title: 231-Kv-1

city: Medford

first: Samantha

last: Payne

address: 200 College Ave

institute: Tufts University

data_processing:
Quality control of raw read was performed using FastQC and adapter trimming and read filtering was done using Trimmomatic using standard settings.
Reads were mapped to the reference human genome (assembly GRCh38) with STAR.
Differential gene expression analysis was performed using EdgeR in R, genes with cpm less than 1 were filtered, and a fold change threshold of 1.5 was used.
Pathway enrichment analysis was performed using Gen Set Enrichment Analysis (GSEA).
Genome_build: Reads were mapped to the reference human genome (assembly GRCh38) with STAR.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample and Differential gene expression analysis

source_name: MDA-MB-231 with Kv1.5 channel

growth_protocol: The MDA-MB-231 breast cancer cell line was obtained from ATCC (Manassa, VA) and cultured in DMEM with 10% FBS (SH30071.03; Cytiva; Marlborough, MA) and penicillin-streptomycin glutamine (10378016; ThermoFisher Scientific; Waltham, MA). Cells were passaged regularly when they reached approximately 70% confluency and used between p5 and p15 for all experiments.  Cells were routinely checked for the presence of mycoplasma by a PCR based method using a Universal Mycoplasma Detection Kit (30-1012K; ATCC, Manassas, VA).

extract_protocol:
RNA was extracted from three separate biological replicates of MDA-MB-231-Control, 231-Kv1.5, and 231-Kir2.1 cells using the the RNA MiniPrep Kit (R1057; Zymo Research; Irvine, CA).  Samples were confirmed to have sufficient quality with Agilent Bioanalyzer before undergoing library preparation.
Library preparation was done by Tufts University Genomics Core using the TruSeq stranded mRNA kit (20020594; Illumina; San Diego, CA).
Samples were run on a HiSeq2500 platform at a depth of 50 million single-end 50 base pair reads to allow for transcript quantitation.

treatment_protocol: For infections, 1µg of constructs expressing human ion channel coding proteins RFP, Kv1.5-T2A-his-EGFP, or KCNJ2(Kir2.1)-Y242F-EGFP were used.  For each construct, HEK293T cells at a confluency of 80% were used to transfect for virus production.  Constructs were mixed with 0.5µg helper (encoding gag/pol) and 0.1µg encoding coat protein (pMD2) along with 6µL TransIT-Lenti transfection reagent (MIR6603; Mirus Bio; Madison, WI) in 200uL Opti-MEM (31985062; ThermoFisher Scientific; Waltham, MA).  Culture media of HEK293T cells was replaced with Opti-MEM and 200µL of transfection mixture and cells were kept in transfection media overnight. Transfection media was replaced with DMEM containing 1% Pen/Strep the following day.  Two days post-transfection media containing virus was collected and stored at -80C.  Collection was repeated on the following day and the total virus collected was combined.  To transduce cells, MDA-MB-231 or MDA-MB-468 cells were seeded in six-well plates at 2 x 105 cells per well in 2mL DMEM containing 10μg/mL polybrene and virus. The plates were centrifuged at 1500 r.p.m., 4°C for 1 h and incubated at 37 °C. Medium was changed after 16 h. Infected cells were sorted by FACS

tag: cell line

value: Triple negative breast cancer

value: Breast

value: Lentiviral transduction


title: Naïve B cell-HC1_Y20

status: Public on Sep 01 2021

type: SRA

city: Guangzhou

first: Binfeng

last: Chen

address: 58 Zhongshan Second Road

country: China

institute: Department of Rheumatology, The First Affiliated Hospital, Sun Yat-sen University

library_source: transcriptomic

data_processing:
Using FastQC (version 0.11.9) for quality assessment and HISAT2 (version 7.5.0) for alignment, with parameter -p for paried sequencing, and others are all default parameters
Using FeatureCounts (version 2.0.1) for transcripts assemble and expression levels calculation
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Naïve B cell

growth_protocol: Naïve human B cells were isolated from 3 donors and stimulated with anti-human IgM (5μg/ml) and anti-human CD40 (1μg/ml) antibodies

extract_protocol:
RNA purification was performed using Qiagen RNeasy Kit (Valencia, CA). 50 pg of total RNA was used as input for the SMART-seq v3 cDNA synthesis kit (Takara). 1 ng of cDNA was used as input for the NexteraXT kit (Illumina) using 9 cycles of PCR amplification. Final libraries were quantitated by qPCR and sized distribution determined by Bioanalyzer prior to pooling and sequencing on a HiSeq2500 using 50bp PE chemistry.
The RNA-seq libraries were made with Illumina HiSeq protocol.

treatment_protocol: YM-58483 or vehicle for 72h

tag: tissue

value: peripheral blood

tag: cell type

value: naive B cell

tag: treatment

value: treated with 20nm YM-58483


title: 10d stressed #2

type: RNA

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

country: Germany

institute: Research Institute for Farm Animal Biology

description: 10 d of repeated handling stress

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA in hybridization buffer was hybridized to 8×60 K Whole Salmon Genome Oligo Microarrays (ID 020938, Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 12.1.1.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Coregonus maraena

source_name: 10 d of repeated handling stress

label_protocol: 50 ng of RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the Low Input Quick Amp protocol. Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Fish were grown in water recirculation tanks of the Fisheries of the State Research Center for Agriculture and Fishery Mecklenburg-Western Pomerania (Born, Germany) and BiMES - Binnenfischerei GmbH (Friedrichsruhe, Germany). Fish were reared in fresh-water recirculation systems with a stocking density of 10 kg/m³ at 18 °C and a 12:12-h day-night cycle. Water quality was maintained by automated purification and disinfection (bio-filter and UV light).

extract_protocol: Fish was dissected and a portion of the head kidney was snap-frozen in liquid nitrogen. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations.

treatment_protocol: The fish (n = 48 in total) used in the experiments were juvenile with a starting size of about 20 cm. They were allowed to acclimatize to the recirculation system and the experimental tanks for at least 3 weeks. Experiments were always carried out in the morning (between 8 a.m. and 11 a.m.). To avoid tank effects, fish were placed in pairs consisting of one control fish and one test fish in identical dark-polyethene tanks (2 × 8 pairs; n = 32) during the acute stress experiments (3 h and 24 h). At the start of the experiment and before the handling procedure, one fish per pair was euthanized. This fish was designated the control fish (0 h). Following the sampling of the control fish, the stress protocol was applied for one minute to the remaining fish, designated the test fish. The stress protocol consisted of hunting and catching fish inside the water with nets, intermittently lifting the fish out of the tanks and finally transferring fish into secondary tanks, where pairs of test fish were left undisturbed for either 3 h or 24 h. After this period, test fish were euthanized and tissues were sampled as described below (see 2.3.). For the chronic handling stress experiment, control fish (n = 8) and test fish (n = 8) were kept in separate tanks for the duration of the experiment. Test fish were hunted and netted in the water for one minute once a day for ten days, while the controls were left undisturbed. The net lifting and tank-transferring steps performed in the acute-stress procedure were skipped in the chronic stress experiment to avoid skin injuries. To minimize habituation, handling was always performed at a random time within the 12 h ‘daylight’ period. Fish were euthanized 10 days after the onset of the chronic-stress procedures, 24 h after the last handling procedure.

value: head kidney

tag: gender

value: unknown

tag: age

value: juvenile fish of ~ 20 cm


title: InjPBS_rep1

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

description:
DEA_IL36_and_IL17a_vs_PBS.tsv
DEA_IL36_vs_PBS.tsv
DEA_IL17a_vs_PBS.tsv
counts.tsv

data_processing:
The RNA-Seq data primary analysis was performed with an in-house pipeline embedded in the QuickNGS workflow management system[45]: Generation of the fastq files and adapter removal was completed using the Illumina demultiplexing and conversion software bcl2fastq [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html]. Quality control checks of the RNA-Seq data were done with fastqc available online (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Subsequently, the reads were aligned to the mm10 reference genome sequence using STAR (v2.5.2b) with default parameters [46]. In the quantification step, reads were counted with featureCounts from the subread package v1.5.1 available online (http://subread.sourceforge.net)
Differential expression analysis was performed in R using the DESeq2 package (v1.30.0) [48]: First, the size factors of each sample were estimated using the function estimateSizeFactors with default parameters, then the dispersions of the counts were estimated by setting the minimal dispersion to 10e-6 and setting the fit type parameter to “local”. Finally, the likelihood ratio test (chi-squared test) for GLMs (negative binomial likelihood ratio test) was used to generate the differentially expressed genes (log2 fold change > 1 and corrected p-value <= 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: For each two pairs of conditions we provide the results table.

organism: Mus musculus

source_name: Injection of PBS

extract_protocol:
The tissues of the mouse ears were mechanically disrupted and homogenized by using tissue lyzer (Qiagen). The Nucleo Spin RNA (Macherey-Nagel, Düren, Germany) kit was used for total RNA extraction, according to the manufacturer’s instructions. Residual genomic DNA was removed by rDNase (RNase-free) digestion.
The cDNA libraries were generated using a TruSeq Stranded Total RNA Sample Preparation Kit (Illumina).

treatment_protocol: The cytokines IL-36γ and IL-17A (1µg of each cytokine dissolved in PBS; volume 5µl) were injected intradermally alone or in combination into the ear pinnae of C57BL/6 mice. PBS was used as control. Ear thickness measurement was performed daily. After 4 days mice were euthanized and a gene expression profiling was conducted.

value: Skin

tag: strain


title: 3h stressed_#6

description: 3 h after handling stress

source_name: 3 h after handling stress


title: InjL17A_rep3

description:
DEA_IL17a_vs_PBS.tsv
DEA_IL36_and_IL17a_vs_IL17a.tsv
counts.tsv

source_name: Injection of IL17A


title: 24h control_#2

description: control fish (w/o stress)

source_name: control fish (w/o stress)


title: 0956A: VCA0956, induced, replicate A

city: Kalamazoo

first: Ben

middle: James

last: Koestler

state: MI

address: 1903 West Michigan Avenue, 3119 Wood Hall

department: Biological Sciences

country: USA

institute: Western Michigan University

data_processing:
Set paired end reads (Geneious)
Raw sequences were trimmed using BBDuk (Geneious)
Reads were mapped to reference (AE014073.1, AF386526.1, AF250878, and VCA0956 from NC_002506) using Geneious mapper
Expression analysis was carried out to determine RPKM, FPKM and TPM (Geneious)
Supplementary_files_format_and_content: .xlsx file contains mapping and differential expression for each Shigella gene

organism: Shigella flexneri 2a str. 2457T

source_name: Bacteria RNA

growth_protocol: S. flexneri grown in LB + DOC (0.05% w/v), supplemented with Kanamycin (50 μg/ml) to maintain pVCA0956. Cultures incubated at 37 C, shaking at 220 rpm for 3 hours.

extract_protocol:
Purelink RNA Mini Kit (Thermo Fisher, 12183020) using the manufacturers protocol with Trizol reagent
RNA libraries were prepared for sequencing using standard protocols (Genewiz). Sequencing was performed by Genewiz.

