title: C1-21-H4_TCCTGAGC-CTAAGCCT_L002_R1_all


title: C1-21-H6_TAGGCATG-CTAAGCCT_L002_R1_all

status: Public on Sep 06 2016

type: SRA

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

country: USA

institute: Yale University School of Medicine

description:
Zika.GEO.humanBrain.singleCell.gene.RPKM.txt.gz
Zika.GEO.humanBrain.singleCell.gene.count.txt.gz

library_source: transcriptomic

data_processing:
We used Illumina CASAVA to purify the low-quality and non-identified reads, and used FastQC to report the fundamental quality parameters.
We trimmed 12 nucleotides in 5’-end and 13 nucleotides in 3’-end, leaving 75 nucleotide long reads for sequence alignment.
We employed Tophat (v1.4.1) to uniquely align the filtered reads to human reference genome with default parameters.
We used RSEQTools and SAMtools to calculate the gene expression. The BAM format alignment was converted into SAM format alignment by using the SAMtools. The "sam2mrf" function in RSEQtools was used to convert the SAM format to Mapped Read Format. The "mrfQuantifier" function in RSEQtools was used to calculated an expression value for each annotation entry by counting all nucleotides from reads that overlap with a given annotation entry in GENCODE project.
Genome_build: hg38
Supplementary_files_format_and_content: [.txt] tab-delimited text files include RPKM values and read count values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Dorsolateral prefrontal cortex

growth_protocol: Cells were resuspended in DMEM/F12 with addition of B27 supplement (1:1000), N2 supplement (1:100), 20 ng/ml FGF-2, 20 ng/ml EGF, 1.6 g/l glucose, 20 µg/ml insulin and 5 ng/ml BDNF. 10 µM rock inhibitor (Y-27632, Stemgent # 04-0012) was added to increase cell viability. The cells were then plated into dishes coated with poly-L-ornithine (0.01%, Sigma #P4957), laminin (5 µg/ml, Invitrogen #23017-015) and fibronectin (1μg/ml, Corning, #354008,). Medium was changed 12 hr after plating and the cells were passaged using 0.25% trypsin within 3 d and replated to obtain a monolayer of cells at a density of 4–5 × 104 cells/cm2. Half of the media was changed every 2–3 d to allow culture conditioning.

extract_protocol:
Fluidigm C1 was used to capture single cell for mRNA sequencing.   Catalog # 100-5760, which is microfluidic IFCs designed to capture cells from 10 to 17 µm.  Since each Fluidigm C1 chip could maximum capture 96 cells,  we sequentially numbered the chips we used during the experiments.  So, the numbers in  the Characteristics "chip" field column indicate the cell was captured from which chip.  This information was provided because it could help the estimation of the systematic effects coming from the chips.
RNA was extracted after single cell capture using C1 single cell auto prep system, with manufacturer protocol.
RNA libraries were prepared for sequencing using with Illumina NEXTERA XT kit
Single cell RNA-Seq

tag: donor

tag: age


title: C1-21-H7_CTCTCTAC-CTAAGCCT_L002_R1_all


title: C1-21-H12_GTAGAGGA-CTAAGCCT_L002_R1_all


title: C1-21-H11_AAGAGGCA-CTAAGCCT_L002_R1_all


title: C1-21-H10_CGAGGCTG-CTAAGCCT_L002_R1_all


title: C1-21-H1_TAAGGCGA-CTAAGCCT_L002_R1_all


title: C1-21-G9_GCTACGCT-AAGGAGTA_L002_R1_all


title: C1-21-G8_CAGAGAGG-AAGGAGTA_L002_R1_all


title: C1-21-G7_CTCTCTAC-AAGGAGTA_L002_R1_all


title: C1-21-H2_CGTACTAG-CTAAGCCT_L002_R1_all


title: C1-21-G6_TAGGCATG-AAGGAGTA_L002_R1_all


title: C1-21-G4_TCCTGAGC-AAGGAGTA_L002_R1_all


title: C1-21-G2_CGTACTAG-AAGGAGTA_L002_R1_all


title: C1-21-G1_TAAGGCGA-AAGGAGTA_L002_R1_all


title: C1-21-G12_GTAGAGGA-AAGGAGTA_L002_R1_all


title: C1-21-G11_AAGAGGCA-AAGGAGTA_L002_R1_all


title: C1-21-G5_GGACTCCT-AAGGAGTA_L002_R1_all


title: C1-21-G10_CGAGGCTG-AAGGAGTA_L002_R1_all


title: C1-21-F7_CTCTCTAC-ACTGCATA_L002_R1_all


title: C1-21-F6_TAGGCATG-ACTGCATA_L002_R1_all


title: C1-21-F4_TCCTGAGC-ACTGCATA_L002_R1_all


title: C1-21-F5_GGACTCCT-ACTGCATA_L002_R1_all


title: C1-21-F8_CAGAGAGG-ACTGCATA_L002_R1_all


title: C1-21-H3_AGGCAGAA-CTAAGCCT_L002_R1_all


title: C1-21-F3_AGGCAGAA-ACTGCATA_L002_R1_all


title: C1-21-F2_CGTACTAG-ACTGCATA_L002_R1_all


title: C1-21-F1_TAAGGCGA-ACTGCATA_L002_R1_all


title: C1-21-F12_GTAGAGGA-ACTGCATA_L002_R1_all


title: C1-21-F10_CGAGGCTG-ACTGCATA_L002_R1_all


title: C1-21-E9_GCTACGCT-GTAAGGAG_L002_R1_all


title: C1-21-E6_TAGGCATG-GTAAGGAG_L002_R1_all


title: C1-21-G3_AGGCAGAA-AAGGAGTA_L002_R1_all


title: C1-21-E7_CTCTCTAC-GTAAGGAG_L002_R1_all


title: C1-21-E3_AGGCAGAA-GTAAGGAG_L002_R1_all


title: C1-21-E5_GGACTCCT-GTAAGGAG_L002_R1_all


title: C1-21-E8_CAGAGAGG-GTAAGGAG_L002_R1_all


title: C1-21-E2_CGTACTAG-GTAAGGAG_L002_R1_all


title: C1-21-E4_TCCTGAGC-GTAAGGAG_L002_R1_all


title: C1-21-E1_TAAGGCGA-GTAAGGAG_L002_R1_all


title: C1-21-E12_GTAGAGGA-GTAAGGAG_L002_R1_all


title: C1-21-E11_AAGAGGCA-GTAAGGAG_L002_R1_all


title: C1-21-D9_GCTACGCT-AGAGTAGA_L002_R1_all


title: C1-21-E10_CGAGGCTG-GTAAGGAG_L002_R1_all


title: C1-21-D6_TAGGCATG-AGAGTAGA_L002_R1_all


title: C1-21-F9_GCTACGCT-ACTGCATA_L002_R1_all


title: C1-21-D8_CAGAGAGG-AGAGTAGA_L002_R1_all


title: C1-21-D4_TCCTGAGC-AGAGTAGA_L002_R1_all


title: C1-21-D5_GGACTCCT-AGAGTAGA_L002_R1_all


title: C1-21-D1_TAAGGCGA-AGAGTAGA_L002_R1_all


title: C1-21-D3_AGGCAGAA-AGAGTAGA_L002_R1_all


title: C1-21-D12_GTAGAGGA-AGAGTAGA_L002_R1_all


title: C1-21-D11_AAGAGGCA-AGAGTAGA_L002_R1_all


title: C1-21-C9_GCTACGCT-TATCCTCT_L002_R1_all


title: C1-21-D2_CGTACTAG-AGAGTAGA_L002_R1_all


title: C1-21-C7_CTCTCTAC-TATCCTCT_L002_R1_all


title: C1-21-C5_GGACTCCT-TATCCTCT_L002_R1_all


title: C1-21-F11_AAGAGGCA-ACTGCATA_L002_R1_all


title: C1-21-C4_TCCTGAGC-TATCCTCT_L002_R1_all


title: C1-21-C3_AGGCAGAA-TATCCTCT_L002_R1_all


title: C1-21-C10_CGAGGCTG-TATCCTCT_L002_R1_all


title: C1-21-C11_AAGAGGCA-TATCCTCT_L002_R1_all


title: C1-21-D7_CTCTCTAC-AGAGTAGA_L002_R1_all


title: C1-21-B8_CAGAGAGG-CTCTCTAT_L002_R1_all


title: C1-21-B7_CTCTCTAC-CTCTCTAT_L002_R1_all


title: C1-21-B9_GCTACGCT-CTCTCTAT_L002_R1_all


title: C1-21-B6_TAGGCATG-CTCTCTAT_L002_R1_all


title: C1-21-B5_GGACTCCT-CTCTCTAT_L002_R1_all


title: C1-21-C6_TAGGCATG-TATCCTCT_L002_R1_all


title: C1-21-B3_AGGCAGAA-CTCTCTAT_L002_R1_all


title: C1-21-B4_TCCTGAGC-CTCTCTAT_L002_R1_all


title: C1-21-B2_CGTACTAG-CTCTCTAT_L002_R1_all


title: C1-21-B11_AAGAGGCA-CTCTCTAT_L002_R1_all


title: C1-21-B12_GTAGAGGA-CTCTCTAT_L002_R1_all


title: C1-21-B1_TAAGGCGA-CTCTCTAT_L002_R1_all


title: C1-21-C8_CAGAGAGG-TATCCTCT_L002_R1_all


title: C1-21-B10_CGAGGCTG-CTCTCTAT_L002_R1_all


title: C1-21-A9_GCTACGCT-TAGATCGC_L002_R1_all


title: C1-21-A7_CTCTCTAC-TAGATCGC_L002_R1_all


title: C1-21-C1_TAAGGCGA-TATCCTCT_L002_R1_all


title: C1-21-C2_CGTACTAG-TATCCTCT_L002_R1_all


title: C1-21-A6_TAGGCATG-TAGATCGC_L002_R1_all


title: C1-21-A5_GGACTCCT-TAGATCGC_L002_R1_all


title: C1-21-A4_TCCTGAGC-TAGATCGC_L002_R1_all


title: C1-21-C12_GTAGAGGA-TATCCTCT_L002_R1_all


title: C1-21-A3_AGGCAGAA-TAGATCGC_L002_R1_all


title: C1-21-A12_GTAGAGGA-TAGATCGC_L002_R1_all


title: C1-21-A1_TAAGGCGA-TAGATCGC_L002_R1_all


title: C1-21-D10_CGAGGCTG-AGAGTAGA_L002_R1_all


title: C1-21-A11_AAGAGGCA-TAGATCGC_L002_R1_all


title: C1-21-A10_CGAGGCTG-TAGATCGC_L002_R1_all


title: C1-21-A2_CGTACTAG-TAGATCGC_L002_R1_all


title: C1-20-H8_CAGAGAGG-CTAAGCCT_L001_R1_all


title: C1-22-C9_GCTACGCT-TATCCTCT_L003_R1_all


title: C1-21-A8_CAGAGAGG-TAGATCGC_L002_R1_all


title: C1-20-H4_TCCTGAGC-CTAAGCCT_L001_R1_all


title: C1-20-H9_GCTACGCT-CTAAGCCT_L001_R1_all


title: C1-20-H6_TAGGCATG-CTAAGCCT_L001_R1_all


title: C1-20-H1_TAAGGCGA-CTAAGCCT_L001_R1_all


title: C1-20-H5_GGACTCCT-CTAAGCCT_L001_R1_all


title: C1-20-H3_AGGCAGAA-CTAAGCCT_L001_R1_all


title: C1-20-H7_CTCTCTAC-CTAAGCCT_L001_R1_all


title: C1-20-H12_GTAGAGGA-CTAAGCCT_L001_R1_all


title: C1-20-H11_AAGAGGCA-CTAAGCCT_L001_R1_all


title: C1-20-G9_GCTACGCT-AAGGAGTA_L001_R1_all


title: C1-20-G7_CTCTCTAC-AAGGAGTA_L001_R1_all


title: C1-20-H10_CGAGGCTG-CTAAGCCT_L001_R1_all


title: C1-20-G6_TAGGCATG-AAGGAGTA_L001_R1_all


title: C1-20-G5_GGACTCCT-AAGGAGTA_L001_R1_all


title: C1-20-G4_TCCTGAGC-AAGGAGTA_L001_R1_all


title: C1-20-G2_CGTACTAG-AAGGAGTA_L001_R1_all


title: C1-21-1000_CAGAGAGG-AGAGTAGA_L001_R1_all


title: C1-20-G1_TAAGGCGA-AAGGAGTA_L001_R1_all


title: C1-20-G3_AGGCAGAA-AAGGAGTA_L001_R1_all


title: C1-21-100_TAGGCATG-AGAGTAGA_L001_R1_all


title: C1-20-G12_GTAGAGGA-AAGGAGTA_L001_R1_all


title: C1-20-H2_CGTACTAG-CTAAGCCT_L001_R1_all


title: C1-20-G10_CGAGGCTG-AAGGAGTA_L001_R1_all


title: C1-20-F7_CTCTCTAC-ACTGCATA_L001_R1_all


title: C1-20-F6_TAGGCATG-ACTGCATA_L001_R1_all


title: C1-20-F4_TCCTGAGC-ACTGCATA_L001_R1_all


title: C1-20-F5_GGACTCCT-ACTGCATA_L001_R1_all


title: C1-20-F12_GTAGAGGA-ACTGCATA_L001_R1_all


title: C1-20-G8_CAGAGAGG-AAGGAGTA_L001_R1_all


title: C1-20-F3_AGGCAGAA-ACTGCATA_L001_R1_all


title: C1-21-10E5_CGTACTAG-GTAAGGAG_L001_R1_all


title: C1-20-F8_CAGAGAGG-ACTGCATA_L001_R1_all


title: C1-20-E6_TAGGCATG-GTAAGGAG_L001_R1_all


title: C1-20-F11_AAGAGGCA-ACTGCATA_L001_R1_all


title: C1-20-E9_GCTACGCT-GTAAGGAG_L001_R1_all


title: C1-20-E7_CTCTCTAC-GTAAGGAG_L001_R1_all


title: EU96_S2

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

data_processing:
Adaptor sequences and low quality score bases (Phred score<20) were first trimmed usingTrim Galore (version 0.2.7).The resulting reads were then mapped to the human genome reference sequence using STAR (version 2.4.1c) and using a hg19 transcript annotation database downloaded from ENSEMBL release 75 and refined for all the splicing junction presents in our samples (2 pass protocol).
Gene-level expression estimates and isoform-level expression values were obtained using RSEM.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: [genes.results] Tab-delimited text files containing expression Expected counts, TPM and FPKM values for genes  for each sample.
Supplementary_files_format_and_content: [isoforms.results] Tab-delimited text files containing expression Expected counts, TPM and FPKM values for isoforms for each sample.

