title: TN1014-Stroma

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

hyb_protocol: Agilent Technlogies SurePrint G3 Hmn GE 8x60K Microarrays (Cat#G4851A) were used for all experiments. RNA samples (300 ng) were subjected to fragmentation followed by 17 h hybridization, washing, and scanning (Agilent Technologies, model G2505C) according to the manufacturer’s protocol (manual ID #G4140-90050). Cy3-labeled samples were hybridized against Cy5-labeled Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA).

scan_protocol: Scanned on an Agilent G2505C scanner. Microarray data were feature extracted using Feature Extraction Software (v. 10.7.3.1) from Agilent with the default parameters.

data_processing: Duplicate arrays were averaged. For genes with multiple probes, the probe with the highest IQR was chosen.

source_name: laser capture microdissected tissue

label_protocol: For samples (ch1), 100 pg to 5 ng of total RNA was subjected to two rounds of T7 linear amplification using the Arcturus® RiboAmp® HS PLUS Kit (Catalog number: KIT0525) and labeled with Cy3 dye (Arcturus® Cy3 Turbo Labeling™ Kit Catalog number: KIT0609)  according to the manufacturer’s protocol. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA). For reference (ch2), RNA was subjected to two rounds of T7 linear amplification using the Arcturus® RiboAmp® HS PLUS Kit (Catalog number: KIT0525) and labeled with Cy5 dye (Arcturus® Cy3 Turbo Labeling™ Kit Catalog number: KIT0610)  according to the manufacturer’s protocol. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

extract_protocol: Tumor epithelium and stroma were separately microdissected from tissue samples using a PixCell IIe LCM system (Arcturus). All microdissections were performed within three hours of tissue staining. Total RNA was extracted from each population of microdissected cells using an Arcturus PicoPure RNA Isolation Kit (Cat# 12204-01).

treatment_protocol: Tissue compartments isolated from OCT-embedded frozen human tissue samples by laser capture microscopy following HistoGene staining and pathologist's evaluation

tag: compartment

value: Tumor Stroma

source_name: Amplified Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)

tag: sample type

value: reference


status: Public on Feb 22 2019

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_0d_CD4

library_source: genomic

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files in bigWig format contain chromatin accessibility profiles and narrowPeak files contain peak calls for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD4 cells

extract_protocol:
Patient PBMCs were thawed and washed twice with PBS containing 0.1% BSA and 5 mM EDTA (PBS + BSA + EDTA). Cells were then incubated with anti-CD16/CD32 (clone 93, Biolegend) to prevent nonspecific binding. Single-cell suspensions were stained with combinations of antibodies against CD3 (clone UCHT1), CD4 (clone OKT4), CD5 (clone UCHT2), CD8 (clone SK1), CD14 (clone M5E2), CD19 (clone HIB19), CD20 (clone 2H7), CD24 (clone ML5), CD25 (clone BC96), CD27 (clone O323), CD38 (clone HB-7), CD45RA (clone HI100), CD45RO (clone 304218), CD56 (clone NCAM16.2), CD127 (clone A019D5), CD197 (CCR7, clone G043H7), CD223 (LAG3, clone 11C3C65), CD279 (PD-1, clone EH12.2H7), CD366 (Tim3, clone F38-2E2) and DAPI viability dye (all from Biolegend) for 30 min at 4 °C followed by two washes with PBS + BSA + EDTA. Cells were either acquired with a LSRFortessa (BD) cell analyzer or sort-purified with a MoFlo Astrois (Beckman Coulter). Data analysis was performed with FlowJo (Tree Star) software. We obtained whole blood from three healthy donors with informed consent, and isolated PBMCs through Ficoll-Paque density gradient centrifugation and stored them in liquid nitrogen. Following sample thawing, up to ten million cells were incubated with anti-CD16/CD32 (clone 93, Biolegend) to prevent nonspecific binding. Single-cell suspensions were stained with antibodies against CD3 (clone UCTH1), CD4 (clone OKT4), CD8 (clone SK1), CD19 (clone HIB19), CD20 (clone 2H7), CD24 (clone ML5), CD27 (clone M-T271), CD38 (clone HB-7), IgD (clone 1A6-2) and fixable Zombie Red viability dye (all from BioLegend) for 30 min at 4 °C followed by two washes with PBS + BSA + EDTA. Sorting was conducted using a Sony SH800 cell sorter, pre-gated on live singlet lymphocytes before sorting cell subpopulations as follows: T cell (CD3+), total B cell (CD19+, CD20+), naive B cell (CD27-, IgD+), natural effector B cell (CD27+, IgD+), and memory B cell (CD27+, IgD-).
Chromatin accessibility mapping was performed using the ATAC-seq method as previously described (Corces et al, Nature Genetics, 2016), with minor adaptations. In each experiment, a maximum of 50,000 sorted cells were pelleted by centrifuging for 5 min at 4 °C at 300 x g. After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 µl 2xTD buffer, 2 µl TDE1 (Illumina) and 10.25 µl nuclease-free water, 0.25 µl 5% Digitonin (Sigma)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 11 µl, 1 µl of the eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers (Buenrostro et al, Nature Methods 2013). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform and the 50-bp single-end configuration.

treatment_protocol: All patients were diagnosed and treated and diagnosed according to the revised guidelines of the International Workshop Chronic Lymphocytic Leukemia/National Cancer Institute. Patients were recruited through clinical trial NCT01804686, aimed at studying the long-term effect of PCI-32765 (ibrutinib) and reflect the clinical and biological heterogeneity of the disease. The study was approved by the ethics committees of the contributing institutions (Semmelweis University and Medical University of Vienna). Informed consent was obtained from all participants.

tag: library

value: ATAC-seq

value: chronic lymphocytic leukemia patient

value: Peripheral blood mononuclear cells (PBMCs)

tag: replicate


title: TN1005-Stroma

type: RNA

molecule: total RNA


description:
ATAC-seq on PBMCs from patient CLL5 on day 150 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL5_150d_Bcell

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_Bcell cells


title: TN1016-Stroma


title: TN1023-Stroma


title: TN1034-Stroma


title: TN1017-Stroma


title: TN1001-Stroma


title: TN1035-Stroma


title: TN1006-Stroma


title: TN1026-Stroma


title: TN1013-Stroma


title: TN1018-Stroma


description:
ATAC-seq on PBMCs from patient CLL5 on day 30 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL5_30d_Bcell

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_Bcell cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 8 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL5_8d_Bcell

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_Bcell cells


title: C57BL/6 monocytes #3

city: New York

first: Stefan

last: Jordan

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: FACS Aria sorted

library_source: transcriptomic

data_processing:
Transcript abundances were quantified using the Ensembl GRCm38 cDNA reference using Kallisto version 0.44.0.
Transcript abundances were summarized to gene level using tximport
Expression matrices were filtered for only transcripts with greater than 5 TPM in all replicates of at least one condition
Genome_build: Ensembl GRCm38 cDNA reference
Supplementary_files_format_and_content: CSV

organism: Mus musculus

source_name: C57BL/6 monocytes #3

growth_protocol: mice were used at the age of 8-12 weeks

extract_protocol:
Rneasy Mini Kit (Qiagen)
Low Input Library Prep Kit v2 (Clontech)

treatment_protocol: food: food and water ad libitum; fast: food was removed from cage for the indicated time and bedding was changed, water ad libitum

tag: strain

tag: organ of origin

value: bone marrow

tag: cell type

value: monocytes

tag: treatment

value: food


title: CCR2-/-mice monocytes #1

description: FACS Aria sorted

source_name: CCR2-/-mice monocytes #1


title: CCR2-/-mice monocytes #2

description: FACS Aria sorted

source_name: CCR2-/-mice monocytes #2


description:
ATAC-seq on PBMCs from patient CLL5 on day 3 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL5_3d_Bcell

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Bcell cells


title: TN1029-Stroma


title: CCR2-/-mice monocytes #3

description: FACS Aria sorted

source_name: CCR2-/-mice monocytes #3


description:
ATAC-seq on PBMCs from patient CLL5 on day 2 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL5_2d_Bcell

source_name: PBMCs_CLL patient_day 2 of ibrutinib treatment_Bcell cells


title: C57BL/6 monocytes #2

description: FACS Aria sorted

source_name: C57BL/6 monocytes #2


description:
ATAC-seq on PBMCs from patient CLL5 on day 1 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL5_1d_Bcell

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_Bcell cells


title: C57BL/6 monocytes fast 17hrs #4

description: FACS Aria sorted

source_name: C57BL/6 monocytes fast 17hrs #4

value: fast


title: C57BL/6 monocytes fast 17hrs #3

description: FACS Aria sorted

source_name: C57BL/6 monocytes fast 17hrs #3


title: C57BL/6 monocytes #1

description: FACS Aria sorted

source_name: C57BL/6 monocytes #1


title: HSCs IVT 12days, C

city: Odense M

first: Kim

last: Ravnskjaer

state: CA

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
SM2099_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt

data_processing:
STAR alignment of reads to mm10 genome
SAM files generated using Homer
Tag-directory generated using Homer (tbp=1)
Exon Coiunt matrices created using Homer (analyzerepeats.pl; -noadj)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files: exon counts, gene accession numbers.

source_name: HSCs IVT 12days

extract_protocol:
HSCs were lyzed in RLT lysis buffer from RNeasy Mini Kit (Qiagen) and total RNA extracted according to manufacturer’s instructions after a standard phenol/chloroform extraction.
RNA concentrations were measured using a Qubit 3.0 Fluorometer (Invitrogen) and quality of the RNA was assessed using a Bioanalyzer 2100 (Agilent Technologies). Purified RNA (3-4 biological replicates) was polyA-selected and subjected to fragmentation before cDNA synthesis. For library construction, we used the NEBNext Ultra™ RNA Library Prep Kit for Illumina and sequenced using the Illumina HiSeq 1500 platform.

value: HSCs In vitro-cultured 12days; DMEM/10%FBS/pen/strep/beta-amphotericin

value: Hepatic stellate cells (HSCs)

tag: preparation

value: Isolated, FACS sorted, cultured


title: ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, Bcells, replicate 2

description:
ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, Bcell_2 cells
ATAC-seq_CLL5_0d_Bcell_2

