title: Untreated3

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

data_processing:
Using FASTX-Toolkit, raw reads in the FASTQ format were trimmed and filtered to remove low quality sequences (a minimum phred quality score of 28).
The BWA-MEM algorithm was employed to align the preprocessed reads into the reference genome.
SAM files containing mapping results were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per each CDS in the pine tree were counted by featureCounts module in the Subread package.
To quantify the gene transcriptional level, we employed the relative transcript abundance with reads per kilobase per million mapped reads (RPKM) method.
Genome_build: Pinus taeda genome (v2.01) obtained from PineRefSeq database (https://treegenesdb.org/FTP/Genomes/Pita/, accessed April-2019)
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Pinus densiflora

source_name: Untreated pine seedlings

growth_protocol: Three-year-old Pinus densiflora were purchased and maintained with a relative humidity of 70%. For pinewood nematode (PWN) infection, Bursaphelenchus xylophilus was cultured on fungal hyphae of Botrytis cinerea grown on potato dextrose agar medium at 25 ℃ for 1 week. A suspension of PWN with distilled water was adjusted to a concentration of approximately 20,000 nematodes/ml.

extract_protocol:
One gram of pinewood nematodes-infected needles was ground in liquid nitrogen and mixed with 15 ml of extraction buffer containing 100 mM Tris-HCl (pH 8), 2% CTAB, 30 mM EDTA, 2 M NaCl, 0.05% spermidine, 2% polyvinylpolypyrrolidinone, 2% 2-mercaptoethanol, and 1.5 mg/ml proteinase K. The suspension was incubated at 42 ℃ for 90 min and extracted with 15 ml chloroform-isoamyl alcohol (24:1), and total RNAs precipitated with 10 M LiCl. After washing with 70% ethanol, the RNA pellets were dissolved in the DEPC water.
Total RNAs of pine trees were converted to cDNA libraries using the TruSeqTM RNA sample preparation kit (Illumina, San Diego, CA, USA), starting with 1 μg of enriched mRNAs. The cDNA libraries were sequenced on the Illumina HiSeq2000 platform with paired-end strategy, according to the manufacturer’s instructions.

treatment_protocol: 5.03% (w/w) acibenzolar-S-methyl and 20% (w/w) methyl salicylic acid were dissolved in water at 1600 μg/ml, and then foliar sprayed with twice at 1-week intervals on pine seedlings. Pine seedlings treated with distilled water containing 250 μg/ml Tween 20 in the same manner were used as a negative control. One week after treatment, the pine seedlings were inoculated with Bursaphelenchus xylophilus (20,000 nematodes/ml).

value: wild type

value: Pine seedlings

value: Distilled water containing 250 μg/ml Tween 20

tag: inoculation


title: SBW25_rep1

status: Public on Nov 02 2020

type: SRA

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

country: Germany

library_source: transcriptomic

data_processing:
library strategy: Y-shaped Adapter-ligated MAture tRNA sequencing (YAMAT-seq)
Sorted into 27 samples using the unique, 6-bp Illumina indices. 0 mismatches allowed.
Per sample: reads between 80 and 151 bp were extracted (in Geneious v11.1.4)
Per sample: 80-151 bp reads were aligned to a set of 42 reference tRNA sequences (all unique primary sequences predicted in the SBW25 genome by GtRNAdb). This was done using Geneious version 11.1.4 (assembly parameters: up to 10% mismatches or gaps of <3 bp per read, up to 5 ambiguities per read, no assignment of reads that map equally well to more than one reference sequence, and no iterations)
Per sample: read numbers for the 42 contigs were used in pairwise comparisons with DESeq2 (in R version 3.6.0)
Genome_build: The 42 tRNA sequence reference file was derived from the SBW25 genome sequence (NCBI accession number: NC_012660.1) using GtRNAdb (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/bacteria/Pseu_fluo_SBW25/pseuFluo_SBW25-tRNAs.fa)
Supplementary_files_format_and_content: 27 text files: the raw read numbers aligned to the 42 reference sequences. One file per sample.
Supplementary_files_format_and_content: "aligned_reads.xlsx" contains a summary of the data for all 27 samples, plus a spreadsheet for each of the 9 strains listing the of the number of reads aligned to each reference sequence in each replicate. "deseq2_comparisons.xlsx"  contains the DESeq2 output for pairwise comparisons between strains of interest.

molecule: total RNA

organism: Pseudomonas fluorescens

source_name: SBW25_liquid cell culture

growth_protocol: Samples were grown from single colonies in liquid culture overnight (28˚C, shaking). A small volume of grown culture was inoculated into fresh medium and grown to mid-exponential phase (approx. 5-7 hours, 28˚C, shaking).

extract_protocol:
Per sample: 1.5 ml aliquots of mid-exponential phase culture were taken, and total RNA extracted (TRIzol Max Bacterial RNA isolation kit; Life Technologies).
The YAMAT-seq method is an adaptation of that published for human cell lines (Shigematsu et al., 2017). For each sample, 5 ug total RNA was subjected to tRNA deacylation treatment by exposure to hydrochloric acid. Hybrid DNA/RNA Y-shaped adapters (Eurofins) were ligated to exposed 5'-CCA-3' tRNA ends using T4 RNA ligase 2 (New England Biolabs). Ligation products were reverse transcribed into cDNA (SuperScript III reverse transcriptase; Thermo Fisher), and amplified PCR (Phusion; Thermo Fisher). One of 27 sample-specific indices (Illumina) was added to each of the 27 reactions. The quality and quantity of each PCR product was checked using an Agilent DNA 7500 kit on a Bioanalyzer (Agilent), and samples combined in equimolar amounts into a single tube. The mixture was run on a 5 % polyacrylaminde gel (Bio-Rad Laboratories), and the group of bands ranging between 180 bp and 250 bp excised. DNA was extracted in deionized water overnight, and agarose removed by centrifugation through filter paper. DNA quality and quantity was checked with a Quant-iT dsDNA BR Assay kit (Invitrogen) on a Fluorescence Nanodrop.High throughput sequencing was performed at the Max Planck Institute for Evolutionary Biology (Ploen, Germany). Single-end, 150 bp reads were generated with a NextSeq 550 Output v2.5 kit (Illumina).

tag: strain type

value: SBW25 (wild type)

tag: genotype

tag: evolution day

tag: molecule subtype

value: mature tRNA


title: Colon_Control_002

type: RNA

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

hyb_protocol: 1.5 ug 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, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mus musculus Sure Print GE 4x44 v2 microarrays with oligonucleotide 45,220 probes (G2519F) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) 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: Mus musculus

source_name: Colon, control_replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: Mouse colon and ileum samples were homogenized using the FastPrep instrument (MP Biomedicals), total RNA was isolated using RNAspin columns (Macherey-Nagel).

treatment_protocol: Three groups of mice (n=4) were randomized to receive distinct doses of ZnCl2 solutions (Sigma–Aldrich, St. Quentin–Fallavier, France) administered in the drinking water (Zn: 250 mg per kg body weight (mg/kg), 50 or 12 mg/kg) while a control group consisted in standard uncontaminated drinking water (n=4). Zn concentration is negligible in drinking water and its concentration is 25 mg/kg in standard chow (Diet A04C-10, Scientific Animal Food and Engineering, Augy, France). After 15 days of Zn treatment, mice are sacrificed and sections (0.5 /1cm in length) from the median colon and terminal ileum were collected and processed with RNA stabilization solution (RNA-later, Ambion, Life Technologies).

tag: tissue

value: colon

tag: gender

value: female

tag: age

value: 7 weeks

tag: diet

value: 15 days of standard uncontaminated drinking water consumption


title: RNA_Ctrl_CRISPRi_rep2

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark Street

department: Molecular Biosciences

country: USA

institute: Northwestern University

data_processing:
3'READS+ : 5' adapters were removed using CutAdapt. Four random nucleotides were removed from 5' end. T tails were removed and saved from 5' ends. Reads > 22 nucleotides were aligned using bowtie2 in end-to-end mode. Reads with a MAPQ score lower than 10 were filtered out. Reads with at least 2 unmappable Ts in their T tails were considered Poly-A supporting reads. Poly-A sites were merged by 24bp. A table of counts was generated for total reads in each PolyA site window. To identify differential usage of poly-A sites, the sum of counts at each gene was calculated. The relative percent usage was then calculated as counts at each site divided by the total counts at the gene associated with that site. EdgeR was used to assess differential usage based on the relative percent usage.
RNA-seq : Reads were aligned using Tophat2. Number of Raw reads at each gene was calculated using in house generated script, and DESeq was used for differential expression analysis in R
Genome_build: hg19
Supplementary_files_format_and_content: 3'READS+ processed data is in format of table with each PolyA-site containing counts. RNA-seq data is in format of table containing counts at each gene and DESeq output information.

organism: Homo sapiens

source_name: human keratinoctyes

growth_protocol: neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium

extract_protocol:
For both 3'READS+ and RNA-seq, RNA were extracted using Quick-RNA™ MiniPrep (Zymo Research), and mRNA were enriched using NEBNext® rRNA Depletion Kit (NEB) or NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB).
For 3'READS+, sequencing libraries were constructed using a modified version of the 3'READS+ protocol.  For RNA-seq, NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) was used for library construction.

treatment_protocol: To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 10 uM of siRNA for each target were nucleofected (Lonza to keratinocytes)

tag: cell type

value: primary human neonatal keratinocytes

tag: strain

value: RNAseq in undifferentiated keratinocytes with Ctrl CRSPRi


title: 3READS_Ctrlsi

value: 3'READS+ in undifferentiated keratinocytes with Ctrl siRNA


title: Colon_Control_001

source_name: Colon, control_replicate 1


title: Untreated1

country: South Korea

tag: treatment

value: Bursaphelenchus xylophilus (20,000 nematodes/ml)


title: Colon_004

source_name: Colon, Zn treatment 15 days_replicate 4

value: 15 days of Zn supplemented diet


title: MeSA2

source_name: Pine seedlings treated with methyl salicylic acid

value: Methyl salicylic acid


title: M_florum 5'-RACE

city: Sherbrooke

first: Sebastien

last: Rodrigue

state: QC

address: 2500 boul. de l'Université

department: Biologie

country: Canada

institute: Université de Sherbrooke

description: 5'-end mRNA sequencing based on monophosphorylated RNA depletion

data_processing:
RNA-Seq and 5'-RACE: Reads were quality trimmed using Trimmomatic version 0.32 and aligned on the M. florum L1 genome (NC_006055.1) in a strand-specific manner using Bowtie 2 version 2.3.3.1. Reads with a MAPQ below 10 were discarded using samtools version 1.5.
RNA-Seq: FPKM values were calculated for each M. florum L1 annotated gene (RAST annotation, see Baby et al 2018) using the GenomicAlignments R package version 1.10.1.
5'-RACE: Reads were clipped to retain only a single base at their 5’ extremity, corresponding to putative 5'-end of transcripts. The number of millions of mapped reads (RSPM) was calculated at each genomic position using Bedtools genomecov version 2.27.1. Peaks with a RSPM signal equal or higher than the average plus one standard deviation single base signal calculated over the entire genome were considered significant and kept for further analysis. Significant peaks located at 10 bp or less of each other were merged to retain only the peak with the highest associated RSPM signal, corresponding to a putative TSS.
Genome_build: NC_006055.1
Supplementary_files_format_and_content: RNA-Seq bigWig (.bw) data files contain strand-specific 1 bp resolution genome coverage tracks generated using Bedtools genomecov version 2.27.1 from MAPQ filtered alignments.
Supplementary_files_format_and_content: 5'-RACE bigWig (.bw) data files contain strand-specific 1 bp resolution genome coverage tracks generated using Bedtools genomecov version 2.27.1 from 5'-end processed alignments.
Supplementary_files_format_and_content: The tab-delimited text file (.tsv) contains raw RNA-Seq read counts calculated by the GenomicAlignments software for each M. florum protein coding gene, as well as corresponding FPKM values.
Supplementary_files_format_and_content: The bed format file (.bed) contains coordinates of all putative TSSs identified by 5'-RACE, along with their corresponding peak height (raw read count) and RSPM values. TSSs are coloured according to their orientation.