source_name: Macrophages

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation.  Monocytes were purified from peripheral blood mononuclear cells by positive selection with magnetic CD14 Mi-croBeads (Miltenyi Biotech). Monocytes were then cultured for 7 days in RPMI-1640 (Fisher) supplemented with 10% heat-inactivated FBS (FBS premium, US origin, Wisent), L-glutamine(Fisher) and M-CSF (20ng/mL; R&D systems). Cell cultures were fed every 2 days with com-plete medium supplemented with the cytokines previously mentioned.   Before infection,  we checked the differentiation/activation status of the monocyte-derived macrophages by flow cy-tometry, using antibodies against CD1a, CD14, CD83, and HLA-DR (BD Biosciences).  Only samples presenting the expected phenotype for non-activated macrophages (CD1a+, CD14+,CD83,  and  HLA-DRlow)  were  used  in  downstream  experiments

extract_protocol:
Total RNA was extracted from the non-infected and infected macrophages using the miRNeasykit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the quality was assessedwith the Agilent 2100 Bioanalyzer (Agilent Technologies).   Only samples with no evidence for RNA degradation (RNA integrity number>8) were kept for further experiments.
RNA-sequencing libraries were prepared using the Illumina TruSeq protocol.
Indexed cDNA libraries were pooled (6 libraries per pool) in equimolar amounts and were sequenced with single-end 100bp/101bp reads.

treatment_protocol: Monocyte-derived macrophages were infected at a multiplicity of infection (MOI) of 10:1 for Salmonella typhimurium and an MOI of 5:1 for Listeria monocytogenes.  A control group of non-infected macrophages was treated the same way but with only medium without bacteria.