treatment_protocol: Induction of the pTac promoter of VCA0956 using IPTG (100 μM)

tag: condition

value: +IPTG

tag: growth

value: LB + DOC, mid-log


title: InjIL36_rep3

description:
DEA_IL36_vs_PBS.tsv
DEA_IL36_and_IL17a_vs_IL36.tsv
counts.tsv

source_name: Injection of IL36γ


title: 231-Kir-3

state: MA

source_name: MDA-MB-231 with Kir2.1 channel


title: 231-Kir-2


title: 10d stressed #1

description: 10 d of repeated handling stress


title: 231-Kv-3


title: 10d stressed #3

description: 10 d of repeated handling stress


title: CM_e1

city: Norwich

first: Wenbo

last: Ma

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

description:
QM2_S284_L006
Biological replicate 1

data_processing:
The quality of the raw sequencing data was checked with FastQC v0.11.9
Read adapters were trimmed from reads using Trimmomatic v 0.36
reads were aligned with the indexed CLas-Psy62 isolate genome assembly (NC_012985.3) and parsed to it using HISAT2 v2.1.0
The number of reads mapped to each gene was counted using the feature counts function of the Rsubread package
Read counts were normalized for each sample for differential expression analysis using DESeq2 v1.30.1
Genome_build: NC_012985.3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized read counts for every genes and every sample

organism: Citrus macrophylla

source_name: midrib

extract_protocol:
Freeze-dried HLB-infected midribs (from 15–25 leaves) were ground to a fine powder in liquid nitrogen. 1ml of TLE extraction buffer was added to 100 mg citrus powder or the pellet obtained after the above bacterial isolation. Then, 60 µL of 500 mM CaCl2 was added, mixed thoroughly, and placed on ice for 10 min. Centrifugation at 12,000 x g for 10 min at 4 °C was performed, followed by two rounds of separation with 500 µl of phenol:Chloroform:isoamyl alcohol (25:25:1) and centrifugation at 15,000 x g for 10 min at 4 °C. The supernatant was mixed with 2 M LiCl and incubated overnight at -20 °C. RNA was precipitated by centrifugation at 15,000 x g for 30 min, washed twice with ice-cold 75% ethanol, centrifuged at 15,000 x g for 15 min and re-suspended in 20 µl of RNAse-free water. 10–15 adult psyllids were ground in liquid nitrogen, immediately suspended in 50 μl TRIzol® (Invitrogen) and ground until complete homogenization. An additional 950 μl of TRIzol® was added to the homogenate, followed by separation with 200 µl of chloroform, precipitation with 500 µl of isopropanol, and two washes with 75% ethanol as indicated by the manufacturer. The pellet was resuspended in 20-30 µl of RNAse-free water.
RNA was converted into sequencing-ready libraries for Illumina sequencing using TruSeq Stranded Total RNA reagents. Poly(A) Polymerase (NEB) treatment (polyA) and Poly(dT)-depleted library construction was tested in parallel. cDNA libraries were subjected to RNASeq, using an Illumina HiSeq-4000 system with 150-bp strand-specific single-end reads with technical duplicates.

treatment_protocol: pre-enrichment (bacterial isolation) performed according to Nobori et al. 2018, 1-step post enrichment using MICROBEnrich, 2-step enrichment using MICROBEnrich followed byRiboMinus Eukaryote Kit. All samples underwent ribodepletion using Illumina Ribo-Zero Plus except a subset of 2-step enrichmed RNA samples that underwent poly(A) polymerase treatment (polyA)

value: midrib

value: 1-step enrichment


title: InjL17A_rep1


title: InjIL17A_IL36_rep1

description:
DEA_IL36_and_IL17a_vs_PBS.tsv
DEA_IL36_and_IL17a_vs_IL36.tsv
DEA_IL36_and_IL17a_vs_IL17a.tsv
counts.tsv

source_name: Joint Injection of IL17A and IL36γ


title: 231-Kv-2


title: BMJ treated High fat diet C57BL/6J mouse liver at 16 weeks, biological rep4

city: Aurora

first: Rajesh

last: Agarwal

state: Colorado

address: 12850 E Montview Blvd

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

description: BMJ treated high fat diet liver

hyb_protocol: Samples were hybridized using the Affymetrix GeneChip®Whole Transcript (WT) Sense Target Labeling Assay. Heat cocktails at 65°C for 5 minutes, at 99°C for 5 minutes, at 45°C for 5 minutes cand entrifuge at maximum speed for 1 minute.

scan_protocol: GeneChip Fluidics Station (FS) 450 / Scanner 3000 and the protocol FS450_0001 for exon arrays

data_processing:
Data were processed using Affymetrix software. Expression estimates and detection above background p-values for individual genes were estimated using Affymetrix Power Tools and the RMA-sketch algorithm. Probe sets were grouped into gene clusters using Ensembl gene annotation (version GRCm38).  A probe set was included in a gene cluster if all of its associated probes aligned to a region completely contained within the exonic region of the gene.
MoEx-1_0-st-v1.r2.C57Bl6.MASKED.perl.pgf
MoEx-1_0-st-v1.r2.dt1.mm10.ensembl.C57.MASKED.mps

label: biotin

source_name: wild-type, BMJ treated high fat diet liver

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: C57BL/6J male mice from 4 weeks to16-weeks of age were fed-high fat diet (HFD), 60 kcal% fat from Research diets Inc., # D12492 to result in diet induced obesity (DIO) ; control group was fed 60 kcal% HFD for additional 40 days; treatment group was 60 kcal% HFD for additional 40 days plus orally gavaged with lyophilized bitter melon juice extract [(200mg/kg body weight/ day)

extract_protocol: RNA was isolated from snap frozen livers using Qiagen kit for both BMJ+DIO and DIO mice

treatment_protocol: Lyophilized bitter melon juice (BMJ) extract (oral gavage 200mg/kg/body weight-daily for 40 days)

value: 16 weeks

tag: Sex

value: male

tag: genotype

value: wild-type


title: 3h stressed_#7

description: 3 h after handling stress


title: CM_n

description:
QM1_S283_L006
Biological replicate 1


title: 10Soy_6

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.0.3, Rstudio V1.3.1093 and biomaRt V2.46.0
DESeq2  V1.30 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Mouse – GRCm38.84  mm10
Supplementary_files_format_and_content: tab-delimited text containing raw counts
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

source_name: liver

growth_protocol: Mice were obtained from JAX at 9 weeks of age and quanrantined in CBC for one week. Then 20 mice were placed on NP diet and 30 were on 20Soy diet for two weeks. At 12 weeks of age, mice were switched to their designated experimental diets and maintained on these diet for a total of 12 weeks. There were 10 mice in each group. Procedures performed during lifetime: Body weights, food and water intake were taken weekly. NMR was also performed weekly. Energy expenditure was measured using Promethion on almost all mice in week 10. Animals were sacrificed after a 4h fast using CO2 inhalation and decapitation.

extract_protocol:
Flash frozen liver was dissected and a small piece was placed in Trizol. After homogenization, BCP was added, samples were vortexed vigorously, and then spun. The aqueous phase was combined with an equal volume of ethanol and the sample was processed through a Qiagen RNeasy column according to the manufacturer's instructions. mRNA was stored at -80°C and samples were diluted to 100ng/µl for RNAseq.
Quant-Seq  3' mRNA-Seq Library Prep Kit
indexed and pooled samples, 50bp forward read

treatment_protocol: The diets used consisted of normal protein diet (NP, 20% casein),  low protein diet (LP, 5% casein), 20Soy (20% soy), 20Soy +SAA (20% soy and Met and Cys was added to match their concentration in NP diet), 10Soy (11.5% soy, the Met concentration was matched to LP diet)

value: Male

tag: dietary protein source

value: 11.5percent soy

tag: methionine and cysteine concentration gm%

value: 6 months


title: 231-RFP-1

source_name: MDA-MB-231 with RFP

value: Triple negative breast cancer

value: Breast

value: Lentiviral transduction


title: 231-Kir-1


title: BMJ treated High fat diet C57BL/6J mouse liver at 16 weeks, biological rep3

description: BMJ treated high fat diet liver


title: InjIL17A_IL36_rep2


title: 10Soy_5


title: InjIL17A_IL36_rep3


title: InjIL36_rep1


title: 24h control_#1

description: control fish (w/o stress)

value: head kidney


title: 24h control_#3

description: control fish (w/o stress)

value: unknown


title: BMJ treated High fat diet C57BL/6J mouse liver at 16 weeks, biological rep1

description: BMJ treated high fat diet liver


title: 24h stressed_#8

description: 24 h after handling stress

source_name: 24 h after handling stress

value: juvenile fish of ~ 20 cm


title: Ribo_U2392_sh2_48_rep2

city: Cambridge

first: Daniel

middle: J

last: Hodson

address: The Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus

department: Department of Haematology

institute: Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge

description: CDScounts.csv

data_processing:
Library strategy: Ribo-Seq
UMI stripping : UMI tools 0.5.3 –bc-pattern NNNNNN
Trimming: cutadapt 1.10, parameters: --quality-base=33 -e 0.1 -m 10 -q 20,20 -u 1 A47 Ribo-Seq only: (-a CTGTAGGCACCATCAATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC )
Alignment: STAR 2.6.0c, parametres: --twopassMode Basic
Counting of ribosomal P-sites and RNA-seq reads was performed as described in Gong et al.
Genome_build: GRCh 38
Supplementary_files_format_and_content: CDScounts.csv contains read counts per CDS (one CDS per gene). To build gene models first 30 nt and last 30 nt of each CDS region were removed to reflect translation elongation intensity.

source_name: U2392 cell line

growth_protocol: Lymphoma cell lines were cultured in RPMI medium (Gibco) supplemented with 10% testified tetracycline-free FBS (Gibco). All cell lines used in this study were confirmed to be free from mycoplasma contamination and identity was verified using a 16-amplicon multiplexed copy number variant fingerprinting assay(Phelan et al., 2018). All cells were cultured at 370C and 5% CO2.

extract_protocol:
For RNA-seq, total RNA was extracted using NucleoSpin RNA extraction kit (Machery-Nagel, Cat No. 740955.250) according to manufacturer’s protocol.  Ribosome profiling was conducted based on Ingolia 2012 protocol with minor modifications. Cells were treated with 100µg/ml of cycloheximide and harvested immediately by centrifugation. Approximately, 5 million cells were lysed in 300µl of buffer containing 20mM Tris-HCl, pH7.4, 150mM NaCl, 5mM MgCl2, 1% NP40, 1mM DTT and 100µg/ml cycloheximide.  100µl of the lysate were reserved for other use and the rest were treated with DNase I and RNase I. The ribosome monomers were purified using Microspin S-400 columns (cat). The ribosome protected RNA fragments (RPF) were extracted using RNA clean up and concentration kit (23600, Norgen Biotek).
For RNA-seq 500ng of total RNA was used for preparing RNA-seq libraries using NEBNext Poly(A) mRNA magnetic isolation module (Cat No. NEB E7490) following manufacturer’s instruction. Final libraries were amplified by PCR for 12 cycles, purified with AMPure XP beads and analysed by Bioanalyser before sending out for high throughput sequencing on Illumina Hi-seq4000. Ribosome protected RNA fragments (RPF) were resolved in 15% Novex TBE-Urea gels, stained with SYBR gold and fragments with 26-34nt were excised from the gel. The RNA was extracted from the gel by electrophoresis with the aid of D-tube (MWCO 3.5 kDa,71506-3, Merck Chemical). The precipitated RNA was dephsphorylated by T4 polynucleotide kinase and ligated to universal miRNA Cloning Linker using T4 RNA ligase 2 truncated. Complementary DNA was prepared with SuperScript III and reverse transcription primer containing 5 random nucleotides. The cDNA was resolved, excised and extracted by D-tube(71504-3, Merk). The extracted DNA was then circularized and PCR amplified with primers containing barcode for specific sample. The final library was separated from PCR primers by electrophoresis and extracted with  D-tube(71504-3,Merk).