organism: Mesoplasma florum

source_name: Bacterial culture

growth_protocol: M. florum cells were grown in ATCC 1161 medium at 34°C with shaking.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research, R2052) according to the manufacturer's specifications.
RNA-Seq: ~300 ng of total RNA was fragmented at 95°C by Mg2+ catalyzed hydrolysis, and then purified using the RNA Clean & Concentrator-5 kit (Zymo Research). RNA molecules were dephosphorylated using Antarctic Phosphatase (NEB), and purified again using the RNA Clean & Concentrator-5 kit. The 3' sequencing adaptor was ligated using the T4 RNA ligase (Enzymatics), and RNA fragments were purified using Agencourt RNAclean XP SPRI beads (Beckman Coulter). RNA fragments were phosphorylated using T4 Polynucleotide Kinase (Enzymatics), purified again using Agencourt RNAclean XP SPRI beads, and the 5' sequencing adaptor was ligated using the T4 RNA ligase. RNA fragments were purified using Agencourt RNAclean XP SPRI beads, and then reverse transcribed to cDNA using the M-MuLV Reverse Transcriptase (Enzymatics). cDNA was purified using Agencourt AMPure XP SPRI beads, amplified by real-time PCR using the VeraSeq 2.0 DNA polymerase (Enzymatics), and purified again using Agencourt AMPure XP SPRI beads. DNA molecules corresponding to rRNA transcripts were depleted using the Duplex-specific nuclease (DSN, Evrogen). Final library size, quality, and concentration was evaluated using a 2100 Bioanalyzer instrument (Agilent Technologies). RNA-Seq libraries were sequenced on a HiSeq 2000 Illumina instrument using 2x50 bp paired-end sequencing. For more details, see Carraro et al 2014.
5'-RACE: ~2 µg of total RNA was fragmented at 75°C by Mg2+ catalyzed hydrolysis, and then purified using the RNA Clean & Concentrator-5 kit (Zymo Research). The 3' sequencing adaptor was ligated using the T4 RNA ligase (Enzymatics), and RNA molecules were purified again using the RNA Clean & Concentrator-5 kit. Monophosphorylated RNA fragments were depleted using the XRN-1 nuclease (NEB), and the remaining RNA molecules were purified with the RNA Clean & Concentrator-5 kit. RNA fragments were treated with the RppH Pyrophosphohydrolase (NEB) to remove a pyrophosphate from the 5'-end of triphosphorylated RNA, and purified once again with the RNA Clean & Concentrator-5 kit. The 5' sequencing adaptor was finally ligated using the T4 RNA ligase, RNA fragments were purified using Agencourt RNAclean XP SPRI beads (Beckman Coulter), and reverse transcribed using the M-MuLV Reverse Transcriptase (Enzymatics). cDNA was purified using Agencourt AMPure XP SPRI beads, amplified by real-time PCR using the VeraSeq 2.0 DNA polymerase (Enzymatics), and purified again using Agencourt AMPure XP SPRI beads. Final library size, quality, and concentration was evaluated using a 2100 Bioanalyzer instrument (Agilent Technologies). The 5'-RACE library was sequenced on an Illumina Genome Analyzer IIx instrument using 40 bp single-end sequencing. For more details, see Carraro et al 2014.

treatment_protocol: Growth medium was removed by centrifugation at 21,000 x g prior to RNA extraction.

value: bacteria

tag: growth phase

value: exponential

tag: growth medium

value: ATCC 1161

tag: growth protocol

value: Batch culture incubated at 34°C in an orbital shaker


title: RNA_CPSF_CRISPRi_rep3

value: RNAseq in undifferentiated keratinocytes with CPSF1 CRSPRi


title: RNA_Ctrl_CRISPRi_rep1


title: MeSA1

value: wild type

value: Pine seedlings


title: RNA_CPSF_CRISPRi_rep2


title: ASM3

source_name: Pine seedlings treated with acibenzolar-S-methyl

value: Acibenzolar-S-methyl


title: Colon_003

source_name: Colon, Zn treatment 15 days_replicate 3

value: colon

value: female


title: ASM2


title: Colon_002

source_name: Colon, Zn treatment 15 days_replicate 2

value: 7 weeks


title: RNA_CPSF_CRISPRi_rep1

value: primary human neonatal keratinocytes


title: ASM1


title: RNAseq_DF_rep3

value: RNAseq in differentiated keratinocytes


title: Untreated2

value: Distilled water containing 250 μg/ml Tween 20


title: MeSA3

value: Bursaphelenchus xylophilus (20,000 nematodes/ml)


title: Colon_001

source_name: Colon, Zn treatment 15 days_replicate 1

value: 15 days of Zn supplemented diet


title: Ileum_Control_004

source_name: Ileum, control_replicate 4

value: ileum

value: 15 days of standard uncontaminated drinking water consumption


title: 033_06_FL_S6

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

description: Basal layer of medium was replaced with infection media (DMEM with 2% FBS, 100 U/mL penicillin and streptomycin, 10 mM HEPES, 0.1 mM nonessential amino acids, 4 mM L-glutamate, and 1mM sodium pyruvate). Wells were left untreated, or treated with 100 ng of IFN-b or 0.1 mM remdesivir in the basal compartment for 1 hr prior to infection. For infection, SARS-CoV-2 strain 2019-nCoV/USA_WA1/2020 (provided by World Reference Center for Emerging Viruses and Arboviruses at the University of Texas Medical Branch) and icSARS-CoV-2-mNG, were added directly to the apical layer of cells for 1 hr at 37°C with rocking every 10 min. The virus was removed from the apical compartment and cells were incubated at 37°C until harvest.

data_processing:
Cellranger 3.0.1 for cell and gene counts
Seurat 2.3.4 for data processing and statistical analysis
Genome_build: Homo_sapiens.GRCh38.dna.chr.fa, MN985325.fa, Homo_sapiens.GRCh38.98.chr.gtf, MN985325.gtf
Supplementary_files_format_and_content: text file and data matrix

source_name: human nHTBE cells

growth_protocol: nHTBE cells (Lonza Bioscience, CC-2540S) harvested from healthy individuals were expanded using Pneumacult-Ex Plus (Stem Cell Technologies) and seeded on 24 well hanging inserts, 0.4 μm pore (Corning, USA) and were maintained at ALI for 21+ days in a Pneumacult ALI growth medium (Stem Cell Technologies) at 37°C/5% CO2 in a humidified incubator. Cells were used 21+ days post ALI for experiments.

extract_protocol:
Cells were washed and trypsinzed using ReagentPack™ Subculture Reagents (Lonza Bioscience). Single cell suspensions were washed with PBS + 5% FBS, resuspended in 200 µL PBS + 5% FBS, passed through a 70 µm filter, and placed on ice. Cells were counted using trypan blue exclusion on a Luna II (Logos Biosystems). The appropriate numbers of cells to achieve a targeted cell input of 5,000 cells per condition were used to generate the GEMs (Gel Bead-In Emulsion). The Chromium Next GEM Single Cell 3’ Gel beads v3.1 kit (10X Genomics, Pleasanton, CA, USA) was used to create GEMs following manufacturer’s instruction. All samples and reagents were prepared and loaded into the chip and ran in the Chromium Controller for GEM generation and barcoding.
GEMs generated were used for cDNA synthesis and library preparation using the Chromium Single Cell 3’ Library Kit v3.1 (10X Genomics) following the manufacturer’s instruction.

treatment_protocol: Basal layer of medium was replaced with infection media (DMEM with 2% FBS, 100 U/mL penicillin and streptomycin, 10 mM HEPES, 0.1 mM nonessential amino acids, 4 mM L-glutamate, and 1mM sodium pyruvate). Wells were left untreated, or treated with 100 ng of IFN or 0.1 M remdesivir in the basal compartment for 1 hr prior to infection. For infection, SARS-CoV-2 strain 2019-nCoV/USA_WA1/2020 (provided by World Reference Center for Emerging Viruses and Arboviruses at the University of Texas Medical Branch) and icSARS-CoV-2-mNG, were added directly to the apical layer of cells for 1 hr at 37C with rocking every 10 min. The virus was removed from the apical compartment and cells were incubated at 37C until harvest.

value: tracheal/bronchial scrapings

value: Normal human tracheal bronchial epithelial

tag: isolate

value: Batch 18TL134625, Tissue acquisition number 35825

tag: Sex

value: Male

value: Remdesivir pretreated

tag: infection status

value: SARS-CoV-2 infected, MOI 5, 48 hours post infection


title: 033_03_FL_S3

value: SARS-CoV-2 infected, MOI 5, 24 hours post infection


title: 033_05_FL_S5

value: untreated


title: RNAseq_DF_rep2


title: 033_02_FL_S2


title: 033_01_FL_S1

value: uninfected


title: Ileum_Control_003

source_name: Ileum, control_replicate 3

value: female

value: 7 weeks


title: Wild-Type vs. Abcb4-/-

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole mouse genome 8x60K microarrays were done according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 3 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: wildtype

label_protocol: RNA labeling was performed with the low input Quick Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Generation and characteristics of knockout lineages C.FVB(129P2)-Abcb4tm1Bor (Abcb4-/-) and BALB/c-ll13tm2Anjm (IL-13) have been described previously. Abcb4-/-- and IL-13-/- mice were crossed to raise double-knockout hybrids C.Cg-ll13tm2Anjm-Abcb4tm1Bor (Abcb4-/-IL-13-/-).