tag: individual

tag: cell type

value: macrophage

tag: infection

value: Salmonella

tag: time

value: 2 hr


title: C1-20-F2_CGTACTAG-ACTGCATA_L001_R1_all


title: C1-20-E5_GGACTCCT-GTAAGGAG_L001_R1_all


title: C1-20-E4_TCCTGAGC-GTAAGGAG_L001_R1_all


title: C1-20-G11_AAGAGGCA-AAGGAGTA_L001_R1_all


title: EU96_NI2

value: Non-infected


title: C1-20-E1_TAAGGCGA-GTAAGGAG_L001_R1_all


title: EU96_L2

value: Listeria


title: C1-20-F9_GCTACGCT-ACTGCATA_L001_R1_all


title: EU56_S2


title: C1-20-E12_GTAGAGGA-GTAAGGAG_L001_R1_all


title: C1-20-E11_AAGAGGCA-GTAAGGAG_L001_R1_all


title: EU40_S2


title: EU306_S2


title: C1-20-F10_CGAGGCTG-ACTGCATA_L001_R1_all


title: EU306_NI2


title: C1-20-D9_GCTACGCT-AGAGTAGA_L001_R1_all


title: C1-20-D5_GGACTCCT-AGAGTAGA_L001_R1_all


title: C1-20-D2_CGTACTAG-AGAGTAGA_L001_R1_all


title: EU302_L2


title: C1-20-E8_CAGAGAGG-GTAAGGAG_L001_R1_all


title: C1-20-D1_TAAGGCGA-AGAGTAGA_L001_R1_all


title: EU302_NI2


title: EU306_L2


title: EU298_NI2


title: EU302_S2


title: C1-20-D11_AAGAGGCA-AGAGTAGA_L001_R1_all


title: C1-20-D7_CTCTCTAC-AGAGTAGA_L001_R1_all


title: C1-20-D10_CGAGGCTG-AGAGTAGA_L001_R1_all


title: C1-20-E10_CGAGGCTG-GTAAGGAG_L001_R1_all


title: EU300_NI2


title: C1-20-D12_GTAGAGGA-AGAGTAGA_L001_R1_all


title: EU298_L2


title: C1-20-F1_TAAGGCGA-ACTGCATA_L001_R1_all


title: C1-20-E3_AGGCAGAA-GTAAGGAG_L001_R1_all


title: EU296_S2


title: C1-20-C9_GCTACGCT-TATCCTCT_L001_R1_all


title: EU296_NI2


title: EU298_S2


title: EU296_L2


title: EU300_L2


title: C1-20-C6_TAGGCATG-TATCCTCT_L001_R1_all


title: C1-20-D4_TCCTGAGC-AGAGTAGA_L001_R1_all


title: C1-20-D3_AGGCAGAA-AGAGTAGA_L001_R1_all


title: EU300_S2


title: C1-20-C4_TCCTGAGC-TATCCTCT_L001_R1_all


title: C1-20-C5_GGACTCCT-TATCCTCT_L001_R1_all


title: EU294_NI2


title: EU294_L2


title: EU294_S2


title: EU290_NI2


title: EU290_L2


title: C1-20-C3_AGGCAGAA-TATCCTCT_L001_R1_all


title: C1-20-C8_CAGAGAGG-TATCCTCT_L001_R1_all


title: EU290_S2


title: C1-20-C1_TAAGGCGA-TATCCTCT_L001_R1_all


title: EU288_S2


title: C1-20-B5_GGACTCCT-CTCTCTAT_L001_R1_all


title: EU288_NI2


title: C1-20-C12_GTAGAGGA-TATCCTCT_L001_R1_all


title: C1-20-B9_GCTACGCT-CTCTCTAT_L001_R1_all


title: EU286_S2


title: EU286_L2


title: C1-20-B4_TCCTGAGC-CTCTCTAT_L001_R1_all


title: EU288_L2


title: C1-20-B6_TAGGCATG-CTCTCTAT_L001_R1_all


title: C1-20-B3_AGGCAGAA-CTCTCTAT_L001_R1_all


title: EU286_NI2


title: C1-20-B2_CGTACTAG-CTCTCTAT_L001_R1_all


title: EU284_L2


title: EU284_NI2


title: C1-20-C11_AAGAGGCA-TATCCTCT_L001_R1_all


title: EU282_NI2


title: C1-20-B12_GTAGAGGA-CTCTCTAT_L001_R1_all


title: EU282_S2


title: C1-20-C2_CGTACTAG-TATCCTCT_L001_R1_all


title: C1-20-B11_AAGAGGCA-CTCTCTAT_L001_R1_all


title: C1-20-A9_GCTACGCT-TAGATCGC_L001_R1_all


title: EU280_S2


title: EU282_L2


title: C1-20-A7_CTCTCTAC-TAGATCGC_L001_R1_all


title: C1-20-B8_CAGAGAGG-CTCTCTAT_L001_R1_all


title: C1-20-A8_CAGAGAGG-TAGATCGC_L001_R1_all


title: C1-20-A6_TAGGCATG-TAGATCGC_L001_R1_all


title: EU280_NI2


title: C1-20-A3_AGGCAGAA-TAGATCGC_L001_R1_all


title: EU278_S2


title: C1-20-A4_TCCTGAGC-TAGATCGC_L001_R1_all


title: EU276_NI2


title: C1-20-A1_TAAGGCGA-TAGATCGC_L001_R1_all


title: EU284_S2


title: C1-20-A5_GGACTCCT-TAGATCGC_L001_R1_all


title: EU278_NI2


title: C1-20-A11_AAGAGGCA-TAGATCGC_L001_R1_all


title: EU276_S2


title: EU274_S2


title: C1-20-A10_CGAGGCTG-TAGATCGC_L001_R1_all


title: EU278_L2


title: C1-20-A2_CGTACTAG-TAGATCGC_L001_R1_all


title: EU274_NI2


title: C1-20-1000-2_CTCTCTAC-TATCCTCT_L001_R1_all


title: C1-20-B1_TAAGGCGA-CTCTCTAT_L001_R1_all


title: C1-20-1000-1_CGAGGCTG-CTCTCTAT_L001_R1_all


title: C1-20-100-2_CTCTCTAC-CTCTCTAT_L001_R1_all


title: EU272_S2


title: C1-20-10E5_CGAGGCTG-TATCCTCT_L001_R1_all


title: EU274_L2


title: C1-4-H9_TAGGCATG-TATCCTCT_L003_R1_all


title: EU270_S2


title: C1-4-H8_AGGCAGAA-TATCCTCT_L003_R1_all


title: EU280_L2


title: EU272_NI2


title: EU268_S2


title: EU270_L2


title: EU270_NI2


title: C1-4-H7_TAGGCATG-CTCTCTAT_L003_R1_all


title: C1-20-100-1_GTAGAGGA-TAGATCGC_L001_R1_all


title: C1-4-H11_TAGGCATG-AGAGTAGA_L003_R1_all


title: C1-4-H4_AGGCAGAA-CTCTCTAT_L003_R1_all


title: EU268_L2


title: C1-4-H10_AGGCAGAA-AGAGTAGA_L003_R1_all


title: EU268_NI2


title: C1-4-G8_AGGCAGAA-TAGATCGC_L003_R1_all


title: EU266_NI2


title: EU266_S2


title: C1-4-G5_CGTACTAG-AGAGTAGA_L003_R1_all


title: C1-4-G4_GGACTCCT-TATCCTCT_L003_R1_all


title: EU264_S2


title: C1-4-G6_GGACTCCT-AGAGTAGA_L003_R1_all


title: EU266_L2


title: C1-4-G3_CGTACTAG-TATCCTCT_L003_R1_all


title: EU264_NI2


title: EU264_L2


title: C1-4-G2_GGACTCCT-CTCTCTAT_L003_R1_all


title: C1-4-G12_TAGGCATG-TAGATCGC_L003_R1_all


title: EU262_S2


title: C1-4-F9_TCCTGAGC-AGAGTAGA_L003_R1_all


title: EU262_NI2


title: EU262_L2


title: EU272_L2


title: C1-4-F7_TCCTGAGC-TATCCTCT_L003_R1_all


title: EU260_L2


title: EU260_S2


title: C1-4-F6_TAAGGCGA-TATCCTCT_L003_R1_all


title: EU260_NI2


title: EU276_L2


title: C1-4-F5_TCCTGAGC-CTCTCTAT_L003_R1_all


title: EU258_S2


title: EU258_L2


title: C1-4-F3_TCCTGAGC-TAGATCGC_L003_R1_all


title: C1-4-F4_TAAGGCGA-CTCTCTAT_L003_R1_all


title: C1-4-F1_TAAGGCGA-TAGATCGC_L003_R1_all


title: EU258_NI2


title: EU254_S2


title: C1-4-F11_GGACTCCT-TAGATCGC_L003_R1_all


title: EU254_L2


title: EU254_NI2


title: C1-4-F10_CGTACTAG-TAGATCGC_L003_R1_all


title: C1-4-F12_CGTACTAG-CTCTCTAT_L003_R1_all


title: C1-4-E8_TAGGCATG-TATCCTCT_L002_R1_all


title: C1-4-E6_AGGCAGAA-TATCCTCT_L002_R1_all


title: EU252_S2


title: EU252_NI2


title: EU248_NI2


title: EU248_S2


title: C1-4-E3_AGGCAGAA-CTCTCTAT_L002_R1_all


title: C1-4-F8_TAAGGCGA-AGAGTAGA_L003_R1_all


title: EU248_L2


title: C1-4-E12_TAGGCATG-AGAGTAGA_L002_R1_all


title: C1-4-E1_TAGGCATG-TAGATCGC_L002_R1_all


title: EU242_S2


title: EU246_L2


title: EU246_S2


title: EU242_NI2


title: C1-4-D9_GGACTCCT-TATCCTCT_L002_R1_all


title: C1-4-E10_AGGCAGAA-AGAGTAGA_L002_R1_all


title: EU240_L2


title: C1-4-D6_CGTACTAG-CTCTCTAT_L002_R1_all


title: EU242_L2


title: EU240_S2


title: C1-4-D7_GGACTCCT-CTCTCTAT_L002_R1_all


title: EU238_S2


title: C1-4-D1_TAAGGCGA-AGAGTAGA_L002_R1_all


title: C1-4-D4_GGACTCCT-TAGATCGC_L002_R1_all


title: C1-4-D2_TCCTGAGC-AGAGTAGA_L002_R1_all


title: EU238_NI2


title: C1-4-D3_CGTACTAG-TAGATCGC_L002_R1_all


title: EU238_L2


title: EU232_S2


title: C1-4-E4_TAGGCATG-CTCTCTAT_L002_R1_all


title: C1-4-D10_CGTACTAG-AGAGTAGA_L002_R1_all


title: C1-4-D12_AGGCAGAA-TAGATCGC_L002_R1_all


title: C1-4-D8_CGTACTAG-TATCCTCT_L002_R1_all


title: C1-4-D11_GGACTCCT-AGAGTAGA_L002_R1_all


title: EU230_L2


title: C1-4-C7_TCCTGAGC-TAGATCGC_L002_R1_all


title: C1-4-C9_TCCTGAGC-CTCTCTAT_L002_R1_all


title: EU230_S2


title: EU232_L2


title: C1-4-C5_TAAGGCGA-TAGATCGC_L002_R1_all


title: C1-4-C4_TAGGCATG-AGAGTAGA_L001_R1_all


title: EU230_NI2


title: EU224_NI2


title: EU224_L2


title: C1-4-C3_AGGCAGAA-AGAGTAGA_L001_R1_all


title: C1-4-C2_TAGGCATG-TATCCTCT_L001_R1_all


title: C1-4-C12_TCCTGAGC-TATCCTCT_L002_R1_all


title: EU232_NI2


title: C1-4-C11_TAAGGCGA-TATCCTCT_L002_R1_all


title: EU216_S2


title: C1-4-B9_TAGGCATG-TAGATCGC_L001_R1_all


title: EU214_S2


title: EU216_L2


title: EU216_NI2


title: C1-4-B8_AGGCAGAA-TAGATCGC_L001_R1_all


title: EU214_NI2


title: EU212_S2


title: EU224_S2


title: EU212_L2


title: C1-4-B7_GGACTCCT-AGAGTAGA_L001_R1_all


title: C1-4-B3_GGACTCCT-CTCTCTAT_L001_R1_all


title: C1-4-C8_TAAGGCGA-CTCTCTAT_L002_R1_all


title: C1-4-B5_GGACTCCT-TATCCTCT_L001_R1_all


title: EU212_NI2


title: EU210_S2


title: EU210_L2


title: C1-4-B1_GGACTCCT-TAGATCGC_L001_R1_all


title: C1-4-B4_CGTACTAG-TATCCTCT_L001_R1_all


title: EU202_S2


title: C1-4-B6_CGTACTAG-AGAGTAGA_L001_R1_all


title: EU214_L2


title: EU210_NI2


title: EU202_NI2


title: C1-4-B10_AGGCAGAA-CTCTCTAT_L001_R1_all


title: EU202_L2


title: EU200_S2


title: C1-4-B12_AGGCAGAA-TATCCTCT_L001_R1_all


title: C1-4-B11_TAGGCATG-CTCTCTAT_L001_R1_all


title: C1-4-A6_TAAGGCGA-TATCCTCT_L001_R1_all


title: EU200_L2


title: EU190_NI2


title: C1-4-A7_TCCTGAGC-TATCCTCT_L001_R1_all


title: C1-4-A4_TCCTGAGC-CTCTCTAT_L001_R1_all


title: EU200_NI2


title: EU190_S2


title: C1-4-A1_TAAGGCGA-TAGATCGC_L001_R1_all


title: EU190_L2


title: C1-4-A3_TAAGGCGA-CTCTCTAT_L001_R1_all


title: C1-4-A12_CGTACTAG-TAGATCGC_L001_R1_all


title: EU186_S2


title: C1-4-B2_CGTACTAG-CTCTCTAT_L001_R1_all


title: C1-4-A2_TCCTGAGC-TAGATCGC_L001_R1_all


title: C1-4-A10_TCCTGAGC-AGAGTAGA_L001_R1_all


title: EU186_NI2


title: C1-4-A9_TAAGGCGA-AGAGTAGA_L001_R1_all


title: EU184_S2


title: EU184_NI2


title: EU186_L2


title: EU170_S2


title: EU170_L2


title: AF55_S2


title: EU170_NI2


title: EU40_L2


title: EU168_S2


title: EU168_NI2


title: EU164_NI2


title: EU164_L2


title: EU40_NI2


title: EU162_S2


title: EU164_S2


title: EU80_NI2


title: EU80_L2


title: EU78_S2


title: EU78_NI2


title: EU56_NI2


title: EU156_NI2


title: EU152_S2


title: EU168_L2


title: EU152_NI2


title: EU78_L2


title: EU74_L2


title: EU72_S2


title: EU184_L2


title: EU162_NI2


title: EU76_S2


title: EU76_NI2


title: EU162_L2


title: EU152_L2


title: EU148_S2


title: EU76_L2


title: EU148_L2


title: EU70_NI2


title: EU156_S2


title: EU74_S2


title: AF55_L2


title: EU156_L2


title: EU74_NI2


title: EU80_S2


title: EU144_L2


title: EU68_NI2


title: EU72_L2


title: EU140_NI2


title: EU68_L2


title: EU66_NI2


title: EU64_S2


title: EU70_L2


title: EU144_S2


title: EU144_NI2


title: EU138_NI2


title: EU138_S2


title: EU68_S2


title: EU140_S2


title: EU66_S2


title: EU64_NI2


title: EU72_NI2


title: EU140_L2


title: EU64_L2


title: EU70_S2


title: EU148_NI2


title: EU56_L2


title: EU136_S2


title: EU138_L2


title: EU136_L2


title: EU136_NI2


title: EU62_L2


title: EU62_S2


title: EU60_S2


title: EU58_S2


title: EU130_L2


title: EU58_NI2


title: EU134_NI2


title: EU128_NI2


title: EU54_S2


title: EU60_NI2


title: EU130_S2


title: EU134_L2


title: EU130_NI2


title: EU128_S2


title: EU58_L2


title: EU128_L2


title: EU54_NI2


title: EU126_L2


title: EU126_S2


title: EU62_NI2


title: EU54_L2


title: EU134_S2


title: EU122_NI2


title: EU126_NI2


title: EU60_L2


title: EU50_NI2


title: EU120_S2


title: EU52_L2


title: EU50_S2


title: EU122_L2


title: EU48_S2


title: EU50_L2


title: EU120_NI2


title: EU48_L2


title: EU118_S2


title: EU46_L2


title: EU46_S2


title: EU52_S2


title: EU122_S2


title: EU42_S2


title: EU48_NI2


title: EU104_S2


title: EU110_S2


title: EU66_L2


title: EU118_NI2


title: EU34_S2


title: EU52_NI2


title: EU118_L2


title: EU110_NI2


title: EU42_NI2


title: EU110_L2


title: AF95_NI2


title: EU36_S2


title: EU104_NI2


title: AF95_L2


title: EU42_L2


title: EU36_NI2


title: EU104_L2


title: EU36_L2


title: AF93_L2


title: EU120_L2


title: AF97_S2


title: EU28_L2


title: EU28_NI2


title: AF91_S2


title: AF97_NI2


title: AF97_L2


title: EU26_S2


title: EU34_NI2


title: EU46_NI2


title: AF93_S2


title: EU30_L2


title: AF95_S2


title: EU26_NI2


title: EU30_S2


title: EU34_L2


title: AF75_S2


title: AF195_NI2


title: EU30_NI2


title: AF89_S2


title: AF193_NI2


title: EU22_S2


title: AF193_S2


title: EU22_NI2


title: EU22_L2


title: AF191_NI2


title: EU28_S2


title: EU16_NI2


title: AF191_L2


title: AF75_NI2


title: EU26_L2


title: AF93_NI2


title: EU24_S2


title: AF189_NI2


title: EU14_NI2


title: AF187_S2


title: AF75_L2


title: EU24_NI2


title: AF195_S2


title: AF189_L2


title: EU24_L2


title: AF195_L2


title: EU20_S2


title: AF193_L2


title: EU06_L2


title: AF79_S2


title: AF185_NI2


title: AF79_L2


title: EU20_NI2


title: AF77_S2


title: AF183_NI2


title: EU16_S2


title: EU14_S2


title: EU16_L2


title: AF191_S2


title: EU14_L2


title: AF77_L2


title: AF183_L2


title: EU06_S2


title: AF189_S2


title: AF71_S2


title: AF181_NI2


title: AF187_NI2


title: AF71_L2


title: AF69_S2


title: AF71_NI2


title: AF187_L2


title: EU06_NI2


title: AF79_NI2


title: AF69_NI2


title: AF185_S2


title: AF69_L2


title: AF185_L2


title: AF183_S2


title: AF177_NI2


title: AF181_L2


title: AF177_L2


title: AF179_S2


title: AF67_L2


title: AF67_NI2


title: AF175_S2


title: AF77_NI2


title: AF179_NI2


title: AF67_S2


title: AF177_S2


title: AF181_S2


title: AF175_L2


title: AF175_NI2


title: AF179_L2


title: AF65_S2


title: AF63_NI2


title: AF65_NI2


title: AF171_S2


title: AF63_L2


title: AF65_L2


title: AF173_NI2


title: AF173_S2


title: AF63_S2


title: AF173_L2


title: AF61_S2


title: AF171_NI2


title: AF61_L2


title: AF59_S2


title: AF167_NI2


title: AF167_S2


title: AF53_S2


title: AF57_L2


title: AF169_NI2


title: AF59_L2


title: AF169_L2


title: AF53_NI2


title: AF61_NI2


title: AF169_S2


title: AF57_NI2


title: AF53_L2


title: AF57_S2


title: AF165_S2


title: AF165_NI2


title: AF163_L2


title: AF171_L2


title: AF59_NI2


title: AF43_S2


title: AF165_L2


title: AF163_NI2


title: AF47_S2


title: AF159_S2


title: AF47_L2


title: AF47_NI2


title: AF41_S2


title: AF161_NI2


title: AF41_NI2


title: AF161_S2


title: AF157_NI2


title: AF167_L2


title: AF157_L2


title: AF155_S2


title: AF159_L2


title: AF39_NI2


title: AF43_L2


title: AF43_NI2


title: AF155_NI2


title: AF39_L2


title: AF157_S2


title: AF159_NI2


title: AF41_L2


title: AF37_S2


title: AF155_L2


title: AF37_NI2


title: AF39_S2


title: AF163_S2


title: AF153_NI2


title: AF37_L2


title: AF161_L2


title: AF153_S2


title: AF31_S2


title: AF35_NI2


title: AF153_L2


title: AF31_NI2


title: AF149_NI2


title: AF149_S2


title: AF31_L2


title: AF35_L2


title: AF29_S2


title: AF151_S2


title: AF151_L2


title: AF29_NI2


title: AF149_L2


title: AF147_L2


title: AF145_S2


title: AF29_L2


title: AF147_NI2


title: AF27_S2


title: AF27_NI2


title: AF145_NI2


title: AF27_L2


title: AF25_S2


title: AF25_NI2


title: AF35_S2


title: AF151_NI2


title: AF143_S2


title: AF25_L2


title: AF143_NI2


title: AF23_S2


title: AF145_L2


title: AF143_L2


title: AF23_NI2


title: AF141_S2


title: AF147_S2


title: AF141_NI2


title: AF21_S2


title: AF141_L2


title: AF19_S2


title: AF139_NI2


title: AF21_NI2


title: AF139_L2


title: AF19_NI2


title: AF137_S2


title: AF17_S2


title: AF137_NI2


title: AF23_L2


title: AF139_S2


title: AF17_NI2


title: AF17_L2


title: AF137_L2


title: AF133_S2


title: AF19_L2


title: AF11_S2


title: AF133_NI2


title: AF133_L2


title: AF11_L2


title: AF11_NI2


title: AF21_L2


title: AF131_S2


title: AF131_L2


title: AF129_S2


title: EU80_S2 (mRNA)

data_processing:
Adaptor sequences and low quality score bases (Phred score<20) were first trimmed usingTrim Galore (version 0.2.7).The resulting reads were then mapped to the human genome reference sequence using TopHat (version 2.0.6) and using a hg19 transcript annotation database downloaded from UCSC (downloaded on 2011-08-30).
Gene-level expression estimates were calculated using featureCounts (version 1.4.6). Transcript-level expression values were obtained using RSEM.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file containing expression count values for genes.
Supplementary_files_format_and_content: Tab-delimited text file containing expression count values for transcripts.

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation.  Monocytes were puri-fied from peripheral blood mononuclear cells by positive selection with magnetic CD14 Mi-croBeads (Miltenyi Biotech). Monocytes were then cultured for 7 days in RPMI-1640 (Fisher)supplemented with 10% heat-inactivated FBS (FBS premium, US origin, Wisent), L-glutamine(Fisher) and M-CSF (20ng/mL; R&D systems). Cell cultures were fed every 2 days with com-plete medium supplemented with the cytokines previously mentioned.   Before infection,  wechecked the differentiation/activation status of the monocyte-derived macrophages by flow cy-tometry, using antibodies against CD1a, CD14, CD83, and HLA-DR (BD Biosciences).  Onlysamples presenting the expected phenotype for non-activated macrophages (CD1a+, CD14+,CD83,  and  HLA-DRlow)  were  used  in  downstream  experiments

extract_protocol:
Total RNA was extracted from the non-infected and infected macrophages using the miRNeasykit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the quality was assessedwith the Agilent 2100 Bioanalyzer (Agilent Technologies).   Only samples with no evidencefor RNA degradation (RNA integrity number>8) were kept for further experiments.
RNA-sequencing libraries were prepared using the Illumina TruSeq protocol.
Indexed cDNA libraries were pooled (6 libraries per pool) in equimolar amounts and were sequenced with single-end 100bp reads.

treatment_protocol: Monocyte-derived macrophages were infected at a multiplicity of infection (MOI) of 10:1 forSalmonellatyphimuriumand an MOI of 5:1 forListeria monocytogenes.  A control group of non-infectedmacrophages was treated the same way but with only medium without bacteria.


