title: BY-Stationary_rep2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description:
BY-Stationary_2
HT-5Pseq with cells at stationary stage

data_processing:
library strategy: RNA-Seq (5PSeq)
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
For HT-5Pseq data, 3’-sequencing adaptor (-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) trimming was applied to 5’ends of reads using cutadapt V1.16. The 8-nt random barcodes on the 5’ ends of reads were extracted and added to the header of fastq file as the UMI using UMItools (v0.5.4). Reads were mapped to the reference genome (SGD R64-1-1 for S. cerevisiae genome, ASM294v2.20 for S.pombe genome) separately by star/2.7.0  with the parameter --alignEndsType Extend5pOfRead1 to exclude soft-clipped bases on the 5’ end. To calculate the fraction of rRNA, tRNA, snRNA snoRNA and mRNA in library compositions,the stepwise alignment was performed by corresponding index generated by star/2.7.0. Duplicated 5’ends of read introduced by PCR during library preparation were removed based on random barcodes sequences using UMItools (v0.5.4).
For The distribution of nucleotide position of 5’ends were performed using Fivepseq package , including relative to start, stop codon and codon specific pausing. Specifically, the unique 5’mRNA reads in biological samples were summed up and normalized to reads per million (rpm). Then the relative position of 5’mRNA reads to all codons of all ORF were summed at each position. The metagene plot was showed as the sum value versus the relative distance from respective codon.
Genome_build: Saccharomyces cerevisiae R64-1-1 , Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.

organism: Saccharomyces cerevisiae

source_name: BY-Stationary

growth_protocol: S. cerevisiae  grown in YPD at 30°C. S.pombe grown in YES at 30°C

extract_protocol:
Total RNA was isolated by the standard phenol: chloroform method, and DNA was removed by DNase I treatment. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
For HT5Pseq libraries construction, we used 6 μg of DNA-free total RNA. Samples were directly subjected to RNA ligation. The treated RNA samples were incubated with 100 μM RNA/RNA rP5_RND oligo (final 10 μM) 2h at 25°C with 10 Units of T4 RNA ligase 1 (NEB). Ligated RNA was purified with RNAClean XP (Beckman Coulter), according to the manufacturer’s instructions. RNA was reverse transcribed with Superscript II (Life Technologies) and primed with Illumina PE2 compatible oligos containing random hexamers (20 μM) and oligo-dT (0.05 μM). Reverse transcription reaction was incubated for 10 min at 25°C, 50 min at 42°C and heat inactivation for 15 min at 70°C. To deplete RNA in RNA/cDNA hybrid after reverse transcription, we used sodium hydroxide (40 mM) for incubation 20 min at 65°C and then neutralized with Tris-HCl, pH =7.0 (40 mM). For DSN (Duplex-specific nuclease) based rRNA depletion, we used a mixture of probes targeted the 18S rDNA, 25S rDNA and 5.8S rDNA. The probes were designed to occupy the whole ribosomal RNA regions with consecutive 25-30nt long unmodified DNA oligos. The hybridization of probes (2 μM each) with cDNAs were incubated at 68 °C for 2 minutes before adding pre-warmed DSN buffer mix with 1 Units of DSN enzyme (Evrogen). The reaction then performed at 68 °C for 20 minutes. To inactive DSN enzyme, we added 2X DSN stop solution and incubate 10 min at 68 °C. The final PCR amplification was used 2X Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) and final 0.1 μM of PE1.0 and corresponding multiplex PE2.0_MTX . The program followed this: 30s 98°C; 15 cycles (20s 98°C; 30s 65°C; 30s 72°C); 7min 72°C. Libraries were size selected using 0.7x-0.9x (v/v) AMpure XP beads (Beckman Coulter) to final 200-500 bp and sequenced by NextSeq 500/550 using 60 sequencing cycles for Read 1 and 15 cycles for Read 2.  5PSeq methods was performed as previously described (PMID: 26820793). 6µg of total RNA was used as input. In brief a RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Illumina).Libraries were PCR amplified (15 cycles). Ampure beads size selected libraries with an average length of 451 nt were sent for sequencing (llumina NextSeq 500 instrument).

treatment_protocol: For cycloheximide (CHX) treatment, CHX was added to final 0.1 mg/mL to the medium and incubated for 5 min at 30°C for S. cerevisiae and 10 min for S.pombe. For glucose deprivation, cells were shifted to pre-warmed YP (lacking glucose) and then grown at 30°C for 5 minutes and 15 minutes prior to harvesting. For glucose re-addition, cultures with already 15 min glucose deprivation were shifted to YPD for 15 min at 30°C. For early exponential phase, strains were grown at 30°C from an initial OD600~0.05 to a final OD600 of 0.3. To reach stationary stage, S. cerevisiae strains were grown during 60h in YPD.

tag: strain background

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

tag: parental strain background

value: BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)


title: BY-Stationary_rep1

status: Public on Apr 02 2021

type: SRA

description:
BY-Stationary_1
HT-5Pseq with cells at stationary stage

library_source: transcriptomic

molecule: total RNA


title: EA rep2

city: Harbin

first: Guangyue

last: Li

state: heilongjang

address: No.26 Hexing Road Xiangfang District

department: College of Life Science

country: China

institute: Northeast Forestry University

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
Cutadapt (v1.9.1) was used to get the "clean reads"
Mapping clean reads to hg19 whole genome using HISAT
Fragments Per Kilobase Million (FPKM) was calculated based on the HTSeq (v0.6.1)
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Liver

growth_protocol: According to previous description,the cells were cultured in the media as suggested by the ATCC (Manassas, VA, USA), supplied with 10% fetal bovine serum and 1% penicillin-streptomycin, and maintained at 37°C in an atmosphere of 5% CO2. Ellagic acid (EA) used in treating cells had purity of over 95% (Cat# E2250, Sigma-Aldrich) and was dissolved in dimethyl sulfoxide (DMSO) as a stock solution.

extract_protocol: Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration.

treatment_protocol: Total RNA was extracted using the TRIzol reagent from the cells after being cultured for 24 h in a medium containing 50 μM EA or an equal volume of DMSO as a control.

tag: tissue

value: Liver

tag: cell line

tag: treatment

value: Ellagic acid


title: scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, unsorted PBMCs 7811BW

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

description:
X025-AP0C1W1_ficoll_perm-cells_0.01dig_ds125M_filtered-fragments.tsv.gz
X025-AP0C1W1_ficoll_perm-cells_0.01dig_ds125M_filtered-metadata.csv.gz
X025-AP0C1W1_ficoll_perm-cells_0.01dig_ds125M_20kb-window-matrix.h5
X025-AP0C1W1
The FASTQs are from human subjects and will be provided via dbGAP

library_source: genomic

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger-atac mkfastq (10x Genomics v.1.1.0).
To assess samples at an equal sequencing depth, FASTQ files were downsampled to a uniform total raw read count among compared samples: 2×108 fragments for comparison of nuclei and cells across FACS conditions (Figure 1 and 2); 1.25×108 fragments for optimization experiments due to lower available total read depth after sequencing.
10x cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis.
genome_build: Ensembl GRCh38-3.0.0
processed_data_files_format_and_content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).

