title: LagPhase_Rep1_240min

source_name: cells, 240 min after inoculation on soft-agar, rep.1

value: WT chromosome; comI_Q12L in natual plasmid


title: LagPhase_Rep2_0min

status: Public on Sep 20 2023

type: SRA

city: Basel

first: Kazuki

last: Nosho

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

library_source: transcriptomic

data_processing:
Sequencing of the cDNA libraries was performed by MPGC (Cologne, Germany) or D-BSSE genomics facilty (Basel, Switzerland)
Sequence reads were trimmed for adaptor sequence/short sequence (<35 nt) using Trimmomatic v0.39
Trimmed sequence reads were mapped to B. subtilis NCIB3610 genome and plasmid (NCBI Accession number: NZ_CP020102 and NZ_CP020103) using HISAT2 v2.2.1 in single-end mode.
Reads mapped to all cetegory of genes (CDS, ncRNA, tmRNA, signal recognition particle RNA, ribonuclease P RNA, tRNA, rRNA) were counted using featureCounts v2.0.1 with fractional counting for multi-mapping and multi-overlapping reads (-OM --fraction) in a strand-specific manner (-s 2). Of those, reads mapped in tRNA and rRNA were removed and the remaining reads were used for the downstream analysis.
All genes for which there were at least 2 samples with a read count of at least 10 were used for the downstream analysis. Samples with remaining reads of < 1 million reads were excluded and the rest of the samples were used for normalization using edgeR (version 3.6.1) and transformed (log2).
Supplementary files format and content: comma-separated files include mapped read count data for each sample
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at expansion phase
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at lag and expansion phase

molecule: total RNA

organism: Bacillus subtilis

source_name: cells, 0 min after inoculation on soft-agar, rep.2

growth_protocol: Bacterial cells were spotted onto the center of a 9 cm petri dish filled with LB soft-agar (0.5% agar) medium and incubated at 30°C for swarm expansion.

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods, 2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using DIY method (Culviner et al, mBio, 2020). Integrity of the prepared RNA was tested using a TapeStation.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB, E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.

treatment_protocol: Cells that started swarm expansion were collected into the lysis buffer by our custom sampling robot. Cells before swarm expansion (lag phase) were collected by being suspened in the lysis buffer.

tag: cell type

value: Bacteria

tag: genotype

tag: strain

tag: time after_inoculation_(min)


title: ZmRPN1-WT-AA-rep1

city: Beijing

first: Luguang

last: Jiang

state: Beijing

address: No.2 Yuanmingyuan West Road, Haidian, Beijing

country: China

institute: China Agricultural University

description:
WT
RPN1-AA-aa-genecounts.txt

data_processing:
Sequencing reads were processed with trimmomatic-0.39 to remove adaptor sequence and low-quality sequence, and then mapped to B73 RefGen_v4 reference genome (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-50/plants/fasta/zea_mays/dna/) using HISAT2 (version: 2.2.1).
Uniquely mapped reads were kept for subsequent gene expression quantification using featureCounts (v1.6.4).
DEGs analysis was performed using the DESeq2 R package.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie (version: 1.3.6).
Assembly: B73 RefGen_v4 reference genome
Supplementary files format and content: tab-delimited text files include read counts for each sample

organism: Zea mays

source_name: anther (S3-S5 stage)

extract_protocol:
Total RNA was extracted using RNAprep Pure Plant Plus kit,treated with RNase-free DNaseI and purified using the RNAclean Kit.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep kit following manufacturer's protocols.

tag: tissue

value: anther (S3-S5 stage)

value: WT


title: LagPhase_Rep1_225min

source_name: cells, 225 min after inoculation on soft-agar, rep.1


title: ET63

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

description: rm.f.results.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the GCF_019320065.1 elk genome using Bowtie2.
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: GCF_019320065.1
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.
Library strategy: MeDIP-Seq

molecule: genomic DNA

organism: Cervus canadensis

source_name: Tendon

growth_protocol: Lower limbs from TAHD-suspect and apparently normal elk and associated metadata were solicited from state, federal, and tribal collaborators for TAHD surveillance conducted during 2018-2020. Elk were harvested, culled for management purposes, or found recently deceased. As such, the study was exempt from review by an Institutional Animal Care and Use Committee. Ecotype was inferred from location of collection. Age class of elk was assigned as adult (>2 years old), juvenile (<2 years old), or unknown.