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Bcells


title: HSCs IVT 12days, B

description:
SM2098_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


title: ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, Bcells, replicate 1

description:
ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, Bcell_1 cells
ATAC-seq_CLL5_0d_Bcell_1


title: SAMPLE 9: 341689-IgG-LPS

city: Houston

first: HUIMING

last: CHEN

state: Texas

address: 1613 Wheeler St

institute: Houston Methodist Research institute

description: replicate 3

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: The HumanHT-12 v4 array (Illumina) was scanned on Illumina HiScan according to the manufacturer's instructions.

data_processing: Raw intensity data was processed using Genome Studio (version 2011.1) Gene Expression Module (version 1.9.0) and further processing was done using the lumi R package from Bioconductor. The data was adjusted for background signal before exporting from BeadStudio, and underwent VST transformation and quantile normalization. Probes with no expression were removed. Differential gene expression analysis was performed using the limma R package, and significantly differentially expressed genes were identified based on fold change≥1.5 and p-value<0.05 with Benjamini & Hochberg false-discovery rate correction.

growth_protocol: 2 ^ 106 CD33+ myeloid cells from healthy PBMC donors were grown in the presence of MCSF for 5 days.

extract_protocol: RNA was extracted using QIAzol reagent (Qiagen), following the manufacturer's instructions.

treatment_protocol: M-CSF-treated myeloid cells were subsequently treated with IL4 or LPS for 18 hours. antiLILRB2 or control Ig were added from the beginning of differentiation (5 day of M-CSF treatment plus 18hr IL4 or LPS treatment).

tag: tissue

value: human CD33 myeloid cells


title: C57BL/6 monocytes fast 17hrs #2

description: FACS Aria sorted

source_name: C57BL/6 monocytes fast 17hrs #2


title: TN1004-Stroma

source_name: laser capture microdissected tissue

source_name: Amplified Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)


description:
ATAC-seq on PBMCs from patient CLL4 on day 3 of ibrutinib treatment, NK cells
ATAC-seq_CLL4_3d_NK

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_NK cells


title: TN1008-Stroma


title: HSCs IVT 12days, A

description:
SM2097_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


title: SAMPLE 5: 199559-IgG-LPS

description: replicate 2

label_protocol: According to the manufacturer's instructions.


title: HSCs IVT 8days, C

description:
SM2096_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: HSCs IVT 8days

value: HSCs In vitro-cultured 8days; DMEM/10%FBS/pen/strep/beta-amphotericin


title: TN1031-Stroma


title: TN1038-Stroma


title: TN1032-Stroma


title: TN1036-Stroma


title: SAMPLE 3: 199542-antiLILRB2-LPS

description: replicate 1


description:
ATAC-seq on PBMCs from patient CLL4 on day 0 of ibrutinib treatment, NK cells
ATAC-seq_CLL4_0d_NK

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_NK cells


title: TN1037-Stroma


title: C57BL/6 monocytes food 17hrs #3

description: FACS Aria sorted

source_name: C57BL/6 monocytes food 17hrs #3


title: HSCs IVT 8days, B

description:
SM2095_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


description:
ATAC-seq on PBMCs from patient CLL4 on day 3 of ibrutinib treatment, Mono cells
ATAC-seq_CLL4_3d_Mono

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Mono cells


title: C57BL/6 monocytes food 17hrs #2

description: FACS Aria sorted

source_name: C57BL/6 monocytes food 17hrs #2


title: HSCs IVT 8days, A

description:
SM2094_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


description:
ATAC-seq on PBMCs from patient CLL4 on day 0 of ibrutinib treatment, Mono cells
ATAC-seq_CLL4_0d_Mono

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Mono cells


title: C57BL/6 monocytes fast 17hrs #1

description: FACS Aria sorted

source_name: C57BL/6 monocytes fast 17hrs #1


title: TN1012-Stroma


title: HSCs IVT 4days, B

description:
SM2092_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: HSCs IVT 4days

value: HSCs In vitro-cultured 4days; DMEM/10%FBS/pen/strep/beta-amphotericin


title: HSCs IVT 4days, C

description:
SM2093_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


title: C57BL/6 hepatocytes fast 12hrs #3

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes fast 12hrs #3

value: liver

value: hepatocytes


description:
ATAC-seq on PBMCs from patient CLL4 on day 2 of ibrutinib treatment, CLL cells
ATAC-seq_CLL4_2d_CLL

source_name: PBMCs_CLL patient_day 2 of ibrutinib treatment_CLL cells


description:
ATAC-seq on PBMCs from patient CLL4 on day 3 of ibrutinib treatment, CLL cells
ATAC-seq_CLL4_3d_CLL

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CLL cells


title: TN1025-Stroma

value: Tumor Stroma


title: C57BL/6 hepatocytes fast 12hrs #2

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes fast 12hrs #2


title: C57BL/6 hepatocytes fast 12hrs #1

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes fast 12hrs #1


title: TN1022-Stroma

value: reference


title: HSCs IVT 4days, A

description:
SM2091_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


title: C57BL/6 monocytes food 17hrs #1

description: FACS Aria sorted

source_name: C57BL/6 monocytes food 17hrs #1


title: HSCs IVT 1day, C

description:
SM2087_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: HSCs IVT 1day

value: HSCs In vitro-cultured 1day; DMEM/10%FBS/pen/strep/beta-amphotericin


description:
ATAC-seq on PBMCs from patient CLL4 on day 3 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL4_3d_CD8

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD8 cells

value: ATAC-seq

value: chronic lymphocytic leukemia patient


title: TN1010-Stroma

source_name: laser capture microdissected tissue

source_name: Amplified Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)


title: C57BL/6 hepatocytes food 12hrs #2

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes food 12hrs #2


description:
ATAC-seq on PBMCs from patient CLL4 on day 0 of ibrutinib treatment, CLL cells
ATAC-seq_CLL4_0d_CLL

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CLL cells

value: Peripheral blood mononuclear cells (PBMCs)


description:
ATAC-seq on PBMCs from patient CLL4 on day 0 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL4_0d_CD8

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_0d_CLL


title: HSCs IVT 1day, A

description:
SM2085_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


title: HSCs IVT 1day, B

description:
SM2086_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


title: C57BL/6 hepatocytes food 12hrs #1

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes food 12hrs #1


description:
ATAC-seq on PBMCs from patient CLL4 on day 3 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL4_3d_CD4

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD4 cells


title: TN1009-Stroma


title: TN1021-Stroma


title: C57BL/6 hepatocytes fast 4hrs #2

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes fast 4hrs #2


title: HSCs IVT 2hrs (t=0), C

description:
SM2081_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: HSCs IVT 2hrs (t=0)

value: HSCs In vitro-cultured 2hrs (t=0); DMEM/10%FBS/pen/strep/beta-amphotericin


title: QM6a_LL_2

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

institute: University of Vienna

description: growth on cellulose, 72h, liquid culture

data_processing:
The mapping of reads was performed using bowtie2 with standard parameter setting
The resulting files were further processed using samtools
The comparison to the annotation was performed using bedtools
Values were calculated for each annotated transcript based on the results of the mapping (RSEM)
Genome_build: https://genome.jgi.doe.gov/Trire2/Trire2.home.html
Supplementary_files_format_and_content: The Excel file contains FPKM values of normalized samples (values for all samples in this file).

organism: Trichoderma reesei

source_name: fungal mycelium

extract_protocol:
Mycelia were harvested by filtration and frozen in liquid nitrogen. Total RNA was isolated essentially as described previously (Tisch et al., 2011 PMID  21220037) using the QIAGEN plant RNA kit (QIAGEN, Hilden, Germany) according to manufacturers instructions. Quality control of total RNA was performed using Bioanalyzer 2100 (Agilent) and only high quality RNA was used for further analysis.
Next generation sequencing was performed at the core facility VetCORE (Vienna, Austria) on a HiSeq2000/SR50 machine.

treatment_protocol: Precultures for cultivation on cellulose were performed on plates with malt extract agar (3 % w/v) in constant darkness for 14 days in order to avoid interference of light pulses or circadian rhythms with transcriptome analysis. An inoculum of 109 conidia/L was applied to 100 ml of Mandels Andreotti minimal medium with 1 % (w/v) microcrystalline cellulose (Alfa Aesar, Karlsruhe, Germany) and 0.1 % (w/v) peptone to induce germination. Strains were grown in constant light (1600 lux) or constant darkness at 28°C for 72 hours at 200 rpm. Harvesting of dark cultures was done under red safety light (darkroom lamp, Philips PF712E, red, 15 W)

tag: genotype/strain

tag: property

value: wildtype

value: constant light


description:
ATAC-seq on PBMCs from patient CLL4 on day 2 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL4_2d_CD4

source_name: PBMCs_CLL patient_day 2 of ibrutinib treatment_CD4 cells


title: HSCs IVT 2hrs (t=0), B

description:
SM2080_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt


title: TN1028-Stroma


title: TN1019-Stroma


title: TN1030-Stroma


title: TN1027-Stroma


title: C57BL/6 hepatocytes food 4hrs #3

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes food 4hrs #3

value: food


title: C57BL/6 hepatocytes food 4hrs #2

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes food 4hrs #2


description:
ATAC-seq on PBMCs from patient CLL4 on day 3 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL4_3d_Bcell

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Bcell cells


description:
ATAC-seq on PBMCs from patient CLL2 on day 150 of ibrutinib treatment, NK cells
ATAC-seq_CLL2_150d_NK

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_NK cells


title: WD 24weeks, D

description:
SM1902_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: WD 24weeks_HSCs

value: Western diet/fructose-fed 24weeks

value: Hepatic stellate cells (HSCs)

value: Isolated, FACS sorted


title: TN1002-Stroma


title: WD 24weeks, C

description:
SM1901_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


title: TN1033-Stroma


title: C57BL/6 hepatocytes food 4hrs #1

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes food 4hrs #1


title: C57BL/6 hepatocytes fast 4hrs #1

description: perfusion & centrifugation isolation

source_name: C57BL/6 hepatocytes fast 4hrs #1

value: fast


title: WD 24weeks, B

description:
SM1900_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


description:
ATAC-seq on PBMCs from patient CLL2 on day 30 of ibrutinib treatment, NK cells
ATAC-seq_CLL2_30d_NK

