaneously and luminescence intensity was measured using an IVIS spectrum in vivo imaging system (Perkin Elmer) with images taken after 1 sec and 1 min exposure times. Once mice showed signs of established BrM defined as a BLI output >1x10e6 photons sec-1 mice were stratified into vehicle and BLZ945 treatment groups at d-1 and treatment was commenced at d0 with daily doses of 20% Captisol or BLZ945 (200 mg/kg). Animals were treated until they developed symptoms from BrM.

extract_protocol:
RNA was isolated from TRIzol via chloroform extraction and isopropanol precipitation using a Glycogen carrier.
cDNA libraries were constructed using the Smart-Seq protocol (Clontech) and fragmented with the Nextera XT kit (illumina).

treatment_protocol: Brain metastasis (BrM) bearing and healthy control mice were anesthetized with 1.25% Avertin, blood collected by cardiac puncture and animals were transcardially perfused with PBS. Tumors were macrodissected guided by ex vivo bioluminescence imaging and dissociated using the Mouse Tumor Dissociation Kit (mTDK, Miltenyi) using the OctoMACS dissociator. Digested tissue was filtered through a 40 μM mesh filter and subjected to RBC lysis (PharmLyse BD). Remaining myelin was removed using the Myelin Removal Beads (Miltenyi). Single cell suspensions were FC blocked (BD) for 15 minutes at 4 degrees Celsius. Cells were then incubated with directly conjugated antibody panels for 15 minutes at 4 degrees Celsius. Cell suspensions were washed (PBS +2% fetal bovine serum) and resuspended in a DAPI solution. Flow cytometry analysis and cell sorting was completed on an Aria III device at the Flow Cytometry Core Facility (FCCF) at MSKCC. Tumor associated microglia (MG) were isolated as Cd45+Cd11b+Ly6c-Ly6g-Cd49d- cells while tumor associated monocyte derived macrophages (MDM) were isolated as Cd45+Cd11b+Ly6c-Ly6g-Cd49d+ cells. Samples were sorted directly into TRIzol LS.

tag: mouse

tag: cell type

value: MDABrM

value: BLZ


title: 66296_MDABrM_BLZ

tag: treatment


title: 66271_MDABrM_BLZ


title: 66273_MDABrM_vehicle

value: vehicle


title: 66276_MDABrM_vehicle


title: 66270_MDABrM_BLZ


title: HIV_ALT_high_13

description: small RNAsequencing analysis


title: HIV_ALT_high_2

description: small RNAsequencing analysis


title: 66370_MDABrM_vehicle


title: 66279_MDABrM_vehicle


title: 66278_MDABrM_vehicle


title: Sample555

type: RNA

city: Seattle

first: Janet

middle: L.

last: Stanford

state: WA

address: 1100 Fairview Ave. N.

country: USA

institute: Fred Hutchinson cancer research center

description: FFPE tumor tissue obtained from a radical prostatectomy sample.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalization + log2 transformation + ComBat to remove batch effects.

label: biotin

source_name: Prostate

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: For each patient, two 1‐mm tumor tissue cores were taken from the areas enriched with ≥ 75% tumor cells from the dominant lesion. The RNeasy® FFPE Kit (Qiagen Inc., Valencia, CA, USA) was used to isolate the RNA from tissue cores.

treatment_protocol: Patients were diagnosed with clinically localized PCa and underwent RP as primary treatment.

tag: race

value: Caucasian

tag: diagnosis

value: Localized prostate cancer (PCa)

value: Local

value: PCa tumor


title: Sample552


title: Sample549

value: Regional


title: Sample554

value: 20+ ng/mL


title: Sample550


title: Sample542


title: Sample545

value: African American


title: Sample553


title: Sample557


title: Sample544


title: Sample546


title: Sample556


title: Sample537

value: missing


title: Sample547


title: Sample548


title: Sample543


title: Sample540


title: Sample533


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title: Sample538


title: Sample539


title: Sample536


title: Sample551


title: Sample532


title: Sample529


title: Sample531


title: Sample534


title: Sample530


title: Sample525


title: LIMB_REP1

source_name: forelimb

value: forelimb

tag: developmental stage

value: Adult


title: Sample526


title: Sample541


title: Sample522


title: Sample521


title: Sample517


title: Sample527


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title: DomA_7_3_S12

city: Woods Hole

first: Jennifer

middle: Martinez

last: Panlilio

state: MA

address: 266 Woods Hole Road

institute: Woods Hole Oceanographic Institution

data_processing:
Data was pre-processed using FastQC. Mapping quality was checked using RSeQC pipeline.
Pre-processed data was mapped to the zebrafish genome using STAR aligner
Htseq-count was used to get the read counts mapped.
EdgeR was used for statistical analysis
Genome_build: ensembl version 84 (GRCz10)
Supplementary_files_format_and_content: text format; count data files include identifier and the raw counts.

source_name: Larvae

growth_protocol: Embryos were raised in 0.3x Danieu's solution during embryonic development in a 48 well plate (with 1 embryo per well).

extract_protocol:
Embryos or larvae were pooled (n= 6 per each tube) then snap frozen in liquid nitrogen. Total RNA from embryos and larval samples was isolated using Zymo Direct-zol RNA purification kit.
Library construction was done using Illumina TruSeq with Ribozero and 50 bp single end strand-specific sequencing was done at Tufts Molecular core facility.
Strand-specific RNAseq

treatment_protocol: Embryos were exposed to saline (0.2x Danieu's solution) or to 0.13 ng domoic acid (nominal dose) through caudal vein microinjection.

value: 7 days post-fertilization

value: 0.13 ng DomA


title: Sample75


title: DomA_7_1_S10


title: Sample71


title: H20_7_2_S8

value: Saline injected


title: SRp_3_RRBS

city: Oslo

first: Magnus

middle: D.

last: Vigeland

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

library_source: genomic

data_processing:
Trimming of fastq files with Trim Galore! (v0.4.3; default parameters)
RRBS alignment to mm10, by Bismark v0.20, powered by bowtie2
RRBS analysis of methylated/unmethylated read counts, by R package edgeR
RNA-Seq alignment and feature counts, by R package Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: Bismark coverage file: Tab-delimited file with one row for each covered cytosine position in the experiment, and the following columns: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: Feature counts: Tab delimited file with one row per gene. The first column has Gene ID (Ensembl), followed by one column per sample, with unnormalised counts.

molecule: genomic DNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). DNA was extracted from NeuN positive nuclei with MasterPure Complete DNA and RNA Purification Kit (Epicentre cat.no. MC85200), following the DNA purification protocol for cell samples.
100ng DNA was digested with MspI (New England Biolabs cat.no. R0106S), followed by gap filling and A-tailing using Klenow fragment (NEB cat.no. M0212S) and dCTP, dGTP, and dATP (NEB cat.no. N0446S). Clean-up was performed using 3 volumes of AMPure XP beads (Beckman Coulter cat.no. A63880). 1 µL of a 1:10 dilution of adaptors from Illumina kit FC-121-3001/2 or FC-121-4001/2 was used for indexing of samples, with ligation performed by T4 ligase (NEB cat.no. M0202S). A two-sided size selection using AMPure XP beads was performed to recover ligation products between approximately 200 and 400 bp. Size selected fragments were bisulfite converted with the EpiTect Bisulfite Kit (Qiagen cat.no. 59104) using the procedure for FFPE samples and two consecutive rounds of the incubations given in the protocol. Bisulfite converted samples were amplified using TruSeq forward and reverse primers and PfuTurbo Cx hotstart DNA polymerase (Agilent cat.no. 600412), followed by AMPure XP clean-up.

