title: 8d tdTomato-MafA (from 6SANgn3 culture) infected organoids_1_3


title: 8d tdTomato-MafA (from 6SANgn3 culture) infected organoids_2_1

status: Public on Dec 26 2018

type: SRA

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

molecule: total RNA

organism: Mus musculus

source_name: Dissociated pancreatic organoid cells

extract_protocol:
Three-dimensional cultures of pancreatic ductal cells (organoids, Huch et al 2013) were infected with multiple vectors expressing GFP-Ngn3, LSS/Orange-Pdx1 and/or tdTomato-MafA. Organoids were dissociated to single cells and FACS sorted  (FACS Influx BD Biosciences). FACS sorting allows us to isolate cells that are expressing each of the transcription factors either individually or in each possible combination by sorting for the associated fluorescent reporter proteins. Pool of 50 cells were sorted by FACS directly into individual wells of a 96-well plate containing lysis buffer. RNA-Seq analysis was performed as described previously (Picelli et al., 2014). Pooled libraries were then run on the Illumina Hi-Seq 2500.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: expression

value: tdTomato-MafA (from 6SANgn3 culture)

tag: tissue

value: Dissociated pancreatic organoid cells

tag: strain

tag: days of transgene induction

value: 8 days

tag: passage


title: uninfected_wt_rep3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

country: USA

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt

source_name: Bone marrow-derived macrophages

growth_protocol: C57Bl/6 and Il1r1-/- mice were purchased from Jackson Laboratory (Stock No:  000664 and 003245).

extract_protocol:
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen).
cDNA synthesis was carrid out using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: Bone marrow-derived macrophages (BMDMs) from WT and Il1r1–/– mice were derived in 7 days in GM-CSF supplemented complete DMEM.  Cells were infected with either Mtb HN878 or Mtb W_7642 (multiplicity of infection = 1) and RNA samples collected after 6 days.

tag: genotype

value: wt

tag: agent

value: uninfected


title: 8d tdTomato-MafA (from 6SANgn3 culture) infected organoids_1_1


title: 8d tdTomato-MafA (from 6SANgn3 culture) infected organoids_1_2


title: 8d tdTomato-MafA (from 6SANgn3 culture) infected organoids_3_1


title: HN878_wt_rep3

value: Mtb HN878


title: HN878_il1r1_rep2


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_2_1


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_3_1


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_1_3


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_2_1


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_3_1


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_1_1


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_1_2


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_3_1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_2_1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_2_2


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_2_2


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_1_3


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_2_1


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_1_2


title: 8d tdTomato-MafA - LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_1_1


title: 8d LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_2_1

value: LSSOrange-Pdx1 (from WTNgn3 culture)


title: 8d LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_1_3


title: 8dLSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_2_2

value: 8dLSSOrange-Pdx1 (from 6SANgn3 culture)


title: 8d LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_1_3

value: LSSOrange-Pdx1 (from 6SANgn3 culture)


title: 8dLSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_1_2


title: 8d LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_1_1


title: 8dLSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_1_1

value: 8dLSSOrange-Pdx1 (from WTNgn3 culture)


title: 8d LSSOrange-Pdx1 (from WTNgn3 culture) infected organoids_1_2


title: 8d GFP-WTNgn3 - tdTomato-MafA infected organoids_3_1

value: GFP-WTNgn3 - tdTomato-MafA


title: 8d GFP-WTNgn3 - tdTomato-MafA infected organoids_2_1


title: 8d GFP-6SANgn3 - tdTomato-MafA infected organoids_3_1

value: GFP-6SANgn3 - tdTomato-MafA


title: 8d GFP-WTNgn3 - tdTomato-MafA infected organoids_1_2


title: 8d GFP-6SANgn3 - tdTomato-MafA infected organoids_2_2


title: 8d LSSOrange-Pdx1 (from 6SANgn3 culture) infected organoids_2_1


title: 8d GFP-6SANgn3 - tdTomato-MafA infected organoids_2_1


title: 8d GFP-6SANgn3 - tdTomato-MafA infected organoids_1_2


title: 8d GFP-6SANgn3 - tdTomato-MafA infected organoids_1_3


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 infected organoids_3_1

value: GFP-WTNgn3 - LSSOrange-Pdx1


title: 8d GFP-6SANgn3 - tdTomato-MafA infected organoids_1_1


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 infected organoids_2_1


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 infected organoids_1_2


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 infected organoids_1_1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 infected organoids_2_2

value: GFP-6SANgn3 - LSSOrange-Pdx1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 infected organoids_2_1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 infected organoids_3_1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 infected organoids_1_3


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 infected organoids_1_1


title: Herb rep4 DNA

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
43-DNA

library_source: genomic

data_processing:
Read trimming: cutadapt version 1.10
Alignment: Bismark version 0.19.0
methylation call: methylKit version 1.0.0
Differential methylation analysis: methylKit version 1.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes methylation values

molecule: genomic DNA

source_name: lung tissue

extract_protocol:
Genomic DNA was extracted with Qiagen kit According to the instructions of the SureSelect MethylSeq
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: Herbal treatment

value: lung

value: BALB/c


title: 8d GFP-WTNgn3 - tdTomato-MafA infected organoids_1_1


title: Herb rep3 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
41-DNA


title: Herb rep1 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
38-DNA


title: Herb rep2 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
40-DNA


title: OVA rep3 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
10-DNA

value: ovalbumin(OVA)-induced asthma model


title: OVA rep2 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
8-DNA


title: OVA rep1 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
7-DNA


title: Saline rep3 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
3-DNA

value: control


title: Saline rep2 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
2-DNA


title: TLR7_72h Rep3

city: Madison

first: Douglas

last: McNeel

state: Wisconsin

address: 111 Highland Ave., Rm 7007

institute: University of Wisconsin

data_processing:
Trimming-Sequencing reads were trimmed using the Skewer trimming program to remove sequencing adapters and bases with quality scores lower than Q20 (Jiang et al., 2014) Version 0.1.123: -q 20 -k 15 -l 25
Aligning-Trimmed reads were subsequently aligned to the Mus musculus reference genome using the STAR aligner (Dobin et al., 2013). Version 2.5.0a
Read count quantification-Quantification of expected read counts for each gene and isoform was calculated by RSEM (Li and Dewey, 2011). Version v1.2.31
Filtering-Transcripts were removed from the analysis if they had fewer than 5 reads in half of the samples.
Differential gene expression analysis-The remaining read counts were used for differential gene expression analysis using edgeR (Robinson, et al., 2010) in the R computing environment (R Core Team, 2017). Versions 3.12.1 and 3.2.1 respectively
Genome_build: GRCm38.85 (ENSEMBL)
Supplementary_files_format_and_content: comma-delimited text files include expected count values for each Sample ...

source_name: Splenocytes from OT-1 Mice

growth_protocol: Spleens were collected from OT-1 mice, processed through a mesh screen, and splenocytes were isolated by centrifugation after red blood cell osmotic lysis with ammonium chloride/potassium chloride lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM EDTA). Splenocytes were cultured at 2x106/mL in RPMI 1640 medium supplemented with L-glutamine, 10% fetal calf serum (FCS), 200 U/mL penicillin/streptomycin, 1% sodium pyruvate, 1% HEPES, 50μM β-MeOH, and 2 µg/mL of the designated peptide. TLR agonists were all purchased from InvivoGen (San Diego, CA) and added one hour before peptides at the following optimal concentrations based on preliminary studies and previously reported results: 300 ng/ml Pam3CSK4, 10 µg/mL Poly(I:C) HMW, 10 μg/ml MPLAs, 3 µg/ml Gardiquimod, 10 µg/ml R848, 5 µM ODN 1826. At the time points indicated, cells were stained, fixed for 15 min at 4°C in cytofix (BD Biosciences (BD), San Jose, CA; 554655), and frozen in FCS + 10% DMSO. After all time points were collected, cells from all times were thawed, rinsed and resuspended in PBS + 3% FCS + 1mM EDTA and analyzed by flow cytometry. Cells were stained for 30 min at 4°C in a 1:4 dilution of brilliant stain buffer (BD 563794) in PBS + 3% FCS + 1mM EDTA. In order to assess co-stimulation, blocking antibodies for CD80 (0.6 µg/mL), CD86 (0.25 µg/mL) or OX40L (0.6 µg/mL) were added 1 hour prior to antigen.

extract_protocol:
Cells were stimulated in vitro as above, and at the times indicated T cells were isolated via immunomagnetic negative selection (StemCell, Vancouver, Canada 19853), RNA was collected as per the manufacturers instruction (Direct-zol RNA MiniPrep Plus w/ TRI Reagent, Zymo Research), treated with DNAse (TURBO DNA-free Kit, Invitrogen), and stored at -80°C until analysis at the UW-Madison Biotechnology Center. Total RNA was verified for purity and integrity via a NanoDrop2000 Spectrophotometer and Agilent 2100 BioAnalyzer, respectively. Samples that met the Illumina sample input guidelines were prepared using the Illumina® TruSeq® Stranded mRNA Sample Preparation kits (Illumina Inc., San Diego, California, USA). For each library preparation, mRNA was purified from 1000 ng total RNA using poly-T oligo-attached magnetic beads. Subsequently, each poly-A enriched sample was fragmented using divalent cations under elevated temperature. The fragmented RNA was synthesized into double-stranded cDNA using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA Polymerase I and RNAse H for removal of mRNA. Double-stranded cDNA was purified by paramagnetic beads (Agencourt AMPure XP beads, Beckman Coulter). The cDNA products were incubated with Klenow DNA Polymerase and DNA fragments, ligated to Illumina adapters, and purified by paramagnetic beads. Adapter ligated DNA was amplified in a Linker Mediated PCR reaction (LM-PCR) for 11 cycles using PhusionTM DNA Polymerase and Illumina's PE genomic DNA primer set and then purified by paramagnetic beads. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit® dsDNA HS Assay Kit (Invitrogen, Carlsbad, California, USA), respectively. Libraries were standardized to 2μM. Cluster generation was performed using standard Cluster Kit (v3) and the Illumina Cluster Station. Single 100bp sequencing was performed, using standard SBS chemistry (v4) on an Illumina HiSeq2500 sequencer. Images were analyzed using the standard Illumina Pipeline, version 1.8.2.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: jackson labs