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_NK cells


title: WD 24weeks, A

description:
SM1899_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


description:
ATAC-seq on PBMCs from patient CLL2 on day 3 of ibrutinib treatment, NK cells
ATAC-seq_CLL2_3d_NK

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_NK cells


description:
ATAC-seq on PBMCs from patient CLL4 on day 0 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL4_0d_CD4

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL2 on day 8 of ibrutinib treatment, NK cells
ATAC-seq_CLL2_8d_NK

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_NK cells


title: HSCs IVT 2hrs (t=0), A

description:
SM2079_cat
processed data file: ivt_ms_data_exon_count_matrix_mm10_noadjust.txt

value: Isolated, FACS sorted, cultured


title: WD 16weeks, D

description:
SM1898_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: WD 16weeks_HSCs

value: Western diet/fructose-fed 16weeks


title: TN1007-Stroma

source_name: laser capture microdissected tissue

source_name: Amplified Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)


title: Female.VmSC5#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

extract_protocol:
1,000 cells were double-sorted by Moflo Astrios cel sorter into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: Pparg-TdTomato+ (C57BL/6)

value: visceral adipose tissue

tag: age

value: 8-10 weeks


title: Female.VmSC4#1


title: Female.VmSC3#2


title: WD 16weeks, B

description:
SM1896_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


title: WD 16weeks, C

description:
SM1897_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


title: Female.VmSC5#2


title: Female.VmSC4#2


title: NAFL_12

city: Hørsholm

first: Kristoffer

last: Rigbolt

address: Hørsholm Kongevej 11B

institute: Gubra

data_processing:
bcl2fastq v2.17.1.14 used for basecalling
Sequenced reads were mapped to Ensembl Mus musculus genome using whole genome using STAR v2.5.2a with default parameters
Filtering for protein coding genes
Genome_build: Ensembl GRCh38 89
Supplementary_files_format_and_content: Count table

molecule: polyA RNA

source_name: Liver needle biopsy

extract_protocol:
TruSeq® Stranded mRNA Library Prep for NeoPrep
RNA was isolated from fine needle biopsies of human livers using NucleoSpin® from MACHEREY-NAGEL according to manufactors protocol

tag: gender

value: Female

value: Liver

tag: disease

value: NAFLD


description:
ATAC-seq on PBMCs from patient CLL2 on day 120 of ibrutinib treatment, CLL cells
ATAC-seq_CLL2_120d_CLL

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CLL cells

value: ATAC-seq

value: chronic lymphocytic leukemia patient

value: Peripheral blood mononuclear cells (PBMCs)


title: TN1011-Stroma

value: Tumor Stroma

value: reference


title: WD 16weeks, A

description:
SM1895_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


title: Female.VmSC3#1


description:
ATAC-seq on PBMCs from patient CLL2 on day 30 of ibrutinib treatment, CLL cells
ATAC-seq_CLL2_30d_CLL

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CLL cells


title: TN1024-Stroma


title: WD 12weeks, D

description:
SM1894_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: WD 12weeks_HSCs

value: Western diet/fructose-fed 12weeks


description:
ATAC-seq on PBMCs from patient CLL2 on day 8 of ibrutinib treatment, CLL cells
ATAC-seq_CLL2_8d_CLL

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CLL cells


title: Female.VmSC2#2


title: WD 12weeks, C

description:
SM1893_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt

value: Hepatic stellate cells (HSCs)


title: Female.VmSC2#1


title: TN1020-Stroma


description:
ATAC-seq on PBMCs from patient CLL2 on day 3 of ibrutinib treatment, CLL cells
ATAC-seq_CLL2_3d_CLL

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CLL cells


title: TN1014-Epithelium

value: Tumor Epithelium


title: TN1015-Stroma


description:
ATAC-seq on PBMCs from patient CLL2 on day 3 of ibrutinib treatment, Mono cells
ATAC-seq_CLL2_3d_Mono

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Mono cells


title: TN1023-Epithelium


title: TN1003-Stroma


title: WD 12weeks, B

description:
SM1892_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt

value: Isolated, FACS sorted


description:
ATAC-seq on PBMCs from patient CLL2 on day 0 of ibrutinib treatment, CLL cells
ATAC-seq_CLL2_0d_CLL

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CLL cells


title: Female.VmSC1#2


title: Male.VmSC5#5


title: WD 0weeks, D

description:
SM1890_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: WD 0weeks_HSCs

value: Western diet/fructose-fed 0weeks


title: WD 12weeks, A

description:
SM1891_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


title: Female.VmSC1#1


title: TN1034-Epithelium


title: TN1005-Epithelium


title: TN1016-Epithelium


title: WD 0weeks, C

description:
SM1889_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


title: TN1026-Epithelium


description:
ATAC-seq on PBMCs from patient CLL2 on day 8 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL2_8d_CD8

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CD8 cells


title: TN1006-Epithelium


title: Male.VmSC5#3


title: Male.VmSC5#2


description:
ATAC-seq on PBMCs from patient CLL2 on day 30 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL2_30d_CD8

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL2 on day 0 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL2_0d_CD8

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL2 on day 120 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL2_120d_CD8

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CD8 cells


title: Male.VmSC5#1


title: TN1035-Epithelium


title: TN1017-Epithelium


title: Male.VmSC5#4


description:
ATAC-seq on PBMCs from patient CLL2 on day 120 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL2_120d_CD4

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL2 on day 3 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL2_3d_CD8

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL2 on day 120 of ibrutinib treatment, Mono cells
ATAC-seq_CLL2_120d_Mono

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_Mono cells


title: CCl4 8weeks, B

description:
SM1808_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: CCl4 8weeks_HSCs

value: CCl4-treated 8weeks


title: Male.VmSC4#3

value: Pparg-TdTomato+ (C57BL/6)


title: Male.VmSC4#4

value: visceral adipose tissue


description:
ATAC-seq on PBMCs from patient CLL2 on day 30 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL2_30d_CD4

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CD4 cells


title: Male.VmSC4#2

value: 8-10 weeks


description:
ATAC-seq on PBMCs from patient CLL2 on day 8 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL2_8d_CD4

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CD4 cells


title: WD 0weeks, A

description:
SM1887_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt


title: CCl4 4weeks, D

description:
SM1805_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: CCl4 4weeks_HSCs

value: CCl4-treated 4weeks


description:
ATAC-seq on PBMCs from patient CLL2 on day 3 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL2_3d_CD4

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD4 cells


title: CCl4 4weeks, C

description:
SM1804_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


description:
ATAC-seq on PBMCs from patient CLL2 on day 0 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL2_0d_CD4

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD4 cells


title: Male.VmSC3#4


description:
ATAC-seq on PBMCs from patient CLL2 on day 120 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL2_120d_Bcell

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_Bcell cells


title: CCl4 4weeks, A

description:
SM1802_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


title: Male.VmSC3#3


title: CCl4 8weeks, C

description:
SM1809_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


title: Male.VmSC4#1


title: CCl4 4weeks, B

description:
SM1803_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


title: TN1029-Epithelium

source_name: laser capture microdissected tissue

source_name: Amplified Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)


title: TN1013-Epithelium


title: TN1001-Epithelium


title: TN1018-Epithelium


description:
ATAC-seq on PBMCs from patient CLL2 on day 30 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL2_30d_Bcell

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_Bcell cells


title: CCl4 1week, C

description:
SM1906_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: CCl4 1week_HSCs

value: CCl4-treated 1week


title: CCl4 8weeks, A

description:
SM1807_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


description:
ATAC-seq on PBMCs from patient CLL2 on day 3 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL2_3d_Bcell

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Bcell cells


title: Male.VmSC3#1


title: CCl4 1week, B

description:
SM1904_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


description:
ATAC-seq on PBMCs from patient CLL2 on day 0 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL2_0d_Bcell

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Bcell cells


title: Male.VmSC2#4


title: CCl4 1week, A

description:
SM1903_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


title: TN1004-Epithelium


title: Male.VmSC2#3


title: TN1031-Epithelium


title: ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, NK cells, replicate 2

description:
ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, NK_2 cells
ATAC-seq_CLL1_120d_NK_2

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_NK cells


title: Male.VmSC3#2


title: TN1008-Epithelium


title: Male.VmSC2#2


description:
ATAC-seq on PBMCs from patient CLL1 on day 3 of ibrutinib treatment, NK cells
ATAC-seq_CLL1_3d_NK

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_NK cells


description:
ATAC-seq on PBMCs from patient CLL1 on day 0 of ibrutinib treatment, NK cells
ATAC-seq_CLL1_0d_NK

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_NK cells


title: ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, NK cells, replicate 1

description:
ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, NK_1 cells
ATAC-seq_CLL1_120d_NK_1


title: TN1038-Epithelium


description:
ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, CLL cells
ATAC-seq_CLL1_120d_CLL

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CLL cells


title: Male.VmSC1#4


title: CCl4 0weeks, A

description:
SM1794_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: CCl4 0weeks_HSCs

value: CCl4-treated 0weeks


title: CCl4 0weeks, D

description:
SM1797_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


title: TN1010-Epithelium


title: Male.VmSC1#3


title: CCl4 0weeks, C

description:
SM1796_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


title: Male.VmSC2#1


title: CCl4 0weeks, B

description:
SM1795_cat
processed data file: ccl4_ms_data_exon_count_matrix_mm10_noadjust.txt


title: TN1032-Epithelium


title: TN1025-Epithelium


title: TN1037-Epithelium


title: TN1036-Epithelium


title: Male.VmSC1#2


title: Male.VmSC1#1


title: TN1022-Epithelium


description:
ATAC-seq on PBMCs from patient CLL1 on day 3 of ibrutinib treatment, CLL cells
ATAC-seq_CLL1_3d_CLL

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CLL cells

value: ATAC-seq


title: TN1021-Epithelium


title: TN1009-Epithelium


description:
ATAC-seq on PBMCs from patient CLL1 on day 030 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL1_030d_CD8

