title: CMT1A iPSC 05148 Schwann-1

description:
CMT1A disease hiPSC derived Schwann cell
11

source_name: CD49d+ CMT1A iPSC 05148 Schwann


title: CMT1A-PGD12-2

status: Public on Aug 15 2019

type: SRA

city: Seoul

first: Macrogen

last: Inc.

address: 12F, World Meridian Venture Center #254 Beotkkot-ro, Geumcheon-gu

country: South Korea

institute: Macrogen Inc.

description:
CMT1A disease hESC derived Schwann cell
Re6

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using TopHat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.2 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for 19 samples.

molecule: total RNA

organism: Homo sapiens

source_name: CD49d+ CMT1A-PGD12

growth_protocol: We cultured undifferentiated hESC and hiPSC lines on mitotically inactivated mouse embryonic fibroblasts, in a medium containing DMEM/F12, 20% knockout serum replacement, 0.1 mM MEM-NEAA, 1 mM L-glutamine, 55 μM β-mercaptoethanol and 4 ng/mL FGF2. For the Fibroblast culture, MEM containing 10% FBS was used. All cells were maintained at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Lysed cells by adding TRIzol
Libraries were constructed from mRNA using the Illumina TruSeq RNA Access Library Prep Kit following  manufacturer's protocols.

treatment_protocol: We differentiated human Schwann cell precursors from hESCs (H9 or PGD CMT1A hESCs) and hiPSCs (healthy donor 00024, 02623, and CMT1A disease line 05148, 05165) by using 2i protocol, and WNT was activated for iNC differentiation.

tag: disease state

value: CMT1A disease

tag: cell type

value: hESC derived Schwann cell


title: CMT1A-PGD12-1

description:
CMT1A disease hESC derived Schwann cell
5


title: H9 Schwann precursor-1

description:
healthy hESC derived Schwann cell
Re1

source_name: CD49d+ H9 Schwann precursor

value: healthy


title: OTX_rep_2

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

country: China

institute: Guangdong Pharmaceutical University

data_processing:
Basecalls performed using bcl2fastq version 2.18
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat 2.1.1
Use Cufflinks version 2.1.1 compute the FPKM, use Refseq GTF file to transcript annotations
RNA-seq data analysis using Excel to compute the Fold change and p-value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample processed by cufflinks

extract_protocol:
mRNA was extracted from DMSO and OTX015 treated cells
mRNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Library Prep Kit for Illumina according to the manusfacture's protocol

tag: treatment


title: CMT1A-PGD11-2

description:
CMT1A disease hESC derived Schwann cell
4

source_name: CD49d+ CMT1A-PGD11


title: H9 Schwann precursor-2

description:
healthy hESC derived Schwann cell
Re2


title: Patient3_KO_Venetoclax_rep2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

country: USA

institute: University of Vermont

data_processing:
Basecalls performed using HiSeq Control Software X, RTA X and CASAVA version X
Quality control of reads were performed using RSeQC v2.6, adapters and low quality reads were removed using using TrimGalore v0.4
Filtered reads were aligned to a hg38 reference index based off of GENCODE Release 25 (GRCh38.p7) using RNA-STAR aligner with the following parameters: --outSAMtype BAM SortedByCoordinate --sjdbGTFfile gencode.m14.annotation.gtf  --outFilterType BySJout --outFilterMultimapNmax 50 --alignSJoverhangMin 1  --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif
Quantification of gene expression was performed with HTSeq-0.11.0 using the aligned bam files and the human GENCODE Release v25 comprehensive GTF annotation file
Genome_build: Hg38 (GRCh38.p7)
Supplementary_files_format_and_content: Raw HTSeq-counts for all files are merged in the CLL_rawcounts.matrix.txt file

source_name: Primary CLL cells

growth_protocol: Primary CLL cells were co-cultured with bone marrow derived mesenchymal stromal cells (BMSCs) from either Wild Type or prkcb-/- mice in vitro in RPMI 1640 medium for totally 48 hours.

extract_protocol:
Primary CLL cells were harvested after purity check (>95% CD5 ve+/CD19 ve+) and total RNA was extracted using the standard protocol from GenElute Mammalian Total RNA Miniprep Kit (Sigma/RTN70).
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB #7420) was used with 100ng of total RNA for the construction of sequencing libraries. mRNA was isolated and purified by using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #7490) before cDNA synthesis.

treatment_protocol: For samples with venetoclax treatment, primary CLL cells were co-cultured with BMSCs for 24 hours before adding venetoclax (1.25nM) into the co-culture system for another 24 hours.

tag: tissue

value: PBMC

value: co-culture with prkcb-/- BMSC, venetoclax treated


title: Patient3_KO_Venetoclax_rep3


title: Patient3_KO_Venetoclax_rep1


title: Patient3_WT_Venetoclax_rep2

value: co-culture with Wild Type BMSC, venetoclax treated


title: Patient3_KO_noTreat_rep3

value: co-culture with prkcb-/- BMSC


title: Patient3_WT_Venetoclax_rep3


title: Patient3_KO_noTreat_rep2


title: Patient3_KO_noTreat_rep1


title: Patient3_WT_noTreat_rep3

value: co-culture with Wild Type BMSC


title: Patient3_WT_noTreat_rep2


title: Patient2_KO_Venetoclax_rep3


title: Patient3_WT_noTreat_rep1


title: Patient2_KO_Venetoclax_rep2


title: Patient2_WT_Venetoclax_rep3


title: CMT1A-PGD11-1

description:
CMT1A disease hESC derived Schwann cell
3


title: Patient2_KO_noTreat_rep1


title: Patient2_KO_noTreat_rep3


title: Patient2_WT_Venetoclax_rep1


title: Patient2_KO_noTreat_rep2


title: Patient2_WT_noTreat_rep2


title: Patient2_WT_noTreat_rep3


title: Patient1_KO_Venetoclax_rep1


title: Patient2_WT_noTreat_rep1


title: Patient1_KO_Venetoclax_rep3


title: Patient1_KO_Venetoclax_rep2


title: Patient1_WT_Venetoclax_rep1


title: Patient1_KO_noTreat_rep3


title: Patient1_KO_noTreat_rep1


title: Patient1_WT_Venetoclax_rep2


title: Patient1_WT_Venetoclax_rep3


title: Patient2_KO_Venetoclax_rep1


title: Patient1_KO_noTreat_rep2


title: Patient1_WT_noTreat_rep2


title: AGO2_mRNA_Susceptible_4

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

description: Ago2 pull down

data_processing:
For mRNA-seq data: Sequenced reads were trimmed for adaptors and aligned to mouse genome GRCm38/mm10 using STARv 2.5.0c with default settings. Aligned reads were annotated to gene exons with HTSeq v0.6.11 using GTF release 86 (update 2016-10), using stranded intersection-nonempty. Count matrixes were TMM and voom normalized with limma and batch adjusted with ComBat.
For miRNA-seq data: The reads were aligned to mouse reference miRNAs (miRBase v21) using miRDeep2 v0.0.7 software package and to mouse genome GRCm38 (GRCm38) using bowtie v1.1.1. The expression of mature miRNAs was quantified using miRDeep2 v0.0.7 quantifier.pl module. Count matrixes were TMM and voom normalized with limma and batch adjusted with ComBat.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log(CPM) values, normalization was done separately for each count matrix.

organism: Mus musculus

source_name: bed nuclei of stria terminalis

growth_protocol: Mice (Charles River Laboratories, Sulzfeld, Germany) were housed in groups in a temperature and humidity controlled facility on a 12h light/dark cycle for the acclimatization period. All mice had ad libitum access to food and water throughout the experiment (except for the durations of behavioral tests). Animal procedures were approved by the Regional State Administration Agency for Southern Finland (license numbers ESAVI-3801-041003-2011 and ESAVI/2766/04.10.07/2014) and carried out in accordance to directive 2010/63/EU of the European Parliament and of the Council, and the Finnish Act on the Protection of Animals Used for Science or Educational Purposes (497/2013).

extract_protocol:
Brain regions were dissected on a sterile chilled petri dish within 7 minutes and tissue was flash-frozen in liquid N2. Total RNA was extracted with TriReagent (Molecular Research Center, Inc.) and RNA integrity was controlled with Bioanalyzer (Agilent). The rRNA was depleted with Ribozero Globin depletion Kit (Illumina, CA, USA) and fragmented using the S2 ultrasonicator (Covaris Inc., MA, USA).
Sequencing libraries were prepared with TruSeq Stranded mRNA Library Prep (Illumina; BNST AGO2 mRNA), TruSeq Stranded Total RNA (Illumina; blood cells RNA), TruSeq Small RNA Library Prep Kit (Illumina; BNST AGO2 miRNA) and NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific; blood cells miRNA) library preparation kits.

treatment_protocol: Mice were killed by cervical dislocation between 8 am and 11 am to avoid circadian differences in gene expression, and the order was counterbalanced across experimental conditions.

tag: strain

tag: age on dissection

value: 8  weeks

tag: Sex

value: male

tag: csds phenotype

value: Susceptible


title: Patient1_WT_noTreat_rep1


title: AGO2_mRNA_Susceptible_3

description: Ago2 pull down


title: X. laevis with thioridazine-induced brain abnormalities at NF stage 47, Biological Replicate 3

city: Medford

first: Kelly

last: McLaughlin

state: MA

address: 200 Boston Avenue

department: Biology

institute: Tufts University

data_processing:
Reads were trimmed to remove adapter sequences and filtered to remove any low-quality reads with Trimmomatic.
Trimmed reads were mapped to the Xenopus laevis genome v9.1 with HISAT2.
Transcript count tables were generated with HTSeq-count.
Differential gene analysis was carried out using the DESeq2 package in R (Love et al., 2014).
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Tabular sheet, gene counts.

organism: Xenopus laevis

source_name: Whole-brain tissue

growth_protocol: All experiments utilizing Xenopus laevis were conducted in accordance with the guide for Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee at Tufts University. Embryo culturing was carried out as previously described (Caine and McLaughlin, 2013). Embryos and tadpoles were reared in 0.1x Marc’s Modified Ringer’s solution (MMR, 10mM NaCl, 0.2 mM KCl, 0.1 mM CaCl, 0.2 mM MgCl2, 0.5 MM HEPES, 1 µM EDTA, pH 7.5) at 14-23 ˚C. The 0.1x MMR rearing media was refreshed at least three times a week. Feeding stage tadpoles were fed Sera Micron powdered growth food three times a week. Embryos and tadpoles were staged based on Nieuwkoop and Faber (P.D. Nieuwkoop and J. Faber, 1994).

extract_protocol:
RNA libraries were generated with the Qiagen RNeasy Mini kit and DNAse treated prior to generating cDNA libraries for RNAseq.
RNAseq cDNA libraries were constructed with the Illumina Truseq RNA Library Preparation Kit v2, following the manufacturer’s protocol. We applied Quibit analysis to quantify the RNAseq cDNA libraries, which were then pooled and run on Illumina Hi-Seq 2500 at the Tufts University Core Facility to generate 100-bp single end reads.

treatment_protocol: Pharmacological exposures to induce brain defects were conducted on neurula stage embryos (NF stage 14-26) that had been reared at 14 ˚C prior to exposure. During the exposure windows, experimental and controls embryos were kept at 18 ˚C, after the exposure they were returned to 14 ˚C until they reached feeding-tadpole stages. Pharmacological treatments included: 90 µM thioridazine (Tocris). Plate densities during exposures were kept at 50 embryos per 10 mL of media.