molecule: genomic DNA

source_name: peripheral blood mononuclear cells

extract_protocol:
Biological specimens were purchased from BioIVT as cryopreserved PBMCs and Bloodworks NW as freshly drawn whole blood. All sample collections were conducted by BioIVT and Bloodworks NW under IRB-approved protocols, and all donors sign informed consent forms.  PBMCs sourced from BioIVT were isolated using either Ficoll-Paque or leukapheresis. Following isolation, PBMCs were subjected to RBC lysis, washing, and counting. PBMC aliquots were cryopreserved in Cryostor CS10 (StemCell Technologies, 07930) and stored in vapor phase liquid nitrogen.   For fresh blood samples from Bloodworks NW, PBMC processing occurred in-house. Blood tubes were pooled, gently swirled until fully mixed, about 30 times, and diluted with an equivalent volume of room temperature PBS (Thermo Fisher Scientific, 14190235). PBMCs were isolated using one or more Leucosep tubes (Greiner Bio-One, 227290) loaded with 15 mL of Ficoll Premium (GE Healthcare, 17-5442-03) to which a 3 mL cushion of PBS had been slowly added on top of the Leucosep barrier. Diluted whole blood (24-30mL) was slowly added to each tube and spun at 1000×g for 10 minutes at 20°C with no brake (Beckman Coulter Avanti J-15RIVD with JS4.750 swinging bucket, B99516). PBMCs were recovered from the Leucosep tube by quickly pouring all volume above the barrier into a sterile 50 mL conical tube (Corning, 352098). 15 mL cold PBS+0.2% BSA (Sigma, A9576; “PBS+BSA”) was added and the cells were pelleted at 400×g for 5-10 minutes at 4-10°C. The supernatant was quickly decanted, the pellet dispersed by flicking the tube, and the cells washed with 25-50 mL cold PBS+BSA. Cell pellets were combined as needed, the cells were pelleted as before, supernatant quickly decanted, and residual volume was carefully aspirated. PBMCs were resuspended in 1 mL cold PBS+BSA per 15 mL whole blood processed and counted with a ViCell (Beckman Coulter) using VersaLyse reagent (Beckman Coulter, A09777) or with a Cellometer Spectrum Cell Counter (Nexcelom) using ViaStain Acridine Orange/Propidium Iodide solution (Nexcelom, C52-0106-5). PBMCs were cryopreserved in Cryostor10 (StemCell Technologies, 07930) or 90% FBS (Thermo Fisher Scientific, 10438026) / 10% DMSO (Fisher Scientific, D12345) at 5×106 cells/mL by slow freezing in a Coolcell LX (VWR, 75779-720) overnight in a -80°C freezer followed by transfer to liquid nitrogen.
Isolation of nuclei suspensions was performed according to the Demonstrated Protocol: Nuclei Isolation for Single Cell ATAC Sequencing (10x Genomics, CG000169 Rev C). Briefly, 8×105 to 1×106 cells were added to a 1.5 mL low binding tube (Eppendorf, 022431021) and centrifuged (300×g for 5 minutes at 4?) using a swinging bucket rotor (Beckman Coulter Avanti J-15RIVD with JS4.750 swinging bucket, B99516). The supernatant was removed using a vacuum aspirator pipette and the cell pellet was resuspended in 100 µl of chilled 10x Genomics Nuclei Isolation Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1 % NP-40 Substitute CAS 9016-45-9 (BioVision 2127-50), 0.01% Digitonin (MP Biomedicals 0215948082), 1% BSA) by pipette-mixing 10 times. Cells were incubated on ice for 3 minutes, followed by dilution with 1 mL of chilled 10x Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20 (BioRad 1610781), 1% BSA) by pipette-mixing 5 times. Nuclei were centrifuged (500×g for 3 minutes at 4?) and the supernatant was slowly removed using a vacuum aspirator pipette. Nuclei were resuspended in chilled 1x Nuclei Buffer (10x Genomics, 2000207) to a target concentration of 3,000 - 6,000 nuclei per µl. Nuclei suspensions were passed through 35 µm Falcon Cell Strainers (Corning, 352235) and counted on a Cellometer Spectrum Cell Counter (Nexcelom) using ViaStain Acridine Orange/Propidium Iodide Staining Solution (Nexcelom, C52-0106-5).  In addition to 10x Nuclei Isolation Buffer (10xNIB), we tested an alternative Nuclei Isolation Buffer (ANIB) as described previously (Mulqueen et al., 2019: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1 % IGEPAL CAS 9002-93-1 (Sigma, I8896), 1x Protease Inhibitor (Roche, 11836170001)). For each buffer, we generated a titration series of detergent concentrations relative to the concentrations described above but did not alter the concentration of other buffer ingredients: 1x, 0.5x, 0.25x, 0.1x for 10xNIB, and 1x and 0.1x for ANIB. The resulting nuclei were imaged using an EVOS M5000 Imaging System (Thermo Fisher Scientific, AMF5000) in transmitted light mode at 40x magnification to visually evaluate nuclear integrity. The 1x 10xNIB, 0.25x 10xNIB, 0.1x 10xNIB, and 1x ANIB were used for 10X scATAC-seq.  For permeabilized cells we prepared a 5% w/v digitonin stock by diluting powdered Digitonin (MP Biomedicals, 0215948082) with 100% DMSO (Fisher Scientific, D12345) and creating 20 µl aliquots which were stored at -20°C. To permeabilize, 1,000,000 cells were added to a 1.5 mL low binding tube (Eppendorf, 022431021) and centrifuged (400×g for 5 minutes at 4°C) using a swinging bucket rotor (Beckman Coulter Avanti J-15RIVD with JS4.750 swinging bucket, B99516). The supernatant was removed using a vacuum aspirator pipette and the cell pellet was resuspended in 100 µl of chilled isotonic Perm Buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.01% Digitonin) by pipette-mixing ten times. Cells were incubated on ice for 5 minutes, after which they were diluted with 1 mL of isotonic Wash Buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2) by pipette-mixing 5 times. Cells were centrifuged (400×g for 5 minutes at 4°C) using a swinging bucket rotor and the supernatant was slowly removed using a vacuum aspirator pipette. The cell pellet was resuspended in chilled TD1 buffer (Illumina, 15027866) by pipette-mixing to a target concentration of 2,300 - 10,000 cells per µl. Cells were passed through 35 µm Falcon Cell Strainers (Corning, 352235) and counted on a Cellometer Spectrum Cell Counter (Nexcelom) using ViaStain Acridine Orange/Propidium Iodide solution (Nexcelom, C52-0106-5). For optimization, we used varying final digitonin concentrations in the Perm Buffer: 0.01% w/v, 0.05% w/v, 0.1% w/v, and 0.2% w/v. The optimal concentration observed was 0.01% w/v.  scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC v1.1 Reagent Kits User Guide (CG000209 Rev B) with several modifications. 15,000 cells or nuclei were loaded into each tagmentation reaction. Nuclei were brought up to a volume of 5 µl in 1x Nuclei Buffer (10x Genomics, 2000207), mixed with 10 µl of a transposition master mix consisting of ATAC Buffer B (10x Genomics, 2000193) and ATAC Enzyme (Tn5 transposase; 10x Genomics, 2000123). Permeabilized cells were brought up to a volume of 9 µl in TD1 buffer (Illumina, 15027866) and mixed with 6 µl of Illumina TDE1 Tn5 transposase (Illumina, 15027916). Transposition was performed by incubating the prepared reactions on a C1000 Touch thermal cycler with 96–Deep Well Reaction Module (Bio-Rad, 1851197) at 37°C for 60 minutes, followed by a brief hold at 4°C. A Chromium NextGEM Chip H (10x Genomics, 2000180) was placed in a Chromium Next GEM Secondary Holder (10x Genomics, 3000332) and 50% Glycerol (Teknova, G1798) was dispensed into all unused wells. A master mix composed of Barcoding Reagent B (10x Genomics, 2000194), Reducing Agent B (10x Genomics, 2000087), and Barcoding Enzyme (10x Genomics, 2000125) was then added to each sample well, pipette-mixed, and loaded into row 1 of the chip. Chromium Single Cell ATAC Gel Beads v1.1 (10x Genomics, 2000210) were vortexed for 30 seconds and loaded into row 2 of the chip, along with Partitioning Oil (10x Genomics, 2000190) in row 3. A 10x Gasket (10x Genomics, 370017) was placed over the chip and attached to the Secondary Holder. The chip was loaded into a Chromium Single Cell Controller instrument (10x Genomics, 120270) for GEM generation. At the completion of the run,

value: BloodWorks NW

value: ficoll

value: permeabilized cells

value: 0.01% digitonin

value: 10x scATAC-seq


title: IR-SAS EVs

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: exo-SAS'

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: cell EVs

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Serum was immediately stored at -80℃ after collected.ど

extract_protocol: Total RNA was extracted from the serum-EVs, cell-EVs using 3D-Gene RNA extraction reagent (Toray, Kamakura, Japan) according to the manufacturer’s instructions.

treatment_protocol: Serum-EVs were extracted using exoRNeasy Serum / Plasma kit (Qiagen), and cell-EVs were extracted using size-exclusion chromatography (SEC) column. Collected EVs were stored at -80℃.

value: cell EVs

tag: disease state

value: oral squamous cell carcinoma

tag: phenotype

value: non-radioresistant (cell culture)


title: SAS EVs

description: exo-SAS


title: HUDEP1_E_C

city: Nicosia

first: Carsten

middle: Werner

last: Lederer

address: 6 Iroon Avenue, Ayios Dometios

department: Molecular Genetics Thalassaemia Department

country: Cyprus

institute: The Cyprus Institute of Neurology and Genetics

data_processing:
Zebra Call (base calling software developed for BGISEQ-500) was used for basecalling
Raw data were filtered to remove low-quality reads, adaptors and other contaminants, and then clean reads were mapped to the reference genome and to other ncRNA databases such as miRBase and Rfam 12.0 by using Bowtie 2 and CMsearch programs.
MiRDeep2 was used to predict novel miRNAs by exploring the characteristic hairpin structure of pre-miRNAs, and Piano was used to predict piRNAs
The small RNA expression level was calculated by using Transcripts Per Million (TPM). DE analysis between sample groups was performed using DEGseq for replicate samples (Wang L, Wang. X (2020). DEGseq: Identify Differentially Expressed Genes from RNA-seq data).
Genome_build: hg18
Supplementary_files_format_and_content: Excel files include raw counts and TPM for each sample

source_name: Umbilical cord blood

growth_protocol:
hCD34+ cells were isolated from PB of healthy individuals by magnetic-activated cell sorting using hCD34 Microbead Kit, human (Miltenyi), after mononuclear cell isolation using Lymphoprep density gradient medium (Axis-Shield), and according to a published protocol (Protocol C). Isolated cells were then expanded in StemSpan SFEM II (Stem Cell Technologies) supplemented with 1 µM Dexamethasone (Sigma-Aldrich), 2 IU/mL EPO (Binocrit 4000 IU/0.4 mL, Sandoz GmbH), 1% StemSpan CC100 (Stem Cell Technologies) and 1× Penicillin-Streptomycin (Thermo Fisher Scientific) at concentrations below 0.5×106 cells/mL. Medium was changed twice a week.
For the induction of differentiation, hCD34+ cells were cultured in Minimum Essential Medium Eagle (Stem Cell Technologies) supplemented with 30% Defined Fetal Bovine Serum (Hyclone), 105 M 2-Mercaptoethanol (Sigma-Aldrich), 10 IU/mL EPO (Binocrit 4000 IU/0.4 mL, Sandoz GmbH) 10 ng/mL hSCF (PeproTech) and 1× Penicillin-Streptomycin (Thermo Fisher Scientific) at a concentration of 0.5–1×106/mL.
HUDEP cells were expanded in StemSpan SFEM II (Stem Cell Technologies) supplemented with 1 µM Dexamethasone (Sigma-Aldrich), 5 μg/mL Doxycycline (Clontech Laboratories), 100 ng/mL Recombinant Human Stem Cell Factor (hSCF) (PeproTech), 3 IU/mL Epoetin alpha (EPO) (Binocrit 4000 IU/0.4 mL, Sandoz GmbH), and 2× Penicillin-Streptomycin (Thermo Fisher Scientific) at concentrations below 0.5×106 cells/mL. Culture medium was changed twice a week and doxycycline was replenished every other day to retain expression of the HPV16-E6/E7 immortalisation system.
To induce erythroid differentiation, cells were cultured in a three-phase erythroid differentiation culture system previously described. Briefly, cells were cultured in Iscove’s Modified Dulbecco’s Medium (Thermo Fisher Scientific) containing 5% Human Serum from plasma male AB (Sigma-Aldrich), 2× Penicillin-Streptomycin (Thermo Fisher Scientific), 1% L-Glutamine (Thermo Fisher Scientific), 200 µg/mL Holo-Transferrin (Sigma-Aldrich), 2 IU/mL Heparin (Sigma-Aldrich), 10 ng/mL Insulin (Sigma-Aldrich), and 3 IU/mL EPO (Binocrit 4000 IU/0.4 mL, Sandoz GmbH). In phase I (days 1–4), culture medium was supplemented with 100 ng/mL hSCF (PeproTech). In phase II (days 5–7), hSCF was withdrawn from culture. In phase III (days 8 and beyond), doxycycline was also removed from culture medium. Cells in differentiation were maintained at 1×106 cells/mL.

extract_protocol:
Total RNA was harvested using TRIzol reagent (Invitrogen). After RNA extraction, small RNAs were size-selected (18-30 nucleotides) using 15% urea-polyacrylamide gel electrophoresis (PAGE).
18-30 bp short-insert library
BGISEQ-500, standard output 40 Million reads per sample, 50bp single-end sequencing reads

value: Umbilical cord blood

tag: stage of erythroid differentation

value: Early (_E)

tag: days in erythroid differentiation culture medium

tag: cell type

value: Cell line HUDEP-1


title: Cy5_labeled_M or OE_Cy3_labeled OE or M

city: Northridge

first: Michael

middle: L.