value: Stock No:003831

tag: cell type

value: CD8+ T cells

tag: time


title: Saline rep1 DNA

description:
Processed data file: meth yl_rawdata.win1000.step500.txt
1-DNA


title: TLR7_72h Rep4


title: TLR7_24h Rep3


title: TLR7_72h Rep1


title: TLR7_24h Rep1


title: TLR2_72h Rep3


title: TLR2_72h Rep4


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 infected organoids_1_2

value: Dissociated pancreatic organoid cells

value: 8 days


title: TLR2_72h Rep1


title: TLR2_72h Rep2


title: TLR7_24h Rep2


title: TLR2_24h Rep2


title: OVA_72h_Rep4

value: OVA


title: TLR7_24h Rep4


title: TLR2_24h Rep1


title: OVA_72h_Rep3


title: OVA_72h_Rep2


title: OVA_72h Rep1


title: OVA_24h Rep4


title: OVA_24h Rep2


title: TLR7_72h Rep2


title: OVA_24h Rep3


title: OVA_24h Rep1


title: CB6R1G

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

description: R_RNA depletion+Poly A selection

data_processing:
Single reads split by barcode into individual files using PERL script. The reads with good quality were aligned to reference sequence databases of  mouse (mm10) genome, RefSeq exons, splicing junctions and contamination databases including ribosome and mitochondria sequences using BWA alignment algorithm and the alignment files in SAM format were generated. After filtering reads mapped to contamination databases, the reads that  have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of corresponding transcript. The read count at exon, splice-junction, transcript and gene levels were summarized and normalized to the similar level across the samples and futher corrected for batch effect  in order to compare transcription level in different groups.
Genome_build: mm10
processed data files format and content: normalized log2 transformed read counts for each sample

source_name: glomeruli

growth_protocol: 8-week old Male mice were fed with Doxycycline Food + water for 6 weeks; Glomeruli extracted after bead perfusion; RNA was extracted from homogenized glomeruli after magnetic separator and sieving

extract_protocol:
Qiagen Rneasy columns
According to Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA hybridized to poly dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first strand synthesis with RTase, randomers second strand synthesis. Then end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode.

treatment_protocol: Littermates non-transgenic for SiRNA sequence were controls

value: BALB-C

tag: genotype/variation

value: Controls

tag: age

value: 14 weeks

tag: gender

value: Male


title: G3

description: R_RNA depletion+Poly A selection


title: G2

description: R_RNA depletion+Poly A selection


title: G1

description: R_RNA depletion+Poly A selection


title: CB6STG

description: R_RNA depletion+Poly A selection

value: 6-weeks Shroom3 knockdown


title: G5

description: R_RNA depletion+Poly A selection


title: G4

description: R_RNA depletion+Poly A selection


title: eralpha_shFbxo_E2-SRC-3

city: Tokyo

first: Yoshikazu

last: Johmura

address: 4-6-1 Shirokanedai, Minato-ku

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

data_processing:
Base calling for single-end reads and alignment were performed using Torrent SuiteTM Software 5.2.2 with default settings.
The reads were mapped to reference human genome hg19 using the Torrent Mapping Alignment Program (TMAP) provided with Torrent SuiteTM.
Tag directories were created with the aligned reads using the makeTagDirectory supplied in HOMER version v4.9.1
Peaks were called using rfindPeaks in HOMER with the default parameters provided, namely a tag density of more than four-fold and a false discovery rate below 0.001 compared with the normalized tag density in the 10kb region surrounding each peak.
Genome_build: hg19
Supplementary_files_format_and_content: To find enriched TF motifs, we utilized findMotifsGenome with a region size of 50 bp and a p-value less than 1e-50, and annotated the regions using annotatePeaks. Overlapping ERα and SRC-3 peaks were identified using a distance of less than 100 bp between the enriched regions of ERα and p160. A hierarchical cluster analysis of the enriched regions was performed using Cluster 3.0. The heatmap data matrix was generated using Homer, and then visualized on Java Tree View. The box-and-whisker plot was created using a logarithm 2 of each density by Excel.

organism: Homo sapiens

growth_protocol: Cells were cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Chromatin immunoprecipitation was performed with a SimpleChIP Enzymatic Chromatin IP kit (CST) according to the manufacturer’s instructions.
Sequencing libraries were prepared with 1.8 ng of the precipitated DNAs using an Ion Xpress Plus Fragment Library kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: E2 (100nM) for 2 hrs, 4OHT (10 nM) for 2 hrs

tag: cell line

value: breast cancer cell line

tag: treatment

value: Fbxo22 depletion-E2

tag: chip antibody


title: Mouse_immature_dentritic cells_Msg_Lyticase_rep1

type: RNA

city: Bethesda

first: Joseph

middle: A.

last: Kovacs

state: MD

address: 10 Center Dr

department: CCMD

institute: NIH

hyb_protocol: Labeled cDNA was hybridized for 18 hours to the GeneChip Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA) following the manufacturer's directions.  Arrays were stained and washed in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix 7G

data_processing:
Data were processed using Partek software. RMA background correction with quantile normalization
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label: biotin

source_name: mouse immature dentritic cells, exposed to lyticase-Msg

label_protocol: cDNA was fragmented and labeled using Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: Normal bone marrow (BM) precursors were isolated from C57BL/6 mice by flushing femurs and washing cells in PBS. BM cells were cultured in RPMI 1640 supplemented with 10% heat-inactivated FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 5 mM glutamine (Invitrogen), 50 µM 2-ME (Sigma) and 30 ng/ml GM-CSF (Peprotech), which was replaced every 3 days. After 7-8 days the loosely adherent or non-adherent cells were collected as immature dendritic cells.

extract_protocol: Cells were collected after 24h, total RNA was extracted from each well using RNeasy Mini Kit (Qiagen) and quantified using a NanoDrop spectrophotometer.

treatment_protocol: Immature dendritic cells were incubated in a 24-well plate (10^6/well) in triplicate  with the following: media alone, LPS (500 ng/ml), SDS-Msg (5 µg/ml), or lyticase-Msg (5 µg/ml).

value: mouse immature dentritic cells

value: exposed to lyticase-Msg


title: Mouse_immature_dentritic cells_Msg_SDS_rep3

source_name: mouse immature dentritic cells, exposed to SDS-Msg

value: exposed to SDS-Msg


title: BgnFru_4

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

description: replicate 4

data_processing:
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the mouse genome (UCSC assembly 10) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

source_name: mouse hippocampus

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent Technologies, CA, USA) and Qubit RNA assay (Life Technologies, NY, USA).
The RNA-Seq libraries were prepared followed the standard Illumina protocol (http://support.illumina.com/sequencing/documentation.ilmn). Briefly, about 1,000 ng total RNA was first enriched for mRNA by poly-A selection, then fragmented, and reverse transcribed using random hexamer-primers to generate first-strand cDNA. Second-strand cDNA was then generated using RNase H and DNA polymerase. Fragments of 200-400 bp in size were next enriched through PCR and multiplex barcodes were also added. Sequencing was performed on HiSeq 2500 (Illumina Inc, CA, USA). Data quality check was done on Sequencing Analysis Viewer and demultiplexing was performed with CASAVA 1.8.2 (Illumina Inc, CA, USA).

value: male

value: Bgn gene knockout (Bgn0/-)

value: hippocampus


title: Mouse_immature_dentritic cells_Msg_SDS_rep2


title: murine WT osteoblasts-4h C5a-#5

city: Ulm

first: Anita

last: Ignatius

address: Helmholtzstraße 14

department: Institute of Orthopaedic Research and Biomechanics

country: Germany

institute: University of Ulm

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 RMA normalization, BRB Array Tools for statistical analysis

source_name: primary murine WT osteoblasts, 4h C5a stimulation

growth_protocol: Primary osteoblasts were expanded and cells of passage 2-3 were sedded in 24-well plates and differentiated for 14 days in osteogenic differentiation medium.

extract_protocol: RNA extraction was performed using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: On day 15 after start of osteogenic differentiation, cells were either left unstimulated (4 h in normal proliferation culture medium) or stimulated with recombinant murine C5a for 4 h (C5a supplied in the proliferation culture medium).

value: WT

tag: age (animal)

value: 8-12 weeks

tag: cell passage

value: Passage 2-3

tag: cell differentiation

value: osteogenic, 14 days

value: 4h C5a


title: Mouse_immature_dentritic cells_Control_rep3

source_name: mouse immature dentritic cells, unexposed control

tag: strain

value: unexposed control


title: Mouse_immature_dentritic cells_LPS_rep3

source_name: mouse immature dentritic cells, exposed to LPS

value: exposed to LPS


title: Mouse_immature_dentritic cells_LPS_rep2


title: Mouse_immature_dentritic cells_Control_rep2


title: Mouse_immature_dentritic cells_Msg_Lyticase_rep3


title: Mouse_immature_dentritic cells_Msg_SDS_rep1


title: murine WT osteoblasts-unstimulated-#4

source_name: primary murine WT osteoblasts, unstimulated

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

value: unstimulated


title: Mouse_immature_dentritic cells_Msg_Lyticase_rep2


title: Mouse_immature_dentritic cells_Control_rep1


title: eralpha_Control_E2+4OHT-SRC-3


title: eralpha_Control_E2-SRC3


title: murine WT osteoblasts-unstimulated-#5


title: Mouse_immature_dentritic cells_LPS_rep1


title: BgnFru_3

description: replicate 3

tag: tissue


title: eralpha_shFbxo_E2-ER

value: ER (CST:D8H8)