value: Hippocampus

value: Sham

tag: neun

value: positive

tag: biol. repl.


title: SRn_3_RRBS

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). DNA was extracted from NeuN negative nuclei with MasterPure Complete DNA and RNA Purification Kit (Epicentre cat.no. MC85200), following the DNA purification protocol for cell samples.
100ng DNA was digested with MspI (New England Biolabs cat.no. R0106S), followed by gap filling and A-tailing using Klenow fragment (NEB cat.no. M0212S) and dCTP, dGTP, and dATP (NEB cat.no. N0446S). Clean-up was performed using 3 volumes of AMPure XP beads (Beckman Coulter cat.no. A63880). 1 µL of a 1:10 dilution of adaptors from Illumina kit FC-121-3001/2 or FC-121-4001/2 was used for indexing of samples, with ligation performed by T4 ligase (NEB cat.no. M0202S). A two-sided size selection using AMPure XP beads was performed to recover ligation products between approximately 200 and 400 bp. Size selected fragments were bisulfite converted with the EpiTect Bisulfite Kit (Qiagen cat.no. 59104) using the procedure for FFPE samples and two consecutive rounds of the incubations given in the protocol. Bisulfite converted samples were amplified using TruSeq forward and reverse primers and PfuTurbo Cx hotstart DNA polymerase (Agilent cat.no. 600412), followed by AMPure XP clean-up.

value: negative


title: H20_7_3_S9


title: DomA_3_3_S6

source_name: Embryos

value: 3 days post fertilization


title: KRp_3_RRBS

value: Kainate


title: Sample67

value: Caucasian

value: Localized prostate cancer (PCa)

value: Local


title: DomA_3_1_S4


title: Sample58

value: PCa tumor


title: Sample69


title: Sample60


title: Sample61

value: Regional

value: 20+ ng/mL


title: Sample70


title: SRp_2_RRBS


title: Sample62


title: H20_3_3_S3


title: Sample64


title: KRn_3_RRBS


title: Sample65


title: Sample63


title: H20_3_2_S2


title: H20_3_1_S1


title: DomA_7_2_S11


title: SRn_2_RRBS


title: H20_7_1_S7


title: KRp_2_RRBS


title: Sample56


title: KRn_2_RRBS


title: 66296_MDM_BLZ

source_name: Tumor-associated MG & MDM

value: MDM

value: BLZ


title: 66296_MG_BLZ

value: MG


title: 66277_MDM_BLZ


title: 66277_MG_BLZ


title: Sample55

value: African American


title: Sample54


title: Sample51

value: missing


title: Sample53


title: Sample57


title: Sample50


title: DomA_3_2_S5

value: 0.13 ng DomA


title: Sample49


title: Sample48


title: 66271_MG_BLZ


title: 66271_MDM_BLZ


title: Sample114


title: Sample47


title: 66270_MDM_BLZ


title: 66270_MG_BLZ


title: Sample45


title: 66370_MDM_vehicle

value: vehicle


title: Sample44


title: iPS-Retro-PAE-iPS-11_P30

type: genomic

city: Miyazaki

first: Koichiro

last: Nishino

state: Miyazaki

address: 1-1 Gakuen-Kibanadai-Nishi

department: Veterinary Medicine

country: Japan

institute: University of Miyazaki

description: placental artery endothelium-derived iPS cslls

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip or Infinium MethylationEPIC using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: Male

tag: sample type

value: inducible pluripotent stem cells

tag: disease state

value: normal


title: 41

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

description: Subject_624 breast milk, group: 1-Never breast cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

data_processing: BeadStudio software

source_name: breast milk

tag: subject

tag: slide

tag: array

tag: age (years)

tag: Sex

value: F

tag: group

value: 1-Never breast cancer

tag: cohort

value: Amherst

tag: breast biopsy

tag: time from delivery (months)


title: EC-NCR-G2

description: Embryonal carcinoma

tag: gender

value: Embryonal carcinoma

value: cancer


title: Sample43

tag: race

value: Localized prostate cancer (PCa)

value: Local

tag: tissue

value: PCa tumor


title: iPS-Retro-MRC-iPS-40_P30

description: Fetal lung fibroblast-derived iPS cslls


title: 66370_MG_vehicle

tag: mouse

tag: cell type

tag: treatment


title: EC-NCR-G3

description: Embryonal carcinoma

tag: sample type


title: 66279_MDM_vehicle

value: MDM


title: EC-NCR-G4

description: Embryonal carcinoma

tag: disease state


title: Sample41

value: Caucasian

tag: diagnosis


title: iPS-Retro-MRC-iPS-19_P4

description: Fetal lung fibroblast-derived iPS cslls


title: 66279_MG_vehicle

value: MG


title: Sample40

value: Regional


title: ES-SEES-06_P45

description: Enbryonic stem cells

value: Enbryonic stem cells


title: 43

description: Subject_664 breast milk, group: 1-Never breast cancer

tag: subject

tag: slide


title: iPS-Retro-PAE-iPS-05_P31


title: iPS-Retro-PAE-iPS-04_P31


title: 39

description: Subject_490 breast milk, group: 1-Never breast cancer

tag: array

tag: age (years)


title: 40

description: Subject_519 breast milk, group: 1-Never breast cancer

tag: Sex

tag: group


title: ES-SEES-03_P30

description: Enbryonic stem cells


title: 30

description: Subject_248 breast milk, group: 1-Never breast cancer

tag: cohort

tag: breast biopsy


title: 29

description: Subject_243 breast milk, group: 1-Never breast cancer

tag: time from delivery (months)


title: 44

description: Subject_667 breast milk, group: 1-Never breast cancer


title: 46

description: Subject_775 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: iPS-Retro-MRC-iPS-11_P4

description: Fetal lung fibroblast-derived iPS cslls

tag: gender


title: Sample42

tag: race

tag: tissue


title: 66278_MG_vehicle

tag: mouse

tag: cell type

value: vehicle


title: 37

description: Subject_417 breast milk, group: 1-Never breast cancer


title: 45

description: Subject_755 breast milk, group: 1-Never breast cancer


title: ES-HUES-2_P21

description: Enbryonic stem cells

value: Male

tag: sample type


title: Sample35

value: African American


title: 66276_MDM_vehicle

tag: treatment


title: 66276_MG_vehicle


title: 42

description: Subject_650 breast milk, group: 1-Never breast cancer


title: 36

description: Subject_403 breast milk, group: 1-Never breast cancer


title: 28

description: Subject_75 breast milk, group: 1-Never breast cancer


title: 33

description: Subject_329 breast milk, group: 1-Never breast cancer


title: Sample39

tag: diagnosis


title: 66273_MDM_vehicle


title: 34

description: Subject_350 breast milk, group: 1-Never breast cancer

tag: subject


title: 66273_MG_vehicle


title: 27

description: Subject_1072 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer

tag: slide


title: 66943_MONO_healthy

value: MONO

value: healthy


title: 32

description: Subject_324 breast milk, group: 1-Never breast cancer

tag: array

value: F

value: 1-Never breast cancer


title: 31

description: Subject_262 breast milk, group: 1-Never breast cancer

tag: age (years)

value: Amherst


title: Sample33

description: FFPE tumor tissue obtained from a radical prostatectomy sample.