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_CD8 cells

value: chronic lymphocytic leukemia patient


title: TN1012-Epithelium


description:
ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL1_120d_CD8

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CD8 cells

value: Peripheral blood mononuclear cells (PBMCs)


description:
ATAC-seq on PBMCs from patient CLL1 on day 030 of ibrutinib treatment, CLL cells
ATAC-seq_CLL1_030d_CLL

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_CLL cells


description:
ATAC-seq on PBMCs from patient CLL1 on day 3 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL1_3d_CD8

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD8 cells


title: TN1019-Epithelium


description:
ATAC-seq on PBMCs from patient CLL1 on day 0 of ibrutinib treatment, CLL cells
ATAC-seq_CLL1_0d_CLL

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CLL cells


title: TN1037

description: Gene expression from patient mcgill.gq.36

hyb_protocol: The fragmented and labeled DNA target was hybridized on GeneChip Human Gene 1.0 ST Array (Affymetrix) and incubated at 450C in the Genechip Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer's instructions (Affymetrix).

scan_protocol: The microarrays were scanned on a GeneChip scanner 3000 (Affymetrix) using the standard Affymetrix protocol.

data_processing: Used Brainarray CDF package (hugene10sthsentrezgcdf_19.0.0)- Duplicate arrays were averaged. For genes with multiple probes, the probe with the highest IQR was chosen.

label: biotin

source_name: Bulk Tumor Tissue

label_protocol: Sense-strand cDNA was synthesized from 250ng of total RNA using the Ambion WT Expression Kit according to the manufacturer instructions (Life Technologies Corporation). The cDNA was fragmented and labeled with the Affymetrix GeneChip WT Terminal Labeling Kit according to manufacturer instructions (Affymetrix)

extract_protocol: RNA was then extracted from these sections using the AllPrep Mini kit (Qiagen). RNA quality was assessed using an Agilent Bioanalyzer

treatment_protocol: All tissues were snap-frozen in O.C.T. Tissue-Tek Compound within 30 minutes of removal.

tag: lymph node

tag: grade

value: III

tag: death

value: no

tag: recurrence

tag: tumor size

tag: patient


title: TN1001

description: Gene expression from patient mcgill.gq.37

value: II


title: ArrayL

city: Wilrijk

first: Isabelle

middle: J

last: Gabriëls

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

hyb_protocol: 825 ng Cy3 and 825 ng Cy5 labeled and purified cRNA were hybridized onto 4x44K full genome zebrafish (version 3, Agilent, Diegem) microarrays for 17 h at 65 °C in a rotating (10 rpm) hybridization oven (Agilent, Diegem). A simple n-loop design (Knapen et al., 2009) was used in which each sample was labelled once in Cy3 and once in Cy5, resulting in 12 arrays for 24 samples (0% and 25% maize, 4 biological replicates per diet, analyzed per sex).

scan_protocol: Microarray slides were scanned using a Genepix 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 µm and excitation wavelengths of 635 nm and 532 nm in an ozone-free environment (NoZone scanner enclosure, SciGene, Sunnyvale, CA, USA). Images were analyzed for spot identification and for quantification of the fluorescent signal intensities using the Genepix Pro software 6.1 (Axon Instruments).

data_processing: The statistical processing of raw microarray data was carried out using the R package Limma as described by Vergauwen et al. (2010). The total number of significantly differentially expressed genes (p<0.05) were calculated for: female 25% vs 0% maize, male 25% vs 0% maize and 25% vs 0% maize sex independently. Spots with FG < BG + 2SD (FG: foreground, BG: background, SD: standard deviation of the local background of the entire array) were excluded from the analysis. The normal-exponential convolution model was used to perform background correction and within-array adjustment was done by Loess normalization. Cut offs were set at FDR < 0.05 (False Discovery rate, multiple testing correction using the Benjamini-Hochberg procedure) and |log2FC| > 0.585 (log2 fold change, corresponding to a fold induction of at least 1.5 or -1.5).

organism: Danio rerio

source_name: male_25% maize

label_protocol: Total RNA was amplified and labeled using the Low Input Quick Amplification Labelling Kit (LIQA, Agilent, Diegem) according to the manufacturer’s instructions. In brief, 100 ng RNA was reverse transcribed into cDNA using oligo dT primers. Subsequently, cDNA was amplified and converted into cRNA and the resulting cRNA of each sample was labeled once with Cy3-CTP and once with Cy5-CTP. The RNeasy mini spin column kit (Qiagen, Venlo) was then used to purify each amplified and labeled cRNA sample. cRNA yield, quality and dye incorporation efficiency were verified using the nanodrop spectrophotometer.

growth_protocol: Zebrafish were kept in reconstituted freshwater at pH 7.5, condutivity 500µS and 28°C. Zebrafish were fed with experimental diets for 28 days (2.5% average wet weight per day).

extract_protocol: Total RNA extracted using Qiazol following manufacturer's instructions

treatment_protocol: Zebrafish livers were pooled per sex per replicate, snap frozen in liquid nitrogen and stored at -80C. Subsequently, samples were homogenized in liquid nitrogen using mortar and pestle and preserved in Qiazol Lysis Reagent at -80°C until RNA extraction

tag: strain

value: AB

tag: genotype/variation

value: wild type

tag: Sex

value: male

tag: diet

value: 25% maize

value: liver

tag: replicate

value: Replicate 3

source_name: male_0% maize

value: 0% maize

value: Replicate 1


title: TN1030-Epithelium

source_name: laser capture microdissected tissue

tag: compartment

value: Tumor Epithelium

source_name: Amplified Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)

tag: sample type

value: reference


title: TN1028-Epithelium


title: TN1008

description: Gene expression from patient mcgill.gq.35


title: TN1010

description: Gene expression from patient mcgill.gq.34


title: ArrayK

source_name: female_0% maize

value: female

tag: tissue


title: TN1014

description: Gene expression from patient mcgill.gq.33

tag: age


title: TN1002-Epithelium


description:
ATAC-seq on PBMCs from patient CLL1 on day 0 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL1_0d_CD8

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD8 cells

tag: library

value: ATAC-seq


title: TN1021

description: Gene expression from patient mcgill.gq.31

value: yes


title: ArrayJ

value: Replicate 2


title: ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, CD4 cells, replicate 2

description:
ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, CD4_2 cells
ATAC-seq_CLL1_120d_CD4_2

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CD4 cells

value: chronic lymphocytic leukemia patient

value: Peripheral blood mononuclear cells (PBMCs)


description:
ATAC-seq on PBMCs from patient CLL1 on day 3 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL1_3d_CD4

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD4 cells


title: TN1027-Epithelium


title: ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, CD4 cells, replicate 1

description:
ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, CD4_1 cells
ATAC-seq_CLL1_120d_CD4_1


description:
ATAC-seq on PBMCs from patient CLL1 on day 120 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL1_120d_Bcell

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_Bcell cells


title: TN1007-Epithelium


description:
ATAC-seq on PBMCs from patient CLL1 on day 3 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL1_3d_Bcell

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Bcell cells


title: TN1003-Epithelium


title: TN1013

description: Gene expression from patient mcgill.gq.32

value: no

value: II


title: ArrayE

value: AB

value: wild type

value: Replicate 4

source_name: female_25% maize


title: ArrayI

value: liver

value: male

value: 25% maize


title: TN1024-Epithelium


title: ArrayH

value: Replicate 1

value: 0% maize


title: TN1012

description: Gene expression from patient mcgill.gq.29

value: III


title: ArrayG

value: female


description:
ATAC-seq on PBMCs from patient CLL1 on day 0 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL1_0d_CD4

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD4 cells

value: ATAC-seq


title: TN1031

description: Gene expression from patient mcgill.gq.28

value: yes


description:
ATAC-seq on PBMCs from patient CLL1 on day 0 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL1_0d_Bcell

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Bcell cells


title: TN1038

description: Gene expression from patient mcgill.gq.30


title: TN1023

description: Gene expression from patient mcgill.gq.27


title: TN1011-Epithelium

value: Tumor Epithelium

value: reference


title: TN1033-Epithelium


title: ArrayD

value: Replicate 3


title: ArrayC


title: WD 0weeks, B

description:
SM1888_cat
processed data file: wd_ms_data_exon_count_matrix_mm10_noadjust.txt

source_name: WD 0weeks_HSCs

tag: treatment

value: Western diet/fructose-fed 0weeks

tag: cell type

value: Hepatic stellate cells (HSCs)

tag: preparation

value: Isolated, FACS sorted


title: ArrayF

value: AB

value: wild type


title: TN1020-Epithelium


title: TN1015-Epithelium


description:
ATAC-seq on PBMCs from donor ND-3, UnswitchedBcell
ATAC-seq_ND-3_UnswitchedBcell

source_name: PBMCs_healthy donor_UnswitchedBcell

value: healthy

value: Peripheral blood mononuclear cells (PBMCs)


description:
ATAC-seq on PBMCs from donor ND-2, UnswitchedBcell
ATAC-seq_ND-2_UnswitchedBcell


description:
ATAC-seq on PBMCs from donor ND-3, Tcell
ATAC-seq_ND-3_Tcell

source_name: PBMCs_healthy donor_Tcell


description:
ATAC-seq on PBMCs from donor ND-1, UnswitchedBcell
ATAC-seq_ND-1_UnswitchedBcell


description:
ATAC-seq on PBMCs from donor ND-2, Tcell
ATAC-seq_ND-2_Tcell


title: ArrayB

value: 25% maize

value: liver

value: Replicate 2

value: male


title: TN1009

description: Gene expression from patient mcgill.gq.26

source_name: Bulk Tumor Tissue

tag: lymph node

value: no

tag: grade

value: III

tag: death


title: Ctl-1

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: flat file with FPKM values reported by Cufflinks for each sample

source_name: Liver

extract_protocol:
Liver were harvested, Total 50 ng RNA was isolated from mouse liver samples using the column-based Aurum Total RNA Fatty and Fibrous Tissue kit (Bio-Rad) for the RNA-seq libraries.
Illumina TruSeq Stranded Total RNA kit

value: Albumin-Cre


title: Ctl-2


title: Li-KO-0

value: Liver-specific Klf15 Knockout


title: Li-KO-1


title: ArrayA

source_name: male_0% maize

value: 0% maize

value: Replicate 1

value: female


title: TN1016

description: Gene expression from patient mcgill.gq.23

value: II

tag: recurrence

tag: tumor size

tag: patient


title: TN1002

description: Gene expression from patient mcgill.gq.25


title: Ctl-0

tag: genotype/variation


title: TN1011

description: Gene expression from patient mcgill.gq.24


title: TN1033

description: Gene expression from patient mcgill.gq.22


title: TN1022

description: Gene expression from patient mcgill.gq.21

value: yes


title: S7_WT_360to390_Mock

city: Cardiff

first: Widad

last: Dantoft

address: Heath Park

country: United Kingdom

institute: Cardiff University

hyb_protocol: Standard Affymetrix hybridization and wash procedure Mouse GeneST V1.0

scan_protocol: GeneChips were scaned using the Affymetrix GeneChip Scanner 3000 HR using the GCOS software tool.