title: eralpha_shFbxo_E2+4OHT-SRC-3

value: breast cancer cell line

value: Fbxo22 depletion-E2+4OHT


title: eralpha_Control_E2+4OHT-ER


title: murine WT osteoblasts-4h C5a-#2

tag: genotype


title: BgnFru_2

description: replicate 2


title: murine WT osteoblasts-4h C5a-#4


title: BgnFru_1

description: replicate 1


title: eralpha_shFbxo_E2+4OHT-ER


title: BgnCtrl_4

description: replicate 4


title: WTFru_2

description: replicate 2

value: wild-type


title: WTFru_3

description: replicate 3


title: BgnCtrl_3

description: replicate 3


title: BgnCtrl_2

description: replicate 2


title: BgnCtrl_1

description: replicate 1


title: WTFru_1

description: replicate 1


title: WTCtrl_4

description: replicate 4


title: WTCtrl_1

description: replicate 1


title: murine WT osteoblasts-unstimulated-#2


title: WTCtrl_2

description: replicate 2


title: eralpha_Control_E2-ER


title: WTFru_4

description: replicate 4


title: WTCtrl_3

description: replicate 3


title: Healthy2a

city: bareilyy

first: Shahid

last: Hussain

address: IVRI campus,Izzatnagar

department: Department of Veterinary Biotechnology

country: India

institute: ICAR-IVRI

description: gene expression of healthy tissue

hyb_protocol: 1.65 _g of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/_g cRNA) was fragmented at 60ÁC for 30 minutes in a reaction volume of 55_l containing 25x Agilent fragmentation buffer and 10x Gene expression blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55_l of 2_ Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent canine (V2) Gene Expression Microarray, 4x44K (G2519F-021193) for 16 hours at 65ÁC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37ÁC in GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned on the AgilentÍs Microarray scanner system (G2505C Scanner, Agilent Technologies) using one color scan setting for 4 x 44K array slides. Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Canis lupus familiaris

source_name: dog healthy mammary tissue

label_protocol: One _ colour microarray gene expression analysis was performed using the Canis familaris microarray slides (4X44K: G2519F-021193). Total RNA (200 ng) was labelled with Low Input Quick Amp Labelling Kit as per manufacturers instructions. RNA samples were proceeded (as biological duplicates) for labelling. The quality check of the labelled cRNA was performed using NanoDrop to check the yield and specific activity.

extract_protocol: RNA isolation from tumor tissue was performed using Trizol reagent as per standard protocol. The purity and concentration of total RNA extracted was checked using Nanodrop spectrophotometer by using 1 µl of total RNA against nuclease free water as blank to determine the absorbance ratio 260/280 nm. The quality check of the isolated RNA was performed in Agilent 2100 Bioanalyzer as per standard protocol using the Agilent RNA 6000 Nano Kit. RNA with RNA integrity number (RIN) greater than 7 was used for microarray experiment.

treatment_protocol: Malignant and benign mammary gland tumors of dog were collected from animals that were suffering from mammary gland cancer and total RNA was isolated

tag: disease state

value: healthy


title: WT_775

city: La Jolla

first: Sandrine

last: Da Cruz

state: Ca

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research-UCSD

data_processing:
fastqs were aligned to a mouse reference genome (mm9, UCSC Genome Browser) by TopHat and the transcript abundance for each annotated protein-coding gene as fragments per kilobase of transcript per million mapped reads (FPKM) were estimated by Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: mFUS-/-/hgFUS WT

extract_protocol:
Total RNA was extracted with TRIzol from 18-month-old spinal cords. RNA quality was measured using the Agilent Bioanalyzer system and processed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to manufacturer’s protocols.
A total of 14 cDNA libraries were simultaneously generated using llumina TruSeq Stranded mRNA Sample Preparation Kit and sequenced using an Illumina HiSeq 2000 sequencer.

value: mFUS-/-/hgFUS WT

value: Spinal cord

value: 18 months


title: Healthy1a

description: gene expression of healthy tissue


title: WT_795


title: Healthy1b

description: gene expression of healthy tissue


title: Benign3b

description: Gene expression of benign tumor tissue

source_name: dog mammary gland tumor

value: tumor

tag: diagnosis

value: benign


title: WT_765


title: Healthy2b

description: gene expression of healthy tissue


title: TLR2_24h Rep3

tag: jackson labs

value: Stock No:003831

value: CD8+ T cells

tag: agent


title: Benign1b

description: Gene expression of benign tumor tissue


title: Benign3a

description: Gene expression of benign tumor tissue


title: Benign2a

description: Gene expression of benign tumor tissue


title: Benign1a

description: Gene expression of benign tumor tissue


title: Malignant5a

description: Gene expression of malignant cancer

value: malignant


title: Benign2b

description: Gene expression of benign tumor tissue


title: Malignant5b

description: Gene expression of malignant cancer


title: Malignant2b

description: Gene expression of malignant cancer


title: Malignant6a

description: Gene expression of malignant cancer


title: Malignant6b

description: Gene expression of malignant cancer


title: WT_638

source_name: Non-Tg

value: Non-Tg


title: Malignant1a

description: Gene expression of malignant cancer


title: Malignant3a

description: Gene expression of malignant cancer


title: Malignant4a

description: Gene expression of malignant cancer


title: Malignant4b

description: Gene expression of malignant cancer


title: Malignant2a

description: Gene expression of malignant cancer


title: WT_55


title: Malignant1b

description: Gene expression of malignant cancer


title: WT_22


title: MT_680

source_name: mFUS-/-/hgFUS R521H

value: mFUS-/-/hgFUS R521H


title: MT_733


title: Follicular lymphoma patient_PP08006619

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

description: Gene expression data from patient 08P6619, frozen Follicular lymphoma biopsy

hyb_protocol: Labeled complementary RNA (cRNA)  from these samples was then fragmented and hybridized to Affymetrix GeneChip® Human Transcriptome Array (HTA) 2.0 microarrays.

scan_protocol: After hybridization, arrays were washed and stained with streptavidin-phycoerythrin (GeneChip   Hybridization Wash and Stain Kit) in a fluidic 450 (Affymetrix). The arrays were scanned with the Genechip scanner 3000 (Affymetrix).

data_processing: The data were analyzed on Expression Console version 1.4.1 (Affymetrix) with "RMA gene full" normalization using default analysis settings.

source_name: Patient n°08P6619, frozen Follicular lymphoma biopsy

label_protocol: RNAs were amplified, prepared and labelled from 100 pg total RNA, with the GeneCHIP® WT PLUS Reagent Kit (Affymetrix)

growth_protocol: No culture was performed, frozen tissues were used for RNA extraction.

extract_protocol: Extraction of total RNA from frozen samples was performed according to the manufacturer's instructions. Post extraction, RNA were purified with clean-up and DNAse I (Rneasy mini kit, Qiagen). RNA quantification was performed on a Nanodrop (ND-1000). RNA quality was controlled with RNA 6000 Nano chip on a Bioanalyzer 2100 (Agilent).

value: Follicular lymphoma biopsy (lymph node)


title: MT_345

source_name: mFUS-/-/hgFUS R521C

value: mFUS-/-/hgFUS R521C


title: Malignant3b

description: Gene expression of malignant cancer


title: MT_329


title: MT_297


title: MT_254


title: MT_250


title: Hodgkin lymphoma patient_RR1108130

description: Gene expression data from patient 11R8130, frozen HL biopsy

source_name: Patient n°11R8130, frozen HL biopsy

value: HL biopsy (lymph node)


title: MT_695


title: TLR2_24h Rep4

source_name: Splenocytes from OT-1 Mice

tag: cell type

tag: time


title: Hodgkin lymphoma patient_PP13002041

description: Gene expression data from patient 13P2041, frozen HL biopsy

source_name: Patient n°13P2041, frozen HL biopsy


title: control_pre_8402

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

institute: The Jenner Institute, University of Oxford

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probes were background corrected using negative control probes followed by quantile normalization using the neqc method of Shi et al. (2010) [PMID:20929874].

source_name: Whole Blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit

extract_protocol: Total intracellular RNA was extracted using the Blood RNA Kit (Qiagen) and the purity and quantity of RNA was assessed prior to storage at -20°C. Globin mRNA was depleted using the GLOBINclear Kit (Ambion), amplified and biotin-labelled using the TotalPrep RNA Amplification Kit (Illumina). RNA was purified and the quality assessed using an Agilent bioanalyser.

value: uninfected control

tag: subject

value: pre

tag: infection group

value: control

tag: eosinophils

value: whole blood


title: HW_pre_8389

value: hookworm infection

tag: treatment

value: HW


title: control_pre_8417


title: HW_post_8386

value: post


title: Follicular lymphoma patient_PP08004926

description: Gene expression data from patient 08P4926, frozen Follicular lymphoma biopsy

source_name: Patient n°08P4926, frozen Follicular lymphoma biopsy


title: control_pre_8418


title: control_pre_8382


title: HW_post_8389


title: Hodgkin lymphoma patient_PP11015820

description: Gene expression data from patient 11P15820, frozen HL biopsy

source_name: Patient n°11P15820, frozen HL biopsy


title: Follicular lymphoma patient_RR09012575

description: Gene expression data from patient 09R12575, frozen Follicular lymphoma biopsy

source_name: Patient n°09R12575, frozen Follicular lymphoma biopsy


title: HW_post_8372


title: ABC DLBCL patient_PP14007995

description: Gene expression data from patient 14P7995, frozen ABC DLBCL biopsy

source_name: Patient n°14P7995, frozen ABC DLBCL biopsy

value: ABC DLBCL biopsy (lymph node)


title: control_pre_8411


title: GCB DLBCL patient_RR12013196

description: Gene expression data from patient 12R13196, frozen GCB DLBCL biopsy

source_name: Patient n°12R13196, frozen GCB DLBCL biopsy

value: GCB DLBCL biopsy (lymph node)


title: GCB DLBCL patient_RR13007950

description: Gene expression data from patient 13R7950, frozen GCB DLBCL biopsy

source_name: Patient n°13R7950, frozen GCB DLBCL biopsy


title: HW_pre_8386


title: GCB DLBCL patient_PP11018905

description: Gene expression data from patient 11P8905, frozen GCB DLBCL biopsy

source_name: Patient n°11P8905, frozen GCB DLBCL biopsy


title: ABC DLBCL patient_RR14006050

description: Gene expression data from patient 14R6050, frozen ABC DLBCL biopsy

source_name: Patient n°14R6050, frozen ABC DLBCL biopsy


title: HW_pre_8372


title: GCB DLBCL patient_RR14002195

description: Gene expression data from patient 14R2195, frozen GCB DLBCL biopsy

source_name: Patient n°14R2195, frozen GCB DLBCL biopsy


title: GCB DLBCL patient_15T019328

description: Gene expression data from patient 15T019328, frozen GCB DLBCL biopsy

source_name: Patient n°15T019328, frozen GCB DLBCL biopsy


title: HW_pre_8365


title: HW_post_8366


title: HW_post_8365


title: HW_pre_8366


title: TP53E10 LS174T cells3

city: yushima bunnkyoku Tokyo

first: Sho

last: Watanabe

department: gastroenterology

institute: Tokyo medical and dental university

description: Gene expression of TP53Exon10 mutated LS174T cells

hyb_protocol: 0.6ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting (Scan resolution 3um).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent)
As normalization algorithm, we imported raw text file that was caliculated with Agilent Feature Extraction 12.0.3.1 soft to GeneSpring. Then we normalized it as 75 percentile shift according to protocol.