last: Summers

state: California

address: 18111 Nordhoff St

department: Dept. of Biology

institute: California State University Northridge

description: Analysis used sigB2 mutant steady state RNA as control samples for comparison to the experimental samples overexpressing sigB2 on a plasmid from tac promoter (pRL490 with sigB2 (Npun_R4091) replacing excised luciferase genes using flanking BamHI sites).

hyb_protocol: Labelled cDNA hybridized using a Tecan 480 Hybridization station. Mutant and overexpression samples were combined, concentrated by vacuum centrifugation, dissolved in 1X GeneFrames hybridization buffer, and applied to spotted array slides. Hybridization was conducted for 16 hours at 50°C using a Tecan 480 hybridization station. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.5x SSC each at 37 °C using a 1 minute soak and 1 minute wash for each prior to drying and scanning.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner and GenePix Pro-6.0 software (Molecular Devices)

data_processing:
Spot analysis for each slide was conducted using the GenePix Pro software after manually confirming/editing automated spot alignments. The resulting .gpr files were normalized and statistically analyzed using R and LIMA GUI packages as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256). Loess was used for within array normalization and aquantile was used for between array normalization.
340480_0091.txt: Cy5_labeled_M_Cy3_labeled OE_BIOLrep1
340629_0091.txt: Cy5_labeled_M_Cy3_labeled OE_BIOLrep2
340478_0091.txt: Cy5_labeled_OE_Cy3_labeled_M_BIOLrep1
340626_0091.txt: Cy5_labeled_OE_Cy3_labeled_M_BIOLrep2

label: Cy3 or Cy5

organism: Nostoc punctiforme

source_name: Exponentially grown cells bearing plasmid overexpressing sigB2 (Npun_R4091) or sigB2 (Npun_R4091) insertional mutant cells

label_protocol: Probes were labelled with Cy3 (Alexia Fluor 555) and Cy5 (Alexa Fluor 647) during cDNA synthesis from total RNA using Superscript Plus Indirect cDNA Labeling System (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN QIAquick PCR purification kit before hybridization.

growth_protocol: Cultures of Nostoc punctiforme ATCC 29133 were grown as 50 mL cultures in 125-mL Erlenmeyer flasks with shaking at 100–120 rpm at 23–25 ̊C with exposure to 19–25 micromol photons m-2 s-1 of cool white fluorescent light in the standard minimal salts medium of Allen and Arnon (1955). Liquid media was diluted four-fold (AA/4), whereas solid media remained undiluted and contained 1% Noble agar (Difco). Both liquid and solid media were supplemented with 5 mM 3-[N-morpholino]propanesulfonic acid, pH 7.8 (MOPS), 2.5 mM NH4Cl, 2.5 mM NaNO3, 2.5 mM KNO3 in combination to make MAN (MOPS, ammonia, nitrate) or MN (MOPS nitrate); neomycin at 10 micrograms ml-1 was added when appropriate. Cultures grown on plates were incubated in 0.5% CO2 at 25 ̊C under 8–12 micromol photons m-2 s-1 continuous light.

extract_protocol: Cultures were harvested by brief centrifugation and flash frozen in a dry ice/ethanol bath.  RNA was isolated using phenol/glass bead agitation, lithium chloride precipitation, (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) followed by further purification using Quiagen RNeasy kit following manufacturers protocol.

treatment_protocol: RNA was extracted from exponential cultures

tag: genotype/variation

value: SigB2 overexpression or loss of SigB2 expression

label: Cy5 or Cy3

source_name: Exponentially grown culture of a sigB2 (Npun_R4091) insertional mutant or cells  bearing plasmid overexpressing sigB2 (Npun_R4091)

value: loss of SigB2 expression or SigB2 overexpression


title: scATAC-seq of ficoll-purified, 1x ANIB isolated nuclei, unsorted PBMCs

description:
X024-AP0C1W4_ficoll_nuclei_ANIB_ds125M_filtered-fragments.tsv.gz
X024-AP0C1W4_ficoll_nuclei_ANIB_ds125M_filtered-metadata.csv.gz
X024-AP0C1W4_ficoll_nuclei_ANIB_ds125M_20kb-window-matrix.h5
X024-AP0C1W4
The FASTQs are from human subjects and will be provided via dbGAP

value: nuclei

value: 1.00x ANIB


title: scATAC-seq of ficoll-purified, 0.1x 10xNIB isolated nuclei, unsorted PBMCs

description:
X024-AP0C1W3_ficoll_nuclei_0.10x10xNIB_ds125M_filtered-fragments.tsv.gz
X024-AP0C1W3_ficoll_nuclei_0.10x10xNIB_ds125M_filtered-metadata.csv.gz
X024-AP0C1W3_ficoll_nuclei_0.10x10xNIB_ds125M_20kb-window-matrix.h5
X024-AP0C1W3
The FASTQs are from human subjects and will be provided via dbGAP


title: BY4741_lowOD_rep1

description:
BY-lowOD_1
HT-5Pseq with cells at OD 0.3

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)


title: CCRT non-responder3

description: Non-responder 3

source_name: serum samples

treatment_protocol: Cell-EVs were extracted using size-exclusion chromatography (SEC) column. Collected EVs were stored at -80℃.

value: serum samples

value: CCRT non-responder


title: HUDEP1_L_C

value: Late (_L)


title: HUDEP1_E_A


title: scATAC-seq of ficoll-purified, 0.25x 10xNIB isolated nuclei, unsorted PBMCs

description:
X024-AP0C1W2_ficoll_nuclei_0.25x10xNIB_ds125M_filtered-fragments.tsv.gz
X024-AP0C1W2_ficoll_nuclei_0.25x10xNIB_ds125M_filtered-metadata.csv.gz
X024-AP0C1W2_ficoll_nuclei_0.25x10xNIB_ds125M_20kb-window-matrix.h5
X024-AP0C1W2
The FASTQs are from human subjects and will be provided via dbGAP

value: BloodWorks NW

value: ficoll


title: CCRT non-responder4

description: Non-responder 4


title: BY4741_lowOD_rep2

description:
BY-lowOD_2
HT-5Pseq with cells at OD 0.3


title: scATAC-seq of ficoll-purified, 0.05% digitonin permeabilized, unsorted PBMCs

description:
X025-AP0C1W2_ficoll_perm-cells_0.05dig_ds125M_filtered-fragments.tsv.gz
X025-AP0C1W2_ficoll_perm-cells_0.05dig_ds125M_filtered-metadata.csv.gz
X025-AP0C1W2_ficoll_perm-cells_0.05dig_ds125M_20kb-window-matrix.h5
X025-AP0C1W2
The FASTQs are from human subjects and will be provided via dbGAP

value: permeabilized cells

value: 0.05% digitonin

value: 10x scATAC-seq


title: CCRT non-responder2

description: Non-responder 2

value: oral squamous cell carcinoma


title: scATAC-seq of ficoll-purified, 1x 10xNIB isolated nuclei, unsorted PBMCs

description:
X024-AP0C1W1_ficoll_nuclei_1.00x10xNIB_ds125M_filtered-fragments.tsv.gz
X024-AP0C1W1_ficoll_nuclei_1.00x10xNIB_ds125M_filtered-metadata.csv.gz
X024-AP0C1W1_ficoll_nuclei_1.00x10xNIB_ds125M_20kb-window-matrix.h5
X024-AP0C1W1
The FASTQs are from human subjects and will be provided via dbGAP


title: BY4741_CHX_rep2

description:
BY-CHX_2
HT-5Pseq with CHX (0.1 mg/mL)


title: BY4741_CHX_rep1

description:
BY-CHX_1
HT-5Pseq with CHX (0.1 mg/mL)


title: CD34_L_A

source_name: Peripheral blood

value: Peripheral blood

value: Primary cells


title: CD34_L_C


title: scATAC-seq of leukapheresis-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs

description:
B003-AP0C1W8_leukopak_perm-cells_neudep-facs_ds125M_filtered-fragments.tsv.gz
B003-AP0C1W8_leukopak_perm-cells_neudep-facs_ds125M_filtered-metadata.csv.gz
B003-AP0C1W8_leukopak_perm-cells_neudep-facs_ds125M_20kb-window-matrix.h5
B003-AP0C1W8
The FASTQs are from human subjects and will be provided via dbGAP

value: BioIVT

value: leukapheresis

value: 0.01% digitonin

value: FACS

value: Dead Cell/Debris/Neutrophil Depletion


title: scATAC-seq of leukapheresis-purified, 0.01% digitonin permeabilized, unsorted PBMCs

description:
B003-AP0C1W7_leukopak_perm-cells_no-facs_ds125M_filtered-fragments.tsv.gz
B003-AP0C1W7_leukopak_perm-cells_no-facs_ds125M_filtered-metadata.csv.gz
B003-AP0C1W7_leukopak_perm-cells_no-facs_ds125M_20kb-window-matrix.h5
B003-AP0C1W7
The FASTQs are from human subjects and will be provided via dbGAP


title: BY_Norm_5P_rep2

description:
BY_Norm_5P_2
5Pseq (PMID: 26046441)

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)


title: HUDEP1_E_B

value: Umbilical cord blood

value: Early (_E)

value: Cell line HUDEP-1


title: CD34_E_C


title: U937 cells, ΔNSPs_3 (RNA-seq)

city: Stanford

first: Purvesh

last: Khatri

address: 279 Campus Dr. Beckman Center B235A

department: BMIR

institute: Stanford University

description: Delta-NSPs plasmid transduced U937 cell line 3

data_processing:
Assessment of FASTQ quality was performed using FASTQC. All included data passed QC checks.
Reads from FASTQ files were aligned to the human genome (GRCh38) using HISAT2 (v. 2.0.0) with default settings.
Aligned BAM files were sorted by position and indexed using samtools (v.1.5.9)
Gene-level counts were generated with HTSeq-Count (v.0.11.1) using the Ensembl GrCh38.p12 GTF file for gene coordinates with the following options: --stranded=yes --order=pos --mode=union --type=exon --idattr=gene_id. Genes with >= 10 counts total (summed across controls and ΔNSPs replicates were retained for downstream analysis)
Genome_build: GRCh38
Supplementary_files_format_and_content: counts_raw.csv contains the compiled HTSeq-Count gene-level counts. The first column contains the Ensembl gene id and the subsequent columns represent each sample.

