title: SRSF1Y19F

city: Beijing

first: Xu

middle: Li

last: ting

address: 56 NanLiShi Road, Xicheng District

institute: Beijing Children’s Hospital

data_processing:
The library preparations were sequenced on an Illumina HiSeq 4000 platform. The 150 bp paired-end reads were generated
reads were aligned to the reference genome (Homo_sapiens.GRCh38.87.chr) using HISAT2 (2.1.0).
HTSeq (0.6.0) was used to count the read numbers, and then the fragments per kilobase million (FPKM) value of each gene was calculated based on the length of the gene and read count mapped to this gene.
Alternative Splicing was analyzed by the Asprofile (b-1.0.4).
Genome_build: Homo_sapiens.GRCh38.87.chr

extract_protocol:
RNA was extraction as described for RT-PCR using TRIZOL. Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit (#E7530L, NEB, USA).
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit

tag: gene overexpressed


title: macrophages F4/80 high MHCII high, from infected spleen [IN_SP_Ma_2]

status: Public on Dec 11 2018

type: SRA

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

library_source: transcriptomic

data_processing:
Paired-end reads were mapped to reference genome using STAR version 2.3
Mapped reads were summaried to gene level using featureCounts version 1.5 and with GENCODE GRCm38 vM10 gene annotation
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Bioconductor edgeR package with normalized library sizes option and log2 transformation
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level log2 transformed FPKM values for all samples

molecule: total RNA

organism: Mus musculus

source_name: infected spleen d35

extract_protocol:
Tissue was digested with collagenase D. Total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to manufacturer's protocol. All mouse RNAs were analyzed on Agilent Bionanlyser for quality assessment; RNA Integrity Number (RIN) range was 6.5-10 and a median of 9.2.
cDNA libraries were prepared starting with 2ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol (Picelli et al., 2014) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All 8 samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2500 Rapid mode (17 samples/lane).

treatment_protocol: P. yoelii infection, 10+6 infected red blood cells

tag: infected with

value: parasitized P. yoelii erythrocytes

tag: tissue

value: spleen

tag: cell type

value: macrophages F4/80 high

tag: samplegroup

value: SP Ma


title: SRSF1Y19D

country: China

molecule: polyA RNA

organism: Homo sapiens

tag: cell line


title: C57Bl/6_4 LF_B6 [jos2145]

type: RNA

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

description: 4 LF_B6

hyb_protocol: 15 ug of cRNA were hybridized to Mu74Av2 arrays, which were then washed and stained with user-generated reagents.

scan_protocol: Chips were scanned using the GCS 3000 scanner from Affymetrix.

data_processing: Data were analyzed using Robust Multi-Array Average (RMA).

label: biotin

label_protocol: 25  g total RNA was pooled from two to three mice and biotin-labeled cRNA was made using the One Cycle Assay protocol.

extract_protocol: Total RNA was extracted and purified with RNeasy (Qiagen, Chatsworth, CA).

value: Epididymal fat pads

tag: diet

value: low-fat

tag: strain


title: 11_Br-M1732_dp12_39g

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse grow in NIDDK animal core facility.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: mRNA is obtained by Co-Ip with FLAG tagged PAB-1 expressed in seam cells and VPCs converted to cDNA and amplified using NuGEN pico amplification kit

value: FVB/129SVEV/Black Swiss at ratios:80%/10%/10%.

tag: genotype/variation

value: Mutant

tag: stage pregnancy


title: Vector

value: plasmid  vector


title: macrophages F4/80 high MHCII high, from uninfected liver [UI_LI_Ma_3]

source_name: Healthy liver

value: none (uninfected)

value: liver

value: LI Ma


title: genomic DNA from paraganglioma 7

type: genomic

city: Brussels

first: Laura

last: Saucedo

address: Laarbeeklaan 103

country: Belgium

institute: Follicle Biology Lab - VUB

description: Paraganglioma/pheochromocytoma sample

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

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2011

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Pheochromocytoma/paraganglioma 7

label_protocol: Standard Illumina Protocol

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

tag: gender

value: female

tag: sample type

value: autonomic lineage cell tumor


title: macrophages F4/80 high MHCII high, from infected lung [IN_LU_Ma_4]

source_name: infected lung d35

value: lung

value: LU Ma


title: 2_Wt-2 V_Virgin_25g

source_name: Wt-V

value: wildtype

value: V


title: SRSF1WT


title: VMRC-LCD_siASCL1 #2

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

data_processing:
CLC Genomics workbench software (Qiagen) was used to generate RPKM data.
Adapter sequences were removed, and read mapping was carried out using the default settings of RNA-Seq analysis package (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, and maximum number of hits for a read set to: 30).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with Expression value (raw counts), TPM and RPKM

source_name: VMRC-LCD

growth_protocol: VMRC-LCD cells were cultured in Eagle's minimum essential medium with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from VMRC-LCD cells 24 h after siRNA transfection using the RNeasy Mini Kit (Qiagen).
The mRNA from eukaryotic organisms was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Small interfering RNAs (siRNAs) for human ASCL1 was purchased from Life technologies. VMRC-LCD cells were transfected with 20 nM siRNA using Lipofectamine RNAiMAX.

value: VMRC-LCD

tag: transfected with

value: ASCL1 siRNAs #2


title: macrophages F4/80 high MHCII high, from infected spleen [IN_SP_Ma_3]

value: parasitized P. yoelii erythrocytes

value: spleen

value: macrophages F4/80 high

value: SP Ma


title: macrophages F4/80 high MHCII high, from infected lung [IN_LU_Ma_3]


title: 3_Wt-3 V_Virgin_23g

value: FVB/129SVEV/Black Swiss at ratios:80%/10%/10%.


title: C57Bl/6_1 LF_B6 [jos2141]

description: 1 LF_B6

value: Epididymal fat pads

value: low-fat


title: VMRC-LCD_siASCL1 #1

value: ASCL1 siRNAs #1


title: VMRC-LCD_siNC

value: control siRNAs


title: macrophages F4/80 high MHCII high, from infected lung [IN_LU_Ma_2]


title: 129S6/SvEvTac_4 HF_129 [jos1760]

description: 4 HF_129

value: Skeletal muscle

value: high-fat


title: C57Bl/6_3 LF_B6 [jos2144]

description: 3 LF_B6


title: 16_1565 Br-M _dp18_

value: Mutant


title: macrophages F4/80 high MHCII high, from infected liver [IN_LI_Ma_3]

source_name: infected liver d35

value: liver

value: LI Ma


title: 8_Wt-2_dp12_42g

value: wildtype


title: 1_Wt-1 V_Virgin_27g

value: V


title: 129S6/SvEvTac_3 HF_129 [jos1759]

description: 3 HF_129


title: 9_Wt-3_dp12_34g


title: macrophages F4/80 high MHCII high, from infected liver [IN_LI_Ma_2]


title: 17_Br-M1763 _dp18_48g (white)


title: MD-111

city: Augusta

first: Hongyan

last: Xu

state: GA

department: Population Health Sciences

institute: Augusta University

description: hiPSC-CMs cultured in RPMI1640/B27 for 50 days

data_processing:
FastQC for quality control
Bowtie2 for alignment
HTSeq 0.9.1 for read count
DESeq2 for normalizaton
Genome_build: human NCBI GRCh38
Supplementary_files_format_and_content: normalized sequence read in comma delimited text format

source_name: hiPSC-CMs

growth_protocol: At day 0, medium for the cultured hiPSCs was changed to RPMI1640 (Life Technologies) with B27 supplement minus insulin (Life Technologies) plus 8 μM ChIR99021 (Cayman). On day 1 (24h), medium was changed to RPMI1640 with B27 supplement minus insulin. On day 3 (72h), media was replaced with combined medium (made by combining 0.5 mL of old medium with 0.5 mL fresh RPMI1640/B27 supplement minus insulin, supplemented with 5 μM IWP2 (Thermo Fisher Scientifics)). On day 5, media was replaced with fresh RPMI1640/B27 supplement minus insulin. On day 7, media was replaced with RPMI1640/B27 supplement (Life Technologies). Cells were then maintained in RPMI1640/B27 medium with medium changed every 3 days. On day 20, hiPSC-CMs were enriched by lactate selection, using glucose free DMEM supplemented with 4 mM lactate, for 5 days. Enriched hiPSC-CMs were maintained in RPMI1640/B27 medium until reached day 50 with medium changed every 3 days.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA Libraries were constructed using Illumina TruSEQ mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA is combined with RNA purficiation beads to bind PolyA RNA to oligodT magnetic beads.  mRNA is eluted and converted to double stranded DNA.  A Tailing, adapter ligation, and PCR amplification using 15 cycles is done to complete the library construction.  Libraries are quantitated via Qubit, analzyed on a Bioanalyzer Tape and diluted to appropriate concentration to run on HiSEQ 4000 High Throughput Flow Cell.

value: Cardiomyocytes

tag: age

value: 50 days


title: 7_Wt-1 _dp12_38g


title: LAMP-2 KO


title: MD-186


title: 129S6/SvEvTac_12 LF_129 [jos1756]

description: 12 LF_129


title: macrophages F4/80 high MHCII high, from infected liver [IN_LI_Ma_4]

value: parasitized P. yoelii erythrocytes


title: MD-506


title: 129S6/SvEvTac_1 HF_129 [jos1757]

description: 1 HF_129


title: CUSO-2


title: CUSO-1


title: C57Bl/6_6 HF_B6 [jos2147]

description: 6 HF_B6


title: silique_poly(A)+ rep4

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

description:
siliquerep3PA
processed data file: lncRNA_exp.xlsx.gz

data_processing:
RNAseq:The adapter or low quality reads were removed by Trimmomatic( Bolger, 2014) .Clean reads were aligned to the Arabidopsis reference genome (TAIR10) by using TopHat version 2.0.10(Trapnell,2009). Parameters were set for strand-specific mapping and up to 5 different alignments were allowed for a given read. The mapped reads which are associated with unique molecular identifiers were further removed PCR duplicates by STL (BIOO SCIENTIFIC) as according to the manufacturer's instructions.
sRNA-seq:After removing bacodes, adapters and low-quality reads, clean reads of size 18-30 nt or 30-60 nt were mapped to the Arabidopsis genome (TAIR10 version) with Bowtie (Langmead et al., Genome Biology, 2009, 10, R25) allowing no mismatches
Genome_build: TAIR10
Supplementary_files_format_and_content: For RNA-Seq processed dataset，our provided file is the expression matrix of our identified lncRNA. The abundance of lncRNAs are estimated FPKM. For sRNA-seq processed datasets, our provided files contain genome match small RNA sequences and their counts.,

organism: Arabidopsis thaliana

growth_protocol: For ABA and dehydration treatment, plants were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C). For cold treatment, plants were grown in short-day conditions(8 h of light/16 h of darkness, 22°C).