data_processing: R/Bioconductor using RMA normalization.

source_name: Bone marrow-derived macrophages_newly transcibed RNA

label_protocol: Biotinylated cRNA were prepared with the standard Affymetrix GeneChip IVT labeling kit.

growth_protocol: Bone marrow was flushed from the femurs and tibia of 10 week old C57BL/6J mice. Cells were the cultured for 7 days in DMEM F12-glutamax with 10% FCS, 10% L929 conditioned medium and penicillin/streptomycin. Cells were phenotyped by flow cytometry analysis of surface CD11b and F4/80 expresson.

extract_protocol: Total RNA was extracted using an Rneasy Midi kit accoring to manufacturers protocol. QC was carried out using an Agilent Bioanalyzer and quantitation was by Nanodrop. Newly transcribed RNA ws isolated using a protocol descibed in Dölken et al. RNA. 2008 Sep;14(9):1959-72.

treatment_protocol: On day 7, cells were mock-infected (2x15cm dishes WT BMDM and 2x15cm dishes Tyk2-/- BMDM) or infected with MCMV (MOI=1, 2x15cm dishes WT BMDM and 2x15cm dishes Tyk2-/- BMDM) for 1h. After 1hr, virus and medium were aspirated and fresh medium was added to all dishes (designated timepoint=0). After 30 or 360 minutes post infection, 4-thiouridine (4sU) was used to label newly transcribed RNA for a period of 30 minutes.

tag: background strain

tag: genetic background

value: wildtype

value: 10 weeks-old

value: femurs and tibia

value: bone marrow-derived macrophages (BMDM)

tag: cell culture age

value: day 7

value: mock infected

tag: time point_minutes

tag: molecule subtype

value: newly transcribed RNA


title: S8_WT_360to390_C3X

tag: age

tag: tissue

value: infected with MCMV


title: TN1019

description: Gene expression from patient mcgill.gq.20


title: S10_Tyk2_360to390_C3X

value: Tyk2 knockout

tag: treatment


title: S9_Tyk2_360to390_Mock

tag: cell type


title: TN1006

description: Gene expression from patient mcgill.gq.18

value: III

value: no


title: S5_Tyk2_60to90_Mock


description:
ATAC-seq on PBMCs from donor ND-3, SwitchedBcell
ATAC-seq_ND-3_SwitchedBcell

source_name: PBMCs_healthy donor_SwitchedBcell

tag: library

value: ATAC-seq

value: healthy

value: Peripheral blood mononuclear cells (PBMCs)

tag: replicate


description:
ATAC-seq on PBMCs from donor ND-1, Tcell
ATAC-seq_ND-1_Tcell


title: S6_Tyk2_60to90_C3X


title: Moderate IOP Replicate 3

first: Edwin

middle: Justin

last: Ostrin

address: 1515 Holcombe Blvd, Unit 1465

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastqs were filtered using fastqc , adapters and kmers trimmed using trimmomatic, and then fastqc filtered agan
Filtered reads aligned to the mm10 genome using a tophat2/cufflinks pipeline to calculate FPKM data and then pairwise comparison using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited FPKM files for each sample

source_name: Retinal Ganglion Cells

extract_protocol:
RGCs were isolated through an improved immunopanning technique.  RNA was harvested using Trizol reagent. 100ng of total RNA per mice for each treatment group were pooled and split into triplicate for the contruction of sequencing libraries.
RNA sequencing libraries were generated according to SMART-seq v4 Ultra low input RNA kit (#634888, Takara Clontech, Mountain View, CA, USA). In brief, purified RNA was incubated with lysis buffer for 5 minutes, 3-SMART-seq CDS primer II (modified Oligo-dT primer) and V4 oligonucleotide were added to isolated RNA for first stranded cDNA synthesis. cDNA was amplified using PCR Primer II A, and subsequently purified using Ampure XP beads (#A63880, Beckman Coulter Life Science, Indianapolis, IN, USA). Illumina library was prepared using Nextera XT DNA library preparation kit (#FC-131-1024, Illumina, San Diego, CA, USA), and sequenced using Illumina HiSeq 2500 using 2x100bp flow cell for 20 million paired-end reads per sample

treatment_protocol: Saline (Control) and Microbeads (treatment) were injected into the anterior chamber of the eyes and IOP were measured 3 times a week for a period of 2 weeks.

tag: strain

value: retina

value: 8 weeks old

value: Moderate IOP


title: Li-KO-2

value: Liver-specific Klf15 Knockout


title: TN1007

description: Gene expression from patient mcgill.gq.17

tag: lymph node

value: yes

tag: grade

tag: death


title: TN1029

description: Gene expression from patient mcgill.gq.19

tag: recurrence

tag: tumor size

tag: patient


title: S4_WT_60to90_C3X

tag: background strain

tag: genetic background

value: wildtype

value: 10 weeks-old

value: femurs and tibia


title: S3_WT60to90_Mock

value: bone marrow-derived macrophages (BMDM)

tag: cell culture age

value: day 7

value: mock infected

tag: time point_minutes


description:
ATAC-seq on PBMCs from donor ND-1, SwitchedBcell
ATAC-seq_ND-1_SwitchedBcell


title: Moderate IOP Replicate 2

tag: age


description:
ATAC-seq on PBMCs from donor ND-2, SwitchedBcell
ATAC-seq_ND-2_SwitchedBcell


description:
ATAC-seq on PBMCs from donor ND-3, NaiveBcell
ATAC-seq_ND-3_NaiveBcell

source_name: PBMCs_healthy donor_NaiveBcell


title: Moderate IOP Replicate 1

tag: tissue


title: TN1027

description: Gene expression from patient mcgill.gq.16


title: Mild IOP Replicate 3

tag: treatment

value: Mild IOP


title: TN1026

description: Gene expression from patient mcgill.gq.15

value: III


title: Mild IOP Replicate 1


title: Control Replicate 3

value: Control


title: Mild IOP Replicate 2


description:
ATAC-seq on PBMCs from donor ND-3, CD8Tcell
ATAC-seq_ND-3_CD8Tcell

source_name: PBMCs_healthy donor_CD8Tcell

value: ATAC-seq


description:
ATAC-seq on PBMCs from donor ND-2, NaiveBcell
ATAC-seq_ND-2_NaiveBcell

value: healthy


title: TN1024

description: Gene expression from patient mcgill.gq.13

value: no


title: Control Replicate 2

value: retina


description:
ATAC-seq on PBMCs from donor ND-2, CD8Tcell
ATAC-seq_ND-2_CD8Tcell

value: Peripheral blood mononuclear cells (PBMCs)


description:
ATAC-seq on PBMCs from donor ND-1, CD8Tcell
ATAC-seq_ND-1_CD8Tcell


title: TN1015

description: Gene expression from patient mcgill.gq.14


title: Control Replicate 1

value: 8 weeks old


description:
ATAC-seq on PBMCs from donor ND-1, NaiveBcell
ATAC-seq_ND-1_NaiveBcell


title: RNAseq of cell line SKM-1 with downregulation of NCAM1 with sh-NCAM1 (72 h)

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

country: Germany

institute: Charité Universitätsmedizin Berlin

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
100 bp single-end reads  (Illumina) were aligned to reference genome hg19 and gtf.-transcriptome annotation release v19 (GENCODE) using STAR two-pass mode ( star 2.4.0.1).
GENCODE v19 gtf.-file was used for quantification, performed by HT-seq (version 0.6.1p1  release date 2014-04-13) , followed by normalisation, transformation and differential gene expression analysis in DEseq2 -1.12.4.
Genome_build: hg19

source_name: acute myeloid leukemia (AML)

extract_protocol:
RNA extraction was performed using Trizol reagent (Invitrogen) according manufacturer instructions.
Library was generated using TruSeq RNA Library Prep Kit v2 (Illumina)

tag: cell line

value: SKM-1, DSMZ number ACC 547

tag: genotype/variation

value: downregulation NCAM1


description:
ATAC-seq on PBMCs from donor ND-2, CD4Tcell
ATAC-seq_ND-2_CD4Tcell

source_name: PBMCs_healthy donor_CD4Tcell

tag: library

tag: replicate


title: TN1020

description: Gene expression from patient mcgill.gq.10

tag: lymph node


title: Mouse liver, control animal, biological replicate 2

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

description: The liver samples were collected from transgenic mice as well as from control animals at the age of 7 weeks

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix Expression Console Software for normalization, BRB Array Tools for statistical analysis

source_name: Wild type mouse

extract_protocol: RNA was purified from frozen liver samples kept in RNAlater (Qiagen) by RNAeasy mini kit (Qiagen) according to manufacturer's instruction.