tag: group (control/thioridazine)

value: Thioridazine

tag: developmental stage

tag: biological replicate


title: X. laevis with thioridazine-induced brain abnormalities at NF stage 47, Biological Replicate 2


title: AGO2_mRNA_Susceptible_2

description: Ago2 pull down


title: X. laevis with thioridazine-induced brain abnormalities at NF stage 45, Biological Replicate 3


title: X. laevis with thioridazine-induced brain abnormalities at NF stage 45, Biological Replicate 2


title: Patient1_WT_noTreat_rep3


title: AGO2_mRNA_Susceptible_1

description: Ago2 pull down


title: X. laevis with thioridazine-induced brain abnormalities at NF stage 45, Biological Replicate 1


title: AGO2_mRNA_Resilient_3

description: Ago2 pull down

value: Resilient


title: Wildtype X. laevis at NF stage 47, Biological Replicate 3

value: Control


title: Wildtype X. laevis at NF stage 47, Biological Replicate 2


title: KD22: siRoq#2, 06h, Rep#2

first: Jaewon

last: Song

state: Seoul

address: 504-407, School of Biological Sciences, College of Natural Sciences, 1 Gwanak-ro, Gwanak-gu

institute: Seoul National  University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence by using CutAdapt version 1.10, in-house python program, and FASTX-Toolkit version 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/).
After preprocessing, the sequenced reads were mapped to human tRNA and rRNA sequences by Bowtie2 version 2.2.7 (-t -k 2 --very-sensitive)
Tophat version 2.1.1 [command-line parameters: with–no-coverage-search–b2-very-sensitive (−b2- score-min L, −0.6, −0.9 only for CLIP-seq due to the high error rate)] was used to align the reads against human and viral genome.
RSEM version 1.2.30 was used to estimate transcript abundance. Differentially expressed genes were assessed using the limma package in R, and voom transformation was applied.
We applied Fisher’s exact test to detect significant peaks (CLIP-seq enriched regions over reference seq) and p-values were calculated for every genomic position in the whole genome background, then adjusted using qvalue package in R.
Genome_build: human (GRCh37.p13), HCMV Toledo (GU937742.2)
Supplementary_files_format_and_content: Files starting with "KD_": tab-delimited text files include genes, transcripts, fold change values and differential expression probabilities, which were made using RSEM.
Supplementary_files_format_and_content: Files starting with "514A_", "515A_", or "Overlap_": CLIP peaks identified using Roquin antibodies. tab-delimited text files include genomic loci of peaks and adjusted p-values. "Overlap" peaks were built by overlapping (by one nucleotide) the libraries derived from the two different antibodies.

source_name: Fibroblast, infected

growth_protocol: Human foreskin fibroblasts (HFFs) (ATCC, passages 10–15) were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin, and 50 µg/mL streptomycin.

extract_protocol:
Total RNAs from HFFs were isolated using the Trizol reagent. For CLIP-seq samples, Roquin-RNA complexes were isolated using antibodies.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: primary cell

value: Human foreskin fibroblast

tag: virus strain

value: HCMV Toledo strain


title: AGO2_mRNA_Resilient_2

description: Ago2 pull down


title: AGO2_mRNA_Resilient_5

description: Ago2 pull down


title: X. laevis with thioridazine-induced brain abnormalities at NF stage 47, Biological Replicate 1


title: AGO2_mRNA_Control_5

description: Ago2 pull down


title: AGO2_mRNA_Resilient_4

description: Ago2 pull down


title: Wildtype X. laevis at NF stage 47, Biological Replicate 1


title: Patient3_WT_Venetoclax_rep1


title: LS174T_LEF1_72h_rep2

type: RNA

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label: Biotin

source_name: pN1-LS174T cells, Dox-induced mLef1-HA, 72h, rep2

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

growth_protocol: LS174T cells were purchased from the Cell Line Service culture collection (CLS #300392, DKFZ, Heidelberg). Cell lines were maintained in growth medium consisting of DMEM supplemented with 10% FCS, 10 mM Hepes, 1/100 MEM non-essential amino acid solution and 1/100 penicillin/streptomycin

extract_protocol: Total RNA was isolated from LS174T cells after treatment with Dox for the indicated time using the PeqGOLD total RNA Kit (#732-2871, Peqlab/VWR Life Science)

treatment_protocol: The generation of pN1-LS174T cells expressing Dox-inducible mSnail1-HA and mLef1-HA was described earlier (Rönsch et al. Mol Oncol.  2015; Schnappauf et al. Biochim Biophys Acta. 2016). For the induction of transgene expression, 0.1 µg/ml Dox was used. For long-term treatment Dox was refreshed after 48 h.

tag: cell line

tag: replicate

value: Replicate 2

tag: overexpression

tag: time


title: LS174T_LEF1_6h_rep1

source_name: pN1-LS174T cells, Dox-induced mLef1-HA, 6h, rep1

value: Replicate 1


title: LS174T_LEF1_24h_rep1

source_name: pN1-LS174T cells, Dox-induced mLef1-HA, 24h, rep1


title: LS174T_LEF1_0h_rep1

source_name: pN1-LS174T cells, Dox-induced mLef1-HA, 0h, rep1


title: LS174T_LEF1_6h_rep2

source_name: pN1-LS174T cells, Dox-induced mLef1-HA, 6h, rep2


title: LS174T_LEF1_72h_rep1

source_name: pN1-LS174T cells, Dox-induced mLef1-HA, 72h, rep1


title: LS174T_LEF1_0h_rep2

source_name: pN1-LS174T cells, Dox-induced mLef1-HA, 0h, rep2


title: LS174T_SNAI1_96h_rep2

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 96h, rep2


title: LS174T_SNAI1_72h_rep1

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 72h, rep1


title: LS174T_SNAI1_96h_rep1

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 96h, rep1


title: AGO2_mRNA_Control_4

description: Ago2 pull down


title: AGO2_mRNA_Resilient_1

description: Ago2 pull down


title: LS174T_SNAI1_48h_rep2

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 48h, rep2


title: AGO2_mRNA_Control_3

description: Ago2 pull down


title: AGO2_mRNA_Control_2

description: Ago2 pull down


title: Wildtype X. laevis at NF stage 45, Biological Replicate 2


title: Wildtype X. laevis at NF stage 45, Biological Replicate 1


title: Wildtype X. laevis at NF stage 45, Biological Replicate 3


title: AGO2_mRNA_Control_1

description: Ago2 pull down


title: AGO2_miRNA_Susceptible_4

description: Ago2 pull down


title: LS174T_SNAI1_24h_rep1

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 24h, rep1


title: LS174T_SNAI1_48h_rep1

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 48h, rep1


title: LS174T_SNAI1_6h_rep2

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 6h, rep2


title: LS174T_SNAI1_0h_rep1

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 0h, rep1


title: LS174T_SNAI1_6h_rep1

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 6h, rep1


title: AGO2_miRNA_Susceptible_2

description: Ago2 pull down

source_name: bed nuclei of stria terminalis


title: LS174T_SNAI1_0h_rep2

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 0h, rep2


title: LS174T_Ctl_72h_rep1

source_name: pN1-LS174T cells, 72h,  rep1


title: AGO2_miRNA_Susceptible_1

description: Ago2 pull down


title: LS174T_SNAI1_3h_rep1

source_name: pN1-LS174T cells, Dox-induced mSnail1-HA, 3h, rep1


title: CAPAN-2_N1_GSK712

city: Collegeville

first: Satyajit

last: Rajapurkar

state: PA

address: 1250S. Collegeville Rd.

institute: GlaxoSmithKline LLC

description: processed data file: CAPAN2_712_DMSO.rMATS.concat.JC.txt

data_processing:
QC of the Fastq files was performed using FastQC.
Fastq files were aligned to GRCh38 version 23 using STAR 2.5.2b.
The BAM files obtained from STAR were filtered, sorted, and indexed using RSeQC and SAMtools.
rMATS was used to identify differential alternative splicing events from the relevant BAM files.
Custom scripts were used to filter the output and generate relevant plots.
Genome_build: GRCh38.v23
Supplementary_files_format_and_content: *.rMATS.concat.JC.txt: Tab-delimited text files containing concatenated rMATS output. The concatenation order is A3SS, A5SS, MXE, RI and SE respectively. Each set contains the list of events given by rMATS with statistics, co-ordinates, counts and inclusion levels for each. SAMPLE_1 is the treated sample, and SAMPLE_2 is the corresponding control (DMSO) sample.

source_name: Pancreatic cancer cell line

extract_protocol:
Total RNA, including miRNA, was isolated from cell pellet using the Qiagen miRNeasy Mini Kit.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina). Samples were sequenced at a depth of 100 million paired-end reads per sample, 100base-pair read length.

value: Replicate #1

value: Treated (GSK3368712)

tag: mtap status


title: Blood_991

city: Leuven

first: Maarten

last: Naesens

address: Herestraat 49

department: Department of Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

hyb_protocol: Fragmented cRNA was hybridized to the Human GeneChip U133 Plus 2.0 Array (Affymetrix).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerytrin on an automated Fluidics Station (Affymetrix) and scanned on the GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing:
The resulting image files were generated using the GeneChip® Command Console® Software (AGCC).
Log 2 RMA-normalized signal intensity (using Bioconductor tools in R version 3.5.3)

label: biotin

label_protocol: Total RNA extracted from the samples was first amplified and biotinylated to complementary RNA (cRNA) using the GeneChip® 3' IVT PLUS Reagent Kit (Affymetrix Inc., High Wycombe HP10 0HH, UK). Biotinylated cRNA was purified and fragmented.

extract_protocol: * BLOOD: Total RNA from peripheral blood samples was extracted using the PAXgene Blood miRNA Kit® (PreAnalytiX GmbH, a Qiagen/ BD Company, Switzerland). The yield and purity of RNA was measured using a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific™, Life Technologies Europe BV, Ghent, Belgium). RNA integrity was assessed using the RNA 6000 Nano LabChip® kit (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument™ (Agilent Technologies Belgium NV, Diegem, Belgium), and globin mRNA was depleted using the GLOBINclear™ Kit (Invitrogen™, Life Technologies Europe BV, Ghent, Belgium). After globin mRNA depletion, the quantity (absorbance at 260nm) and purity (ratio of the absorbance at 230, 260 and 280nm) of the isolated RNA were measured using the NanoDrop ND-1000™ spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE, USA). The extracted RNA samples were stored at -80°C.   ** BIOPSY: Total RNA from renal allograft biopsies was extracted using the Allprep DNA/RNA/miRNA Universal Kit® (Qiagen Benelux BV, Venlo, The Netherlands) on a QIAcube instrument (Qiagen Benelux BV, Venlo, The Netherlands). The quantity (absorbance at 260nm) and purity (ratio of the absorbance at 230, 260 and 280nm) of the RNA isolated from the biopsies were measured using the NanoDrop ND-1000™ spectrophotometer (Thermo Scientific™, Life Technologies Europe BV, Ghent, Belgium). RNA integrity was evaluated using the Eukaryote nano/pico RNA Kit® (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument™ (Agilent Technologies Belgium NV, Diegem, Belgium). Samples were stored at -80°C until further analysis.

treatment_protocol: * BLOOD: Peripheral blood samples were collected at time of the renal allograft biopsies, directly in PAXgene Blood RNA tubes® (PreAnalytiX GmbH, a Qiagen/ BD Company, Switzerland). The Paxgene tubes were stored at ambient temperature for at least 24 hours, and then stored at -80°C until extraction.   ** BIOPSY: Two needle cores were taken at each kidney allograft biopsy. One was used for histology, at least half of the other one was immediately stored in Allprotect Tissue Reagent® (Qiagen Benelux BV, Venlo, The Netherlands). The Allprotect tubes were stored at 4°C (minimum 24 hours and maximum 72 hours), and then stored at -20°C until extraction.

value: BLOOD

tag: tcmr (no

tag: abmr (no

tag: date of sample


title: AGO2_miRNA_Resilient_4

description: Ago2 pull down

tag: strain


title: BT054: bf631_UI_VA;Ru_kidney

city: New York

first: Atlas

last: Khan

state: NY

address: 1150 St Nicholas Ave, 408B

department: Medicine

institute: Columbia University

data_processing: Reads were mapped to the mouse reference genome (mm9) using Tophat (version 2.0.4) allowing 4 mismatches (--read-mismatches = 4) and a maximum of 10 multiple hits (--max-multihits = 10). Counts tables were generated with HTSeq (https://htseq.readthedocs.io/) version 0.6.1. Transcripts with 0 counts across all samples were removed and mathematical artifacts (e.g. negative infinites) were replaced with “NA”. Statistical analysis was performed in R version 3.4.2.