source_name: TP53Exon10 mutated LS174T cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LS174T cells were cultured in Dulbecco’s modified Eagle’s medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol: Total RNA was isolated using an RNeasy Micro Kit (Qiagen, Venlo, Netherlands) according to the manufacturer's instructions.

treatment_protocol: Lenti-CRISPR v2® (Plasmid #52961; Addgene, Cambridge, MA, USA), which includes S. pyogenes Cas9 and sgRNA in an improved one-vector system, were ligated with the target array according to the provided instructions. The lentivirus generated from Lenti-CRISPR v2® vector with target array were infected to LS174T cells

tag: genotype/variation

value: mutated in TP53 Exon10


title: HW_pre_7837


title: HW_pre_7819


title: TP53E3 LS174T cells3

description: Gene expression of TP53Exon3 mutated LS174T cells

source_name: TP53Exon3 mutated LS174T cells

value: mutated in TP53 Exon3


title: HW_post_7837


title: TP53E10 LS174T cells2


title: control_pre_7834


title: control_pre_7828


title: Follicular lymphoma patient_15T010556

description: Gene expression data from patient 15T010556, frozen Follicular lymphoma biopsy

source_name: Patient n°15T010556, frozen Follicular lymphoma biopsy


title: HW_post_7819


title: TP53E3 LS174T cells2


title: HW_pre_7796


title: HW_pre_7802


title: Hodgkin lymphoma patient_14T027341

description: Gene expression data from patient 14T027341, frozen HL biopsy

source_name: Patient n°14T027341, frozen HL biopsy


title: ABC DLBCL patient_15T011542

description: Gene expression data from patient 15T011542, frozen ABC DLBCL biopsy

source_name: Patient n°15T011542, frozen ABC DLBCL biopsy


title: TP53E10 LS174T cells1


title: HW_post_7801


title: ABC DLBCL patient_14T024678

description: Gene expression data from patient 14T024678, frozen ABC DLBCL biopsy

source_name: Patient n°14T024678, frozen ABC DLBCL biopsy


title: HW_post_7796

source_name: Whole Blood


title: HW_post_7802


title: TP53WT LS174T cells3

description: Gene expression of TP53WT LS174T cells

source_name: TP53WT LS174T cells


title: HW_pre_7801


title: ABC DLBCL patient_RR13015923

description: Gene expression data from patient 13R15923, frozen ABC DLBCL biopsy

source_name: Patient n°13R15923, frozen ABC DLBCL biopsy


title: HW_pre_7794


title: TP53E3 LS174T cells1


title: GCB DLBCL patient_15T001992

description: Gene expression data from patient 15T001992, frozen GCB DLBCL biopsy

source_name: Patient n°15T001992, frozen GCB DLBCL biopsy


title: HW_post_7794


title: ABC DLBCL patient_RR13020351

description: Gene expression data from patient 13R20351, frozen ABC DLBCL biopsy

source_name: Patient n°13R20351, frozen ABC DLBCL biopsy


title: rice_RSV.rep1 (RNA-Seq)

city: Fuzhou

first: Liu

last: Renyi

state: Fujian Province

address: Shangxiadian Road 15, Fujian University of Agriculture and Forestry, Fuzhou, Fujian, P.R.China

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of raw RNA sequencing reads was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). To obtain clean reads, low quality regions and adapter sequences were removed using SolexQA (v2.2) (Cox et al., 2010) and cutadapt, respectively. Reads shorter than 25 bases were discarded
Clean reads were mapped to the host (rice or planthopper, depending on the sample source) genome sequence using HISAT2 (Kim et al., 2015).
Read counts of the annotated genes were summarized by HTSeq-count (Anders et al., 2015)
Genome_build: MSU7 for rice and in-house assmbly genome for planthopper (Zhu, J.J., Jiang, F., Wang, X.H., Yang, P.C., Bao, Y.Y., Zhao, W., Wang, W., Lu, H., Wang, Q.S., Cui, N., Li, J., Chen, X.F., Luo, L., Yu, J.T., Kang, L., and Cui, F. (2017). Genome sequence of the small brown planthopper, Laodelphax striatellus. Gigascience 6.)
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values

organism: Oryza sativa

source_name: Leaves

growth_protocol: The viruliferous and non-viruliferous small brown planthopper strains used in this work were derived from a rice field population in Hai'an, Jiangsu Province, China, and maintained in the laboratory for nearly nine years. The planthoppers were reared on 2 cm to 3 cm seedlings of rice (Oryza sativa Huangjinqing) in glass incubators, which were sealed with a nylon mesh, at 25 ± 1°C, 80% relative humidity, and 16 h of light per day. The planthoppers were transferred to fresh rice seedlings every 8 days to ensure sufficient nutrition.

extract_protocol:
Total RNA was isolated from rice plants or planthoppers by using the TRIzol Reagent (Invitrogen) according to manufacturer’s instructions. Approximately 100 mg rice leaves or 10 small brown planthoppers were ground in liquid nitrogen and mixed with 1 ml of TRIzol Reagent for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4th instar nymphs of viruliferous planthoppers were transferred to fresh rice seedlings for RSV inoculation. After 24 h feeding, the planthoppers were removed and the inoculated seedlings were cultured at 25 ± 1°C with 16 h of light daily for 20 d until disease symptom appeared. Each rice seedling was fed by three viruliferous planthoppers, and three seedlings were used as a replicate. Meanwhile, healthy rice seedlings without inoculation were prepared and maintained at the same condition as the negative control. Leaves with typical disease symptoms from RSV-infected rice plants and leaves from healthy rice plants were collected at the same time and three biological replicates for each group were prepared for sequencing analysis

tag: infection

value: RSV

tag: treatment time

value: Leaves

tag: genome build


title: rice_RSV.rep2 (RNA-Seq)


title: rice_mock.rep2 (RNA-Seq)


title: TP53WT LS174T cells2

description: Gene expression of TP53WT LS174T cells


title: p(45-103)

first: Younghoon

last: Lee

address: KAIST 291 Daehak-ro, Yuseong-gu

department: Chemistry

institute: KAIST

data_processing:
The sequence data for the reference genome were retrieved from the NCBI database.
Qualityfiltered reads were aligned to the reference‐genome sequence using Bowtie2.
The relative transcript abundance was measured in RLE.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: For all processed data files, the relative transcript abundance was measured in RLE.

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

growth_protocol: E. coli cells containing SdsR or SdsR(45-103) were grown for 3 h post-inoculation (OD600 of 1.5~1.7) and induced with 1mM IPTG for 10 min before the cell harvest.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: containing a pHM4T derivative carrying the 45-103 sequence of sdsR

tag: treated with

value: 1 mM (final concentration)

tag: time point

value: 10 min before the cell harvest


title: control_pre_7790

tag: tissue


title: pSdsR

source_name: E. coli_pSdsR

value: containing a pHM4T derivative carrying the full sdsR sequence


title: GCB DLBCL patient_RR12011145

description: Gene expression data from patient 12R11145, frozen GCB DLBCL biopsy

source_name: Patient n°12R11145, frozen GCB DLBCL biopsy


title: ALK+ anaplastic large cell lymphoma patient_RR11019637

description: Gene expression data from patient 11R19637, frozen ALK+ anaplastic large cell lymphoma biopsy

source_name: Patient n°11R19637, frozen ALK+ anaplastic large cell lymphoma biopsy

value: ALK+ anaplastic large cell lymphoma biopsy (lymph node)


title: control_pre_7785

tag: disease state

value: uninfected control

value: pre


title: dH2O_5

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data were quantile normalised using Lumi for R.

label: Biotin

source_name: Total B cells from healthy donors.  Day3 cells treated with 10 μM control (dH2O), RNA extracted and analysed on Day6.

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted with Trizol and amplified using Illumina® TotalPrepTM-96 RNA Amplification Kit

value: peripheral blood

tag: gender

value: Female


title: ABC DLBCL patient_RR13008462

description: Gene expression data from patient 13R8462, frozen ABC DLBCL biopsy

source_name: Patient n°13R8462, frozen ABC DLBCL biopsy


title: dH2O_6

value: Male


title: TP53WT LS174T cells1

description: Gene expression of TP53WT LS174T cells


title: ALK- anaplastic large cell lymphoma patient_RR11015469

description: Gene expression data from patient 11R15469, frozen ALK- anaplastic large cell lymphoma biopsy

source_name: Patient n°11R15469, frozen ALK- anaplastic large cell lymphoma biopsy

value: ALK- anaplastic large cell lymphoma biopsy (lymph node)


title: dH2O_2


title: dH2O_1


title: dH2O_3


title: dH2O_4


title: PF-429242_2

source_name: Total B cells from healthy donors.  Day3 cells treated with 10 μM of S1P inhibitor PF-42924, RNA extracted and analysed on Day6.