value: missing


title: 26

description: Subject_1072 breast milk, group: 4-Contralateral, new diagnosed breast cancer

tag: Sex


title: 66278_MDM_vehicle


title: 25

description: Subject_244 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer

tag: group


title: 66943_MG_healthy


title: Sample32

value: Localized prostate cancer (PCa)


title: Sample30


title: Sample31


title: 66942_MONO_healthy


title: 35

description: Subject_352 breast milk, group: 1-Never breast cancer

tag: cohort


title: 66942_MG_healthy


title: Sample29


title: 66941_MONO_healthy


title: 21

description: Subject_465 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer

tag: breast biopsy


title: Sample28

value: Local


title: Sample27

value: PCa tumor


title: 66941_MG_healthy


title: Sample34


title: 18

description: Subject_172 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer

tag: time from delivery (months)


title: 17

description: Subject_161 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: 16

description: Subject_532 breast milk, group: 4-Contralateral, new diagnosed breast cancer


title: Sample26


title: 22

description: Subject_775 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: Sample36


title: Panc.10.05 Pdx1 Si

city: San Francisco

first: Nilotpal

last: Roy

state: CA

address: 513 Parnassus Ave.

department: Diabetes Center

institute: UCSF

description:
Panc.10.05 transfected with Pdx1 Si
processed data file: Panc.10.05.xlsx

data_processing:
10 nM library was loaded and sequenced using a Hi-Seq 2000 instrument, generating paired 100 bp reads.
Reads were then mapped to the human genome(hg38) using tophat version 2 with default parameters.
Transcript assembly and differential expression analysis was performed using Cufflinks and Cuffdiff with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-limited text file include RPKM values for each pair (control vs Pdx1 siRNA) for each cell line.

source_name: Human PDA_Pdx si

extract_protocol:
RNA was harvested using RNA isolation kit (Qiagen RNeasy mini kit). Quality control was performed using bio-analyzer.
Standard Illumina Protocol

tag: cell line

value: PDA tumor cell


title: 11

description: Subject_401 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: 23

description: Subject_844 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: 15

description: Subject_532 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: Panc.10.05 Con Si

description:
Panc.10.05 transfected with Con Si
processed data file: Panc.10.05.xlsx

source_name: Human PDA_control si


title: 20

description: Subject_370 breast milk, group: 3-Ipsilateral previously diagnosed breast cancer


title: 19

description: Subject_263 breast milk, group: 3-Ipsilateral previously diagnosed breast cancer


title: Sample25

tag: race

value: Caucasian


title: 24

description: Subject_931 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: 10

description: Subject_377 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: Panc.05.04 Pdx1 Si

description:
Panc.05.04 transfected with Pdx1 Si
processed data file: Panc.05.04.xlsx


title: 9

description: Subject_377 breast milk, group: 4-Contralateral, new diagnosed breast cancer


title: 7

description: Subject_357 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: 6

description: Subject_300 breast milk, group: 2-Contralateral, previously diagnosed breast cancer


title: Sample24

description: FFPE tumor tissue obtained from a radical prostatectomy sample.

tag: tissue


title: Sample23


title: 12

description: Subject_401 breast milk, group: 4-Contralateral, new diagnosed breast cancer


title: HPAF-II Pdx1 Si

description:
HPAF-II transfected with Pdx1 Si
processed data file: HPAF-II.xlsx

value: HPAF-II


title: Sample22

value: Regional


title: HPAF-II Con Si

description:
HPAF-II transfected with Con Si
processed data file: HPAF-II.xlsx


title: 2174_L

description: Subject_2174 breast milk, group: 1-Never breast cancer

value: NHBCS


title: 2174_R


title: 2

description: Subject_177 breast milk, group: 5-Ipsilateral, new diagnosed breast cancer


title: Sample21


title: 8

description: Subject_357 breast milk, group: 4-Contralateral, new diagnosed breast cancer


title: Panc.8 Pdx1 Si

description:
Panc.8 transfected with Pdx1 Si
processed data file: Panc.8.xlsx

source_name: Human PDA Pdx1 si


title: 2325_R

description: Subject_2325 breast milk, group: 1-Never breast cancer


title: 2272_L

description: Subject_2272 breast milk, group: 1-Never breast cancer


title: 2335_R

description: Subject_2335 breast milk, group: 1-Never breast cancer


title: 1

description: Subject_177 breast milk, group: 4-Contralateral, new diagnosed breast cancer


title: Panc.8 Con Si

description:
Panc.8 transfected with Con Si
processed data file: Panc.8.xlsx


title: 2325_L


title: 2335_L


title: Sample20

value: 20+ ng/mL


title: Sample17


title: SRn_3_mRNA

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN negative nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

value: Hippocampus

value: Sham

tag: neun

value: negative

tag: biol. repl.


title: Sample19


title: SRp_3_mRNA

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN positive nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

value: positive


title: KRp_3_mRNA

value: Kainate


title: Combo_3

city: NEW YORK

first: Kivanc

last: Birsoy

state: NY

address: 1230 YORK AVENUE,

institute: ROCKEFELLER UNIVERSITY

data_processing:
Sequence reads generated using NextSeq Control Software v1.4
Reads were aligned using STAR RNA-seq aligner; BAM files were sorted by coordinate and translated into transcript coordinates using quantMode SAM options
Normalized abundance measurements (FPKM values) were calculated using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene for a given treatment condition

growth_protocol: HEK 293T cells grown in RPMI, 10% FBS, 5% CO2, 21% O2.

extract_protocol:
Cells were washed 2x with cold PBS and RNA was harvested using RNAeasy mini kit (Qiagen)
RNA-Seq libraries using Illumina TruSeq stranded mRNA LT kit

treatment_protocol: +/- 24h preincubation with Ferric Ammonium Citrate (0.1mg/ml) followed by 24h treatment +/- BafA1 (10nM)

tag: genotype

value: wild type

value: Ferric Ammonim Citrate (0.1mg/ml); BafilomycinA1 (10nM)


title: Panc.05.04 Con Si

description:
Panc.05.04 transfected with Con Si
processed data file: Panc.05.04.xlsx

tag: cell type


title: Combo_2

tag: treatment


title: Sample15

tag: diagnosis


title: KRn_3_mRNA


title: 2249_R

description: Subject_2249 breast milk, group: 1-Never breast cancer

tag: subject

tag: slide

value: F

value: 1-Never breast cancer


title: 2076_R

description: Subject_2076 breast milk, group: 1-Never breast cancer

tag: array

tag: age (years)


title: SRp_2_mRNA


title: Sample16

value: Localized prostate cancer (PCa)


title: 2272_R

tag: Sex

tag: group


title: SRn_2_mRNA


title: FAC_2

value: Ferric Ammonim Citrate (0.1mg/ml); BafilomycinA1 (0nM)


title: 2076_L

tag: cohort

tag: breast biopsy


title: 2105_L

description: Subject_2105 breast milk, group: 1-Never breast cancer

tag: time from delivery (months)


title: KRp_2_mRNA


title: 2105_R


title: FAC_1

tag: cell line


title: Sample13

description: FFPE tumor tissue obtained from a radical prostatectomy sample.

tag: race

value: Local

tag: tissue

value: PCa tumor


title: Sample12

value: Caucasian


title: KRn_2_mRNA

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN negative nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify approximately 0.05 ng mRNA from total RNA, with 15 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

tag: neun

tag: biol. repl.