source_name: Kidney

extract_protocol:
Total RNA was extracted by Trizol and in vitro biotinylation of RNA was prepared by using EZ-link Biotin HPDP (Pierce Biotechnology, #21341), and subsequently purified using µMACS Streptavidin Kit (Miltenyi Biotec, Cat#: 130-074-101). RNA concentration and integrity for each sample were assessed on RNA 6000 Pico Chips using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Poly-A pull-down was used to enrich mRNAs)
Libraries were prepared using single-end 100bp reads for each sample with Illumina TruSeq® RNA prep kits (Illumina, San Diego, CA).
Libraries were sequenced using Illumina HiSeq2000 at the Columbia Genome Center.

treatment_protocol: UTI model: transurethral inoculation of ~50µL of 1E9 CFU/mL of uropathogenic E. coli strain CFT073 in female mice

tag: cell type

value: kidney intercalated cells

value: Female

tag: condition

value: UTI 24 hours


title: BT056: bf636_UI_VA;Ru_kidney

tag: Sex


title: AGO2_miRNA_Resilient_5

description: Ago2 pull down

tag: age on dissection

tag: csds phenotype


title: LS174T_Ctl_24h_rep1

source_name: pN1-LS174T cells, 24h,  rep1


title: LS174T_Ctl_48h_rep1

source_name: pN1-LS174T cells, 48h,  rep1


title: LS174T_Ctl_6h_rep2

source_name: pN1-LS174T cells, 6h,  rep2


title: LS174T_Ctl_96h_rep1

source_name: pN1-LS174T cells, 96h,  rep1


title: BT044: bf480_UI_VA;Ru_kidney


title: BT053: bf624_UI_VA;Ru_kidney


title: LS174T_Ctl_6h_rep1

source_name: pN1-LS174T cells, 6h,  rep1


title: Blood_9804

tag: tissue


title: BT043: bf452_UI_VA;Ru_kidney


title: LS174T_Ctl_0h_rep1

source_name: pN1-LS174T cells, 0h,  rep1


title: BT055: bf633_UI_VA;Ru_kidney


title: Blood_9843


title: AGO2_miRNA_Resilient_3

description: Ago2 pull down


title: Blood_9662


title: LS174T_Ctl_3h_rep1

source_name: pN1-LS174T cells, 3h,  rep1


title: Blood_9431


title: LS174T_Ctl_0h_rep2

source_name: pN1-LS174T cells, 0h,  rep2


title: Blood_9429


title: BT042: bf451_UI_VA;Ru_kidney


title: AGO2_miRNA_Control_5

description: Ago2 pull down


title: AGO2_miRNA_Resilient_2

description: Ago2 pull down


title: BT119: bf1254_UI_12_VA;Ru_kidney

value: UTI 12 hours


title: Blood_9410


title: BT041: bf447_UI_VA;Ru_kidney


title: BT118: bf1205_UI_12_VA;Ru_kidney


title: AGO2_miRNA_Control_4

description: Ago2 pull down

value: 8  weeks


title: BT036: bf277_UI_VA;Ru_kidney


title: BT117: bf1203_UI_12_VA;Ru_kidney


title: AGO2_miRNA_Resilient_1

description: Ago2 pull down

value: male


title: BT116: bf1123_UI_12_VA;Ru_kidney


title: BT115: bf1122_UI_12_VA;Ru_kidney


title: AGO2_miRNA_Control_3

description: Ago2 pull down


title: Blood_9400


title: AGO2_miRNA_Control_2

description: Ago2 pull down


title: BT035: bf275_UI_VA;Ru_kidney


title: BT114: bf1113_UI_12_VA;Ru_kidney


title: BT098: bf892_NC5_VA;Ru_kidney


title: BT060: bf647_NC_VA;Ru_kidney


title: miRNA_blood_ED6_5

description: size selection

source_name: blood

value: Susceptible


title: BT039: bf286_NC_VA;Ru_kidney


title: BT038: bf284_NC_VA;Ru_kidney


title: miRNA_blood_ED6_40

description: size selection


title: Blood_9321


title: Blood_9397


title: BT080: bf734_NC5_VA;Ru_kidney


title: miRNA_blood_ED6_39

description: size selection


title: BT113: bf1097_UI_12_VA;Ru_kidney


title: WT_76_D6

city: Taipei

first: Li-Jung

last: Juan

address: 128 Academia Road, Section 2, Nankang

department: GRC

country: Taiwan

institute: Academia Sinica

data_processing:
Illumina Casava1.8 pipeline used for basecalling
RNAseq reads trimmed for adaptor sequence and masked for low-complexity or low-quality sequence were aligned to mm10 reference using TopHat-v2.0.13
The aligend reads were annotated and called for Reads Per Kilobase of exon per Megabase  (RPKM) for gene expression using Htseq-v0.9.1
Genome_build: GRCm38, mm 10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: subcutaneous inguinal WAT (iWAT)

growth_protocol: iWATs were excised from 8-week old male mice, minced into pieces with scissors, and then incubated with digestion buffer containing type II collagenase (2 mg/ml) and 0.2% BSA in PBS in a ratio of 5 ml/g tissue at 37°C for 45 min. Tissue homogenates were passed through 40 µm mesh to remove undigested tissues, followed by centrifugation at 500 g for 5 min. Pellets containing SVF cells were incubated with red blood cell lysis buffer on ice for 5 min, collected by centrifugation at 500 g for 5 min, and resuspended with DMEM/F12 (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific), penicillin (100 U/ml) and streptomycin (100 µg/ml, Thermo Fisher Scientific). The SVF cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNAs purified from SVF cells with or without beige adipocyte induction for 2 and 6 days using RNeasy Plus Mini Kit (Qiagen) were treated with DNase I to remove residual genomic DNA, enriched by oligo-dT magnetic beads, and sonicated (Bioruptor, Diagenode) into roughly 200 bp fragments.
cDNAs were synthesized with random hexamer-primers, purified by silicon-coated magnetic beads, blunted in the ends, added with a single adenine at 3'-end, ligated with sequencing adaptors and PCR-amplified. The quality and quantity of the resulting library were determined by Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, respectively.

treatment_protocol: Beige adipocyte differentiation in vitro was carried out as described (Seale et al., 2011). Briefly, confluent SVF cells (designated as Day 0, D0) were cultured in the induction media containing 0.5 mM 3-isobutyl-1-methylxanthine (IBMX, Sigma), 5 µM dexamethasone (DEX, Sigma), 125 µM indomethacin (IDM, Sigma), 850 nM insulin (Sigma), 1 nM 3,3′,5-Triiodo-L-thyronine (T3, Sigma) and 1 µM rosiglitazone (Rosg, Sigma) for 2 days (designated as Day 2, D2) and switched to the maintenance media containing 850 nM insulin, 1 nM T3 and 1 µM rosiglitazone every other day (designated as Day 4, D4) till Day 6 (designated as Day 6, D6).

value: stromal-vascular fraction of iWAT

tag: beige adipocyte induction

value: 6 days


title: WT_77_D6


title: WT_77_D2

value: 2 days


title: WT_77_D0


title: WT_76_D0


title: miRNA_blood_ED4_4

description: size selection


title: AGO2_miRNA_Control_1

description: Ago2 pull down

value: Control


title: miRNA_blood_ED4_3

description: size selection


title: miRNA_blood_ED6_38

description: size selection


title: WT_76_D2


title: miRNA_blood_ED4_1

description: size selection


title: miRNA_blood_ED4_15

description: size selection


title: miRNA_blood_ED3_4

description: size selection


title: Adult Opn4-Cre/GFP RGC Rep3 [DJB35]

city: Palo Alto

first: Daniel

last: Berg

state: CA

address: 1050 Arastradero Road

institute: Stanford University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and removed for low-quality sequence; aligned to mm9 whole genome using tophat2; converted to SAM using samtools; and reads counted using htseq-count
count-based differential expression analysis with EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: Annotated Excel file with companion PDF including highlighting of differentially expressed genes and count values for each Sample. Sample BAM and companion index files for IGV visualization of read allignments

source_name: Adult Opn4-Cre/GFP RGC

extract_protocol:
Retinas were removed, enzymatically dissociated, enriched for retinal ganglion cells using Magnetic Associated Cell Sorting by surface protein Thy-1, cells selected by FACS, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using Nugen Ovation for cDNA amplification and Illumina TruSeq (DNA Sample Prep Kit v2-Set A) for the construction of sequencing libraries.

tag: strain background

value: mixed

tag: mouse line

tag: genotype/variation

tag: age

value: post natal day 27-33

value: retina

value: retinal ganglion cells (RGC)

tag: molecule subtype

value: mRNA enriched


title: Adult Opn4-Cre/GFP RGC Rep4 [DJB41]


title: Postnatal Opn4-GFP RGC Rep3 [DJB43]

source_name: Postnatal Opn4-GFP RGC

value: post natal day 4-6


title: Postnatal Opn4-GFP RGC Rep2 [DJB25]


title: Adult Opn4-Cre/GFP ipRGC Rep3 [DJB32]

source_name: Adult Opn4-Cre/GFP ipRGC

value: intrinsically photosensitive retinal ganglion cells (ipRGCs)


title: Adult Opn4-Cre/GFP ipRGC Rep2 [DJB22]


title: Adult Opn4-Cre/GFP RGC Rep1 [DJB06]


title: Adult Opn4-Cre/GFP ipRGC Rep4 [DJB40]


title: Adult Opn4-Cre/GFP RGC Rep2 [DJB23]


title: Postnatal Opn4-GFP RGC Rep1 [DJB04]


title: Adult Opn4-Cre/GFP ipRGC Rep1 [DJB05]


title: miRNA_blood_EC4_8

description: size selection

value: Resilient


title: Postnatal Opn4-GFP ipRGC Rep2 [DJB24]

source_name: Postnatal Opn4-GFP ipRGC


title: miRNA_blood_ED3_12

description: size selection


title: Postnatal Opn4-GFP ipRGC Rep1 [DJB03]


title: Patient2_WT_Venetoclax_rep2

source_name: Primary CLL cells

value: PBMC

tag: treatment

value: co-culture with Wild Type BMSC, venetoclax treated


title: Adult Opn4-GFP RGC Rep4 [DJB21]

source_name: Adult Opn4-GFP RGC


title: Adult Opn4-GFP RGC Rep6 [DJB39]


title: miRNA_blood_EC4_4

description: size selection

value: 8  weeks


title: Adult Opn4-GFP RGC Rep5 [DJB37]


title: miRNA_blood_EC4_20

description: size selection

value: male


title: Adult Opn4-GFP RGC Rep3 [DJB29]


title: Adult Opn4-GFP RGC Rep2 [DJB31]


title: miRNA_blood_EC4_19

description: size selection


title: miRNA_blood_EC4_3

description: size selection

value: Susceptible


title: Adult Opn4-GFP RGC Rep1 [DJB08]


title: Adult Opn4-GFP ipRGC Rep6 [DJB38]

source_name: Adult Opn4-GFP ipRGC


title: miRNA_blood_EC4_17

description: size selection


title: Adult Opn4-GFP ipRGC Rep5 [DJB36]


title: Adult Opn4-GFP ipRGC Rep4 [DJB16]


title: Blood_9035

value: BLOOD

tag: tcmr (no


title: Blood_923

tag: abmr (no


title: Blood_9027

tag: date of sample


title: Blood_9017


title: Adult Opn4-GFP ipRGC Rep3 [DJB28]


title: miRNA_blood_EC4_12

description: size selection

tag: strain


title: Blood_8905


title: Blood_9264


title: Blood_8597


title: Blood_8950


title: Blood_8682


title: Blood_86


title: Blood_8972


title: Adult Opn4-GFP ipRGC Rep2 [DJB30]

tag: cell type


title: miRNA_blood_EC4_10

description: size selection


title: n-6 PolyI:C Male H25_1

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
DNA sequencing data from 24 samples were aligned to mouse reference genome (mm10) using the BSMAP program by activating RRBS function and minimum fragment length 20bp. Final methylation data was reported as the fraction of reads that were methylated.  The ratio of cytosine bases to total reads for each CpG locations were calculated using MethylKit. Methylated cytosines are protected and unmethylated cytosines converted to thymine bases during the bisulfite conversion process.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include methylratio comparison between the groups. Col Chromosme locatioon, statistical significance and methylation difference.