source_name: Monocytic cell line

growth_protocol: U937 cells were cultured in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (ATCC), glutamine (Gibco), and penicillin/streptomycin and selected with 500ug/ml geneticin

extract_protocol:
U937 cells RNA was prepared using the Rneasy Plus mini kit (Qiagen) following the manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: genetically modified U937

tag: genetic modification

value: ΔNSPs

tag: genotype

value: depleted of CTSG, ELANE, and PRTN3 simultaneously (deltaNSPs)


title: CCRT responder2

description: Responder 2

value: serum samples

value: CCRT responder


title: BY_Norm_5P_rep1

description:
BY_Norm_5P_1
5Pseq (PMID: 26046441)


title: CD34_E_B

value: Peripheral blood


title: U937 cells, ΔNSPs_2 (RNA-seq)

description: Delta-NSPs plasmid transduced U937 cell line 2


title: CCRT responder3

description: Responder 3

value: oral squamous cell carcinoma


title: BY4741_NonProbes_rep2

description:
BY-NP_2
HT-5Pseq with DSN treatment without probes


title: BY4741_NonProbes_rep1

description:
BY-NP_1
HT-5Pseq with DSN treatment without probes


title: CCRT non-responder1

description: Non-responder 1

value: CCRT non-responder


title: U937 cells, ΔNSPs_1 (RNA-seq)

description: Delta-NSPs plasmid transduced U937 cell line 1


title: E15_singlecell_control

city: LA

first: Xia

last: Han

state: CA

address: 2250 Alcazar Street

institute: University of Southern California

description:
mRNA
E15_5_Control

data_processing:
Raw read counts were analyzed using the Seurat R 3.4.1 package. Cell clusters and variably expressed genes in each cluster were identified by using Log Normalize, Find Variable Genes, Scale Data and RunPCA functions.
assembly: mm10

organism: Mus musculus

source_name: E15.5 singlecell control

extract_protocol:
Soft palate tissue (posterior third of the palatal region) was digested from E15.5 wild type embryos by TrypLE express enzyme (Thermo Fisher Scientific) at 37°C with shaking at 600 rpm for 20 min.
Full-length cDNA was reverse transcribed from poly-adenylated mRNA using primers containing: an illumina TruSeq Read 1, 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI) and 30 nt poly(dT) sequence. Silane magnetic beads are used to purify the first-strand cDNA from post GEM-RT reaction mixture. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, a sample index and TruSeq Read 2 are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplication.
Chrominum Single Cell 3' Gene Expression Library

tag: strain

tag: Stage

value: soft palate


title: BY4741_NonDSN_rep2

description:
BY-NonDSN_2
HT-5Pseq without DSN treatment


title: CD34_L_B

value: Late (_L)

value: Primary cells


title: CD34_E_A


title: s200709a8

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Star 2.5.3a software was used for comparative analysis between sequencing data of single cell RNA and reference genome of Ensembl database
Quantify gene expression using read2 by featureCounts1.6.2 software
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

extract_protocol:
A moderate amount of renal tissue was taken from the selected patients during renal puncture, and GEXSCOPE ® Single Cell RNA Library Kit Tissue was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: IgA nephropathy

tag: age

tag: proteinuria

value: proteinuria not conform to nephrotic syndrome

value: kidney


title: CCRT responder1

description: Responder 1


title: s200702a5


title: s200707a7


title: E14_singlecell_control2

description:
mRNA
E14com_barcodes.tsv.gz
E14com_features.tsv.gz
E14com_matrix.mtx.gz
JF-C2

source_name: E14.5 singlecell control2

extract_protocol:
Soft palate tissue (posterior third of the palatal region) was digested from E14.5 wild type embryos by TrypLE express enzyme (Thermo Fisher Scientific) at 37°C with shaking at 600 rpm for 20 min.
Full-length cDNA was reverse transcribed from poly-adenylated mRNA using primers containing: an illumina TruSeq Read 1, 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI) and 30 nt poly(dT) sequence. Silane magnetic beads are used to purify the first-strand cDNA from post GEM-RT reaction mixture. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, a sample index and TruSeq Read 2 are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplication.
Chrominum Single Cell 3' Gene Expression Library


title: U937 cells, Control_3 (RNA-seq)

description: Control plasmid transduced U937 cell line 3

value: Control plasmids

value: control


title: BY4741_NonDSN_rep1

description:
BY-NonDSN_1
HT-5Pseq without DSN treatment

tag: strain background

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)


title: BY4741_DSN_rep2

description:
BY-DSN_2
HT-5Pseq with DSN treatment and probes

tag: parental strain background


title: E14_singlecell_control1

description:
mRNA
E14com_barcodes.tsv.gz
E14com_features.tsv.gz
E14com_matrix.mtx.gz
XH-A10

source_name: E14.5 singlecell control1

tag: tissue


title: SC-BactRS-12S-SCR-346_S12_R1_001

status: Public on Apr 01 2021

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
FastQ files from Illumina NextSEQ500 were processed using the CLC genomics workbench (Qiagen) RNA-seq data analysis pipeline.
Reads were mapped to the coding regions of the Caulobacter crescentus NA1000 genome (accession CP001340)
Genome_build: GenBank accession CP001340
Supplementary_files_format_and_content: Processed files report the results of expression analysis in CLC Genomics Workbench in tab-delimited .txt format.

organism: Caulobacter vibrioides

source_name: ∆chvI chvI(D52E)++

growth_protocol: 2 mL PYE cultures were inoculated with ∆chvI EV and ∆chvI chvI(D52E)++ cells and grown overnight. Cultures were diluted to OD660 = 0.001 in 2 mL fresh PYE and grown for 22.5 hours. Cultures were diluted to OD660 = 0.075 in 5 mL PYE + 0.15% xylose and grown for 3.5 hours before TRIzol extraction.

extract_protocol:
Total RNA was isolated from C. crescentus cell pellets using TRIzol per manufacturer protocol, followed by purification with a Qiagen RNeasy kit.
RNA-seq libraries were prepared using an Illumina TruSeq stranded RNA kit and sequenced on an Illumina NextSEQ500 instrument

value: delta_chvI xylX::pMT585-chvI(D52E)


title: SC-BactRS-12S-SCR-345_S11_R1_001


title: U937 cells, Control_1 (RNA-seq)

description: Control plasmid transduced U937 cell line 1

tag: cell line

value: genetically modified U937


title: E13_singlecell_control

description:
mRNA
Control_SP

source_name: E13.5 singlecell control

extract_protocol:
Soft palate tissue (posterior third of the palatal region) was digested from E13.5 wild type embryos by TrypLE express enzyme (Thermo Fisher Scientific) at 37°C with shaking at 600 rpm for 20 min.
Full-length cDNA was reverse transcribed from poly-adenylated mRNA using primers containing: an illumina TruSeq Read 1, 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI) and 30 nt poly(dT) sequence. Silane magnetic beads are used to purify the first-strand cDNA from post GEM-RT reaction mixture. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, a sample index and TruSeq Read 2 are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplication.
Chrominum Single Cell 3' Gene Expression Library


title: s200525a4


title: BY4741_DSN_rep1

description:
BY-DSN_1
HT-5Pseq with DSN treatment and probes


title: s200707N5

value: Normal control

value: normal urine


title: SC-BactRS-12S-SCR-344_S10_R1_001


title: SC-BactRS-12S-SCR-343_S9_R1_001


title: SC-BactRS-12S-SCR-340_S6_R1_001

source_name: ∆chvI EV

value: delta_chvI xylX::pMT585


title: SC-BactRS-12S-SCR-341_S7_R1_001


title: SC-BactRS-12S-SCR-342_S8_R1_001


title: SC-BactRS-12S-SCR-339_S5_R1_001


title: SC-BactRS-12S-SCR-338_S4_R1_001


title: SC-BactRS-12S-SCR-337_S3_R1_001


title: QA_1_1 Queen

city: Seoul

first: Igojo

last: Kang

state: Seoul

address: Gwanak_1 Gwanak-ro, Gwanak-gu

department: Applied Biology and Chemistry

country: South Korea

institute: Seoul National University

data_processing:
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
small RNA-seq reads were aligned to the ACSNU 2.0 genome
Transcripts Per Million (TPM) were calculated using Kallisto program.
Genome_build: ACSNU 2.0
Supplementary_files_format_and_content: Text files include TPM values for each Sample.

organism: Apis cerana

source_name: Queen

extract_protocol:
Dissect organs from Apis cerana, flash frozen on dry ice, and RNA was isolated using Trizol reagent. Small RNA-Seq Library Prep Kit (Cat. No. 052.96) was used with 1 ug of total RNA for the construction of sequencing libraries.
small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: Adult

value: wild type


title: SC-BactRS-12S-SCR-335_S1_R1_001


title: U937 cells, Control_2 (RNA-seq)