title: 2249_L


title: BafA1_3

tag: genotype

value: Ferric Ammonim Citrate (0mg/ml); BafilomycinA1 (10nM)


title: Sample14


title: FAC_3

tag: treatment


title: Combo_1


title: Sample9

tag: diagnosis

value: Regional


title: BafA1_2


title: 2144_L

description: Subject_2144 breast milk, group: 1-Never breast cancer

tag: subject

value: NHBCS


title: 2124_L

description: Subject_2124 breast milk, group: 1-Never breast cancer

tag: slide


title: 2186_R

description: Subject_2186 breast milk, group: 1-Never breast cancer

tag: array


title: BafA1_1


title: Sample10


title: Sample7


title: Sample8


title: 2186_L

tag: age (years)


title: 2236_L

description: Subject_2236 breast milk, group: 1-Never breast cancer

tag: Sex


title: Ctrl_2

value: Ferric Ammonim Citrate (0mg/ml); BafilomycinA1 (0nM)


title: 2224_R

description: Subject_2224 breast milk, group: 1-Never breast cancer

tag: group


title: Ctrl_3


title: Ctrl_1


title: Sample5


title: Sample3

value: African American


title: 2144_R

tag: cohort


title: Sample2


title: Sample4


title: SRn_1_mRNA

value: Hippocampus

value: Sham

value: negative


title: SRp_1_mRNA

value: positive


title: KRp_1_mRNA

value: Kainate


title: Sample1


title: 2124_R

value: F

tag: breast biopsy


title: 2236_R

value: 1-Never breast cancer

tag: time from delivery (months)


title: KRn_1_mRNA


title: SRp_1_RRBS


title: kidney mutant biological rep3

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

label: bioin

source_name: kidneys from 6 weeks old mutant mice

label_protocol: Fragmented, biotinylated cDNAs were prepared from 100 ng total RNA using  GeneChip WT Plus Kit according to the manufacturers instructions.

growth_protocol: kidney tissues were collected from 6 weeks old wildtype and mutant mice

extract_protocol: Total RNA was extracted frim renal cortex from mice using the Rneasy Mini Kit (Qiagen)

treatment_protocol: tissue was cut in small pieces, stored in RNAlater solution (Invitrogen) for 24 hours and frozen at -80°C till RNA extraction

value: kidney

value: Foxd1_Cre Pdgfrb_mutant

tag: strain

tag: gender

value: male

tag: age

value: 6 weeks


title: kidney mutant biological rep2

tag: tissue


title: CD8+ T cells, LP52

city: Yuseong-gu

first: Ji Won

last: Han

state: Daejeon

address: Daehak-ro 291

country: South Korea

institute: KAIST

description: Ex vivo gene expression

hyb_protocol: cDNAs were labeled with Cy3 dye and hybridized to an Agilent Human 4 X 44K microarray (GenomicWorks, Daejeon, Korea)

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent).

source_name: Ex vivo LSMC

extract_protocol: RNA was extracted from each sorted cell population using the Ribospin kit (Geneall).

value: Liver

tag: cell type

value: LSMC

tag: sorted cell type

value: CD8+ T cells


title: CD8+ T cells, LP51

description: Ex vivo gene expression

label_protocol: cDNAs were labeled with Cy3 dye and hybridized to an Agilent Human 4 X 44K microarray (GenomicWorks, Daejeon, Korea)


title: SRn_1_RRBS

tag: treatment

tag: neun

tag: biol. repl.


title: kidney mutant biological rep1

tag: genotype

value: female


title: 2123_R

description: Subject_2123 breast milk, group: 1-Never breast cancer

tag: subject

tag: slide

tag: array

value: NHBCS


title: CD8+ T cells, LP1

description: Ex vivo gene expression


title: kidney wildtype biological rep3

source_name: kidneys from 6 weeks old wildtype mice

value: Foxd1_wt Pdgfrb_wt


title: 2190_R

description: Subject_2190 breast milk, group: 1-Never breast cancer

tag: age (years)

tag: Sex

tag: group


title: 2190_L

tag: cohort

tag: breast biopsy

tag: time from delivery (months)


title: KRp_1_RRBS

value: Hippocampus


title: CD8+ T cells, LP36

description: Ex vivo gene expression


title: CD8+ T cells, B52

description: Ex vivo gene expression

source_name: Ex vivo PBMC

value: Blood

value: PBMC


title: 2217_R

description: Subject_2217 breast milk, group: 1-Never breast cancer


title: kidney wildtype biological rep2

tag: strain

tag: gender

tag: age


title: plus Fe Rep3

city: Hanover

first: Mary Lou

last: Guerinot

address: 78 College St

department: Biological Sciences

institute: Dartmouth College

data_processing:
ChIP reads were trimmed using Trimmomatic version 0.33
Truseq version 2 single-end adapters were removed using a maximum of two seed mismatches, a palindrome clip threshold of 30, and a simple clip threshold of 10
Low-quality bases were removed using sliding window trimming with a window size of 3 bp and an average required quality score of 20
After trimming, reads were mapped to the A. thaliana TAIR10 reference genome using Bowtie 1.2.2 with the following parameters: -v 2 –best –strata -m 1
Aligned reads then were sorted using SAMtools 1.3.1. Clonal reads were removed using Picard 2.4.1. The final reads were converted to BED format using BEDTools 2.26.0
Genome_build: TAIR10
Supplementary_files_format_and_content: BAM files were loaded and analyzed with Galaxy (http://usegalaxy.org). Peaks were called using MACS2 with default settings (effective genome size 120 Mb, lower mfold bound 5, upper mfold bound 50, and the band width at 300). The reads file from the library of the IgG fraction were used as a control for all three replicates. The binding regions were detected using the DiffBind tool.

organism: Arabidopsis thaliana

source_name: Arabidopsis roots

extract_protocol: Library construction was carried in the laboratory of Robert Schmitz at the University of Georgia.

tag: binding

value: URI


title: KRn_1_RRBS

tag: tissue

tag: treatment

value: Kainate

value: negative


title: 2217_L

value: F

value: 1-Never breast cancer


title: minus Fe Rep3


title: 2211_L

description: Subject_2211 breast milk, group: 1-Never breast cancer


title: 2211_R


title: kidney wildtype biological rep1

value: kidney


title: IP_Control

city: Bern

first: Pauline

middle: Emilie

last: Jullien

address: Altenbergrain 21

department: Institute of Plant Biology

institute: University of Bern

data_processing:
alignment: Bowtie for sRNA and hisat2 for mRNA
HiCdat was used to assign sRNA reads to 500 bp fragments
Rsubread function featureCounts() was used to assign aligned reads to genomic features
Genome_build: TAIR10
Supplementary_files_format_and_content: tab separated files containing mRNA sequencing counts per genomic feature (RNAseq_counts.txt )
Supplementary_files_format_and_content: tab separated files containing small RNA sequencing counts per 500 bp genomic bin (sRNA_per_500bp_fragments.txt )

source_name: siliques

extract_protocol:
sRNA eluted from Flag beads
Illumina library protocol

value: 1-5 days after polination siliques

tag: ecotype

tag: genotype/variation

value: wild type


title: plus Fe Rep2


title: TOTAL_smRNA

extract_protocol:
total sRNA extracted with trizol
Illumina library protocol


title: CD8+ T cells, B51

description: Ex vivo gene expression

tag: cell type

tag: sorted cell type


title: minus Fe Rep2


title: CD8+ T cells, B36

description: Ex vivo gene expression


title: IP_AGO3

value: ago3-3 pAGO3:FHA-AGO3


title: plus Fe Rep1


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample3

city: Singapore

first: Sarah

last: Daud

address: 1E Kent Ridge Road,NUHS Tower Blk,Lvl 12,

country: Singapore

institute: National University of Singapore

description: Cynomolgus macaque peripheral blood CD27+CD11b+ NK subset

hyb_protocol: The hybridization cocktails containing 1µg of Cy3-labeled cDNA targets were heated at 95ºC for 3 minutes before hybridization. Equal volume of aliquots from each sample were hybridized onto Agilent oligonucleotides custom GE microarray (8x60K format) at 65ºC for 17 hours at 20 rpm in a rotating hybridization oven. The slide was washed according to the gene expression was buffer pack protocol (Agilent Technologies) in the presence of 0.005% Triton X-102.