molecule: genomic DNA

source_name: Hypothalamus

extract_protocol:
DNA was isolated from biological triplicates of adult hypothalamus using the Qiagen EZ1 DNA kit as per manufacturer’s protocol.
Reduced representation bisulfite sequencing (RRBS) method was used for library preparation. 2.5µg of genomic DNA was digested overnight with MspI enzyme (New England Biolabs, Ipswich, MA), using 20 units of enzyme per µg of DNA. The fragments were size-selected and bisulfite converted using EZ DNA methylation kit (Zymo Research, Irvine, CA). The fragment sizes were confirmed on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and quantified in a Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY). A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system. These libraries were PCR amplified and single end sequenced in a HiSeq 2000 system with 51bp read length.

treatment_protocol: A total of n = 11 pregnant mice were used. Six were exposed to PolyI:C (5 mg/kg, injection via the tail vein) and 5 to saline vehicle, on gestation day 9. After weaning n = 39 offspring exposed to MIA and n = 38 exposed to saline were split to generate n = 12 MIA units (of 2-6 same-sex offspring); and n = 12 control units (of 2-6 same-sex offspring). The same-sex offspring from each litter were housed together in an experimental unit. Then the experimental units were randomly allocated to n-3 PUFA enriched diet or n-6 PUFA control diet.

value: Hypothalamus

value: 12 weeks


title: Adult Opn4-GFP ipRGC Rep1 [DJB07]


title: n-6 PolyI:C Female H24_1


title: miRNA_blood_EC3_6

description: size selection


title: miRNA_blood_EC3_5

description: size selection


title: n-6 PolyI:C Female H22_1


title: n-6 PolyI:C Male H23_1


title: n-6 PolyI:C Male H21_1


title: Blood_904


title: n-6 PolyI:C Female H20_1


title: miRNA_blood_EC3_3

description: size selection


title: n-3 PolyI:C Male H17_1


title: miRNA_blood_EC3_2

description: size selection


title: n-3 PolyI:C Male H19_1


title: Blood_8389


title: n-3 PolyI:C Female H16_1


title: Blood_8283


title: n-3 PolyI:C Male H15_1


title: Blood_8585


title: Blood_8142


title: miRNA_blood_EC3_15

description: size selection

value: Control


title: Blood_8135


title: Blood_8287


title: Blood_8464


title: Blood_8117


title: Blood_8044


title: n-3 PolyI:C Female H14_H18_1


title: Blood_8006


title: Blood_7908


title: Postnatal Opn4-GFP ipRGC Rep3 [DJB42]


title: n-3 PolyI:C Female H13_1


title: miRNA_blood_EC3_12

description: size selection


title: Blood_8756


title: miRNA_blood_EC3_10

description: size selection


title: genomic DNA_T_143

type: genomic

city: Shinjyuku-ku

first: Yae

last: Kanai

state: Tokyo

address: 35, Shinano-machi

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450K Beadchip using standard Illumina protocol.

scan_protocol: Hybridization fluorescence signals were read by the iScan reader  using standard recommended Illumina scanner setting.

data_processing: GenomeStudio methylation software

label: Cy5 and Cy3

source_name: cancerous tissue obtained from patient with urothelial carcinomas

label_protocol: Standard Illumina Protocol

extract_protocol: High-molecular-weight DNA was extracted from fresh frozen tissue samples using phenol–chloroform, followed by dialysis.

tag: diagnosis

value: urothelial carcinoma

tag: gender

value: Male


title: n-6 Saline Female H9_1


title: n-6 Saline Male H12_1


title: n-6 Saline Male H11_1


title: mRNA_blood_ED6_5

description: ribo-zero globin depletion

tag: age on dissection

tag: Sex


title: genomic DNA_T_134

tag: tissue

value: cancerous tissue obtained from patient with urothelial carcinomas


title: n-6 Saline Male H8_1


title: genomic DNA_T_118

value: Female


title: n-6 Saline Female H10_1


title: mRNA_blood_ED6_39

description: ribo-zero globin depletion

tag: csds phenotype


title: genomic DNA_T_115


title: mRNA_blood_ED6_38

description: ribo-zero globin depletion


title: mRNA_blood_ED6_40

description: ribo-zero globin depletion


title: n-3 Saline Female H6_1


title: n-6 Saline Female H7_1


title: genomic DNA_T_114


title: mRNA_blood_ED4_4

description: ribo-zero globin depletion


title: n-3 Saline Male H5_1


title: mRNA_blood_ED4_3

description: ribo-zero globin depletion


title: genomic DNA_T_109


title: Blood_7569


title: Blood_7549


title: Blood_7992


title: mRNA_blood_ED4_1

description: ribo-zero globin depletion


title: genomic DNA_T_099


title: genomic DNA_T_095


title: Blood_7376


title: Blood_7548


title: Blood_7427


title: n-3 Saline Male H2_1


title: n-3 Saline Male H4_1


title: Blood_7864


title: mRNA_blood_ED4_15

description: ribo-zero globin depletion


title: genomic DNA_T_088


title: Blood_7218


title: Blood_7419


title: n-3 Saline Female H1_1


title: mRNA_blood_ED3_4

description: ribo-zero globin depletion


title: mRNA_blood_ED3_12

description: ribo-zero globin depletion


title: genomic DNA_T_087


title: genomic DNA_T_064


title: mRNA_blood_EC4_8

description: ribo-zero globin depletion


title: genomic DNA_T_061


title: mRNA_blood_EC4_3

description: ribo-zero globin depletion


title: genomic DNA_T_091


title: mRNA_blood_EC4_4

description: ribo-zero globin depletion


title: genomic DNA_T_074


title: Blood_7019


title: genomic DNA_T_073


title: Blood_704


title: genomic DNA_T_060


title: mRNA_blood_EC4_19

description: ribo-zero globin depletion


title: Blood_6611


title: Blood_6608


title: mRNA_blood_EC4_17

description: ribo-zero globin depletion


title: MDA-MB-231 cells - Allstar siRNA + 5-ALA [Sample 12]

city: Berlin

first: Wolfgang

last: Kemmner

state: Berlin

address: Lindenberger Weg 80

department: ECRC

institute: Max-Delbrueck-Center

hyb_protocol: Hybridization was done according to the manufacturer's instructions using GeneChip Hybridization, Wash and Stain.

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

data_processing: The resulting microarray data were preprocessed using the robust multichip average (RMA) algorithm via the BioConductor oligo package.

source_name: Breast cancer cell MDA-MB-231

label_protocol: Preparation of labelled cRNA was done according to the manufacturer's instructions using GeneChip Hybridization, Wash and Stain.

growth_protocol: Breast cancer cell MDA-MB-231 were grown in monolayer cultures in RPMI medium supplemented with 10% fetal calf serum, 2 mM glutamine.

extract_protocol: RNA extraction with RNeasy Mini Kit. RNA quality and yield were assessed using Bioanalyzer Agilent 2100 and Nanodrop ND-1000. RIN was always above 9.0.

treatment_protocol: For silencing FECH the following sequence was used: 5'-gaauauccucuugguuccg-3', covering FECH mRNA, accession NM_001012515.1.

tag: cell line

value: Breast cancer cells

value: Allstar siRNA + 5-ALA


title: genomic DNA_T_048


title: mRNA_blood_EC4_20

description: ribo-zero globin depletion


title: Blood_7181


title: mRNA_blood_EC4_12

description: ribo-zero globin depletion


title: Blood_6986


title: Blood_6531


title: genomic DNA_T_028


title: mRNA_blood_EC4_10

description: ribo-zero globin depletion


title: MDA-MB-231 cells - No treatment [Sample 9]

value: No treatment


title: Blood_6131


title: Blood_6111


title: mRNA_blood_EC3_6

description: ribo-zero globin depletion

value: Resilient


title: MDA-MB-231 cells - FECH siRNA + 5-ALA [Sample 11]

value: FECH siRNA + 5-ALA


title: MDA-MB-231 cells - only 5-ALA [Sample 10]

value: Only 5-ALA


title: genomic DNA_T_023


title: genomic DNA_T_007


title: MDA-MB-231 cells - Allstar siRNA + 5-ALA [Sample 8]


title: MDA-MB-231 cells - FECH siRNA + 5-ALA [Sample 7]


title: Blood_6078


title: MDA-MB-231 cells - only 5-ALA [Sample 6]


title: mRNA_blood_EC3_5

description: ribo-zero globin depletion

value: 8  weeks


title: MDA-MB-231 cells - No treatment [Sample 5]


title: mRNA_blood_EC3_3

description: ribo-zero globin depletion

value: male


title: Blood_606


title: Blood_6019


title: Blood_6064


title: Blood_5690


title: genomic DNA_T_024


title: Blood_5910


title: mRNA_blood_EC3_2

description: ribo-zero globin depletion


title: mRNA_blood_EC3_15

description: ribo-zero globin depletion


title: Control Dawn 17.5h Rep 1

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

department: Biochemistry

institute: NCSU

description:
7-17.5h_C
processed data file: Pannicle_timecourse_WNT.csv

data_processing:
Trimmed files were aligned using Hisat v2. MH63 (rigw.com). The resulting bam files were then piped to htseq count version 0.6.0. Using the options -f bam, -s reverse, and -m union counts per gene were generated for the annotated genes in MH63. Counts were than normalized to counts per million.
Genome_build: MH63RS1
Supplementary_files_format_and_content: Pannicle_timecourse_WNT.csv: Comma-separated text file includes raw counts.
Supplementary_files_format_and_content: Pannicle_gradient_24_26_28_30C.csv: Comma-separated text file includes raw counts.

organism: Oryza sativa Indica Group

source_name: Rice Panicle

growth_protocol: An IR64 land variety was grown on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.

extract_protocol:
Tissue samples were stored at -80C until needed. The panicle samples were first grinded in liquid nitrogen with a metal pestle. The tissue then lyophilized at -60C overnight before RNA extractions. Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) with the recommended RLT lysis buffer. The RNA extraction provided protocol was followed the inclusion of DNase step. RNA concentration was then measured with NANOdrop 2000. 2ug of RNA was used with NEBNext Poly(A) Magnetic mRNA isolation kit (NEB). Oligo(dT) attached to magnetic beads isolate mRNA by attaching to ploy(A) modified mRNA.
RNA libraries were prepared for sequencing using NEB ultra directional library prep kit.

treatment_protocol: Plants were grown in a field setting. WNT were treated with IR heater at night. 24C, 26C, 28C, and 30C rice were treated with field tents for increased night temperatures.

tag: variety

tag: developmental stage

value: 50% flowering

value: Panicle

tag: time point

value: Dawn 17.5h


title: Control Dawn 14h Rep 4

description:
6-14h_C.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 14h


title: genomic DNA_T_050

tag: age


title: genomic DNA_T_057


title: Blood_5672

value: BLOOD


title: genomic DNA_T_047

value: urothelial carcinoma


title: Control Dawn 14h Rep 3

description:
6-14h_C.2
processed data file: Pannicle_timecourse_WNT.csv

tag: treatment

value: Control


title: mRNA_blood_EC3_12

description: ribo-zero globin depletion


title: genomic DNA_T_040

value: cancerous tissue obtained from patient with urothelial carcinomas

value: Male


title: mRNA_blood_EC3_10

description: ribo-zero globin depletion

value: Susceptible


title: Control Dawn 14h Rep 2

description:
6-14h_C.1
processed data file: Pannicle_timecourse_WNT.csv


title: Blood_5666

tag: tcmr (no


title: genomic DNA_T_031

value: Female


title: MDA-MB-231 cells - only 5-ALA [Sample 2]

value: Breast cancer cells


title: Control Dawn 14h Rep 1

description:
6-14h_C
processed data file: Pannicle_timecourse_WNT.csv


title: genomic DNA_T_026


title: MDA-MB-231 cells - No treatment [Sample 1]

value: No treatment


title: Control Dusk Rep 4

description:
5-Dusk_C.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dusk


title: MDA-MB-231 cells - FECH siRNA + 5-ALA [Sample 3]

value: FECH siRNA + 5-ALA


title: MDA-MB-231 cells - Allstar siRNA + 5-ALA [Sample 4]

value: Allstar siRNA + 5-ALA


title: Blood_5513

tag: abmr (no


title: Blood_5458

tag: date of sample


title: genomic DNA_T_013


title: genomic DNA_T_008


title: Control Dusk Rep 3

description:
5-Dusk_C.2
processed data file: Pannicle_timecourse_WNT.csv


title: Blood_5331


title: Cells_C

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description:
small RNA (15 to 200 nt)
Cells, replicate 3

data_processing:
Sample demultiplexing and FastQ file generation was performed using bcl2fastq v.1.8.4 (Illumina).
For miRNA-tailored analysis, the raw sequence reads were cleaned from adapter sequences and size-selected in the range 19-25 nucleotides (plus 8 random bases from the adapters) using Cutadapt v.1.7.1 (http://cutadapt.readthedocs.org).
Reads containing low-quality bases were filtered with the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit) and deduplicated based on full sequence identity (library insert plus 8 random bases from the library adapters).
Mapping to the mouse reference genome NCBIM37 (mm9) with concomitant trimming of the random adapter bases was performed using Bowtie v.0.12.8 (http://bowtie-bio.sourceforge.net) with parameters “-v 3 -M 1 -y --sam --best --strata --nomaqround --trim5 4 --trim3 4”.
Mature miRNA annotation from miRbase (http://www.mirbase.org/) was used to estimate the number of reads per miRNA using Subread featureCounts v.1.4.6-p4 (http://subread.sourceforge.net/).
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with miRNA read counts from Subread featureCounts

source_name: Cells

growth_protocol: Primary oligodendrocytes derived from embryonic day 14 mice were cultured in Sato 1 % horse serum (Thermo Fisher Scientific).