title: ABC DLBCL patient_RR12001665

description: Gene expression data from patient 12R1665, frozen ABC DLBCL biopsy

source_name: Patient n°12R1665, frozen ABC DLBCL biopsy

value: ABC DLBCL biopsy (lymph node)


title: PF-429242_5


title: PF-429242_6


title: pHM4T

source_name: E. coli_pHM4T

value: containing an IPTG-inducible pHM4T RNA expression vector


title: GCB DLBCL patient_PP12019020

description: Gene expression data from patient 12P19020, frozen GCB DLBCL biopsy

source_name: Patient n°12P19020, frozen GCB DLBCL biopsy

value: GCB DLBCL biopsy (lymph node)


title: rice_mock.rep1 (RNA-Seq)

value: control


title: PF-429242_1


title: Follicular lymphoma patient_RR10002808

description: Gene expression data from patient 10R02808, frozen Follicular lymphoma biopsy

source_name: Patient n°10R02808, frozen Follicular lymphoma biopsy

value: Follicular lymphoma biopsy (lymph node)


title: PF-429242_3


title: Peripheral T cell lymphoma (NOS) patient_PP14006021

description: Gene expression data from patient 14P06021, frozen Peripheral T cell lymphoma (NOS) biopsy

source_name: Patient n°14P06021, frozen Peripheral T cell lymphoma (NOS) biopsy

value: Peripheral T cell lymphoma biopsy (lymph node)


title: WT_Stressed

city: Deagu

first: Young-Saeng

last: Kim

address: 80, Daehak-ro

institute: Kyungpook National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Synechococcus elongatus PCC 7942 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: Synechococcus elongatus PCC 7942; https://www.ncbi.nlm.nih.gov/assembly/GCF_000012525.1/
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Cyanobacterial cell

growth_protocol: After culturing for 2 days at 30 ºC with shaking; aliquots of each sample were collected and the absorbance was measured at 730 nm. When the OD730 value was 0.3, the aliquots were diluted, and new measurements were taken.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). rRNA was removed using Ribo-Zero Magnetic kit (epicentre, Inc., USA) from each 5ug of total RNA.
RNA libraries were prepared for sequencing using Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

treatment_protocol: Cyanobacteria cells were cultured in BG11 medium containing 2.5 mM H2O2 for 2 days. To evaluate the response to oxidative stress, cells were allowed to reach the growth phase (OD730 = 0.30–0.35), exposed to 2.5 mM H2O2 for 2 days at 30 ºC with shaking.

tag: strain

tag: sample type

value: Cyanobacterial cell

value: wild type

tag: growth condition

value: stress; 2.5 mM H2O2 for 2 days


title: WT_Normal

value: normal


title: OT_Stressed

value: OsTPX-expressing


title: Mantle cell lymphoma patient_PP13021046

description: Gene expression data from patient 13P21046, frozen Mantle cell lymphoma biopsy

source_name: Patient n°13P21046, frozen Mantle cell lymphoma biopsy

value: Mantle cell lymphoma biopsy (lymph node)


title: PF-429242_4


title: Hodgkin lymphoma patient_PP13010349

description: Gene expression data from patient 13P10349, frozen HL biopsy

source_name: Patient n°13P10349, frozen HL biopsy

value: HL biopsy (lymph node)


title: GCB DLBCL patient_PP12019610

description: Gene expression data from patient 12P19610, frozen GCB DLBCL biopsy

source_name: Patient n°12P19610, frozen GCB DLBCL biopsy


title: Burkitt lymphoma patient_PP13004440

description: Gene expression data from patient 13P4440, frozen Burkitt lymphoma biopsy

source_name: Patient n°13P4440, frozen Burkitt lymphoma biopsy

value: Burkitt lymphoma biopsy (lymph node)


title: Mantle cell lymphoma patient_PP12016407

description: Gene expression data from patient 12P16407, frozen Mantle cell lymphoma biopsy

source_name: Patient n°12P16407, frozen Mantle cell lymphoma biopsy


title: ABC DLBCL patient_PP12013729

description: Gene expression data from patient 12P13729, frozen ABC DLBCL biopsy

source_name: Patient n°12P13729, frozen ABC DLBCL biopsy


title: Hodgkin lymphoma patient_PP12005999

description: Gene expression data from patient  12P5999, frozen HL biopsy

source_name: Patient n° 12P5999, frozen HL biopsy


title: HepG2 shSND1-#1-1

city: Tianjin

first: Xiaoteng

last: Cui

address: NO. 22, Qixiangtai Road, Heping district

institute: Tianjin Medical University

description: Gene expression data from HepG2 pLKO-shSND1-#1 stable cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HepG2 pLKO-shSND1-#1 stable cell lines treated with 5-Fu for 48h

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

growth_protocol: HepG2 stable cell lines of shSND1-#1 and pLKO-Vector was grown in DMEM with 10% fetal bovine serum.

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

treatment_protocol: HepG2 stable cell lines of shSND1-#1 and pLKO-Vector were treated with 6μg/mL 5-Fu, respectively.

tag: cell line

tag: gene expression

value: SND1 knockdown


title: HepG2 sh-Vector-2

description: Gene expression data from HepG2 pLKO-Vector stable cell lines

source_name: HepG2 pLKO-Vector stable cell lines treated with 5-Fu for 48h


title: HepG2 sh-Vector-3


title: Hodgkin lymphoma patient_PP12005647

description: Gene expression data from patient 12P5647, frozen HL biopsy

source_name: Patient n°12P5647, frozen HL biopsy


title: HepG2 sh-Vector-1


title: ABC DLBCL patient_PP12009422

description: Gene expression data from patient 12P9422, frozen ABC DLBCL biopsy

source_name: Patient n°12P9422, frozen ABC DLBCL biopsy


title: Hodgkin lymphoma patient_PP12007177

description: Gene expression data from patient  12P7177, frozen HL biopsy

source_name: Patient n° 12P7177, frozen HL biopsy


title: Peripheral T cell lymphoma patient_PP12013625

description: Gene expression data from patient 12P13625, frozen peripheral T cell lymphoma biopsy

source_name: Patient n°12P13625, frozen peripheral T cell lymphoma biopsy


title: HepG2 shSND1-#1-3


title: FANTOM-20-39866214

city: GLASGOW

first: Simon

last: Milling

address: 120 UNIVERSITY PLACE, ROOM B421, Sir Graeme Davies Building

department: Immunobiology

institute: University of Glasgow

data_processing:
the sequencing was done on the Illumina NextSeq 500 using High Throughput flow-cells multiplexing eight samples per flow cell to produce 50M read-pairs per sample on average.
Sample-specific fastq files were generated using bcl2fastq software.
Statistical analysis: Data was aligned using HISAT2 and the reads summarised and normalised using the Feature Counts tool.
Differential expression was performed using the DESeq2 R package. Significant differential expression was defined as adjusted P-value < 0.05.
Supplementary_files_format_and_content: Deseq files contain abundance table comparisons

source_name: Colonic macrophages

extract_protocol:
Sample preparation: Histologically normal margins of healthy colonic resections were processed, digested and stained for FACS analysis as previously described. CD45+ CD64+ HLA-DR+ CD206+ and CD45+ CD64+ HLA-DR+ CD206- cells were sorted using a FACSAria II/III. Cells were sorted into 300 μl RLT buffer (Qiagen) and stored at -80°C prior to RNA extraction using a MicroRNA kit (Qiagen).
Sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq kit-Pico Input Mammalian (Clontech), starting with 1ng of RNA and following the manufactures protocol with 15 cycles of PCR.

treatment_protocol: Intestinal tissue processing. To remove the epithelial layer from biopsies, tissue was incubated in 2 mM EDTA/HBSS (Gibco) for three minutes at 37°C in a shaking incubator.  For resected tissue samples, fat and muscle layers were first removed; tissue was washed in HBSS and subsequently dissected into 0.5 cm pieces. To remove the epithelial layer from resections, tissue was incubated in 2 mM EDTA/HBSS for 15 minutes at 37°C in a shaking incubator. Tissue was vigorously shaken; supernatant discarded and the process was repeated three times. After the final EDTA step, all samples were washed in HBSS and resuspended in 2 ml (20 ml for resections) of pre-warmed 10% complete media (RPMI 1640 supplemented with 10% foetal calf serum (FCS), 100 U ml-1 penicillin, 100 U ml-1 streptomycin, 2 mM L-glutamine and 50 μM 2-mercaptoethanol) containing: Collagenase VIII (1 mg/ml, Sigma-Aldrich), Collagenase D (1.25 mg/ml, Roche), Dispase (1 mg/ml, Gibco) and DNase. Samples were returned to the shaking incubator (37°C) for 30-40 minutes; additional vigorous shaking was performed every 10 minutes to aid digestion. Cell suspension was first filtered through a 100 μM then a 40 μM cell strainer (BD Falcon) and washed in PBS containing 2 mM EDTA and 2% FCS.

tag: cell type


title: FANTOM-18-39875204


title: BH13811-3_Muxing-3

city: Zhengzhou

first: Xuexiang

last: Cha

state: Henan

address: Kexue Avenue 100

department: Basic Medical Science

institute: Zhengzhou University

description: human umbilical vein endothelial cells(HUVECs)

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

organism: Homo

source_name: HUVECs undergoing hypoxia/reoxygenation-induced injury

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: HUVECs (ATCC® CRL1730™) were cultured in RPMI1640 (Gibco) containing 10% fetal bovine serum (FBS) in a humidified incubator with 5% CO2 at 37°C.

treatment_protocol: hypoxia/reoxygenation-induced injury was induced by Na2S2O4(5mM) and 1%O2. Inulin-type oligosaccharides(30μM) was administrated when reoxygenation

value: HUVEC

tag: condition


title: BH13811-3_Zhengchang-3

source_name: Normal HUVECs


title: BH13811-2_Yao-1

source_name: HUVECs undergoing hypoxia/reoxygenation-induced injury and Inulin-type oligosaccharides administration


title: FANTOM-16-39875200


title: BH13811-3_Zhengchang-1


title: BH13811-3_Yao-3

value: undergoing hypoxia/reoxygenation-induced injury and Inulin-type oligosaccharides administration


title: BH13811-3_Muxing-2


title: FANTOM6_6-30126329


title: FANTOM-14-39865231


title: Burkitt lymphoma patient_PP11019167

description: Gene expression data from patient n°11P19167, frozen Burkitt Lymphoma biopsy

source_name: Patient n°11P19167, frozen Burkitt lymphoma biopsy


title: FANTOM12-39879394


title: FANTOM10-39721055


title: FANTOM-19-39867266


title: HepG2 shSND1-#1-2


title: FANTOM-17-39867256


title: FANTOM13-39887242


title: FANTOM-15-39884241


title: FANTOM11-39721057


title: FANTOM9-39722091


title: FANTOM6_7-30124311


title: BH13811-3_Yao-2


title: BH13811-2_Mouxing-1


title: epithelial type #2

city: Omaha

first: Yaping

last: Tu

state: NE

address: 2500 California Plaza

institute: Creighton University

description: Beas-2b cells with epithelial phenotype

data_processing:
trim adapter using cutadapt.
map trimmed reads on miRNA precursors using SHiMPS aligner
counts reads associated to mature miRNAs
Genome_build: miRBase 21
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Beas-2b cell line

growth_protocol: Cells were cultured in BEGM medium obtained from Lonza/Clonetics Corporation as a kit: BEGM, Kit Catalog No. CC-3170.