scan_protocol: The scanning of microarray slide was performed using Agilent DNA Microarray Scanner (Agilent Technologies) according to manufacturer’s instruction for AgilentG3_GX_1Color protocol. Assignment of grid template was performed based on AMADID 064853. This design ID contains a total of 62976 Feature Numbers corresponding to 43973 of unique Probe IDs.

data_processing: Raw signal data extraction, spot intensities, grid measurements and removal of outlier pixels were performed using Feature Extraction Software v10.7.1.1 (Agilent Technologies). The Feature Extraction output file containing intensity and annotation information for each hybridized samples were transferred into Partek® Genomics Suite® software, version 7.0 (Partek Inc.) for duplicate Probe IDs summarization and data normalization. Duplicate Probe ID (Probe Name) handling:- The processed data table contains 43973 of unique Probe IDs after mean signals were taken as the imported values on all duplicate Probe IDs. The first line on the duplicate Probe IDs were taken as the annotation information (Feature Number).

organism: Macaca fascicularis

source_name: Vietnam

label_protocol: Purified total RNA of 50ng as input was amplified using the Ovation® Pico WTA System V2 kit (NuGEN Technologies Inc.) that includes first-strand cDNA synthesis, second-strand cDNA synthesis and SPIA isothermal linear amplification. The purification of the final SPIA cDNA product was performed using MinElute® Reaction Cleanup Kit (Qiagen). For each sample, 400ng of amplified product was Cy3-labeled using the SureTag DNA Labeling kit (Agilent Technologies) with restriction digestion step based on Agilent’s recommended protocol for 8-pack microarrays. Dye incorporation, specific activity and cDNA yield were analyzed using MicroArray Measurement DNA-50 menu, NanoDrop ND-1000.

growth_protocol: unstimulated NK cell subpopulations

extract_protocol: Total RNA was extracted from flow-sorted cells using TRIzol reagent (Invitrogen) method combined with RNeasy MinElute kit (Qiagen) purification steps.

treatment_protocol: Cryopreserved samples were thawed in a 37°C water bath, re-suspended in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum to wash away the freezing media. Macaque cells were stained for NK surface markers NKG2A/CD159a, CD8a, CD27, CD11b, NKp80 and lymphocyte lineage markers CD45, CD3, CD14, CD20, HLA-DR. After the addition of DAPI stain to distinguish dead cells, NK subsets were subjected to fluorescence-activated cell sorting using a four laser MoFlo® Astrios™ cell sorter (Beckman Coulter) and cells were flow sorted directly into TriZol solution. All NK cell subsets were derived from CD45+ CD3- CD14- CD20- HLA-DR- live gate.

value: Female

value: 4 years old


title: 2103_L

description: Subject_2103 breast milk, group: 1-Never breast cancer

tag: subject

tag: slide

tag: array


title: 2123_L

tag: age (years)

tag: Sex

tag: group


title: WT_rep1_1

extract_protocol:
total RNA extracted with Rneasy kit
Illumina library protocol


title: 2134_L

description: Subject_2134 breast milk, group: 1-Never breast cancer

tag: cohort

tag: breast biopsy

tag: time from delivery (months)


title: CD8+ T cells, B1

description: Ex vivo gene expression

value: CD8+ T cells


title: EC-NCCIT-A3

description: Embryonal carcinoma

tag: gender

value: Male

tag: sample type

value: Embryonal carcinoma

tag: disease state

value: cancer


title: minus Fe Rep1

tag: binding


title: 2103_R

value: NHBCS


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample2

description: Cynomolgus macaque splenic CD27+CD11b+ NK subset

source_name: Singapore

tag: tissue

value: Spleen

tag: age

value: 5 years old


title: EC-NEC14

description: Embryonal carcinoma


title: ago3_HO_rep1_1

tag: ecotype

tag: genotype/variation


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample1

value: 9 years old


title: minus Fe_IgG control

value: IgG control


title: EC-1777N-Rpmet

description: Embryonal carcinoma


title: EC-PA-1

description: Embryonal carcinoma


title: ago3_HE_rep2_1


title: sid2_L-Glu_48_h_rep3

city: Yokohama

first: Yukihisa

last: Goto

address: 1-7-22 Suehiro-cho

institute: RIKEN

data_processing:
The 50 bp single-end reads were sequenced on an Illumina Hiseq 4000 platform. The Fastx toolkit 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/) was used for quality filtering. The first 6 bp sequences were trimmed to remove barcode sequences. Low-quality nucleotides (<30 quality score) were removed from the 3’ ends and short reads (<39 bp) and reads showing at least 95 % of nucleotides with less than 20 quality score were removed.
Filtered reads were mapped to Arabidopsis genome TAIR10.30 by tophat v2.1.0 (Trapnell et al., 2009)　(https://ccb.jhu.edu/software/tophat/index.shtml).
Read counts were extracted by HTSeq version 0.6.0 (Anders et al., 2015) (https://htseq.readthedocs.io/)
Read counts were filtered such that there was at least one count per million in at least half of the samples and subsequently normalized using the trimmed mean of M-values (TMM) method in the Bioconductor package edgeR 3.22.3 (Robinson et al., 2010).
Genome_build: Arabidopsis genome TAIR10.30
Supplementary_files_format_and_content: comma separated text files includeTMM-normalized expression

source_name: seedlings

growth_protocol: Arabidopsis ecotype Columbia (Col-0) was sown on soil or half-strength Murashige-Skoog media containing 1 % sucrose. After a 2 day cold treatment to break seed dormancy, Liquid culture seedlings were grown under continuous-light at 23℃.

extract_protocol:
Sample preparation was performed using a High-throughput RNA-Seq method as described previously (Kumar et al., 2012)
RNA-Seq library preparation was also carried out using a High-throughput RNA-Seq method (Kumar et al., 2012)

treatment_protocol: The 14-day-old Arabidopsis seedlings were treated with 20 mM urea, 20 mM L-Glu, or 1mM SA after 6 h, 12 h, 24 h, and 48 h

tag: treatment

value: L-Glu

tag: genotype

tag: timepoint


title: ago3_HE_rep1_1


title: 2189_L

description: Subject_2189 breast milk, group: 1-Never breast cancer

tag: subject

tag: slide

tag: array

tag: age (years)

value: F

value: 1-Never breast cancer


title: 2322_L

description: Subject_2322 breast milk, group: 1-Never breast cancer

tag: Sex

tag: group

tag: cohort

tag: breast biopsy


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample2

description: Cynomolgus macaque splenic CD27loCD11b+ NK subset

tag: gender


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample3

description: Cynomolgus macaque peripheral blood CD27loCD11b+ NK subset

value: PBMC


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample1


title: 2131_R

description: Subject_2131 breast milk, group: 1-Never breast cancer

tag: time from delivery (months)


title: Wild Type-powder chow-animal 115

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Samples were hybridized to Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on a GeneArray Scanner 3000 7G, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done using the Robust Multichip Average (RMA) algorithm and the MBNI custom CDF (http://brainarray.mbni.med.umich.edu/) version #14 for the mouse gene 1.0 ST array. Normalization output consisted of data for 21225 probe sets each corresponding to unique Entrez Gene IDs.