extract_protocol:
Frozen elk tendon samples were thawed for analysis. Genomic DNA from tendon samples was prepared as follows: DNA was isolated from tendon samples by cutting a 2mm x 2mm x 2mm cube of tendon and rinsing twice in 1 ml PBS followed by centrifugation at 13,000g for 1 min to remove the Allprotect Tissue Reagent™. Each sample was minced and incubated with 1 mg/ml collagenase I in 1 ml PBS at 37° with rotation overnight.  Samples were then processed using the DNeasy Blood and Tissue Kit™ (Qiagen) to extract DNA, following the manufacturer’s protocols. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20 min at 4 C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min then centrifuged again at 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: Frozen lower limbs (-20) were submitted to the Washington Disease Diagnostic Laboratory (WADDL) for TAHD diagnosis and sample collection. Feet were thawed, grossly examined, and sampled under the direction of a board-certified veterinary pathologist. Tissue samples used to determine TAHD status were placed in formalin and processed for histologic examination with H&E and Warthin Starry silver stains. Cases that exhibited characteristic gross lesions with inflammation and spirochetes on histologic examination were diagnosed as TAHD positive. An approximately 1 cm section of the superficial or deep flexor tendon at about the level of the fetlock was collected from one foot from each elk for epigenetic analysis. Tendon appeared grossly normal and was collected proximal to the location of TAHD lesions. The sample was placed in AllProtect Tissue Reagent™ (Qiagen, Germantown, Maryland) storage solution and frozen at -80 until use.

tag: subspecies

value: nelsoni

tag: group

value: tahd negative

tag: Sex

value: female

value: Tendon


title: Cav1 knockout (KO) week 70 aging brain rep2

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

description: Illumina

data_processing:
The quality of raw sequences was checked with FastQC followed by trimming the adaptors from the sequence reads by cutadapt. The trimmomatic tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides). The quality reads were then mapped to the mouse reference genome GRCm38 using Hisat2 aligner.
Read counting from the alignment data was performed by FeatureCounts. The feature count data was then analyzed by edgeR to determine significance of differential expression of KO compared to WT brain.
Assembly: GRCm39
Supplementary files format and content: comma separated file

organism: Mus musculus

source_name: whole brain

extract_protocol:
Total RNA was isolated from day 15 fetal brain of WT and KO mice, in three biological replicates, using an AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) following the manufacturer’s instruction. Sample was homogenized with 500 ul -1 ml RLT buffer (Qiagen, Cat No./ID: 79216) supplemented with 5μl of 2-mercaptoethanol. The homogenate was transferred to a fresh tube and centrifuged for 1 minute at ≥ 8000 x g. From the supernatant, 750μl was transferred to fresh tube and mixed with 1 volume 70% ethanol to precipitate RNA. RNA was eluted in 30μl nuclease-free water twice to a total volume of 60μl. Concentration of RNA was determined using Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific). RNA Integrating Number (RIN) was determined (using Agilent2100).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: whole brain

tag: age

value: week 70

value: Cav1 KO


title: Wildtype (W) day 15 fetal brain rep1

description: Illumina

value: day 15 fetus


title: notaddDrug_2, input

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description: notaddDrug_2, input

data_processing:
Clean reads were mapped the hg19 genome using STAR
MACS2 were used to identify peaks
Peaks from each sample were merged to a set of union peaks using BEDTools merge.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: m6A-seq

organism: Homo sapiens

growth_protocol: Total RNA from cell lines was isolated by using Trizol reagent (Invitrogen). The RNA samples were quantified by measuring absorbance at 260 nm with a UV spectrophotometer, and only analytes with an RNA integrity number (RIN) ≥ 7.0 were used in further experiments.

extract_protocol:
One tenth of the fragmented RNA served as an input control in RNA sequencing.
RNA fragments from the m6A-IP and input samples were used for cDNA library preparation and sequenced on an Illumina HiSeqX Ten PE150 platform.