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) and treated with DNase I (Ambion). Polyadenylated [poly(A)+] RNAs were isolated from total RNA through two rounds of purification with oligo(dT) beads (QIAGEN).
Libraries for RNA-seq were generated using NEXTflex Rapid Directional qRNA-Seq Kit (dUTP based) according to the manufacturer's instructions.

treatment_protocol: For ABA treatment, 2-week-old seedlings were transferred to 1/2 MS liquid medium with 100 μM ABA for 0, 2, 4, 6, 8 hours. For dehydration treatment, 2-week-old seedlings were removed from the agar and desiccated in dishes for 0, 2, 4, 6, 8 hours. For cold treatment, 2-week-old seedlings (grown under SD conditions) were transferred to 4°C and cultured under SD conditions for 20 days.

tag: ecotype

value: Columbia

value: Wild type

tag: treatment

value: siliques, 5.5-week-old plant

tag: molecule subtype

value: poly(A)+ RNA


title: 129S6/SvEvTac_11 LF_129 [jos1755]

description: 11 LF_129

value: low-fat


title: 15_Wt-3_dp18_50g(brown)

value: FVB/129SVEV/Black Swiss at ratios:80%/10%/10%.


title: silique_poly(A)+ rep3

description:
siliquerep2PA
processed data file: lncRNA_exp.xlsx.gz

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) and treated with DNase I (Ambion). Polyadenylated [poly(A)+] RNAs were isolated from total RNA through two rounds of purification with oligo(dT) beads (QIAGEN).
Libraries for RNA-seq were generated using NEXTflex Rapid Directional qRNA-Seq Kit  (dUTP based) according to the manufacturer's instructions.

value: siliques,5.5-week-old plant


title: 14_Wt-2_dp18_40g(white)


title: 129S6/SvEvTac_10 LF_129 [jos1752]

description: 10 LF_129

value: Skeletal muscle


title: silique_poly(A)+ rep2

description:
siliquerep1PA
processed data file: lncRNA_exp.xlsx.gz


title: 129S6/SvEvTac_9 LF_129 [jos1751]

description: 9 LF_129


title: leaf_poly(A)+ rep4

description:
leafrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: leaves, 5.5-week-old plant


title: C57Bl/6_8 HF_B6 [jos1754]

description: 8 HF_B6

value: high-fat


title: 13_Wt-1_dp18_


title: leaf_poly(A)+ rep3

description:
leafrep2PA
processed data file: lncRNA_exp.xlsx.gz


title: C57Bl/6_6 HF_B6 [jos1749]

description: 6 HF_B6


title: 19_Wt-1_Lac10_28g(white)


title: C57Bl/6_7 HF_B6 [jos1750]

description: 7 HF_B6


title: INV 1_RNASeq

city: Pretoria

first: Moleboheng

last: Lekota

state: Choose a State

address: Corner of Lynwood Road & Roper street

department: Plant and soil sciences

country: South Africa

institute: University of Pretoria

data_processing:
cDNA libraries were sequenced with an Illumina Hi Seq 2000 sequencer generating 90 bp paired-end reads
Quality of individual sequences was evaluated using TrimGalore (Cutadapt and FastQC) tool
High quality sequence reads were aligned and mapped to the potato reference genome sequence (Solanum tuberosum Group Phureja DM v4.04) using Hisat2 v2.1 spliced aligner.(http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml), using Hisat2 v2.1 spliced aligner
A False Discovery Rate (FDR) threshold of 10% and an absolute log 2-fold change > 1 were used to determine differentially expressed genes
G-fold (v1.1.4) analysis tool was used to perform differential expression (DE) analysis.
Genome_build: Solanum tuberosum Group Phureja DM v4.04
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each Sample

organism: Solanum tuberosum

source_name: Potato tubers

growth_protocol: Potato plants were individually planted in plastic pots filled with pasteurised sandy-loam soil and grown in a greenhouse maintained at 22 ± 2 °C with a 16-hr photoperiod. Plants were watered every second day with 200 ml of sterile distilled water for maintenance of moist soil conditions, favourable for tuber infection by Sss.

extract_protocol:
RNA was extracted using a Direct Zol™ RNA extraction kit (Zymo Research, USA) together with Tri-Reagent® (Sigma-Aldrich, Germany) following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two plants were inoculated with Spongospora subterranea inoculum 7 days after planting and the other two plants were mock-inoculated with distilled water and maintained as control plants. Plants were harvested seven weeks after emergence.

tag: cultivar

value: Innovator

tag: response to sss

value: Tolerant

value: Inoculated

value: Tuber peels


title: VDP 2_RNASeq

value: Vanderplank

value: Susceptible

value: Un-inoculated /control

tag: tissue


title: VDP 1_RNASeq


title: leaf_poly(A)+ rep2

description:
leafrep1PA
processed data file: lncRNA_exp.xlsx.gz

value: Columbia


title: C57Bl/6_5 HF_B6 [jos1747]

description: 5 HF_B6


title: 129S6/SvEvTac_2 HF_129 [jos1758]

description: 2 HF_129


title: 20_Wt -2_Lac10_39g (brown)

value: wildtype


title: INV 2_RNASeq


title: nucleus pulposus-IDD-rep3

city: shanghai

first: jian

last: chen

address: shanghai pudong district minfeng road NO.351  Room 406  Building 1

description: miRNAs expression in nucleus pulposus from IDD patients

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: nucleus pulposus-IDD-rep3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: male

value: nucleus pulposus

tag: diagnosis

value: intervertebral disc degeneration


title: C57Bl/6_14 LF_B6 [jos1745]

description: 14 LF_B6

value: low-fat


title: 21_Wt-3_Lac10_39g(brown)

value: FVB/129SVEV/Black Swiss at ratios:80%/10%/10%.


title: inflorescence_poly(A)+ rep4

description:
inflorescencerep3PA
processed data file: lncRNA_exp.xlsx.gz

value: Wild type

value: inflorescences, 5.5-week-old plant

value: poly(A)+ RNA


title: C57Bl/6_13 LF_B6 [jos1744]

description: 13 LF_B6

value: Skeletal muscle


title: inflorescence_poly(A)+ rep3

description:
inflorescencerep2PA
processed data file: lncRNA_exp.xlsx.gz


title: C57Bl/6_15 LF_B6 [jos1753]

description: 15 LF_B6


title: 129S6/SvEvTac_10 HF_129 [jos1819]

description: 10 HF_129

value: Liver

value: high-fat


title: inflorescence_poly(A)+ rep2

description:
inflorescencerep1PA
processed data file: lncRNA_exp.xlsx.gz

value: Inflorescences, 5.5-week-old plant


title: nucleus pulposus-IDD-rep1

source_name: nucleus pulposus-IDD-rep1


title: nucleus pulposus-IDD-rep2

source_name: nucleus pulposus-IDD-rep2


title: drought_8h_poly(A)+ rep4

description:
drought8hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 8 hour post drought treatment

value: 2-week-old seedlings


title: nucleus pulposus-control-rep3

description: miRNAs expression in nucleus pulposus from control

source_name: nucleus pulposus-control-rep3

value: traumatic lumbar fracture


title: nucleus pulposus-control-rep2

source_name: nucleus pulposus-control-rep2


title: drought_8h_poly(A)+ rep3

description:
drought8hrep2PA
processed data file: lncRNA_exp.xlsx.gz

value: Columbia


title: nucleus pulposus-control-rep1

source_name: nucleus pulposus-control-rep1


title: drought_8h_poly(A)+ rep2

description:
drought8hrep1PA
processed data file: lncRNA_exp.xlsx.gz


title: drought_6h_poly(A)+ rep4

description:
drought6hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 6 hour post drought treatment


title: drought_6h_poly(A)+ rep3

description:
drought6hrep2PA
processed data file: lncRNA_exp.xlsx.gz


title: drought_6h_poly(A)+ rep2

description:
drought6hrep1PA
processed data file: lncRNA_exp.xlsx.gz


title: drought_4h_poly(A)+ rep4

description:
drought4hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 4 hour post drought treatment


title: 129S6/SvEvTac_8 HF_129 [jos1807]

description: 8 HF_129


title: drought_4h_poly(A)+ rep3

description:
drought4hrep2PA
processed data file: lncRNA_exp.xlsx.gz


title: 129S6/SvEvTac_7 HF_129 [jos1806]

description: 7 HF_129


title: 129S6/SvEvTac_9 HF_129 [jos1809]

description: 9 HF_129


title: 129S6/SvEvTac_6 LF_129 [jos1805]

description: 6 LF_129


title: 129S6/SvEvTac_12 LF_129 [jos1864]

description: 12 LF_129


title: 129S6/SvEvTac_11 LF_129 [jos1863]

description: 11 LF_129


title: drought_2h_poly(A)+ rep4

description:
drought2hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 2 hour post drought treatment


title: C57Bl/6_16 HF_B6 [jos1868]

description: 16 HF_B6


title: drought_4h_poly(A)+ rep2

description:
drought4hrep1PA
processed data file: lncRNA_exp.xlsx.gz


title: 129S6/SvEvTac_5 LF_129 [jos1804]

description: 5 LF_129


title: drought_2h_poly(A)+ rep2

description:
drought2hrep1PA
processed data file: lncRNA_exp.xlsx.gz


title: drought_0h_poly(A)+ rep4

description:
drought0hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 0 hour post drought treatment


title: drought_0h_poly(A)+ rep3

description:
drought0hrep2PA
processed data file: lncRNA_exp.xlsx.gz


title: C57Bl/6_14 HF_B6 [jos1866]

description: 14 HF_B6


title: C57Bl/6_13 HF_B6 [jos1865]

description: 13 HF_B6


title: drought_0h_poly(A)+ rep2

description:
drought0hrep1PA
processed data file: lncRNA_exp.xlsx.gz


title: C57Bl/6_2 LF_B6 [jos1762]

description: 2 LF_B6

value: low-fat


title: C57Bl/6_15 HF_B6 [jos1867]

description: 15 HF_B6


title: C57Bl/6_3 LF_B6 [jos1763]

description: 3 LF_B6


title: ABA_8h_poly(A)+ rep3

description:
ABA8hrep2PA
processed data file: lncRNA_exp.xlsx.gz

value: 8 hour post ABA treatment


title: C57Bl/6_1 LF_B6 [jos1761]

description: 1 LF_B6


title: drought_2h_poly(A)+ rep3

description:
drought2hrep2PA
processed data file: lncRNA_exp.xlsx.gz

value: Wild type


title: ABA_8h_poly(A)+ rep4

description:
ABA8hrep3PA
processed data file: lncRNA_exp.xlsx.gz


title: ABA_6h_poly(A)+ rep4

description:
ABA6hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 6 hour post ABA treatment

value: poly(A)+ RNAs


title: tre antiCD3+ide

city: Modena

first: silvia

last: martinelli

address: via del pozzo 71

country: Italy

institute: University of Modena and Reggio Emilia

description: gene expression after 1 hr treatment + 4 hrs stimulation

hyb_protocol: Cy3-labeled cRNAs (1.65 µg) were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized for 17 hours at 65°C on 4x44K Whole Human Genome Microarray (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Fluorescence data were analyzed with Feature Extraction Software v.10.7 (Agilent Technologies) to obtain background subtracted, spatially detrended Processed Signal intensities and quality control analyses. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: T cells pre-treated with idelalisib and stimulated with antiCD3

label_protocol: High quality RNAs were amplified and Cy3-labeled using Low Input Quick Amp Labeling kit (Agilent Technologies, Palo alto, CA, USA). Agilent RNA One-Color Spike-In was added in each sample to provide positive controls for monitoring the microarray workflow from sample amplification and labelling to microarray processing. All cRNA products were purified using RNeasy columns (QIAGEN). Dye incorporation and cRNA yield were checked with InfiniteM200 (Tecan). Samples had to contain at least 6 pmole of cyanine dye/µg of cRNA to be considered suitable for subsequent hybridization.