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: Mice at  8 weeks of age were used.

value: Wild-Type

value: FVB/N

value: liver

source_name: knock out (KO)


title: Ileum_Control_002

source_name: Ileum, control_replicate 2


title: N87_24h_Afa_3

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
fastq file generation by bcl2fastq2ConversionSoftwarev2.20 (Illumina)
raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file.
Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with default settings
Feature counts were determined using R package “Rsubread”.
Genome_build: hg38
Supplementary_files_format_and_content: Text file with raw counts

molecule: polyA RNA

growth_protocol: MKN1, MKN7 and NCI-N87 cells were grown in RPMI medium (10 % FCS, 0.5 % penicillin/streptomycin). Hs746T cells were grown in DMEM medium (10 % FCS, 0.5 % penicillin/streptomycin)

extract_protocol:
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher)
NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols

treatment_protocol: Cells were treated with EGF (5 ng/ml, Sigma Aldrich), cetuximab (Cet, 1 µg/ml, Merck), trastuzumab (Tra, 5 µg/ml, Roche) or afatinib (Afa, 0.5 µM, Biozol) for 4 h or 24 h

tag: cell line

value: Gastric cancer cell line

tag: time

tag: treat

value: Afa


title: N87_24h_Tra_3

value: Tra


title: RNAseq_UD_rep2

value: primary human neonatal keratinocytes

value: RNAseq in undifferentiated keratinocytes


title: N87_4h_Afa_3


title: N87_24h_Tra+Afa_3

value: Tra+Afa


title: Ileum_004

source_name: Ileum, Zn treatment 15 days_replicate 4

value: ileum

value: 15 days of Zn supplemented diet


title: RNAseq_UD_rep1


title: N87_4h_Tra_3


title: 3READS_DF_rep2

value: 3'READS+ in differentiated keratinocytes


title: MKN7_24h_Tra+Afa_3


title: Ileum_003

source_name: Ileum, Zn treatment 15 days_replicate 3


title: RNAseq_DF_rep1

source_name: human keratinoctyes

value: RNAseq in differentiated keratinocytes


title: Ileum_002

source_name: Ileum, Zn treatment 15 days_replicate 2


title: MKN7_24h_Tra_3


title: 3READS_DF_rep1


title: 3READS_UD_rep2

value: 3'READS+ in undifferentiated keratinocytes


title: M3L_rep3

institute: Max Planck Institute for Evolutionary Biology

source_name: M3L_liquid cell culture

tag: strain type

value: engineered then evolved

tag: genotype

tag: evolution day

tag: molecule subtype

value: mature tRNA


title: Ileum_001

source_name: Ileum, Zn treatment 15 days_replicate 1

tag: tissue

tag: gender

value: female

tag: age

value: 7 weeks

tag: diet


title: MKN7_24h_unb_3

tag: cell type

value: untreated


title: N87_4h_Tra+Afa_3


title: RNAseq_UD_rep3

tag: strain


title: 3READS_UD_rep1


title: MKN7_24h_Afa_3


title: Ileum_Control_001

source_name: Ileum, control_replicate 1

value: 15 days of standard uncontaminated drinking water consumption


title: MKN7_4h_Tra_3

value: Gastric cancer cell line


title: N87_24h_unb_3


title: MKN7_4h_Afa_3

value: Afa


title: D4_latent_activated

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

data_processing:
Raw reads were trimmed to remove low quality reads and adapter sequences. Filtered reads for the samples were mapped to the collection of human mature miRNA from miRBase v21 using Novoalign (3.02.03). Only reads that were uniquely aligned to the mature miRNA were considered for further analysis.
Read counting was conducted using HTSeq (version 0.6.1) and annotation derived from miRBase v21.
The miRNA expression data were filtered to preserve miRNA with a minimum of 2 counts per million reads (cpm) in at least 25% of samples.
Differential expression testing was conducted using the Bioconductor package EdgeR (version 3.4.2). The data were normalized to adjust for sample library sizes using the trimmed mean of M values (TMM) method. Differentially expressed miRNAs were identified by fitting the data to a generalized linear model (GLM) followed by GLM likelihood ratio test. The p-values were adjusted for multiple testing using the Benjamini and Hochberg approach. A false discovery rate (FDR) corrected p-value < 0.05 was considered a significant difference.
Genome_build: miRBase v21 built from hg38
Supplementary_files_format_and_content: Tab delimited file with rows for host miRNAs and columns for sample label.

source_name: CD4+ T-cell RNA extract

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (cat. #74134), according to manufacturer’s instructions, with addition of extra ethanol to the flow through from the gDNA columns (1.5 volumes of 100% Ethanol) to recover small RNAs. On-column DNase treatment was included as part of the protocol to remove genomic DNA.
Library construction and sequencing were conducted at Expression Analysis, Inc. Briefly, the Illumina TruSeq Small RNA Library Prep kit was used to prepare libraries, and the BluePippin system was used for size selection. Libraries were sequenced to a read depth of 5 million reads using the Illumina HiSeq2000 to generate 50 base pair single end reads.

treatment_protocol: Peripheral blood mononuclear cells were collected from 4 HIV-seronegative donors. CD4+ T cells were isolated and utilized to generate an in vitro model of latent HIV infection (model developed by Bosque and Planelles, 2009, 2016). Mock-infected cells were cultured in parallel under the same culture conditions, but without exposure to the virus. Following generation of the model, both mock-infected and latently infected cells were activated using T cell receptor stimulus (antiCD3/antiCD28 coated magnetic beads) for 48 hours.

value: CD4+ T cell

value: model of HIV latency

tag: activation

value: activated


title: MKN7_4h_unb_3


title: CPSF1i_RNAseq_rep2

data_processing:
5' adapters were removed using CutAdapt. Four random nucleotides were removed from 5' end. T tails were removed and saved from 5' ends. Reads > 22 nucleotides were aligned using bowtie2 in end-to-end mode. Reads with a MAPQ score lower than 10 were filtered out. Reads with at least 2 unmappable Ts in their T tails were considered Poly-A supporting reads. Poly-A sites were merged by 24bp. A table of counts was generated for total reads in each PolyA site window. To identify differential usage of poly-A sites, the sum of counts at each gene was calculated. The relative percent usage was then calculated as counts at each site divided by the total counts at the gene associated with that site. EdgeR was used to assess differential usage based on the relative percent usage.
Reads were aligned using Tophat2. Number of Raw reads in each peak was calculated using in house generated script, and DESeq was used for differential expression analysis in R
Genome_build: hg19
Supplementary_files_format_and_content: 3'READS+ processed data is in format of table with each PolyA-site containing counts, relative counts, and EdgeR output. RNA-seq data is in format of table containing counts at each gene and DESeq output information.

source_name: human keratinoctyes with Ctrl si

extract_protocol:
For both 3'READS+ and RNA-seq, RNA were extracted using Quick-RNA™ MiniPrep (Zymo Research), rRNA were removed using using NEBNext® rRNA Depletion Kit (NEB).
For 3'READS+, sequencing libraries were constructed using a modified version of the 3'READS+ protocol.  For RNA-seq, NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) was used for library construction.

value: primary human neonatal keratinocytes

tag: sample type

value: undifferentiated keratinocytes with CPSF1 siRNA nucleofection


title: CPSF1i_RNAseq_rep1


title: N87_4h_unb_3


title: Hs746T_24h_Afa_3


title: D4_latent_resting

value: resting


title: M2L_rep3

source_name: M2L_liquid cell culture


title: Hs746T_24h_Tra_3

value: Tra


title: D4_mock_activated

value: mock-infected


title: MKN7_4h_Tra+Afa_3

value: Tra+Afa


title: CTRLi_RNAseq_rep2

source_name: human keratinoctyes with Brg1/Brm si

value: undifferentiated keratinocytes with CTRL siRNA nucleofection


title: Hs746T_24h_EGF+Cet_3

value: EGF+Cet


title: Hs746T_24h_Cet_3

value: Cet


title: D4_mock_resting


title: CTRLi_RNAseq_rep1


title: CTL-72 hrs_rep 1

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization within lumi package in R

label: biotin

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

growth_protocol: HCT116 cells were cultured in DMEM/F12 with 5% Horse serum, at 37oC, 5%CO2.

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: SUNO1 was depleted by using siRNA. Control siRNA was used as control in HCT116 cells. We performed the microarray in biologicl duplicates. We used to two time points (36 hrs and 72 hrs post siRNA treatment) to identify the gene sets that showed differential expression during early and late time points post SUNO1 depletion.

tag: sirna

value: Control

tag: time point


title: Hs746T_24h_unb_3

tag: cell line

value: untreated


title: Hs746T_4h_Afa_3

tag: time


title: D3_latent_resting

tag: infection status


title: D3_mock_activated


title: Hs746T_4h_Tra_3

tag: treat


title: Hs746T_4h_EGF+Cet_3


title: Hs746T_4h_Cet_3


title: Hs746T_24h_Tra+Afa_3


title: NC3_shRNA_RNA-Seq_rep2

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
RNA-seq analysis and identification of differentially expressed genes was performed using LCDB workflow (https://github.com/lcdb/lcdb-wf)
For visualization, bigwig files created by the LCDB workflow were loaded onto IGV.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig

growth_protocol: Human embryonic stem (hES) H1 cells were maintained under feeder free conditions on Matrigel-coated plates (#354277, BD Biosiences) in mTeSRTM1, (#05871/05852, StemCell Technologies Inc.) and were routinely passaged with collagenase (#07909, StemCell Technologies Inc.). Neural induction of hES H1 cells expressing different shRNA constructs was performed using STEMdiffTM Neural Induction Medium (#05831, StemCell Technologies Inc.) in combination with a monolayer culture method according to the manufacturer’s technical bulletin (#28044). In brief, single cell suspensions were prepared by treatment of hES cells with accutase and 1.5 – 2.0 x 106 cells were seeded per well of a 6-well plate in 4mL STEMdiffTM Neural Induction Medium supplemented with 10 μM Y-27632 ROCK inhibitor. Neural induction was performed for indicated time periods with daily medium change.

extract_protocol:
RNA from three replicates for cells treated with control shRNA or shRNA against OTUD5, at each stage of neural-conversion, was isolated using Trizol.
After confirming that the RNA integration number for each sample was above 8, libraries were prepared using TruSeq Stranded mRNA prep kit with PolyA purificaton.
Libraries were sequenced on HiSeq 2500 using a 1x50 single read mode.

treatment_protocol: Lentiviruses were produced in 293T cells by cotransfection of lentiviral constructs with packaging plasmids (Addgene) for 48–72 hr. Transduction was carried out by infecting 2x105 hES H1 cells per well of a 6-well plate with lentiviruses in the presence of 6 μg/ml Polybrene (Sigma) and 10 μM Y-27632 ROCK inhibitor. For transduction of lentiviruses carrying ectopic expression vectors, cells were centrifuged at 1,000g at 30C for 90min. Media was replaced with 2mL mTESR1 containing 10 μM Y-27632 ROCK inhibitor.  After 4-6d of selection with appropriate antibiotic (1 μg/ml puromycin for pLKO1-puro-shRNA constructs, 200 μg/ml G418 for pINDUCER20 constructs), hES H1 cells were analyzed and used in differentiation experiments.