treatment_protocol: ShRNA vectors were generated by cloning annealed oligonucleotides into the retroviral vector backbone pRSMX-PG. Sequences were designed to avoid cross-targeting of DDX3X and DDX3Y.

tag: time (h)

tag: molecule

value: Ribosomal footprints


title: InjIL36_rep2

value: Skin


title: 3h control_#2

description: control fish (w/o stress)


title: 231-RFP-2


title: Ribo_U2392_sh2_48_rep1

description: CDScounts.csv


title: 3h control_#1

description: control fish (w/o stress)


title: 10Soy_2


title: 231-RFP-3


title: Ribo_U2392_sh1_48_rep1

description: CDScounts.csv


title: 10Soy_1


title: BMJ treated High fat diet C57BL/6J mouse liver at 16 weeks, biological rep2

description: BMJ treated high fat diet liver

source_name: wild-type, BMJ treated high fat diet


title: 24h stressed_#7

description: 24 h after handling stress


title: High fat diet C57BL/6J mouse liver at 16 weeks, biological rep 3

description: high fat diet liver

source_name: wild-type, high fat diet liver


title: 24h stressed_#6

description: 24 h after handling stress


title: 10Soy_4


title: 3h stressed #5

description: 3 h after handling stress


title: Ribo_U2392_sh1_48_rep2

description: CDScounts.csv


title: High fat diet C57BL/6J mouse liver at 16 weeks, biological rep 2

description: high fat diet liver


title: P6_C3

city: Mol

first: Mohamed

last: Mysara

state: Belgium

address: Boeretang 200

country: Belgium

institute: Belgian nuclear research center (SCK-CEN)

description: raw_count.tsv column "P6_C3"

data_processing:
Illumina Casava software used for basecalling.
Obtained RNAseq reads were aligned to the Limnospira sp. PCC 8005 reference genome ARTHRO_v5 of 2014 using bowtie2 software (version 2.2.5) set at its default parameters. Raw counts per gene were calculated based on the most recent genome annotation of Limnospira sp. PCC 8005 i.e. currently available on the MaGe platform (https://mage.genoscope.cns.fr/). Reads for coding regions were allowed to map between the start and stop codon. Reads that were mapped to ribosomal or transfer RNA were removed from the raw count data to prevent bias in detecting differential expression.
Differential expression was calculated using the edgeR package (version 3.2.4) (Robinson et al., 2010) in BioConductor (release 3.0, R version 3.1.2), resulting in a fold change (FC) or logarithmic fold change (log2FC) value and a corresponding p-value corrected for multiple testing for each individual gene, resulting in False Discovery Rate (FDR) values. Genes were considered as being differentially expressed if they abided to the selection criteria: -1 >= log2FC >= 1 and an FDR equal or below 0.05.
For visualization of the controls, a multidimensional scaling (MDS) or principle component analysis (PCA) plot that assumes the normality (uses parametric measures of distance) was plotted. The function in R called plotMDS is used with an adaption for RNAseq data where the distance between each pair of samples (e.g. P2C1fw and P6Rfw, etc) with the root-mean-square deviation (Euclidean distance) for the top genes are used, instead of all genes. Therefore, the genes are sorted by fold-change and the top 500 genes are used to calculate the distance between the two samples. This is different from traditional MDS were all genes are taken into consideration to overcome the missed gene and static genes; this is applied in the Bioconductor packages DESeq and DESeq2
Genome_build: ARTHROv5 – updated version 5 of 15 February 2014, available at NCBI under GenBank assembly accession number GCA_000973065.1 (reference genome); P2 and P6 genomic sequences are available as BioProject number PRJNA517821 and  BioSample number SUB5105069 (Yadav et al. 2019 - https://doi.org/10.1080/09670262.2019.1675763)
Supplementary_files_format_and_content: tab-delimited text files including the raw count value

organism: Limnospira indica PCC 8005

source_name: cyanobacterial cell

growth_protocol: Axenic Arthrospira sp. PCC8005 cultures of helical (P6) and straight (P2) morphotypes were grown in a large volume (1 L) in an Erlenmeyer flask (Thermofisher Scientific, Merelbeke, Belgium) at a constant temperature of 30 °C in a Binder KBW400 growth chamber (Analis SA, Namur, Belgium), using a Heidolph Unimax 2010 rotatory shaker (Analis SA) at 121 rpm and a photon irradiance of 45 μmol photons per square meter per second  (µE.m-2.s-1) produced by Osram Daylight fluorescent tubes.

extract_protocol:
Three replicates of 30 mL each of the retrieved irradiated cultures and the non-irradiated control cultures were immediately put on ice after gamma irradiation and centrifuged for 20 mins at 10,000 g and 4 °C, to collect the cell pellets in 15 mL conical FalconTM centrifuge tubes (BD Biosciences, Erembodegem, Belgium). The cell pellets were then transferred to 2 mL Eppendorf centrifuge tubes (Fisher Scientific) and as much as possible all Zarrouk medium was removed by additional centrifugation for 2 min at maximal speed. The pellets were washed three times with 1x Phosphate-Buffered Saline (PBS) and finally flash-frozen in liquid nitrogen until further analysis. RNA extraction was performed at 4oC using RiboPureTM- Bacteria Kit (Ambion-Life Technologies, Gent, Belgium), Direct-zolTM RNA miniPrep (Zymo Research, BaseClear Lab Products, Leiden, The Netherlands), RNA Clean and Concentrator-25 (Zymo Research) and the Turbo DNA-free kit (Ambion-Life Technologies, Gent, Belgium). The breakage of cell was performed by the RiboPureTM-Bacteria kit using Zirconia Beads in the lysis RNAwiz solution (both are kit components). The final volume of the lysis solution was adjusted according to the volume of the pellet. The released RNA was separated from cell debris by centrifugation at 10,000 g for 10 min at 4oC. The further purification of the released RNA was performed with the Direct-zolTM RNA Miniprep kit maintaining a 1:1 ratio of organic and aqueous phase, following the manufacturer’s instructions. DNA was degraded with DNase 1 treatment (1 U/µL) and incubating at 37 °C for 30 mins. Obtained RNA was concentrated with the RNA Clean and Concentrator-25 kit. The quality and integrity of the RNA was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Diegem, Belgium).
Library preparation was done using TruSeq Stranded Total RNA kit (Illumina, Brussels, Belgium) with fragmentation at 94°C for 3 minutes instead of 8 mins as to generate long fragments (an adaptation to the manual protocol for generation of long fragments). The amplification was performed using a PCR with 14 cycles. The quality check of the library was performed with an Agilent 2100 Bioanalyzer High Sensitivity Chip by means of qPCR. The amplicons were pooled together with size selection on a 2% E-GelTM Agarose Gel (ThermoFisher Scientific) and a final amplicon quality check was performed on the Agilent 2100 Bioanalyzer High Sensitivity Chip by means of qPCR. The final sequencing was performed on a HiSeq 3000 system (Illumina, San Diego, USA) with a single-read paired end preset at 150 bp (PE150 specifications).

treatment_protocol: When cultures reached an OD750 of 0.5 as measured on a Genesys UV-Vis Spectrophotometer (Thermofisher Scientific) they were divided as triplicates into three separate volumes of 50 mL each using 250 mL Erlenmeyer flasks and subjected to a dose rate of 80 Gy.h-1 for a period of 3 days at the GEUSE II facility of SCK•CEN. An inbuilt LED light chamber was used in the experiment for a continuous white light exposure of 45 μE.m-2.s-1 irradiance. Triplicates of a non-irradiated control per dose were kept at otherwise similar conditions in the lab. Culture samples were collected in time intervals at three prechosen time points T1 to T3 of exposure (roughly at 15, 40, and 71 hours) corresponding to approximate cumulative doses of respectively 1400, 3200, and 5700 Gy

value: non-irradiated (0 Gy)

tag: morphology

value: helical trichomes

tag: buoyancy

value: sedimenting


title: Ribo_U2392_sh2_24_rep2

description: CDScounts.csv


title: 3h control_#4

description: control fish (w/o stress)


title: 20Soy_SAA_6

value: 20percent soy + Methionine + Cysteine


title: FFPE SG_rep8

city: Tianjin

first: chuanli

last: zhang

address: Fu kang Road251,Nankai Strict

institute: Tianjin Medical University Eye Hospital

description:
SG67987
miRNAs screening in human SG FFPE sample.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent miRNA Microarray (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction software 10.7.1.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data was normalized with the quantile algorithm with GeneSpring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as "Detected" were maintained.
Processed_data.txt file includes normalized signal intensities.

source_name: Human FFPE SG

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SGC and SG FFPE tissue samples were selected for differentially miRNAs detection. Immunohistochemical staining was used to detect whether the carcinoma tissues contained TP53 mutation.

value: eyelid sebaceous gland

value: female


title: 20Soy_SAA_5

value: Male


title: Ribo_U2392_sh2_24_rep1

description: CDScounts.csv


title: P6_R3

description: raw_count.tsv column "P6_R3"

value: irradiated (3200 Gy)


title: 24h stressed_#5

description: 24 h after handling stress


title: 10Soy_3

value: 11.5percent soy

value: 6 months


title: P6_R2

description: raw_count.tsv column "P6_R2"


title: 20Soy_SAA_4


title: FFPE SG_rep7

description:
SG36001
miRNAs screening in human SG FFPE sample.


title: P6_C2

description: raw_count.tsv column "P6_C2"


title: P6_R1

description: raw_count.tsv column "P6_R1"


title: Ribo_U2392_sh1_24_rep1

description: CDScounts.csv


title: P6_C1

description: raw_count.tsv column "P6_C1"


title: 20Soy_SAA_3


title: Ribo_U2392_ctl_48_rep2

description: CDScounts.csv

value: control


title: FFPE SG_rep5

description:
SG190178
miRNAs screening in human SG FFPE sample.


title: FFPE SG_rep6

description:
SG130118
miRNAs screening in human SG FFPE sample.


title: Ribo_U2392_sh1_24_rep2

description: CDScounts.csv


title: Ribo_U2392_ctl_48_rep1

description: CDScounts.csv


title: FFPE SG_rep4

description:
SG170113
miRNAs screening in human SG FFPE sample.

value: male


title: FFPE SG_rep3

description:
SG60733
miRNAs screening in human SG FFPE sample.


title: P2_R3

description: raw_count.tsv column "P2_R3"

value: straight trichomes

value: surface floating


title: FFPE SG_rep1

description:
SG71668
miRNAs screening in human SG FFPE sample.


title: P2_R2

description: raw_count.tsv column "P2_R2"


title: 20Soy_SAA_2


title: 20Soy_SAA_1


title: FFPE SG_rep2

description:
SG61443
miRNAs screening in human SG FFPE sample.


title: P2_R1

description: raw_count.tsv column "P2_R1"


title: Ribo_U2392_ctl_24_rep2

description: CDScounts.csv


title: 20Soy_6

value: 20percent soy


title: 20Soy_4


title: P2_C2

description: raw_count.tsv column "P2_C2"


title: FFPE SGC_rep8 and without TP53 mutation_rep4

description:
SGC170220
miRNAs screening in human SGC FFPE sample.