growth_protocol: Purified T cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNAs were extracted from purified T cells using RNeasy Mini kit Plus (QIAGEN, Valencia, CA, USA) following the manufacturer's recommendations.  RNAs were quantified using InfiniteM200 (Tecan)

treatment_protocol: Purified T cells were cultured with the three following conditions: i) ctrl (no treatment/no stimulation), ii) antiCD3 (stimulation with 500 ng/ml antiCD3 antibody for 4 hours), iii) antiCD3 + ide (treatment with 5 µM idelalisib for 1 hour followed by antiCD3 stimulation for 4 hours).

tag: cell type

value: T cells

value: peripheral blood

tag: disease state

value: CLL patient


title: tre antiCD3

description: gene expression after 4 hrs stimulation

source_name: T cells stimulated with antiCD3

value: stimulated with antiCD3


title: C57Bl/6_4 LF_B6 [jos1764]

description: 4 LF_B6

value: Liver

tag: diet


title: ABA_8h_poly(A)+ rep2

description:
ABA8hrep1PA
processed data file: lncRNA_exp.xlsx.gz

value: 8hour post ABA treatment

value: 2-week-old seedlings

value: poly(A)+ RNA


title: ABA_6h_poly(A)+ rep3

description:
ABA6hrep2PA
processed data file: lncRNA_exp.xlsx.gz

value: Columbia


title: gar antiCD3+ide

value: pre-treated with idelalisib and stimulated with antiCD3


title: leaf_feeding_L1_rep1

city: Berlin

first: Daniel

last: Geuss

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Biology

country: Germany

institute: Freie Universität Berlin

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer’s protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Data were analyzed using the “limma” software packages from Bioconductor in “R” (R Core Team; Ritchie et al. 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, 1.8 fold the fluorescence value of the 90% percentile of non-labelled hairpin DNA probes (dark-corner spots) was set as limit of detection on each microarray. About 20% of the probes showed fluorescence values below this threshold in at least one microarray within each treatment group. These probes were considered non-expressed and removed from further analysis in the paper. Background-correction and normalization across arrays was then performed after removal of the non-expressed genes.

organism: Solanum dulcamara

source_name: leaf, S. exigua fed

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacture’s protocol.

growth_protocol: Solanum dulcamara plants were grown from stem cuttings in a greenhouse at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol/ m s

extract_protocol: For each microarray sample, leaf material from three independent biological replicates was pooled. Leaf material was ground under liquid nitrogen and RNA was extracted with the NucleoSpin® RNA Plant kit (Macherey-Nagel GmbH & Co. KG) according to the manufacturer’s instructions using double the amount of RAP lysis buffer. RNA was DNase digested using TURBO DNA-free™ (AmbionTM) according to the manufacturer’s instructions.

treatment_protocol: The fifth fully developed was subjected to either Spodoptera exigua oviposition, received no eggs but feeding, received both egg deposition and feeding or remained untreated. Egg load ranged from 10 to 150 eggs and they were removed 3 d after oviposition. 12 neonate larvae per plant started feeding 12 hrs after egg removal on the previously egg-laden leaf or the corresponding leaf position of non-oviposited plants encaged in clip cages for 24 hrs. Then, this leaf and the corresponding leaf of unfed control- and egg-plants was cut at the petiole (the transcriptome analysis of this L0 leaf is uploaded as seperate data set) and the larvae were transferred to the adjacent upper leaf, which was harvested another 24 hours later (L1-leaf).

tag: genotype location

value: Erkner

value: S. exigua fed

value: L1 leaf


title: ABA_6h_poly(A)+ rep2

description:
ABA6hrep1PA
processed data file: lncRNA_exp.xlsx.gz

tag: genotype/variation


title: leaf_feeding_L1_rep2

value: Friesland


title: mat antiCD3

description: gene expression after 4 hrs stimulation


title: gar antiCD3

description: gene expression after 4 hrs stimulation


title: mat antiCD3+ide


title: tre ctrl

description: gene expression after 4 hrs culture

source_name: T cells not treated/not stimulated

value: not treated/not stimulated


title: leaf_eggs+feeding_L1_rep3

source_name: leaf, S. exigua oviposited + fed

value: Siethen

value: S. exigua oviposited + fed


title: leaf_feeding_L1_rep3


title: leaf_eggs+feeding_L1_rep2


title: ABA_4h_poly(A)+ rep4

description:
ABA4hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: Wild type

value: 4 hour post ABA treatment


title: PBS rep3

city: fuzhou

first: Zhe

last: Zhang

state: Fujian

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

department: Haixia Institute of Science and Technology

institute: Fujian Agriculture and Forestry University

description:
PBS3_L8_I396
processed data file: PBS.edgeR.DEG.all.Annotation.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality and quantity of RNA were checked using a NanoDrop 2000 spectrophotometer. mRNA was then purified using magnetic beads with Oligo (dT), and fragmented into short fragments, thus worked as templates for cDNA synthesis. Purified short cDNA fragments were connected with Illumina Truseq adapters. Subsequently, suitable cDNA fragments (350-450bp) separated by 2% agarose gel electrophoresis were selected for the PCR amplification as templates. Quantification and qualification of the sample libraries were assessed using an ABI StepOnePlus Real-Time PCR System. Finally, each library was sequenced using Illumina Hiseq2500 V4 at Berry Genomics Corporation in Beijing, China.(Borodina et al., 2011)
After removing reads containing sequencing adapters and reads of low quality, the paired-end reads were aligned to the moso bamboo genome.(Kim et al., 2013) Only the unique aligened reads were retained for the followed analysis. In order to identify the genes associated with BR regulation of shoot and root growth, each gene expression levels were normalized as fragments per kilobase of transcript per million mapped reads (FPKM)
Genome_build: EMBL: ERP001340
Supplementary_files_format_and_content: Excel files include RPKM values, fold change, FDR and gene annotation between each sample.

organism: Phyllostachys edulis

source_name: 1 μM BL after PPZ pretreatment_Shoot

growth_protocol: Moso bamboo seeds for RNA-seq were sterilized by chlorine gas for 4 hours then imbibed water for 24 hours at room temperature. Seeds were sowed onto half Murashige and Skoog medium with 0.7% phytagel and 1% sucrose, then grew under long-day conditions (16 h light / 8 h dark) at 24 °C for 18 days.

extract_protocol:
Total RNA  isolated by SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, Shanghai, China) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 18-day moso bamboo seedlings were transferred to 10 μM PPZ and mock medium for another 5 days. PPZ pre-treated seedlings were then treated with 1 μM BL or mock solution for 4 hours. Harvested seedling shoot and root separately, then frozen into liquid nitrogen immediately for further RNA sequencing analysis.

value: 23-day seedling

value: 1 μM BL after PPZ pretreatment

value: Shoot


title: gar ctrl

description: gene expression after 4 hrs culture

value: T cells

value: peripheral blood

value: CLL patient


title: leaf_eggs+feeding_L1_rep1


title: mat ctrl

description: gene expression after 4 hrs culture


title: PBS rep2

description:
PBS2_L8_I395
processed data file: PBS.edgeR.DEG.all.Annotation.xls


title: sga ctrl

description: gene expression after 4 hrs culture


title: sga antiCD3

description: gene expression after 4 hrs stimulation

value: stimulated with antiCD3


title: sga antiCD3+ide

value: pre-treated with idelalisib and stimulated with antiCD3


title: leaf_eggs_L1_rep3

source_name: leaf, S. exigua oviposited

value: S. exigua oviposited


title: PBS rep1

description:
PBS1_L8_I394
processed data file: PBS.edgeR.DEG.all.Annotation.xls


title: ABA_2h_poly(A)+ rep4

description:
ABA2hrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: Columbia

value: 2 hour post ABA treatment

value: 2-week-old seedlings

value: poly(A)+ RNA


title: ABA_4h_poly(A)+ rep3

description:
ABA4hrep2PA
processed data file: lncRNA_exp.xlsx.gz


title: PMS rep2

description:
PMS2_L4_I389
processed data file: PMS.edgeR.DEG.all.Annotation.xls

source_name: 10 μM PPZ treatment_Shoot

value: 10 μM PPZ treatment


title: Bham2_RNA(LM4)

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

data_processing:
Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score < 20) were removed with cutadapt (v.1.11) while processing both read pairs at the same time.
The filtered reads were mapped to the reference genome (GCA_001632505.1) using tophat2 (v.2.1.0).
The read counts for genes were extracted with HTSeq (v.0.9.1) using unstranded union mode for genes.
Gene expression in Daphnia magna Bham2-strain was compared to publicly available RNA-seq data on Daphnia magna Xinb3-strain (nature.com/articles/sdata201630) using age matched (5 day old) control samples, using DESeq2 (v1.18.1).
Genome_build: GCA_001632505.1
Supplementary_files_format_and_content: txt (gene expression count from RNA-seq mapping and differential expression analysis from DESeq2: expression_Bham2_Xinb3.txt.gz)

organism: Daphnia magna

source_name: whole organism

growth_protocol: Daphnia magna Bham 2 clones were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in high hardness COMBO medium (HH COMBO). Media were prepared using a protocol adapted from Baer & Goulden (1998) and Kilham et al. (1998), and renewed once a week. Animals were fed every other day with Chlorella vulgaris at a concentration of ≈27,550 cells of algae per individual Daphnia.

extract_protocol:
RNA was extracted using RNeasy micro kit (Qiagen) according to the manufactures protocol.
Daphnia magna RNA-seq libraries were prepared and sequenced using Illumina HiSeq-2500 platform at the Environmental Omics Sequencing Facility, University of Birmingham, UK

treatment_protocol: Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1).