extract_protocol:
Total RNA was isolated from samples using mirVana miRNA isolation kit (Invitrogen). NEXTflexTM Small RNA-Seq Kit v3 (Bioo Scientic #5132-05) was used with 1 ug of total RNA for the construction of small RNA sequencing libraries.
small RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Beas-2b cell subclones with mesenchymal type were obtained by serial enrichment of poorly adherent cells.

tag: mophology

value: epithelial-like

tag: passage


title: mesenchymal type #2

description: Beas-2b cells with mesenchymal phenotype

value: mesenchymal-like


title: mesenchymal type #1


title: epithelial type #1

description: Beas-2b cells with epithelial phenotype


title: 485Siglec9plus

city: Basel

first: Heinz

last: Läubli

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Alignment to hg38 using STAR
knownGene counting
edgeR (3.20.9) Bioconductor normalization for library size
edgeR differential gene expression between Siglec9 plus vs Siglec9 minus using QLF function with batch correction for patients
Genome_build: hg38
Supplementary_files_format_and_content: tab separated values. Table of raw gene level counts.

source_name: tumor-infiltrating CD8+ T cells

growth_protocol: none, tumor tissue was digested and single cell suspension was stained and sorted directly

extract_protocol:
cells were sorted directly into RNA lysis buffer (provided by Microsynth AG) and frozen to -80°C. isolation of RNA performed by Microsynth AG, Switzerland
NuGene low input RNA libraries for Illumina, Poly-A enrichment, Illumina TrueSeq single-end library construction

value: tumor-infiltrating CD8+ T cells

tag: tumor type

value: non-small cell lung cancer

tag: patient id

tag: siglec9 status

value: plus

value: CD8+ T cells


title: 485Siglec9minus

value: minus


title: 477Siglec9minus


title: 474Siglec9plus


title: 469Siglec9minus


title: 475Siglec9plus


title: 474Siglec9minus


title: 475Siglec9minus


title: 483Siglec9minus


title: 477Siglec9plus


title: 469Siglec9plus


title: T47D_R5020+TPA_input-2

city: Chicago

first: Julie

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Illumina adapters were trimmed using cutadapt (v1.13) with default parameters
Trimmed reads were aligned to the human reference genome using Bowite (v1.1.2) using default parameters
Peaks were called using HOMER
Differential peak analysis was performed using HOMER
Big Wig files were generated using HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: T47D cells were grown in RPMI supplemented with 10% FBS, 1% Sodium pyruvate, 100 units/ml penicillin/streptomycin. Before treatment cells were cultured in phenol-free RPMI media supplemented with 5% stripped charcoal-stripped FBS and 1% sodium pyruvate and 100 units/ml penicillin/streptomycin.

extract_protocol:
Chromatin was extracted using SimpleChIP chromatin IP kit (cell signaling) and immunoprecipitated with PR antibody.
Libraries were prepared using Kapa Biosystems Hyper Prep kit (#KK8500) according to manufacturer’s protocol. 1ng of DNA was used and 12 cycle library amplification was performed.

treatment_protocol: Cells were treated with vehicle (ethanol), R5020 10nM, TPA 1uM, R5020+TPA for 30 mins

tag: treatment

tag: chip antibody


title: T47D_R5020+TPA_input-1


title: T47D_R5020+TPA_PR-2

value: PR (Santa Cruz SC-7208X)


title: T47D_TPA_PR-3

value: TPA


title: T47D_TPA_input-3


title: T47D_R5020+TPA_PR-3


title: T47D_R5020+TPA_input-3


title: T47D_R5020+TPA_PR-1


title: T47D_TPA_input-2


title: T47D_TPA_input-1


title: T47D_R5020_PR-3


title: T47D_R5020_PR-2


title: T47D_TPA_PR-1


title: T47D_R5020_input-3


title: 483Siglec9plus


title: T47D_R5020_input-1


title: T47D_R5020_PR-1


title: T47D_TPA_PR-2


title: T47D_VC_PR-3

value: VC


title: T47D_VC_input-3


title: T47D_VC_PR-2


title: T47D_VC_PR-1


title: T47D_VC_input-1


title: T47D_VC_input-2


title: E protein_2

city: Gurugram

first: Reshma

last: Bhagat

state: Haryana

address: Near Nainwal mode,Manesar

department: Cellular and molecular neuroscience

institute: National Brain Research Centre

description:
Small RNA sequencing.
Human fetus-derived stem cells.
Highly proliferating fNSCs.
Control fNSCs were transfected with E protein-pCAGIG expression vector for 24 hours (n=2).
S1P - S1P14_T (GE) - RPKM
processed data file: Vec_vs_S1P.txt

data_processing:
Sequenced data has been processed to generate FASTQ files. Quality of fastq reads was checked using fastQC tool set in CLC bio Genomic Workbench ver 9.0 (CGWB). A minimum of 70% of the read pairs are of Q30 value.
Raw data for each sample were aligned to human microRNAnome database (miRBase release 21) with remaining reads aligned to the most recent human genome GRCh38 build in order to identify previously unknown regions that may encode for unique miRNAs. Pairwise comparison of the alignment results was done for identification of miRNAs that are differentially expressed at a significant level, i.e. up- or down-regulated.
Genome_build: GRCh38
Supplementary_files_format_and_content: Vec_vs_S1P.txt: Tab-delimited text file includes Reads Per Kilobase per Million (RPKM) for each sample.

source_name: human fetal stem cells

growth_protocol: Telencephalon of 10-15 week-old human aborted fetus was used to isolate Neural stem cells (NSCs). Isolated fNSCs were cultured in poly-D-lysine (Sigma-Aldrich, St. Louis, MO, USA) coated culture dishes in neurobasal media (Invitrogen, San Diego, CA, USA). The media was supplemented with Neural Survival Factor-1 (Lonza, Charles City, IA, USA), N2 supplement (Invitrogen), Bovine Serum Albumin (Sigma-Aldrich, St. Louis, MO, USA), glutamine (Sigma), 25 ng/ml basic fibroblast growth factor (bFGF) (Peprotech), 20 ng/ml epidermal growth factor (EGF) (Peprotech), penicillin and streptomycin solution (Invitrogen) and gentamicin (Sigma). Cells were passaged for at least 9 times and characterized before performing experiments. fNSCs were maintained in sterile humidified chamber at 37°C and 5% CO2 in above cocktail of media.

extract_protocol:
Total RNA was extracted from fNSCs using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the Bioanalyzer.
SMARTer smRNA-Seq Kit for Illumina (Clonetech) was used for preparing libraries for the samples. The workflow involves polyadenylation, cDNA synthesis, and PCR amplification steps resulting in indexed cDNA library, followed by library purification, validation, gel-free bead based size selection and post-size selection library validation. The resulting validated cDNA indexed libraries have been sequenced on Illumina NextSeq 500 to generate ≥20 million reads per sample (paired-end analysis).

treatment_protocol: The empty pCAGIG and full-length E protein expressing pCAGIG vector were transfected in fNSCs at confluency of 70-80% using Lipofectamine 2000 (Invitrogen) according to manufacturer’s protocol. Cells were harvested after 24 hours of transfection.

value: control fetal neural stem cells (fNSCs)

tag: passages

tag: transfection

value: Zika Virus E protein expression vector


title: T47D_R5020_input-2


title: Empty vector_2

description:
Small RNA sequencing.
Human fetus-derived stem cells.
Highly proliferating fNSCs.
Control fNSCs were transfected with empty pCAGIG for 24 hours (n=2).
Vec - VECTORP14_T (GE) - RPKM
processed data file: Vec_vs_S1P.txt

value: empty vector


title: E protein_1

description:
Small RNA sequencing.
Human fetus-derived stem cells.
Highly proliferating fNSCs.
Control fNSCs were transfected with E protein-pCAGIG expression vector for 24 hours (n=1).
S1P - S1P13_T (GE) - RPKM
processed data file: Vec_vs_S1P.txt


title: Empty vector_1

description:
Small RNA sequencing.
Human fetus-derived stem cells.
Highly proliferating fNSCs.
Control fNSCs were transfected with empty pCAGIG for 24 hours (n=1).
Vec - VECTORP13_T (GE) - RPKM
processed data file: Vec_vs_S1P.txt


title: ROCK1 KO Liver (rep 1)

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were normalized using quantile normalization method after transforming the raw intensities into log2-scale

source_name: ROCK1 KO Liver

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: The mice were  growth under controlled temperatures at 22−24°C and 14 h light/10 h dark cycle.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were fed a normal chow ad libitum for 16 weeks.

tag: genotype/variation

value: liver-specific ROCK1 KO

tag: diet

value: normal chow ad libitum for 16 weeks

tag: tissue

value: liver


title: Control Liver (rep1)

source_name: Control Liver

value: control


title: BGN_L_rep2

city: Los Angeles

first: Xia

last: Yang

address: 610 Charles E. Young Dr. East

institute: UCLA

description: F

data_processing: The data were normalised using a robust spline normalization (RSN) with lumi (v2.10.0) in R (v2.15.0)

label_protocol: Standard Illumina label protocol

extract_protocol: RNA was extracted with QIAGEN RNeasy Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain background

tag: gender

value: male

value: BGN knockout

tag: age

value: 13 weeks


title: BGN_L_rep4

description: H


title: WT_L_rep1

description: A

value: wild type


title: BGN_L_rep1

description: E


title: STAT2-/- 3

city: Pittsburgh

first: John

middle: F

last: Alcorn

state: PA

address: 4401 Penn Ave

department: Pediatrics

institute: Children's Hospital of Pittsburgh

data_processing:
Raw sequencing reads from Illumina sequencing platform that was converted into FASTQ file format were quality checked for potential sequencing issues and contaminants using FastQC.
Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and Trimmomatic. Reads with a remaining length of fewer than 20bp after trimming were discarded.
Single reads were mapped to the mouse genome (m10) using STAR in a strand specific manner.
Cufflinks was used to determine FPKM levels for each gene from the STAR alignment and was used as input for Cuffdiff.
Read counts were then normalized across all samples and significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: .diff file. Contains differential gene expression results between WT vs STAT2-/-. Includes gene_ID, locus, log2 (fold_change), test_stat, p_value, and q_value.