title: EU80_NI2 (mRNA)


title: AF129_NI2


title: AF129_L2


title: EU80_L2 (mRNA)


title: EU78_NI2 (mRNA)


title: EU78_S2 (mRNA)


title: EU78_L2 (mRNA)


title: AF127_S2


title: EU76_NI2 (mRNA)


title: EU76_S2 (mRNA)


title: AF127_L2


title: AF127_NI2


title: EU74_S2 (mRNA)


title: EU72_S2 (mRNA)


title: AF119_L2


title: AF125_NI2


title: AF125_L2


title: EU74_NI2 (mRNA)


title: EU76_L2 (mRNA)


title: EU74_L2 (mRNA)


title: AF115_NI2


title: AF119_S2


title: AF119_NI2


title: AF115_L2


title: AF131_NI2


title: EU72_L2 (mRNA)


title: EU68_S2 (mRNA)


title: EU70_S2 (mRNA)


title: AF115_S2


title: AF113_L2


title: AF117_S2


title: AF117_NI2


title: EU70_L2 (mRNA)


title: EU66_S2 (mRNA)


title: AF113_S2


title: AF113_NI2


title: AF111_L2


title: EU70_NI2 (mRNA)


title: AF125_S2


title: EU64_NI2 (mRNA)


title: EU68_L2 (mRNA)


title: EU66_NI2 (mRNA)


title: AF111_NI2


title: EU72_NI2 (mRNA)


title: EU62_S2 (mRNA)


title: EU62_NI2 (mRNA)


title: AF107_S2


title: EU64_S2 (mRNA)


title: EU66_L2 (mRNA)


title: AF109_L2


title: EU64_L2 (mRNA)


title: AF111_S2


title: EU68_NI2 (mRNA)


title: AF109_NI2


title: AF109_S2


title: EU62_L2 (mRNA)


title: EU60_NI2 (mRNA)


title: AF107_NI2


title: AF105_S2


title: EU60_L2 (mRNA)


title: AF105_L2


title: EU58_S2 (mRNA)


title: AF101_NI2


title: EU54_S2 (mRNA)


title: AF101_L2


title: EU52_L24 (mRNA)

value: 24 hr


title: EU58_L2 (mRNA)


title: EU66_L24 (mRNA)


title: AF107_L2


title: EU306_L24 (mRNA)


title: EU34_L24 (mRNA)


title: EU302_L24 (mRNA)


title: AF105_NI2


title: EU52_NI2 (mRNA)


title: EU54_L2 (mRNA)


title: EU60_S2 (mRNA)


title: EU52_L2 (mRNA)


title: EU66_NI24 (mRNA)


title: EU50_NI2 (mRNA)


title: EU28_L24 (mRNA)


title: EU50_S2 (mRNA)


title: EU50_L2 (mRNA)


title: EU52_NI24 (mRNA)


title: EU48_NI2 (mRNA)


title: EU52_S2 (mRNA)


title: EU48_S2 (mRNA)


title: AF101_S2


title: EU58_NI2 (mRNA)


title: EU48_L2 (mRNA)


title: EU302_NI24 (mRNA)


title: EU34_NI24 (mRNA)


title: EU54_NI2 (mRNA)


title: EU66_S24 (mRNA)


title: EU46_NI2 (mRNA)


title: EU42_S2 (mRNA)


title: EU46_L2 (mRNA)


title: EU306_S24 (mRNA)


title: EU36_S2 (mRNA)


title: EU42_NI2 (mRNA)


title: EU306_S2 (mRNA)


title: EU36_NI2 (mRNA)


title: EU28_S24 (mRNA)


title: EU36_L2 (mRNA)


title: EU306_NI2 (mRNA)


title: EU306_L2 (mRNA)


title: EU34_NI2 (mRNA)


title: EU302_S2 (mRNA)


title: EU306_NI24 (mRNA)


title: GEK69

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: total RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Jatropha curcas

source_name: immature seeds

growth_protocol: Jatropha curcas plants were grown in an open environment (15°16'16.68"S 39°05'34.50"W). Flowers were tagged upon opening and fruits from different plants were collected in the middle of a light cycle at 40 to 60 days after flower opening (DAF) (mature seeds). The seeds were dissected from the fruits and immediately frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing and sequencing by Illumina HiSeq2000. Three libraries were generated from immature, intermediate and mature seeds. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.

tag: sample

value: pool

tag: daf

tag: tissue

value: seeds


title: GEK89

description: total RNA

source_name: mature seeds


title: GEK87

description: total RNA

source_name: intermediate seeds


title: EU28_NI24 (mRNA)


title: EU302_NI2 (mRNA)


title: EU46_S2 (mRNA)


title: EU302_L2 (mRNA)


title: EU52_S24 (mRNA)


title: EU34_S24 (mRNA)


title: EU186_S2 (mRNA)


title: EU42_L2 (mRNA)


title: EU302_S24 (mRNA)


title: EU30_L2 (mRNA)


title: EU30_NI2 (mRNA)


title: EU186_NI2 (mRNA)


title: EU34_S2 (mRNA)


title: EU26_S2 (mRNA)


title: EU186_L2 (mRNA)


title: EU66_S24 (miRNA)

data_processing:
After demultiplexing, sequences matching the 30 adaptor sequence were identified and trimmed.A minimum matching of the 6 first bases of the adaptor sequence was required, following which we discarded all reads shorter than 16 or longer than 26 bases,  corresponding to the known length distribution of mammalian miRNAs.
Sequences were aligned to the human reference genome (build GRCh37/hg19) using bowtie (v0.12.7) ( (13)) allowing for 2 mismatches (-v 2) and reported all best alignments for reads that mapped equally well to more than one genomic location (-a best strata).
We suppressed reads with more than 50 possible alignments (-m 50). On average, 96% of reads aligned to the human genome, of which 60% aligned uniquely. The remaining40% of reads had more than one best alignment, which is expected given that miRNAs are short and tend to occur in families that share highly similar sequences. To avoid cross-mapping artefacts, we used a correction strategy that assigns weights to each of the candidate mapping loci of multiply aligning reads.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file containing corrected expression count values for miRNAs.

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation.  Monocytes were purified from peripheral blood mononuclear cells by positive selection with magnetic CD14 Mi-croBeads (Miltenyi Biotech). Monocytes were then cultured for 7 days in RPMI-1640 (Fisher)supplemented with 10% heat-inactivated FBS (FBS premium, US origin, Wisent), L-glutamine(Fisher) and M-CSF (20ng/mL; R&D systems). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned.   Before infection,  we checked the differentiation/activation status of the monocyte-derived macrophages by flow cytometry, using antibodies against CD1a, CD14, CD83, and HLA-DR (BD Biosciences).  Only samples presenting the expected phenotype for non-activated macrophages (CD1a+, CD14+,CD83,  and  HLA-DRlow)  were  used  in  downstream  experiments

extract_protocol:
Total RNA was extracted from the non-infected and infected macrophages using the miRNeasykit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the quality was assessedwith the Agilent 2100 Bioanalyzer (Agilent Technologies).   Only samples with no evidence for RNA degradation (RNA integrity number>8) were kept for further experiments.
miRNA libraries were prepared using the Illumina TruSeq Small RNA library protocol.
We multiplexed 36 libraries per lane and sequenced the pool in two lanes with single-end 100bp reads

treatment_protocol: Monocyte-derived macrophages were infected at a multiplicity of infection (MOI) of 10:1 for Salmonellatyphimuriumand an MOI of 5:1 for Listeria monocytogenes.  A control group of non-infected macrophages was treated the same way but with only medium without bacteria.


title: EU34_S24 (miRNA)


title: EU34_L2 (mRNA)


title: EU28_S2 (mRNA)


title: EU52_S24 (miRNA)


title: EU28_NI2 (mRNA)


title: EU24_S2 (mRNA)


title: EU24_NI2 (mRNA)


title: EU28_L2 (mRNA)


title: EU26_NI2 (mRNA)


title: EU26_L2 (mRNA)


title: EU302_S24 (miRNA)


title: EU66_S2 (miRNA)


title: EU306_S24 (miRNA)


title: EU30_S2 (mRNA)


title: EU28_S24 (miRNA)


title: EU24_L2 (mRNA)


title: EU52_S2 (miRNA)


title: EU22_S2 (mRNA)


title: EU34_S2 (miRNA)


title: EU22_L2 (mRNA)


title: EU22_NI2 (mRNA)


title: EU20_S2 (mRNA)


title: EU306_S2 (miRNA)


title: EU302_S2 (miRNA)


title: EU28_S2 (miRNA)


title: EU20_NI2 (mRNA)


title: EU34_NI24 (miRNA)


title: EU66_NI24 (miRNA)


title: EU16_NI2 (mRNA)


title: EU14_S2 (mRNA)


title: EU66_NI2 (miRNA)


title: EU302_NI24 (miRNA)


title: EU16_L2 (mRNA)


title: EU28_NI24 (miRNA)


title: EU16_S2 (mRNA)


title: EU52_NI2 (miRNA)


title: EU14_NI2 (mRNA)


title: EU306_NI24 (miRNA)


title: AF79_S2 (mRNA)


title: EU06_L2 (mRNA)


title: EU14_L2 (mRNA)


title: EU306_NI2 (miRNA)


title: EU34_NI2 (miRNA)


title: EU06_S2 (mRNA)


title: EU06_NI2 (mRNA)


title: EU302_NI2 (miRNA)


title: EU28_NI2 (miRNA)


title: AF79_NI2 (mRNA)


title: EU66_L24 (miRNA)


title: EU52_L24 (miRNA)


title: AF79_L2 (mRNA)


title: AF77_S2 (mRNA)


title: EU34_L24 (miRNA)


title: EU52_NI24 (miRNA)


title: AF77_NI2 (mRNA)


title: EU20_L2 (mRNA)


title: EU302_L24 (miRNA)


title: EU28_L24 (miRNA)


title: EU306_L24 (miRNA)


title: EU66_L2 (miRNA)


title: AF71_NI2 (mRNA)


title: AF71_S2 (mRNA)


title: EU52_L2 (miRNA)


title: AF77_L2 (mRNA)


title: EU34_L2 (miRNA)


title: EU302_L2 (miRNA)


title: EU306_L2 (miRNA)


title: AF69_NI2 (mRNA)


title: AF71_L2 (mRNA)


title: AF69_L2 (mRNA)


title: AF69_S2 (mRNA)


title: AF67_NI2 (mRNA)


title: EU28_L2 (miRNA)


title: AF67_S2 (mRNA)


title: AF65_S2 (mRNA)


title: AF65_NI2 (mRNA)


title: AF67_L2 (mRNA)


title: AF65_L2 (mRNA)


title: AF63_NI2 (mRNA)


title: fus3-3 mutant Arabidopsis seed 17daf

city: Irapuato

first: Sandra

middle: Isabel

last: Gonzalez-Morales

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: LANGEBIO

country: Mexico

institute: CINVESTAV

data_processing:
The SOLiD BioScope Whole Transcriptome Analysis (WTA) version 1.2.1 pipeline for single reads was used to align the reads to the Col-0 reference genome TAIR10
Two perfect matches per location were allowed, count aligned reads per exon, and calculate per base coverage. WTA pipeline CountTags module provides normalize RPKM (reads per kilobase of exon sequence, per million reads) values along with read counts per exon. Using BASH and MySQL scrips were calculated the gene counts per gene model
Gene counts were normalized using edgeR’s TMM [trimmed mean M (¼ log fold-change gene expression)] algorithm
Genome_build: TAIR 10
Supplementary_files_format_and_content: counts_libraries_matrix.csv: raw counts of sequencing reads
Supplementary_files_format_and_content: cpm_normalized_edgeR.csv: normalized counts of sequencing reads

organism: Arabidopsis thaliana

source_name: seed

growth_protocol: Plants of A. thaliana were grown in a sterile mix of vermiculite and soil in a growth chamber at 22 °C with a 16-h photoperiod at 200 mmol m2 s.  the flowers were marked, and at given time intervals following anthesis (15, 17 and 21 DAF), siliques were collected from 24 plants, seeds were dissected, immediately frozen in liquid nitrogen, and stored at -80°C. Samples were collected in triplicates

extract_protocol:
For RNA-Seq total RNA was isolated using the TRIZOL reagent (Invitrogen) according to the manufacturer's instructions and further purificated using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions.
Five μg of RNA from each experimental condition was pooled to obtain a single RNA sample. First and second strand cDNA synthesis was performed with 3 μg of the total RNA mixture using Message Amp-II kit (Ambion) following the manufacturers recommendations. Each sample was treated separately 10-12 ng of synthesized cDNA was amplified by in vitro transcription and the resulting 70-90 μg of antisense RNA (aRNA) purified using RNAeasy columns (Qiagen). A second round of cDNA synthesis was performed using the mRNA as template (20 μg). cDNA synthesis was performed as described above except that random primers (mostly hexamers) were used at the first strand synthesis stage. This procedure yielded approximately 10 μg of cDNA that was purified using the DNA Clear Kit for cDNA purification (Ambion). Samples were barcoded for multiplexing using the SOLiD RNA Barcoding Kit

tag: genotype/variation

value: fus3-3 mutant Arabidopsis seed 17daf

tag: ecotype

value: Columbia 0

tag: developmental stage

tag: phenotype

value: Desiccation intolerant seed


title: col0 ecotype Arabidospsis seed 15daf

value: Wildtype

value: Desiccation tolerant seed


title: fus3-3 mutant Arabidopsis seed 21daf

value: fus3-3 mutant Arabidopsis seed 21daf


title: fus3-3 mutant Arabidopsis seed 15daf

value: fus3-3 mutant Arabidopsis seed 15daf


title: col0 ecotype Arabidospsis seed 21daf


title: abi3-1 mutant Arabidopsis seed 21daf

value: abi3-1 mutant Arabidopsis seed 21daf

value: Landsberg erecta


title: AF63_L2 (mRNA)

value: macrophage


title: abi3-1 mutant Arabidopsis seed 15daf

value: abi3-1 mutant Arabidopsis seed 15daf


title: abi3-5 mutant Arabidopsis seed 21daf

value: abi3-5 mutant Arabidopsis seed 21daf


title: AF61_S2 (mRNA)

value: Salmonella

value: 2 hr


title: AF59_S2 (mRNA)


title: Ler ecotype Arabidopsis seed 21daf


title: AF61_L2 (mRNA)

value: Listeria


title: AF59_L2 (mRNA)