tag: strain

tag: clone

value: Clone 2

tag: exposure

value: control

value: female

tag: replicate

value: 5 days

value: Maintained under standard condition with normal levels of oxygen (6 mg/L) for 5 days

tag: culturing media

value: HH COMBO


title: leaf_eggs_L1_rep2

value: Friesland

value: L1 leaf


title: leaf_control_L1_rep3

source_name: leaf, undamaged control

value: Siethen

value: undamaged control


title: ABA_0h_poly(A)+ rep4

description:
ABA0hrep3PA
processed data file: lncRNA_exp.xlsx.gz

tag: ecotype

value: Wild type

value: 0 hour post ABA treatment


title: Bham2_RNA(LM1)

tag: gender

tag: age

tag: treatment


title: ABA_2h_poly(A)+ rep3

description:
ABA2hrep2PA
processed data file: lncRNA_exp.xlsx.gz

value: Columbia

tag: molecule subtype


title: Bham2_RNA(LM2)


title: PMS rep1

description:
PMS1_L5_I388
processed data file: PMS.edgeR.DEG.all.Annotation.xls

value: 23-day seedling

tag: tissue

value: Shoot


title: Bham2_RNA(LM3)


title: MS rep3

description:
MS3_L5_I384
processed data file: PMS.edgeR.DEG.all.Annotation.xls

source_name: Mock treatment_Shoot

value: Mock treatment


title: leaf_control_L1_rep2


title: ABA_4h_poly(A)+ rep2

description:
ABA4hrep1PA
processed data file: lncRNA_exp.xlsx.gz

value: 4 hour post ABA treatment

value: 2-week-old seedlings

value: poly(A)+ RNA


title: ABA_2h_poly(A)+ rep2

description:
ABA2hrep1PA
processed data file: lncRNA_exp.xlsx.gz

value: 2 hour post ABA treatment


title: ABA_0h_poly(A)+ rep2

description:
ABA0hrep1PA
processed data file: lncRNA_exp.xlsx.gz


title: ABA_0h_poly(A)+ rep3

description:
ABA0hrep2PA
processed data file: lncRNA_exp.xlsx.gz


title: cold_20d_poly(A)+ rep4

description:
20Vrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 20 days post cold treatment


title: PMS rep3

description:
PMS3_L5_I390
processed data file: PMS.edgeR.DEG.all.Annotation.xls

value: 10 μM PPZ treatment


title: MS rep2

description:
MS2_L5_I383
processed data file: PMS.edgeR.DEG.all.Annotation.xls


title: MS rep1

description:
MS1_L5_I382
processed data file: PMS.edgeR.DEG.all.Annotation.xls


title: leaf_eggs_L1_rep1

value: Erkner

value: S. exigua oviposited


title: leaf_eggs+feeding_L0_rep2

data_processing: Data were analyzed using the “limma” software packages from Bioconductor in “R” (R Core Team; Ritchie et al. 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, 1.5 fold the fluorescence value of the 90% percentile of non-labelled hairpin DNA probes (dark-corner spots) was set as limit of detection on each microarray. About 15% of the probes showed fluorescence values below this threshold in at least one microarray within each treatment group. These probes were considered non-expressed and removed from further analysis in the paper. Background-correction and normalization across arrays was then performed after removal of the non-expressed genes.

growth_protocol: Solanum dulcamara plants were grown from seeds in a greenhouse at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol/ m s

treatment_protocol: The fifth fully developed was subjected to either Spodoptera exigua oviposition, received no eggs but feeding, received both egg deposition and feeding or remained untreated. Egg load ranged from 10 to 150 eggs and they were removed 3 d after oviposition. 12 neonate larvae per plant started feeding 12 hrs after egg removal on the previously egg-laden leaf or the corresponding leaf position of non-oviposited plants encaged in clip cages for 24 hrs. Then, this leaf and the corresponding leaf of unfed control- and egg-plants was cut at the petiole and immediately flash frozen in liquid nitrogen (L0-leaf).

value: Friesland

value: S. exigua oviposited + fed

value: L0 leaf


title: PBR rep3

description:
PBR3_L2_I393
processed data file: PBR.edgeR.DEG.all.Annotation.xls

source_name: 1 μM BL after PPZ pretreatment_Root

value: 1 μM BL after PPZ pretreatment

value: Root


title: leaf_eggs+feeding_L0_rep3

value: Siethen


title: leaf_feeding_L0_rep3

value: S. exigua fed


title: leaf_eggs+feeding_L0_rep1


title: leaf_feeding_L0_rep2


title: PBR rep2

description:
PBR2_L8_I392
processed data file: PBR.edgeR.DEG.all.Annotation.xls

value: 23-day seedling


title: cold_20d_poly(A)+ rep3

description:
20Vrep2PA
processed data file: lncRNA_exp.xlsx.gz

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) and treated with DNase I (Ambion). Polyadenylated [poly(A)+] RNAs were isolated from total RNA through two rounds of purification with oligo(dT) beads (QIAGEN).
Libraries for RNA-seq were generated using NEXTflex Rapid Directional qRNA-Seq Kit (dUTP based)according to the manufacturer's instructions.

value: Columbia

value: Wild type


title: leaf_control_L1_rep1

value: undamaged control

value: L1 leaf


title: cold_20d_poly(A)+ rep2

description:
20Vrep1PA
processed data file: lncRNA_exp.xlsx.gz

value: 2-week-old seedlings

value: poly(A)+ RNA


title: PMR rep3

description:
PMR3_L5_I387
processed data file: PMR.edgeR.DEG.all.Annotation.xls

source_name: 10 μM PPZ treatment_Root

value: 10 μM PPZ treatment


title: cold_0d_poly(A)+ rep4

description:
0Vrep3PA
processed data file: lncRNA_exp.xlsx.gz

value: 0 day post cold treatment


title: cold_0d_poly(A)+ rep2

description:
0Vrep1PA
processed data file: lncRNA_exp.xlsx.gz


title: Col-0 [ncRNA-seq]

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen) followed by PEG precipitation to enrich low molecular-weight sRNAs. The resulting sRNAs were resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-30nt were excised, and the RNAs were eluted and purified for small RNA library contruction.
Libraries for sRNA-seq were generated using NEBNext Small RNA Library Prep Set for Illumina (NEB) according to the manufacturer's instructions.


title: amiR-NAT569 [ncRNA-seq]


title: cold_0d_poly(A)+ rep3

description:
0Vrep2PA
processed data file: lncRNA_exp.xlsx.gz


title: PMR rep2

description:
PMR2_L5_I386
processed data file: PMR.edgeR.DEG.all.Annotation.xls


title: MR rep2

description:
MR2_L4_I380
processed data file: PMR.edgeR.DEG.all.Annotation.xls

source_name: Mock treatment_Root

value: Mock treatment


title: MR rep3

description:
MR3_L5_I381
processed data file: PMR.edgeR.DEG.all.Annotation.xls


title: PBR rep1

description:
PBR1_L5_I391
processed data file: PBR.edgeR.DEG.all.Annotation.xls


title: leaf_eggs_L0_rep2

value: Friesland

value: S. exigua oviposited


title: leaf_eggs_L0_rep3

value: L0 leaf


title: amiR-NAT3872 [ncRNA-seq]


title: Mock control (Aft2)

city: Paris

first: Antonin

last: Thiébaut

address: 7-9 quai Saint Bernard, building C, floor 3, room C321B

country: France

institute: Sorbonne Université

library_source: genomic

data_processing:
Quality of FASTQ files was controlled, using FASTQC program.
Nucleotides with a QC < 20 in 5' and 3' were trimmed using a home made Python program.
Reads were mapped on the reference genome (downloaded from Genolevures – http://genolevures.org/download.html#, C. glabrata CBS138) with default parameters, except for -m 1
BAM files were converted into BED files for peak calling with bPeaks program, using the genomeCov tool available in Bedtools.
Genome_build: C. glabrata CBS138
Supplementary_files_format_and_content: Bed files used to perform peak calling with bPeaks.

organism: Nakaseomyces glabratus

source_name: Candida glabrata cell culture

growth_protocol: All cultures were conducted in a rotative shaker at 30°C in YPD (Glucose 2%, yeast extract 1%, Bactopeptone 1%).

extract_protocol:
Cells were lysed and DNA was sheared by sonication into ~500 bp fragments. DNA-protein complexes were selected using the antibody specifically targeting the protein of interest.
Libraries were prepared according to Illumina's instructions

treatment_protocol: For ChIP, myc-tagged CgAft2 strains were grown in YPD until exponential phase (OD=0.8). They were then treated by 0.5 mM of BPS for 60 minutes. Cross-linking of the cells and ChIP were performed as described previously (Lelandais et al., Methods Mol Biol, 2016). Meanwhile, the parental DHTL (untagged strain) was grown and processed the same way to provide the mock-IP sample.

value: Mock

tag: antibody

value: parental


title: MR rep1

description:
MR1_L4_I301
processed data file: PMR.edgeR.DEG.all.Annotation.xls

value: Root


title: Input DNA control (Aft2)

value: BPS

value: input

value: myc-tagged CgAft2


title: leaf_control_L0_rep3

value: Siethen


title: Aft2 IP BPS treated sample


title: leaf_control_L0_rep1

value: Erkner

value: undamaged control


title: amiR-NAT3034 [ncRNA-seq]

value: Columbia

value: 2-week-old seedlings


title: 6PAE-2

city: Kaifeng

first: Jiasheng

last: Song

address: Jinming RD

institute: Henan University

description:
miRNA_exp.xlsx
6P-3

data_processing:
Illumina Casava1.7 software used for basecalling.
The clean reads were obtained by eliminating the low-quality reads, empty adapters, reads shorter than 18 nt. Sequences of tRNA, rRNA, snRNA, snoRNA and piRNA were removed by similarity search using the Rfam12.1 and piRNABank database. miRNAs were identified by blasting the rest sequences with miRbase (V21.0) and referring to the locust genome
Then the RPKM value were calculated for expression level quantification.
Genome_build: V2.4.1

organism: Locusta migratoria

source_name: fat body

extract_protocol:
total RNA was extracted using TRIzol
RNA library were prepared using standard Illumina protocols

tag: Sex

value: Female

tag: time point


title: amiR-NAT2680 [ncRNA-seq]


title: leaf_feeding_L0_rep1

value: S. exigua fed


title: amiR-NAT2671 [ncRNA-seq]


title: leaf_eggs_L0_rep1


title: 6PAE-1

description:
miRNA_exp.xlsx
6P-2


title: leaf_control_L0_rep2


title: 6PAE-3

description:
miRNA_exp.xlsx
6P-4


title: amiR-NAT2384 [ncRNA-seq]


title: 4PAE-3

description:
miRNA_exp.xlsx
4P-4


title: amiR-NAT2358 [ncRNA-seq]


title: 4PAE-1

description:
miRNA_exp.xlsx
4P-2


title: 4PAE-2

description:
miRNA_exp.xlsx
4P-3


title: DU145, olaparib treatment, 18h

city: bethesda

first: james

middle: w

last: hodge

state: md

address: 10/8b13, 9000 rockville pike

department: LTIB

institute: NCI

description: Du145 Ola 18h

data_processing: We used nSolver 2.0 (mac) for data analysis.  We compared 2 paired samples at a time, i.e. du145 prostate cancer cells, no treatment, 6 hours versus du145 prostate cancer cells, olaparib treated, 6 hours.  We used background thresholding with a threshold count of 20.   We used positive control normalization and geometric mean to compute.  Fold change estimation was compared to beseline (set as no treatment for each respective timepoint).  Ratio data was exported with RCC collector tool format export.