source_name: Human FFPE SGC

value: eyelid sebaceous gland carcinoma

tag: tp53 status

value: without TP53 mutation


title: P2_C3

description: raw_count.tsv column "P2_C3"

value: non-irradiated (0 Gy)


title: RNA_U2392_sh2_48_rep1

description: CDScounts.csv

data_processing:
UMI stripping : UMI tools 0.5.3 –bc-pattern NNNNNN
Trimming: cutadapt 1.10, parameters: --quality-base=33 -e 0.1 -m 10 -q 20,20 -u 1 A47 Ribo-Seq only: (-a CTGTAGGCACCATCAATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC )
Alignment: STAR 2.6.0c, parametres: --twopassMode Basic
Counting of ribosomal P-sites and RNA-seq reads was performed as described in Gong et al.
Genome_build: GRCh 38
Supplementary_files_format_and_content: CDScounts.csv contains read counts per CDS (one CDS per gene). To build gene models first 30 nt and last 30 nt of each CDS region were removed to reflect translation elongation intensity.

value: polyA RNA


title: RNA_U2392_sh1_48_rep1

description: CDScounts.csv


title: FFPE SGC_rep7 and without TP53 mutation_rep3

description:
SGC120446
miRNAs screening in human SGC FFPE sample.

tag: tissue


title: P2_C1

description: raw_count.tsv column "P2_C1"


title: 20Soy_3


title: High fat diet C57BL/6J mouse liver at 16 weeks, biological rep 1

description: high fat diet liver

value: 16 weeks

value: wild-type


title: RNA_U2392_sh2_24_rep1

description: CDScounts.csv


title: 1512_W

city: Saint-Genès Champanelle

first: Etienne

last: Lefai

address: INRA Auvergne Rhône -Alpes

country: France

institute: INRA

data_processing:
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the data was assessed using FastQC (v0.11.5) from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.2.9), was used to align the RNA-Seq reads to the Ursus arctos genome (NCBI GCA_003584765.1 ASM358476v1 assembly) with a set of gene model annotations (GCA_003584765.1_ASM358476v1_genomic.gff.gz downloaded from NCBI on June 17 2019).
Final read alignments having more than 3 mismatches were discarded.
Samtools (v1.9) was used to sort the alignment files.
Then, the counting was performed with featureCounts (version 1.6.2). The data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene.
Genome_build: GCA_003584765.1 ASM358476v1 assembly
Supplementary_files_format_and_content: Tab-separated text file. First column is the gene identifier, the following columns are the raw counts for each sample.

organism: Ursus arctos

source_name: Skeletal muscle

extract_protocol:
Muscle biopsie was flash frozen on dry ice, and total and RNA was harvested using Trizol reagent
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions.  Briefly, poly-A RNAs were purified using oligo-d(T) magnetic beads from 1µg of total RNA. The poly-A RNAs were fragmented into small pieces using divalent cations under elevated temperature and reverse transcribed using random hexamers, Super Script II (Thermo Fisher Scientific, Carlsbad, CA) and Actinomycin D. During the second strand generation step, dUTP substitued dTTP. This prevents the second strand to be used as a matrix during the final PCR amplification. Double stranded cDNAs were adenylated at their 3' ends before ligation was performed using Illumina's indexed adapters. Ligated cDNAs were amplified following 15 cycles PCR and PCR products were purified using AMPure XP Beads (Beckman Coulter Genomics, Brea, CA, USA). Libraries were validated using a Fragment Analyzer  (Agilent Technologies, Santa Clara, CA, USA) and quantified using the KAPA Library quantification kit (Roche, Bâle, CHE).

value: 2-3 years old

tag: season

value: winter

value: vastus lateralis


title: FFPE SGC_rep6 and without TP53 mutation_rep2

description:
SGC130118
miRNAs screening in human SGC FFPE sample.

value: female


title: 20Soy_2

value: Male


title: 20Soy_5

value: 6 months


title: 1512_S

value: summer


title: Ribo_U2392_ctl_24_rep1

description: CDScounts.csv

value: control

value: Ribosomal footprints


title: FFPE SGC_rep5 and without TP53 mutation_rep1

description:
SGC190178
miRNAs screening in human SGC FFPE sample.


title: RNA_U2392_sh1_24_rep2

description: CDScounts.csv


title: LP_6

value: 5percent casein


title: 3h control_#3

description: control fish (w/o stress)

source_name: control fish (w/o stress)

value: head kidney

value: unknown

value: juvenile fish of ~ 20 cm


title: LP_5


title: RNA_U2392_sh1_24_rep1

description: CDScounts.csv


title: FFPE SGC_rep3 and TP53 mutation_rep3

description:
SGC160185
miRNAs screening in human SGC FFPE sample.

value: eyelid sebaceous gland carcinoma

value: TP53 mutation


title: FFPE SGC_rep2 and TP53 mutation_rep2

description:
SGC160217
miRNAs screening in human SGC FFPE sample.


title: RNA_U2392_ctl_48_rep1

description: CDScounts.csv

value: polyA RNA


title: 1509_S


title: RNA_U2392_sh2_24_rep2

description: CDScounts.csv


title: 1511_W


title: 1511_S


title: LP_4


title: LP_3


title: FFPE SGC_rep1 and TP53 mutation_rep1

description:
SGC170553
miRNAs screening in human SGC FFPE sample.


title: RNA_U2392_ctl_24_rep3

description: CDScounts.csv


title: FFPE SGC_rep4 and TP53mutation_rep4

description:
SGC170113
miRNAs screening in human SGC FFPE sample.

value: male


title: LP_2


title: 20Soy_1

value: 20percent soy


title: RNA_U2392_ctl_24_rep1

description: CDScounts.csv


title: RNA_U2392_ctl_48_rep2

description: CDScounts.csv


title: 1317_S

value: 2-3 years old


title: 1316_W

value: winter

value: vastus lateralis


title: Ribo_Mutu_sh2_48_rep1

description: CDScounts.csv

source_name: Mutu cell line


title: 1305_W


title: NP_6

value: Male

value: 20percent casein


title: RNA_U2392_ctl_24_rep2

description: CDScounts.csv


title: Ribo_Mutu_sh1_48_rep1

description: CDScounts.csv


title: +NO3_Rep3_re-analyzed

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

data_processing:
base-calling and demultiplexing with Illumina CASAVA 1.8
adapter clipping and quality filtering with Trimmomatic 0.33
mapping with tophat-2.0.13; parameters: -N 3 --read-gap-length 3 --read-edit-dist 3 --b2-very-sensitive -i 5 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000 --library-type fr-firststrand
Differential expression analysis usign Cufflinks version 2.2.1 --multi-read-correct, --compatible-hits-norm, --dispersion-method per-condition and --library-norm-method quartile
Genome_build: RefGen ZmB73 Assembly AGPv4
Supplementary_files_format_and_content: tab-delimited matrix with normalized RPKM values for all the samples

molecule: polyA RNA

organism: Zea mays

source_name: primary root apexes

growth_protocol: Maize seeds were germinated on wet filter paper at 25°C in the dark; after three days, seedlings were moved to a controlled environmental chamber in 500 ml tanks containing a nutrient medium (Quaggiotti et al. 2003).

extract_protocol:
Total RNA was extracted using TRIzol reagent, followed by DNAse treatment
TruSeq Stranded RNA Library Prep Kit

treatment_protocol: 24h of growth in nutrient solution supplemented with 1mM KNO3 or 1mM NH4Cl or 1 mM KNO3 plus 1 mM cPTIO (-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide)

value: primary root apexes

tag: cultivar

tag: treatment


title: NP_3

tag: age

value: 6 months


title: NP_2

tag: strain


title: Ribo_Mutu_sh1_24_rep1

description: CDScounts.csv

tag: condition

value: Ribosomal footprints


title: +NO3_Rep1_re-analyzed


title: NP_4


title: 1316_S

value: summer


title: exp_3_monoculture

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description: RNA expression value derived from Affymetrix Launcher software

hyb_protocol: Samples were hybridized with: miRNA-4_0 or HuGene-1_1-st-v1, as indicated (Affymetrix) and scanned at the HUJI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed in R for background correction and RMA normalization. Normalized expression data were log-transformed.

source_name: WM3682 melanoma line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Exp.1-  WM1716  melanoma cells were grown in 10% serum DMEM. Exp.2- WM3682  melanoma cells were grown in adipocytes medium.

extract_protocol: RNA was isolated from WM1716 and WM3682 cells using Trizol (Qiagen), according to the manufacturer’s instructions. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA.

treatment_protocol: Exp.1 - WM1716 melnaoma cells were stably trasfected with scrambled control or miR-211. Exp.2 - WM3682 melnaoma cells were co-cultured with adipocytes or mono-cultured. RNA was extracted at day 5.

tag: cell line

tag: protocol

value: monoculture


title: +NO3_Rep2_re-analyzed


title: NP_5

tag: Sex


title: 1317_W


title: 1305_S


title: Ribo_Mutu_ctl_48_rep2

description: CDScounts.csv

value: control


title: NP_1

tag: dietary protein source


title: LP_1

value: 5percent casein

tag: methionine and cysteine concentration gm%


title: Ribo_Mutu_sh2_24_rep1

description: CDScounts.csv

tag: time (h)


title: -N_control_Rep3_re-analyzed


title: Spermidine-fed_2_DspeG

city: Chandigarh

first: Dipak

last: Dutta

email: dutta@imtech.res.in, ddutta25@gmail.com

state: Chandigarh

address: Sector 39-A

department: Molecular Biochemistry

country: India

institute: CSIR IMTECH

description: Gene expression_Plus manganase_1

hyb_protocol: 2000ng ng of labeled cRNA sample were fragmented at 60° C and hybridized on to a Agilent custom Microarray Gene expression 8x15k Array (AMADID: 068043). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Raw data was normalized using  quantile normalization method using R Scripts (https://cran.r-project.org/). Gene based analysis was performed.

organism: Escherichia coli

source_name: Bacteria_LB_1 mM manganese grown_1

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight culture of DspeG strain was diluted to 1:100 in Luria broth and grown for 1.5 hours followed by addition of spermidine (3.8 mM), whereever required, for 2.5 hours at 37°C. 2.5 ml stop solution (5% phenol in ethanol) was added in 25 ml of growing culture for 10 minutes to prevent the RNA degradation and the cell pellets were collected by centrifuging at 5000 rpm for 10 minutes at 4°C.

extract_protocol: RNA Extraction was perforemd using Qiagen RNeasy Mini kit (Cat. No. 74106) as per the manufacturer's recommendations.