title: abi3-5 mutant Arabidopsis seed 15daf

value: abi3-5 mutant Arabidopsis seed 15daf


title: AF59_NI2 (mRNA)

value: Non-infected


title: AF61_NI2 (mRNA)


title: AF57_S2 (mRNA)


title: Ler ecotype Arabidopsis seed 17daf


title: AF63_S2 (mRNA)


title: Ler ecotype Arabidopsis seed 15daf


title: lec2-1 mutant Arabidopsis seed 21daf

value: lec2-1 mutant Arabidopsis seed 21daf

value: Wassilewskija


title: lec2-1 mutant Arabidopsis seed 17daf

value: lec2-1 mutant Arabidopsis seed 17daf


title: AF57_L2 (mRNA)


title: AF57_NI2 (mRNA)


title: col0 ecotype Arabidospsis seed 17daf

value: Wildtype

value: Columbia 0


title: AF53_S2 (mRNA)


title: lec2-1 mutant Arabidopsis seed 15daf

value: lec2-1 mutant Arabidopsis seed 15daf

value: Desiccation tolerant seed


title: abi3-1 mutant Arabidopsis seed 17daf

value: abi3-1 mutant Arabidopsis seed 17daf

value: Desiccation intolerant seed


title: lec1-1 mutant Arabidopsis seed 21daf

value: lec1-1 mutant Arabidopsis seed 21daf


title: AF53_L2 (mRNA)

value: macrophage


title: lec1-1 mutant Arabidopsis seed 15daf

value: lec1-1 mutant Arabidopsis seed 15daf


title: AF53_NI2 (mRNA)


title: Ws ecotype Arabidopsis seed 21daf


title: AF49_NI2 (mRNA)


title: abi3-5 mutant Arabidopsis seed 17daf

value: abi3-5 mutant Arabidopsis seed 17daf

value: Landsberg erecta


title: Ws ecotype Arabidopsis seed 17daf


title: AF49_S2 (mRNA)

value: Salmonella

value: 2 hr


title: AF49_L2 (mRNA)

value: Listeria


title: Ws ecotype Arabidopsis seed 15daf


title: AF47_S2 (mRNA)


title: wt_UF.rep3

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: small RNA

data_processing:
Illumina CASAVA-1.8.2 software used for basecalling.
Prior to read mapping, small-RNA reads were processed using the FASTX-Toolkit to demultiplex, remove adaptor sequences (CTGTAGGCACCATCAAT) and the first 4 bases (corresponding to random barcode).
Sequence quality reads (phred quality  ≥ 20 in 100% of nucleotides), reads length (18-30 nt) were filted. Fastq files were collapsed to fasta files.
Filtered reads were mapped to Drosophila Genome Release 5.50 using Bowtie 0.12.8 with parameters -f -v 0  --best --sam --al.
Genome_build: flybase: dmel-all-chromosome-r5.50
Supplementary_files_format_and_content: tab-delimited text file of sequence that were trimmed adaptor and the first 4 bases (corresponding to barcode), all bases quality score ≥ 20 for each Sample. Sequence count included.

organism: Drosophila melanogaster

source_name: unfertilized eggs

growth_protocol: Flies were kept at 25ºC with 12 hours light/dark cycles

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol. The small-RNA fraction was isolated from the total RNA sample using a modification protocol of mirVana™ (MirVANA kit, Invitrogen) as Gu et al Methods Mol Biol 2011, 725:251
2S rRNA depletion using a protocol from Seitz H et al, Curr Biol 2008, 18:147
RNA libraries were prepared for sequencing using a protocol from Gu et al Methods Mol Biol 2011, 725:251.

value: unfertilized eggs

tag: time-window

tag: genotype

value: gfp-vas,Pr Dr/TM3


title: AF45_NI2 (mRNA)

value: Non-infected


title: wt_UF.rep2

description: small RNA


title: wt2_4h.rep3

description: small RNA

source_name: embryos

value: embryos


title: wt_UF.rep1

description: small RNA


title: AF47_NI2 (mRNA)


title: AF47_L2 (mRNA)


title: wt2_4h.rep2

description: small RNA


title: AF45_L2 (mRNA)


title: AF45_S2 (mRNA)


title: AF43_S2 (mRNA)


title: lec1-1 mutant Arabidopsis seed 17daf

value: lec1-1 mutant Arabidopsis seed 17daf

value: Wassilewskija


title: wt0_2h.rep2

description: small RNA


title: AF43_L2 (mRNA)


title: AF43_NI2 (mRNA)


title: smg_UF.rep3

description: small RNA


title: AF41_S2 (mRNA)


title: AF41_NI2 (mRNA)


title: smg_UF.rep1

description: small RNA


title: smg2_4h.rep3

description: small RNA


title: AF39_NI2 (mRNA)


title: smg_UF.rep2

description: small RNA


title: smg2_4h.rep2

description: small RNA


title: AF39_L2 (mRNA)


title: AF37_S2 (mRNA)


title: smg2_4h.rep1

description: small RNA


title: wt2_4h.rep1

description: small RNA


title: wt0_2h.rep3

description: small RNA


title: smg0_2h.rep3

description: small RNA


title: AF37_NI2 (mRNA)


title: smg0_2h.rep1

description: small RNA


title: AF35_S2 (mRNA)


title: smg0_2h.rep2

description: small RNA


title: AF35_NI2 (mRNA)


title: AF35_L2 (mRNA)


title: AF31_S2 (mRNA)


title: AF31_NI2 (mRNA)


title: wt0_2h.rep1

description: small RNA


title: AF39_S2 (mRNA)


title: AF31_L2 (mRNA)


title: DNase I 0h glucose

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: processed data file: DNase_peakfile.txt

library_source: genomic

data_processing:
alignment: DNase-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
peakdetection, quantification and visualization: Mapped DNAse-seq reads were peak detected and quantified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589). Tag directories were generated by calling makeTagDirectory (only including 1 tag pr bp, parameter: -tbp 1), and peak detection was performed  using findPeaks -style factor (FDR ≤ 0. 1%). Peak locations and normalized counts (Pr. 10 M reads) for each condition  are provided in DNAse_peakfile.txt. BedGraph files for visualization were generated using makeUCSCfile.
Genome_build: rn5

molecule: genomic DNA

organism: Rattus norvegicus

source_name: β-cell_DNase I 0h glucose

growth_protocol: INS-1E cells were cultured in  RPMI 1640 w. 11 mM glucose supplemented with 5% Heat inactivated FCS, 50 uM β-MeOH, 1mM NaPyruvate, and 100 U/ml Penicilin + 100 mg/ml streptomycin. Cells were used between passages 60 and 90

extract_protocol:
DNase-seq was performed on ~10 mill. nuclei essentially as described in (Siersbaek et al. 2011, EMBO J, 30: 1459-1472.).
RNA-, DNase-, and ChIP-seq libraries were constructed using PentAdapters (Pentabase) essentially as previously described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Prior to exposure to high (25 mM) glucose, cells were preincubated with 5 mM glucose medium for 24 h. Time course experiments were performed in a reverse manner, i.e. medium was changed on all cells at time point 0 h, where after 25 mM glucose was added to the medium at consecutive time points and all cells were harvested at the 12 h time point.

tag: cell line

value: beta-cell


title: DNase I 12h glucose

description: processed data file: DNase_peakfile.txt

source_name: β-cell_DNase I 12h glucose


title: AF29_S2 (mRNA)


title: Input 12h

data_processing:
alignment: ChIP-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
peakdetection, quantification and visualization: BedGraph files for visualization were generated using makeUCSCfile.
Genome_build: rn5

source_name: β-cell_Input 12h

extract_protocol:
ChIP experiments were performed according to standard protocol as described in (Siersbæk et al. 2012, MCB, 32: 3452-3463)
RNA-, DNase-, and ChIP-seq libraries were constructed using PentAdapters (Pentabase) essentially as previously described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).


title: Input 0h

source_name: β-cell_Input 0h


title: AF29_NI2 (mRNA)


title: ChREBP 12h glucose B

description: processed data file: ChREBP_peakfile.txt

data_processing:
alignment: ChIP-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
peakdetection, quantification and visualization: Mapped ChREBP ChIP-seq reads were peak detected and quantified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589). Tag directories were generated by calling makeTagDirectory (only including 1 tag pr bp, parameter: -tbp 1), and peak detection was performed on pooled libraries of replicate experiments using findPeaks -style factor (FDR ≤ 0. 1%). Individual ChREBP peak files were subsequently merged using mergePeaks, and reads within 500 bp around the center of each peak were quantified for each replicate and each condition using annotatePeaks.pl. Peak locations and normalized counts (Pr. 10 M reads) for each condition and replicate are provided in ChREBP_peakfile.txt. BedGraph files for visualization were generated using makeUCSCfile.
Genome_build: rn5

source_name: β-cell_ChREBP 12h glucose

tag: chip-antibody

value: anti-ChREBP (NB400-135, Novus Biologicals)


title: ChREBP 12h glucose A


title: AF29_L2 (mRNA)


title: ChREBP 2h glucose B

source_name: β-cell_ChREBP 2h glucose


title: DNase I 2h glucose

description: processed data file: DNase_peakfile.txt

source_name: β-cell_DNase I 2h glucose


title: AF37_L2 (mRNA)


title: AF27_NI2 (mRNA)


title: Input 2h

source_name: β-cell_Input 2h


title: ChREBP 2h glucose A


title: ChREBP 0h glucose A

source_name: β-cell_ChREBP 0h glucose


title: AF27_L2 (mRNA)


title: AF25_S2 (mRNA)


title: ChREBP 0h glucose B


title: MED1 12h glucose B

description: processed data file: MED1_peakfile.txt

data_processing:
alignment: ChIP-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
peakdetection, quantification and visualization: Mapped MED1 ChIP-seq reads were peak detected and quantified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589). Tag directories were generated by calling makeTagDirectory (only including 1 tag pr bp, parameter: -tbp 1), and peak detection was performed on pooled libraries of replicate experiments using findPeaks -style factor (FDR ≤ 0. 1%). Individual MED1 peak files were subsequently merged using mergePeaks, and reads within 500 bp around the center of each peak were quantified for each replicate and each condition using annotatePeaks.pl. Peak locations and normalized counts (Pr. 10 M reads) for each condition and replicate are provided in MED1_peakfile.txt. BedGraph files for visualization were generated using makeUCSCfile.
Genome_build: rn5

source_name: β-cell_MED1 12h glucose

value: anti-MED1 (M-255, sc-8998, Santa Cruz)


title: AF25_NI2 (mRNA)

source_name: Macrophages


title: HDAC3-KO_rest_ZT10_GROseq

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

description: nascent RNA

data_processing:
Library strategy: GRO-Seq
Bowtie 1 was used to align GRO-seq samples to mm9 genome, followed by generation of tag directories and ucsc visualization tracks using HOMER, and enhancer-RNA calling using a custom script.
Genome_build: mm9

organism: Mus musculus

source_name: quadriceps muscle

growth_protocol: C57BL/6 mice were grown on normal chow on normal light/dark schedule

extract_protocol:
DNA or RNA is extracted using Qiagen kits
Library contruction follows illumina kits

treatment_protocol: no specific treatment was performed

tag: strain

value: 4-months old

tag: gender

value: male

value: HDAC3 Knock-out


title: MED1 12h glucose A

description: processed data file: MED1_peakfile.txt


title: AF25_L2 (mRNA)

tag: individual

value: macrophage


title: WT_rest_ZT10_GROseq

description: nascent RNA

tag: age

value: HDAC3 Wild-type


title: AF23_S2 (mRNA)

tag: cell type

tag: infection

value: Salmonella


title: HDAC3-KO_rest_ZT10_rep3_RNAseq

data_processing:
Tophat 2 was used to align RNA-seq samples to mm9 genome, followed by cuffdiff to measure normalized abundance and differential gene expression.
Genome_build: mm9


title: HDAC3-KO_rest_ZT10_rep2_RNAseq


title: MED1 0h glucose B

description: processed data file: MED1_peakfile.txt

source_name: β-cell_MED1 0h glucose


title: AF23_L2 (mRNA)

tag: time

value: 2 hr


title: MED1 2h glucose A

description: processed data file: MED1_peakfile.txt

source_name: β-cell_MED1 2h glucose


title: HDAC3-KO_rest_ZT10_rep1_RNAseq


title: AF27_S2 (mRNA)


title: MED1 2h glucose B

description: processed data file: MED1_peakfile.txt


title: AF21_S2 (mRNA)


title: AF23_NI2 (mRNA)


title: WT_rest_ZT10_rep3_RNAseq


title: WT_rest_ZT10_rep2_RNAseq


title: AF21_NI2 (mRNA)


title: RNA siBHLHE40 12h glucose C

description: processed data file: Knockdowns_exon.txt

data_processing:
alignment: RNA-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
quantification: mRNA-seq coverage within  exons of Ensembl (Rnor_5.0) genes were quantified  using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40), to asses mature transcript levels. EdgeR normalized readcounts are provided in  Knockdowns_exon.txt
Genome_build: rn5

source_name: β-cell_RNA siBHLHE40 12h glucose

extract_protocol:
Following Isol-RNA lysis Reagent® (5-Prime) extraction and EconoSpin (Epoc Life) column purification of total RNA, polyadenylated RNA was isolated using poly-dT beads and RNA fragmentation and cDNA synthesis was performed according to the manufacturers (Truseq 2® , Illumina) instructions.
RNA-, DNase-, and ChIP-seq libraries were constructed using PentAdapters (Pentabase) essentially as previously described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: One day prior to transfection INS-1E cells were seeded in antibiotic-free culture medium at a density of 800.000 cells/cm2. A transfection mix (750nM siRNA and 5% v/v DharmaFECT (Thermo) prepared in serum- and antibiotic-free OptiMEM media (Gibco) was added to the cells in a 1:5 ratio. The following day, the media was changed to standard RPMI, and the cells were incubated for 2 days and then switched to 5mM glucose medium for 24 h before exposure to (25 mM) or low (5mM) glucose for 12 h.