treatment_protocol:
Purified RNA was fragmented and incubated with anti-m6A antibody (Synaptic Systems, 202003)-conjugated beads in RIP reaction buffer overnight at 4 °C
After incubation, the bound RNAs were purified via proteinase K treatment, acidic phenol/chloroform extraction and ethanol precipitation

tag: cell line

value: Human PDAC cell lines

value: not Cytochalasin D treatment

tag: treatment


title: LagPhase_Rep1_210min

source_name: cells, 210 min after inoculation on soft-agar, rep.1


title: Cav1 knockout (KO) day 15 fetal brain rep3

description: Illumina


title: ET62

description: rm.f.results.csv.gz


title: notaddDrug_1, input

description: notaddDrug_1, input


title: LagPhase_Rep1_195min

source_name: cells, 195 min after inoculation on soft-agar, rep.1


title: ET67

description: rm.f.results.csv.gz

value: tahd positive


title: Cav1 knockout (KO) day 15 fetal brain rep2

description: Illumina


title: ET61

description: rm.f.results.csv.gz


title: notaddDrug_2, ip

description: notaddDrug_2, ip


title: LagPhase_Rep1_180min

source_name: cells, 180 min after inoculation on soft-agar, rep.1


title: ET60

description: rm.f.results.csv.gz


title: notaddDrug_1, ip

description: notaddDrug_1, ip


title: LagPhase_Rep1_150min

source_name: cells, 150 min after inoculation on soft-agar, rep.1


title: ET59

description: rm.f.results.csv.gz


title: addDrug_2, input

description: addDrug_2, input

value: CFL1 inhibitor Cytochalasin D


title: Wildtype (W) day 15 fetal brain rep2

description: Illumina


title: LagPhase_Rep1_120min

source_name: cells, 120 min after inoculation on soft-agar, rep.1


title: Cav1 knockout (KO) fetal brain

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The base call (BCL) files generated from Illumina machine were processed by Cell Ranger pipeline (v. 3.0.1) to generate the FASTQ files. The STAR aligner  was used to map the reads in the FASTQ files to the mouse reference genome to generate read count data of genes expressed in the single cells.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single nuclei from fetal brain were isolated using Pure Prep Nuclei Isolation kit (Sigma, St. Louis, MO, USA). Briefly, frozen brain samples after thawing were minced into small pieces and added to the lysis buffer. Using a dounce homogenizer, the sample were be homogenized till the solution looks evenly mixed, which generally requires 15-20 dounces. A 70µm cell strainer was be used to filter the nuclei from the lysed cells, diluted and layered over a freshly prepared 1.8M sucrose cushion solution to collect single nuclei. After centrifugation and suspension with the kit provided storage buffer (ice cold), final purification of single nuclei was be performed by filtering through a 40µm cell strainer. The purified nuclei were then counted using a Countess II FL Automated Cell Counter (ThermoFisher).
The freshly prepared nuclei were used to prepare sequencing libraries using 10X Genomics Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 at the University of Missouri Genomics Technology Core. The nuclei suspension, reverse transcription master mix, and partitioning oil were loaded on a Chromium Next GEM G chip with a capture target of 10,000 nuclei per sample.  Post-Chromium controller GEMs were transferred to a PCR strip tube and reverse transcription performed on an Applied Biosystems Veriti thermal cycler at 53°C for 45 minutes.  cDNA was amplified for 12 cycles and purified using Axygen AxyPrep MagPCR Clean-up beads.  cDNA fragmentation, end-repair, A-tailing, and ligation of sequencing adaptors was performed according to manufacturer specifications.  The final library was quantified with the Qubit HS DNA kit and the fragment size was analyzed using an Agilent Fragment Analyzer system.  Libraries were pooled and sequenced on an Illumina NovaSeq to generate 50,000 reads per cell with a sequencing configuration of 28 base pair (bp) on read1 and 98 bp on read2. Each library was sequenced to a depth of 20,000 paired-end (single-indexing) reads per nucleus using NovaSeq 6000.