extract_protocol:
EVs were isolated by differential centrifugation (130 x g for 10 min, 10 000 x g for 30 min, 100 000 x g for 2 h). Pellet or cells were mixed with QIAzol and small RNA was isolated using the miRNeasy micro Kit (Qiagen). RNA was size-selected between 15 to 200 nt on 10% TBE-urea gel. Gel-purified RNA was eluted overnight in 0,3 M NaCl and then precipitated with 100% isopropanol and Glycoblue for 1 h at -20°C. The pellet was washed once with 75% ethanol and dissolved in nuclease-free water. The purified fraction was confirmed by Bioanalyzer Small RNA chip (Agilent).
Library preparation was based on the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) with slight modification. In brief, RNA was first ligated to the 3’ adapter and then to the 5’ adapter, both of which contained 4 random bases and were chemically synthesized by Bio Scientific. Adapter-ligated RNA was reverse-transcribed and PCR-amplified for 14 cycles using index primers. The PCR-amplified cDNA construct was purified using AMPure XP beads (Beckman Coulter) and was checked on the Bioanalyzer using High Sensitivity DNA chip (Agilent). Size selection of the RNA library was performed on LabChip XT instrument (Perkin Elmer) using DNA 300 assay kit in the range 140-300 bp, the libraries were pooled in equal molar ratio and sequenced on Illumina HiSeq 2500 for 51 cycles plus 7 cycles index read.

treatment_protocol: Oligodendrocytes were washed in PBS and subsequently EVs were collected for 24 h in serum-free Sato supplemented with B27 (Gibco).

tag: strain

value: Primary cultured oligodendrocytes

tag: cell compartment

value: whole cells

tag: days in vitro

value: DIV 6


title: Cells_B

description:
small RNA (15 to 200 nt)
Cells, replicate 2

tag: cell type


title: Cells_A

description:
small RNA (15 to 200 nt)
Cells, replicate 1


title: Control Dusk Rep 2

description:
5-Dusk_C.1
processed data file: Pannicle_timecourse_WNT.csv

value: 50% flowering

value: Panicle


title: genomic DNA_T_033

tag: diagnosis

tag: gender


title: EVs_C2

description:
small RNA (15 to 200 nt)
EVs, replicate 3

source_name: Extracellular vesicles (EVs)

value: Extracellular vesicles (EVs)

value: DIV 5-6


title: Control Dusk Rep 1

description:
5-Dusk_C
processed data file: Pannicle_timecourse_WNT.csv

tag: tissue

value: Control


title: EVs_B2

description:
small RNA (15 to 200 nt)
EVs, replicate 2


title: genomic DNA_T_004

value: cancerous tissue obtained from patient with urothelial carcinomas

value: urothelial carcinoma


title: Control Dawn 10.5h Rep 4

description:
4-10.5h_C.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 10.5h


title: Blood_5243

value: BLOOD


title: Blood_5147


title: Control Dawn 10.5h Rep 3

description:
4-10.5h_C.2
processed data file: Pannicle_timecourse_WNT.csv


title: Blood_5385


title: Blood_5370


title: EVs_A2

description:
small RNA (15 to 200 nt)
EVs, replicate 1


title: genomic DNA_T_927

value: Male


title: genomic DNA_T_017


title: Control Dawn 10.5h Rep 2

description:
4-10.5h_C.1
processed data file: Pannicle_timecourse_WNT.csv


title: Control Dawn 10.5h Rep 1

description:
4-10.5h_C
processed data file: Pannicle_timecourse_WNT.csv


title: genomic DNA_T_926


title: genomic DNA_T_924

value: Female


title: Control Dawn 7h Rep 4

description:
3-7h_C.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 7h


title: genomic DNA_T_923


title: HCM

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

country: Sweden

institute: Lund University

data_processing:
Base-calling using Illumina 1.9
Paired-end reads were quality-filtered, aligned to the human genome reference GRCh38_86v2 and demultiplexed using the ST Pipeline v. 1.6.2
Image alignment was performed using the ST Spot Detector Software
Genome_build: GRCh38_86v2
Supplementary_files_format_and_content: Spatial transcriptomics count matrices in.tsv format with spot coordinates and normalized read counts

source_name: Cardiac biopsy (explanted)

extract_protocol:
Tissue sections were placed on Spatial Transcriptomics Library Preparation slides containing an array of reverse transcription primers with unique positional barcodes. Sections were fixed, stained with Hematoxylin/Eosin and imaged before tissue permeabilization, RNA hybridization and cDNA synthesis.
Libraries were constructed according to the Spatial Transcriptomics Library Preparation Manual

tag: subject status

value: hypertrophic cardiomyopathy patient

value: Cardiac biopsy (explanted)


title: ICM

value: ischemic cardiomyopathy patient


title: DCM

value: dilated cardiomyopathy patient


title: Normal control

source_name: Cardiac biopsy (transplantation)

value: Normal control

value: Cardiac biopsy (transplantation)


title: Control Dawn 7h Rep 2

description:
3-7h_C.1
processed data file: Pannicle_timecourse_WNT.csv

value: 50% flowering

value: Panicle


title: Blood_4942


title: Blood_5062


title: genomic DNA_T_921


title: Control Dawn 7h Rep 1

description:
3-7h_C
processed data file: Pannicle_timecourse_WNT.csv


title: genomic DNA_T_920


title: Blood_4634


title: Blood_4843


title: Blood_4543


title: Blood_4535


title: Blood_4611


title: genomic DNA_T_918


title: Blood_4422


title: Control Dawn 3.5h Rep 3

description:
2-3.5h_C.2
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 3.5h


title: genomic DNA_T_917


title: n-3 Saline Female H3_1

value: Hypothalamus

value: 12 weeks


title: Control Dawn 3.5h Rep 2

description:
2-3.5h_C.1
processed data file: Pannicle_timecourse_WNT.csv

value: Control


title: genomic DNA_T_922

value: cancerous tissue obtained from patient with urothelial carcinomas

value: urothelial carcinoma


title: Control Dawn Rep 4

description:
1-Dawn_C.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn


title: genomic DNA_T_916

value: Male


title: Control Dawn 7h Rep 3

description:
3-7h_C.2
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 7h


title: Control Dawn 3.5h Rep 1

description:
2-3.5h_C
processed data file: Pannicle_timecourse_WNT.csv


title: genomic DNA_T_913


title: genomic DNA_T_915


title: Control Dawn Rep 3

description:
1-Dawn_C.2
processed data file: Pannicle_timecourse_WNT.csv


title: Control Dawn 3.5h Rep 4

description:
2-3.5h_C.3
processed data file: Pannicle_timecourse_WNT.csv


title: genomic DNA_T_912


title: Control Dawn Rep 2

description:
1-Dawn_C.1
processed data file: Pannicle_timecourse_WNT.csv


title: genomic DNA_N_143

source_name: non-cancerous urothelium obtained from patient with urothelial carcinomas


title: genomic DNA_N_134

value: non-cancerous urothelium obtained from patient with urothelial carcinomas


title: genomic DNA_N_115


title: genomic DNA_N_095


title: genomic DNA_N_109


title: genomic DNA_N_099


title: genomic DNA_T_909


title: Control Dawn Rep 1

description:
1-Dawn_C
processed data file: Pannicle_timecourse_WNT.csv


title: genomic DNA_N_118

value: Female


title: genomic DNA_N_114


title: genomic DNA_N_088


title: genomic DNA_N_064


title: genomic DNA_N_061


title: Blood_3373

value: BLOOD


title: Blood_377


title: Blood_4047


title: Blood_3795


title: Blood_4219


title: genomic DNA_N_091


title: Blood_3458


title: Blood_3976


title: Blood_3295


title: genomic DNA_N_087


title: Blood_3631


title: Blood_4254


title: Blood_3105


title: Blood_3117


title: Blood_2973


title: Blood_4033


title: Blood_2855


title: Blood_2877


title: Blood_3947


title: Blood_3561


title: genomic DNA_N_074


title: Blood_2768


title: Blood_3314


title: Blood_3644


title: genomic DNA_N_060


title: genomic DNA_N_073


title: Hdn null ESCs day 6 rep2

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

institute: Georg-Speyer-Haus

data_processing:
RNA-seq
STAR aligner using default settings with the option --outSAMtype BAM SortedByCoordinate
DESeq2 with padj < 0.01 and LFC=0.59 cutoff
Genome_build: mm10
Supplementary_files_format_and_content: RPKM Data are represented as a XLSX

source_name: ESC day 6 BMP4 differentiation

growth_protocol: Embryos were harvested at E9.5 and the embryonic heart dissected.

extract_protocol:
To isolate RNA either from heart tissue or cultivated cardiomyocytes the cells were lysed in 900 µl Qiazol (Qiagen, #79306). To remove the DNA 100 µl gDNA Eliminator solution was added and 180 µl Chloroform (AppliChem, #A3633) to separate the phases. The extraction mixture was centrifuge at full speed, 4°C for 15min. The aqueous phase was mixed with the same amount of 70 % Ethanol and transferred to a micro or mini columns depending of the amount of tissue and cells. The following steps were done according to the manufactural protocol.
Libraries for RNA-seq were constructed according to the ScriptSeq v2 Complete (Mouse/Human/Rat) Low Input Kit (Illumina/Epicenter)

treatment_protocol: Feeder cells were removed from mESCs by serial plating and cultivated in 2i media. mESCs were aggregated by the hanging drop method overnight in ES-Serum media (40 cells per μL, 5μL per drop). The next day, embryoid bodies were washed thoroughly with Advanced DMEM (Gibco #12491015), and approximately 600 drops were plated onto 6 cm tissue culture dish coated with fibronectin (2,µg/ml in 1x PBS, Millipore #341631-5MG) in serum-free media (1:1 Neurobasal:F12/DMEM, 2mM L-glutamine, 50U/mL penicillin, 50μg/mL streptomycin, 0.5x B-27 supplement, 0.5x N-2 supplement, 0.05% Albumin, bovine Fraction V (7.5%; Sigma-Aldrich, # A8412), 0.001% 1-thioglycerol (Sigma-Aldrich, #M6145)) containing recombinant BMP4 (20ng/mL, R&D Systems, #5020-BP). The media was changed daily at the same time point.

value: ESC BMP4 differentiation

tag: Stage

value: differentiated day 6

tag: genotype/variation

value: Hdn mutant


title: Hdn null ESCs day 6 rep3


title: F1(G4) wt E9.5 hearts

description:
F1G4
This sample is not part of the expression analysis.
This sample is just used for visualization of transcripts of the Handsdown locus for Figure 1A.