value: stem cells - Neural_Conversion_day3

tag: shRNA


title: NC3_shRNA_RNA-Seq_rep3


title: NC3_shRNA_RNA-Seq_rep1


title: Hs746T_4h_unb_3

value: Gastric cancer cell line


title: Hs746T_4h_EGF_3

value: EGF


title: MKN1_24h_Tra+Afa_3


title: D3_mock_resting

value: CD4+ T cell


title: NC3_ctrl_RNA-Seq_rep3


title: D2_latent_activated

value: model of HIV latency


title: MKN1_24h_Afa_3

value: Afa


title: MKN1_24h_Cet_3


title: MKN1_24h_EGF+Cet_3


title: D2_latent_resting


title: NC3_ctrl_RNA-Seq_rep2


title: Hs746T_24h_EGF_3


title: D3_latent_activated

value: activated


title: NC3_ctrl_RNA-Seq_rep1


title: MKN1_24h_Tra_3


title: MKN1_24h_unb_3


title: D2_mock_activated


title: Hs746T_4h_Tra+Afa_3


title: MKN1_24h_EGF_3


title: D2_mock_resting


title: D1_latent_activated


title: MKN1_4h_Tra+Afa_3


title: MKN1_4h_Afa_3


title: hESC_shRNA_RNA-Seq_rep2

source_name: hESC

value: hESC


title: MKN1_4h_Tra_3


title: D1_latent_resting

value: resting


title: hESC_shRNA_RNA-Seq_rep1


title: MKN1_4h_Cet_3


title: hESC_ctrl_RNA-Seq_rep3


title: MKN1_4h_EGF_3


title: MKN1_4h_EGF+Cet_3


title: MKN1_4h_unb_3


title: D1_mock_resting


title: N87_24h_Tra+Afa_2


title: hESC_ctrl_RNA-Seq_rep2


title: N87_24h_Tra_2

value: Tra


title: N87_24h_Afa_2


title: N87_24h_unb_2


title: hESC_ctrl_RNA-Seq_rep1


title: hESC_O5_shRNA_RNA-Seq_rep3


title: N87_4h_Tra+Afa_2


title: NC3_shRNA_ATAC-Seq_rep3

description: Accessible Chromatin

library_source: genomic

data_processing:
Raw reads were processed using the ENCODE pipeline  (encodeproject.org/atac-seq/)
For visualization, bigwig files generated by the ENCODE pipeline that represent the p value signal of pooled true replicates were loaded into Integrated Genomics Viewer (IGV).
ATAC peaks identified by the ENCODE analysis pipeline were selected using the most restrictive approach (0.05 IDR of pseudo replicates).
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig and NarrowPeak

molecule: genomic DNA

extract_protocol:
ATAC-seq was performed using the OMNI-ATAC protocol
Briefly, cells were dissociated using Accutase, and 50,000 cells were subjected to the tagmentation reaction. Cells were first washed in resuspension buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, and 3 mM MgCl2 in water), following which nuclei were isolated in 1 ml lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin in water) on ice for three minutes. Nuclei were rinsed once in wash buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and tagmentation was carried out using 2.5ul Tn5 transposase (Illumina 15027865) for 30 mins. Following tagmentation, DNA was purified using the Zymo DNA Clean and Concentrator kit.
Libraries were prepared by PCR using Q5 High Fidelity DNA polymerase (NEB) polymerase and using primers carrying Illumina Nextera i7 barcodes. First, gap filling was performed at 72°C for 5mins followed by five cycles of 98°C, 20secs, 63°C, 30secs, and 720C 1min. After initial amplification, tubes were held on ice, while quantitative PCR was run on 1l of the pre-amplified library to determine additional number of cycles needed. Libraries were sequenced on HiSeq2500 using PE50.


title: sh_SKA3_1

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

country: China

institute: Shanxi Medical University

data_processing:
Basecalls performed using Perl package developed by Novogene.
Contaminant reads were filtered from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads.
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default. The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Then coding potential analysis was performed with CNCI, CPC, Pfam-sca, and phyloCSF, Transcripts predicted with coding potential by either/all of the four tools above were filtered out, and those without coding potential were candidate set of lncRNAs. Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

source_name: sh_SKA3 transfected cells

growth_protocol: The LSCC cell line TU-177 obtained from the China Center for Type Culture Collection was cultured in DMEM (Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS) (BI, Cromwell, CT). The cells were maintained at 37 °C in a humidified chamber supplied with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TU-177 cells were transduced with lentiviruses carrying shRNA targeting SKA3 or negative control, puromycin was added to screen positive cells 48 hours after transduction, puromycin-resistant cells were harvested for RNA sequencing.

value: laryngeal squamous cell carcinoma cell

tag: materials

value: cultured cells

tag: transfection


title: sh_SKA3_2


title: N87_4h_Afa_2


title: NC3_shRNA_ATAC-Seq_rep2

description: Accessible Chromatin


title: sh_NC_2

source_name: Negative Control transfected cells

value: negative control


title: N87_4h_Tra_2


title: N87_4h_unb_2


title: sh_NC_1


title: NC3_shRNA_ATAC-Seq_rep1

description: Accessible Chromatin


title: D1_mock_activated

value: mock-infected


title: MKN7_24h_Afa_2


title: MKN7_24h_Tra_2


title: MKN7_4h_Tra+Afa_2

value: Tra+Afa


title: MKN7_24h_unb_2


title: NC3_ctrl_ATAC-Seq_rep2

description: Accessible Chromatin

value: Control


title: MKN7_4h_Tra_2


title: NC3_ctrl_ATAC-Seq_rep1

description: Accessible Chromatin


title: MKN7_4h_unb_2

value: untreated


title: MKN7_4h_Afa_2


title: Hs746T_24h_Tra+Afa_2


title: Hs746T_24h_Afa_2


title: hESC_shRNA_ATAC-Seq_rep2

description: Accessible Chromatin


title: Hs746T_24h_Tra_2


title: Hs746T_24h_EGF+Cet_2

value: EGF+Cet


title: Hs746T_24h_EGF_2

value: Gastric cancer cell line


title: hESC_shRNA_ATAC-Seq_rep1

description: Accessible Chromatin


title: hESC_ctrl_ATAC-Seq_rep3

description: Accessible Chromatin


title: Hs746T_24h_unb_2


title: Hs746T_4h_Tra+Afa_2


title: MKN7_24h_Tra+Afa_2


title: Hs746T_4h_Afa_2


title: Hs746T_4h_Tra_2


title: hESC_ctrl_ATAC-Seq_rep1

description: Accessible Chromatin


title: hESC_ctrl_ATAC-Seq_rep2

description: Accessible Chromatin


title: NC3_ctrl_ATAC-Seq_rep3

description: Accessible Chromatin

value: stem cells - Neural_Conversion_day3


title: Hs746T_4h_EGF+Cet_2


title: Patient5_PrimaryTumour

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform as 50bp single-end data.
Raw sequence reads had the first 9 base pairs clipped off the 5' end to remove the 9N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.4, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 9). The remaining sequences were then aligned to the GRC38 genome in single-end mode using Bismark (v0.22.1; parameters: --pbat). Methylation calls were extracted after duplicate sequences had been excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

source_name: Primary tumour

extract_protocol:
Sample collection protocol: Tissue specimens of colorectal primary tumor, normal adjacent tissue (NAT) and at least one lymph node metastasis (LNM) were obtained by surgery, fixed in tamponed formaline and paraffin-embedded.
DNA extraction was performed using QIAamp DNA FFPE Tissue Kit (Qiagen, Germantown, MD, USA), after manual microdissection.
Bisulfite treated DNA was ligated with adaptors by using random probing method. Library amplification using indexed primers and library purification. Purified library DNA was eluted in 12 μl of water.

value: Primary tumour

tag: diagnosis

value: Colorectal cancer

tag: patient


title: Hs746T_4h_unb_2


title: MKN1_24h_Tra+Afa_2


title: hESC_O5_shRNA_ATAC-Seq_rep3

description: Accessible Chromatin


title: Hs746T_4h_EGF_2

value: EGF


title: Patient5_NormalAdjacentTissue

source_name: Normal adjacent tissue

value: Normal adjacent tissue

tag: age


title: MKN1_24h_Afa_2

value: Afa


title: MKN1_24h_Cet_2

value: Cet


title: MKN1_24h_Tra_2

value: Tra


title: Hs746T_4h_Cet_2


title: Patient4_PrimaryTumour


title: MKN1_24h_EGF+Cet_2


title: Patient5_LymphNodeMetastasis

source_name: Lymph node metastasis

value: Lymph node metastasis


title: MKN1_24h_EGF_2


title: Patient4_NormalAdjacentTissue


title: MKN1_4h_Tra+Afa_2


title: Hs746T_24h_Cet_2


title: Patient4_LymphNodeMetastasis


title: MKN1_24h_unb_2


title: MKN1_4h_Afa_2


title: Patient3_PrimaryTumour


title: MKN1_4h_Tra_2


title: MKN1_4h_Cet_2


title: Patient3_NormalAdjacentTissue


title: MKN1_4h_EGF+Cet_2


title: MKN1_4h_EGF_2


title: Patient3_LymphNodeMetastasis


title: MKN1_4h_unb_2


title: N87_24h_Afa_1


title: N87_24h_Tra+Afa_1


title: Patient2_PrimaryTumour


title: Patient2_NormalAdjacentTissue


title: N87_24h_Tra_1


title: N87_4h_Tra+Afa_1


title: N87_24h_unb_1


title: Patient2_LymphNodeMetastasis


title: N87_4h_Afa_1


title: N87_4h_Tra_1


title: Patient1_PrimaryTumour


title: MKN7_24h_Afa_1


title: MKN7_24h_Tra_1


title: MKN7_24h_unb_1


title: Patient1_LymphNodeMetastasis


title: MKN7_4h_Tra+Afa_1


title: MKN7_4h_Afa_1


title: M_7R2

city: Pretoria

first: Teresia

middle: Nyambura

last: Macharia

state: Gauteng

address: cnr Lynnwood Road and Roper Street

department: Biochemistry, Genetics and Microbiology

country: South Africa

institute: University of Pretoria

description:
Treated  7 day post infection
M_7R3

data_processing:
FASTQC package was used to perform quality analysis of sequenced reads
Trimmomatic v 0.36 was used to trim and remove reads containing adapter and low quality reads
The paired clean reads were mapped onto the genome  (v4.03) using histat2 v2.1.0 software. Subsequent re-mapping was done by progressively trimming at the 3'end and re-mapped to the genome until a match was found
FeatureCounts package was used to perform raw-read counts in the R enviroment
The read counts were then used for differential analysis using edgeR package. The expression profiles of 3 and 7 dpi were compared to the mock-inoculated samples.False discovery rate (0.05) and log2 fold change ≥ 1 or ≤ -1 were used as cut-off values to detemine the up and down-regulated genes
Genome_build: Solanum tuberosum genome  (v4.03)
Supplementary_files_format_and_content: xls Files with False discovery rate  and log2 fold change values for  differentially expressed genes at  3 and 7 dpi and input read file with the counts provided to histat software, featureCounts and edgeR package

organism: Solanum tuberosum

source_name: Roots

growth_protocol: Potato plants were grown under green house conditions and inoculated with 1000 Infective stages of M.javanica

extract_protocol:
Total RNA for individual time course and replicate was extracted using TiaGen extraction kit. Libraries were constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: whole roots tissues were sampled at 0, 3 and 7 days post infection. The roots were washed with sterilized water, brifiely dried with a paper towel. The samples were immediately flash frozen in liquid nitrogen and stored at -80 °C until further use.

tag: cultivar

value: Mondial

tag: infection

value: Melodoigyne javanica

tag: tissue

value: Roots

value: 7 dpi


title: M_7R1

description:
Treated 7 day post infection
M_7R2


title: M_3R2

description:
Treated 3 day post infection
M_3R3

value: 3 dpi


title: MKN7_4h_Tra_1

tag: cell type


title: MKN7_4h_unb_1

value: untreated


title: PDS_rep3

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

institute: Institut Imagine

data_processing:
Mapping with STAR v2.7 with the ENCODE processing pipeline standard settings for RNA-seq data
Deduplication with Picard 1.9.2 MarkDuplicates (AS=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true)
Sort with samtools 1.4 sort (-n)
Assign to features using featureCounts 1.5.0 (-p -F GTF; GENCODE-annotated genes )
Genome_build: Human v37 (hg19)
Supplementary_files_format_and_content: Tab-delimited table of raw read counts for GENCODE genes and for each sample
Supplementary_files_format_and_content: Tab-delimited table with the layout for processing

source_name: Fibrosarcoma

growth_protocol: HT1080-ST fibrosarcoma cells were cultured in monolayers in Dulbecco’s Modified Essential Medium (DMEM) medium (10% SVF)

extract_protocol:
Cells were collected for RNA extraction and processed using the miRNeasy Mini Kit (Qiagen, #217004) according to the manufacturer’s guidelines. RNA concentration and purity were assessed using NanoDrop equipment (NanoDrop Technologies Inc.) and size profiles and integrity were analyzed on a 2100 TapeStation (Agilent, RNA ScreenTape).
Strand specific library preparation were performed using the TruSeq Stranded Total RNA kit (Illumina) following manufacturer’s instructions.