value: fetal

value: Cav1 knockout (KO)


title: wildtype fetal brain

description: 10x Genomics

value: wildtype


title: ET58

description: rm.f.results.csv.gz


title: LagPhase_Rep1_90min

source_name: cells, 90 min after inoculation on soft-agar, rep.1

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid


title: addDrug_1, input

description: addDrug_1, input


title: addDrug_2, ip

description: addDrug_2, ip


title: LagPhase_Rep1_60min

source_name: cells, 60 min after inoculation on soft-agar, rep.1


title: LagPhase_Rep1_30min

source_name: cells, 30 min after inoculation on soft-agar, rep.1


title: Control_2, input [nuclear RNA]

description:
Control_2, input
Ctrl12_IPtoinput.bw

molecule: nuclear RNA

value: Control


title: sample683+sample684 blood ADT

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description: New-onset diabetic NOD mice

library_source: other

data_processing:
Raw sequencing reads were de-multiplexed using the Cell Ranger pipeline (10x Genomics Inc.) and gene expression and cell surface protein matrices were created.
These matrices were processed with Seurat v4.1.0. Cells expressing >200 genes were retained. Subsequent filtering based on number of features, unique molecular identifiers (UMIs) and percentage of mitochondrial DNA was applied.
Data was normalized employing natural-log and centered-log ratio (CLR) normalization for mRNA-based and ADT-based clustering respectively.
To identify the different cell types of the dataset, we clustered the cells with principal component analysis (PCA) linear dimensional reduction and uniform manifold approximation and projection (UMAP) non-linear dimensional reduction for visualization.
Assembly: GRCm38.99
Supplementary files format and content: raw and filtered count matrices in a .h5 file containing the cDNA, ADT and HTO library counts

molecule: protein

source_name: blood

growth_protocol: Following tissue dissociation, total cells from blood and pancreas were resuspended in RPMI+10%+ FBS+1%P/S media and kept on ice until the sorting of CD45+ leucocytes

extract_protocol:
Cells were incubated for 10 min with Fc block to block nonspecific antibody binding. Subsequently, cells were incubated with a pool of 190 barcoded TotalSeq™-A antibodies (Biolegend) for 30 min at 4 °C mixed with an antibody against CD45 (clone 30-F11, Thermo Fisher Scientific). After labelling, cells were washed with FACS buffer and CD45+ immune cells were sorted with BD FACS Aria™ II cell sorter (BD Biosciences). Cells were sorted, spun down, and resuspended in PBS with 0.04% BSA at an estimated final concentration of 1,000 cells/μL. Cellular suspensions (target recovery of 10,000 cells) were loaded on a GemCode Single-Cell Instrument (10x Genomics, Inc., Pleasanton, CA, USA) to generate single-cell Gel Bead-in-EMulsion (GEMs).
Single-cell RNA-sequencing libraries were prepared using GemCode Single-Cell 3ʹ V3.1 Gel Bead and Library Kit (10x Genomics) according to the manufacturer’s instructions.  The cDNA amplification mix was modified to include ADT PCR additive primer (5’-CCTTGGCACCCGAGAATT*C*C-3’ where * indicates a phosphorotioate bond) and HTO PCR additive primer (5’-GTGACTGGAGTTCAGACGTGTGC*T*C-3’). Size selection via a SPRIselect Reagent kit (Beckman Coulter, Brea, CA, USA) was used to separate the amplified cDNA molecules for 3′ gene expression and cell surface protein library construction.
Sequencing libraries were loaded on an Illumina HiSeq4000 or an Illumina NovaSeq 6000 flow cell with sequencing settings according to the recommendations of 10x Genomics Inc. (read 1: 26 cycles; read 2: 98 cycles; index i7: eight cycles; index i5: no cycles, pooled in a 75:20:5 ratio with a 115 pM loading concentration + 1% PhiX for the combined 3′ gene expression and cell surface / hashing libraries respectively).