source_name: earl heart loop in E9.5 embryos

value: Embryo heart loops

value: wild type


title: genomic DNA_N_028


title: Blood_2833


title: genomic DNA_N_024


title: genomic DNA_N_023


title: Hdn null ESCs day 6 rep1


title: genomic DNA_N_007


title: Blood_2755


title: genomic DNA_N_050


title: genomic DNA_N_048


title: Hdn null ESCs day 5 rep2

source_name: ESC day 5 BMP4 differentiation

value: differentiated day 5


title: Hdn null ESCs day 5 rep3


title: genomic DNA_N_057


title: Blood_2728


title: Hdn null ESCs day 5 rep1


title: Hdn null ESCs day 4 rep3

source_name: ESC day 4 BMP4 differentiation

value: differentiated day 4


title: genomic DNA_N_047


title: genomic DNA_N_040


title: Blood_2639


title: Blood_2582


title: Hdn null ESCs day 4 rep2


title: wildtype

city: Rochester

first: Xiaolei

last: Xu

state: MN

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
The flow cells were sequenced as 50×2 paired-end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software.
Raw RNA-seq reads were aligned to the zebrafish genome assembly (Zv9) for each sample using the Ensembl annotation Zv9 (Danio_rerio.Zv9.79.gtf) by TopHat (Version 2.0.12) . Each transcriptome was assembled by Cufflinks (Version 2.2.1) .
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) was calculated using a protocol from Cufflinks. Isoform_exp.diff was the result form Cuffdiff script, and isoforms.fpkm_table was the result from Cuffnorm script.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Danio rerio

source_name: heart

extract_protocol:
Tissues were homogenized using a mortar and pestle (Fisher Scientific), and total RNA was extracted using TRIzol (Sigma) according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument (Agilent Technologies) in the Mayo DNA sequencing core facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: genotype

value: 3 months


title: bag3

value: bag3 knockout

value: 6 months


title: Blood_2461


title: genomic DNA_N_031

value: urothelial carcinoma


title: Blood_2389


title: genomic DNA_N_026

value: Male


title: Hdn null ESCs day 3 rep3

source_name: ESC day 3 BMP4 differentiation

value: differentiated day 3


title: genomic DNA_N_013

value: non-cancerous urothelium obtained from patient with urothelial carcinomas


title: genomic DNA_N_008


title: Hdn null ESCs day 3 rep2


title: TUT4/7 Double Knockout (DKO)  endogenous miRNAs rep3

city: Frederick

first: Shuo

last: Gu

state: MD

address: 1050 Boyles Str. Building 560 Room 11-6B

institute: National Cancer Institute

description:
DKO_vs_WT.isomir.tsv
DKO_vs_WT.isomir.sequence_info.tsv

data_processing:
3ʹ adaptor sequences were removed by customized scripts. Reads without the 3′ adaptor sequences or shorter than 18 nt were discarded
For miRNA isoform analyses based on small-RNA-seq, QuagmiR (on Seven Bridges Cancer Genomics Cloud) was used with default or custermized motif files
For gene expression analyses based on RNA-seq, Raw reads were aligned to the human genome (GRCh37.75) using STAR 2.5.1.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: 1) isomiR profile (tsv files) (small-RNA-seq) 2) gene expression counts (tab files) (RNA-seq)

source_name: human embryonic kidney Cells

growth_protocol: HEK293T cells were maintained in DMEM (high glucose) (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1X MEM Non-Essential Amino Acids (Gibco), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco). HEK293T-TUT4/TUT7 DKO cells were generated by using CRISPR/Cas9.

extract_protocol:
RNAs were extracted by using Trizol.
Sequencing libraries were constructed by either Illumina® TruSeq® RNA sample preparation kit or NEBNext® Multiplex Small RNA Library Prep Set according to the manufacturer's’ protocol with minor modifications.

treatment_protocol: HEK293T and DKO cells were transfected with Lipofectamine 3000 (Life Technologies) according to the manufacturer's’ instructions

value: TUT4 and TUT7 Double Knockout

tag: ip antibody


title: Blood_2672

value: BLOOD


title: TUT4/7 Double Knockout (DKO)  endogenous miRNAs rep4


title: TUT4/7 Double Knockout (DKO)  endogenous miRNAs rep1


title: Blood_2195


title: Blood_1886


title: Blood_2117


title: Blood_2127


title: Hdn null ESCs day 4 rep1

value: ESC BMP4 differentiation


title: Hdn null ESCs day 3 rep1


title: Hdn null ESCs rep3

source_name: ESC

value: ESC

value: undifferentiated


title: genomic DNA_N_033

value: Female

tag: age


title: Blood_2153


title: Hdn null ESCs rep2

value: Hdn mutant


title: Blood_1854


title: genomic DNA_N_017


title: Blood_156


title: TUT4/7 Double Knockout (DKO)  endogenous miRNAs rep2


title: Hdn null ESCs rep1


title: TUT7 rescue

source_name: TUT7 rescue

tag: cell line

value: human embryonic kidney Cells

value: TUT4 and TUT7 Double Knockout with TUT7 rescue


title: 7AA target biotin-pull-down

source_name: 7AA target biotin-pull-down

value: WT


title: genomic DNA_N_927


title: TUT4 rescue

source_name: TUT4 rescue

value: TUT4 and TUT7 Double Knockout with TUT4 rescue


title: TUT4/7 Double Knockout (DKO) with miR-27a O/E

value: TUT4 and TUT7 Double Knockout with ectopic expression of miR-27a


title: genomic DNA_N_926


title: F1(G4) wt ESCs day 6 rep2

value: differentiated day 6

value: wild type


title: F1(G4) wt ESCs day 6 rep3


title: Ago2-IP with ectopic expression of miR-27a rep3

value: WT with ectopic expression of miR-27a

value: Sigma M8823-1ML Anti-FLAG M2 Magnetic Beads


title: Blood_1340

tag: tcmr (no


title: F1(G4) wt ESCs day 6 rep1


title: Blood_1435

tag: abmr (no


title: Ago2-IP with ectopic expression of miR-27a rep2


title: F1(G4) wt ESCs day 5 rep3

value: differentiated day 5


title: genomic DNA_N_922

value: non-cancerous urothelium obtained from patient with urothelial carcinomas

value: urothelial carcinoma

value: Male


title: Ectopic expression of miR-27a rep3

source_name: Ectopic expression of miR-27a


title: Blood_1181

value: BLOOD

tag: date of sample


title: Blood_1086


title: Blood_1153


title: F1(G4) wt ESCs day 5 rep2

value: ESC BMP4 differentiation

tag: strain


title: genomic DNA_N_921


title: F1(G4) wt ESCs day 5 rep1


title: Ectopic expression of miR-27a rep2


title: genomic DNA_N_920


title: F1(G4) wt ESCs day 4 rep3

value: differentiated day 4


title: genomic DNA_N_924

value: Female


title: genomic DNA_N_918


title: F1(G4) wt ESCs day 4 rep2


title: BIOPSY_9895

value: kidney allograft biopsy


title: genomic DNA_N_004


title: HEK293T-endogenous-miRNAs rep3

value: human embryonic kidney Cells


title: Blood_1183


title: BIOPSY_9558


title: genomic DNA_N_923


title: Ago2-IP with ectopic expression of miR-27a rep1


title: BIOPSY_9385


title: genomic DNA_N_917


title: HEK293T-endogenous-miRNAs rep2

value: WT


title: F1(G4) wt ESCs day 4 rep1


title: genomic DNA_N_916


title: BIOPSY_9171


title: F1(G4) wt ESCs day 3 rep3

value: differentiated day 3


title: Ectopic expression of miR-27a rep1


title: BIOPSY_9023


title: HEK293T-endogenous-miRNAs rep1


title: genomic DNA_N_915


title: BIOPSY_9157


title: BIOPSY_9025


title: BIOPSY_9513


title: 30C Rep4 Dusk

description:
Dusk_30_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv

source_name: Rice Panicle

tag: variety

tag: developmental stage

value: 50% flowering

value: Panicle

tag: treatment

tag: time point

value: Dusk


title: F1(G4) wt ESCs day 3 rep1

tag: cell type

value: wild type


title: F1(G4) wt ESCs day 3 rep2


title: 30C Rep3 Dusk

description:
Dusk_30_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv

tag: tissue


title: F1(G4) wt ESCs rep3

value: ESC

value: undifferentiated


title: 30C Rep4 Dawn

description:
Dawn_30_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv

value: Dawn


title: genomic DNA_N_913

value: non-cancerous urothelium obtained from patient with urothelial carcinomas

tag: diagnosis

value: urothelial carcinoma

tag: gender


title: F1(G4) wt ESCs rep2

tag: Stage

tag: genotype/variation


title: 30C Rep3 Dawn

description:
Dawn_30_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: 30C Rep2 Dusk

description:
Dusk_30_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: BIOPSY_8778


title: F1(G4) wt ESCs rep1


title: BIOPSY_8598


title: 30C Rep1 Dusk

description:
Dusk_30_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: genomic DNA_N_909

value: Male


title: 30C Rep2 Dawn

description:
Dawn_30_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: I5

city: Pontevedra

first: Maria

last: Tortosa

state: Galicia

address: Pazo de Salcedo nº8

country: Spain

institute: Mision Biologica de Galicia (MBG-CSIC)

data_processing:
Library strategy: MACE
HCS from Illumina HiSeq 2000
Assemblies were performed with NovoAlign v3.00.05; reads mapping to multiple locations were limited to 10
Differential expression analysis was performed with the R package DESeq (Anders and Huber 2010) with the standard parameters
Genome_build: ENSEMBL Brassica oleracea (v2.1), UniProtKB/Swiss-Prot, UniProtKB and Ref-Seq
Supplementary_files_format_and_content: tab-delimited text files including Gene annotation, Expression values, logFC and FDR

organism: Brassica oleracea

source_name: leaf

growth_protocol: The doubled haploid broccoli line “Early Big” (B. oleracea var. italica) was used in this study. Plants were sown in plastic pots containing Sphagnum peat (GRAMOFLOR GmbH & Co, Germany) in a greenhouse with a minimum temperature of 20 ºC day and 15°C night venting at 25°C and 60% of humidity

extract_protocol:
Individual sample tissues were grounded in liquid nitrogen and total RNA from three biological replicates of each treatment was extracted using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich, MO, USA)
Massive Analysis of 3′-cDNA Ends (MACE) was performed from each sample (GenXPro GmbH, Frankfurt am Main, Germany) as described by Zawada et al. (2014)

treatment_protocol: Plants at six leaf stage were inoculated at the third leaf following the method described by Taylor (2002). Control plants were mock-inoculated following the same procedure

value: leaf

value: Inoculated with Xantomonas campestris pv. Campestris

tag: days post-inoculation

tag: ecotype

value: Early Big (B. oleracea var. italica)


title: I4


title: I3


title: I6


title: 30C Rep1 Dawn

description:
Dawn_30_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: I1


title: I2


title: BIOPSY_8327

value: kidney allograft biopsy


title: 28C Rep4 Dawn

description:
Dawn_28_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: C6

value: Control


title: 28C Rep4 Dusk

description:
Dusk_28_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: BIOPSY_8640


title: BIOPSY_8521


title: BIOPSY_7972


title: BIOPSY_8107


title: BIOPSY_8340


title: C5


title: BIOPSY_8138


title: 28C Rep3 Dusk

description:
Dusk_28_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: WT Control

city: Boston

first: Shashi

last: Kant

address: 4 Blackfan Circle, Room 614

department: Cardiovascular Medicine

institute: Brigham Women's Hospital

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: data processing

source_name: RNA form gastonimeus muscle of 3 mice after 3 days of hindlimb ischemia were pooled totgether

label_protocol: standard affymetrix protocol

extract_protocol: Gastrocnemius and thigh adductor muscle of mice were isolated and total RNA was extracted from gastonimeus muscle  after 3 days of hindlimb ischemia TRIzol reagent (Invitrogen). Then RNA  were pooled totgether and  Microarray was performed using affymetrix mogene-2_0-st chip at UMASS.

treatment_protocol: Heterozygous Mapk10-null animals on the C57Bl6/J background were bred to create homozygous Mapk10-/- and wild-type age-matched controls. Male mice at 8 to 12 weeks of age were anesthetized via intraperitoneal injection with a combination of 100 mg/kg ketamine hydrochloride and 5 mg/kg xylazine (Webster Veterinary, Devens, MA) before surgery. Unilateral hindlimb ischemia in the right leg was introduced in the mice.