treatment_protocol: G-quadruplex ligand treatment was initiated by replacing culture media with fresh media containing 10 μM final concentration of either PhenDC3, PhenDC6, Pyridostatin or Bisquinolinium control compound (stock in DMSO; 3 culture plates each), or DMSO only (3 culture plates).

tag: treatment

value: PDS

value: Fibrosarcoma

tag: status


title: PhenDC6_rep3

tag: time point


title: PhenDC3_rep3

tag: cell line


title: N87_4h_unb_1

value: Gastric cancer cell line

tag: time


title: BisQn_rep3

value: BisQn

value: Control


title: Hs746T_24h_Tra+Afa_1

value: Tra+Afa


title: M_0R2

description:
Mock-inoculated 0 day post infection
M_0R3

value: mock

value: 0 dpi


title: DMSO_rep3

value: DMSO


title: Hs746T_24h_Afa_1

value: Afa


title: M_3R1

description:
Treated 3 day post infection
M_3R1


title: MKN7_24h_Tra+Afa_1


title: Patient1_NormalAdjacentTissue

value: Normal adjacent tissue

value: Colorectal cancer


title: Untreated_rep3

value: Untreated


title: FK

type: genomic

city: Bristol

first: Keith

middle: William

last: Brown

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

institute: University of Bristol

description:
Processed data shows the ratio between microarray hybridisation signal from input total genomic DNA (Cy3 labelled) and methylated DNA purified by MCIP (methyl CpG immunoprecipitation) (Cy5 labelled).
36250002

hyb_protocol: The labeled MCIP and input DNAs were co-hybridized to the array for 16 - 20 hours (Nimblegen Inc).

scan_protocol: Nimblegen Inc.

data_processing:
NimbleScan
Scaled log2 ratio between MCIP DNA signal and input DNA signal

source_name: Input DNA from FK

label_protocol: 1.2 to 1.4 micrograms of DNA was labelled using Klenow fragment-catalyzed primer extension using Cy dye coupled 9mer primers (Nimblegen Inc).

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from Wilms tumor cell lines with a DNeasy kit (Qiagen). Human fetal kidney genomic DNA was obtained from BioChain. Input DNA was total purified genomic DNA. MCIP DNA was the methylated fraction of genomic DNA, purified using Methyl CpG Immunoprecipitation (MCIP) with recombinant methyl-binding protein-Fc fusion as described by Gedhard et al (2006) Cancer Res. 66 (12): 6118-28 and Szemes et al (2013) Hum. Mol. Genet. 22(1):74-83.

value: Fetal Kidney

tag: tissue type

value: Human fetal tissue

tag: passage number

value: not applicable

source_name: MCIP DNA from FK


title: Hs746T_24h_Tra_1

tag: treat

value: Tra


title: PhenDC6_rep2


title: Hs746T_24h_Cet_1

value: Cet


city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

description: Gene expression Data from Mouse Midbrain, Fibril injected side, 90dpi, rep6

hyb_protocol: cDNA was hybridized onto Affymetrix Mouse Gene 2.0 ST Arrays and the Affymetrix GeneChip Hybridization GeneChip® Expression Wash, Stain and Scan Kit was used.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) for images and intensities.

data_processing: The data was pre-processed using Partek GS software and further processed using R/bioconductor and GC-RMA with default parameters.

label_protocol: The fragmented cDNA was labelled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labelling Reagent that is covalently linked to biotin; 5.5 μg of single-stranded cDNA are required for fragmentation and labelling, then 3.5 mg of labeled DNA + hybridization controls were injected into an Affymetrix cartridge

extract_protocol: For RNA extraction the Qiagen RNEasy Universal Kit (Qiagen, # 73404)

treatment_protocol: 10µg of PFFs, or respective PBS solution (control mice)  were administered, in volumes of 2 µl, within the right dorsal striatum at the following relative-to-bregma coordinates: anterior +0.5 mm, lateral +2.1 mm; depth +3.2 mm.

tag: strain

value: Mouse Midbrain

value: Fibrils


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 90dpi, rep5


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 90dpi, rep1


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 90dpi, rep2


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 90dpi, rep4


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 90dpi, rep6


title: PDS_rep2

value: PDS

value: Fibrosarcoma


title: 17-94 p36

description:
Processed data shows the ratio between microarray hybridisation signal from methylated DNA purified by MCIP (methyl CpG immunoprecipitation) (Cy5 labelled) and input total genomic DNA (Cy3 labelled).
36248402

source_name: Input DNA from 17-94

growth_protocol: DME + 10% fetal bovine serum

value: Wilms tumour

value: 17-94 cell line

source_name: MCIP DNA from 17-94


title: M_0R1

description:
Mock-inoculated 0 day post infection
M_0R2

value: Mondial

value: mock

value: Roots

value: 0 dpi


title: PhenDC3_rep2


title: Wit49 p78

description:
Processed data shows the ratio between microarray hybridisation signal from input total genomic DNA (Cy3 labelled) and methylated DNA purified by MCIP (methyl CpG immunoprecipitation) (Cy5 labelled).
36248602

source_name: Input DNA from Wit49

value: Wit49 cell line

source_name: MCIP DNA from Wit49


title: 6752 3pUTR3

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

description:
6752
HilD overexpressing

data_processing:
Fastq reads were trimmed of adapter using custom script
Fastx toolkit was used for quality trimming and filtering
Reads were mapped to SL1344 genome (NC_016810.1) using Bowtie2
Reads mapping to genes were counted using htseq-count
Data normalization and differential gene expression were performed using DESeq2
Genome_build: NC_016810.1
Supplementary_files_format_and_content: tab delimited text file of deseq2 normalized read counts.

organism: Salmonella enterica

source_name: cells

growth_protocol: Liquid cultures were grown in LB-Miller broth (10 g/L salt) and were incubated at 37°C with shaking (225 rpm).

extract_protocol:
RNA was extracted from bacteria using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad)
Total RNA was depleted of ribosomal RNA using RiboZero Bacterial rRNA depletion kit  followed by library generation using Illumina TruSeq Stranded mRNA Library Preparation kit.

tag: genotype/variation

value: HilD overexpressing


title: 6750 WT3

description:
6750
Wildtype

value: wild type


title: DMSO_rep2

value: DMSO

value: Control


title: Hs746T_4h_Tra+Afa_1

value: Gastric cancer cell line

value: Tra+Afa


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 90dpi, rep5

value: Mouse Midbrain


title: Hs746T_24h_EGF_1

value: EGF


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 90dpi, rep3

value: Fibrils


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 90dpi, rep3


title: Hs746T_24h_EGF+Cet_1

value: EGF+Cet


title: 6748 3pUTR1

description:
6748
HilD overexpressing


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 90dpi, rep2


title: 6746 WT2

description:
6746
Wildtype


title: Hs746T_4h_Afa_1

value: Afa


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 90dpi, rep1


title: BisQn_rep2

value: BisQn

value: Fibrosarcoma


title: PhenDC6_rep1


title: Hs746T_4h_Tra_1

value: Tra


title: Hs746T_4h_Cet_1

value: Cet


title: 6739 3pUTR2

description:
6739
HilD overexpressing


title: PDS_rep1

value: PDS


title: Hs746T_24h_unb_1

value: untreated


title: PhenDC3_rep1


title: Hs746T_4h_EGF+Cet_1


title: BisQn_rep1


description: Gene expression Data from Mouse Midbrain, PBS injected side, 90dpi, rep5

value: PBS


description: Gene expression Data from Mouse Midbrain, PBS injected side, 90dpi, rep6


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 90dpi, rep4


description: Gene expression Data from Mouse Midbrain, PBS injected side, 90dpi, rep4


title: Hs746T_4h_EGF_1


title: Untreated_rep2

value: Untreated


title: DMSO_rep1

value: DMSO


description: Gene expression Data from Mouse Midbrain, PBS injected side, 90dpi, rep3


title: 6741 WT1

description:
6741
Wildtype

value: wild type


title: MKN1_24h_Tra+Afa_1

value: Gastric cancer cell line


title: Untreated_rep1

value: Control


title: K171R_RUNX3_IP_2 (ChIP-seq)

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

description:
RUNX3 bound DNA from K171R SNU484 cells [rep2]
MACS_K171R_2_peaks.bed

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.12, and then aligned to Homo sapiens reference genome (GRCh38) using Bowtie2 v2.2.6 with default parameters.
After removing duplicate reads, peak calling was performed using MACS2 v2.1.1 for each pair of ChIP and Input DNA samples. DiffBind v2.6.5 was used to identify consensus peaks which are the peaks consistently detected in at least two pairs of samples among the total 6 pairs of samples and count the number of reads mapped onto these consensus peaks for each of the 6 ChIP samples.
The number of reads were converted to counts per million (CPM) based on the library size of each ChIP sample; and the CPM values were converted to log2-CPM values after adding one to the CPM values (MATLAB R2016a).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files including peaks called by MACS2 and a tab-delimited text file including log2-CPM values for each ChIP sample

source_name: SNU484 cell line

growth_protocol: SNU484 cells were passaged in our laboratory according to Korean Cell Line Bank (KCLB, Seoul, Korea) protocol.

extract_protocol:
ChIP experiment was performed using iDeal ChIP-seq kit for Transcription Factors (Diagenode SA, Belgium). Briefly, cells were fixed for 15 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and chromatin was sonicated in the mixture of shearing buffer and protease inhibitor cocktail to an average size of 220 bp. Sonicated chromatin was used for immunoprecipitation by incubation with anti-RUNX3 antibodies (ab11905, Abcam) (40 μg) overnight at 4ºC. One per cent of chromatin used for each ChIP reaction was kept as input DNA. Washed protein A-coated magnetic beads (120 μl) were added to each ChIP reaction and reactions were incubated 2 hr at 4ºC. The beads were then incubated in 400 μl elution buffer at 65ºC for 4 hr to elute immunoprecipitated materials.
Libraries were prepared using DNA SMART ChIP-Seq Kit (Clontech Laboratories, USA), according to the manufacturer’s protocol.

treatment_protocol: SNU484 cells were maintained and exposed to hypoxic conditions as described elsewhere.

value: SNU484 gastric carcinoma cell line

tag: genotype

value: RUNX3 K171R mutant

value: 8h after the exposure to hypoxia

tag: chip antibody

value: anti-RUNX3 (ab11905, Abcam)


title: MKN1_24h_Afa_1

value: Afa


title: K171R_RUNX3_IP_1 (ChIP-seq)

description:
RUNX3 bound DNA from K171R SNU484 cells [rep1]
MACS_K171R_1_peaks.bed


title: MKN1_24h_Tra_1


description: Gene expression Data from Mouse Midbrain, PBS injected side, 90dpi, rep2

value: Mouse Midbrain


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 13dpi, rep4

value: Fibrils


title: K171R_Input_2 (ChIP-seq)

description:
Input DNA from RUNX3 K171R mutant SNU484 cells [rep2]
MACS_K171R_2_peaks.bed


description: Gene expression Data from Mouse Midbrain, PBS injected side, 90dpi, rep1


title: MKN1_24h_Cet_1


title: K171R_Input_1 (ChIP-seq)

description:
Input DNA from RUNX3 K171R mutant SNU484 cells [rep1]
MACS_K171R_1_peaks.bed