value: NOD mouse

value: blood

value: CD45+ leukocytes

tag: library type

value: ADT

value: 14-18 weeks


title: ET55

description: rm.f.results.csv.gz

value: nelsoni

value: tahd negative

value: female

value: Tendon


title: sample683+sample684 blood cDNA

description: New-onset diabetic NOD mice

value: mRNA


title: sample676+sample681 blood HTO

description: New-onset diabetic NOD mice

value: HTO


title: LagPhase_Rep1_0min

source_name: cells, 0 min after inoculation on soft-agar, rep.1


title: Cav1 knockout (KO) day 15 fetal brain rep1

description: Illumina

value: whole brain

value: day 15 fetus

value: Cav1 KO


title: ET57

description: rm.f.results.csv.gz


title: ET53

description: rm.f.results.csv.gz


title: Control_1, input [nuclear RNA]

description:
Control_1, input
Ctrl12_IPtoinput.bw

value: Human PDAC cell lines


title: Treated-3

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

country: United Kingdom

institute: Brunel University London

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl2fastq (2.20.0.422)
Read mapping was performed with HISAT
Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R and were normalized using edgeR’s Trimmed Mean of M values algorithm.  Subsequent values were then converted to counts per million (cpm).
Assembly: NZ_CP008706.1
Supplementary files format and content: Matrix table (tab-delimited file) with raw gene counts for every gene and every sample
Supplementary files format and content: Individual tab-delimited files with normalize counts (cpm) for every sample.

organism: Acinetobacter baumannii AB5075

source_name: Acinetobacter baumannii AB5075

growth_protocol: A. baumannii AB5075 (6 independent replicates) was inoculated from stock and incubated overnight in LB (37 C, 180 rpm). Then, cultures were diluted in cation-adjusted Muller-hinton (pH 7.2) (suplemented wth 0.375 mM Kaempferol or with a mock treatment of DMSO) to OD600 0.05 and incubated at 37 C, 180 rpm until reaching mid-exponential phase (OD600 0.6 approx.).

extract_protocol:
Cultures were harvested by centrifugation and washed in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Samples were additionally treated with RNAse-free DNAse (Invitrogen). cDNA library was prepared with Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: The treatment (0.375 mM Kaempferol or a DMSO control) was applied as a supplement in the LB medium and was present since the beginning of the growth.

value: 0.375 mM Kaempferol

tag: culture conditions

value: 42 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.)


title: ET54

description: rm.f.results.csv.gz


title: sample683+sample684 blood HTO

description: New-onset diabetic NOD mice

value: NOD mouse


title: Treated-2

value: 41 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.)


title: sample676+sample681 blood ADT

description: New-onset diabetic NOD mice

value: blood

value: CD45+ leukocytes


title: Control_2, ip [nuclear RNA]

description:
Control_2, ip
Ctrl12_IPtoinput.bw

value: Control


title: ET52

description: rm.f.results.csv.gz

value: nelsoni


title: Control_1, ip [nuclear RNA]

description:
Control_1, ip
Ctrl12_IPtoinput.bw


title: ET56

description: rm.f.results.csv.gz

value: tahd negative


title: ET51

description: rm.f.results.csv.gz

value: female


title: sample683+sample684 pancreas HTO

description: New-onset diabetic NOD mice

source_name: pancreas

value: pancreas

value: 14-18 weeks


title: KO METTL3_2, input [nuclear RNA]

description:
KO METTL3_2, input
M3KO12_IPtoinput.bw

value: KO METTL3


title: sample676+sample681 blood cDNA

description: New-onset diabetic NOD mice

value: mRNA


title: Treated-1

value: 40 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.)


title: ET50

value: roosevelti

value: tahd omit

value: male

value: Tendon


title: addDrug_1, ip

description: addDrug_1, ip

value: Human PDAC cell lines

value: CFL1 inhibitor Cytochalasin D


title: Untreated-3

value: DMSO control

value: 39 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.)


title: sample683+sample684 pancreas ADT

description: New-onset diabetic NOD mice

value: NOD mouse

value: CD45+ leukocytes

value: ADT


title: KO METTL3_1, input [nuclear RNA]

description:
KO METTL3_1, input
M3KO12_IPtoinput.bw


title: sample683+sample684 pancreas cDNA

description: New-onset diabetic NOD mice


title: Untreated-2

value: 38 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.)