tag: strain background

value: wild-type

value: Gastrocnemius and thigh adductor muscle


title: BIOPSY_7765

tag: tcmr (no


title: MLL-AF9/Mn1null replicate 3

city: Hannover

first: Amit

last: Sharma

address: Carl neuberg str-1

department: Hematology

institute: Hannover Medical School

description: Gene expression data from sorted mouse bone marrow cells transduced with EGFP control vector

hyb_protocol: Samples were hybridized to an identical lot of Affymetrix GeneChip for 16 hours at 45ﾰC on MOE430 2.0. Steps for washing and SA-PE staining were processed on the fluidics station 450 using the mini_euk2v3_FS450 protocol (Affymetrix; Santa Clara, CA)

scan_protocol: Image Analysis was performed on GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA)

data_processing: RMA (Robust Multichip Average; Bioconductor)

label_protocol: For biotin-labeled target synthesis starting from 3 ﾵg of total RNA, reactions were performed using standard protocols supplied by the manufacturer (Affymetrix; Santa Clara, CA). Briefly, 3 ﾵg total RNA were converted to dsDNA using 100 pmol of a T7T23V primer (Eurogentec; Seraing, Belgium) containing a T7 promotor. The cDNA was then used directly in an in-vitro transcription reaction in the presence of biotinylated nucleotides

growth_protocol: cells cultured in DMEM+15%FCS+1%P/S supplemented with mIL3, hIL6 and mSCF cytokines

extract_protocol: Trizol extraction

value: sorted mouse bone marrow cells


title: BIOPSY_8128

tag: abmr (no


title: 28C Rep3 Dawn

description:
Dawn_28_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv

value: 50% flowering

value: Panicle


title: C4


title: JNK3 knockout

value: homozygous Mapk10-/-


title: MLL-AF9/Mn1null replicate 1


title: MLL-AF9/Mn1null replicate 2


title: BIOPSY_7933

tag: date of sample


title: 28C Rep2 Dusk

description:
Dusk_28_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv

value: Dusk


title: MLL-AF9/Mn1wt replicate 3


title: C3


title: MLL-AF9/Mn1wt replicate 2


title: 28C Rep2 Dawn

description:
Dawn_28_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: C2


title: 28C Rep1 Dusk

description:
Dusk_28_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: C1


title: 28C Rep1 Dawn

description:
Dawn_28_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: MLL-AF9/Mn1wt replicate 1


title: BIOPSY_7635


title: 26C Rep4 Dusk

description:
Dusk_26_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: 26C Rep4 Dawn

description:
Dawn_26_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: BIOPSY_7522


title: 26C Rep3 Dusk

description:
Dusk_26_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: BIOPSY_7393


title: BIOPSY_7565


title: HFD6: Ing-46

city: Cologne

first: Eva

last: Hucklenbruch-Rother

state: North rhine Westphalia

address: Robert Straße 14, Gebäude 44a

department: Department of Pediatric and Adolescent Medicine

institute: University Hospital of Cologne

description: The hypothalamus was cut immediately caudal to the optic chiasm. The dissection was limited laterally by the hypothalamic sulci and dorsally by the mammillothalamic tract (46).

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was hybridized to the array using the Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: After scanning microarray raw data were extracted using Agilent’s Feature Extraction Software (version 10.8) using default parameters. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hypothalamic tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0ug total RNA using the One-Color Low RNA Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from hypothalamus of CO and HFD animals using TRI-Reagent® (Sigma-Aldrich) according to the manufacturer’s guidelines. RNA quantity and purity were determined by measuring UV absorption with a Tecan spectrophotometer (Tecan, Nano Quant infinite M200 Pro).

treatment_protocol: On P21, male pups were sacrificed and the hypothalamus was dissected. The hypothalamus was cut immediately caudal to the optic chiasm. The dissection was limited laterally by the hypothalamic sulci and dorsally by the mammillothalamic tract. Hypothalamic tissue was immediately frozen at −80° C.

value: hypothalamus

value: male

tag: age

value: Postnatal day (P) 21


title: granulosa cells_sownr2723_follicle6_smallfollicle_HighVAR_HighCOChealth

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 8*60K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

organism: Sus scrofa

source_name: granulosa cells

label_protocol: Approximately 40 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). 32 Cy3-labeled samples with the highest cRNA yield were used for the reference pool.

extract_protocol: Total RNA was isolated from granulosa cells isolated using laser capture micro-dissection (Arcturus) and the Picopure RNA Isolation kit (Arcturus), quantified using Nanodrop (IsoGen Life Science) and qualified using TapeStation (Agilent).

treatment_protocol: A total of 29 multiparous Dutch Landrace sows (parity 3 to 5; Topigs Norsvin, Vught, the Netherlands) were used. The sows were fed a standard lactation diet (ca. 12.5MJ NE/kg, 154 g/kg CP, 9.3 g/kg lysine; Lacto Excellent, Agrifirm, Apeldoorn, The Netherlands). Within 24 hours after parturition, piglets were cross-fostered to ensure 13 suckling piglets per sow. The sows had a lactation period of 26.1±0.2 (25 to 27) days and weaned 13.0±0.9 piglets. The sows were slaughtered at the slaughterhouse by stunning and exsanguination within 2 hours after weaning.

tag: origin

value: TopigsNorsvin N-line, multiparous sows

tag: follicle size

value: small

tag: var

value: high

tag: coc health

tag: sample type

value: reference


title: HFD5: Ing-37

tag: tissue


title: granulosa cells_sownr2633_follicle6_smallfollicle_LowVAR_HighCOChealth

value: low


title: granulosa cells_sownr2434_follicle6_smallfollicle_LowVAR_LowCOChealth


title: BIOPSY_7314

city: Leuven

first: Maarten

last: Naesens

address: Herestraat 49

institute: KU Leuven

data_processing:
The resulting image files were generated using the GeneChip® Command Console® Software (AGCC).
Log 2 RMA-normalized signal intensity (using Bioconductor tools in R version 3.5.3)

extract_protocol: * BLOOD: Total RNA from peripheral blood samples was extracted using the PAXgene Blood miRNA Kit® (PreAnalytiX GmbH, a Qiagen/ BD Company, Switzerland). The yield and purity of RNA was measured using a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific™, Life Technologies Europe BV, Ghent, Belgium). RNA integrity was assessed using the RNA 6000 Nano LabChip® kit (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument™ (Agilent Technologies Belgium NV, Diegem, Belgium), and globin mRNA was depleted using the GLOBINclear™ Kit (Invitrogen™, Life Technologies Europe BV, Ghent, Belgium). After globin mRNA depletion, the quantity (absorbance at 260nm) and purity (ratio of the absorbance at 230, 260 and 280nm) of the isolated RNA were measured using the NanoDrop ND-1000™ spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE, USA). The extracted RNA samples were stored at -80°C.   ** BIOPSY: Total RNA from renal allograft biopsies was extracted using the Allprep DNA/RNA/miRNA Universal Kit® (Qiagen Benelux BV, Venlo, The Netherlands) on a QIAcube instrument (Qiagen Benelux BV, Venlo, The Netherlands). The quantity (absorbance at 260nm) and purity (ratio of the absorbance at 230, 260 and 280nm) of the RNA isolated from the biopsies were measured using the NanoDrop ND-1000™ spectrophotometer (Thermo Scientific™, Life Technologies Europe BV, Ghent, Belgium). RNA integrity was evaluated using the Eukaryote nano/pico RNA Kit® (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument™ (Agilent Technologies Belgium NV, Diegem, Belgium). Samples were stored at -80°C until further analysis.

value: kidney allograft biopsy


title: 26C Rep2 Dusk

description:
Dusk_26_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv

tag: variety

tag: developmental stage

tag: treatment

tag: time point


title: HFD1: Ing-1

tag: gender


title: BIOPSY_7310


title: HFD4: Ing-36


title: granulosa cells_sownr2279_follicle6_smallfollicle_HighVAR_HighCOChealth


title: HFD3: Ing-14


title: BIOPSY_7244


title: BIOPSY_7248


title: HFD2: Ing-8


title: 26C Rep3 Dawn

description:
Dawn_26_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv

value: Dawn


title: 26C Rep2 Dawn

description:
Dawn_26_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: 26C Rep1 Dusk

description:
Dusk_26_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: 26C Rep1 Dawn

description:
Dawn_26_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: granulosa cells_sownr2124_follicle6_smallfollicle_HighVAR_HighCOChealth


title: BIOPSY_7031


title: BIOPSY_7158


title: 24C Rep4 Dusk

description:
Dusk_24_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: granulosa cells_sownr2673_follicle6_smallfollicle_LowVAR_LowCOChealth


title: 24C Rep4 Dawn

description:
Dawn_24_P4
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: SD3: 65-5


title: SD5: 89-5


title: granulosa cells_sownr1808_follicle6_smallfollicle_LowVAR_LowCOChealth


title: BIOPSY_6921


title: BIOPSY_6878


title: Uninfected control cells at 9 days post infection replicate 1 [UI9DPI1]

city: Providence

first: Walter

last: Atwood

address: 70 Ship Street

institute: Brown University

data_processing:
Mapping was performed using Tophat version 2.0.10 in conjuction with Bowtie version 1.0.0, reads were trimmed for adpater sequence if required using Flexbar version 2.4.
Cufflinks version 2.1.1 was used to detect genes and transcripts that are expressed and Cuffdiff version 2.1.1 was used to collect FPKM expression values across all samples.
The edgeR R Bioconductor 2.12 package was used for differential expression
Genome_build: human genome reference sequence GRCh38
Supplementary_files_format_and_content: differential epression data are in "csv" format. They include the comparisons between JCPyV infected sample with BKPyV infected samples and between each virus (JCPyV or BKPyV) with the uninfected control sample at each time point tested (3, 6 and 9 days post infection)

extract_protocol:
Total RNA was harvested using the RNAeasy kit from qiagen adding the DNAse treatment step
The library was generated by Beckman Coulter Genomics using the the Illumina Truseq stranded total RNA with Ribo Zero kit

tag: cell type

value: Primary Human Renal Epithelial Cells (ATCC)

tag: cell source

value: 13 months old female

value: none (uninfected)

value: at 9 days post infection


title: Uninfected control cells at 9 days post infection replicate 2 [UI9DPI2]


title: 24C Rep3 Dusk

description:
Dusk_24_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv

value: 50% flowering

value: Panicle


title: granulosa cells_sownr2684_follicle6_smallfollicle_HighVAR_LowCOChealth


title: SD4: 89-2


title: granulosa cells_sownr2279_follicle5_smallfollicle_HighVAR_HighCOChealth


title: granulosa cells_sownr2434_follicle5_smallfollicle_LowVAR_LowCOChealth


title: BIOPSY_6800

tag: tcmr (no


title: granulosa cells_sownr2124_follicle5_smallfollicle_HighVAR_HighCOChealth


title: SD2: 65-3


title: Uninfected control cells at 6 days post infection replicate 3 [UI6DPI3]

value: at 6 days post infection


title: BIOPSY_6719

tag: abmr (no


title: Uninfected control cells at 9 days post infection replicate 3 [UI9DPI3]


title: SD1: 65-1

value: hypothalamus


title: 24C Rep3 Dawn

description:
Dawn_24_P3
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: BIOPSY_6402

tag: date of sample


title: granulosa cells_sownr1808_follicle5_smallfollicle_LowVAR_LowCOChealth


title: BIOPSY_6352


title: genomic DNA_N_912

source_name: non-cancerous urothelium obtained from patient with urothelial carcinomas

tag: diagnosis

value: urothelial carcinoma

value: Male

tag: age


title: Uninfected control cells at 6 days post infection replicate 2 [UI6DPI2]


title: 24C Rep2 Dusk

description:
Dusk_24_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv

value: Dusk


title: Uninfected control cells at 6 days post infection replicate 1 [UI6DPI1]


title: BIOPSY_6175


title: 24C Rep1 Dusk

description:
Dusk_24_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: 24C Rep2 Dawn

description:
Dawn_24_P2
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: 24C Rep1 Dawn