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 13dpi, rep2


title: MKN1_24h_EGF+Cet_1

value: EGF+Cet


title: MKN1_24h_EGF_1

value: EGF


title: K129R_RUNX3_IP_2 (ChIP-seq)

description:
RUNX3 bound DNA from K129R SNU484 cells [rep2]
MACS_K129R_2_peaks.bed

value: RUNX3 K129R mutant


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 13dpi, rep1


title: Hs746T_4h_unb_1

value: untreated


title: K129R_RUNX3_IP_1 (ChIP-seq)

description:
RUNX3 bound DNA from K129R SNU484 cells [rep1]
MACS_K129R_1_peaks.bed


title: MKN1_24h_unb_1


title: K129R_Input_2 (ChIP-seq)

description:
Input DNA from RUNX3 K129R mutant SNU484 cells [rep2]
MACS_K129R_2_peaks.bed


title: MKN1_4h_Tra+Afa_1

value: Tra+Afa


description: Gene expression Data from Mouse Midbrain, PBS uninjected side, 13dpi, rep2

value: PBS


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 13dpi, rep6


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 13dpi, rep3


description: Gene expression Data from Mouse Midbrain, Fibril uninjected side, 13dpi, rep5


title: K129R_Input_1 (ChIP-seq)

description:
Input DNA from RUNX3 K129R mutant SNU484 cells [rep1]
MACS_K129R_1_peaks.bed


description: Gene expression Data from Mouse Midbrain, PBS uninjected side, 13dpi, rep4


title: MKN1_4h_Afa_1


description: Gene expression Data from Mouse Midbrain, PBS uninjected side, 13dpi, rep1


title: WT_RUNX3_IP_1 (ChIP-seq)

description:
RUNX3 bound DNA from WT SNU484 cells [rep1]
MACS_WT_1_peaks.bed


title: D1763-1

city: Christchurch

first: Andrew

last: Dodgshun

address: 2 Riccarton Avenue

department: Children’s Haematology/Oncology Centre

country: New Zealand

institute: Christchurch Hospital

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

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

data_processing: CHaMP package, R language

label: Cy3 and Cy5

source_name: Tumour tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using commercially available kits (differing by source of tissue) according to standard protocols

tag: age at diagnosis

tag: tissue source

value: FFPE

tag: histology

value: GBM

tag: primary (p) or recurrent (r)

value: R

tag: Sex

value: F


title: WT_RUNX3_IP_2 (ChIP-seq)

description:
RUNX3 bound DNA from WT SNU484 cells [rep2]
MACS_WT_2_peaks.bed

value: SNU484 gastric carcinoma cell line

value: wild type

tag: treatment


title: D1424

value: P


description: Gene expression Data from Mouse Midbrain, PBS uninjected side, 13dpi, rep6

tag: tissue


description: Gene expression Data from Mouse Midbrain, PBS uninjected side, 13dpi, rep5

tag: time point


title: MKN1_4h_Cet_1

tag: cell line

tag: cell type

value: Gastric cancer cell line

value: Cet


title: MKN1_4h_Tra_1

tag: time

value: Tra


title: D1121

value: M


title: MKN1_4h_EGF_1


description: Gene expression Data from Mouse Midbrain, PBS uninjected side, 13dpi, rep3

value: Mouse Midbrain


title: WT_Input_2 (ChIP-seq)

description:
Input DNA from WT SNU484 cells [rep2]
MACS_WT_2_peaks.bed

value: 8h after the exposure to hypoxia


title: D1122


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 13dpi, rep3

value: Fibrils


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 13dpi, rep6


title: D1423-1


title: VEH_3

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

data_processing:
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.36). Next, the reads were mapped to the Homo sapiens reference genome from Ensembl database and aligned using the STAR alignment tool (Version 2.5.3). After this, the read counts were generated from SUBREAD (Version 1.5.2) and featured counts were outputted for statistical analysis in R. Quality control and normalization was conducted in R using edgeR (Version 3.20.9).
Statistical Analysis and DEGs: Statistical analysis was conducted in R using limma (Version 3.34.9). Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >1.5 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: Bam count files and list of differentially expressed genes

source_name: mammary cell

growth_protocol: MCF-7 ESR1Y537S cells were seeded at a density of 1x106 cells on 10-cm plates and incubated in a 37 °C incubator for 48 hours. Next day, RNA was extracted from these cells and prepared for sequencing procedure.

extract_protocol:
* The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.
* The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a NovaSeq 6000

value: MCF-7 ESR1Y560

tag: agent

value: VEH


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 13dpi, rep2


title: VEH_2

value: MCF-7 ESR1Y559


title: D1410

value: FFPE


title: NZO_L2-CRD_62+63: Pancreatic_islets_HFD_39wk_CRD_2d_rep5

city: Nuthetal

first: Richard

last: Kehm

address: Arthur-Scheunert-Allee 114-116

department: Molecular Toxicology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep5
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
NZO_L2-CRD_62+63

hyb_protocol: Agilent Gene Expression Hybridization Kit was used according to manufacturer´s instructions. Approximately 600 ng of each cRNA was hybrized on 6x80K microarray at 65°C for 17 minutes using Agilent´s recommended hybridization chamber and oven. After hybridization, microarrays were washed twice, first with Agilent gene expression wash buffer 1 at room temperature for one minute and second with preheated (37°C) Wash Buffer 2 also for one minute.

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

data_processing: The scanned images were analyzed with Agilent´s Feature Extraction software version 11 to read and process TIFF files, using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: Pancreatic islets, HFD, 39wk + CRD, 2d

label_protocol: Low-input QuickAmp Labeling Kit (Agilent technologies) was used to genereate fluorescent complementary RNA (cRNA). CRNA was labelled with Cyanine 3-CTP (Cy3) and 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 manufacturer's instructions First strand synthesis was conducted by using oligo-dT primer or a mixture of radnom primer/oligo-dT primer. After second strand synthesis, in vitro transcription for cRNA synthesis was performed.

growth_protocol: Mice were housed in open cages of 4-5 animals at a controlled environment (20±2°C, 12/12 h light/dark cycle) with ad libitum access to diets and water.

extract_protocol: RNA extraction was performed by using RNeasy Mini Kit (Quiagen) according to manufacturer´s instructions. Subsequently, DNAase digestion was carried out with nuclease-free DNase (Qiagen), purified using the NucleoSpin RNA Clean-up Kit (Macherey-Nagel). RNA extracts underwent a quality control with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) using RNA 6000 Pico Kit for total RNA samples. Samples with a minimal RNA integrity number (RIN) of > 8.0 were included in microarray analysis.

treatment_protocol: Islet isolation from mice before and after 2 days of CRD feeding was performed as follows. After perfusion by injection of 3 ml Collagenase Type IV from Clostridium histolyticum diluted in Hank´s buffered salt solution (plus 25 mM HEPES, 0,5% BSA) into the common bile duct, the pancreas was digested in 2 ml of collagenase for 10-15 min at 37°C. After mechanical tissue disruption by using a 18G needle, islets were separated from exocrine tissue by manual selection in RPMI 1640 (plus 10% FCS, 2% L-Glutamine, 1% penicillin/streptomycin) and frozen at -80°C.

value: Pancreas

tag: gender

value: male

tag: age

value: 39 weeks + 2 days

value: NZO/HIBomDife

tag: feeding


title: D1805-2

value: GBM

value: R

value: F


title: P2B TCR

last: Seder

address: 40 Convent Dr

institute: Vaccine Research Center

description:
Pool 2 rep 2 (P2B)
P2B_filtered_contig_annotations.csv

data_processing:
Cell Ranger mkfastq used to convert Illumnia BCLs to FASTQ files
Cell Ranger Count used to generate count matrix from FASTQ files for both gene expression and hashtag libraries
Cellranger VDJ used to annotate TCRs from the TCR library
Raw feature matrix processed in R using the Seurat pipeline (v3.1) for gene expression and hashtag libraries, cell barcodes were demultiplexed using Seurat v3.1 HTODemux function.
TCR cell barcode pairs were matched to processed gene expression matrix
Genome_build: mm9
Supplementary_files_format_and_content: 10X output in the raw_feature_bc_matrix contains the three files below
Supplementary_files_format_and_content: raw feature count matrices  (mtx)
Supplementary_files_format_and_content: barcode information (barcodes.tsv)
Supplementary_files_format_and_content: feautre information (features.tsv)

source_name: Spleen

extract_protocol:
According to 10X genomics VDJ pipeline, V1
Gene Expression Library constructed according to 10X genomics VDJ pipeline protocl, V1 Rev. C
TCR library constructed according to 10X genomics pipeline protocol, V1 Rev. C
Hashtag library constructed according to 10X genomics pipeline protecol, V1 Rev. C
single cell RNA seq

treatment_protocol: Mice were vaccinated twice 2 weeks apart, and antigen specific CD8 T cells sorted by FACS from processed spleens

value: antigen specific CD8 T cells

tag: strain


title: D1423-2

value: P


title: VEH_1

value: MCF-7 ESR1Y558


title: P2A TCR

description:
Pool 2 rep 1 (P2A)
P2A_filtered_contig_annotations.csv


title: D1120

value: M


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 13dpi, rep5

value: Mouse Midbrain


title: NZO_L2-CRD_61: Pancreatic_islets_HFD_39wk_CRD_2d_rep4

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep4
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
NZO_L2-CRD_61


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 13dpi, rep4

value: Fibrils


title: NZO_L2-CRD_60: Pancreatic_islets_HFD_39wk_CRD_2d_rep3

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep3
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
NZO_L2-CRD_60


title: 4-OHT+SEL_3

growth_protocol: MCF-7 ESR1Y537S cells were seeded at a density of 1x106 cells on 10-cm plates and incubated in a 37 °C incubator for 24 hours. Next day, cells were treated with 10-7 M Selinexor in combination with 10-6 M 4-OHT for 24 hours and incubated in a 37 °C incubator. After 48 hours period, RNA was extracted from these cells and prepared for sequencing procedure.