source_name: mouse lung

extract_protocol:
Whole lung RNA was isolated using the Agilent Absolutely RNA Miniprep Kit
Total RNA libraries were generated using Illumina TruSeq Stranded mRNA sample preparation kit. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by using dUTP in the Second Strand Marking Mix, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.The cDNA libraries are validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer. Quality is examined using Agilent Tapestation 2200.

treatment_protocol: Mice were infected with 100 PFU of influenza A/PR/8/34 (FLU) in 50 ul of sterile PBS by oropharyngeal aspiration. Six days later mice were challenged with 5x10^7 MRSA USA300 in 50ul of sterile PBS by oropharyngeal aspiration for one additional day

tag: strain


title: WT_L_rep4

description: D


title: OT_Normal

source_name: Cyanobacterial cell

tag: sample type

value: Cyanobacterial cell

value: OsTPX-expressing

tag: growth condition

value: normal


title: brain tumor cell line sample 6

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description: Methylation data from brain tumor cell line sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'

label: biotin/DNP

source_name: brain tumor cell line

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: brain tumor cell line

value: ependymoma


title: WT_L_rep3

description: C


title: STAT2-/- 2


title: Control Liver (rep2)


title: BGN_L_rep3

description: G


title: WT_L_rep2

description: B


title: STAT2-/- 4


title: BH13811-3_Zhengchang-2

tag: cell type

value: HUVEC

tag: condition


title: ROCK1 KO Liver (rep 2)


title: brain tumor cell line sample 5


title: WT 3


title: STAT2-/- 1


title: WT 4


title: brain tumor cell line sample 4


title: BGN_KO_rep3

description:
replicate 3
C

data_processing: The data were normalised using a robust spline normalization (RSN) with lumi (v2.10.0) in R (v2.15.0).

source_name: mouse hypothalamus

tag: background strain

value: hypothalamus


title: brain tumor cell line sample 15

value: high-grade glioma


title: WT_rep4

description:
replicate 4
H

value: WT


title: BGN_KO_rep2

description:
replicate 2
B


title: WT 1


title: WT_rep2

description:
replicate 2
F


title: WT_rep3

description:
replicate 3
G


title: brain tumor cell line sample 16


title: BGN_KO_rep4

description:
replicate 4
D


title: WT_rep1

description:
replicate 1
E


title: BGN_KO_rep1

description:
replicate 1
A


title: WT 2


title: brain tumor cell line sample 1


title: brain tumor cell line sample 14

value: medulloblastoma


title: brain tumor cell line sample 13


title: Herb rep4 RNA

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
Herb.sample_43

data_processing:
Read trimming: cutadapt version 1.10
Alignment: Hisat2 alignemnt to mm10 (version 2.1.0)
Abundance estimation: stringtie (version 1.3.3b)
FPKM table: ballgown version 2.6.0
Differential gene expression: edgeR version 3.16.5
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: lung tissue

extract_protocol:
Lung tissue were removed, flash frozen on dry ice, and RNA was harvested    using Trizol reagent.    Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of    total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Herbal treatment

value: lung

value: BALB/c


title: Herb rep3 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
Herb.sample_41


title: brain tumor cell line sample 12


title: Herb rep2 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
Herb.sample_40


title: brain tumor cell line sample 11


title: brain tumor cell line sample 2


title: brain tumor cell line sample 10


title: brain tumor cell line sample 3


title: Herb rep1 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
Herb.sample_38


title: Liver-Sutent rep3

city: 上海市

first: Yan

last: Qiu

address: 上海岳阳路320号

institute: University of Chinese Academy of Sciences

description:
Liver_C_vs_S_all_expression_rlog.txt
Liver_S1

data_processing:
Basecalls performed using illumina Bcl2fastq version 2.17.1.14
Map to mouse genome mm9 using Tophat(v 2.1.1)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Gene expression level was calculated using Deseq2
Genome_build: mm9
Supplementary_files_format_and_content: Counts

source_name: Liver-Sutent

extract_protocol:
Total RNA was extracted from tissues using TRIzol reagent in accordance with the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 24-weeks old

value: sutent

value: liver


title: Liver-Sutent rep4

description:
Liver_C_vs_S_all_expression_rlog.txt
Liver_S2


title: OVA rep3 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
OVA.sample_10

value: ovalbumin(OVA)-induced asthma model


title: OVA rep2 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
OVA.sample_08


title: iWAT-Sutent rep2

description:
iWAT_C_vs_S_all_expression_rlog.txt
iWAT_S2

source_name: iWAT-Sutent

value: inguinal white adipose tissue


title: brain tumor cell line sample 9


title: dis2Δ, Spt5-T1E total-Pol II_input_2 ChIP-seq

city: Oxford

first: Tea

last: Kecman

address: South Parks Road

department: Biochemistry

institute: University of Oxford

data_processing:
ChIP-seq: Single end reads with a Phred score of less than 20 were removed using the the program Trimmomatic (version 0.36) and the remaining reads were aligned to the S. pombe genome (ASM294v2.25 from Pombase.org) using the short read aligner Bowtie (version 2.2.6).
Genome_build: S. pombe genome version ASM294v2.28
Supplementary_files_format_and_content: ChIP-Seq: the data is provided as bigwig files

organism: Schizosaccharomyces pombe

source_name: Yeast cell extract

growth_protocol: S. pombe were grown in YES medium to exponential phase at 30°C

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270) or Illumina (E7335).

tag: genotype

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX

tag: method

value: ChIP-Seq


title: brain tumor cell line sample 8

value: brain tumor cell line


title: OVA rep1 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
OVA.sample_07


title: iWAT-Sutent rep1

description:
iWAT_C_vs_S_all_expression_rlog.txt
iWAT_S1

tag: treatment


title: brain tumor cell line sample 7


title: genomic DNA from MG cells

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate school

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: HCT116 cells

label_protocol: Standard Illumina Protocol

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

tag: cell line


title: Liver-Control rep1

description:
Liver_C_vs_S_all_expression_rlog.txt
Liver_C1

source_name: Liver-Control

value: vehicle


title: Saline rep3 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
Saline.sample_03

value: control


title: Saline rep2 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
Saline.sample_02


title: iWAT-Control rep2

description:
iWAT_C_vs_S_all_expression_rlog.txt
iWAT_C2

source_name: iWAT-Control


title: genomic DNA from non-MG cells


title: Liver-Control rep2

description:
Liver_C_vs_S_all_expression_rlog.txt
Liver_C2


title: Saline rep1 RNA

description:
Processed data file: bg_mouse.FPKM.gene_symbol.txt
Saline.sample_01


title: eWAT-Sutent rep1

description:
eWAT_C_vs_S_all_expression_rlog.txt
eWAT_S1

source_name: eWAT-Sutent

value: epididymal white adipose tissue


title: dis2Δ, Spt5-WT total-Pol II_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: eWAT-Sutent rep2

description:
eWAT_C_vs_S_all_expression_rlog.txt
eWAT_S2


title: eWAT-Control rep2

description:
eWAT_C_vs_S_all_expression_rlog.txt
eWAT_C2

source_name: eWAT-Control


title: dis2+, Spt5-T1E total-Pol II_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX


title: dis2Δ, Spt5-T1A total-Pol II_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX


title: KPC_Tumor_DapiNeg biological rep2

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

data_processing:
Basecalls performed using CASAVA version 1.4.   FASTQ files generated using CellRanger mkfastq version 2.0.0 (10X Genomics)
scRNA-seq reads were aligned to the mm10 genome assembly using CellRanger version 2.0.0 (10X Genomics) with the default parameters.  Gene-barcode matrices from individual samples were generated by CellRanger count version 2.0.0, and aggregated into a single, depth-normalized matrix using the Cellranger aggr function.
Genome_build: mm10 (GRChm38)
Supplementary_files_format_and_content: matrix files contain digital gene expression counts

molecule: polyA RNA

source_name: all live cells from KPC tumor

extract_protocol:
KPC tumors were dissociated into single cell suspensions at 37C, 600rpm for 45 min using collagenese, liberase and Dnase,  and passed through a 100 um FlowMi cell strainer.  Cells were stained with DAPI, anti-mouse CD31 Alexa Fluor 647, anti-mouse CD45 Alexa FLuor 647, anti-mouse PDPN Alexa APC/Cy7, anti-mouse PDGFRa PE. DAPI- cells and DAPI-CD45-CD31-EpCAM-PDPN+ cells were sorted in 2 different collection tubes. Viability was confirmed to be >75% using a Countess FL II cell counter (Life Technologies #AMQAF1000) before proceeding to single cell library prep.
Single cell libraries were prepared using a 10X Genomics Chromium Controller (cat #120223) and the 10X Genomics Single Cell 3' Gene Expression kit (cat #120237) according to the manufacturer's instructions
Single cell 3' digital gene expression with cell barcodes and unique molecular identifiers (UMIs).

tag: strain/genotype

value: KPC (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre) mouse

tag: mouse background

value: pancreatic tumor

value: all tumor cells


title: dis2+, Spt5-T1A total-Pol II_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX


title: iWAT-Control rep1

description:
iWAT_C_vs_S_all_expression_rlog.txt
iWAT_C1

value: 24-weeks old


title: KPC_Tumor_CAFs biological rep2

source_name: live CAFs from KPC tumors

value: CAFs


title: eWAT-Control rep1

description:
eWAT_C_vs_S_all_expression_rlog.txt
eWAT_C1


title: KPC_Tumor_DapiNeg biological rep1


title: dis2+, Spt5-WT total-Pol II_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: BAT-Sutent rep2

description:
BAT_C_vs_S_all_expression_rlog.txt
BAT_S2

source_name: BAT-Sutent

value: sutent

value: brown adipose tissue


title: dis2Δ, Spt5-T1E total-Pol II_IP_2 ChIP-seq

description: Crosslinked DNA

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX

value: ChIP-Seq

tag: antibody

value: RNAPII (8WG16) antibody, Millipore, Cat#05-952


title: BAT-Sutent rep1

description:
BAT_C_vs_S_all_expression_rlog.txt
BAT_S1

tag: tissue


title: CM-JAKi biological rep3

city: Cold Spring Harbor

first: Giulia

last: Biffi

address: 1 Bungtown Rd

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298868

data_processing:
Illumina NextSeq platform
Paired-end sequenced reads were mapped to Gencode mouse (vM1/NCBIM37) whole genome using STAR program (v2.5.1b) with parameters from ENCODE 3 STAR-RSEM pipeline. Gene/Transcript expressions were quantified using RSEM program (v1.2.29).
Differential expression analysis was conducted using DESeq2 program and customized R script
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data in tab-delimited text format.