description:
Dawn_24_P1
processed data file: Pannicle_gradient_24_26_28_30C.csv


title: Uninfected control cells at 3 days post infection replicate 2 [UI3DPI2]

value: at 3 days post infection


title: Uninfected control cells at 3 days post infection replicate 1 [UI3DPI1]


title: granulosa cells_sownr1808_follicle4_smallfollicle_LowVAR_LowCOChealth

tag: origin

value: TopigsNorsvin N-line, multiparous sows

tag: follicle size

value: small


title: WNT Dawn 23h Rep 4

description:
8-23h_WNT.3
processed data file: Pannicle_timecourse_WNT.csv

value: WNT

value: Dawn 23h


title: granulosa cells_sownr2124_follicle4_smallfollicle_HighVAR_HighCOChealth

tag: var

value: high

tag: coc health

value: reference


title: granulosa cells_sownr2673_follicle4_smallfollicle_LowVAR_LowCOChealth

value: low

tag: sample type


title: WNT Dawn 23h Rep 3

description:
8-23h_WNT.2
processed data file: Pannicle_timecourse_WNT.csv

tag: variety

tag: tissue


title: granulosa cells_sownr2684_follicle4_smallfollicle_HighVAR_LowCOChealth


title: BIOPSY_5976

value: kidney allograft biopsy


title: Uninfected control cells at 3 days post infection replicate 3 [UI3DPI3]

value: Primary Human Renal Epithelial Cells (ATCC)

value: 13 months old female

tag: treatment

value: none (uninfected)


title: JC infected cells at 9 days post infection replicate 2 [JC9DPI2]

value: JC polyomavirus (JCPyV)

tag: time point

value: at 9 days post infection


title: WNT Dawn 23h Rep 2

description:
8-23h_WNT.1
processed data file: Pannicle_timecourse_WNT.csv

tag: developmental stage

value: 50% flowering

value: Panicle


title: granulosa cells_sownr2434_follicle4_smallfollicle_LowVAR_LowCOChealth

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: JC infected cells at 9 days post infection replicate 1 [JC9DPI1]

tag: cell type


title: granulosa cells_sownr2633_follicle4_smallfollicle_LowVAR_HighCOChealth


title: granulosa cells_sownr2723_follicle4_smallfollicle_HighVAR_HighCOChealth


title: BIOPSY_5869


title: BIOPSY_5646


title: WNT Dawn 23h Rep 1

description:
8-23h_WNT
processed data file: Pannicle_timecourse_WNT.csv


title: BIOPSY_5649


title: BIOPSY_5756


title: JC infected cells at 6 days post infection replicate 3 [JC6DPI3]

tag: cell source

value: at 6 days post infection


title: WNT Dawn 17.5h Rep 4

description:
7-17.5h_WNT.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 17.5h


title: BIOPSY_5495

tag: tcmr (no


title: WNT Dawn 17.5h Rep 3

description:
7-17.5h_WNT.2
processed data file: Pannicle_timecourse_WNT.csv


title: JC infected cells at 6 days post infection replicate 2 [JC6DPI2]


title: JC infected cells at 6 days post infection replicate 1 [JC6DPI1]


title: JC infected cells at 9 days post infection replicate 3 [JC9DPI3]


title: WNT Dawn 17.5h Rep 2

description:
7-17.5h_WNT.1
processed data file: Pannicle_timecourse_WNT.csv


title: JC infected cells at 3 days post infection replicate 3 [JC3DPI3]

value: at 3 days post infection


title: JC infected cells at 3 days post infection replicate 2 [JC3DPI2]


title: granulosa cells_sownr2279_follicle3_largefollicle_HighVAR_HighCOChealth

value: TopigsNorsvin N-line, multiparous sows

value: large


title: WNT Dawn 14h Rep 4

description:
6-14h_WNT.3
processed data file: Pannicle_timecourse_WNT.csv

value: WNT

value: Dawn 14h


title: granulosa cells_sownr1808_follicle3_largefollicle_LowVAR_LowCOChealth

value: reference


title: granulosa cells_sownr2279_follicle4_smallfollicle_HighVAR_HighCOChealth

value: small

value: high


title: WNT Dawn 14h Rep 3

description:
6-14h_WNT.2
processed data file: Pannicle_timecourse_WNT.csv


title: BIOPSY_5589

value: kidney allograft biopsy

tag: abmr (no


title: JC infected cells at 3 days post infection replicate 1 [JC3DPI1]

value: Primary Human Renal Epithelial Cells (ATCC)

value: 13 months old female


title: BIOPSY_5357

tag: date of sample


title: WNT Dawn 17.5h Rep 1

description:
7-17.5h_WNT
processed data file: Pannicle_timecourse_WNT.csv


title: WNT Dawn 14h Rep 1

description:
6-14h_WNT
processed data file: Pannicle_timecourse_WNT.csv


title: BK infected cells at 9 days post infection replicate 2 [BK9DPI2]

value: BK polyomavirus (BKPyV)


title: granulosa cells_sownr2434_follicle3_largefollicle_LowVAR_LowCOChealth

value: low


title: granulosa cells_sownr2673_follicle3_largefollicle_LowVAR_LowCOChealth


title: granulosa cells_sownr2633_follicle3_largefollicle_LowVAR_HighCOChealth


title: BIOPSY_5226


title: granulosa cells_sownr2124_follicle3_largefollicle_HighVAR_HighCOChealth


title: BIOPSY_5431


title: granulosa cells_sownr2723_follicle3_largefollicle_HighVAR_HighCOChealth


title: BIOPSY_5306


title: BIOPSY_5131


title: BIOPSY_5204


title: BIOPSY_5164


title: granulosa cells_sownr2684_follicle3_largefollicle_HighVAR_LowCOChealth


title: BK infected cells at 9 days post infection replicate 1 [BK9DPI1]

value: at 9 days post infection


title: WNT Dusk Rep 3

description:
5-Dusk_WNT.2
processed data file: Pannicle_timecourse_WNT.csv

value: 50% flowering

value: Panicle

value: Dusk


title: BK infected cells at 6 days post infection replicate 3 [BK6DPI3]

value: at 6 days post infection


title: WNT Dawn 14h Rep 2

description:
6-14h_WNT.1
processed data file: Pannicle_timecourse_WNT.csv


title: granulosa cells_sownr2723_follicle2_largefollicle_HighVAR_HighCOChealth

value: TopigsNorsvin N-line, multiparous sows


title: BK infected cells at 6 days post infection replicate 2 [BK6DPI2]


title: BIOPSY_5041


title: WNT Dusk Rep 2

description:
5-Dusk_WNT.1
processed data file: Pannicle_timecourse_WNT.csv


title: granulosa cells_sownr2279_follicle2_largefollicle_HighVAR_HighCOChealth

value: large


title: WNT Dusk Rep 1

description:
5-Dusk_WNT
processed data file: Pannicle_timecourse_WNT.csv

value: WNT


title: BIOPSY_4964


title: WNT Dawn 10.5h Rep 4

description:
4-10.5h_WNT.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 10.5h


title: BK infected cells at 3 days post infection replicate 3 [BK3DPI3]

value: at 3 days post infection


title: BK infected cells at 6 days post infection replicate 1 [BK6DPI1]


title: WNT Dusk Rep 4

description:
5-Dusk_WNT.3
processed data file: Pannicle_timecourse_WNT.csv


title: BIOPSY_4949


title: BIOPSY_51


title: BIOPSY_4567


title: WNT Dawn 10.5h Rep 3

description:
4-10.5h_WNT.2
processed data file: Pannicle_timecourse_WNT.csv


title: BK infected cells at 3 days post infection replicate 2 [BK3DPI2]


title: BK infected cells at 3 days post infection replicate 1 [BK3DPI1]


title: granulosa cells_sownr2434_follicle2_largefollicle_LowVAR_LowCOChealth

value: reference


title: granulosa cells_sownr2673_follicle2_largefollicle_LowVAR_LowCOChealth


title: BIOPSY_4396


title: granulosa cells_sownr2633_follicle2_largefollicle_LowVAR_HighCOChealth

value: high


title: WNT Dawn 10.5h Rep 1

description:
4-10.5h_WNT
processed data file: Pannicle_timecourse_WNT.csv


title: granulosa cells_sownr2124_follicle2_largefollicle_HighVAR_HighCOChealth

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: granulosa cells_sownr1808_follicle2_largefollicle_LowVAR_LowCOChealth


title: BK infected cells at 9 days post infection replicate 3 [BK9DPI3]


title: Medium

city: Suzhou

first: Xiao-Ming

last: Gao

address: 199 Ren’ai Road

department: Institute of Biology and Medical Sciences, School of Biology and Basic Medical Sciences,

institute: Soochow University

data_processing:
Reads were mapped to human reference genome hg19 using BWA/Bowtie2 tool
Genes expression level is quantified by RSEM package.The differentially expression was indentified by EBSeq package.
Peak calling was done for individual samples using macs (version 1.4.2 20120305).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Human blood monocytes

growth_protocol: Freshly isolated CD14+ human blood monocytes were cultured for 24 hrs in R10 medium in microtiter tissue culture plates pre-coated with IVIG (cIgG), or without (RPMI), at 37°C and 5% CO2.

extract_protocol:
Monocytes were pre-incubated either with cell culture medium (Medium), LFIC (10μg/ml) or cIgG (10 μg/ml) for 24 hrs.After wash-out, cells were harvested and processed into RNA extraction.
Total RNA was polyA enriched, fragmented and converted into a library of Illumina-compatible sequencing templated with Illumina mRNA-seq sample preparation kit according to the manufacturer’s instructions. The cDNA library was size-fractionated in a 1% agarose gel. 200-250 bp fragments were isolated and amplified by PCR with Illumina primers PE1 and PE2 for 15 cycles. The integrity and quality of total RNA and size-selected libraries was evaluated with Bioanalyzer 2100 (Agilent Tech).

treatment_protocol: Freshly fractionated monocytes  were cultured for 24 hrs in RPMI-10 medium for preparation of Mo(Medium),Mo(LF-IC) and Mo(cIgG).

value: Peripheral blood

value: CD14+ human blood monocytes

value: RPMI culture for 24 hrs


title: cIgG

value: cIgG priming for 24 hrs


title: BIOPSY_4357

value: kidney allograft biopsy


title: granulosa cells_sownr2684_follicle1_largefollicle_HighVAR_LowCOChealth

value: low


title: BIOPSY_4327


title: WNT Dawn 7h Rep 3

description:
3-7h_WNT.2
processed data file: Pannicle_timecourse_WNT.csv

value: 50% flowering

value: Dawn 7h


title: LF-IC

value: LFIC priming for 24 hrs


title: granulosa cells_sownr2684_follicle2_largefollicle_HighVAR_LowCOChealth


title: WNT Dawn 7h Rep 4

description:
3-7h_WNT.3
processed data file: Pannicle_timecourse_WNT.csv

value: Panicle


title: BIOPSY_4091


title: BIOPSY_4531


title: WNT Dawn 10.5h Rep 2

description:
4-10.5h_WNT.1
processed data file: Pannicle_timecourse_WNT.csv


title: DKO-anti-miR-148b

molecule: polyA RNA

tag: genotype

value: TUT4 and TUT7 Double Knockout

tag: ip antibody


title: WNT Dawn 7h Rep 2

description:
3-7h_WNT.1
processed data file: Pannicle_timecourse_WNT.csv


title: granulosa cells_sownr2673_follicle1_largefollicle_LowVAR_LowCOChealth

tag: origin

value: TopigsNorsvin N-line, multiparous sows

value: large


title: granulosa cells_sownr2723_follicle1_largefollicle_HighVAR_HighCOChealth

tag: follicle size


title: WT-anti-miR-148b

value: WT


title: WNT Dawn 3.5h Rep 4

description:
2-3.5h_WNT.3
processed data file: Pannicle_timecourse_WNT.csv

value: WNT

value: Dawn 3.5h


title: granulosa cells_sownr2279_follicle1_largefollicle_HighVAR_HighCOChealth

tag: var

value: high

value: reference


title: WT-control_treament (WT-anti-miR-148b)


title: granulosa cells_sownr2633_follicle1_largefollicle_LowVAR_HighCOChealth

tag: coc health