value: MCF-7 ESR1Y557


title: P1B TCR

description:
Pool 1 rep 2 (P1B)
P1B_filtered_contig_annotations.csv


description: Gene expression Data from Mouse Midbrain, Fibril injected side, 13dpi, rep1


title: D1764


title: 4-OHT+SEL_2

value: MCF-7 ESR1Y556


title: D1244


title: P1A TCR

description:
Pool 1 rep 1 (P1A)
P1A_filtered_contig_annotations.csv


title: NZO_L2-CRD_57: Pancreatic_islets_HFD_39wk_CRD_2d_rep2

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep2
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
NZO_L2-CRD_57


title: NZO_L0-HFD_88+89: Pancreatic_islets_HFD_39wk_rep5

description:
Pancreatic_islets_HFD_39wk_rep5
Gene expression after 39 weeks of HFD feeding
NZO_L0-HFD_88+89

source_name: Pancreatic islets, HFD, 39wk

value: 39 weeks

value: 39 weeks of HFD feeding


title: 4-OHT+SEL_1

value: MCF-7 ESR1Y555


title: MKN1_4h_unb_1

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
fastq file generation by bcl2fastq2ConversionSoftwarev2.20 (Illumina)
raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file.
Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with default settings
Feature counts were determined using R package “Rsubread”.
Genome_build: hg38
Supplementary_files_format_and_content: Text file with raw counts

extract_protocol:
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher)
NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols

value: Gastric cancer cell line

tag: treat

value: untreated


title: NZO_L2-CRD_55+56: Pancreatic_islets_HFD_39wk_CRD_2d_rep1

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep1
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
NZO_L2-CRD_55+56

value: Pancreas

value: male

value: 39 weeks + 2 days

value: NZO/HIBomDife


description: Gene expression Data from Mouse Midbrain, PBS injected side, 13dpi, rep6

value: PBS


title: RCH6

tag: age at diagnosis

value: FFPE

value: GBM

value: P


title: RCH3

tag: tissue source

value: M


title: RCH4

tag: histology

value: F


title: RCH5

value: AA

tag: primary (p) or recurrent (r)


title: D1243

tag: Sex


title: P2B Hashtag

description:
Pool 2 rep 2 (P2B)
P2B_barcodes.tsv
P2B_features.tsv
P2B_matrix.mtx

value: antigen specific CD8 T cells


title: P2A Hashtag

description:
Pool 2 rep 1 (P2A)
P2A_barcodes.tsv
P2A_features.tsv
P2A_matrix.mtx


title: RCH2


title: 4-OHT_3

value: MCF-7 ESR1Y554


title: P1B Hashtag

description:
Pool 1 rep 2 (P1B)
P1B_barcodes.tsv
P1B_features.tsv
P1B_matrix.mtx


title: P1A Hashtag

description:
Pool 1 rep 1 (P1A)
P1A_barcodes.tsv
P1A_features.tsv
P1A_matrix.mtx


title: 4-OHT_2

value: MCF-7 ESR1Y553


title: SEL_3

growth_protocol: MCF-7 ESR1Y537S cells were seeded at a density of 1x106 cells on 10-cm plates and incubated in a 37 °C incubator for 24 hours. Next day, cells were treated with 10-7 M Selinexor for 24 hours and incubated in a 37 °C incubator. After 48 hours period, RNA was extracted from these cells and prepared for sequencing procedure.

value: MCF-7 ESR1Y551

value: SEL


title: RCH1

value: PNET/GBM


title: P2B Gene Expression


title: SEL_2

value: MCF-7 ESR1Y550


description: Gene expression Data from Mouse Midbrain, PBS injected side, 13dpi, rep2

value: Mouse Midbrain

tag: treatment


description: Gene expression Data from Mouse Midbrain, PBS injected side, 13dpi, rep3

tag: tissue


title: NZO_L0-HFD_56+57: Pancreatic_islets_HFD_39wk_rep3

description:
Pancreatic_islets_HFD_39wk_rep3
Gene expression after 39 weeks of HFD feeding
NZO_L0-HFD_56+57

value: Pancreas

value: male

value: 39 weeks

value: 39 weeks of HFD feeding


title: P2A Gene Expression


title: NZO_L0-HFD_54+55: Pancreatic_islets_HFD_39wk_rep2

description:
Pancreatic_islets_HFD_39wk_rep2
Gene expression after 39 weeks of HFD feeding
NZO_L0-HFD_54+55

value: NZO/HIBomDife


title: NZO_L0-HFD_20: Pancreatic_islets_HFD_39wk_rep1

description:
Pancreatic_islets_HFD_39wk_rep1
Gene expression after 39 weeks of HFD feeding
NZO_L0-HFD_20


title: 4-OHT_1

value: MCF-7 ESR1Y552


description: Gene expression Data from Mouse Midbrain, PBS injected side, 13dpi, rep4

value: PBS

tag: time point


description: Gene expression Data from Mouse Midbrain, PBS injected side, 13dpi, rep1


title: CD3 enriched T cells DONOR7_(miRNA-3_0)

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

description:
CD3 enriched T cells
miRNA expression profiling

hyb_protocol: Hybridization was performed according to the manufactorers' recommendations (GeneChip miRNA 3.0 arrays (Affymetrix, Santa Clara, CA).

scan_protocol: Scanning was performed according to the manufactorers' recommendations (GeneChip miRNA 3.0 arrays (Affymetrix, Santa Clara, CA).

data_processing: The data were extracted from the images, background corrected (RMA), quantile-normalized, summarized (median polish), and log2-transformed with Partek Genomic Suite (Partek Incorporated, St. Louis, MO, USA). Differentially expressed miRNAs were determined by Student´s t-test and p-values were corrected for multiple testing.

source_name: CD3 positive T cells

label_protocol: One μg of total RNA including miRNA from each sample was labeled with biotin using the FlashTag Biotin HSR Kit (Genisphere, Hatfield, PA).

extract_protocol: Total RNA was extracted with the miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: CD 3positive T-cells from five healthy donors were immunomagnetically purified from peripheral blood. T-PLL cells were FACS sorted from ten patients with T-PLL.

value: unknown


title: NZO_K2-CRD_58: Pancreatic_islets_HFD_18wk_CRD_2d_rep5

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep5
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
NZO_K2-CRD_58

source_name: Pancreatic islets, HFD, 18wk + CRD, 2d

value: 18 weeks + 2 days


title: CD3 enriched T cells DONOR6_(miRNA-3_0)


title: P1B Gene Expression

value: antigen specific CD8 T cells


title: P1A Gene Expression


title: PALB+SEL_3

growth_protocol: MCF-7 ESR1Y537S cells were seeded at a density of 1x106 cells on 10-cm plates and incubated in a 37 °C incubator for 24 hours. Next day, cells were treated with 10-7 M Selinexor in combination with 10-6 M Palbociclib for 24 hours and incubated in a 37 °C incubator. After 48 hours period, RNA was extracted from these cells and prepared for sequencing procedure.

tag: cell line

value: MCF-7 ESR1Y548

value: PALB+SEL


title: WT_Input_1 (ChIP-seq)

description:
Input DNA from WT SNU484 cells [rep1]
MACS_WT_1_peaks.bed

value: SNU484 gastric carcinoma cell line

tag: genotype

value: wild type

value: 8h after the exposure to hypoxia

tag: chip antibody


title: MKN1_4h_EGF+Cet_1

last: Geffers

address: Inhoffenstr. 7

tag: cell type

value: Gastric cancer cell line

tag: time

value: EGF+Cet


title: PALB+SEL_2

value: MCF-7 ESR1Y547

tag: agent


description: Gene expression Data from Mouse Midbrain, PBS injected side, 13dpi, rep5

value: Mouse Midbrain


title: CD3 enriched T cells DONOR5_(miRNA-3_0)

tag: gender


title: CD3 enriched T cells DONOR1_(miRNA-3_0)


title: NZO_K2-CRD_56: Pancreatic_islets_HFD_18wk_CRD_2d_rep3

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep3
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
NZO_K2-CRD_56

value: Pancreas

value: male

tag: age

tag: strain

tag: feeding


title: NZO_L0-HFD_58+59: Pancreatic_islets_HFD_39wk_rep4

description:
Pancreatic_islets_HFD_39wk_rep4
Gene expression after 39 weeks of HFD feeding
NZO_L0-HFD_58+59

value: 39 weeks

value: NZO/HIBomDife

value: 39 weeks of HFD feeding


title: NZO_K2-CRD_57: Pancreatic_islets_HFD_18wk_CRD_2d_rep4

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep4
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
NZO_K2-CRD_57


title: Mouse Placenta E12.5

city: San Francisco

first: Bryan

last: Marsh

address: 35 Medical Center Way, RMB 912E, None

institute: University of California, San Francisco

description: cell barcodes appended with "_3"

data_processing:
Processing of raw sequencing to a counts matrix was performed using CellRanger v3.0.2 using default settings. This includes alignment to the mm10 genome (using a premRNA GTF file generated according to 10x Genomics instructions) using STAR (v2.6). Processing of counts matrix was performed in Seurat v3.1.3. Raw counts were normalized, scaled, and batch corretion and integration performed using Seurat. Additional details can be found in the manuscript.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of normalized and batch corrected gene expression.
Supplementary_files_format_and_content: AllStages_AllNuclei_clusters.txt contains annotations of the cellular barcodes in AllStages_AllNuclei_datamatrix.txt to computationally identified clusters.
Supplementary_files_format_and_content: AllStages_TrophoblastNuclei_clusters.txt contains annotations of the cellular barcodes in AllStages_TrophoblastNuclei_datamatrix.txt to computationally identified clusters.

source_name: Nuclei Isolated from Placental Tissue

extract_protocol:
Nuclei extractions using a modification of the Nuclei EZ kit protocol followed by FACS cleanup and collection using 10x Genomics Single Cell 3' v3 Library. Additional details included in the manuscript.
10x Genomics Single Cell 3' v3 Protocol

tag: cell types

value: Nuclei from placental tissue


title: PALB+SEL_1

value: MCF-7 ESR1Y546


title: NZO_K2-CRD_52+53: Pancreatic_islets_HFD_18wk_CRD_2d_rep2

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep2
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
NZO_K2-CRD_52+53

value: 18 weeks + 2 days


title: Mouse Placenta E10.5

description: cell barcodes appended with "_2"


title: PALB_3

growth_protocol: MCF-7 ESR1Y537S cells were seeded at a density of 1x106 cells on 10-cm plates and incubated in a 37 °C incubator for 24 hours. Next day, cells were treated with 10-6 M Palbociclib for 24 hours and incubated in a 37 °C incubator. After 48 hours period, RNA was extracted from these cells and prepared for sequencing procedure.

value: MCF-7 ESR1Y545

value: PALB


title: PALB_2

value: MCF-7 ESR1Y544


title: ISWI RNAi rep 4

city: Philadelphia

first: Matthew

middle: S

last: Kayser

state: PA

address: 320 Clinical Research Building

institute: University of Pennsylvania

data_processing:
RNA-seq reads were mapped to the Drosophila melanogaster assembly BDGP6 pre-indexed with transcript models from Ensembl 87 using STAR 2.5.0b with default parameters except --alignIntronMax set to 10,000. Aligned reads were assigned to gene models using the summarizeOverlaps function of the GenomicRanges R package.
Reads per kilobase per million (RPKMs) were calculated with a slight modification, whereby only reads assigned to annotated protein-coding genes were used in the denominator, to minimize batch variability due to different amounts of contaminant ribosomal RNA.
Differential expression was determined using the DESeq2 package. The annotated genes exhibiting an adjusted P-value > 0.1 were considered to be differentially expressed compared to control. Visualization of differentially expressed genes was done using R-package ggplot2 v3.2.0.
Genome_build: BDGP6
Supplementary_files_format_and_content: tab-delimited files

organism: Drosophila melanogaster

source_name: mid-3rd larval instar brain

extract_protocol:
40 brains per sample at the mid-3rd instar stage were dissected in cold AHL (108 mM NaCl, 5 mM KCl, 2 mM CaCl2, 8.2 mM MgCl2, 4mM NaHCO3, 1 mM NaH2PO4-H2O, 5 mM trehalose, 10 mM sucrose, 5 mM HEPES). Three biological replicates for the control group and four for the experimental, each with 40 brains, were dissected. Brains were transferred to 1 mL of Trizol and incubated for 5 minutes at room temperature (RT). 0.2 mL of chloroform was added and samples were inverted. Samples were incubated 2-3 minutes at RT, then centrifuged at 12,000g for 15 minutes at 4oC. Genomic DNA was removed using a gDNA eliminator column (RNeasy Plus Micro Kit, Qiagen). RNA was then extracted using the RNeasy MinElute Cleanup Kit (Qiagen).
Sequence libraries for each sample were synthesized using the NEBNext Ultra II Directional RNA kit following supplier recommendations and were sequenced on Illumina HiSeq-4000 sequencer as single reads of 100 base reads following Illumina’s instructions.