source_name: prostate carcinoma cell line

growth_protocol: All cell lines were passaged for less than 6 months, free of Mycoplasma and cultured at 37°C/5% CO2. 22RV1were maintained in RPMI, DU145 were maintained in EMEM. All media was supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 0.5% gentamicin, nonessential amino acids, and L-glutamine.

extract_protocol: RNAzol

treatment_protocol: Olaparib was obtained from Selleck Biochemical (Houston, TX). For cytotoxic assays, adherent tumor cells in log-growth phase based on real-time cell analysis were exposed for 24h to olaparib (20µM). For flow cytometry, Western blots, and NanoString, cells at 50-80% confluency were exposed to olaparib (20µM) while incubating at 37C/5% CO2.

tag: agent

value: olaparib

tag: cell line


title: DU145, olaparib treatment, 12h

description: Du145 Ola 12h


title: amiR-NAT3043 [ncRNA-seq]

tag: genotype/variation


title: DU145, no treatment, 18h

description: Du145 NT 18h


title: DU145, olaparib treatment, 6h

description: Du145 Ola 6h


title: DU145, no treatment, 12h

description: Du145 NT 12h


title: 2PAE-3

description:
miRNA_exp.xlsx
2P-4


title: amiR-NAT2195 [ncRNA-seq]


title: 22rv1, olaparib treatment, 18h

description: 22rv1 Ola 18h


title: 2PAE-2

description:
miRNA_exp.xlsx
2P-3


title: 22rv1, olaparib treatment, 12h

description: 22rv1 Ola 12h


title: 22rv1, olaparib treatment, 6h

description: 22rv1 Ola 6h


title: amiR-NAT1336 [ncRNA-seq]


title: 0PAE-3

description:
miRNA_exp.xlsx
0P-4


title: amiRMAS-2 [ncRNA-seq]


title: 0PAE-2

description:
miRNA_exp.xlsx
0P-3


title: 22rv1, no treatment, 18h

description: 22rv1 NT 18h


title: amiRMAS-1 [ncRNA-seq]


title: 22rv1, no treatment, 12h

description: 22rv1 NT 12h


title: DU145, no treatment, 6h

description: Du145 NT 6h


title: 0PAE-1

description:
miRNA_exp.xlsx
0P-1


title: Nip 1

status: Public on Dec 10 2018

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

data_processing:
After removing the adapter and primer sequences and low quality reads with more than 20% low quality bases (quality < 20) were filtered out. The the clean reads were mapped to the reference genome using Tophat262 and gene expression level was calculated by Cufflinks using default parameters.
Genome_build: Nip-BRI
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Oryza sativa

source_name: Whole plant

growth_protocol: Rice plants were grown on Yoshida solution in a growth chamber under short day (SD) condition (10 h light/14 h dark) with a light intensity of 800 μmol m-2 s-1。

extract_protocol:
RNAs from 3-week-old Nip seedlings were extracted by RNeasy Plus Mini Kit (Qiagen).
We generated the cDNA libraries using an NEBNext Ultra RNA Library Prep Kit (Neb). The quantified libraries were then prepared for sequencing on the Illumina HiSeq X-ten sequencing platform.

value: Whole plant

tag: cultivar

value: Nipponbare

tag: developmental stage


title: 93-11 1

data_processing:
After removing the adapter and primer sequences and low quality reads with more than 20% low quality bases (quality < 20) were filtered out. The the clean reads were mapped to the reference genome using Tophat2 and gene expression level was calculated by Cufflinks using default parameters.
Genome_build: 93-11-BRI
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
RNAs from 3-week-old 93-11 seedlings were extracted by RNeasy Plus Mini Kit (Qiagen).
We generated the cDNA libraries using an NEBNext Ultra RNA Library Prep Kit (Neb). The quantified libraries were then prepared for sequencing on the Illumina HiSeq X-ten sequencing platform.


title: Nip 2


title: 93-11 2


title: PMR rep1

description:
PMR1_L5_I385
processed data file: PMR.edgeR.DEG.all.Annotation.xls

value: 23-day seedling

value: 10 μM PPZ treatment


title: amiR-NAT2088 [ncRNA-seq]


title: amiR-NAT1427 [ncRNA-seq]


title: 2PAE-1

description:
miRNA_exp.xlsx
2P-2


title: 22rv1, no treatment, 6h

description: 22rv1 NT 6h


title: c3p: Posterior part Control (Lhx1+/flox; Meox2+/Cre), replicate 3

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

hyb_protocol: not provided

scan_protocol: not provided

data_processing: GenomeStudio was used to convert .idat files to summarised probe-level data. The beadarray library in R was used to recalculate detection scores prior to normalisation, and a detection score of 0 was assigned to beads with a higher intensity than all the negative controls. Subsequently, the expression data was quantile normalised and log2 transformed. Probes with missing or poor annotation according to the illuminaMousev2.db library were removed from subsequent analysis. This library was also used to convert probe annotation to gene annotation. Genes with multiple probes were summarised the avereps function in the Limma. Genes with a detection p-value <0.05 were considered as expressed. Genes were considered significantly differentially expressed if they had an adjusted p-value <0.05

source_name: 5 x E7.75 embryos

label_protocol: not provided

growth_protocol: Embryos of the genotype Lhx1-/flox; Meox2+/Cre (Lhx1epiCKO) and Lhx1+/flox; Meox2+/Cre were collected at E7.75 from early bud to early head-fold stage and the anterior and posterior region of the epiblast dissected separately.

extract_protocol: RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Three biological replicates consisting of five anterior or posterior halves pooled each were used for each genotype.

value: embryonic head

tag: region

value: Posterior part

tag: genotype

value: Lhx1+/flox; Meox2+/Cre


title: m1p: Posterior part Lhx1epiCKO (Lhx1-/flox; Meox2+/Cre), replicate 1

value: Lhx1-/flox; Meox2+/Cre


title: m2p: Posterior part Lhx1epiCKO (Lhx1-/flox; Meox2+/Cre), replicate 2


title: m3a: Anterior part Lhx1epiCKO (Lhx1-/flox; Meox2+/Cre), replicate 3

value: Anterior part


title: m1a: Anterior part Lhx1epiCKO (Lhx1-/flox; Meox2+/Cre), replicate 1


title: c1a: Anterior part Control (Lhx1+/flox; Meox2+/Cre), replicate 1


title: c2p: Posterior part Control (Lhx1+/flox; Meox2+/Cre), replicate 2


title: c3a: Anterior part Control (Lhx1+/flox; Meox2+/Cre), replicate 3


title: m3p: Posterior part Lhx1epiCKO (Lhx1-/flox; Meox2+/Cre), replicate 3


title: c1p: Posterior part Control (Lhx1+/flox; Meox2+/Cre), replicate 1


title: m2a: Anterior part Lhx1epiCKO (Lhx1-/flox; Meox2+/Cre), replicate 2


title: FOXO3 - FOXO3dn transfection - mouse 6

city: Stockholm

first: Leonidas

middle: S

last: Lundell

state: Stockholm

address: Von Eulers Väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

hyb_protocol: Hybridized to Affymetrix Human Mouse Gene ST Array 2.1 according to manufacturer's protocols in a GeneChip Hybridization Oven 640 (Affymetrix). Arrays were washed and stained with a GeneChip Gluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Pre-processing of data was performed using Robust Multi-array Average (RMA) using oligo, mogene21sttranscriptcluster.db, and collapsed using WGCNA.

source_name: Tibialis anterior, 2 hours post oral glucose tolerance test, FOXOdn plasmid

label_protocol: Sense strand cDNA was synthesized from total RNA with Ambion® WT Expression Kit (Life Techniologies) and biotin labeled with the Affymetrix® GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: EZ RNA extraction kit according to manufacturer instruction

treatment_protocol: Male, 30 weeks, C57BL/6J

value: male

tag: strain

value: 30 weeks

value: Tibialis anterior


title: FOXO3 - control plasmid transfection - mouse 5

source_name: Tibialis anterior, 2 hours post oral glucose tolerance test, control plasmid


title: c2a: Anterior part Control (Lhx1+/flox; Meox2+/Cre), replicate 2


title: HSC_6 OE Tr.4

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description: overexpression

hyb_protocol: The samples were hybridized to HuGene ST1.0 microarrays according to standardized protocols from Affymetrix.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were normalized by RMA (Affymetrix Power Tools).

source_name: Cord blood 6

label_protocol: biotin

growth_protocol: Cord blood samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (Permit number: EK 187-08). CD34+ HSPCs were isolated from cord blood and cultured in StemSpan Serum-Free Expansion Medium supplemented with 10 μg/mL heparin, 20 ng/mL thrombopoietin, 10 ng/mL stem cell factor, 10 ng/mL fibroblast growth factor 1 and 100 U/mL penicillin/streptomycin.

extract_protocol: Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel) acording to the manufacturers instructions

treatment_protocol: For knockdown (KD) or overexpression (OE) of specific transcripts the HSPCs were lentivirally infected 1 day after isolation and selected with 2.5 µg/mL puromycin at day 2 post infection. To knockdown DNMT3A transcripts we designed short hairpin RNAs (shRNAs) to target transcript-specific exons: exon 5 of  transcript 1+3 (ENSE00001486208), exon 2 of  transcript 2 (ENSE00001486123), and exon 4  of  transcript 4 (ENSE00001559474). In brief, forward and reverse oligonucleotides (Metabion, Planegg, Germany) were joined and ligated into the pLKO.1 vector (Addgene, Cambridge, MA, USA) that drives shRNA expression from the human U6 promoter and carries the puromycin resistance gene. For constitutive overexpression of DNMT3A transcripts the sequences of the transcripts were amplified from cDNA of human blood cells with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA, USA) using exon-specific primers.