treatment_protocol: The cells were grown in the presence or absence of 3.8mM of spermidine for 2.5 hours at 37°C

tag: genotype

value: deltaspeG

tag: agent

value: spermidine (3.8 mM)


title: Purkinje cell p56 RNA-Seq Tet1fl/fl/Tet2fl/fl/Tet3fl/fl rep1

city: NYC

first: Elitsa

last: Stoyanova

state: NY

address: 1230 York Ave

department: Molecular Biology

institute: Rockefeller University

data_processing:
RNA-Seq data: RNA-seq reads were aligned using STAR and genome assemblies from UCSC. In addition to default STAR parameters, we used the following for paired-end data (--outFilterMismatchNmax 999 --alignMatesGapMax 1000000 -- outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 60 -- outFilterMismatchNoverLmax 0.05) UCSC gene model annotations for whole genes were downloaded using the UCSC Table Browser tool.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts generated by ht-seq count
Supplementary_files_format_and_content: bigWigs generated using deepTools, 0 to 1 modification status per cytosine
Supplementary_files_format_and_content: peak text files from macs2

source_name: Cerebellum

extract_protocol:
Cerebella were dissected and flash frozen. Nuclei were extracted, fixed, stained with antibodies and sorted. RNA/gDNA was extracted using Qiagen FFPE RNA/DNA sample prep.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cerebellum

tag: cell type

value: Purkinje cells

value: post natal day 56


title: Ribo_Mutu_ctl_48_rep1

description: CDScounts.csv

tag: molecule


title: ATAC-Seq MGT_siAJSZ_2

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

library_source: genomic

data_processing:
Cell Ranger-ATAC (1.1.0) pipeline was used to filter and align reads, count barcodes, identify transposase cut sites, detect chromatin peaks, prepare t-SNE dimensionality reduction plots, and compare differential accessibility between clusters.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed file containing peaks

molecule: genomic DNA

source_name: dermal fibroblasts

growth_protocol: HDFs were added to 384-well plates at 2.5×103 cells/well in iCRM and transfected with siRNAs.

extract_protocol:
Cells were collected 2 days later using trypsin-EDTA. Cells from 40 wells were pooled to obtain ≥2×105 cells per sample, with two biological replicates per condition. Cells were washed with FCM, centrifuged in conical tubes, and the pellets were frozen in Freezing Medium (DMEM, 10% DMSO, 20% FBS), transferred to cryotubes, and placed in Mr, Frosty containers (Thermo Fisher) at −80°C.
Samples were processed for scATAC-seq at UCSD CMME. Samples were processed for scATAC-seq at UCSD CMME using 10x Genomics
Libraries were sequenced on a NovaSeq 6000 at a depth of 20-25k read pairs per nucleus

treatment_protocol: The next day (day 0), cells were transduced mouse MGT retrovirus

tag: sample type

value: HDFs overexpressing MGT _ siAJSZ


title: Purkinje cell p56 RNA-Seq Tet1fl/fl/Tet2fl/fl/Tet3fl/fl rep2

tag: tissue


title: Ribo_Mutu_ctl_24_rep2

description: CDScounts.csv


title: -N_control_Rep2_re-analyzed

tag: cultivar


title: NO3-+cPTIO_Rep3

tag: treatment

value: cPTIO


title: NO3-+cPTIO_Rep2


title: ATAC-Seq HDF_2

value: Untreated HDFs (baseline)


title: Purkinje cell p56 BS-Seq  Pcp2-Cre::Tet1-/-/Tet2-/-/Tet3-/-  rep1

data_processing:
OxBS-Seq and BS-Seq data: Reads were processed with trim_galore with parameters “--stringency 3 --fastqc --paired --clip_R1 5 --clip_R2 10”. Trimmed reads were mapped to mm10 using bismark with parameters “--bowtie2 -p 4 --multicore 4” (v0.20.0). Duplicates were removed using deduplicate_bismark. The following tools from methpipe (v3.4.2) were used for downstream statistical estimation of the methylation and hydroxymethylation levels. First, bismark aligned reads were converted to the custom .mr format and sorted with default parameters. Methylation calls were extracted with methcounts with default parameters. Methylation and hydroxymethylation levels were estimated using the mlml tool with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts generated by ht-seq count
Supplementary_files_format_and_content: bigWigs generated using deepTools, 0 to 1 modification status per cytosine
Supplementary_files_format_and_content: peak text files from macs2

extract_protocol: Cerebella were dissected and flash frozen. Nuclei were extracted, fixed, stained with antibodies and sorted. RNA/gDNA was extracted using Qiagen FFPE RNA/DNA sample prep.

tag: age


title: exp_2_adipocytes co-culture

value: adipocytes co-culture


title: -N_control_Rep1_re-analyzed


title: Purkinje cell p56 RNA-Seq Pcp2-Cre+::Tet1-/-/Tet2-/-/Tet3-/- rep1

tag: strain


title: ATAC-Seq MGT_siAJSZ_1


title: RNA_Mutu_sh2_48_rep1

description: CDScounts.csv

tag: condition

value: polyA RNA


title: RNA_Mutu_sh2_48_rep2

description: CDScounts.csv


title: NO3-+cPTIO_Rep1

value: primary root apexes


title: ATAC-Seq HDF_1


title: Ribo_Mutu_ctl_24_rep1

description: CDScounts.csv


title: Purkinje cell p56 RNA-Seq Pcp2-Cre+::Tet1-/-/Tet2-/-/Tet3-/-  rep2


title: Purkinje cell p56 OxBS-Seq Pcp2-Cre::Tet1-/-/Tet2-/-/Tet3-/- rep1

data_processing:
Library strategy: OxBS-Seq
OxBS-Seq and BS-Seq data: Reads were processed with trim_galore with parameters “--stringency 3 --fastqc --paired --clip_R1 5 --clip_R2 10”. Trimmed reads were mapped to mm10 using bismark with parameters “--bowtie2 -p 4 --multicore 4” (v0.20.0). Duplicates were removed using deduplicate_bismark. The following tools from methpipe (v3.4.2) were used for downstream statistical estimation of the methylation and hydroxymethylation levels. First, bismark aligned reads were converted to the custom .mr format and sorted with default parameters. Methylation calls were extracted with methcounts with default parameters. Methylation and hydroxymethylation levels were estimated using the mlml tool with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts generated by ht-seq count
Supplementary_files_format_and_content: bigWigs generated using deepTools, 0 to 1 modification status per cytosine
Supplementary_files_format_and_content: peak text files from macs2


title: ATAC-Seq MGT_2

value: HDFs overexpressing MGT


title: RNA_Mutu_sh1_48_rep1

description: CDScounts.csv


title: Control 1_unfed_DspeG

description: Gene expression_minus manganase_1

source_name: Bacteria_LB grown_1


title: RNA_Mutu_sh2_24_rep1

description: CDScounts.csv


title: Control 2_unfed_DspeG

description: Gene expression_minus manganase_2

source_name: Bacteria_LB grown_2


title: exp_2_monoculture

tag: cell line


title: exp_3_adipocytes co-culture

tag: protocol


title: Spermidine-fed 1_DspeG

description: Gene expression_minus manganase_3

source_name: Bacteria_LB grown_3


title: RNA_Mutu_sh1_24_rep1

description: CDScounts.csv


title: s22

city: Bethesda

first: Martina

last: Absinta

address: 10 Center Drive MSC 1400

department: NINDS

institute: NIH

data_processing:
CellRanger software was implemented for library demultiplexing, barcode processing, fastq file generation, gene alignment to the human genome (pre-mRNA GRCh38-3.0 human genome), and unique molecular identifier (UMI) counts.
Genome_build: pre-mRNA GRCh38-3.0 human genome
Supplementary_files_format_and_content: Comma-separated values files containing read counts for each gene by nucleus in matrix format.

source_name: Brain

extract_protocol:
Snap-frozen autopsy human brain tissue sampling used a 3mm-punch biopsy tool and a cold blade. Nuclei extraction from snap-frozen human autopsy brains was performed according to the following protocol. On wet ice, the frozen, dissected tissue was lysed using a Dounce homogenizer (10 strokes with the loose pestle followed by 20 strokes with the tight pestle) in 600-μl of freshly made cold lysis buffer (low sucrose buffer, Triton X-100 20%, Rnase inhibitor 40U/μl). Part of the homogenate (200 μl) was collected for bulk RNA extraction (Qiagen RNAeasy kit) and stored at -80°C for future applications. The remaining homogenate was filtered through a 40-μm cell strainer for nuclei extraction with 4-ml of low sucrose buffer (0.64M sucrose, HEPES pH8, CaCl2, MgAc, EDTA, DTT, nuclease-free water). Sonication of the homogenate was performed for 10 sec. To remove cellular and myelin debris, a sucrose gradient (12-ml of high sucrose buffer [2M sucrose, HEPES pH8, MgAc, DTT, nuclease-free water] underneath the low sucrose buffer) was centrifuged at 3,200 g for 30 minutes, and the supernatant was discarded. Nuclei were resuspended in 1-ml resuspension solution (PBS, 5% BSA and RNAse inhibitor 40U/μl) and centrifuged for 12-min at 3,200 g. Nuclei were again resuspended in 50-μl cold resuspension solution. Nuclei were counted using trypan blue and a haemocytometer under bright field. A yield of 700–1,200 nuclei/μl per sample was targeted.
Immediately after extraction, 5,000 nuclei/sample were loaded onto a Chromium Single Cell 3′ Chip (10X Genomics) and processed for the single-nucleus cDNA library preparation (Chromium Single Cell 3’ version 3, 10X Genomics) according to the manufacturer’s instructions without modifications.
Chromium Single Cell 3’ version 3, 10X Genomics

tag: clinical phenotype

value: progressive multiple sclerosis


title: RNA_Mutu_ctl_48_rep3

description: CDScounts.csv


title: Purkinje cell p56 BS-Seq WT rep1

description: Purkinje cell p56 BS-Seq WT rep1

value: wild type


title: Purkinje cell p7 BS-SeqWT rep1

description: Purkinje cell p7 BS-SeqWT rep1

value: post natal day 7


title: s23


title: RNA_Mutu_ctl_48_rep2

description: CDScounts.csv

value: control


title: Purkinje cell p0 BS-Seq WT rep2

description: Purkinje cell p0 BS-Seq WT rep2

value: post natal day 0


title: Purkinje cell p56 BS-Seq WT rep2

description: Purkinje cell p56 BS-Seq WT rep2


title: s20


title: RNA_Mutu_ctl_48_rep1

description: CDScounts.csv


title: Purkinje cell p7 BS-Seq WT rep2

description: Purkinje cell p7 BS-Seq WT rep2


title: s19


title: Purkinje cell p0 BS-Seq WT rep1

description: Purkinje cell p0 BS-Seq WT rep1


title: s18


title: ATAC-Seq MGT_1


title: RNA_Mutu_sh1_48_rep2

description: CDScounts.csv


title: RNA_Mutu_ctl_24_rep2

description: CDScounts.csv


title: RNA_Mutu_ctl_24_rep1

description: CDScounts.csv


title: Purkinje cell p7 OxBS-Seq WT rep2

description: Purkinje cell p7 OxBS-Seq WT rep2


title: TGFR2G357W_IPH3K27ME3

city: Boston

first: SAUMYA

last: Das

address: 185 Cambridge Street

institute: MGH

description: Clean_151202_I137_FCH3L72BBXX_L2_wHAPSI023969-16_1

data_processing:
Then, fastqs files were aligned to the human genome (hg19, ENSEMBL version 75) using bowtie2 aligner11 with up to 50 alignments reported. Reads that were multimapped, duplicated or those that contained more than 2 mismatches were filtered out using samtools v1.3.112. The filtered alignment files in the form of bam files were indexed for the ability to view them on Integrative Genome Viewer13.  Peak calling was performed using macs2 v. caller between aneurysm (ACTA2R179H) smooth muscle cells and their corresponding control sample at a p-value threshold of 0.05. The annotation of the peaks from macs2 was performed using the ChipSeeker package in R14. Briefly, the reads that are mapped to unplaced scaffolds are removed from the analysis. Before annotating the peaks with UCSC’s hg19 knownGene database, the genomic coordinates are first converted from ENSEMBL to UCSC and all peaks with a transcription start site region defined at 5 kilobases of the gene location are annotated.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files - Aneurysm sample versus control for each pulldown.