value: elav-GAL4>UAS-ISWI RNAi

value: mid-3rd instar larval central brain + ventral nerve cord

value: 4 days post-egg lay at 25 C


title: Mouse Placenta E14.5

description: cell barcodes appended with "_4"


title: Mouse Placenta E9.5

description: cell barcodes appended with "_1"

value: 9.5 dpc


title: PALB_1

value: MCF-7 ESR1Y543


title: FULV+SEL_3

growth_protocol: MCF-7 ESR1Y537S cells were seeded at a density of 1x106 cells on 10-cm plates and incubated in a 37 °C incubator for 24 hours. Next day, cells were treated with 10-7 M Selinexor in combination with 10-6 M Fulvestrant for 24 hours and incubated in a 37 °C incubator. After 48 hours period, RNA was extracted from these cells and prepared for sequencing procedure.

value: MCF-7 ESR1Y542

value: FULV+SEL


title: ISWI RNAi rep 3


title: M_florum RNAseq - rep 3B

city: Sherbrooke

first: Sebastien

last: Rodrigue

address: 2500 boul. de l'Université

department: Biologie

institute: Université de Sherbrooke

description: Strand-specific RNA-Seq protocol

data_processing:
RNA-Seq and 5'-RACE: Reads were quality trimmed using Trimmomatic version 0.32 and aligned on the M. florum L1 genome (NC_006055.1) in a strand-specific manner using Bowtie 2 version 2.3.3.1. Reads with a MAPQ below 10 were discarded using samtools version 1.5.
RNA-Seq: FPKM values were calculated for each M. florum L1 annotated gene (RAST annotation, see Baby et al 2018) using the GenomicAlignments R package version 1.10.1.
5'-RACE: Reads were clipped to retain only a single base at their 5’ extremity, corresponding to putative 5'-end of transcripts. The number of millions of mapped reads (RSPM) was calculated at each genomic position using Bedtools genomecov version 2.27.1. Peaks with a RSPM signal equal or higher than the average plus one standard deviation single base signal calculated over the entire genome were considered significant and kept for further analysis. Significant peaks located at 10 bp or less of each other were merged to retain only the peak with the highest associated RSPM signal, corresponding to a putative TSS.
Genome_build: NC_006055.1
Supplementary_files_format_and_content: RNA-Seq bigWig (.bw) data files contain strand-specific 1 bp resolution genome coverage tracks generated using Bedtools genomecov version 2.27.1 from MAPQ filtered alignments.
Supplementary_files_format_and_content: 5'-RACE bigWig (.bw) data files contain strand-specific 1 bp resolution genome coverage tracks generated using Bedtools genomecov version 2.27.1 from 5'-end processed alignments.
Supplementary_files_format_and_content: The tab-delimited text file (.tsv) contains raw RNA-Seq read counts calculated by the GenomicAlignments software for each M. florum protein coding gene, as well as corresponding FPKM values.
Supplementary_files_format_and_content: The bed format file (.bed) contains coordinates of all putative TSSs identified by 5'-RACE, along with their corresponding peak height (raw read count) and RSPM values. TSSs are coloured according to their orientation.

source_name: Bacterial culture

growth_protocol: M. florum cells were grown in ATCC 1161 medium at 34°C with shaking.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research, R2052) according to the manufacturer's specifications.
RNA-Seq: ~300 ng of total RNA was fragmented at 95°C by Mg2+ catalyzed hydrolysis, and then purified using the RNA Clean & Concentrator-5 kit (Zymo Research). RNA molecules were dephosphorylated using Antarctic Phosphatase (NEB), and purified again using the RNA Clean & Concentrator-5 kit. The 3' sequencing adaptor was ligated using the T4 RNA ligase (Enzymatics), and RNA fragments were purified using Agencourt RNAclean XP SPRI beads (Beckman Coulter). RNA fragments were phosphorylated using T4 Polynucleotide Kinase (Enzymatics), purified again using Agencourt RNAclean XP SPRI beads, and the 5' sequencing adaptor was ligated using the T4 RNA ligase. RNA fragments were purified using Agencourt RNAclean XP SPRI beads, and then reverse transcribed to cDNA using the M-MuLV Reverse Transcriptase (Enzymatics). cDNA was purified using Agencourt AMPure XP SPRI beads, amplified by real-time PCR using the VeraSeq 2.0 DNA polymerase (Enzymatics), and purified again using Agencourt AMPure XP SPRI beads. DNA molecules corresponding to rRNA transcripts were depleted using the Duplex-specific nuclease (DSN, Evrogen). Final library size, quality, and concentration was evaluated using a 2100 Bioanalyzer instrument (Agilent Technologies). RNA-Seq libraries were sequenced on a HiSeq 2000 Illumina instrument using 2x50 bp paired-end sequencing. For more details, see Carraro et al 2014.
5'-RACE: ~2 µg of total RNA was fragmented at 75°C by Mg2+ catalyzed hydrolysis, and then purified using the RNA Clean & Concentrator-5 kit (Zymo Research). The 3' sequencing adaptor was ligated using the T4 RNA ligase (Enzymatics), and RNA molecules were purified again using the RNA Clean & Concentrator-5 kit. Monophosphorylated RNA fragments were depleted using the XRN-1 nuclease (NEB), and the remaining RNA molecules were purified with the RNA Clean & Concentrator-5 kit. RNA fragments were treated with the RppH Pyrophosphohydrolase (NEB) to remove a pyrophosphate from the 5'-end of triphosphorylated RNA, and purified once again with the RNA Clean & Concentrator-5 kit. The 5' sequencing adaptor was finally ligated using the T4 RNA ligase, RNA fragments were purified using Agencourt RNAclean XP SPRI beads (Beckman Coulter), and reverse transcribed using the M-MuLV Reverse Transcriptase (Enzymatics). cDNA was purified using Agencourt AMPure XP SPRI beads, amplified by real-time PCR using the VeraSeq 2.0 DNA polymerase (Enzymatics), and purified again using Agencourt AMPure XP SPRI beads. Final library size, quality, and concentration was evaluated using a 2100 Bioanalyzer instrument (Agilent Technologies). The 5'-RACE library was sequenced on an Illumina Genome Analyzer IIx instrument using 40 bp single-end sequencing. For more details, see Carraro et al 2014.

value: bacteria

tag: growth phase

value: exponential

tag: growth medium

value: ATCC 1161

tag: growth protocol

value: Steady-state culture grown in a chemostat system set at 34°C

tag: biological replicate


title: Sorted T cells 8_A_(miRNA-3_0)

description:
Sorted T cells
miRNA expression profiling

source_name: Sorted T-PLL cells

value: m


title: FULV+SEL_2

value: MCF-7 ESR1Y541


title: NZO_K2-CRD_27: Pancreatic_islets_HFD_18wk_CRD_2d_rep1

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep1
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
NZO_K2-CRD_27

tag: tissue

value: Pancreas

value: male

value: 18 weeks + 2 days

value: NZO/HIBomDife


title: NZO_K0-HFD_33+34: Pancreatic_islets_HFD_18wk_rep5

description:
Pancreatic_islets_HFD_18wk_rep5
Gene expression after 18 weeks of HFD feeding
NZO_K0-HFD_33+34

source_name: Pancreatic islets, HFD, 18wk

value: 18 weeks

value: 18 weeks of HFD feeding


title: ISWI RNAi rep 2

value: elav-GAL4>UAS-ISWI RNAi

value: mid-3rd instar larval central brain + ventral nerve cord

value: 4 days post-egg lay at 25 C


title: NZO_K0-HFD_26: Pancreatic_islets_HFD_18wk_rep1

description:
Pancreatic_islets_HFD_18wk_rep1
Gene expression after 18 weeks of HFD feeding
NZO_K0-HFD_26


title: Sorted T cells 11_1_(miRNA-3_0)

value: f


title: Sorted T cells 7_(miRNA-3_0)


title: NZO_K0-HFD_30: Pancreatic_islets_HFD_18wk_rep2

description:
Pancreatic_islets_HFD_18wk_rep2
Gene expression after 18 weeks of HFD feeding
NZO_K0-HFD_30


title: CD3 enriched T cells DONOR2_(miRNA-3_0)

value: unknown


title: Sorted T cells 10_(miRNA-3_0)


title: NZO_K0-HFD_31: Pancreatic_islets_HFD_18wk_rep3

description:
Pancreatic_islets_HFD_18wk_rep3
Gene expression after 18 weeks of HFD feeding
NZO_K0-HFD_31


title: M_florum RNAseq - rep 3A

description: Strand-specific RNA-Seq protocol

value: bacteria


title: FULV+SEL_1

value: MCF-7 ESR1Y540

value: FULV+SEL


title: Sorted T cells 38_A_(miRNA-3_0)


title: NZO_K0-HFD_32: Pancreatic_islets_HFD_18wk_rep4

description:
Pancreatic_islets_HFD_18wk_rep4
Gene expression after 18 weeks of HFD feeding
NZO_K0-HFD_32


title: M_florum RNAseq - rep 2B

description: Strand-specific RNA-Seq protocol

value: exponential

value: ATCC 1161

value: Steady-state culture grown in a chemostat system set at 34°C


title: SEL_1

value: MCF-7 ESR1Y549

value: SEL


title: ISWI RNAi rep 1


title: FULV_3

growth_protocol: MCF-7 ESR1Y537S cells were seeded at a density of 1x106 cells on 10-cm plates and incubated in a 37 °C incubator for 24 hours. Next day, cells were treated with 10-6 M Fulvestrant for 24 hours and incubated in a 37 °C incubator. After 48 hours period, RNA was extracted from these cells and prepared for sequencing procedure.

value: MCF-7 ESR1Y539

value: FULV


title: Control rep 3

value: elav-GAL4; +


title: M_florum RNAseq - rep 2A

description: Strand-specific RNA-Seq protocol


title: M_florum RNAseq - rep 1B

description: Strand-specific RNA-Seq protocol


title: Control rep 2


title: FULV_2

value: MCF-7 ESR1Y538


title: Sorted T cells 3_1_(miRNA-3_0)

value: m


title: Sorted T cells 4_A_(miRNA-3_0)


title: FULV_1

value: MCF-7 ESR1Y537


title: Sorted T cells 2_A_(miRNA-3_0)


title: Sorted T cells 5_1_(miRNA-3_0)


title: Control rep 1

source_name: mid-3rd larval instar

value: mid-3rd instar larval central brain + ventral nerve cord

value: 4 days post-egg lay at 25 C


title: M_florum RNAseq - rep 1A

description: Strand-specific RNA-Seq protocol


title: Sorted T cells 1_A_(miRNA-3_0)

value: f