value: liver

tag: genotype

value: wild type

value: the generated mice were on a C57BL/6 and NMRI mixed background and were backcrossed at least 4-times to C57BL/6 background


description:
ATAC-seq on PBMCs from donor ND-1, CD4Tcell
ATAC-seq_ND-1_CD4Tcell


title: Mouse liver, constitutively active FoxO3, metformin administered, biological replicate 3

source_name: Trangenic mouse, Metformin treated, biol. Replicate 3

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

value: constitutively active FoxO3 transgene

value: metformin


title: Mouse liver, constitutively active FoxO3, metformin administered, biological replicate 2

source_name: Trangenic mouse, Metformin treated, biol. Replicate 2


title: Mouse liver, control animal, biological replicate 1


description:
ATAC-seq on PBMCs from donor ND-3, CD4Tcell
ATAC-seq_ND-3_CD4Tcell


title: TN1003

description: Gene expression from patient mcgill.gq.9

tag: grade

tag: death


title: TN1025

description: Gene expression from patient mcgill.gq.11

tag: recurrence

tag: tumor size


title: Mouse liver, constitutively active FoxO3, metformin administered, biological replicate 4

source_name: Trangenic mouse, Metformin treated, biol. Replicate 4


description:
ATAC-seq on PBMCs from donor ND-3, Bcell
ATAC-seq_ND-3_Bcell

source_name: PBMCs_healthy donor_Bcell


title: RNAseq of cell line NOMO-1 with control shRNA transfection (72 h)

value: NOMO-1, DSMZ number ACC 542

value: control


title: RNAseq of cell line NOMO-1 with downregulation of NCAM1 with sh-NCAM1 (72 h)


title: RNAseq of cell line SKM-1 with control shRNA transfection (72 h)


title: Mouse liver, control animal, biological replicate 3


description:
ATAC-seq on PBMCs from donor ND-2, Bcell
ATAC-seq_ND-2_Bcell


title: RNAseq of cell line MOLM-14 with downregulation of NCAM1 with sh-NCAM1 (72 h)

value: MOLM-14, DSMZ number ACC 777


title: Mouse liver, control animal, biological replicate 4


title: Mouse liver, constitutively active FoxO3, metformin administered, biological replicate 1

source_name: Trangenic mouse, Metformin treated, biol. Replicate 1


description:
ATAC-seq on PBMCs from donor ND-1, Bcell
ATAC-seq_ND-1_Bcell


title: Mouse liver, constitutively active FoxO3, biological replicate 3

source_name: Trangenic mouse, biol. Replicate 3


title: RNAseq of cell line MOLM-14 with control shRNA transfection (72 h)


title: Mouse liver, constitutively active FoxO3, biological replicate 4

source_name: Trangenic mouse, biol. Replicate 4


title: TN1030

description: Gene expression from patient mcgill.gq.8

source_name: Bulk Tumor Tissue

value: yes

value: III

tag: patient


title: Mouse liver, constitutively active FoxO3, biological replicate 2

source_name: Trangenic mouse, biol. Replicate 2

tag: genetic background


title: hBMMSCs printed with CdECM bioink 2

city: Pohang

first: Dong-woo

last: Cho

state: Gyeongbuk

address: 77 Cheongam-ro, Nam-gu

department: Department of Mechanical Engineering

country: South Korea

institute: POSTECH

description: Gene expression data from hBMMSCs printed with CdECM bioink 2

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix)

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC). Data processed with RMA.

source_name: 3D cell-printed construct (pre-tissue)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Human bone marrow derived mesenchymal stem cells (hBMMSCs) (Cefobio, Korea) were cultured using DMEM/F12 (1:1) from Gibco with 10% fetal bovine serum (FBS) (Gibco, USA) and 1% penicillin/streptomycin (Gibco, USA)

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

treatment_protocol: After 80-90% confluence, hBMMSCs were detached using 0.05% trypsin-EDTA (Sigma-Aldrich, USA), and encapsulated in 1.5% (w/v) of liver, heart, skin and cornea dECM bioink (5×10^6 cells/ml). Then, the cell-laden constructs were printed using an in-house-developed 3D cell printing system. Cell-printed constructs were incubated at 37°C for 30 minutes to induce thermal crosslinking. The cell-printed constructs were cultured for seven days in the same culture media condition.

tag: cell type

value: human bone marrow derived mesenchymal stem cells  printed with Cornea dECM bioink 2, 3D cell-printed construct, 7 days culture


title: hBMMSCs printed with CdECM bioink 1

description: Gene expression data from hBMMSCs printed with CdECM bioink 1

value: human bone marrow derived mesenchymal stem cells  printed with Cornea dECM bioink 1, 3D cell-printed construct, 7 days culture


title: TN1036

description: Gene expression from patient mcgill.gq.7

value: no


title: TN1017

description: Gene expression from patient mcgill.gq.6


title: TN1028

description: Gene expression from patient mcgill.gq.4


title: Mouse liver, constitutively active FoxO3, biological replicate 1

source_name: Trangenic mouse, biol. Replicate 1


title: M3

city: Rome

first: Bruno

last: Arca

address: P.le Aldo Moro 5

department: Public Health and Infectious Diseases

country: Italy

institute: Sapienza University

description: M3 cpm

data_processing:
Raw reads were quality control checked by FastQC and then trimmed by cutadapt to remove 3’ adapters and discard reads shorter than 14 nucleotides.
Processed reads from each sample were mapped using Bowtie (-n 0 -l 18 -e 80) to the A. gambiae AgamP4 genome Assembly. Reads aligned to AgamP4 were then mapped (-n 0 -l 18 -e 80 – norc) to a collection of A. gambiae rRNA sequences obtained from VectorBase by the BioMart tool. After subtraction of ribosomal RNAs the remaining reads were mapped (-n 0 -l 18 -a --best --strata -e 80 --norc) to a list of miRNA precursors (known and predicted by MapMi and MiRDeep* software) and other non coding RNAs from A. gambiae (including tRNAs, snoRNAs, snRNAs, 7SL, 7SK and Rnase P) and finally to A. gambiae transcripts and repeats downloaded from VectorBase (-n 0 -l 18 -a --best --strata -e 80).
Raw read counts for each  A. gambiae mature miRNA were computed from SAM files using a Python custom script. Reads with multiple highest score mappings were discarded. Expression values were calculated as count per millions (CPM) using the edgeR software. Reads mapping to precursor miRNAs were assigned to mature miRNAs based on their mapping position; an overhang of maximum 3 nucleotides for each side of the mature form was tolerated.
Genome_build: AgamP4
Supplementary_files_format_and_content: Tab-delimited text file including CPM values for each Sample.

organism: Anopheles coluzzii

source_name: adult males

growth_protocol: A. coluzzii mosquitoes were reared under standard insectary conditions  (28°C, 60%-70% humidity, 14:10 hours light:dark photoperiod).

extract_protocol:
Saliva was collected in microcapillary tubes. Salivary glands were dissected in Phosphate Buffered Saline.
Libraries were prepared at the EMBL Genomic Core facility using the Illumina TruSeq Small RNA Sample preparation kit.

treatment_protocol: Adults 2-6 days post-emergence (dpe) were used for the experiments reported here. Saliva was collected in microcapillary tubes. Salivary glands were dissected in Phosphate Buffered Saline.

tag: strain

value: laboratory strain (Xag, 2R+, 2L+, 3R+, 3L+)

tag: origin

value: originally collected in Cameroon

value: whole body (adult male)

tag: molecule subtype

value: small RNA


title: hBMMSCs printed with SdECM bioink 2

description: Gene expression data from hBMMSCs printed with SdECM bioink 2

value: human bone marrow derived mesenchymal stem cells  printed with Skin dECM bioink 2, 3D cell-printed construct, 7 days culture


title: hBMMSCs printed with SdECM bioink 1

description: Gene expression data from hBMMSCs printed with SdECM bioink 1

value: human bone marrow derived mesenchymal stem cells  printed with Skin dECM bioink 1, 3D cell-printed construct, 7 days culture


title: M2

description: M2 cpm

tag: tissue


title: Vn-LB3-37-2

city: BOSTON

first: Henry

middle: Hung-Yi

last: Lee

state: Massachusetts

address: 77 AVENUE LOUIS PASTEUR, NRB 233

department: Genetics

description:
Directional RNASeq
processed data file: SupplementaryTable6_Transcriptome_Analysis.xlsx

data_processing:
Basecalling and demultiplexing via Basespace (Illumina).
Trimmed UMI with cutadapt <= 1.16.
Alignment with bowtie2 2.2.8 to protein-encoding genes from RAST, organism 691.12 (RefSeq NZ_CP009977, NZ_CP009978).
Transcripts were quantified with Salmon 0.8.1 and counts were summarized with tximport for differential expression analysis with DESeq2.
Genome_build: RAST, organism 691.12 (RefSeq NZ_CP009977.1, NZ_CP009978.1)
Supplementary_files_format_and_content: SupplementaryTable6_Transcriptome_Analysis.xlsx: Excel file including differential expression analysis results and salmon analyses results for each sample.

organism: Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

source_name: microbial culture

growth_protocol: Cultures were grown overnight in LB3 or minimal media with glucose at 37C and subcultured 1:1000 (~10E6 cfu/mL) into 25mL of fresh media in a 250mL baffled flask at ~250rpm until OD600 ~0.3-0.5.

extract_protocol:
Samples were resuspended in RNAProtect (Qiagen) and frozen overnight at -80C, RNA extracted with RNeasy (Qiagen) protocol with lysozyme digestion and DNase on column digestion, rRNA depleted with Ribo-Zero rRNA Removal Kit Bacteria (Illumina).
Prepared according to manufacturer's protocol NEXTflexTM Rapid Directional qRNA-SeqTM Kit - 5130-01D.