source_name: Aneurysm Smooth Muscle Cells

extract_protocol:
Human wild-type or aneurysm (ACTA2R179H)10 smooth muscle cells (10 million) were fixed with 1% of formaldehyde at 37 C for 20 min, quenched with 125 mM glycine for 5 min (RT) and protein lysates were prepared using EpiTect ChIP kit according to the manufacturer’s instructions (Qiagen, USA). Next, total protein lysates were sonicated to shear chromatin to an average length of 500–1,000 bp, followed by centrifugation for 10 minutes at max speed. Supernatants were collected into a 2 mL tube containing 6 μg of monoclonal antibody against HDAC9 (ab59718), BGR1 (ab110641), H3K27me3 (Abcam, ab4729) or IgG isotype control (ab171870) and 1 ml of lysis buffer supplemented with 1× of protease inhibitor cocktail (Roche Diagnostics), followed by incubation overnight (14 hours) at 4°C. Immunoprecipitates were analyzed using EpiTect ChIP kit according to the manufacturer’s instructions (Qiagen). Then, ChIP-ed DNA was quantified and used for DNA-end repair (3’-dA) followed by PCR amplification and size selection (usually 100-400bp, including adaptor sequence).
The, qualified libraries were used for HiSeq sequencing (Illumina HiSeq 50 SE sequencing).

tag: genotype/variation

value: Aneurysm Smooth Muscle Cells

tag: chip antibody

value: H3K27me3 (Abcam, ab4729)


title: Purkinje cell p56 OxBS-Seq WT rep1

description: Purkinje cell p56 OxBS-Seq WT rep1

value: Cerebellum


title: s17

value: non-neurological control


title: TGFR2G357W_IPHDAC9

description: Clean_151202_I137_FCH3L72BBXX_L2_wHAPSI023971-14_1

value: HDAC9 (Abcom, ab59718)


title: Purkinje cell p56 OxBS-Seq WT rep2

description: Purkinje cell p56 OxBS-Seq WT rep2

value: Purkinje cells

value: post natal day 56


title: N9 LPS replicate 3

city: Madison

last: Shippy

address: 1111 Highland Avenue

institute: UW-Madison

data_processing:
Library preparations were sequenced on an Illumina platform and paired-end reads were generated
Paired-end clean reads were aligned to the reference genome using HiStat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: mm10
Supplementary_files_format_and_content: read counts and differential expression analysis

source_name: microglia

growth_protocol: Murine N9 microglial cells were routinely cultured in RPMI 1640 media with FBS (10%) and pen/strep (1%)

extract_protocol:
RNA was extracted from cells using Qiagen Rneasy Plus Mini Kit.
RNA libraries were prepared for sequencing using standard protocols by Novogene.

treatment_protocol: cells were either untreated (control) or treated with LPS (1 µg/ml) for 6 hours

value: N9 microglia cell line

value: LPS


title: Purkinje cell p7 OxBS-Seq WT rep1

description: Purkinje cell p7 OxBS-Seq WT rep1


title: N9 LPS replicate 2


title: N9 control replicate 3

value: untreated


title: N9 LPS replicate 1


title: TGFR2G357W_IPBRG1

description: Clean_151202_I137_FCH3L72BBXX_L2_wHAPSI023968-15_1

value: BRG1 (Abcam, ab110641)


title: RAZZ_447

city: San Francisco

first: Marina

last: Sirota

state: CA

address: 490 Illinois St, Floor 2

department: Bakar Computational Health Sciences Institute

institute: UCSF

data_processing:
Following demultiplexing, sequencing reads were aligned against the human genome (NCBI GRC h38) using STAR to extract gene counts.
Samples retained in the dataset had a total of at least 3e+05 gene counts, and the median across all samples was 5.8e+05 gene counts.
Differentially expressed genes were identified using the R package DEseq2.
Genome_build: NCBI GRC h38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole blood_activity_tertile_three

extract_protocol:
Whole blood was collected and stored at -80C. Following RNA extraction (Zymo Pathogen Magbead Kit) and DNase treatment, human cytosolic and mitochondrial ribosomal RNA was depleted using FastSelect (Qiagen). RNA was then fragmented and underwent library preparation using the NEBNext Ultra II RNAseq Kit (New England Biolabs).
Libraries underwent 146 nucleotide paired-end Illumina sequencing on an Illumina Novaseq 6000 instrument.

tag: tissue/cell type

value: Whole blood

value: three

tag: Sex

value: female

tag: race

value: white

tag: hispanic

value: zero

tag: bmi

tag: biologicis

value: one

tag: dmard


title: Purkinje cell p0 OxBS-Seq WT rep1

description: Purkinje cell p0 OxBS-Seq WT rep1

tag: tissue

tag: cell type

value: post natal day 0

tag: genotype

value: wild type


title: RAZZ_429

source_name: Whole blood_activity_tertile_one

tag: age


title: RAZZ_419

value: dk


title: RAZZ_460


title: CTRL_IPBRG1

description: Clean_151202_I137_FCH3L72BBXX_L2_wHAPSI023963-111_1

source_name: Wild type Smooth Muscle Cells

value: Wild Type

value: Wild type Smooth Muscle Cells


title: RAZZ_462

source_name: Whole blood_activity_tertile_two

value: two


title: RAZZ_389


title: Purkinje cell p56 ChIP-Seq H3K27me3 WT rep1

data_processing:
ChIP-Seq data: Reads were processed with trim_galore with parameters “--stringency 3 --fastqc --paired”. Trimmed reads were mapped to mm10 using bowtie2 (v2.1.0) with default parameters. Duplicates were removed using samtools. QC was performed with ChIPQC and that estimated fragment size was used for broad peak calling with macs2 (--nomodel -f BAM --keep-dup all --broad -g mm -B -q 0.01).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts generated by ht-seq count
Supplementary_files_format_and_content: bigWigs generated using deepTools, 0 to 1 modification status per cytosine
Supplementary_files_format_and_content: peak text files from macs2

tag: strain

value: Cerebellum

value: Purkinje cells

value: post natal day 56

value: H3K27me3 (Active Motif, 39155)


title: CTRL_H3K27ME3

description: Clean_151202_I137_FCH3L72BBXX_L2_wHAPSI023956-112_1

value: H3K27me3 (Abcam, ab4729)


title: N9 control replicate 1

value: N9 microglia cell line

tag: treatment

value: untreated


title: CTRL_IPHDAC9

description: Clean_160811_I137_FCHC7KNBBXX_L3_wHAPSI033194-39+4_1

value: HDAC9 (Abcom, ab59718)


title: Purkinje cell p0 OxBS-Seq WT rep2

description: Purkinje cell p0 OxBS-Seq WT rep2


title: RAZZ_379

value: Whole blood

value: three

value: female

value: multi


title: ACTA2R179H_IPHDAC9

description: Clean_160726_I136_FCHC2MMBBXX_L2_wHAPSI033199-40+2_1

value: Aneurysm Smooth Muscle Cells


title: Purkinje cell p7 ChIP-Seq H3K27me3 WT rep1

value: post natal day 7

value: wild type


title: Purkinje cell p56 ChIP-Seq H3K27me3 WT rep2


title: RAZZ_369

value: one

value: dk


title: ACTA2R179H_IPH3K27ME3

description: Clean_151202_I137_FCH3L72BBXX_L2_wHAPSI023967-102_1


title: 1509_W

source_name: Skeletal muscle

value: 2-3 years old

tag: season

value: winter

value: vastus lateralis


title: ACTA2R179H_IPBRG1

description: Clean_160726_I136_FCHC2MMBBXX_L2_wHAPSI033198-41+1_1

value: BRG1 (Abcam, ab110641)


title: RAZZ_360

value: two

value: zero


title: LPSCLU_B3 [ZM_CTX_LPSCLU_B3]

city: Palo Alto

first: Nathalie

last: Khoury

state: CA California

address: 3801 Miranda Avenue Blvd. 100 VAPA D3-111 - Neurology

institute: Stanford University

data_processing:
Bulk RNAseq of cortex:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25)
Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered.
Data visualization and analysis was performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file including raw counts for each sample

source_name: Cortex

extract_protocol:
Bulk RNAseq of cortex:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

value: LPS (lipopolysaccharide) + clusterin

value: All cortical cells


title: N9 control replicate 2

value: N9 microglia cell line

value: untreated


title: LPSCLU_B4 [ZM_CTX_LPSCLU_B4]


title: LPSCLU_B2 [ZM_CTX_LPSCLU_B2]


title: LPSCLU_B1 [ZM_CTX_LPSCLU_B1]


title: Purkinje cell p56 ChIP-Seq H3K4me3 WT rep2

value: Cerebellum

value: Purkinje cells

value: post natal day 56

value: H3K4me3 (Active Motif, 39159)


title: RAZZ_348

value: Whole blood

value: female

value: black


title: Purkinje cell p0 ChIP-Seq H3K27me3 WT rep1

value: post natal day 0

value: wild type

value: H3K27me3 (Active Motif, 39155)


title: Purkinje cell p56 ChIP-Seq H3K4me3 WT rep1


title: LPSCLU_A3 [ZM_CTX_LPSCLU_A3]


title: RAZZ_338

value: one

value: white


title: Purkinje cell p7 ChIP-Seq H3K27me3 WT rep2

value: post natal day 7


title: D28_preg_4

city: Neustadt

first: Claudia

last: Klein

address: Höltystr. 10

institute: Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality ends and reads shorter than 50 bp were removed
Reads were then mapped to the equine EquCab3 genome allowing two mismatches per read
Total counts and transcripts per million (TPM) were generated for all transcripts
Genome_build: EquCab3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Equus caballus

source_name: pregnant mare

extract_protocol:
Total RNA was isolated using the RNEasy Mini kit. TruSeq Stranded mRNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endometrium

tag: days after ovulation


title: D28_preg_2


title: D28_preg_3


title: LPSCLU_A1 [ZM_CTX_LPSCLU_A1]

value: LPS (lipopolysaccharide) + clusterin

value: All cortical cells


title: RAZZ_359

value: three

value: dk


title: RAZZ_352

value: zero


title: LPSCLU_A4 [ZM_CTX_LPSCLU_A4]


title: RAZZ_287

value: two

value: male


title: LPS_B4 [ZM_CTX_LPS_B4]

value: LPS (lipopolysaccharide)


title: Purkinje cell p0 ChIP-Seq H3K27me3 WT rep2

value: Cerebellum

value: Purkinje cells


title: D22_preg_5

value: female


title: D22_preg_3


title: D22_preg_4


title: Purkinje cell p0 ChIP-Seq H3K4me3 WT rep2

value: post natal day 0

value: wild type

value: H3K4me3 (Active Motif, 39159)