description: Control plasmid transduced U937 cell line 2


title: QR_1_3 Queen

value: Pupae


title: QA_1_3 Queen


title: QDR_1_1 Queen


title: QR_1_1 Queen


title: QR_1_2 Queen


title: QDR_1_3 Queen


title: QA_1_2 Queen


title: QW_1_3 Queen


title: QW_1_1 Queen


title: QW_1_2 Queen


title: D_1_3 Drone

source_name: Drone


title: QL_1_2 Queen

value: Larvae


title: SC-BactRS-12S-SCR-336_S2_R1_001


title: QL_1_3 Queen


title: D_1_1 Drone


title: OA_1_2 Worker

source_name: Worker


title: OA_1_1 Worker


title: OA_1_3 Worker


title: YA_1_3 Worker


title: YA_1_1 Worker


title: YA_1_2 Worker


title: QDR_1_2 Queen


title: DRB_1_1 Honey bee

source_name: Honey bee


title: DRB_1_3 Honey bee


title: R_1_2 Honey bee


title: DR_1_1 Honey bee


title: DR_1_3 Honey bee


title: R_1_1 Honey bee


title: DR_1_2 Honey bee


title: R_1_3 Honey bee


title: W_1_1 Honey bee


title: L5_1_3 Honey bee


title: L5_1_2 Honey bee


title: L5_1_1 Honey bee


title: W_1_3 Honey bee


title: W_1_2 Honey bee


title: QL_1_1 Queen


title: L4_1_3 Honey bee


title: D_1_2 Drone


title: L4_1_1 Honey bee


title: L3_1_3 Honey bee


title: L4_1_2 Honey bee


title: L3_1_2 Honey bee


title: DRB_1_2 Honey bee


title: L3_1_1 Honey bee


title: L2_1_1 Honey bee


title: L1_1_3 Honey bee


title: L1_1_2 Honey bee


title: L2_1_3 Honey bee


title: L2_1_2 Honey bee


title: E_1_3 Honey bee

value: Egg


title: E_1_2 Honey bee


title: L1_1_1 Honey bee


title: QO_1_1 Queen

value: Ovary


title: WO_2_1 Worker


title: Wvenom_2_1 Worker

value: Venom Gland


title: QO_2_1 Queen


title: WO_1_1 Worker


title: WR_2_1 Worker

value: Rectum


title: WR_1_1 Worker


title: WV_2_1 Worker

value: Ventriculus


title: WB_2_1 Worker

value: Brain


title: DT_2_1 Drone

value: Testis


title: WB_1_1 Worker


title: DR_2_1 Drone


title: DMGld_2_1 Drone

value: Mucus Gland


title: DMGld_1_1 Drone


title: DV_1_1 Drone


title: DV_2_1 Drone


title: DB_2_1 Drone


title: DR_1_1 Drone


title: E_1_1 Honey bee


title: DB_1_1 Drone


title: WV_1_1 Worker


title: Wvenom_1_1 Worker


title: dinorΔ Rep3

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.5 and processed by Trim Galore version 0.4.4 to remove adapters and low-quality reads.
Clean reads were aligned to the C. auris B8441 reference genome using the STAR version 020201 and Subjunc version 1.5.3 software.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 1 were considered to represent significantly differentially expressed genes (DEGs). The GO term analysis of biological processes represented in DEGs was performed using clusterProfiler version 3.10.1.
Genome_build: C. auris B8441 (GCA_002759435.2)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Candidozyma auris

source_name: C. auris

growth_protocol: Overnight cultures were diluted 1:100 into 50 mL of YPD medium and grown at 30 °C with shaking for 18 h.

extract_protocol:
Hot phenol method
NEBNext Ultra II RNA Library Prep Kit (NEB, E7770).

value: CBS10913 leu2[delta]:FRT arg4:PB[LEU2] dinor[delta]:FRT

tag: treatment

value: Untreated


title: dinorΔ:DINOR Rep3

value: CBS10913 leu2[delta]:FRT arg4:PB[LEU2] dinor[delta]:FRT DINOR:ARG4


title: WT Rep3


title: dinorΔ Rep2


title: DT_1_1 Drone


title: WT Rep1


title: dinorΔ Rep1


title: dinorΔ:DINOR Rep2


title: WT Rep2


title: dinorΔ:DINOR Rep1


title: Skin-S.aureus-rep3

city: Baltimore

first: Luis

last: Garza

state: Maryland

address: 1551 Orleans Street

department: Dermatology

institute: Johns Hopkins University

description:
S. aureus treated mice scar on wound day 12
SA 3

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.na36.mm10.transcript.csv

label: biotin

source_name: Skin treated with S. aureus on wound day3

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip 3' IVT Plus Kit per manufacturer's instructions.

growth_protocol: 21-day-old, 8 to 12 -gram male and female mice in their first telogen phase were selected.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Mice were anesthetized with vaporizing anesthesia (Baxter, Isoflurane), shaved, and denuded of 1.44 cm² full thickness skin using sterile procedures. PBS and 1e7 /100ul  S. aureus were injected under the scab on wound day3.

value: 21 days old mice

tag: time

value: Wound day 12

value: wounded back skin


title: Skin-S.aureus-rep1

description:
S. aureus treated mice scar on wound day 12
SA 1


title: Skin-S.aureus-rep2

description:
S. aureus treated mice scar on wound day 12
SA 2


title: Skin-SPF-rep1

description:
SPF mice scar on wound day 12
SPF1

source_name: SPF mice

growth_protocol: 21-day-old, 8 to 12 -gram male and female Germ free (GF) and specific pathogen free (SPF) mice in their first telogen phase were selected.

treatment_protocol: Mice were anesthetized with vaporizing anesthesia (Baxter, Isoflurane), shaved, and denuded of 1.44 cm² full thickness skin using sterile procedures.

tag: condition

value: SPF


title: VPA 6M-3

city: Kodaira

last: Watanabe

state: Tokyo

address: 4-1-1 Ogawa Higashi

institute: National Center of Neurology and Psychiatry

description: Gene expression data from VPA 6M

hyb_protocol: The arrays were hybridized and washed using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were normalized by GCRMA.

organism: Callithrix jacchus

source_name: Cortical tissue of Area8B/9 from VPA 6M marmoset

label_protocol: Biotin-labeled cRNA was generated using the GeneChip 3'IVT Express Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: For production of VPA marmoset, pregnant marmoset was administered with VPA at post-conception days 60-66, and the offspring were used.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Marmosets were anesthesized with ketamine followed by pentobarbital. Diethylpyrocarbonate-treated phosphate-buffered saline was transcardially perfused. Cortical tissues were isolated and immersed in RNAlater (Thermo Fisher).

tag: animal id

tag: Sex

value: M

value: VPA

tag: age (days)

tag: area


title: VPA 3M-6

description: Gene expression data from VPA 3M

source_name: Cortical tissue of Area8B/9 from VPA 3M marmoset


title: Skin-SPF-rep2

description:
SPF mice scar on wound day 12
SPF2


title: Skin-PBS-rep3

description:
PBS treated mice scar on wound day 12
Con 3

source_name: Skin treated with PBS on wound day3

value: control


title: VPA 3M-3

description: Gene expression data from VPA 3M

value: F


title: Skin-PBS-rep2

description:
PBS treated mice scar on wound day 12
Con 2


title: VPA 6M-6

description: Gene expression data from VPA 6M


title: Skin-GF-rep3

description:
GF mice scar on wound day 12
GF3

source_name: GF mice

value: GF


title: Skin-GF-rep2

description:
GF mice scar on wound day 12
GF2


title: Skin-GF-rep1

description:
GF mice scar on wound day 12
GF1


title: Skin-PBS-rep1

description:
PBS treated mice scar on wound day 12
Con 1


title: Skin-SPF-rep3

description:
SPF mice scar on wound day 12
SPF3


title: VPA 0M-11

description: Gene expression data from VPA 0M

source_name: Cortical tissue of Area8B/9 from VPA 0M marmoset


title: VPA 0M-10

description: Gene expression data from VPA 0M


title: frac_inf_7hpi_cyto_rep2

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
RNA-seq of the cytosolic, nuclear and total cell fractions.
frac_reads.txt

data_processing:
The reads were trimmed with cutadapt to remove the linker CTGTAGGCACCATCAAT in the ribo-seq libraries and the linker AGATCGGAAGAGCACACGT in the mRNA libraries. The reads of the fractionation samples were trimmed to length 50 nucleotides.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus : Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files. For the mRNA and ribo-seq samples, the files include the number of uniquely aligned reads to the transcript, coding sequence, introns of the host genes, and to the coding sequence of the virus. For the total samples (no polyA selection), and to the mRNA and ribo-seq samples, a file with the breakdown of the aligned reads to the rRNA/tRNA, viral genome, host genome, host transcriptome, etc. For the fractionation samples, the number of uniquely aligned reads to the host transcripts. For the slam-seq samples, the per gene output of the GRAND-SLAM pipeline.
Supplementary_files_format_and_content: frac_reads.txt: Number of reads aligned uniquely to host genes in the fractionation samples
Supplementary_files_format_and_content: slam_inf_params.txt: Output of the GRAND-SLAM pipeline on the Infected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: slam_uninf_params.txt: Output of the GRAND-SLAM pipeline on the UnInfected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: frac_abs_TPM.txt: Absolute localization TPM values (calculated based on the linear regression of the total fraction as function of the cytosolic and nuclear fractions).

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Calu 3 cells, ATCC HTB-55

growth_protocol: Calu3 cells (ATCC HTB-55) were cultured in 6-well or 10cm plates with RPMI supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, 2mM L-Glutamine, 100Units/ml Penicillin and 1% Na-pyruvate.

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered. For SLAM-seq libraries Cells were harvested with Tri-reagent at 1, 2, 3, and 4 hours after addition of 4sU (corresponding to 4,5,6 and 7hpi for infected cells) . RNA was extracted under reducing conditions and treated with Iodoacetamide. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For fractionation, first a fraction of 10% of the cells was transferred to a new tube and RNA was extracted in Tri-reagent to obtain whole cellular extract. Nuclear fraction was separated from cytoplasmic fraction by centrifugation following cell lysis. RNA was then extracted from both fraction in Tri-reagent. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen).
RNA-seq: mRNA samples were subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products were then used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. Ribo-seq: Cells were treated with 100µg/mL CHX for 1 minute. Cells were then placed on ice, washed twice with PBS containing 100µg/mL CHX, scraped from 10cm plates, pelleted and lysed with lysis buffer (1% triton in 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol supplemented with 10 U/ml Turbo DNase and 100µg/ml cycloheximide). After lysis samples stood on ice for 2h and subsequent Ribo-seq library generation was performed. Briefly, cell lysate was treated with RNAseI for 45min at room temperature followed by SUPERase-In quenching. Sample was loaded on sucrose solution (34% sucrose, 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol and 100µg/ml cycloheximide) and spun for 1h at 100K RPM using TLA-110 rotor (Beckman) at 4c. Pellet was harvested using TRI reagent and the RNA was collected using chloroform phase separation. For size selection, 15uG of total RNA was loaded into 15% TBE-UREA gel for 65min, and 28-34 nt footprints were excised using 28 nt and 34 nt flanking RNA oligos, followed by RNA extraction and ribo-seq protocol (Finkel Y. et. al., 2020, ELife)
RNA-seq of whole cells as well as nuclear and cytoplasmic fractions, ribosome profiling, and SLAM-seq.

treatment_protocol: Cells were infected for indicated time points before treatment or left uninfected. For Ribo-seq libraries, samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX. For SLAM-seq, 200μM 4sU was added to the growth media of the cells 3hpi.