title: ET49

description: ro.m.results.csv.gz

value: tahd negative


title: KO METTL3_2, ip [nuclear RNA]

description:
KO METTL3_2, ip
M3KO12_IPtoinput.bw


title: KO METTL3_1, ip [nuclear RNA]

description:
KO METTL3_1, ip
M3KO12_IPtoinput.bw


title: Untreated-1

value: 37 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.)


title: sample676+sample681 pancreas HTO

description: New-onset diabetic NOD mice

value: pancreas

value: HTO

value: 14-18 weeks


title: ET48

description: ro.m.results.csv.gz

value: roosevelti

value: tahd positive


title: KO CFL1_2, input [nuclear RNA]

description:
KO CFL1_2, input
CFL1KO12_IPtoinput.bw

value: KO CFL1


title: ET47

description: ro.m.results.csv.gz

value: male

value: Tendon


title: sample676+sample681 pancreas ADT

description: New-onset diabetic NOD mice


title: testis

city: Lund

first: Helena

last: Persson

address: Scheelevagen 2

department: Dept of Clinical Sciences, Oncology

country: Sweden

institute: Lund University

description: testis

data_processing:
Basecalling and demultiplexing were done with Guppy version 4.2.3.
Reads were aligned using minimap2 version 2.17 with the settings -ax splice -G 500k and --junc-bed together with a merged and filtered set of annotated and novel ESR1 splice junctions.
Full-length reads were identified and assigned to individual amplicons through comparison with the coordinates of forward and reverse primers used for RT-PCR. Transcripts were filtered to only retain isoforms with an intron size ≥70 bp and GU-AG intron ends and then divided into three tiers depending on the available support: Tier 1 isoforms only had exon ends present in the curated set of exons from SCAN-B breast tumours, GENCODE and RefSeq, tier 2 isoforms had one or more exon ends that were only present in the unfiltered SCAN-B junction set and tier 3 isoforms had one or more exon ends unsupported by new or existing annotation.
Assembly: hg38
Supplementary files format and content: Tab-delimited read count table for all full-length transcripts with an intron size ≥70 bp and GU-AG intron ends. Columns are: isoform ID = named by RT-PCR amplicon, unique transcript number and annotation tier; exon coordinates hg38 chr6 = comma-separated list of start-end coordinates for all included exons on chromosome 6 in the hg38 genome assembly, for the first and last exon the coordinates refer to RT-PCR primer ends; unannotated splice junctions = comma-separated list of splice junctions with 0 corresponding to splice junctions in the merged set of known and novel splice junctions and 1 denoting splice junctions without previous support. The remaining 15 columns have isoform read counts per sample.

source_name: testis

extract_protocol:
RNA was extracted with TRI Reagent (Sigma-Aldrich) from the BT-474, MCF7, and T47D cell lines (purchased from ATCC) according to the manufacturer’s instructions and treated with DNase I (Thermo Fisher Scientific). The FirstChoice Human Total RNA Survey Panel with normal tissue RNA was purchased from Ambion/Thermo Fisher Scientific.
First-strand cDNA was generated using RevertAid H minus (Thermo Fisher Scientific) and an anchored oligo(dT) primer (Integrated DNA Technologies) as per the manufacturer’s recommendations. Primers for reverse transcription polymerase chain reaction (RT-PCR) were designed to amplify full-length transcripts from seven different locations in first exons. PCR was done using AccuPrime GC-Rich DNA Polymerase (Thermo Fisher Scientific) with the following conditions: 98 °C for 3 minutes, followed by 34 cycles of 95 °C for 30 seconds, 55 °C for 30 seconds, 72 °C for 2 minutes, and a final extension step of 72 °C for 10 minutes. Products were purified using AMPure XP beads (Beckman Coulter) and quantitated with the Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific) before pooling all amplicons per sample at equimolar concentrations to a final mass of 150 ng (~140 fmol) per pool. Pools underwent end-repair with the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs) before clean-up with AMPure XP beads. Barcoding ligation was performed with the PCR Native Barcoding Expansion 1-12 PCR-free kit (Oxford Nanopore Technologies) and Blunt/TA Ligase Master Mix (New England Biolabs) to allow sample pooling and multiplexing. Barcoded amplicon pools were purified using AMPure XP beads and quantitated with the Qubit dsDNA High Sensitivity Assay Kit before pooling equimolar amounts of each barcoded sample (1-12) to reach a final concentration of 200 femtomoles. Library quality was assessed on a Bioanalyzer with a High Sensitivity DNA chip (Agilent Technologies) and measured using the Qubit dsDNA Broad Range Assay kit. Adapter ligation was performed using the Ligation Sequencing Kit (Oxford Nanopore Technologies), followed by purification using AMPure XP beads and elution in Elution Buffer.