title: RAZZ_258

value: Whole blood

value: one


title: Purkinje cell p56 ATAC-Seq WT rep2

description: Purkinje cell p56 ATAC-Seq WT rep2

data_processing:
ATAC-Seq data: Reads were processed with trim_galore with parameters “--stringency 3 --fastqc --paired”. Trimmed reads were mapped to mm10 using bowtie2 (version 2.1.0) with parameters “-X 2000 --no-mixed --no-discordant”. Duplicates were removed using samtools. Reads were normalized to RPKM using deepTools bamCompare module, ignoring chrX, chrY, chrM and filtering reads for minimum mapping quality of 30. Metagene and heatmap profiles were generated using deepTools modules computeMatrix, plotProfile and plotHeatmap. Unique fragments under 100 nt were used to call peaks with macs2 with parameters “--nomodel -q 0.01 --call-summits”. Broad peaks were called with macs2 as well with parameters “--nomodel -f BAM --keep-dup all --broad -g mm -B -q 0.01”. The peaks were filtered to remove chrY and chrM peaks and peaks that overlap with the mm10 blacklist from ENCODE.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts generated by ht-seq count
Supplementary_files_format_and_content: bigWigs generated using deepTools, 0 to 1 modification status per cytosine
Supplementary_files_format_and_content: peak text files from macs2

value: post natal day 56


title: RAZZ_320

value: white


title: D28_preg_1

value: endometrium


title: Purkinje cell p7 ChIP-Seq H3K4me3 WT rep1

value: post natal day 7


title: D14_preg_4


title: RAZZ_247

value: three

value: dk


title: RAZZ_251

value: zero


title: RAZZ_277

value: two


title: LPS_B2 [ZM_CTX_LPS_B2]

value: LPS (lipopolysaccharide)

value: All cortical cells


title: Purkinje cell p0 ChIP-Seq H3K4me3 WT rep1

value: Cerebellum

value: Purkinje cells


title: RAZZ_241

value: female


title: LPS_A2 [ZM_CTX_LPS_A2]


title: D22_preg_2


title: D14_preg_2


title: LPS_B1 [ZM_CTX_LPS_B1]


title: Purkinje cell p7 ChIP-Seq H3K4me3 WT rep2

value: wild type


title: LPS_A1 [ZM_CTX_LPS_A1]


title: Purkinje cell p0 ATAC-Seq WT rep2

description: Purkinje cell p0 ATAC-Seq WT rep2

value: post natal day 0


title: Purkinje cell p0 ATAC-Seq WT rep1

description: Purkinje cell p0 ATAC-Seq WT rep1


title: LPS_A3 [ZM_CTX_LPS_A3]


title: D14_preg_3


title: LPS_A4 [ZM_CTX_LPS_A4]


title: D22_preg_1


title: Purkinje cell p7 ATAC-Seq WT rep2

description: Purkinje cell p7 ATAC-Seq WT rep2


title: LPS_B3 [ZM_CTX_LPS_B3]


title: After 7 days of incubation from non-inoculated roots; Bio. Rep. 1

city: Bremen

first: Barbara

last: Reinhold-Hurek

state: Bremen

address: Leobener Str. 5

department: Microbe-Plant Interactions

institute: University of Bremen

description: RNA isolated after seven days of incubation from non-inoculated rice roots; Biological Replicate 1

data_processing:
Generated libraries were sequenced on an Illumina NextSeq 500 platform (Illumina, Inc., USA) where 150-bp paired-end reads were generated.
Raw reads were then filtered, trimmed (PHRED > 33) and mapped (minimal length fraction of 1, and minimal similarity fraction of 0.98) onto IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare genome using CLC Genomics Workbench 8.5.1 (Qiagen, Germany)
In order to perform differential gene expression analysis, raw read counts were then extracted from CLC software and analyzed using the DEseq2 package from Bioconductor in R-studio (http://www.rproject.org) based on the protocol (Anders et al., 2013). Genes were considered as differentially regulated (DEG) when the expression levels exhibited FDR < 0.05 and the fold change (FC) ³ 1.5.
Genome_build: IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

organism: Oryza sativa Japonica Group

source_name: 6 rice roots, non-inoculated (sterile)

growth_protocol: Surface sterilization of dehusked rice caryopsis was carried out as described by Hurek et al., 1994. For germination, seeds were then transferred into GA7 Magenta boxes (Sigma-Aldrich, USA) filled with 100 ml of solid plant medium (Egener et al., 1999), supplemented with 8 g per l Bacto Agar, 20 mg of neutralized DL-malic acid per l and a potassium phosphate buffer (0,439 g KH2PO4, 0,561 g K2HPO4 at pH 6.8), and incubated at 300C in the dark for three days, and in light in the phytotron (at 30°C, at 80% humidity and with a 14-h-day and 10-h-night cycle at approximately 100 μmol photons m–2 s–1) for one day. Then, one day before inoculation with bacteria, seedlings were transferred into hydroponic cultures: they were placed on top of metal mash adaptors in 200 x 30,00 x 1,1-1,2 mm glass tubes containing 50 ml of liquid plant medium (as described above but without addition of Bacto agar) and transferred back to the phytotron for an additional 24 h incubation. Certain modifications in the composition of the liquid plant medium were made according to the experimental set-up: for the boosted-colonization, liquid plant medium was supplemented with 400 mg of neutralized DL-malic acid per l instead of 20 mg, and for ammonia-containing controls 68 mg per l (NH4)2SO4 was added.

extract_protocol:
In order to extract total RNA, six rice roots were pooled together and the protocol of RNeasy Plant Mini Kit (Qiagen, Germany) was followed. Afterward, RNA quality and purity were evaluated via NanoDrop 2000 (Thermo Fisher Scientific, USA) and Agilent Bioanalyzer 2100 system (Agilent Technologies, USA), and only RNA samples with an RNA integrity number >8 were chosen for further analysis.
mRNA fraction was purified from 1 μg of the total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) and libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s recommendations. Quality of prepared libraries was assessed using Agilent Bioanalyzer 2100 system and quantity via NEBNext Library Quant Kit for Illumina (NEB, USA).

treatment_protocol: Parallel to seed preparation, bacterial cells of Azoarcus olearius BH72 or mutant strains were grown until the late exponential growth phase (optical density at 578 nm [OD578nm] = 1.0 to 1.2), washed in an N-free medium (Egener et al., 1999), and directly added to hydroponic cultures to yield an optical density of 0.067. Inoculated plants were then incubated in the phytotron for one, three or seven days depending on the experimental set-up.

value: total root

value: 12 days after planting the seeds

tag: concentration of carbon source in the medium

value: 20 mg/L of neutralized DL-malic

tag: days of incubation

value: 7 days

value: non-inoculated plants


title: Purkinje cell p7 RNA-Seq WT rep2

description: Purkinje cell p7 RNA-Seq WT rep2

value: post natal day 7


title: D14_preg_1

value: endometrium


title: RAZZ_199

tag: tissue/cell type

value: Whole blood

value: white

value: one


title: RAZZ_202

value: two

tag: Sex

value: asian

value: zero


title: TT25

city: New York

first: Michelle

middle: E

last: Ehrlich

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: 4 Months old mouse striatum-Ct

data_processing:
Paired-end reads were aligned to the reference genome using STAR
FeatureCounts was used to count the read numbers mapped per gene
Readcounts were adjusted by TMM normalisation
edgeR R package was used to perform differential expression analysis.
P-values were adjusted using Benjamini Hochberg method
Mus musculus Grch38
.txt file containing a matrix of genes with readcounts against samples

source_name: striatum

extract_protocol:
The striatum  from one hemisphere was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA sequencing was performed by Novogene (https://en.novogene.com) on an Illumina Novaseq 6000 S4 flow cells platform

tag: injection group

value: N-TAF MiRNA

tag: age of injection


title: Purkinje cell p0 RNA-Seq WT rep2

description: Purkinje cell p0 RNA-Seq WT rep2

source_name: Cerebellum

value: Cerebellum

value: Purkinje cells


title: Purkinje cell p7 ATAC-Seq WT rep1

description: Purkinje cell p7 ATAC-Seq WT rep1

value: wild type


title: RAZZ_238

value: three

value: female

tag: race

tag: hispanic

tag: bmi


title: Purkinje cell p56 ATAC-Seq WT rep1

description: Purkinje cell p56 ATAC-Seq WT rep1

tag: tissue

value: post natal day 56


title: RAZZ_163

tag: biologicis

tag: dmard


title: Purkinje cell p0 RNA-Seq WT rep1

description: Purkinje cell p0 RNA-Seq WT rep1

tag: cell type

tag: age

value: post natal day 0

tag: genotype


title: RAZZ_223


title: Sal_B2 [ZM_CTX_Sal_B2]

tag: strain

tag: treatment

value: Saline

value: All cortical cells


title: RB22

description: 4 Months old mouse striatum-Ct


title: HFHS ertugliflozin 4

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and treated with ertugliflozin.
WC_HFHS-ERTU-16

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.6.0c).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 92 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Regularized logarithmic (rlog) transformation was accomplished using the rlog() function in the DESeq2 R package (version 1.22.1).
Genome_build: mm10
Supplementary_files_format_and_content: count, rlog

source_name: left ventricle of heart

growth_protocol: 8 week old C57BL/6J male mice were fed either a control low fat diet (CD) +/- Ertugliflozin or a high fat high sucrose (HFHS) diet +/- Ertugliflozin (drug formulated into diet, 0.5 mg/g) for 4 months

extract_protocol:
Snap frozen left ventricular tissue was ground with mortar & pestle into a fine powder under liquid nitrogen, and RNA was extracted with Qiagen RNeasy Universal Mini kit with on-column DNAse digest.
Libraries were prepared from 250 ng total RNA input, enriched for mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module, and the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (New England Biolabs, USA).

treatment_protocol: Mice were fed diet +/- drug ad libitum for 4 months.

tag: diet

value: high-fat, high-sugar diet (HFHS)

tag: drug

value: ertugliflozin

tag: group

value: HFHS ertugliflozin


title: After 3 days of incubation from non-inoculated roots; medium supplemented with 400 mg/L malic acid; Bio. Rep. 2

description: RNA isolated after three days of incubation from non-inoculated rice roots; medium supplemented with 400 mg/L malic acid; Biological Replicate 2

value: Oryza sativa ssp. japonica cv. Nipponbare

value: total root

value: 8 days after planting the seeds

tag: concentration of carbon source in the medium

value: 400 mg/L of neutralized DL-malic

tag: days of incubation

value: 3 days

value: non-inoculated plants


title: 7 days after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 2

description: RNA isolated seven days after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 2

source_name: 6 rice roots, colonized with Azoarcus olearius BH72

value: 12 days after planting the seeds

value: 20 mg/L of neutralized DL-malic

value: 7 days

value: plants inoculated with Azoarcus olearius BH73


title: After 7 days of incubation from non-inoculated roots; Bio. Rep. 3

description: RNA isolated after seven days of incubation from non-inoculated rice roots; Biological Replicate 3


title: HFHS ertugliflozin 3

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and treated with ertugliflozin.
WC_HFHS-ERTU-15


title: Purkinje cell p56 RNA-Seq WT rep2

description: Purkinje cell p56 RNA-Seq WT rep2

value: Cerebellum

value: Purkinje cells

value: post natal day 56

value: wild type


title: Sal_B1 [ZM_CTX_Sal_B1]

value: Saline

value: All cortical cells


title: RAZZ_218

tag: tissue/cell type

value: Whole blood

value: one

tag: Sex

value: female

value: black

value: zero


title: Sal_A2 [ZM_CTX_Sal_A2]


title: Sal_A1 [ZM_CTX_Sal_A1]