tag: cell type

value: CD34+ HSCs

tag: primary tissue

value: cord blood

tag: dnmt3a transcript

value: DNMT3A transcript 4


title: HSC_6 Empty

description: overexpression

value: Control


title: FOXO3 - FOXO3dn transfection - mouse 5

tag: gender

tag: age


title: HSC_6 OE Tr.2

description: overexpression

value: DNMT3A transcript 2


title: FOXO3 - control plasmid transfection - mouse 4

tag: tissue


title: HSC_6 OE Tr.1+3

description: overexpression

value: DNMT3A transcripts 1+3


title: HSC_5 OE Tr.2

description: overexpression

source_name: Cord blood 5


title: FOXO3 - FOXO3dn transfection - mouse 3


title: FOXO3 - FOXO3dn transfection - mouse 4


title: FOXO3 - control plasmid transfection - mouse 6


title: HSC_5 Empty

description: overexpression


title: HSC_5 OE Tr.4

description: overexpression


title: FOXO3 - control plasmid transfection - mouse 3


title: HSC_5 OE Tr.1+3

description: overexpression


title: HSC_4 Empty

description: overexpression

source_name: Cord blood 4


title: FOXO3 - control plasmid transfection - mouse 2


title: HSC_4 OE Tr.2

description: overexpression


title: FOXO3 - FOXO3dn transfection - mouse 2


title: HSC_4 OE Tr.4

description: overexpression


title: HSC_3 KD Tr.2

description: knockdown

source_name: Cord blood 3


title: FOXO3 - FOXO3dn transfection - mouse 1


title: HSC_3 KD Tr.4

description: knockdown


title: HSC_3 Scramble

description: knockdown


title: HSC_4 OE Tr.1+3

description: overexpression


title: HSC_2 Scramble

description: knockdown

source_name: Cord blood 2


title: FOXO1 - control plasmid transfection - mouse 5


title: FOXO1 - FOXO1dn transfection - mouse 5


title: HSC_3 KD Tr.1+3

description: knockdown


title: FOXO1 - FOXO1dn transfection - mouse 6


title: FOXO1 - FOXO1dn transfection - mouse 4


title: HSC_2 KD Tr.1+3

description: knockdown


title: FOXO3 - control plasmid transfection - mouse 1


title: HSC_2 KD Tr.4

description: knockdown


title: FOXO1 - control plasmid transfection - mouse 3


title: SS6_Combination

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Base calling was performed using RTA (Illumina) and converted to fastq format using bcl2fastq (version 2.17).
RNA-sequencing reads were aligned to GRCh38 using STAR v2.5 with default parameter settings.
Read counts were summarized to the gene-level using featureCounts (from Subread package).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read count matrix summarized to the gene-level by featureCounts is provided.

source_name: Primary Sample

growth_protocol: Primary cells were cultured in RPMI 1640 medium + 2.05mM L-Glutamine (Hyclone) supplemented with penicillin (100µg/mL), streptomycin (50µg/mL), 10% human serum (Sigma-Aldrich), 10ug/mL IL-2, 10ug/mL IL-7 (PeproTech, Rocky Hill, NJ, USA). Prior to drug treatments, the cells were stimulated for 48 hours with 10ug/mL plated anti-CD3 and 2ug/mL soluble anti-CD28 (Thermo Fisher). Cell lines were cultured in RPMI 1640 medium + 2.05mM L-Glutamine (Hyclone, Logan, UT, USA) supplemented with penicillin (100µg/mL), streptomycin (50µg/mL), and 10% Fetal Bovine Serum (FBS) for SeAx and HH, and 20% FBS for Hut78. All cells were incubated at 37°C in a humidified atmosphere containing 5% CO2 and checked periodically for mycoplasma contamination using MycoSensor qPCR Assay Kits (Agilent, Santa Clara, CA, USA).

extract_protocol:
Cells treated for 24 hours under the 4 treatment conditions were washed with sterile PBS and flash frozen in liquid nitrogen. Total RNA was extracted from cell pellets by guanidinium thiocyanatephenol-chloroform extraction (TriZol, Sigma-Aldrich) and purified using RNeasy mini kit (QIAGEN, Germantown, MD, USA). Quantity and quality of isolated RNA were assessed using an Agilent Bioanalyzer 2100 and samples were stored at -80ºC.
RNA-seq libraries were generated at the Sulzberger Genome Center at Columbia University Medical Center using the TruSeq Stranded RNA Library Prep kit with RiboZero gold (Illumina). Libraries were multiplexed and sequenced on an Illumina HiSeq2500 to obtain 100bp, paired-end reads to a target depth of 30 million reads per sample.

treatment_protocol: Cell lines and primary samples were each treated with vehicle, single agents and the drug combination, using doses equivalent to the 48-hour IC50 of each drug.

value: CD4+ T cells

value: Combination


title: FOXO1 - control plasmid transfection - mouse 4


title: FOXO1 - control plasmid transfection - mouse 1


title: HSC_1 Scramble

description: knockdown

source_name: Cord blood 1


title: SS6_Mechlorethamine

value: Mechlorethamine


title: FOXO1 - control plasmid transfection - mouse 6


title: HSC_2 KD Tr.2

description: knockdown


title: HSC_1 KD Tr.1+3

description: knockdown


title: SS6_Romidepsin

value: Romidepsin


title: FOXO1 - FOXO1dn transfection - mouse 1


title: SS6_DMSO

value: DMSO


title: SS5_Romidepsin


title: SS5_Mechlorethamine


title: FOXO1 - FOXO1dn transfection - mouse 2


title: SS5_DMSO


title: FOXO1 - FOXO1dn transfection - mouse 3


title: HSC_1 KD Tr.2

description: knockdown


title: SS4_Romidepsin


title: SS4_Mechlorethamine


title: SS4_DMSO


title: S-LSER3-6DAF: Stress Lateral  Starchy Endosperm Replicate 3

city: Niigata

first: Tsutomu

last: Ishimaru

address: 1-2-1 Inada, Joetsu, Niigata

institute: Central Region Agricultural Research Center, National Agriculture and Food Research Organization (CARC/NARO)

description:
Raw data file: US22502560_251524110676_S01_GE2-v5_95_Feb07_1_4.txt
A microdissected samples of  lateral starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 3 of 3.

hyb_protocol: 1250 ng of labeled cRNAs were fragmented and hydridized on a slide glass of rice 4 × 44K microarray RAP-DB (G2519F#1524 ; Agilent Technologies).

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner, and background of the Cy3 and Cy5 raw signals was corrected using the Feature Exraction (ver. 10.5.1.1, Agilent Technologies).

data_processing:
The two channels Agilent microarray expression data of 12 microdissected samples of dorsal aluerone cells (AL), dorsal starchy endosperm (DSE), central starchy endosperm (CSE) and lateral starchy endosperm (LSE) at 7DAF from control and at 6DAF from heat stressed tissues consisting of three replicates was further processed (ratio computation, log transformation and baseline transformation) using the software GeneSpring GX version 12 (Agilent, Santa Carla, CA).
Limma R (Ritchie et al., 2015) package is used following the empirical Bayes method (Smyth, 2004) to shrink the probe-wise sample variances towards a common value and to augmenting the degrees of freedom for the individual variances. The P-values adjustment method was used (Bonferroni, 1936). The top-ranked genes having an adjusted P-value below <=0.05 and log2 fold change above +/- 1 were selected.

source_name: LSE Lateral  Starchy Endosperm

label_protocol: Total RNA (5.0 ng) was amplified to obtain complementary RNA (cRNA) using two-color Quick Amp Labeling kit (Agilent technologies). RNA extracted from control and high-temperature condition was labeled with cyanine-3 (Cy3)-CTP and cyanine-5 (Cy5)-CTP, respectively. Three biological replicates were prepared from high temperature conditions as well under control conditions.

growth_protocol: Rice plants cv. 'Koshihikari' were grown in 1/2000 pots. At three days after flowering (DAF), pots were moved to the naturally-illuminated temperature controlled chamber.

extract_protocol: Developing caryopses was fixed with the ice-cooled mixture of ethanol-acetic acid (3 :1), embeded in 2% carboxymethyl cellulose following the method of Ishimaru et al. (2007). After making the cryo-section, fine tissues of developing endosperm were microdissected with AS LMD system (Leica Microsystems, Germany). Total RNA was extracted with Picopure RNA isolation kit (Arcturus Engineering).

treatment_protocol: Control and high temperature condition were set at 26/20 oC and 33/27 oC (day/night), respectively. Day and night length was 13 (0600-1900 h) and 11 (1900-0600 h) hours, respectively. Plants were kept in the chambers from three days after flowering until 30-35 DAF

value: Koshihikar

value: Endosperm

value: Lateral  Starchy Endosperm


title: S-CSER3-6DAF: Stress Central Starchy Endosperm Replicate 3

description:
Raw data file: US22502560_251524110216_S01_GE2-v5_91_0806_1_3.txt
A microdissected samples of  central starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 3 of 3.

source_name: CSE Central Starchy Endosperm

value: Central Starchy Endosperm


title: SS3_Combination


title: SS5_Combination


title: S-LSER1-6DAF: Stress Lateral  Starchy Endosperm Replicate 1

description:
Raw data file: US22502560_251524110676_S01_GE2-v5_95_Feb07_1_2.txt
A microdissected samples of  lateral starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 1 of 3.


title: SS3_Mechlorethamine


title: HSC_1 KD Tr.4

description: knockdown


title: SS4_Combination


title: S-CSER1-6DAF: Stress Central Starchy Endosperm Replicate 1

description:
Raw data file: US22502560_251524110216_S01_GE2-v5_91_0806_1_1.txt
A microdissected samples of  central starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 1 of 3.


title: SS3_Romidepsin


title: SS3_DMSO


title: S-DSER1-6DAF: Stress Dorsal Starchy Endosperm Replicate 1

description:
Raw data file: US22502560_251524111743_S01_GE2-v5_95_Feb07_1_1.txt
A microdissected samples of  dorsal starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 1 of 3.

source_name: DSE Dorsal Starchy Endosperm

value: Dorsal Starchy Endosperm


title: S-CSER2-6DAF: Stress Central Starchy Endosperm Replicate 2

description:
Raw data file: US22502560_251524110216_S01_GE2-v5_91_0806_1_2.txt
A microdissected samples of  central starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 2 of 3.


title: S-ALR1-6DAF: Stress Aleurone Cell Replicate 1

description:
Raw data file: US22502560_251524110215_S01_GE2-v5_91_0806_1_1.txt
A microdissected samples of  aluerone cells  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 1 of 3.

source_name: AL Aleurone Cell

value: Aleurone Cell


title: S-LSER2-6DAF: Stress Lateral  Starchy Endosperm Replicate 2

description:
Raw data file: US22502560_251524110676_S01_GE2-v5_95_Feb07_1_3.txt
A microdissected samples of  lateral starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 2 of 3.


title: S-DSER2-6DAF: Stress Dorsal Starchy Endosperm Replicate 2

description:
Raw data file: US22502560_251524111743_S01_GE2-v5_95_Feb07_1_2.txt
A microdissected samples of  dorsal starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 2 of 3.


title: S-ALR2-6DAF: Stress Aleurone Cell Replicate 2

description:
Raw data file: US22502560_251524110215_S01_GE2-v5_91_0806_1_2.txt
A microdissected samples of  aluerone cells  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 2 of 3.


title: C-LSER2-7DAF: Control Lateral  Starchy Endosperm Replicate 2

description:
Raw data file: US22502560_251524110676_S01_GE2-v5_95_Feb07_1_3.txt
A microdissected samples of  lateral starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 2 of 3.


title: C-LSER3-7DAF: Control Lateral  Starchy Endosperm Replicate 3

description:
Raw data file: US22502560_251524110676_S01_GE2-v5_95_Feb07_1_4.txt
A microdissected samples of  lateral starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 3 of 3.


title: S-DSER3-6DAF: Stress Dorsal Starchy Endosperm Replicate 3

description:
Raw data file: US22502560_251524111892_S01_GE2-v5_95_Feb07_1_4.txt
A microdissected samples of  dorsal starchy endosperm  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 3 of 3.