source_name: forebrain

label_protocol: RNA samples were processed using the Affymetrix GeneChip WT PLUS kit.

growth_protocol: Mice were housed in standard cages with food and water ad libitum and a light/dark cycle of 12h. Female C57Bl/6J mice (Jackson Laboratory, Bar Harbor, ME) were crossed with Ts1Cje males (B6 T(12:16)1Cje/CjeDnJ, a mouse model of Down syndrome), to generate pregnancies in which approximately half of the fetuses were affected with Down syndrome and half were wild-type. Only outcomes from wild-type fetuses and offspring (exposed to the intrauterine environment of a wild-type/C57Bl/6J dam) were examined here. This study was part of a larger research program examining the impact of maternal nutrient supplementation in pregnancy on fetal and offspring brain development in the setting of fetal Down Syndrome compared to wild-type fetuses.

extract_protocol: On embryonic day 15.5 (E15.5), pregnant dams were euthanized with isoflurane followed by decapitation.  Embryos were rapidly dissected from the uterine horns and placed in ice-cold 1X phosphate-buffered saline (PBS) containing RNA preservative (RNALater, Qiagen). Theiler staging was performed to confirm E15.5. Embryonic brains were rapidly removed from skulls on a cold platform, forebrain was isolated and snap frozen in liquid nitrogen, prior to storage at -80C.  Tail snips were obtained for Ts1Cje and sex genotyping. In this study, only mice that had the wild-type genotype were used. Five embryos per maternal diet group were used for microarray analyses. Total RNA was isolated from embryonic forebrains using the NucleoSpin II RNA/protein kits (Machery-Nagel, Duren, Germany) per the manufacturer’s instructions.

treatment_protocol: Breeder pairs received either a standard commercially-available pelleted chow (Teklad 2918, 14 dams) or a standard commercially-available purified powdered chow diet (Bioserv F3197, 14 dams). Dams were started on the study diet at the time of initial breeding with a sire. They continued on the diet throughout pregnancy and lactation.

tag: diet

value: Powder Chow


title: Wild Type-powder chow-animal 111


title: sid2_L-Glu_48_h_rep2


title: EC-NEC8

description: Embryonal carcinoma

tag: sample type

tag: disease state


title: sid2_L-Glu_48_h_rep1


title: WT_rep2_1

tag: tissue

value: 1-5 days after polination siliques

tag: ecotype

tag: genotype/variation

value: wild type


title: Arabidopsis XVE:PAN_24 hours after induction_third biological replicate

city: Raleigh

first: Maria

middle: Angels

last: de Luis Balaguer

state: NC

address: 2115 Gardner Hall, Box 7612

department: Plant and Microbial Biology

institute: North Carolina State University

data_processing:
cDNA libraries were sequenced using an Illumina HiSeq 2500 sequencing machine
Adapters and low quality reads were filtered out using ea-utils software. Reads longer than 30bp with a quality score was greater than 30 were kept.
Clean reads were mapped against the TAIR 10 reference genome using the TopHat v2.0.13
Transcripts were assembled using Cufflinks (version 2.1.1). Normalized reads (FPKM values) were calculated at this step.
Cuffdiff was used to test for differential expression.
Genome_build: TAIR 10

source_name: Arabidpsis whole root

growth_protocol: Seeds were grown on 1X MS supplemented with 1% sucrose plates, and then were transferred to 1X MS supplemented with 1% sucrose and 10 uM β-estradiol for 0, 6, or 24 hours.

extract_protocol:
Roots were dissected at approximately 0.5 cm from the root tip for RNA extraction. RNA was extracted using the RNeasy Micro Kit (Qiagen).
cDNA synthesis, amplification, and library preparation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries were sequenced on an Illumina HiSeq 2500 with 100 bp single-end reads.

treatment_protocol: Induction of PAN expression for 0, 6, or 24 hours

value: XVE:PAN transgenic line

tag: time point

value: 24hrs after induction of PAN expression


title: Arabidopsis XVE:PAN_24 hours after induction_first biological replicate


title: Arabidopsis XVE:PAN_24 hours after induction_second biological replicate


title: sid2_urea_48_h_rep3

tag: treatment

value: urea

tag: genotype

tag: timepoint


title: 2134_R

tag: subject

tag: slide

tag: array

tag: age (years)


title: 2224_L

tag: Sex

tag: group

tag: cohort

tag: breast biopsy


title: Wild Type-powder chow-animal 108

tag: diet


title: sid2_urea_48_h_rep2


title: 2147_R

description: Subject_2147 breast milk, group: 1-Never breast cancer

tag: time from delivery (months)


title: Arabidopsis XVE:PAN_6 hours after induction_third biological replicate

value: 6hrs after induction of PAN expression


title: Wild Type-powder chow-animal 88


title: 2189_R


title: 2020_L

description: Subject_2020 breast milk, group: 1-Never breast cancer


title: 002279_SK8: uri +Fe Root Biological Rep2

description: Gene expression data from roots

hyb_protocol: Labelled cRNA were hybridized on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array following standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to the standard Affymetrix protocol.

data_processing: Dara were normalized from .cel files using the RMA protocol.

source_name: Arabidopsis root

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol.

growth_protocol: Plants were grown on half-strength Gamborg's B5 medium for 14 days and transferred to +Fe or -Fe conditions for 3 days.

extract_protocol: Total RNA was extracted using a Rnease Mini kit (Qiagen) following manufacturere's instruction.

treatment_protocol: Basal medium was prepared with 2 mM Ca(NO3)2, 0.75 mM K2SO4, 0.65 mM MgSO4, 0.1 mM KH2PO4, 10 µM H3BO3, 0.1 µM MnSO4, 0.05 µM CuSO4, 0.05 µM ZnSO4, 0.005 µM (NH3)6Mo7O24, 1 mM MES, 0.7% (w/v) type M agar, and adjusted to pH 6.0. For +Fe conditions, 50 µM Fe(III)-EDTA was added to the agar medium. The iron chelator ferrozine [3-(2-pyridyl)-5,6-diphenyl-1,2,4-triazine sulfonate] (HACH Chemical) was added at 300 µM to the agar medium for -Fe conditions.