tag: media


title: V3-M9


title: M1

description: M1 cpm


title: hBMMSCs printed with HdECM bioink 2

description: Gene expression data from hBMMSCs printed with HdECM bioink 2

value: human bone marrow derived mesenchymal stem cells  printed with Heart dECM bioink 2, 3D cell-printed construct, 7 days culture


title: Vn-LB3-37-1


title: hBMMSCs printed with LdECM bioink 2

description: Gene expression data from hBMMSCs printed with LdECM bioink 2

value: human bone marrow derived mesenchymal stem cells  printed with Liver dECM bioink 2, 3D cell-printed construct, 7 days culture


title: V2-M9


title: V1-M9


title: hBMMSCs printed with HdECM bioink 1

description: Gene expression data from hBMMSCs printed with HdECM bioink 1

value: human bone marrow derived mesenchymal stem cells  printed with Heart dECM bioink 1, 3D cell-printed construct, 7 days culture


title: F2

description: F2 cpm

source_name: adult females

value: whole body (adult female)


title: F3

description: F3 cpm


title: TN1005

first: Benjamin

last: Haibe-Kains

address: 610 University Avenue

description: Gene expression from patient mcgill.gq.2

tag: age


title: AgSal2

description: AgSal2 cpm

source_name: saliva

value: saliva from adult females


title: F1

description: F1 cpm


title: AgSal1

description: AgSal1 cpm


title: Young Leaf Replicate 3

city: Subang Jaya

first: Kanagesswari

last: Muniandy

state: Selangor

address: Jalan Lagoon Selatan

department: School of Science

country: Malaysia

institute: Monash University Malaysia

data_processing:
Trimming with Trimmomatic v36.0
Alignment with Bismark v16.3 with default parameters except max. length set at 800bp
Methylation calling of CpG, CHG and CHH context with Bismark v16.3
Analysis and visualization of differential CpG, CHG and CHH methylation with SeqMonk v40.0
Genome_build: Chloroplast: assembled MR219 chloroplast genome
Supplementary_files_format_and_content: Bismark methylation extractor context text file

organism: Oryza sativa Indica Group

source_name: Leaf

growth_protocol: MR219 seeds were germinated and grown in ambient conditions

extract_protocol:
Total genomic DNA was extracted using  Qiagen DNAeasy Plant Mini Kit protocol
DNA libraries were prepared for sequencing using standard Illumina protocols with methylated adaptors. Sodium bisulfite treatment was carried out during library preparation.

value: 33 days aftyer germination

value: leaf

tag: developmental stage

value: vegetative stage


title: G2

description: G2 cpm

source_name: salivary glands

value: salivary glands from adult females


title: 9993000009_RingStage(C+)_Cultured Cells

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

description: Triplicate 2ug total RNA aliquots of sample 9993000009 was submitted for sequencing due to not having a 5ug aliquot sample present at the time. Samples were not pooled before submission to avoid an additional freeze/thaw. These triplicate 2ug aliquots were eventually pooled together by the Yerkes Genomics Core and the appropriate quantity was used for library prep.

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters. Note all values for ERCC abundances will be zero as no spike ins were included in sequenced samples. See readme for details.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: RNA-Seq reads were mapped to a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0), created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under BioProject accession  PRJNA214746. Parasite: Plasmodium knowlesi Malayan Strain Pk1 (A+) genome assembly was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA377737.
Supplementary_files_format_and_content: Excel files contain either normalized transcript abundances or raw counts at the gene level, for each individual.  Abundances and raw counts are further classified by experimental Time Point (RingStage), and Specimen Type (Cultured Cells).
Supplementary_files_format_and_content: Host, Parasite, and ERCC Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Raw File List / Sample Identifier / Abundances': Samples were sequenced across multiple lanes and all fastq files are listed for each sample. Rawread counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point.      Notes:  There are 9 columns representing 9 subjects.    There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.
Supplementary_files_format_and_content: Host DESeq2Normalized Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Raw File List / Sample Identifier / Abundances': Samples were sequenced across multiple lanes and all fastq files are listed for each sample. DESeq2 normalized read counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point.      Notes:  There are 9 columns representing 9 subjects.    There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.

organism:
Plasmodium knowlesi
Macaca mulatta

source_name: Cultured Cells

growth_protocol: Animals approved for use were already in experimental housing. Sample dates range from 9/14/07 to 6/14/17. All Non Human Primates used in this experiment were naive for the particular clone of P. knowlesi used to generate the time course. Macaca mulatta were inoculated with a particular parasite clone and allowed to reach a targeted peak parasitemia of 5% - 10% proportion of infected RBCs. Whole blood was collected at the early ring stage while subjects were under anesthesia, and an ex vivo culture was established using standard protocols, which include but are not limited to the processing of the whole blood by removing platelets and white blood cells. Samples were collected starting at 1.5-2 hours after establishing cultures, followed by collections every 4 hours for a 24 hour period.

extract_protocol:
(Ex_vivo_prep_of_RBCs.pdf SOP)  1.RBCs are obtained from an infected rhesus monkey.  1.a. 10 ml of blood/kg of weight are drawn  1.b. Sample is collected in heparin tubes  1.c. Pool individuals tubes in a 50ml-tube to obtain total volume  2. Platelets are removed by the addition of adenosine diphosphate (SIGMA A-4386; Stock: 40 mg/ml prepared in PBS)  2.a. Add 0.5 ml per 10 ml of blood  2.b. Incubate 5 min at room temperature  3. Preparation of columns:  3.a. Glasperlen Glass bead column  3.a.i. Use a ___ ml syringe  3.a.ii. Bed volume of glass beads: 1/2 volume of blood  3.a.iii. Pre-wet beads with Hanks Solution (HBSS)  3.b. Cf11 Column:  3.b.i. Use __ml syringe  3.b.ii. Volume of cellulose: 2X of total volumne  3.b.iii. Mix cellulose with HBSS, 50ml of cellulose + 100ml of HBSS gives aprox. 37ml of bed  3.b.iv. Pour into syringe at once and don't allow to drip until ready to start  3.c. Add blood carefully into glass bead column  3.d. Push with the plug gently  3.e. Wash with one column volume of HBSS  3.f. Remove the plug from CF11 column  3.g. Drip blood through CF11 column  3.h. Allow blood to flow completely into cellulose matrix  3.i. Wash CF11 column with one column volume  3.j. Collect fraction in 50ml tubes  3.k. Centrifuge 2000 rpm for 5 min  (RPMI recipe.pdf SOP)  1. RPMI - 1640 Complete medium or McCoys  1.a. 1 package RPMI 1640 powder or McCoys powder  1.b. 0.5 ml gentamicin (50 mg/ml)  1.c. 7.2 gm HEPES  1.d. 2 ml (25mg/ml) Hypoxanthine in 1 M NaOH  1.e. 2 gm Glucose (Dextrose) for RPMI or 1 gm for McCoys  2. Dissolve RPMI-1640 in 500 ml Gibco distilled H2O in 1 liter volumetric flask  3. Add various ingredients and mix  4. Adjust pH to 7.2 with 1M NaOH  5. Bring to total volume 1000ml with H2O  6. Filter sterilization  7. Add 48ml serum (10%) and 16ml bicarbonate (0.25%) to 432ml RPMI  8. Filter sterilization  (Cell_Culture)  1. Processed RBCs are put into standard culture medium in culture flasks with plug seal caps.  2. Culture flasks are then gassed with blood gas mix  3. Incubate cultures at 37 degrees celsius  (Total_RNA_Extraction_from_Parasite_Cultures.docx SOP)  1. Spin down the cultures at 700 g for 5 min. Aspirate off the supernatant.  2. Add 5 volumes of pre-warmed TRIzol LS (37°C) and shake vigorously for 1 min.  3. Incubate at 37°C for 5 min.  4. Keep the samples on ice. For each 5 mL of TRIzol LS that was used in step 2, add 1 mL of chloroform and vortex/shake for 1 min and transfer to a Teflon tube.  5. Centrifuge at 12000 g for 30 min at 4°C.  6. Carefully transfer the upper aqueous layer to a fresh polypropylene tube and add 0.8 volume of pre-chilled isopropanol to precipitate the RNA. Mix carefully by inverting.  7. Mix by inverting and centrifuge at 12000 g for 30 min and 4°C. Carefully aspirate off the supernatant.  8. Allow the pellet to air-dry on ice for 5 min and add 30-100 μL of RNase-free non-DEPC treated water.  9. Heat tubes at 60°C for 10 min and then place on ice.  10. Clean up RNA with the Qiagen RNeasy kit, with the optional DNAse digest on the column.   11. Measure the RNA conc and absorbance on Nanodrop.   12. Store aliquots for northern blots (30 ug total RNA in ETOH+NaAc), PCR (2 ug in water), and RNAseq (5 ug in water).   13. Total RNA (5 µg) of each sample (except sample  9993000009, see sample section for more information) were used for sequencing.  14. The quality of all RNA samples was then confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.  As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 100 million paired-end 100 base pair (bp) reads per library.

tag: time point

value: RingStage

tag: gender

value: Male

tag: non human primate individual id

tag: infected with

value: Plasmodium knowlesi


title: G1

description: G1 cpm

value: laboratory strain (Xag, 2R+, 2L+, 3R+, 3L+)

value: originally collected in Cameroon


title: Young Leaf Replicate 2

value: 32 days aftyer germination


title: Young Leaf Replicate 1

value: 31 days aftyer germination


title: 9993000008_RingStage(B+1+)_Cultured Cells


title: Old Leaf Replicate 2

value: 125 days after germination

value: ripening stage


title: 9993000007_RingStage(A+)_Cultured Cells


title: Old Leaf Replicate 3


title: S2

description: S2 cpm

value: small RNA


title: 9993000006_RingStage(C+)_Cultured Cells

value: NHPX


title: 9993000005_RingStage(B+1+)_Cultured Cells


title: Old Leaf Replicate 1


title: TN1018

city: Toronto

institute: Princess Margaret Cancer Centre

description: Gene expression from patient mcgill.gq.12

tag: lymph node

value: yes

tag: grade

value: III

tag: death

value: no


title: hBMMSCs printed with LdECM bioink 1

description: Gene expression data from hBMMSCs printed with LdECM bioink 1

value: human bone marrow derived mesenchymal stem cells  printed with Liver dECM bioink 1, 3D cell-printed construct, 7 days culture


title: TN1032

description: Gene expression from patient mcgill.gq.1

tag: recurrence

tag: tumor size

tag: patient


title: Grain Replicate 3

source_name: Grain

value: grain


title: 9993000003_RingStage(C+)_Cultured Cells


title: Grain Replicate 2


title: G3

description: G3 cpm

tag: strain

value: salivary glands from adult females


title: 9993000002_RingStage(B+1+)_Cultured Cells

value: RingStage


title: S3

description: S3 cpm

tag: origin

value: saliva from adult females


title: 9993000001_RingStage(A+)_Cultured Cells

value: Male

value: Plasmodium knowlesi


title: Grain Replicate 1


title: Processed RA data at time t30 after Auxin addition

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: cDNA labelling for BY25598 strain, t30: 30 min after Auxin addition

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Typhoon FLA7000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing:
Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.
Value is the result of the Median Absolute Deviation normalization of each triplicate of the raw data.