title: WT_rest_ZT10_rep1_RNAseq


title: MED1 0h glucose A

description: processed data file: MED1_peakfile.txt


title: RNA siBHLHE40 0h glucose C

source_name: β-cell_RNA siBHLHE40 0h glucose


title: RNA siATF4 0h glucose C

source_name: β-cell_RNA siATF4 0h glucose


title: RNA siATF4 12h glucose C

source_name: β-cell_RNA siATF4 12h glucose


title: AF19_S2 (mRNA)


title: AF19_NI2 (mRNA)


title: Input ChIP-seq at ZT22 (Wild Type)

data_processing:
Bowtie 1 was used to align ChIP-seq samples to mm9 genome, followed by peak-calling and generation of ucsc visualization files using HOMER.
Genome_build: mm9

tag: antibody

value: none (input)


title: Input ChIP-seq at ZT10 (HDAC3 Knock-out)


title: RNA siGATA4 12h glucose C

source_name: β-cell_RNA siGATA4 12h glucose


title: AF17_S2 (mRNA)


title: AF19_L2 (mRNA)

value: Listeria


title: RNA siGATA4 0h glucose C

source_name: β-cell_RNA siGATA4 0h glucose


title: HDAC3 ChIP-seq at ZT10 (HDAC3 Knock-out)


title: HDAC3 ChIP-seq at ZT22 (Wild Type)


title: RNA siMYCN 12h glucose C

source_name: β-cell_RNA siMYCN 12h glucose


title: HDAC3 ChIP-seq at ZT10 (Wild Type)


title: AF41_L2 (mRNA)


title: AF17_L2 (mRNA)


title: RNA siMYCN 0h glucose C

source_name: β-cell_RNA siMYCN 0h glucose


title: AF17_NI2 (mRNA)


title: AF11_S2 (mRNA)


title: RNA siRORC 12h glucose A

source_name: β-cell_RNA siRORC 12h glucose


title: RNA siRORC 0h glucose C

source_name: β-cell_RNA siRORC 0h glucose


title: Adiponectin-cre Nova2flox/flox 9

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing: GEO'S REQUEST FOR PROCESSED DATA WAS DENIED

source_name: eWAT 24 week-old male mouse

growth_protocol: 8-week old male mice were fed with a chow diet for 16 weeks.

extract_protocol: Total RNA was extracted using the RNAeasy kit (Qiagen), including the DNaseI treatment.

treatment_protocol: Mice were fasted overnight

value: 24 week-old

tag: tissue

value: Epididymal adipose tissue

tag: diet

value: Control Chow diet


title: AF11_L2 (mRNA)


title: Input ChIP-seq at ZT10 (Wild Type)

tag: genotype/variation


title: Adiponectin-cre Nova2flox/flox 8


title: WT Group_PFC_Rep_2

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

institute: University of Virginia

data_processing:
Base calling an quality scoring performed by real-Time Analysis (RTA) v2.
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Reads were splice-aware aligned to the UCSC mm9 genome using STAR.
Reads overlapping UCSC mm9 gene regions were counted using featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: Prefrontal cortex

growth_protocol: C57BL/6J mice 8 weeks old

extract_protocol:
RNA was isolated using RNAeasy mini kit (Qiagen)
cDNA library was generated with a TruSeq Stranded mRNA Library Prep Kit (Illumina) with Agencourt AMPure XP beads for PCR cleanup.

treatment_protocol: 6 days group or single housed

value: prefrontal cortex

value: 8-10 weeks

value: wild type

tag: housing

value: group


title: Adiponectin-cre Nova2flox/flox 7


title: Adiponectin-cre Nova1flox/flox 5


title: Adiponectin-cre Nova1flox/flox 6


title: WT Group_PFC_Rep_3


title: RNA siRORC 0h glucose A

value: beta-cell


title: WT Group_PFC_Rep_1


title: RNA siChREBP 12h glucose B

source_name: β-cell_RNA siChREBP 12h glucose


title: Adiponectin-cre Nova1flox/flox 4


title: Adiponectin-cre Wild type 3

value: Wild type


title: WT Isolated_PFC_Rep_3

value: single


title: RNA siRORC 12h glucose C


title: RNA siChREBP 0h glucose B

source_name: β-cell_RNA siChREBP 0h glucose


title: RNA siChREBP 12h glucose A


title: AF11_NI2 (mRNA)

source_name: Macrophages

value: Non-infected


title: RNA siChREBP 0h glucose A


title: Adiponectin-cre Wild type 2

value: male


title: Adiponectin-cre Nova1flox/floxNova2flox/flox 23

growth_protocol: 8-week old male mice were fed with a chow or a high fat diet for 16 weeks.

value: High fat diet 16 week

value: Nova1- and Nova2-deficient


title: WT Isolated_PFC_Rep_1


title: RNA siCtrl 12h glucose C

source_name: β-cell_RNA siCtrl 12h glucose


title: RNA siCtrl 12h glucose B


title: Adiponectin-cre Nova1flox/floxNova2flox/flox 22


title: RNA siCtrl 12h glucose A


title: Adiponectin-cre Nova1flox/floxNova2flox/flox 21


title: mRNA_adult_heart_mm771_A7060_wtwt_female

city: Berkeley

first: Diane

last: Dickel

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

data_processing:
Basecalls performed using CASAVA
Reads were filtered cutadapt and aligned to the mm9 genome assembly using tophat
Genome_build: mm9
Supplementary_files_format_and_content: fpkm values of genes calculated by cufflinks

growth_protocol: Mice were maintained in an animal facilty under standard conditions.

extract_protocol:
Total RNA was extracted with TRIzol Reagent and physical homogenization
Ambion TURBO DNase treatment, Illumina TruSeq Stranded mRNA Sample Prep (according to manuf. protocol)

treatment_protocol: None.  WT and KO mice were not subjected to any treatment.

value: mixed 129S6 and C57BL/6J

value: wild-type (WT)

value: female

value: adult

tag: mouse line

value: mm771 line

value: ventricular portion of heart


title: mRNA_adult_heart_mm771_A7062_koko_female

value: mm771 KO


title: mRNA_adult_heart_mm771_A7063_koko_female


title: RNA siCtrl 0h glucose B

source_name: β-cell_RNA siCtrl 0h glucose


title: RNA siCtrl 0h glucose A

extract_protocol:
Following Isol-RNA lysis Reagent® (5-Prime) extraction and EconoSpin (Epoc Life) column purification of total RNA, contaminant genomic DNA was removed from purified total RNA by TURBO® DNase digestion (Life Technologies), and ribosomal RNAs were removed using the Ribo-Zero® Human/Mouse/Rat kit (Epicentre). RNA fragmentation and cDNA synthesis was performed according to the manufacturers (Truseq 2® , Illumina) instructions.
RNA-, DNase-, and ChIP-seq libraries were constructed using PentAdapters (Pentabase) essentially as previously described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: One day prior to transfection INS-1E cells were seeded in antibiotic-free culture medium at a density of 800.000 cells/cm2. A transfection mix (750nM siRNA and 5% v/v DharmaFECT (Thermo) prepared in serum- and antibiotic-free OptiMEM media (Gibco) was added to the cells in a 1:5 ratio. The following day, the media was changed to standard RPMI, and the cells were incubated for 2 days and switched to 5mM glucose medium for 24 h before exposure to (25 mM) or low (5mM) glucose for 12 h.


title: mRNA_adult_heart_mm77_A5362_wtwtF

value: adult (~6 months postnatal)

value: mm77 line


title: Adiponectin-cre Wild type 19

value: 24 week-old

value: Epididymal adipose tissue


title: WT Isolated_PFC_Rep_2

value: prefrontal cortex

value: 8-10 weeks

value: wild type


title: Van 1h riboZ RNA-Seq

city: Seoul

first: Sun

last: Kim

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Basecalls performed using CASAVA version 1.8.2
mRNA, riboZ sequence reads were trimmed for adaptor sequences and mapped to IRGSP-1.0 reference genome using Tophat2. The abundance of isoforms and genes were measured using Cufflinks.
small RNA sequence reads were trimmed for adaptor sequences and mapped to IRGSP-1.0 reference genome using Bowtie1 with perfect match and allowing up to 5 multiple alignments. The abundance of reads were normalized by the library size.
long non-codingRNAs were assembled using the riboZ RNA-seq data following the lincRNA assembly protocol from Hada Hezroni et al., Cell Reports, 2015. Only intergenic lncRNA(lincRNA)s were assembled since our RNA-seq data is not strand specific.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: gene_expression.txt: tab delimitedtab-delimited text file that includes FPKM values of all mRNA-seq samples
Supplementary_files_format_and_content: lincRNA_expression.txt: tab delimitedtab-delimited text file that includes FPKM values of assembled lincRNAs from riboZ RNA-seq samples
Supplementary_files_format_and_content: miRNA_expression.txt: tab delimitedtab-delimited text file that includes sample normalized read count values of miRNAs from small RNA-seq samples

organism: Oryza sativa Indica Group

source_name: drought tolerant Indica rice variety

growth_protocol: The rice plants were cultured in Yoshida solution at pH 5.8 (Yoshida et al. 1972) and maintained in a temperature-controlled culture room at 29°C under 16-hr/8-hr light/dark conditions.

extract_protocol:
Total RNA was extracted from control and drought-stressed rice plants using Tri-Reagent (MRC, Cincinnati OH, USA) according to the manufacturer’s instructions.
First and second cDNAs were then strands were synthesized. After the cDNA ends were repaired, the 3’ ends were adenylated and the adaptors were ligated. After PCR amplification of cDNAs, NGS was conducted using a TruSeqTM RNA sample preparation Guide.

treatment_protocol: Rice plants at the three-leaf stage were subjected to drought-stress for 1 and 6 hr by removal of the culture solution. Untreated plants were used as control. After treatment, entire plants were immediately transferred into liquid nitrogen.

tag: cultivar

value: wild type vandana

tag: developmental stage

value: three-leaf stage

value: Whole plant


title: RNA Ad-CA-ChREBP B

description: processed data file: CAChREBP_exon.txt

data_processing:
alignment: RNA-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
quantification: Total RNA-seq coverage within  introns of Ensembl (Rnor_5.0) genes were quantified  using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40), to asses primary transcript levels and in exons to asses mature transcript levels. EdgeR normalized readcounts are provided in  CAChREBP_exon.txt
Genome_build: rn5

source_name: β-cell_RNA Ad-CA-ChREBP

treatment_protocol: INS-1E cells were preincubated for 24 hours, incubated with equal titers of CA-ChREBP or GFP control adenovirus for 2 hours, and incubated with 5 mM glucose for 12 hours before harvest of RNA.

tag: cell line

value: beta-cell


title: Adiponectin-cre Wild type 17

value: male

value: High fat diet 16 week

value: Wild type


title: RNA Ad-CA-ChREBP A

description: processed data file: CAChREBP_exon.txt


title: mRNA_adult_heart_mm77_A5355_wtwtF

value: mixed 129S6 and C57BL/6J

value: wild-type (WT)

value: female


title: Adiponectin-cre Wild type 16


title: Adiponectin-cre Wild type 1

value: Control Chow diet


title: RNA Ad-GFP B

description: processed data file: CAChREBP_exon.txt

source_name: β-cell_RNA Ad-GFP B


title: Van 0h riboZ RNA-Seq


title: mRNA_adult_heart_mm77_A5351_kokoF

value: mm77 KO

value: adult (~6 months postnatal)

value: mm77 line

value: ventricular portion of heart


title: RNA Ad-GFP A

description: processed data file: CAChREBP_exon.txt

source_name: β-cell_RNA Ad-GFP A


title: RNA siCtrl 0h glucose C


title: mRNA_adult_heart_mm771_A7068_wtwt_female

value: adult

value: mm771 line


title: Van 6h riboZ RNA-Seq

value: wild type vandana


title: mRNA_adult_heart_mm77_A5407_wtwtM


title: Adiponectin-cre Wild type 18

value: 24 week-old

value: Epididymal adipose tissue


title: eWAT high fat diet 2

value: Epididymal white adipose tissue

tag: genotype


title: eWAT high fat diet 1

tag: strain

value: male


title: AP2 6h riboZ RNA-Seq

source_name: AP2 over-expressed transgenic Oryza Sativa

value: nipponbare AP2 transgenic

value: three-leaf stage

value: Whole plant


title: AP2 1h riboZ RNA-Seq


title: mRNA_adult_heart_mm77_A5287_kokoM

value: mixed 129S6 and C57BL/6J

tag: gender


title: mRNA_adult_heart_mm77_A5398_wtwtM

value: wild-type (WT)


title: WT 6h riboZ RNA-Seq

source_name: Wildtype Oryza Sativa

value: wild type nipponbare


title: eWAT control diet 3

value: Control Chow diet

value: Wild type


title: mRNA_adult_heart_mm77_A5347_kokoM

value: mm77 KO

value: adult (~6 months postnatal)

value: mm77 line


title: eWAT control diet 2


title: eWAT high fat diet 3

value: High fat diet 16 week


title: RNA 4h glucose A

description: processed data file: Glucose_exon.txt, Glucose_intron.txt

data_processing:
alignment: RNA-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
quantification: Total RNA-seq coverage within  introns of Ensembl (Rnor_5.0) genes were quantified  using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40), to asses primary transcript levels and in exons to asses mature transcript levels. edgeR normalized readcounts are provided in  Glucose_intron.txt and Glucose_exon.txt
Genome_build: rn5

source_name: β-cell_RNA 4h glucose

value: beta-cell


title: totalRNA_rRNAminus_e11.5_heart_mm77_5294-9_koko

source_name: heart_enhancer-null_e11.5_mm77 line

extract_protocol:
Total RNA was extracted with Ambion RNAqueous Total RNA Isolation Kit
Ambion TURBO DNase treatment, Illumina Ribo-Zero rRNA removal followed by Illumina TruSeq Stranded Total RNA Sample Prep (according to manuf. protocol)

value: embryonic day 11.5

value: heart


title: mRNA_adult_heart_mm77_A5358_kokoF

value: female

value: ventricular portion of heart


title: WT 0h riboZ RNA-Seq


title: RNA 2h glucose B

source_name: β-cell_RNA 2h glucose


title: eWAT control diet 1

value: male

value: 24 week-old

value: Epididymal white adipose tissue


title: totalRNA_rRNAminus_e11.5_heart_mm77_5294-1_wtwt

source_name: heart_wild-type_e11.5_mm77 line

value: mixed 129S6 and C57BL/6J


title: Van 6h small RNA-Seq

value: wild type vandana

value: three-leaf stage

value: Whole plant


title: AP2 0h riboZ RNA-Seq

value: nipponbare AP2 transgenic


title: AF21_L2 (mRNA)

data_processing:
Adaptor sequences and low quality score bases (Phred score<20) were first trimmed usingTrim Galore (version 0.2.7).The resulting reads were then mapped to the human genome reference sequence using TopHat (version 2.0.6) and using a hg19 transcript annotation database downloaded from UCSC (downloaded on 2011-08-30).
Gene-level expression estimates were calculated using featureCounts (version 1.4.6). Transcript-level expression values were obtained using RSEM.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file containing expression count values for genes.
Supplementary_files_format_and_content: Tab-delimited text file containing expression count values for transcripts.