value: uri mutant

tag: tissue

value: root


title: 002278_SK7: uri +Fe Root Biological Rep1

description: Gene expression data from roots


title: ago3_HO_rep2_1

tag: ecotype


title: sid2_urea_48_h_rep1


title: EC-NTERA-2-cloneD1

description: Embryonal carcinoma

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: Embryonal carcinoma

tag: disease state

value: cancer


title: Wild Type-pelleted chow-animal 15

value: Pelleted Chow


title: Col-0_L-Glu_48_h_rep3

tag: treatment

value: L-Glu

tag: genotype


title: Arabidopsis XVE:PAN_6 hours after induction_second biological replicate

tag: genotype/variation

tag: time point


title: 002277_SK6: WT +Fe Root Biological Rep2

description: Gene expression data from roots

value: wild-type


title: Wild Type-pelleted chow-animal 11


title: 2127_L

description: Subject_2127 breast milk, group: 1-Never breast cancer

tag: subject

tag: slide

tag: array

value: F

value: 1-Never breast cancer

value: NHBCS


title: 002276_SK5: WT +Fe Root Biological Rep1

description: Gene expression data from roots


title: 2147_L

tag: age (years)

tag: Sex

tag: group


title: plus Fe_IgG control

tag: binding

value: IgG control


title: Arabidopsis XVE:PAN_0 hours after induction_third biological replicate

value: 0hr after induction of PAN expression


title: Arabidopsis XVE:PAN_0 hours after induction_second biological replicate

value: XVE:PAN transgenic line


title: Arabidopsis XVE:PAN_0 hours after induction_first biological replicate


title: 2322_R

tag: cohort

tag: breast biopsy

tag: time from delivery (months)


title: Arabidopsis XVE:PAN_6 hours after induction_first biological replicate

tag: ecotype


title: Col-0_urea_48_h_rep2

tag: timepoint


title: Col-0_urea_48_h_rep3


title: Postnatal day 7 melanocytes

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
The reads were mapped to mm9 with Tophat.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Melanocytes

growth_protocol: The  RNASeq samples  were derived from the GFP-positive melanocytic cells isolated from four developmental time points: Embryonic day (E) 15.5 and 17.5, and Postnatal day (P) 1 and 7.

extract_protocol:
Isolation of melanoblasts and melanocytes: FVB/N iDct-GFP dams were fed doxycycline-fortified chow for the entire duration of gestation until collection of E15.5, E17.5 and P1 pups. Doxycycline was injected intraperitoneally at 80 μg/g body weight 24 hr before collection of P7 pups. A single cell suspension was generated from embryos and skin of newborn pups. Multiple litters were used for each developmental stage, and embryos/pups from each stage were pooled to ensure adequate numbers of GFP+ cells. The head was removed to prevent collection of GFP positive cells in the embryonic telencephalon, and melanocytes from the inner ear or from the retinal pigmented epithelium (RPE) were discarded. Excess tissue was also removed. The spinal cord was kept intact as some melanoblasts still remain in the neural crest area. At E17.5, P1 and P7 stages, most melanocytes have reached the dermis, thus only the skin was collected from these developmental stages. Back skin was immersed in a shallow layer of 1X PBS and subcutaneous fat was scraped off until skin appeared translucent. E15.5 was the youngest age assessed due to the necessity to capture sufficient cells for RNA-sequencing. Preparation of single cell suspensions and Fluorescence-Activated Cell Sorting (FACS): Tissue was minced and incubated for 30 min at 37°C in digestion media containing RPMI 1640 (Gibco Life Technologies) with 200 units/ml Liberase TL (Roche Applied Science). Up to 1g of tissue was digested per 5 ml digestion media. Tissue was processed using a Medimachine (BD Biosciences) and sterile medicon units (BD Biosciences). Cells were extracted using 1.5-2 ml of RFD solution (24 ml RPMI media, 6 ml FBS, 300 µl 5% DNase I) through a 20 ml syringe with 18-gauge needle. Collected cells were filtered through a 50-micron filter (BD Biosciences). This process was repeated until all the tissue was processed. Cells were spun at 1200 rpm, 4°C for 5 min and resuspended twice in a solution of 1% BSA in PBS and filtered through a 30-micron filter for sorting. Embryos of the same developmental age that were heterozygous for the TRE-H2B-GFP gene but lacked the Dct-rtTA gene were used as negative controls. Cell doublets were excluded from the analysis. Cells were sorted based on GFP expression and SSC-A. Based on these reference sorts, gates were set so that background cells represented less than 10% of sorted cells. RNA Isolation: Cells were lysed in 10-fold TRIzol reagent (w/v), phases were separated by addition of 0.2X volume of chloroform, the aqueous phase was combined with an equal volume of 70% ethanol and applied to a RNeasy Micro column (Qiagen) and processed as per the manufacturer’s instructions. Paired-end sequencing libraries were prepared using 1 μg of purified RNA following the mRNA-Seq Sample Prep Kit according to the manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: These four stages represent embryonic melanoblast development from the neural crest into differentiated quiescent melanocytes of the postnatal pup.

tag: strain

value: FVB/N iDct-GFP

tag: tissue

value: skin

tag: in vivo timepoint

value: Postnatal day 7


title: Postnatal day 1 melanocytes

value: Postnatal day 1


title: Col-0_L-Glu_48_h_rep1

tag: treatment

tag: genotype


title: Col-0_L-Glu_48_h_rep2


title: Wild Type-pelleted chow-animal 09

tag: diet


title: Arabidopsis root_hb13 mutant genetic background_third biological replicate

source_name: Arabidpsis whole root_hb13

growth_protocol: Growth Media: Standard media for 5 days

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen).
cDNA synthesis, amplification, and library preparation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries were sequenced on an Illumina HiSeq 2500 with 100 bp single-end reads.

treatment_protocol: Roots were dissected at approximately 0.5 cm from the root tip for RNA extraction 5 days after germination.

tag: genotype/variation

value: hb13 mutant

value: whole root


title: Wild Type-pelleted chow-animal 07


title: 002187_SK4: uri -Fe Root Biological Rep2

description: Gene expression data from roots

value: uri mutant

value: root


title: 002186_SK3: uri -Fe Root Biological Rep1

description: Gene expression data from roots


title: Col-0_urea_48_h_rep1

value: urea


title: Wild Type-pelleted chow-animal 05

value: Pelleted Chow


title: 2127_R

source_name: breast milk

tag: subject

tag: slide

tag: array


title: 002185_SK2: WT -Fe Root Biological Rep2

description: Gene expression data from roots

value: wild-type


title: 2020_R

tag: age (years)

tag: Sex

value: F

tag: group


title: Embryonic day 17.5 melanoblasts

source_name: Melanoblasts

value: Embryonic day 17.5


title: Arabidopsis root_hb13 mutant genetic background_first biological replicate


title: Col-0_SA_48_h_rep3 time course

value: SA

tag: time


title: Embryonic day 15.5 melanoblasts

value: whole embryo with heads removed

value: Embryonic day 15.5


title: Col-0_SA_48_h_rep2 time course


title: Arabidopsis root_WT genetic background_third biological replicate

source_name: Arabidpsis whole root_WT

value: wild type


title: s06

city: Vienna

first: Loan

last: Vulliard

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM

data_processing:
Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0.
Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
Read counts per exon were obtained in R 3.4.0 with Rsubread_1.26.1, with the featureCount function, either allowing or not both parameters allowMultiOverlap and countMultiMappingReads.
Genome_build: mm9
Supplementary_files_format_and_content: Feature counts with and without multimapping reads, in two objects called respectively fcMulti and fcStrict, were exported as binary file using R's save function.