title: SS2_Mechlorethamine


title: S-ALR3-6DAF: Stress Aleurone Cell Replicate 3

description:
Raw data file: US22502560_251524110215_S01_GE2-v5_91_0806_1_3.txt
A microdissected samples of  aluerone cells  at 7DAF (days after fertilization) from high-temperature condition;Biological replicate 3 of 3.


title: SS2_DMSO


title: SS2_Combination


title: C-CSER3-7DAF: Control Central Starchy Endosperm Replicate 3

description:
Raw data file: US22502560_251524110216_S01_GE2-v5_91_0806_1_3.txt
A microdissected samples of  central starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 3 of 3.


title: SS2_Romidepsin


title: C-CSER2-7DAF: Control Central Starchy Endosperm Replicate 2

description:
Raw data file: US22502560_251524110216_S01_GE2-v5_91_0806_1_2.txt
A microdissected samples of  central starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 2 of 3.


title: SS1_Mechlorethamine


title: SS1_DMSO


title: SS1_Combination


title: SS1_Romidepsin


title: Hut78_Romidepsin


title: Hut78_Combination


title: WTD16R3: FLAG-Lhx1 wild-type doxycycline at 16 h repiicate 3

data_processing:
Trimmomatic version 0.33 was used to trim adapters and loq quality reads using the following paramters: ILLUMINACLIP:Illumina_trueSeq_Adapters 2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:15 MINLEN:36.
Tophat version 2.1.1 was used to align trimmed reads to the mm10 genome using the parameters --library-type fr-firststrand and --no-novel-juncs
Genes were qualified using summarizeOverlaps in R and differential gene expression analysis was performed using Limma Voom with the FDR<0.05 as a significance threshold.

source_name: ESC-derived embryoid bodies

growth_protocol: FLAG-Lhx1 mutant/FLAG-Lhx1 wild-type expressing embryonic stem cells were differentiated into embryoid bodies over a 2 day period.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
TruSeq RNA Sample Prep Kit

treatment_protocol: Embryoid bodies were either treated or not treated with doxycycline for 16 h.

value: ESC-derived embryoid bodies

tag: differentiation time

value: 2 days

value: FLAG-Lhx1 wild-type A2lox.cre ESCs


title: Hut78_DMSO


title: WTD16R2: FLAG-Lhx1 wild-type doxycycline at 16 h repiicate 2


title: Hut78_Mechlorethamine


title: WTC16R3: FLAG-Lhx1 wild-type no doxycycline control at 16 h repiicate 3


title: C-CSER1-7DAF: Control Central Starchy Endosperm Replicate 1

description:
Raw data file: US22502560_251524110216_S01_GE2-v5_91_0806_1_1.txt
A microdissected samples of  central starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 1 of 3.


title: C-DSER2-7DAF: Control Dorsal Starchy Endosperm Replicate 2

description:
Raw data file: US22502560_251524111743_S01_GE2-v5_95_Feb07_1_2.txt
A microdissected samples of  dorsal starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 2 of 3.


title: C-DSER1-7DAF: Control Dorsal Starchy Endosperm Replicate 1

description:
Raw data file: US22502560_251524111743_S01_GE2-v5_95_Feb07_1_1.txt
A microdissected samples of  dorsal starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 1 of 3.


title: WTC16R1: FLAG-Lhx1 wild-type no doxycycline control at 16 h repiicate 1


title: C-ALR3-7DAF: Control Aleurone Cell Replicate 3

description:
Raw data file: US22502560_251524110215_S01_GE2-v5_91_0806_1_3.txt
A microdissected samples of  aluerone cells  at 7DAF (days after fertilization) from control condition;Biological replicate 3 of 3.


title: C-ALR2-7DAF: Control Aleurone Cell Replicate 2

description:
Raw data file: US22502560_251524110215_S01_GE2-v5_91_0806_1_2.txt
A microdissected samples of  aluerone cells  at 7DAF (days after fertilization) from control condition;Biological replicate 2 of 3.


title: C-DSER3-7DAF: Control Dorsal Starchy Endosperm Replicate 3

description:
Raw data file: US22502560_251524111892_S01_GE2-v5_95_Feb07_1_4.txt
A microdissected samples of  dorsal starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 3 of 3.


title: WTC16R2: FLAG-Lhx1 wild-type no doxycycline control at 16 h repiicate 2


title: HH_Combination

source_name: HH

value: HH


title: HH_DMSO


title: MUTD16R3: FLAG-Lhx1 mutant doxycycline at 16 h repiicate 3

value: FLAG-Lhx1 mutant A2lox.cre ESCs


title: MUTD16R1: FLAG-Lhx1 mutant doxycycline at 16 h repiicate 1


title: HH_Mechlorethamine


title: HH_Romidepsin


title: C-ALR1-7DAF: Control Aleurone Cell Replicate 1

description:
Raw data file: US22502560_251524110215_S01_GE2-v5_91_0806_1_1.txt
A microdissected samples of  aluerone cells  at 7DAF (days after fertilization) from control condition;Biological replicate 1 of 3.


title: WTD16R1: FLAG-Lhx1 wild-type doxycycline at 16 h repiicate 1


title: MUTD16R2: FLAG-Lhx1 mutant doxycycline at 16 h repiicate 2


title: FOXO1 - control plasmid transfection - mouse 2

value: male

value: 30 weeks

value: Tibialis anterior


title: MUTC16R2: FLAG-Lhx1 mutant no doxycycline control at 16 h repiicate 2


title: MUTC16R3: FLAG-Lhx1 mutant no doxycycline control at 16 h repiicate 3


title: C-LSER1-7DAF: Control Lateral  Starchy Endosperm Replicate 1

description:
Raw data file: US22502560_251524110676_S01_GE2-v5_95_Feb07_1_2.txt
A microdissected samples of  lateral starchy endosperm  at 7DAF (days after fertilization) from control condition;Biological replicate 1 of 3.


title: SeAx_DMSO

source_name: SeAx

value: SeAx


title: SeAx_Mechlorethamine

value: Mechlorethamine


title: MMTV-Neu.180152.Entinostat.CRtoPD.expression

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: gene expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

scan_protocol: Agilent Technologies Scanner Using Feature Extraction Software

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Whole Mouse Reference RNA

extract_protocol: Qiagen Rneasy Kit

tag: mouse RNA reference

tag: sample type

value: MMTV/Neu

tag: treatment


title: MMTV-Neu.180225.Entinostat.CRtoPD.expression

description: gene expression


title: MMTV-Neu.180226.Entinostat.de_novo.expression

description: gene expression


title: MMTV-Neu.180165.Entinostat.de_novo.expression

description: gene expression


title: MMTV-Neu.180165.Entinostat.CRtoPD.expression

description: gene expression


title: MMTV-Neu.180153.Entinostat.CRtoPD.expression

description: gene expression


title: MMTV-Neu.180238.Entinostat.CRtoPD.expression

description: gene expression


title: MMTV-Neu.178117.Entinostat.CRtoPD.expression

description: gene expression


title: SeAx_Romidepsin

tag: cell line

tag: agent

value: Romidepsin


title: MMTV-Neu.177758.Entinostat.6wk.expression

description: gene expression


title: MMTV-Neu.177754-2.Entinostat.6wk.expression

description: gene expression


title: MMTV-Neu.180221.Entinostat.6wk.expression

description: gene expression


title: MMTV-Neu.180161.Entinostat.6wk.expression

description: gene expression


title: MMTV-Neu.179063.Entinostat.6wk.expression

description: gene expression


title: MMTV-Neu.176662.Entinostat.3wk.expression

description: gene expression


title: MMTV-Neu.177754.Entinostat.6wk.expression

description: gene expression


title: MMTV-Neu.178267.Entinostat.3wk.expression

description: gene expression


title: MMTV-Neu.177757.Entinostat.3wk.expression

description: gene expression


title: MMTV-Neu.177755.Entinostat.3wk.expression

description: gene expression


title: MMTV-Neu.173360.Untreated.expression

description: gene expression

value: Untreated


title: MMTV-Neu.179059.Untreated.expression

description: gene expression


title: SeAx_Combination

value: Combination


title: MMTV-Neu.175389.Untreated.expression

description: gene expression


title: MMTV-Neu.179065.Untreated.expression

description: gene expression


title: MMTV-Neu.178113.Entinostat.3wk.expression

description: gene expression


title: MMTV-Neu.180264.Untreated.expression

description: gene expression


title: MMTV-Neu.176661.Untreated.expression

description: gene expression


title: HMPV

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
For data analysis, FASTQ files were generated using CASAVA v1.8.1.
FastQC software (Version 0.9.6) was used to evaluate the quality of the files.
The trimming of adapter sequences from the reads was performed using fastq-mcf utility
Reads were then aligned to mature human microRNAs, release 21, from miRBase using miRNAkey v1.2
EBSeq was used to perform differential expression testing at a false discovery rate (FDR) of 5% or less
Genome_build: miRBASE Release 21
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each sample

source_name: moDC infected with HMPV

growth_protocol: Monocyte-derived dendritic cells (moDC) were generated from human peripheral blood mononuclear cells (PBMC) from healthy donors

extract_protocol:
RNA from uninfected, RSV- and HMPV-infected moDC was isolated using the RNAeasy plus kit (Qiagen).
Library preparation was performed  from 1µg of total RNA using the TruSeq Small RNA Sample Preparation kit (Illumina Inc., San Diego, CA).

treatment_protocol: moDC (10^6) were plated in 12-multiwell plates in a total volume of 1 ml of medium. Cells were infected with RSV or HMPV at a multiplicity of infection (MOI) of 3, or were left uninfected (control), for 24h before RNA extraction.

tag: intrinsic subtype

value: HMPV

value: monocyte-derived dendritic cells


title: MMTV-Neu.180266.Untreated.expression

description: gene expression


title: RSV

source_name: moDC infected with RSV

value: RSV


title: Uninfected

source_name: moDC

value: Uninfected


title: MMTV-Neu.180265.Untreated.expression

description: gene expression


title: MUTC16R1: FLAG-Lhx1 mutant no doxycycline control at 16 h repiicate 1

value: ESC-derived embryoid bodies

value: 2 days


title: SKBR3.Untreated.A

description: cell line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software

source_name: Human Reference B

extract_protocol: Total RNA isolated by stratagene

value: Human Reference B

source_name: Breast cancer, Cell_lines, Untreated

value: Untreated for 72 hours


title: SKBR3.Untreated.C

description: cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: SKBR3.Untreated.D

description: cell line


title: SKBR3.Untreated.B

description: cell line


title: SKBR3.Entinostat.D

description: cell line

source_name: Breast cancer, Cell_lines, Entinostat-treated

value: Treated by Entinostat for 72 hours at the IC50 doses


title: Ecoli_MG1655(Δpnp)_T0_rep3_re-analysis

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

institute: TBI

description:
SAMPLE 9
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing: Raw probe intensities ( .pair files three replicates for each strain) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Raw probe intensities were processed and analyzed with the R computing environment using the affy and limma packages of Bioconductor. Raw data were submitted to a RMA-based background correction [Irizarry et al, 2003, Biostatistics 4(2): 249-264]. After background correction, intra-replicate quantile normalization was performed for each strain. A set of probes in the background for which the ranks were roughly invariant across all nine arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition. Intensity values were multiplied by the total RNA extraction yield (in µg total RNA per mg of dry cell weight) to provide the mRNA concentration value in arbitrary units per mg of dry cell weight.