organism: Saccharomyces cerevisiae

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC to 0.5 OD600. Each sample was done in triplicate.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: BY25598 (Xrn1-Auxin degron)

tag: time

value: t30 (30 min after Auxin addition)

tag: sample type

value: mRNA


title: S1

description: S1 cpm

value: laboratory strain (Xag, 2R+, 2L+, 3R+, 3L+)

value: originally collected in Cameroon

tag: tissue

tag: molecule subtype


title: L3_salivary_gland_H3K9R_rep1

status: Public on Feb 21 2019

city: Chapel Hill

first: Robert

last: Duronio

state: NC

address: CB #3280, Coker Hall

institute: University of North Carolina at Chapel Hill

data_processing:
Paired-end 100bp reads were trimmed using Trimmomatic (v0.36) with LEADING:30 and TRAILING:30 parameters and aligned to the dm6 reference genome (release 6.04) using Bowtie2 (v2.3.2) default parameters. Reads with a MAPQ score greater than 10 were retained with SAMtools (v1.6). BEDTools coverage (v2.25.0) was used to quantify the number of reads mapping to 10kb windows tiled across the genome, with results normalized to read depth (RPM). CNVnator 0.3.3 was used for detection of under-replicated sequences using a bin size of 1000. Under-replicated domains were called if they were: 1) detected by CNVnator and 2) greater than 10kb in size.
Genome_build: dm6
Supplementary_files_format_and_content: [under_replication_arms.txt]  CNVnator 0.3.3 was used for detection of under-replicated sequences using a bin size of 1000. Under-replicated domains were called if they were: 1) detected by CNVnator and 2) greater than 10kb in size. Under-replicated domains located in chromosome arms are included here.
Supplementary_files_format_and_content: [under_replication_pericentromere.txt]  CNVnator 0.3.3 was used for detection of under-replicated sequences using a bin size of 1000. Under-replicated domains were called if they were: 1) detected by CNVnator and 2) greater than 10kb in size. Under-replicated domains located in pericentric heterochromatin are included here.

organism: Drosophila melanogaster

growth_protocol: All stocks were maintained on standard corn media. 50 ΔHisC, twi-GAL4/CyO females and 20 ΔHisC, UAS-2xEYFP/CyO ; HWT/HWT, H4K16R/H4K16R, or H3K9R/H3K9R males were placed in a cage at 25C and allowed to lay eggs on a grape juice agar plate.~50 GFP positive larvae were moved to a corn media vial 48 hours after egg laying to separate ΔHisC, UAS-2xEYFP / ΔHisC, twi-GAL4 mutants from their siblings. Culture vials were cleared of wandering third instar larvae, and after 4-6 hours newly wandering larvae were selected.

extract_protocol:
Salivary glands from female, wandering third-instar larvae were isolated and flash frozen in liquid N2 until all samples were collected. Nuclei were isolated from replicates of 25 salivary glands and sonicated with a Branson Sonifier 450 to an average fragment size distribution of 500-1000bp. Sonicated samples were treated with 100 µg/mL RNaseA at 37°C for 1 hour and with 200 µg/mL proteinase K at 37°C for 2 hours. Genomic DNA was phenol chloroform extracted and stored at -80°C prior to library preparation.
Libraries were prepared from 20 ng of genomic DNA with the ThruPLEX DNA-seq kit (Rubicon Genomics) and sequenced on an Illumina HiSeq2500 at the UNC High-Throughput Sequencing Core Facility.

tag: developmental stage

value: 3rd instar wandering larvae

value: salivary gland

tag: genotype

tag: Sex

value: female


title: Ce_adult_polyp_3

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

data_processing:
All libraries were quality checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reaper v16-098 (https://www.ebi.ac.uk/~stijn/reaper/reaper.html) was used to remove the Illumina small RNA Adapter sequences, and PullSeq 1.0.2 (https://github.com/bcthomas/pullseq) to keep reads that were at least 16 nucleotides long.
Tally v16-098 (https://www.ebi.ac.uk/~stijn/reaper/tally.html) was used to collapse all reads to a single occurrence in a FASTA file, keeping the counts of each read in the header. These are provided as processed files.
The alignment component of ShortStack 3.8.3 was used, with parameters: --nostitch, --mismatches 2, --mmap u, --bowtie_m 500 and --ranmax 500.
All the sRNA-seq results for each genome were used to predict novel ncRNA producing regions or clusters. All libraries for each genome were combined as a single input, and ShortStack 3.8.3 was used with the following parameters: --pad 10, --mincov 10, --dicermin 18, --dicermax 32. All the clusters were then split at exon-intron boundaries.
In order to obtain a level of expression for each sRNA-producing cluster, mapped reads were counted using the findOverlaps function from GenomicRanges R package with parameters minoverlap=16 and ignore.strand=TRUE. Only reads between 20-25nt were counted. Count tables were produced for each genome, where each cluster is a row and each library a column. These are provided as supplementary files.
Genome_build: The reference genome assembly for H. bakeri genome was nHp_v2.0 from http://parasite.wormbase.org/Heligmosomoides_polygyrus_prjeb15396 and for C. elegans WBcel235 from http://parasite.wormbase.org/Caenorhabditis_elegans_prjna13758.
Supplementary_files_format_and_content: Contains all reads of at least 16 nucleotides collapsed to a unique occurrences and saved in FASTA format. Read count is included in the tab files.

organism: Caenorhabditis elegans

source_name: Adult worms

growth_protocol: C. elegans cultures were grown at a density of 100,000 worms per plate, on 150mm plates with 2ml of 5X concentrated OP50 to the gravid adult stage (containing embryos; 65h post L1 at 20°C).

extract_protocol:
Total RNA was treated with RNA 5' Polyphosphatase (Epicenter) following manufacturer's instructions, before library preparation.
Total RNA was extracted using a miRNAeasy mini kit (Qiagen) following manufacturer's instructions. RNA was treated with Turbo DNA-free kit (Thermo Fisher) to remove residual DNA.
Libraries were prepared using the CleanTag small RNA library prep kit according to manufacturer’s instructions, using total RNA from adult worms (30 ng), and sucrose-gradient purified EVs (equivalent 1E10 EVs measured by Nanosight, Malvern). For all samples, 1:12 dilutions of both adapters were used with 18 amplification cycles (TriLink BioTechnologies). Fragments between 140-170bp were size selected and sequenced on an Illumina HiSeq high output v4 50bp SE in Edinburgh Genomics.

value: Adult worms

tag: agent

value: polyphosphatase

tag: treatment protocol

value: Nematodes were harvested from the plates and flash frozen.


title: Ce_adult_polyp_2


title: L3_salivary_gland_HWT_rep1

value: HWT


title: L3_salivary_gland_H4K16R_rep1


title: L3_salivary_gland_H3K9R_rep2


title: 9993000004_RingStage(A+)_Cultured Cells

tag: time point

tag: gender

tag: non human primate individual id

tag: infected with


title: Processed RA data at time t0

description: cDNA labelling for BY25598 strain, t0: before Auxin addition

value: t0 (before Auxin addition)


title: L3_salivary_gland_H4K16R_rep2


title: L3_salivary_gland_HWT_rep2


title: Ce_adult_polyp_1


title: Processed TR data at time t30 after Auxin addition

description: GRO labelling for BY25598 strain, t30: 30 min after Auxin addition

value: GRO


title: Ce_adult_monop_1

extract_protocol:
Total RNA was used directly for library preparation.
Total RNA was extracted using a miRNAeasy mini kit (Qiagen) following manufacturer's instructions. RNA was treated with Turbo DNA-free kit (Thermo Fisher) to remove residual DNA.
Libraries were prepared using the CleanTag small RNA library prep kit according to manufacturer’s instructions, using total RNA from adult worms (30 ng), and sucrose-gradient purified EVs (equivalent 1E10 EVs measured by Nanosight, Malvern). For all samples, 1:12 dilutions of both adapters were used with 18 amplification cycles (TriLink BioTechnologies). Fragments between 140-170bp were size selected and sequenced on an Illumina HiSeq high output v4 50bp SE in Edinburgh Genomics.


title: Ce_adult_monop_3


title: Ce_adult_monop_2


title: Experiment_2_DAF-mut9_3

city: Columbus

first: Emily

middle: Rose

last: Theisen

address: 700 Childrens Drive

department: Center For Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to hg19 whole genome using STAR-2.5.1b using --outSAMunmapped within and otherwise default
Raw counts were generated for each sample using htseq-count with -t exon -i gene -r pos
Normalized counts were generated using default settings in ComBat.
Differential expression was calculated using default settings and blind = TRUE in DEseq2.
Genome_build: hg19
Supplementary_files_format_and_content: csv; Counts are organized by gene (row) and sample (column); ComBat counts are the raw counts filtered and normalized with ComBat to correct for batch effects; Differential expression contains information for gene (Ensembl ID and HGNC symbol), the base mean expression level, and the log2(FoldChange), stdev(log2(FoldChange)), and the adjusted p-value (Benjamini-Hochberg) for each construct as compared to the iEF samples as reference control.

source_name: A673 cells

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase digestion.  2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq

treatment_protocol: A673 cells were seeded at 50% confluency and left to adhere overnight (day 0). shRNAs were retrovirally delivered on day 1. Selection in 2 µg/mL puromycin (Sigma P8833) occurred on days 2-5. Cells were infected with retrovirus containing the cDNA in the pMSCV-hygro backbone on day 5. Double selection in puromycin and 400 µg/mL hygromycin B (Thermo Fisher 10687010) began on day 6 and continued until day 16. Cells were subsequently harvested for RNA, protein, and seeded for soft agar assays.

tag: cell line

tag: transduced shrna

value: iEF

tag: transduced cdna

tag: replicate


title: Processed TR data at time t0

description: GRO labelling for BY25598 strain, t0: before Auxin addition

tag: strain

tag: time


title: Experiment_2_mut9_3


title: Experiment_2_DAF-mut9_1


title: Experiment_2_mut9_2


title: Experiment_2_mut9_1


title: Experiment_2_DAF_1

value: DAF


title: Experiment_2_DAF_2


title: Experiment_2_DAF_3