tag: individual

value: macrophage

value: Listeria

value: 2 hr


title: GFP_H3K4me3_2

city: Davis

first: Gina

middle: Marie

last: Turco

address: University of California, Davis

institute: UC Davis

description: Input ID: GFPKINPUT2

data_processing:
low quality reads were filtered
Bowtie software was used for the mapping to the Arabidopsis TAIR10 reference genome
SICER.SH ran at "redundancy threshold" (1), "window size" (200), "fragment size" (300), "effective genome fraction" (0.85), "gap size" (200), "FDR" (0.01)
Windowbed was used for the identification of the genes affected by the histone modification
Genome_build: Tair 10
Supplementary_files_format_and_content: wig

source_name: GFP positive protoplast (pWOL:GFP marker line)

growth_protocol: Plants were grown under standard conditions at 24ºC in a 16-h light 8-h dark cycle.

extract_protocol:
Root protoplast were prepared as described in (Brady et al., 2007). The MoFlo cell sorter?s electronic configuration was modified to identify intact protoplasts above electronic and sample buffer ?noise? levels by choosing a side scatter electronic threshold and by applying logarithmic scaling to the forward angle and side angle 488nm laser light scatter signals.  To collect the GFP positive protoplasts, the green fluorescence of the GFP (530/50 detection filter) was separated from the red fluorescence (emission 670/30) of chlorophyl. Protoplast chromatin was crosslinked with 0.1% formaldehyde for 5 min and the reaction was stopped by adding glycine (0.125M final concentration). The chromatin immunoprecipitation assay performed in this study is a modification of the protocol described in (Bouyer et al., 2011). We used four independent biological replicates (100,000 GFP positive protoplast each) and two antibodies: H3K27me3 (Millipore 07-449) and H3K4me3 (Millipore 07-473).
DNA recovered after ChIP and the input chromatin were both amplified using SeqPlex Enhanced DNA amplification kit (SEQXE, Sigma) for the bioreps 1&2 and GenomePlex Complete (WGA-Sigma) for the bioreps A&B, following the manufacturer's instructions. Amplified DNA was used to synthesize a barcoded Illumina-compatible library (Kumar et al., 2012). Libraries were pooled and sequenced on the HiSeq2500 50SR. WGA adaptors from bioreps A&B were trimmed before mapping to the refference genome.

value: root

value: FACS treated GFP positive root protoplasts

tag: genetic background/cultivar

tag: chip antibody

value: H3K4me3 (Millipore 07-473)


title: RNA 12h glucose A

source_name: β-cell_RNA 12h glucose

tag: cell type

value: beta-cell


title: GFP_H3K27me3_2

description: Input ID: GFPKINPUT2

value: H3K27me3 (Millipore 07-449)


title: totalRNA_rRNAminus_e11.5_heart_mm77_5283-2_wtwt

value: wild-type (WT)

tag: age

value: embryonic day 11.5

value: mm77 line

value: heart


title: Van 1h small RNA-Seq


title: WT_H3K4me3_2

description: Input ID: WTKINPUT2

source_name: Root protoplasts (Col0)

value: FACS treated wild type root protoplasts

value: wildtype


title: Van 0h small RNA-Seq

value: wild type vandana

value: three-leaf stage


title: totalRNA_rRNAminus_e11.5_heart_mm77_5283-1_koko

value: mixed 129S6 and C57BL/6J

value: mm77 KO


title: RNA 1h glucose A

source_name: β-cell_RNA 1h glucose


title: RNA 4h glucose B


title: WT 1h riboZ RNA-Seq

value: wild type nipponbare

value: Whole plant


title: totalRNA_rRNAminus_e11.5_heart_mm771-19_wtwt

source_name: heart_wild-type_e11.5_mm771 line

value: mm771 line


title: RNA 0h glucose B

source_name: β-cell_RNA 0h glucose


title: RNA 12h glucose B


title: totalRNA_rRNAminus_e11.5_heart_mm771-16_koko

source_name: heart_enhancer-null_e11.5_mm771 line

value: mm771 KO


title: WT_H3K27me3_2

description: Input ID: WTKINPUT2

value: root


title: GFP_INPUT_2

value: FACS treated GFP positive root protoplasts


title: RNA 0h glucose A

value: beta-cell


title: AP2 6h small RNA-Seq

value: nipponbare AP2 transgenic


title: AP2 1h small RNA-Seq


title: totalRNA_rRNAminus_e11.5_heart_mm771-7_koko

value: embryonic day 11.5


title: RNA 2h glucose A


title: WT 6h small RNA-Seq


title: GFP_H3K4me3_1

description: Input ID: GFPKINPUT1

value: H3K4me3 (Millipore 07-473)


title: totalRNA_rRNAminus_e11.5_heart_mm771-5_wtwt

value: wild-type (WT)

value: heart


title: RNA 1h glucose B


title: Lgr6- rep1

city: London

first: Axel

last: Behrens

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Gene level abundance estimates were generated using RSEM (v1.2.22) by mapping 50bp paired-end reads against the Mus musculus mm10 Refseq transcriptome and reference genome with the STAR (v2.4.2a) aligner.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene level raw abundance estimates for each sample.

source_name: mammary gland

extract_protocol:
Mammary glands from Lgr6-eGFP-CreErt2 mice were dissected, mashed gently with a MACS dissociator (Miltenyi Biotec) and incubated in HBSS with 300U ml-1 collagenase (Sigma) plus 300 μg hyaluronidase (300U ml-1activity) (Sigma) and digested for 30m at 37°C. Red blood cells were lysed and samples digested with Trypsin for 3 min at 37°C before being filtered with a 70 by 40 μm-mesh. LIN- cells where then FACS sorted for LGR6+ cells.
RNA concentrations were determined with a Qubit fluorometer (ThermoFisher) as 7-25 pg/ul before analysis of RNA quality on a Bioanalyzer (Agilent) (RIN 5-8). cDNA (50-75ng/μl) was generated from 5μl RNA (NuGEN/Next-Gen), sheared (Covaris S-series), and cDNA fragments were cleaned-up (Zymo Research) before 10ng were used to generate an amplified cDNA library (NuGEN Ovation) over 18 PCR cycles. cDNA was sequenced on a HiSeq 4000 system (illumina) in paired-end 50 mode

value: Lgr6 negative

value: 5-week old

tag: Sex

value: female


title: GFP_H3K27me3_1

description: Input ID: GFPKINPUT1

tag: tissue

value: H3K27me3 (Millipore 07-449)


title: Lgr6- rep2


title: WT 1h small RNA-Seq

value: three-leaf stage


title: WT_INPUT_2

value: FACS treated wild type root protoplasts

value: wildtype


title: WT 0h small RNA-Seq

value: wild type nipponbare

value: Whole plant


title: Nosema/BQCV1

city: Avignon

first: Cédric

last: Alaux

address: Domaine Saint-Paul

department: UMR 406 Abeilles et Environnement

country: France

institute: INRA

data_processing:
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2).
Reads were mapped to the Apis mellifera genome (Amel_4.5) using the eland_rna module of CASAVA 1.8.2 (Illumina). NCBI annotation file (seq_gene.md.gz; 2012-12-17) was used to retrieve annotations on genes and exons.
The counting was performed with HTSeq count (union mode). As the sequencing was strand-specific, the reads had to map to the opposite strand of the gene.
Genome_build: Apis mellifera (Amel_4.5)
Supplementary_files_format_and_content: tab-delimited text files include raw abundance measurements

organism: Apis mellifera

growth_protocol: Bees were reared in cages (30 worker honey bees per cage) for 13 days post infection, and fed with ad libidum with sugar water (50%).

extract_protocol:
Bees were flash frozen in liquid nitrogen and brain dissected in dry ice. RNA was extracted from pool of 4 brains using Trizol reagent and the Qiagen RNeasy Mini Kit (QIagen).  Illumina TruSeq Stranded mRNA Sample Preparation kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-Seq libraries were constructed with the Truseq stranded mRNA sample preparation (Low throughput protocol) kit from Illumina.

treatment_protocol: Bees were infected either with Nosema ceranae, Black Queen Cell Virus, or both.

value: 15 days old bees

tag: infected with

value: Nosema and BQCV

tag: time point

value: 13 days post infection

value: brain (pool of 4 brains)


title: Lgr6+ rep2

value: Lgr6 positive


title: Nosema/BQCV2


title: WT_H3K4me3_1

description: Input ID:  WTKINPUT1

value: root

value: H3K4me3 (Millipore 07-473)


title: WT_H3K27me3_1

description: Input ID:  WTKINPUT1


title: BQCV3

value: Black Queen Cell Virus (BQCV)


title: Van 6h RNA-Seq

source_name: drought tolerant Indica rice variety

value: wild type vandana


title: Lgr6+ rep1

extract_protocol:
Mammary glands from Lgr6-eGFP-CreErt2 were dissected, mashed gently with a MACS dissociator (Miltenyi Biotec) and incubated in HBSS with 300U ml-1 collagenase (Sigma) plus 300 μg hyaluronidase (300U ml-1activity) (Sigma) and digested for 30m at 37°C. Red blood cells were lysed and samples digested with Trypsin for 3 min at 37°C before being filtered with a 70 by 40 μm-mesh. LIN- cells where then FACS sorted for LGR6+ cells.
RNA concentrations were determined with a Qubit fluorometer (ThermoFisher) as 7-25 pg/ul before analysis of RNA quality on a Bioanalyzer (Agilent) (RIN 5-8). cDNA (50-75ng/μl) was generated from 5μl RNA (NuGEN/Next-Gen), sheared (Covaris S-series), and cDNA fragments were cleaned-up (Zymo Research) before 10ng were used to generate an amplified cDNA library (NuGEN Ovation) over 18 PCR cycles. cDNA was sequenced on a HiSeq 4000 system (illumina) in paired-end 50 mode

value: 5-week old


title: BQCV2


title: WT_INPUT_1


title: Nosema3

value: Nosema ceranae spores


title: AP2 0h small RNA-Seq

value: nipponbare AP2 transgenic


title: YKL rep2

city: Boston

first: Marc

last: Wein

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

data_processing:
Basecalls performed using CASAVA version 1.7
Subsequent to demultiplexing and adapter trimming, fastqs were mapped to mm10 with splice-aware aligner STAR vers-2.3.0 using mm10 Ensembl gtf version 75
To calculate RPKM expression values, sequencing reads were counted over an assembly of all putative exons for each gene and normalized by the length of the exon assembly and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values for each sample are given in tab-delimited txt files.  A matrix of RPKM values for those samples is also available.

growth_protocol: Ocy454 cells were allowed to reach confluency at 33C, then were switched to 37C for 14 days, with medium changes every 3-4 days. Medium was changed 24 hours prior to sample collection. All samples were treated identically prior to compound treatment.

extract_protocol:
RNA was isolated using Rneasy columns (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either vehicle (PBS + 25 mM HCl), PTH 1-34 (1 nM), or YKL-05-093 (0.5 uM) for 4 hours.