tag: virus strain

value: Calu 3 cells, ATCC HTB-55

tag: hours post infection


title: frac_inf_7hpi_total_rep2


title: frac_inf_7hpi_nuc_rep2


title: UE 6M-9

description: Gene expression data from UE 6M

source_name: Cortical tissue of Area8B/9 from UE 6M marmoset

value: UE


title: UE 3M-7

description: Gene expression data from UE 3M

source_name: Cortical tissue of Area8B/9 from UE 3M marmoset


title: UE 0M-10

description: Gene expression data from UE 0M

source_name: Cortical tissue of Area8B/9 from UE 0M marmoset


title: UE 6M-7

description: Gene expression data from UE 6M


title: UE 3M-9

description: Gene expression data from UE 3M


title: VPA 0M-7

description: Gene expression data from VPA 0M


title: UE 0M-9

description: Gene expression data from UE 0M


title: frac_inf_7hpi_total_rep1


title: frac_inf_7hpi_cyto_rep1


title: frac_inf_7hpi_nuc_rep1


title: UE 6M-8

description: Gene expression data from UE 6M


title: Calu3_fp_8hpi_2

description: Ribo-seq after treatment with Cycloheximide

data_processing:
Library strategy: Ribo-seq
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from  our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files with the number of reads on the transcripts, coding sequence, introns of the host genes, on the coding sequence of the virus, and also global number of reads aligned to the rRNA abd tRNA
Supplementary_files_format_and_content: global.txt: Global number of reads aligned to rRNA, host and Virus
Supplementary_files_format_and_content: transcript_host.txt: For each host gene, number of read aligned uniquely to the transcript
Supplementary_files_format_and_content: cds_host.txt: For each host gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: cds_virus.txt: For each viral gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: transcript_introns.txt: For each host gene, number of read aligned uniquely to the transcript

source_name: Homo Sapiens, SARS-CoV-2

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA samplewas subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. Ribo-seq:

treatment_protocol: Cells were infected for 3, 5 or 8 hours before treatment or left uninfected. For Ribo-seq libraries, samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.


title: slam_inf_5hpi_2h_4sU_rep1

description:
RNA-seq after 4sU labeling
slam_inf_params.txt

data_processing:
The reads were trimmed with cutadapt to remove the linker CTGTAGGCACCATCAAT in the ribo-seq libraries and the linker AGATCGGAAGAGCACACGT in the mRNA libraries. The reads of the fractionation samples were trimmed to length 50 nucleotides.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus : Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files. For the mRNA and ribo-seq samples, the files include the number of uniquely aligned reads to the transcript, coding sequence, introns of the host genes, and to the coding sequence of the virus. For the total samples (no polyA selection), and to the mRNA and ribo-seq samples, a file with the breakdown of the aligned reads to the rRNA/tRNA, viral genome, host genome, host transcriptome, etc. For the fractionation samples, the number of uniquely aligned reads to the host transcripts. For the slam-seq samples, the per gene output of the GRAND-SLAM pipeline.
Supplementary_files_format_and_content: frac_reads.txt: Number of reads aligned uniquely to host genes in the fractionation samples
Supplementary_files_format_and_content: slam_inf_params.txt: Output of the GRAND-SLAM pipeline on the Infected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: slam_uninf_params.txt: Output of the GRAND-SLAM pipeline on the UnInfected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: halflife.txt: Half-life values (calculated based on regression of the log old fraction, estimated by the GRAND-SLAN, as function of time)


title: slam_inf_6hpi_3h_4sU


title: slam_inf_5hpi_2h_4sU_rep2


title: slam_inf_4hpi_1h_4sU


title: UE 3M-8

description: Gene expression data from UE 3M


title: slam_inf_no4sU

data_processing:
The reads were trimmed with cutadapt to remove the linker CTGTAGGCACCATCAAT in the ribo-seq libraries and the linker AGATCGGAAGAGCACACGT in the mRNA libraries. The reads of the fractionation samples were trimmed to length 50 nucleotides.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus : Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files. For the mRNA and ribo-seq samples, the files include the number of uniquely aligned reads to the transcript, coding sequence, introns of the host genes, and to the coding sequence of the virus. For the total samples (no polyA selection), and to the mRNA and ribo-seq samples, a file with the breakdown of the aligned reads to the rRNA/tRNA, viral genome, host genome, host transcriptome, etc. For the fractionation samples, the number of uniquely aligned reads to the host transcripts. For the slam-seq samples, the per gene output of the GRAND-SLAM pipeline.
Supplementary_files_format_and_content: frac_reads.txt: Number of reads aligned uniquely to host genes in the fractionation samples
Supplementary_files_format_and_content: slam_inf_params.txt: Output of the GRAND-SLAM pipeline on the Infected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: slam_uninf_params.txt: Output of the GRAND-SLAM pipeline on the UnInfected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: halflife.txt: Half-life values (calculated based on regression of the log old fraction, estimated by the GRAND-SLAN, as function of time)^SAMPLE = GSM5049227
The reads were trimmed with cutadapt to remove the linker CTGTAGGCACCATCAAT in the ribo-seq libraries and the linker AGATCGGAAGAGCACACGT in the mRNA libraries. The reads of the fractionation samples were trimmed to length 50 nucleotides.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus : Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files. For the mRNA and ribo-seq samples, the files include the number of uniquely aligned reads to the transcript, coding sequence, introns of the host genes, and to the coding sequence of the virus. For the total samples (no polyA selection), and to the mRNA and ribo-seq samples, a file with the breakdown of the aligned reads to the rRNA/tRNA, viral genome, host genome, host transcriptome, etc. For the fractionation samples, the number of uniquely aligned reads to the host transcripts. For the slam-seq samples, the per gene output of the GRAND-SLAM pipeline.
Supplementary_files_format_and_content: frac_reads.txt: Number of reads aligned uniquely to host genes in the fractionation samples
Supplementary_files_format_and_content: slam_inf_params.txt: Output of the GRAND-SLAM pipeline on the Infected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: slam_uninf_params.txt: Output of the GRAND-SLAM pipeline on the UnInfected slam-seq samples. Includes, number of reads, NTR mean and MAP, and more.
Supplementary_files_format_and_content: halflife.txt: Half-life values (calculated based on regression of the log old fraction, estimated by the GRAND-SLAN, as function of time)


title: Calu3_mrna_8hpi_1

description: RNA-seq with polyA selection

data_processing:
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from  our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : hg19 genome and annotation from UCSC, besides the mitochendria genes which are from Ensembl. Virus Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: All processed files are tab delimited files with the number of reads on the transcripts, coding sequence, introns of the host genes, on the coding sequence of the virus, and also global number of reads aligned to the rRNA abd tRNA
Supplementary_files_format_and_content: global.txt: Global number of reads aligned to rRNA, host and Virus
Supplementary_files_format_and_content: transcript_host.txt: For each host gene, number of read aligned uniquely to the transcript
Supplementary_files_format_and_content: cds_host.txt: For each host gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: cds_virus.txt: For each viral gene, number of read aligned uniquely to the coding sequence
Supplementary_files_format_and_content: transcript_introns.txt: For each host gene, number of read aligned uniquely to the transcript


title: Calu3_mrna_3hpi_total

description: RNA-seq without polyA selection


title: Calu3_fp_3hpi


title: Calu3_fp_8hpi_1


title: Calu3_fp_5hpi


title: Calu3_mrna_8hpi_2_total

description: RNA-seq without polyA selection


title: Calu3_mrna_5hpi_total

description: RNA-seq without polyA selection


title: Calu3_mrna_5hpi

description: RNA-seq with polyA selection


title: Calu3_mrna_8hpi_1_total

description: RNA-seq without polyA selection


title: Calu3_mrna_8hpi_2

description: RNA-seq with polyA selection


title: slam_inf_7hpi_4h_4sU


title: Calu3_mrna_3hpi

description: RNA-seq with polyA selection


title: CO7

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

data_processing:
Illumina Casava software
Sequencing adaptors, low-complexity reads, and reads containing low quality bases were removed in an initial data-filtering step. Reads with a PhredScore lower than 30 were filtered out. Quality control (QC) and read statistics were estimated with FastQC v0.11.8 and MultiQC v1.9 software. After QC, 29 and 31 samples (seven or eight samples per group) remained for further analyses from CAR and COT, respectively. Reads were mapped to the Bos taurus reference genome (ARS-UCD 1.2) [31] using the STAR aligner v. 2.7.3a. Raw counts per gene were obtained using the –quantMode GeneCounts flag from STAR based on the gene annotation file (release 100, Ensembl). MultiQC, NOISeq, and edgeR software were used to perform the post-mapping quality control. Genes with expression values lower than 1 count per million in 50% of the samples were filtered out. After filtering, the genes of CAR and COT tissues were analyzed using the DESeq2 v.1.22.1 software to identify DEGs.
Genome_build: Bos taurus ARS-UCD 1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every tissue, gene and every sample

organism: Bos taurus

source_name: coyledon

extract_protocol:
Total RNA of eight female samples per treatment was isolated from the CAR and COT tissues using the RNeasyâ kit (Qiagenâ, Germantown, MA) followed by on-column DNase treatment, according to the manufacturer's protocol.
Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA). Library preparation and paired-end sequencing with 150-bp reads at a depth of 20 M reads/sample were carried out at Novogene Co. (Nanjing, China).

treatment_protocol: The factors examined included vitamin and mineral supplementation (VTM or NoVTM) and rate of gain (low gain – LG or moderate gain – MG). The treatments were arranged as follows: (1) no vitamin and mineral supplementation and low gain (NoVTM_LG, n = 9); (2) vitamin and mineral supplementation and low gain (VTM_LG, n = 9); (3) no vitamin and mineral supplementation and moderate gain (NoVTM_MG, n = 9), and (4) vitamin and mineral supplementation and moderate gain (VTM_MG, n = 8).

value: placental cotyledon

tag: developmental stage

value: 83 days of preganancy

tag: farm


title: CO76


title: CO68


title: CO65


title: Exosome_P_PDLSCs_rep1

city: Xi'an

first: zheng

middle: ya

last: wang

address: Changle West Road

institute: The Fourth Military Medical University

description: miRNA expression in P-PDLSCs-derived exosomes (P-Exo)

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: P-PDLSCs culture supernatants

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: The culture supernatants of healthy PDLSCs (H-PDLSCs, obtained from healthy periodontal ligament tissue) and inflammatory PDLSCs(P-PDLSCs, obtained from periodontitis periodontal ligament tissue; L-PDLSCs,H-PDLSCs treated with 100 ng/mL lipopolysaccharide for 7 days) were used for exosomes extraction by using ultracentrifuge.