source_name: pancreatic stellate cell line (PSC5-II)_pancreatic tumor organoid conditioned media 3 with JAK inhibitor

growth_protocol: Cells were cultured in 5%FBS DMEM control media (MG-CM)  or tumor organoid conditioned media (CM) for 4 days in the presence or absence of JAKi. An independent source of CM was used for each cohort.

extract_protocol:
RNA was extracted using the PureLink RNA mini kit (Thermo Fisher Scientific)
TruSeq Stranded Total RNA Kit with RiboZero Human/Mouse/Rat (Illumina)

treatment_protocol: Treated cells were cultured with 500 nM JAKi for 4 days. JAKi = AZD1480 from Selleck, catalog number S2162.

value: Pancreata

value: WT PSC cells


title: CM biological rep3

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298867

source_name: pancreatic stellate cell line (PSC5-II)_pancreatic tumor organoid conditioned media 3


title: MG-CM biological rep3

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298866

source_name: pancreatic stellate cell line (PSC5-II)_Matrigel-conditioned media or control media


title: dis2Δ, Spt5-WT total-Pol II_IP_2 ChIP-seq

description: Crosslinked DNA

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: CM-JAKi biological rep2

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298865

source_name: pancreatic stellate cell line (PSC5-I)_pancreatic tumor organoid conditioned media 2 with JAK inhibitor


title: BAT-Control rep1

description:
BAT_C_vs_S_all_expression_rlog.txt
BAT_C1

source_name: BAT-Control

value: vehicle


title: CM biological rep2

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298864

source_name: pancreatic stellate cell line (PSC5-I)_pancreatic tumor organoid conditioned media 2


title: dis2+, Spt5-T1A total-Pol II_IP_2 ChIP-seq

description: Crosslinked DNA


title: KPC_Tumor_CAFs biological rep1


title: MG-CM biological rep2

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298863

source_name: pancreatic stellate cell line (PSC5-I)_Matrigel-conditioned media or control media


title: dis2+, Spt5-WT total-Pol II_IP_2 ChIP-seq

description: Crosslinked DNA


title: CM-JAKi biological rep1

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298862

source_name: pancreatic stellate cell line (PSC4)_pancreatic tumor organoid conditioned media 1 with JAK inhibitor


title: dis2Δ, Spt5-T1E total-Pol II_input_1 ChIP-seq

source_name: Yeast cell extract

growth_protocol:
S. pombe were grown in YES medium to exponential phase at 30°C
S. pombe were grown in YES medium to exponential phase at 30°C

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Illumina (E7335).
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270) or Illumina (E7335).


title: dis2Δ, Spt5-T1A total-Pol II_input_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX


title: CM biological rep1

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298861

source_name: pancreatic stellate cell line (PSC4)_pancreatic tumor organoid conditioned media 1


title: dis2Δ, Spt5-T1A total-Pol II_IP_2 ChIP-seq

description: Crosslinked DNA


title: dis2Δ, Spt5-WT total-Pol II_input_1 ChIP-seq


title: dis2+, Spt5-T1E total-Pol II_input_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX


title: MG-CM biological rep1

description:
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298860

source_name: pancreatic stellate cell line (PSC4)_Matrigel-conditioned media or control media


title: dis2+, Spt5-T1E total-Pol II_IP_2 ChIP-seq

description: Crosslinked DNA


title: BAT-Control rep2

description:
BAT_C_vs_S_all_expression_rlog.txt
BAT_C2


title: dis2+, Spt5-T1A total-Pol II_input_1 ChIP-seq


title: dis2Δ Rhn1-TAP_input_1 ChIP-seq

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by ChIP DNA Clean & Concentrator (Zymo Research).
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).

value: h+:leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Rhn1-3XHA-TAP::kanMX

tag: molecule

value: genomic DNA


title: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, salt stress condition, rep. 3

city: Espinardo

first: Irene

last: Albaladejo

state: Murcia

address: Campus Universitario Espinardo

country: Spain

institute: CEBAS-CSIC

description: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, salt stress condition, replicate 3

hyb_protocol: Following fragmentation and labeling, 3.5 ug of cDNA was hybridized for 20 hr at 48ºC on TomGene-1-1-st-v1 array using the GeneAtlas Hybridization Station. After hybridization, arrays were washed and stained in the GeneAtlas Fluidics Station (GeneAtlasTM System, Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station (GeneAtlasTM System, Affymetrix)

data_processing: Data were analyzed with RMA (Robust Multiarray Analysis) using Affymetrix default analysis settings and global scaling as normalization method. Non-supervised Principal Components Analysis (PCA) and hierarchical clustering were performed and they showed that samples tend to separate according to genotype and condition. Partek Genomics Suite and Partek Pathways software (Partek Incorporated, St. Louis, USA) were used for obtaining the annotation of probesets and performing the statistical analysis. An ANOVA test was applied with a restrictive threshold at p-value ≤ 0.05, and multiple test corrections was performed using the FDR (Benjamini and Hochberg, 1995).

organism: Solanum lycopersicum

source_name: WT leaflets, salt stress condition

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 100ng of total RNA (GeneChip WT Plus Reagent Kit. Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays).

growth_protocol: Plants of the res mutant and Solanum lycopersicum L. cv. Moneymaker (background genotype), were used. Seeds were germinated in darkness, in a 8:3 (v/v) mixture of peat:perlite, at 28ºC temperature and 90% of relative humidity (RH). After emergence, plants were grown in a controlled growth chamber with 16 h light/8 h darkness photoperiod, with light of a photosynthetic photon flux (400-700 nm) of 350 µmol m-2 s-1 at the plant level, provided by fluorescent tubes (Philips Master TL-D 58W/840 REFLEX, Holland), and 25 ºC and 50-60% of temperature and RH, respectively. Two-week old plantlets were transferred to hydroponics. The hydroponic system consisted in tanks of 50 L volume (219 x 20 x 17 cm) filled with half-strength (½) Hoagland nutritive solution (Hoagland and Arnon, 1950), which was continuously aerated by means of a compressor (Puska N-150-150, with a 115 L min-1 flow, 10 Kg cm-2 maximum pressure). The nutritive solution was controlled by monitoring pH and electrical conductivity (EC), renewing it at least once per week.

extract_protocol: Total RNA from 24 samples was extracted by means of Rneasy Mini Kit (Qiagen) according to instrutions from manufacturer.The amount and quality of the RNA was checked by Bioanalyzer and spectrophotometrically by Nanodrop.

treatment_protocol: Salt stress was applied in hydroponics to six-week old WT and res plants, and consisted in ½ Hoagland plus 200 mM NaCl for 5 days. Leaflets from the first fully-expanded leaf and roots were harvested and immediately frozen in liquid N2 prior to stress application (control) and after 5 days of salt treatment. Three biological replicates (each one including three plants) were considered for each genotype and treatment.

value: leaflet

value: WT

tag: background cultivar

value: Moneymaker

value: six-week old plants

value: salt stress (200 mM NaCl for 5 days)


title: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, salt stress condition, rep. 1

description: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, salt stress condition, replicate 1

tag: age


title: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, salt stress condition, rep. 2

description: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, salt stress condition, replicate 2


title: dis2Δ, Spt5-T1E total-Pol II_IP_1 ChIP-seq

description: Crosslinked DNA


title: WT Rhn1-TAP_IP_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Rhn1-3XHA-TAP::kanMX

value: Rabbit IgG Agarose, Sigma-Aldrich, Cat# A2909

value: Crosslinked DNA


title: dis2+, Spt5-WT total-Pol II_input_1 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX

value: ChIP-Seq


title: WT Rhn1-TAP_input_1 ChIP-seq


title: dis2Δ, Spt5-T1A total-Pol II_IP_1 ChIP-seq

description: Crosslinked DNA

value: RNAPII (8WG16) antibody, Millipore, Cat#05-952


title: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, control condition, rep. 3

description: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, control condition, replicate 3

source_name: WT leaflets, control condition

value: control (optimal growth condition)


title: dis2Δ Pcf11-TAP_input_2 ChIP-seq

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Pcf11-TAP::kanMX


title: dis2Δ, Spt5-WT total-Pol II_IP_1 ChIP-seq

description: Crosslinked DNA

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; dis2::ura4+; Seb1-3XHA-TAP::kanMX; Spt5-wt-3xFlag::natMX


title: res tomato mutant, leaflets, salt stress condition, rep. 3

description: res tomato mutant, leaflets, salt stress condition, replicate 3

source_name: res mutant leaflets, salt stress condition

value: res mutant


title: dis2+, Spt5-T1E total-Pol II_IP_1 ChIP-seq

description: Crosslinked DNA

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1A-3xFlag::natMX


title: res tomato mutant, leaflets, salt stress condition, rep. 2

description: res tomato mutant, leaflets, salt stress condition, replicate 2


title: dis2Δ Pcf11-TAP_input_1 ChIP-seq

value: genomic DNA


title: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, control condition, rep. 2

description: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, control condition, replicate 2

value: leaflet


title: res tomato mutant, leaflets, control condition, rep. 3

description: res tomato mutant, leaflets, control condition, replicate 3

source_name: res mutant leaflets, control condition


title: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, control condition, rep. 1

description: Tomato (S. lycopersicum) cv. Moneymaker, leaflets, control condition, replicate 1

value: WT


title: dis2Δ Pcf11-TAP_IP_2 ChIP-seq


title: dis2+, Spt5-T1A total-Pol II_IP_1 ChIP-seq

description: Crosslinked DNA

value: h+; leu1-32; ura4-[delta]18; ade6-M216; his3[delta]::1; Seb1-3XHA-TAP::kanMX; Spt5-T1E-3xFlag::natMX