organism: Escherichia coli str. K-12 substr. MG1655

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit

growth_protocol: The laboratory strain E. coli K12 MG1655 and two mutant strains E. coli MG1655_rnr) and E. coli MG1655_pnp) were grown in baffled flasks in LB medium at 37 °C and 180 rpm. Initial pH was set to 7. All cultures were inoculated at OD 0.1 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Cultures were performed in triplicate.

extract_protocol: After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively. Total RNA extraction profiles were checked to be similar for all the three tested strains.

treatment_protocol: Three hours after the stationary phase of growth was reached, samples were collected for transcriptomic analysis; this time point was also the reference time point (T0) for the half-life determination procedure.

tag: genotype/variation

value: {delta}pnp

tag: sampling time point

value: before rifampicin addition

tag: repetition

value: repetition 3


title: Ecoli_MG1655_T0_rep3_re-analysis

description:
SAMPLE 3
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.

value: wild type


title: MMTV-Neu.180152.Entinostat.CRtoPD.aCGH

description: aCGH

hyb_protocol: hybridized to Agilent 244k CGH arrays (model G4415A)

scan_protocol: scanned on Agilent scanner (model G2505B)

source_name: DNA reference - UCSC mm7/NCBI release 35 (August 2005)

label_protocol: labeled according to the direct incorporation method (Agilent)

extract_protocol: genomic DNA isolated using Dneasy kit (Qiagen)

treatment_protocol: 4 different treatments: Untreated, 3 week treatment, 6 week treatment, and Entinostat Progression

tag: characteristics

value: reference:DNA reference

value: MMTV-Neu

value: Entinostat Progression


title: Ecoli_MG1655_T0_rep1_re-analysis

description:
SAMPLE 1
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.

value: repetition 1


title: Ecoli_MG1655_T0_rep2_re-analysis

description:
SAMPLE 2
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.

value: repetition 2


title: Gametocytes of P.falciparum 3D7 in Day 12

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

institute: Nanyang Technological University

hyb_protocol: Equal amounts of Cy5- and Cy3-labelled cDNA samples were hybridised on a P. falciparum 8×15K Agilent gene expression microarray for 16 hours at 65°C in an Agilent hybridisation oven (G2545A) (Painter et al., 2013).

scan_protocol: Slides were scanned using the GenePix scanner 4000B and GenePix pro 6.0 software (Molecular Devices).

data_processing: All the samples were Loess normalized within arrays and quantile normalized between arrays using Limma package of R. Probes showing weak signals were ignored at the threshod of forground intensity < 1.5 background intensity for both Cy5 and Cy3 channels.

organism: Plasmodium falciparum

label_protocol: All the cDNA samples were equally Cy5- and Cy3-labelled (1 mg each)

growth_protocol: P. falciparum 3D7/HP1-GFP-DD ON parasites were cultured at 5% haematocrit, 4 nM WR99210 and 625 nM Shield-1 as described (Brancucci et al., 2014). Growth synchronisation was achieved by repeated treatment with 5% D-sorbitol (Lambros and Vanderberg, 1979). Gametocytogenesis was triggered by removing Shield-1 from the growth medium of ring stage cultures (4-12 hpi), which leads to activation of pfap2-g and the consequential commitment to sexual development in over 50% of schizonts (Brancucci et al., 2014). The RBCs from a 150 ml ring stage culture (5-6% parasitaemia) were pelleted and washed once in medium lacking Shield-1. After addition of 15 ml uninfected RBCs (packed cell volume (PCV)) and 450 ml growth medium lacking Shield-1, 15 equal 30 ml cultures of 3D7/HP1-GFP-DDOFF parasites were prepared (1.75% parasitaemia) (day -1). After schizogony (day 0) and re-invasion, these cultures reached 6-8% total ring stage parasitaemia with approximately half of all parasites representing sexually committed ring stages (day 1). Note that PfHP1-depleted sexual ring stages differentiate normally into stage V gametocytes over the following 8 to 10 days, whereas PfHP1-depleted asexual ring stages enter cell cycle arrest at the late ring/early trophozoite stage (Brancucci et al., 2014). This highly enriched early gametocyte bulk culture was used to isolate total RNA daily from day 1 to 12 to cover the entire gametocyte differentiation period (one 30 ml culture aliquot each was harvested for days 1 to 9; two 30 ml culture aliquots each were harvested for days 10 to 12)

extract_protocol: Total parasite RNA from the day 1 sample was harvested directly from the mixture of asexual and sexual ring stage parasites. For each of the eleven consecutive time points (days 2 to 12; early stage I to mature stage V gametocytes) total RNA was harvested from MACS column-enriched gametocyte samples. RNA extraction and cDNA synthesis was carried out as described (Bozdech et al., 2003).

tag: strain

tag: transgenic line

value: HP1 transgenic line

tag: time point

source_name: Reference pool

tag: reference

value: Mixture of asexual stages from ring to schizont


title: Gametocytes of P.falciparum 3D7 in Day 10


title: Ecoli_MG1655(Δpnp)_T0_rep2_re-analysis

description:
SAMPLE 8
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Ecoli_MG1655(Δpnp)_T0_rep1_re-analysis

description:
SAMPLE 7
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: MMTV-Neu.180238.Entinostat.CRtoPD.aCGH

description: aCGH


title: SKBR3.Entinostat.B

description: cell line


title: SKBR3.Entinostat.C

description: cell line


title: Tg2 (IFNα Tg #2)

city: Kato

first: Shunichi

last: Shiozawa

address: 944-25 Fujita

institute: Institute for Rheumatic Diseases

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: splenocyte, IFNα Tg mice

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from splenocytes using RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: spleen

tag: cell type

value: splenocyte

tag: genotype

value: IFNa transgenic


title: Gametocytes of P.falciparum 3D7 in Day 11


title: Gametocytes of P.falciparum 3D7 in Day 5


title: Gametocytes of P.falciparum 3D7 in Day 4


title: MMTV-Neu.180226.Entinostat.de_novo.aCGH

description: aCGH


title: C1 (control #1)

source_name: splenocyte, control mice

tag: tissue

value: control


title: Tg1 (IFNα Tg #1)


title: Ecoli_MG1655(Δpnp)_T3_rep3

description:
the cells were in stationary phase, the sampling was performed 3 minutes after rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 33

data_processing:
Raw probe intensities ( .pair files three replicates for each strain before and after transcription arrest by rifampicin addition) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Twelve arrays (three reference T0 samples, and nine time points after addition of rifampicin) were used. Only a normalization between arrays according to an invariant probeset intensities was performed. For each strain, a set of probes in the background for which the ranks were roughly invariant across all twelve arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition.
After normalization, in each array, transcript-specific intensity was computed as the median value of the 16 targeting probe intensities.

growth_protocol: The laboratory strain E. coli K12 MG1655 and two mutant strains E. coli MG1655(Δrnr) and E. coli MG1655(Δpnp) were grown in baffled flasks in LB medium at 37 °C and 180 rpm. Initial pH was set to 7. All cultures were inoculated at OD 0.1 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Cultures were performed in triplicate.

treatment_protocol: Three hours after the stationary phase of growth was reached, samples were collected for transcriptomic analysis; this time point was also the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (500 µg.mL-1) was added to inhibit the initiation of transcription, and cells were harvested at three different time points after this addition. Cultures were performed in triplicate. Samples were taken at either at 0’, 2’, 8’ and 15’, or 0’, 5’, 10’ and 18’ or 0’, 3’, 12’ and 30’ min after rifampicin addition. Samples were immediately frozen in liquid nitrogen upon collection.

value: 3 minutes after rifampicin addition


title: Ecoli_MG1655(Δpnp)_T0_rep3

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 32


title: SKBR3.Entinostat.A

description: cell line

value: Human Reference B

value: Treated by Entinostat for 72 hours at the IC50 doses


title: MMTV-Neu.180225.Entinostat.CRtoPD.aCGH

description: aCGH


title: C2 (control #2)


title: Ecoli_MG1655(Δrnr)_T0_rep1_re-analysis

description:
SAMPLE 4
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.

value: {delta}rnr

value: before rifampicin addition


title: Ecoli_MG1655(Δpnp)_T30_rep3

description:
the cells were in stationary phase, the sampling was performed 30 minutes after rifampicin addition .It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 35

value: {delta}pnp

value: 30 minutes after rifampicin addition

value: repetition 3


title: Ecoli_MG1655(Δpnp)_T12_rep3

description:
the cells were in stationary phase, the sampling was performed 12 minutes after rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 34

value: 12 minutes after rifampicin addition


title: MCF-7.Untreated.D

description: cell line

value: Untreated for 72 hours


title: Gametocytes of P.falciparum 3D7 in Day 9


title: Ecoli_MG1655(Δrnr)_T0_rep2_re-analysis

description:
SAMPLE 5
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.

value: repetition 2


title: Ecoli_MG1655(Δpnp)_T18_rep2

description:
the cells were in stationary phase, the sampling was performed 18 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 31

value: 18 minutes after rifampicin addition


title: MMTV-Neu.180165.Entinostat.de_novo.aCGH

description: aCGH

value: reference:DNA reference

value: MMTV-Neu

value: Entinostat Progression


title: Ecoli_MG1655(Δrnr)_T0_rep3_re-analysis

description:
SAMPLE 6
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: MMTV-Neu.180165.Entinostat.CRtoPD.aCGH

description: aCGH


title: Gametocytes of P.falciparum 3D7 in Day 7

value: HP1 transgenic line

value: Mixture of asexual stages from ring to schizont


title: MMTV-Neu.180153.Entinostat.CRtoPD.aCGH

description: aCGH


title: Gametocytes of P.falciparum 3D7 in Day 6


title: Gametocytes of P.falciparum 3D7 in Day 3


title: Gametocytes of P.falciparum 3D7 in Day 8


title: MMTV-Neu.178117.Entinostat.CRtoPD.aCGH

description: aCGH


title: Gametocytes of P.falciparum 3D7 in Day 1


title: MCF-7.Untreated.B

description: cell line


title: MCF-7.Entinostat.D

description: cell line


title: MCF-7.Untreated.A

description: cell line


title: Ecoli_MG1655(Δpnp)_T10_rep2

description:
the cells were in stationary phase, the sampling was performed 10 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 30

value: 10 minutes after rifampicin addition


title: MMTV-Neu.180221.Entinostat.6wk.aCGH

description: aCGH

value: Entinostat 6wks


title: MCF-7.Entinostat.C

description: cell line

value: Human Reference B

value: Treated by Entinostat for 72 hours at the IC50 doses