tag: source

value: culture supernatants

tag: cell type

value: inflammatory periodontal ligament stem cells (P-PDLSCs)

tag: cell source

tag: sample type

value: P-PDLSCs-derived exosomes


title: Exosome_L_PDLSCs_rep1

description: miRNA expression in L-PDLSCs-derived exosomes (L-Exo)

source_name: L-PDLSCs culture supernatants

value: inflammatory periodontal ligament stem cells (L-PDLSCs)

value: H-PDLSCs treated with lipopolysaccharide for 7 days

value: L-PDLSCs-derived exosomes


title: CO67

tag: tissue


title: CO52


title: CO48


title: CO45


title: CO47


title: CO46


title: Exosome_H_PDLSCs_rep1

description: miRNA expression in H-PDLSCs-derived exosomes (H-Exo)

source_name: H-PDLSCs culture supernatants

value: healthy periodontal ligament stem cells (H-PDLSCs)

value: obtained from healthy periodontal ligament tissue

value: H-PDLSCs-derived exosomes


title: CO44


title: CO43


title: CO37


title: CO36


title: CO34


title: CO31


title: CO28


title: CO35


title: CO3


title: CO24


title: CO25


title: CO59


title: CO23


title: CO60


title: CO20


title: CO22


title: CO18


title: CO16


title: CO15


title: CA74

source_name: caruncle

value: placental caruncle


title: CA76


title: CA65


title: CA60


title: CA7


title: CA52


title: CA59


title: CO41


title: CA47


title: CA48


title: CA36


title: CA35


title: CA44


title: CA31


title: CA23


title: CA37


title: CA46


title: CA34


title: CA75


title: CA20


title: CA22


title: CA28


title: CO13


title: CA16


title: CA18


title: CA24


title: Chow_Input-rep2

city: Cambridge

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

country: United Kingdom

institute: Univerity of Cambridge

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were trimmed using trimgalore with the --trim1 option for paired end aligments. ChIP and ATAC reads were aligned using Bowtie version 1.2.3 using the following parameters --best --tryhard -p 14 -X 500 --chunkmbs 200 -m 1. RNA reads were aligned using STAR version 2.6.0 using the ensemble transcripts .gtf with the following parameters --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMstrandField intronMotif
ATAC and ChIP reads were filtered for PCR duplicates using picardTools Mark Duplicates with the REMOVE_DUPLICATES=true option ; reads were further filtere to remove all reads mapping to blacklisted regions.
Peaks were called in MACS2 version 2.2.5 using the  -f BAMPE -q 0.00001 options. Peaks were additionally filtered to select for only the loci that had a summit height greater than 20 reads, and less then 500 reads to filter out biological noise
Read coverage of genes exons was preformed using bedtools coverage. total reads mapping to genes was found by totalling to sum of reads mapping to across exons.
Pileups of fragments were generated using bedtools coverage version2.29.0.  the --split option was added for RNA-seq pileups, while the -pc option was added for paired end files. bigWigs were generates using ucsctools wigToBigWig
Genome_build: rheMac10
Supplementary_files_format_and_content: bigWig : un-normalised coverage of filtered fragments (reconstructed, duplicate-filtered fragments : see above)

organism: Macaca mulatta

source_name: Liver biopsy

growth_protocol: 11-12 year old male rhesus macaques were fed a standard chow diet, (15% calories from fat, 27% from protein, and 59% from carbohydrates). Livers were then biopsied. Rhesus macaques were then switched to a high fat diet (36% calories from fat, 18% from protein, 45% from carbohydrates) for 6 months. Livers were biopsied again after the end of the six month period.

extract_protocol:
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with respective antibodies.
Sequencing library preparation and reactions were conducted at City of Hope’s Integrative Genomics Core. ChIP-seq libraries were made using Illumina Tru-Seq library preparation kit and multiplexing barcodes compatible with Illumina HiSeq 2500 technology. RNAseq libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems)

tag: diet

value: Chow

tag: animal id#


title: CA13

tag: treatment


title: HFD_H3K27ac-rep2

value: High fat

tag: antibody

value: ab4729, Abcam


title: HFD_Input-rep2


title: CA45


title: Chow_Input-rep1


title: CA15


title: R493_4h_r3 [1649.L]

city: Cologne

first: Deepak

middle: Dharamchand

last: Bhandari

email: bhandari@mpipz.mpg.de, dharamch@msu.edu

state: nrw

address: Carl-von-linne-weg, 10

department: Plant-Microbe interactions

country: Germany

institute: Employer

data_processing:
RNA-seq reads were mapped to the annotated genome of Arabidopsis thaliana (TAIR10) using TOPHAT2 (a = 10, g = 10) and transformed into a read count per gene per sample using the htseq-count script (s = reverse, t = exon) in the package HTSeq
Genes with less than 100 reads in all samples together were discarded; subsequently, the count data of the remaining genes were TMM normalized and log2 transformed using functions ‘calcNormFactors’ and ‘voom’
Genome_build: TAIR10
Supplementary_files_format_and_content: counts

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis seeds were grown in soil under controlled environment chambers under a 10 h light regime (150-200 μE/m2s) at 22 °C and 60 % relative humidity

extract_protocol:
Total RNA purification with an RNeasy Plant Mini Kit (Qiagen)
RNA-seq libraries were prepared from 1 µg total RNA according to TruSeq RNA sample preparation v2 guide (Illumina)

treatment_protocol: leaves from four-week-old plants were syringe infiltrated with Pst AvrRps4 (OD600=0.005). Total RNA isolated from 4 different plants was pooled as a biological replicate. 3 replicates were sequenced.

tag: genotype

value: 4-week old leaves

tag: pathogen

value: Pst AvrRps4

tag: time point

value: 4 hpi

tag: replicate


title: R493_4h_r1 [1649.J]


title: R493_4h_r2 [1649.K]


title: eds1_2_4h_r1 [1649.G]


title: CA29

value: 83 days of preganancy


title: eds1_2_4h_r3 [1649.I]


title: Chow_H3K27ac-rep2


title: HFD_H3K4me3-rep2

value: ab37415, Abcam


title: Chow_H3K4me3-rep2


title: HFD_H3K4me3-rep1


title: HFD_Input-rep1


title: HFD_RNA-rep2


title: CA25


title: eds1_2_4h_r2 [1649.H]


title: Chow_H3K27ac-rep1


title: w.tEDS1_4h_r2 [1649.E]


title: w.tEDS1_4h_r1 [1649.D]


title: Chow_RNA-rep2


title: 35S:TEM1_1

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

data_processing:
Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4
QC check was performed on the raw sequencing data, removing low-quality portions. The minimum length established was 35 and the quality score 25. FastQC was performed before and after the trimming.
High-quality reads were mapped to using Spliced Transcripts Alignment to Reference (STAR) software (v2.4.0)
STAR alignment files were used as input for Cuffdiff (v2.2.1) together with the TAIR 10 annotation file to calculate gene expression values
Genome_build: Arabidopsis thaliana reference genome (TAIR10)
Supplementary_files_format_and_content: xlsx file include RPKM values for each Sample

source_name: Whole plants

growth_protocol: Each sample was pooled from twenty 10-day old plants grown at LD 22ºC and collected at ZT18

extract_protocol:
Total RNA was extracted with PureLink™ RNA Mini Kit (Invitrogen), treated with TURBO DNA-free™ Kit (Invitrogen), and used for the construction of cDNA libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample

value: 20 pooled 10-day old plants

tag: growth conditions

value: LD 22ºC and collected at ZT18


title: Col_4h_r2 [1649.B]


title: Chow_H3K4me3-rep1


title: Chow_RNA-rep1


title: Col_4h_r3 [1649.C]


title: Col_4h_r1 [1649.A]


title: 35S.TEM1_2


title: HFD_RNA-rep1


title: WT_Arabidopsis_2

value: WT


title: HFD_ATAC-rep2


title: w.tEDS1_4h_r3 [1649.F]


title: WT_Arabidopsis_1


title: Timepoint16_ATAC-Seq

city: Boston

first: Salvador

last: Casani

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
Fastq files were trimmed using trimmomatic software with options LEADING:25 TRAILING:25 SLIDINGWINDOW:5:25 MINLEN:25
Files were mapped to S. cerevisiae reference genome with bowtie 2 basic options. Mapped files were sorted and dup removed
Peaks from files were called using MACS2 software, peaks were merged to obtain consensus peaks and then used as features to count using feature counts software, which released a peak counts file, provided as processed data.
Genome_build: Scerevisiae R64
Supplementary_files_format_and_content: Peak count matrix

source_name: Yeast Metabolic Cycle

growth_protocol: Cells were grown at illumina bioFlo 120 fermenter.

extract_protocol:
~30 Million cycling yeast cells were extracted from the fermentor and fixed for 5 minutes with 1% formaldehyde, fixation was stopped with 2.5M glycine. Cells were washed and treated with zymoliase for 12 minutes, after sorbitol washes cells were incubated with lysis buffer, nuclei was extracted and transposition reaction was applied as specified in Illumina protocol. When reaction finishes DNA is decroslinked and proceeded to library preparation and PCR amplification
Library construction and sequencing were performed following the Illumina protocol. Briefly, DNA was end repaired and A-tailed. PCR products were gel-extracted again and quantified on an Agilent Bioanalyzer.

tag: time points

tag: metabolic cycle

value: Reductive Charging


title: Timepoint15_ATAC-Seq

value: Reductive Building


title: HFD_H3K27ac-rep1


title: Timepoint14_ATAC-Seq


title: Timepoint18_ATAC-Seq


title: Chow_ATAC-rep1


title: Timepoint17_ATAC-Seq


title: Chow_ATAC-rep2


title: HFD_ATAC-rep1


title: Timepoint11_ATAC-Seq


title: Timepoint12_ATAC-Seq


title: Timepoint9_ATAC-Seq

value: Oxidative


title: Timepoint10_ATAC-Seq


title: Timepoint8_ATAC-Seq


title: Timepoint13_ATAC-Seq


title: Timepoint6_ATAC-Seq


title: Timepoint7_ATAC-Seq


title: Timepoint5_ATAC-Seq


title: Timepoint4_ATAC-Seq


title: HCT69-1T PDO

city: Koto-ku

first: Ryoji

last: Yao

address: 3-8-31 Ariake

institute: The JFCR-Cancer Institute

description: gene expression data of PDO derived from primary tumor

hyb_protocol: Following fragmentation, 5.2 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip Human transcriptome Array 2. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome analysis console 4.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: PDO established from surgical specmen HCT69-1T

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA ( GeneChip WT PLUS Reagent Kit (Affymetrix)).

growth_protocol: PDOs were collected and matrigel were removed using cell recovery solution.

extract_protocol: RNA was extracted using an RNeasy Micro Kit (Qiagen). RNA quality was validated using an Agilent Bioanalyzer.

treatment_protocol: Collected PDOs were directly used for RNA isolation.