source_name: Preosteoclasts

growth_protocol: Bone marrow was culutred for three days with 100 ng/ml M-CSF, scratched and replated in 30 ng/ml M-CSF and/or 50 ng/ml RANKL and  for 24 hours

extract_protocol:
RNA-seq was performed as described previously with slight modification (Hirahara et al., Immunity 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol  following manufacture’s protocol (Life Technologies).
Total RNA was subsequently processed to mRNA-seq library using NeoPrep Library Prep System and TruSeq Stranded mRNA Library Prep Kit for NeoPrep (Illumina).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

treatment_protocol: Cells were either plated on day 3 either with M-CSF, M-CSF+RANKL, M-CSF+RANKL+recArg1 (MCSF+RANKL+recArg1) in full medium or with M-CSF (M-CSF+depl), MCSF+arginine (MCSF+rescue), MCSF+RANKL (MCSF+RANKL+depl), MCSF+RANKL+arginine (MCSF+RANKL+rescue) in arginine-free medium

tag: condition

value: MCSF+rescue

tag: mouse


title: Col-0_SA_48_h_rep1 time course

tag: ecotype


title: Arabidopsis root_WT genetic background_second biological replicate


title: s08

value: MCSF+RANKL+rescue


title: Arabidopsis root_WT genetic background_first biological replicate


title: 170331_0038_s082


title: 002184_SK1: WT -Fe Root Biological Rep1

description: Gene expression data from roots


title: 170331_0038_s080

value: MCSF+RANKL+depl


title: Col-0_SA_24_h_rep1 time course


title: 170331_0038_s078

value: MCSF+RANKL


title: Arabidopsis root_hb13 mutant genetic background_second biological replicate

value: hb13 mutant


title: Small intestine, Hnf4aKO_rep5

city: Amsterdam

first: Sander

last: Meisner

address: Meibergdreef 69-71

department: Tytgat institute

institute: AMC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: small intestine, Hnf4a knockout

label_protocol: Biotinylated cRNA were prepared with the Invitrogen Illumina Totalprep RNA amplification kit for Illumina arrays

growth_protocol: VillinCreERT2+-Hnf4afl/fl mice and VillinCreERT2--Hnf4afl/fl mice were given 1 mg of tamoxifen (Sigma, Saint Louis, MO, USA) administered by oral gavage for 5 consecutive days.

extract_protocol: The intestinal tissue RNA was extracted with TRI Reagent (Sigma-Aldrich) and RNA clean-up was performed with the RNeasy kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 3 weeks after tamoxifen-induced Cre recombination, the animals were treated with 14 Gy whole-body γ-irradiation and sacrificed 96 hours afterwards.

value: small intestine

value: irradiated

tag: time point

value: 96h after irradiation


title: Small intestine, Hnf4aKO_rep7

tag: tissue


title: Wild Type-powder chow-animal 87

value: Powder Chow


title: 170331_0038_s075

value: MCSF+depl


title: Col-0_SA_12_h_rep2 time course


title: 170331_0038_s073

value: MCSF


title: Col-0_SA_24_h_rep2 time course


title: Small intestine, Hnf4aKO_rep3


title: Col-0_SA_12_h_rep1 time course


title: Col-0_SA_06_h_rep3 time course

value: 6 h


title: 170331_0038_s071


title: 170227_s48


title: Small intestine, Hnf4aKO_rep2


title: Col-0_SA_12_h_rep3 time course


title: Healthy patient 5

city: Moscow

first: German

last: Osmak

address: 3-ya Cherepkovskaya

country: Russia

institute: National Medical Research Center for Cardiology

description: Gene expression data from patients with MI

hyb_protocol: Following fragmentation, 5.5 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip™ Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G.

data_processing: Computational analysis of the microarray data files was performed using R programming language version 3.5.1. Data processing was carried out based on the affy package written in R [Gautier L, Cope L, Bolstad BM, Irizarry RA (2004). “affy—analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics, 20(3), 307–315. ISSN 1367-4803, doi: 10.1093/bioinformatics/btg405]. A biomaRt package was used to annotate the obtained data [Durinck S. et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis //Bioinformatics. – 2005. – Т. 21. – №. 16. – С. 3439-3440].

source_name: Blood sample from Healthy patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Array User Guide, 2018, Thermo Fisher Scientifi).

growth_protocol: Six patients with first ST-segment elevation myocardial infarction (MI) were enrolled in this study. All patients were diagnosed at the National Medical Scientific Center for Cardiology (Moscow, Russia) based on symptoms of myocardial ischemia, increase of high-sensitivity cardiac troponin I (hs-cTn-I) and/or emergence of new or presumed new ST-segment elevation, new left bundle branch block or development of pathological Q waves in accordance with Third Universal Definition of MI. Hs-cTn-I was measured during the initial patient assessment (from 1 to 18 h after the onset of disease symptoms). All patients underwent coronary angiography on admission. All patients and were treated according to contemporary guidelines. A total of 6 healthy controls (HCs) (all men, mean age 51.0 ± 7.1 years) with normal electrocardiogram, no history of cardiovascular diseases (CVD) and diabetes mellitus were included in the study; healthy controls (HCs characteristics by smoking status and body mass index were compatible to MI patients. All participants lived in European Russia.

extract_protocol: Blood samples were collected from MI patients 24-36 h after the disease onset and from HCs in the morning. PBMCs were isolated using Ficoll-Hypaque density gradient method (Sigma-Aldrich, St. Louis, MO, USA) within 3 h of sampling. Total RNA including small RNA was extracted using miRNeasy Mini Kit (Qiagen, Hildren, Germany) following the manufacturer's instructions. The RNA quantity was measured using the NanoDropTM spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA); the RNA integrity was assessed by QIAxcel Advanced System (Qiagen, Hilden, Germany). Samples with a RNA integrity number (RIN) value above eight were included in subsequent experiments.

tag: subject group

value: Healthy patient

tag: gender

value: male

tag: subject status

value: Normal electrocardiogram, no history of cardiovascular diseases (CVD) and diabetes mellitus

value: blood


title: Col-0_SA_06_h_rep2 time course

tag: treatment

value: SA


title: Col-0_SA_24_h_rep3 time course


title: Small intestine, Hnf4aKO_rep6

tag: genotype


title: Small intestine, Hnf4aKO_rep1


title: Small intestine, Hnf4aWT_rep8

source_name: small intestine, Hnf4a wildtype


title: 170227_s46


title: 170227_s43


title: Healthy patient 4


title: Col-0_L-Glu_48_h_rep3 time course

value: L-Glu


title: 170227_s41

value: MCSF+rescue


title: Small intestine, Hnf4aKO_rep4


title: Healthy patient 3


title: Col-0_L-Glu_48_h_rep2 time course


title: Small intestine, Hnf4aWT_rep7


title: 170227_s39


title: Small intestine, Hnf4aWT_rep6


title: Small intestine, Hnf4aWT_rep5


title: Small intestine, Hnf4aWT_rep4


title: Healthy patient 2


title: Col-0_L-Glu_48_h_rep1 time course


title: Patient with MI 6

source_name: Blood sample from patient with MI

value: patient with Myocardial infarction (MI)

value: Increase of high-sensitivity cardiac troponin I (hs-cTn-I) and new ST-segment elevation


title: Healthy patient 1


title: Healthy patient 6


title: 170227_s36

value: MCSF+RANKL+depl


title: Patient with MI 5


title: 170227_s35


title: Small intestine, Hnf4aWT_rep2

value: small intestine


title: Col-0_L-Glu_24_h_rep3 time course


title: Small intestine, Hnf4aWT_rep3

value: irradiated


title: 170227_s33


title: Patient with MI 4


title: Small intestine, Hnf4aWT_rep1

value: 96h after irradiation


title: Patient with MI 3


title: Col-0_L-Glu_24_h_rep1 time course


title: Patient with MI 2


title: Col-0_L-Glu_12_h_rep3 time course


title: 170227_s15

value: MCSF+RANKL


title: 170227_s14


title: Col-0_L-Glu_24_h_rep2 time course


title: 170227_s16


title: Col-0_L-Glu_12_h_rep1 time course


title: Col-0_L-Glu_12_h_rep2 time course


title: Col-0_L-Glu_06_h_rep3 time course