value: osteocytic cell line

tag: treated with


title: Van 1h RNA-Seq

value: three-leaf stage


title: Van 0h RNA-Seq


title: AP2 6h RNA-Seq


title: Nosema2


title: BQCV1


title: AP2 0h RNA-Seq


title: PTH rep2

value: PTH (1 nM) for 4 hrs


title: AP2 1h RNA-Seq


title: Nosema1


title: Control3

value: Control


title: Control2


title: Control1


title: PTH rep1


title: YKL rep1


title: GFP_INPUT_1

value: FACS treated GFP positive root protoplasts


title: VEH rep1

value: vehicle for 4 hrs


title: WT 0h RNA-Seq

value: wild type nipponbare

value: Whole plant


title: VEH rep2


title: DCKO DN3_2

status: Public on Sep 05 2016

city: Cambridge

first: Martin

last: Turner

address: Babraham Hall

department: Lymphocyte Signalling and Development

institute: Babraham Institute

data_processing:
Libraries were sequenced by Hiseq 2000 in 100bp single-end reads
Basecalling was done using Illumina default pipeline
Reads were trimmed to remove adapter sequences using Trim Galore
Reads were mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly
Read counts for each gene were generated in htseq-count: transcripts from the same gene were collapsed into a single transcript containing all exons
Differences in the abundance of transcripts between DCKO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised read counts for each sample, and output from DESeq2 analysis

source_name: thymus

extract_protocol:
Cells FACS sorted from thymus as described in summary above (methods). RNA was extracted using RNeasy Micro Kit
20-200 ng of RNA used to make libraries using TruSeq Stranded Total RNA and rRNA Removal Mix – Gold from Illumina

value: pre-T cell, lymphocyte

value: Zfp36l1fl/fl, Zfp36l2fl/fl, CD2cre


title: DCKO iCLIP

data_processing:
Library strategy: iCLIP-Seq
Libaries were sequenced using Illumina’s HiSeq2000 (100 bp single end sequencing)
Basecalling was done using Illumina default pipeline
Sample demultiplexing was performed by identification of the 3 known bases of the 7 bases barcode introduced in the 5’ end of the read by the RCLIP primer.  The remaining four random bases were used to remove PCR duplicate reads
Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome GRCm38 using Bowtie
Identification of highly significant ZFP36L1 binding sites was performed using iCount to assign a FDR to each crosslink site. Data generated by having sequenced the same sample on two lanes (sample 2 and sample 3) was merged during iCOUNT processing.
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated text file includes output from iCOUNT pipeline

extract_protocol:
Cells were lysed and ZFP36L1-RNA complexes were pulled down with Brf1/2 antibody using protein A Dynabeads.  RNA-protein complexes were run on an SDS-PAGE gel, transfered to nitrocellulose and visualised by radiolabelling a proportion of the immunoprecipitated material.  Correctly sized complexes were cut out of the membrane and used to generate libraries.
Wild-type cDNA libraries from two independent experiments and a DCKO cDNA library from one experiment were prepared using the RCLIP primers indicated and sequenced using Illumina’s HiSeq2000 (100 bp single end sequencing).  RCLIP primers used for RNA reverse transcription included a barcode at the 5’end with three known bases and four random nucleotides

treatment_protocol: Intact cells were irradiated with UV-light (300 mJ/cm2, Stratalinker 2400)

value: total naive thymocytes

value: DCKO


title: DCKO DN3_4


title: DCKO DN3_1


title: DCKO DN3_3


title: Control DN3b_3

value: Zfp36l1fl/fl, Zfp36l2fl/fl


title: Control DN3a_3


title: Control DN3a_2


title: Control DN3b_1


title: Control DN3b_4


title: WT 6h RNA-Seq


title: Control DN3b_2


title: HuR_iClip_siADAR1

city: Newcastle Upon Tyne

first: Konstantinos

last: Stellos

state: England

address: Central Parkway, Centre for Life

department: Faculty of Medical Sciences

institute: Newcastle University

description: HuR iCLIP

data_processing:
RNA-Seq: Reads which contained unknown bases were discarded.Reads were aligned to the human reference genome (hg19) by BWA (v0.6.2), with maximal 2 missmatches in the seed sequence. Afterwards used cufflinks (v2.2.1)to estimate the transcript expression.  Next we evaluated the RNA editing by following the steps of a previously described bioinformatic method (Ramaswami et al. Nat Methods. 2013; 10(2):128-32)
ICLIP-Data: 3bp were trimmed from the reads. Demultiplexing was done with the following index sequences:  ADAR_Knockdown TGGC  Control1 CGGA. Reads were mapped by tophat2 (v.2.0.9) to hg19. Afterwards Homer was utilized with the following attributes:-makeTagDirectory BAMFILE -keepAll -fragLength 15 findPeaks PEAKDIR -size 8 fragment-size 20 -style factor -o auto
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file wich includes FPKM values for each sample
Supplementary_files_format_and_content: Homer Peak file for ScrambleG and siADAR1

source_name: human umbilical vein endothelial cells

growth_protocol: Pooled HUVECs were purchased from Lonza and cultured in endothelial basal medium (EBM;Lonza) supplemented with EGM-SingleQuots (Lonza) and 10% fetal calf serum (FCS; Invitrogen (San Diego, CA ) until the third passage.

extract_protocol:
Total RNA was extracted from HUVECs and where applicable HUVECs were previously transfected with siADAR1, siADAR2 or scrambled siRNAs using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. The cDNA and the final sequencing libraries were prepared as described before (Wang et.al, EMBO Mol Med, 2013).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: HUVECs were transfected at 70% confluency using GeneTrans II (Mobitec) according to the manufacturer's protocol with a final concentration of 55nM siRNA. The following siRNA sequences were used: Scrambled 1/ScrambleG (5’-UCUCUCACAACGGGCAU[dT][dT]-3’)   ADAR1:(5’-GCUAUUUGCUGUCGUGUCA[dT][dT]-3’). All siRNAs were purchased by Sigma Aldrich.

value: human umbilical vein endothelial cells

tag: passage

value: passage 3

tag: RNAi treatment


title: HuR_iClip_scrambled

description: HuR iCLIP

value: scrambled nucleotides (Scramble G)


title: Control DN3a_1


title: Huvec_siADAR1_hypoxia_rep2

description: Hypoxic conditions


title: Huvec_siADAR1_hypoxia_rep3

description: Hypoxic conditions


title: Huvec_siADAR1_hypoxia_rep1

description: Hypoxic conditions


title: WT2 iCLIP

value: WT


title: Control DN3a_4


title: WT 1h RNA-Seq

tag: cultivar

tag: developmental stage


title: Huvec_siADAR1_basal_rep2

description: Basal conditions


title: Huvec_siADAR1_basal_rep1

description: Basal conditions


title: Huvec_Scrambled_hypoxia_rep2

description: Hypoxic conditions


title: Huvec_Scrambled_hypoxia_rep1

description: Hypoxic conditions


title: Huvec_siADAR1_basal_rep3

description: Basal conditions


title: Huvec_Scrambled_basal_rep3

description: Basal conditions


title: Huvec_Scrambled_basal_rep2

description: Basal conditions


title: Huvec_Scrambled_basal_rep1

description: Basal conditions


title: Adiponectin-cre Nova1flox/floxNova2flox/flox 20

source_name: eWAT 24 week-old male mouse

value: male

value: 24 week-old

value: Epididymal adipose tissue

tag: diet

value: High fat diet 16 week

tag: genotype/variation

value: Nova1- and Nova2-deficient


title: Huvec_Scrambled_hypoxia_rep3

description: Hypoxic conditions


title: Icm2

data_processing:
Illumina Casava 1.8.2 software was used for basecalling and demultiplexing. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
The reads were mapped by tophat2 v2.0.11 to GRCH37 with the default parameters.
The gene quantification was done by cuffdiff with the parameters -p 20 -T --library-norm-method classic-fpkm. Afterwards the FPKM values were combined with the cummeRbund package in R.
Genome_build: GRCH37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: human peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. The cDNA and the final sequencing libraries were prepared as described before (Wang et.al, EMBO Mol Med, 2013). The libraries were sequenced using the Illumina HiSeq 2000 following the TruSeq RNA protocol.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: The peripheral blood mononuclear cells were not treated. The hypoxia endothelial cell samples (n=2 biological replicates) were treated with hypoxia 1% for 24h.

value: peripheral blood mononuclear cells

tag: condition

value: chronic ischemic heart failure


title: Icm4


title: Cad_rep4

value: stable coronary heart disease


title: Icm1


title: Icm3


title: Cad_rep3


title: norm_24h_rep1

value: umbilical vein endothelial cells

tag: treatment

value: control


title: Cad_rep2


title: norm_24h_rep2


title: Control_rep1

value: healthy


title: Control_rep3


title: Control_rep4


title: Huvec_scrambled1_rep2

data_processing:
Reads which contained unknown bases were discarded. To demultiplex the reads we used the following index Sequences:   scramble1_rep1 ATCACG  scramble2_rep1 TTAGGC  Adar1_kd_rep1 GATCAG  adar2_kd_rep1 CTTGTA  scramble1_rep2 ACTTGA  scramble2_rep2 TAGCTT  Adar1_kd_rep2 GGCTAC  Adar2_kd_rep2 CGATGT.  Reads were aligned to the human reference genome (hg19) by BWA (v0.6.2), with maximal 2 missmatches in the seed sequence. Afterwards used cufflinks (v2.2.1)to estimate the transcript expression.  Next we evaluated the RNA editing by following the steps of a previously described bioinformatic method (Ramaswami et al. Nat Methods. 2013; 10(2):128-32)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file wich includes RPKM values for each sample

extract_protocol:
Total RNA was extracted from HUVECs previously transfected with siADAR1, siADAR2 or scrambled siRNAs using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. The cDNA and the final sequencing libraries were prepared as described before (Wang et.al, EMBO Mol Med, 2013). The libraries were sequenced using the Illumina HiSeq 2000 for 1 x 51cycles following the TruSeq RNA protocol.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: HUVECs were transfected at 70% confluency using GeneTrans II (Mobitec) according to the manufacturer's protocol with a final concentration of 55nM siRNA. The following siRNA sequences were used: Scrambled 1/Scrambled (5’-UCUCUCACAACGGGCAU[dT][dT]-3’) or   Scrambled 2 (5’-GUGGGCACCGAUAUCUUGA[dT][dT]-3’)   ADAR1:(5’-GCUAUUUGCUGUCGUGUCA[dT][dT]-3’), the human ADAR2 targeting siRNA: ADAR2: (5’-GAUCGUGGCCUUGCAUUAA[dT][dT]-3’). All siRNAs were purchased by Sigma Aldrich.

value: scrambled nucleotides (Scrambled 1)


title: Huvec_scrambled2_rep2

value: scrambled nucleotides (Scrambled 2)


title: Huvec_Adar1kd_rep2


title: Control_rep2


title: Huvec_Adar2kd_rep2


title: Huvec_scrambled2_rep1


title: Huvec_Adar2kd_rep1


title: Huvec_scrambled1_rep1


title: Huvec_Adar1kd_rep1


title: Cad_rep1


title: hyp_24h_rep2

value: 24h hypoxia treatment


title: hyp_24h_rep1


title: C2_4

city: Edinburgh

first: José

middle: Roberto

last: Bermúdez-Barrientos

state: Lothian

address: Charlotte Auerbach Rd

department: Institute of Immunology & Infection

institute: The University of Edinburgh

description: small RNAs

data_processing:
adapter trimming using reaper (version reaper-13-100), part of Kraken software tools suite (Enright group, EBI), with parameters: -geom no-bc -3pa TGGAATTCTCGGGTGCCAAGG -3p-global 12/2/1 -3p-prefix 8/2/1 -3p-head-to-tail 1 -nnn-check 3/5 -format-clean @%    I%n%C%n+%n%Q%n -dust-suffix 20 -polya 5 -qqq-check 0/10 -tri 0 -tabu GTTCAGAGTTCTACAGTCCGACGATC -mr-tabu 14/2/1
reads were then mapped to S. carpocapsae Breton genome using ShortStack version 3.3 (Axtell group, Penn State Univeristy, USA), which internally uses Bowtie1 internally with the following parameters --mmap u --bowtie_m 101 --ranmax 101 --mismatches 2 --align_only
reads mapping to microRNAs loci were counted with the function featureCounts, part of the Rsubread (version 1.22.1) R package. Using th following parameters minOverlap=1, allowMultiOverlap=FALSE, countMultiMappingReads=FALSE
The microRNA count table was analyzed for differential expression using edgeR (version 3.14.0) R package, microRNAs with a False Discovery Rate (FDR) below 0.1 were considered differentially expressed
Genome_build: S. carpocapsae Breton
Supplementary_files_format_and_content: The processed data file consists of a table of microRNAs and their counts of reads mapping, only reads of 20-24 length were considered for microRNA differential expression analysis and therefore for the processed file

organism: Steinernema carpocapsae

source_name: Infective juvenile

growth_protocol: Nematodes were grown using an in vitro mass production protocol modified from Bedding 1981 Bedding, R.A. Low cost in vitro mass production of Neoaplectana and Heterorhabditis species (Nematoda) for field control of insect pests. Nematologica 27, 109-114 (1981).

extract_protocol:
total RNA was extracted using the Trizol reagent
TruSeq Small RNA
Sequencing one lane of Illumina HiSeq 2500 in fast mode of the six libraries metioned here along with other 9 libraries

treatment_protocol: Nematodes were incubated with Galleria mellonella Haemolymph. Control nematodes weren't added haemolymph. Nematodes were collected after two hours of haemolymph treatment

tag: strain

value: Breton

tag: incubation time

value: 2 hours without induction

tag: rna integrity number rin

tag: number of reads raw files


title: C2_2

description: small RNAs


title: H2_4

description: small RNAs

value: 2 hours post induction


title: H2_2

description: small RNAs


title: C2C12_notreatment

status: Public on Sep 04 2016

city: Pasadena

first: Nagarajan

last: Nandagopal

address: 1200 E. California Blvd, M/C 114-96

institute: California Institute of Technology

data_processing:
fastq files concatenated and trimmed to ensure fastqc values >28
aligned to mm9 assembly using tophat
cufflinks run to extract FKPM values
Genome_build: mm9
Supplementary_files_format_and_content: .tabular files represent cufflinks output

molecule: polyA RNA

source_name: C2C12 cells

growth_protocol: Cells grown in DMEM, 20% FBS, 4 mM L-glutamine, Pen/Strep, NEAA, Sodium Pyruvate at 37 C, 5% CO2

extract_protocol:
Qiagen Rneasy RNA extraction
Libraries were prepared according to Illumina's instructions, with barcodes and polyT enrichment.

treatment_protocol: Cells cultured in 10 uM DAPT, which was washed out in samples of interest for 1h or 6h

tag: cell type

value: mouse myoblast


title: C2C12_1h_noDAPT


title: C2C12_6h_noDAPT


title: H2_1

description: small RNAs


title: WT1 iCLIP

value: total naive thymocytes

tag: genotype

value: WT


title: C2_1

description: small RNAs