value: colorectal cancer

tag: pdo derived from

value: primary tumor


title: HCT83-4LM PDO

description: gene expression data of PDO derived from metastasis tumor

source_name: PDO established from surgical specmen HCT83-4LM

value: metastasis tumor


title: HCT83-6LMR PDO

description: gene expression data of PDO derived from recurrent tumor

source_name: PDO established from surgical specmen HCT83-6LMR

value: recurrent tumor


title: HCT71-1T PDO

source_name: PDO established from surgical specmen HCT71-1T


title: HCT83-1T PDO

source_name: PDO established from surgical specmen HCT83-1T


title: HCT69-3LM PDO

source_name: PDO established from surgical specmen HCT69-3LM


title: HCT71-3LM PDO

source_name: PDO established from surgical specmen HCT71-3LM


title: HCT67-3LM PDO

source_name: PDO established from surgical specmen HCT67-3LM


title: HCT64-3LM PDO

source_name: PDO established from surgical specmen HCT64-3LM


title: HCT67-1T PDO

source_name: PDO established from surgical specmen HCT67-1T


title: HCT64-5LM PDO

source_name: PDO established from surgical specmen HCT64-5LM


title: Timepoint2_ATAC-Seq


title: HCT67-4LMR PDO

source_name: PDO established from surgical specmen HCT67-4LMR


title: HCT64-1T PDO

source_name: PDO established from surgical specmen HCT64-1T


title: Timepoint3_ATAC-Seq


title: Timepoint1_ATAC-Seq


title: HCT60-1T PDO

source_name: PDO established from surgical specmen HCT60-1T


title: HCT59-4LM PDO

source_name: PDO established from surgical specmen HCT59-4LM


title: HCT51-2LN PDO

description: gene expression data of PDO derived from lymph node

source_name: PDO established from surgical specmen HCT51-2LN

value: lymph node


title: HCT60-3LM PDO

source_name: PDO established from surgical specmen HCT60-3LM


title: HCT59-1T PDO

source_name: PDO established from surgical specmen HCT59-1T


title: HCT51-4LM PDO

source_name: PDO established from surgical specmen HCT51-4LM


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 10, replicate 1

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

hyb_protocol: 3.5 µg of sense DNA was hybridized, with rotation, onto an Affymetrix GeneChip® Arabidopsis Gene 1.0 ST Array for 16 h at 45 °C. Arrays were washed on a Fluidics Station 450 (ThermoFisher Scientific, Catalog # 00-0079) using the Hybridization Wash and Stain Kit (Thermofisher Scientific, Catalog # 900720) and the Washing Procedure FS450_0002.

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files from each microarray experiment were loaded into the RStudio (v1.1.453) environment and normalized with the Robust Multichip Average (RMA) algorithm using the Oligo package. Tests of differential gene expression were performed using the Limma package, with cutoff criteria of: FDR of q < 0.05 and greater than two-fold change. Differentially-expressed genes (DEGs) were output and probe IDs were annotated using the TAIR10 version of the annotation for the AraGene 1.0 ST array. R version 4.0.0 was used. Scripts for microarray differential expression analysis were derived from scripts from the US National Aeronautics and Space Administration (NASA) GeneLab, which have been made publicly-available.

source_name: Roots of seedlings fixed after the tenth parabola, replicate 1

label_protocol: cDNA was synthesized from 100 ng of total RNA, and the cDNA was used as a template for in vitro transcription (IVT). The antisense RNA synthesized during the IVT reaction was used to generate sense DNA. Sense strand DNA was fragmented, biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (ThermoFisher Scientific, Catalog # 900670) per the manufacturer’s protocol.

growth_protocol: Petri dishes (100 mm x 15 mm; Fisher Scientific, Pittsburgh, PA, USA), containing 50 mL of a 0.5% Phytagel™-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg’s Vitamin Mixture, were prepared aseptically for planting. Seeds were sterilized via treatment with 70% ethanol for 10 minutes, and then with 50% bleach supplemented with Tween-20 at 2-3 drops per mL for 20 minutes, with seeds being mixed throughout the process. Seeds were washed with sterile water at least 6 times, and stored at 4 °C for 3-5 days. Seeds were dispensed onto the media surface in a laminar flow hood in one row of 12-15 seeds, and plates were sealed with Micropore® tape (3M, Maplewood, MN, USA). Plates were grown vertically at the University of florida in growth rooms at 19 ± 2 °C, and 24-h fluorescent lighting at approximately 80 µmol m-2 s-1 PAR until the time of transport to the experimental location. Plates were transported to Ellington Airport in Houston, Texas, inside a cooler lit with an LED light bank, and maintained onsite in a mobile growth setup consisting of a fluorescent light bank, with room temperature similar to that used for early growth.

extract_protocol: RNALater™-fixed samples were removed from -80 °C storage, and thawed overnight at 4°C. Seedlings were disentangled, and roots were dissected from shoots. Root tissues were used for RNA extraction, and shoots were restored to -80 °C storage. For each experimental condition, 3-4 biological replicates, derived from roots fixed in a single KFT, were used. Excess RNALater™ was removed from roots, and RNA was extracted using the QIAshredder and RNAeasy kits from QIAGEN (QIAGEN Sciences, MD, USA), using the manufacturer’s instructions. RNase-free DNase (QIAGEN GmbH, Hilden, Germany) was used for on-column digestion and removal of DNA

treatment_protocol: The morning before the flight, seedlings were transplanted from plates into Kennedy Space Center Fixation Tubes (KFTs) loaded with RNALater™ fixative internally fitted with wetted Kimwipes™ cut into a cylinder. On the flight day, KFTs were taken onboard the C-9 aircraft. Members of the group actuated the KFTs in level flight before the first parabola, and after the first, third, and tenth parabolas, fixing seedlings in RNALater™.

value: Whole Root

tag: cultivar

value: Wassilewskija (WS)

tag: age

value: 10 days, 24h light grown

tag: fixative

value: RNALater-fixed Sample


title: HCT50-1T PDO

source_name: PDO established from surgical specmen HCT50-1T

tag: tissue


title: HCT59-3LM PDO

source_name: PDO established from surgical specmen HCT59-3LM


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 10, replicate 2

source_name: Roots of seedlings fixed after the tenth parabola, replicate 2


title: HCT50-5LMR PDO

source_name: PDO established from surgical specmen HCT50-5LMR


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 10, replicate 3

source_name: Roots of seedlings fixed after the tenth parabola, replicate 3


title: HCT51-1T PDO

source_name: PDO established from surgical specmen HCT51-1T


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 3, replicate 4

source_name: Roots of seedlings fixed after the third parabola, replicate 4


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 3, replicate 2

source_name: Roots of seedlings fixed after the third parabola, replicate 2


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 1, replicate 4

source_name: Roots of seedlings fixed after the first parabola, replicate 4


title: HCT50-4LM PDO

source_name: PDO established from surgical specmen HCT50-4LM


title: HCT47-1T PDO

source_name: PDO established from surgical specmen HCT47-1T


title: HCT64-4LM PDO

source_name: PDO established from surgical specmen HCT64-4LM


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 3, replicate 3

source_name: Roots of seedlings fixed after the third parabola, replicate 3


title: HCT47-3LM PDO

source_name: PDO established from surgical specmen HCT47-3LM


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 3, replicate 1

source_name: Roots of seedlings fixed after the third parabola, replicate 1


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 1, replicate 2

source_name: Roots of seedlings fixed after the first parabola, replicate 2


title: HCT45-3LM PDO

source_name: PDO established from surgical specmen HCT45-3LM


title: pCaMV35S:14-3-3κ:GFP Root, Level Flight, replicate 4

source_name: Roots of seedlings fixed during level flight, replicate 4


title: pCaMV35S:14-3-3κ:GFP Root, Level Flight, replicate 3

source_name: Roots of seedlings fixed during level flight, replicate 3


title: HCT43-2Ov PDO

source_name: PDO established from surgical specmen HCT43-2Ov


title: pCaMV35S:14-3-3κ:GFP Root, Level Flight, replicate 1

source_name: Roots of seedlings fixed during level flight, replicate 1


title: HCT45-1T PDO

source_name: PDO established from surgical specmen HCT45-1T


title: pCaMV35S:14-3-3κ:GFP Root, Level Flight, replicate 2

source_name: Roots of seedlings fixed during level flight, replicate 2


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 1, replicate 3

source_name: Roots of seedlings fixed after the first parabola, replicate 3


title: HCT43-6LuMRRR PDO

source_name: PDO established from surgical specmen HCT43-6LuMRRR


title: HCT41-5LuMRR PDO

source_name: PDO established from surgical specmen HCT41-5LuMRR


title: WS, Parabola 10 End, replicate 3

source_name: Roots from seedlings fixed at the end of the tenth parabola, replicate 3

extract_protocol: RNALater™-fixed samples were removed from -80 °C storage, and thawed overnight at 4°C. Seedlings were disentangled, and roots were dissected from shoots. Root tissues were used for RNA extraction, and shoots were restored to -80 °C storage. For each experimental condition, 3-4 biological replicates, derived from roots fixed in a single KFT, were used. Excess RNALater™ was removed from roots, and RNA was extracted using the QIAshredder and RNAeasy kits from QIAGEN (QIAGEN Sciences, MD, USA), using the manufacturer’s instructions. RNase-free DNase (QIAGEN GmbH, Hilden, Germany) was used for on-column digestion and removal of DNA.

treatment_protocol: The morning before the flight, seedlings were transplanted from plates into Kennedy Space Center Fixation Tubes (KFTs) loaded with RNALater™ fixative internally fitted with wetted Kimwipes™ cut into a cylinder. On the flight day, KFTs were taken onboard the C-9 aircraft. Members of the group actuated the KFTs in level flight soon before the first parabola, immediately at the start of the first parabola, mid-way through the first parabola, and after the first, third, and tenth parabolas, fixing seedlings in RNALater™.

value: Wild-type

value: 12 days, 24h light grown


title: WS, Parabola 3 End, replicate 1

source_name: Roots from seedlings fixed at the end of the third parabola, replicate 1


title: HCT41-1T PDO

source_name: PDO established from surgical specmen HCT41-1T


title: WS, Parabola 10 End, replicate 1

source_name: Roots from seedlings fixed at the end of the tenth parabola, replicate 1


title: WS, Parabola 3 End, replicate 2

source_name: Roots from seedlings fixed at the end of the third parabola, replicate 2


title: HCT43-5LMRR PDO

source_name: PDO established from surgical specmen HCT43-5LMRR