title: RAZZ_143

value: male

tag: race

tag: hispanic


title: TT20

description: 4 Months old mouse striatum-Ct

tag: injection group

value: N-TAF MiRNA

tag: age of injection


title: HFHS ertugliflozin 2

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and treated with ertugliflozin.
WC_HFHS-ERTU-14

value: high-fat, high-sugar diet (HFHS)

value: ertugliflozin

value: HFHS ertugliflozin


title: 7 days after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 3

description: RNA isolated seven days after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 3

value: Oryza sativa ssp. japonica cv. Nipponbare

tag: tissue

value: total root

value: 12 days after planting the seeds

value: 20 mg/L of neutralized DL-malic

value: 7 days

value: plants inoculated with Azoarcus olearius BH74


title: Purkinje cell p7 RNA-Seq WT rep1

description: Purkinje cell p7 RNA-Seq WT rep1

value: Cerebellum

tag: cell type

value: Purkinje cells

value: post natal day 7

value: wild type


title: RAZZ_116

value: Whole blood

value: two

tag: age

value: female

value: white

tag: bmi

tag: biologicis

value: one

tag: dmard


title: RB17

description: 4 Months old mouse striatum-Ct

value: N-TAF MiRNA

tag: strain


title: RT16

description: 4 Months old mouse striatum-Ct


title: RAZZ_166

value: three

value: zero


title: 7 days after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 1

description: RNA isolated seven days after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 1

value: Oryza sativa ssp. japonica cv. Nipponbare

value: total root

tag: treatment

value: plants inoculated with Azoarcus olearius BH72


title: HFHS untreated 4

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and left untreated.
WC_HFHS-12

tag: diet

value: high-fat, high-sugar diet (HFHS)

tag: drug

value: untreated

tag: group

value: HFHS untreated


title: Purkinje cell p56 RNA-Seq WT rep1

description: Purkinje cell p56 RNA-Seq WT rep1

value: Cerebellum

value: Purkinje cells

value: post natal day 56

tag: genotype


title: RAZZ_203

tag: tissue/cell type

value: Whole blood

tag: Sex


title: LB24

description: 4 Months old mouse striatum-Ct


title: After 7 days of incubation from non-inoculated roots; Bio. Rep. 2

description: RNA isolated after seven days of incubation from non-inoculated rice roots; Biological Replicate 2

value: 12 days after planting the seeds

tag: concentration of carbon source in the medium

value: 20 mg/L of neutralized DL-malic

tag: days of incubation

value: 7 days

value: non-inoculated plants


title: LT23

description: 4 Months old mouse striatum-Ct

tag: injection group

value: N-TAF MiRNA

tag: age of injection


title: After 3 days of incubation from non-inoculated roots; medium supplemented with 400 mg/L malic acid; Bio. Rep. 3

description: RNA isolated after three days of incubation from non-inoculated rice roots; medium supplemented with 400 mg/L malic acid; Biological Replicate 3

tag: tissue

value: 8 days after planting the seeds

value: 400 mg/L of neutralized DL-malic

value: 3 days


title: HFHS untreated 3

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and left untreated.
WC_HFHS-11


title: RAZZ_105

value: two

tag: age

value: female

tag: race

value: dk

tag: hispanic

value: one


title: HFHS untreated 2

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and left untreated.
WC_HFHS-10

value: high-fat, high-sugar diet (HFHS)

value: untreated

value: HFHS untreated


title: After 3 days of incubation from non-inoculated roots; medium supplemented with 400 mg/L malic acid; Bio. Rep. 1

description: RNA isolated after three days of incubation from non-inoculated rice roots; medium supplemented with 400 mg/L malic acid; Biological Replicate 1

value: Oryza sativa ssp. japonica cv. Nipponbare

value: total root


title: HFHS ertugliflozin 1

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and treated with ertugliflozin.
WC_HFHS-ERTU-13

value: ertugliflozin

value: HFHS ertugliflozin


title: 3 days after inoculation from roots inoculated with A. olearius BH72; supplemented with 400 mg/L malic acid; Bio. Rep. 2

description: RNA isolated three days after inoculation from rice roots inoculated with Azoarcus olearius BH72; medium supplemented with 400 mg/L malic acid to boost bacterial growth; Biological Replicate 2

value: plants inoculated with Azoarcus olearius BH73


title: HuMSC_2D

city: Beijing

first: Junhao

last: Deng

state: Beijing

address: Fuxing Road,  Beijing, 100853, People’s Republic of China.

institute: Chinese PLA General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: mesenchymal stem cells

extract_protocol:
Cells were collected and prepared for RNA extractionusing Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta

tag: cell type

value: mesenchymal stem cells

tag: passage

value: 2D-conventional culture


title: HFHS untreated 1

description:
Left ventricular tissue obtained from an animal fed a high-fat, high-sugar diet and left untreated.
WC_HFHS-9


title: RAZZ_137

value: Whole blood

value: three

value: multi

value: zero

tag: bmi

tag: biologicis

tag: dmard


title: RAZZ_130

value: two

value: female


title: RT21

description: 4 Months old mouse striatum-Ct

value: N-TAF MiRNA

tag: strain


title: 3 days after inoculation from roots inoculated with A. olearius BH72; supplemented with 400 mg/L malic acid; Bio. Rep. 3

description: RNA isolated three days after inoculation from rice roots inoculated with Azoarcus olearius BH72; medium supplemented with 400 mg/L malic acid to boost bacterial growth; Biological Replicate 3

value: 8 days after planting the seeds

value: 400 mg/L of neutralized DL-malic

value: 3 days

tag: treatment

value: plants inoculated with Azoarcus olearius BH74


title: CD ertugliflozin 4

description:
Left ventricular tissue obtained from an animal fed a control diet and treated with ertugliflozin.
WC_CD-ERTU-8

tag: diet

value: control diet (CD)

tag: drug

value: ertugliflozin

tag: group

value: CD ertugliflozin


title: RT12

description: 4 Months old mouse striatum-Ct

value: C/N-TAF MiRNA


title: 3 days after inoculation from roots inoculated with A. olearius BH72; supplemented with 400 mg/L malic acid; Bio. Rep. 1

description: RNA isolated three days after inoculation from rice roots inoculated with Azoarcus olearius BH72; medium supplemented with 400 mg/L malic acid to boost bacterial growth; Biological Replicate 1

value: Oryza sativa ssp. japonica cv. Nipponbare

value: total root

tag: concentration of carbon source in the medium

tag: days of incubation

value: plants inoculated with Azoarcus olearius BH72


title: RAZZ_127

tag: tissue/cell type

value: Whole blood

tag: Sex

value: one


title: ΔPus7 293T cellular 6SG PA-Ψ-Seq

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description:
Cell extract polyA+ RNA
Aligned to hg19

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
For hg19 alignments: tophat -N 1 --no-convert-bam --b2-N 1
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
When comparing WT to Pus KO samples, the dataset with the higher read depth down sampled to match the one with the lower read depth using "macs2 randsample"
Filtered out all reads that lack a G>A or T>C mutation (for 6SG or 4SU-pulsed samples, respectively)
Peaks called with: "macs2 callpeak --nomodel -q $q --extsize 32 --shift 0 --keep-dup 5 -g hs" where $q is 0.0005 for WT samples, $q=0.05 for KO samples
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
For WT samples, peaks further screened with "awk '{if($1!="#" && $1!="chr" && $6>=3 && $8>=5) {print $1 "\t" $2-1 "\t" $3 "\t" $10 "\t" $6 "\t."}}' macs_called_peaks.xls > significant_peaks.bed" For KO samples, the if statement in the awk script is "if($1!="#" && $1!="chr" && $6>=1 && $8>=3)"
Genome_build: NL4-3 genome: 551-9626nt of GenBank AF324493.2
Genome_build: Human hg19
Genome_build: tRNA sequences from tRNAdb (Juhling Morl 2016)
Genome_build: rRNA: GenBank #U13369 nts 7935-12969, X03205, and U13369 nts 6623-6779
Genome_build: snRNA: NC_000001.11:c16514285-16514122, NC_000017.11:c43233977-43233790, NC_000012.12:c120293237-120293094, NC_000015.10:65296051-65296167, NC_000015.10:c67840045-67839940, NC_000001.11:28648600-28648734, NC_000022.11:42615244-42615393, NC_000002.12:121530880-121531009, NC_000009.12:c134164564-134164440, all from GRCh38.p13
Supplementary_files_format_and_content: bed files, aligned to hg19, HIV-1 NL4-3 genome, or tRNA, rRNA, snRNA sequences

source_name: ΔPus7 293T

extract_protocol:
PA-Ψ-seq or PA-m6A-seq (PAR-CLIP done with a pasudouridine or m6A RNA targeting antibody)
All samples were processed with the NEB Next small RNA-seq library prep kit for Illumina

tag: virus strain

value: HIV-1 NL4-3

tag: technique

value: PA-Psi-Seq

tag: pulldown antibody

value: anti-pseudouridine (anti-Psi) (MBL #347-3)


title: HuMSC_3D

tag: tissue

value: placenta

tag: cell type

value: mesenchymal stem cells

value: 3D-spheroid culture


title: LT14

description: 4 Months old mouse striatum-Ct

tag: injection group

tag: age of injection


title: TT15

description: 4 Months old mouse striatum-Ct


title: After 3 days of incubation from non-inoculated roots; Bio. Rep. 3

description: RNA isolated after three days of incubation from non-inoculated rice roots; Biological Replicate 3

tag: age

value: 8 days after planting the seeds

value: 20 mg/L of neutralized DL-malic

value: 3 days

value: non-inoculated plants


title: 3 days after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 2

description: RNA isolated three days after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 2

tag: strain

value: plants inoculated with Azoarcus olearius BH73


title: RAZZ_110

value: two

value: female

tag: race

value: asian

tag: hispanic

value: zero

tag: bmi

tag: biologicis

tag: dmard


title: RB13

description: 4 Months old mouse striatum-Ct

value: C/N-TAF MiRNA


title: After 3 days of incubation from non-inoculated roots; Bio. Rep. 1

description: RNA isolated after three days of incubation from non-inoculated rice roots; Biological Replicate 1

value: Oryza sativa ssp. japonica cv. Nipponbare

value: total root

tag: concentration of carbon source in the medium

tag: days of incubation

tag: treatment


title: 3 days after inoculation from roots inoculated with A. olearius BH72; Bio. Rep. 3

description: RNA isolated three days after inoculation from rice roots inoculated with Azoarcus olearius BH72; Biological Replicate 3

value: plants inoculated with Azoarcus olearius BH74


title: RT7

description: 4 Months old mouse striatum-Ct

value: control miRNA


title: CD ertugliflozin 3

description:
Left ventricular tissue obtained from an animal fed a control diet and treated with ertugliflozin.
WC_CD-ERTU-7

tag: diet

value: control diet (CD)

tag: drug

value: ertugliflozin

tag: group

value: CD ertugliflozin


title: Cas9-control 293T cellular 6SG PA-Ψ-Seq

description:
Cell extract polyA+ RNA
Aligned to hg19

source_name: ΔGFP 293T

tag: virus strain

value: HIV-1 NL4-3

tag: technique

value: PA-Psi-Seq

tag: pulldown antibody

value: anti-pseudouridine (anti-Psi) (MBL #347-3)


title: CD ertugliflozin 1

description:
Left ventricular tissue obtained from an animal fed a control diet and treated with ertugliflozin.
WC_CD-ERTU-5