value: testis


title: ET46

description: ro.m.results.csv.gz


title: sample676+sample681 pancreas cDNA

description: New-onset diabetic NOD mice

value: mRNA


title: KO CFL1_1, input [nuclear RNA]

description:
KO CFL1_1, input
CFL1KO12_IPtoinput.bw

value: Human PDAC cell lines


title: spleen

description: spleen

source_name: spleen

value: spleen


title: skeletal muscle

description: skeletal muscle

source_name: skeletal muscle

value: skeletal muscle


title: ET45

description: ro.m.results.csv.gz

source_name: Tendon


title: mtKeima_Veh_replicate_5

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
RNAseq analysis was provided by Novogene. For quality control, raw data (raw reads) of FASTQ format were first processed through fastp to obtain clean data (clean reads) by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses are based on this high quality, clean data.
Original image data file from Illumina was transformed to sequenced reads (raw data) by CASAVA base recognition (base calling).
Raw data was subjected to data QC including error rate distribution, GC content distribution, and data filtering.
Mapping was performed using STAR (v2.6.1d, mismatch=2) and reads were mapped to the mouse reference genome mm10. Quantification was conducted by FeatureCounts (v1.5.0) under default mode.
Normalization and differential gene expression used DESeq2 (v1.26.0)(45). Genes with p-value ≤0.05 were passed on for enrichment analysis (Gene Ontology and KEGG) using ClusterProfiler (v3.8.1) and terms with padj <0.05 were considered significant.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include readcount values for each sample.

source_name: Cochlea

growth_protocol: Mice (mt-Keima, Jackson Lab) were fed and had access to water ad libitum and group housed per NIH animal experimental protocol #361-OSD-2023.

extract_protocol:
Total RNA was extracted from cochlear tissue using Trizol Reagent (Zymo Research, #R2050-1-50) and Direct-zol RNA Miniprep (Zymo Research, #R2050) as described by Patil et al. (Hear. Res., 2015)
Library construction and sequencing were performed by Novogene. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Oral supplementation with NR (7 mg/ml, 24 mM) in the drinking water started at 2 months of age and lasted until 12 months of age, while non-treated control groups received regular water.

value: Cochlea

value: mtKeima

value: Female

value: 12 months

value: Vehicle

tag: treatment duration


title: prostate

description: prostate

source_name: prostate

value: prostate


title: KO CFL1_2, ip [nuclear RNA]

description:
KO CFL1_2, ip
CFL1KO12_IPtoinput.bw


title: ET44

description: ro.m.results.csv.gz


title: mtKeima_Veh_replicate_4


title: ovary

description: ovary

source_name: ovary

value: ovary


title: KO CFL1_1, ip [nuclear RNA]

description:
KO CFL1_1, ip
CFL1KO12_IPtoinput.bw


title: Control_2, input

description:
Control_2, input
m6Aseq_control12.bw
control12_merge.narrowPeak

data_processing:
Clean reads were mapped the hg19 genome using STAR
MACS2 and MeTPeak were used to identify peaks, and the cutoff of the P-value for MACS2 was 1e-4.
To obtain high-confidence m6A peaks, we chose those peaks based on the following conditions: (1) Peaks that appeared in ≥ 5 samples were retained. (2) Possible m6Am peaks containing an adenosine at the TSS were filtered out.
Peaks from each sample were merged to a set of union peaks using BEDTools merge.
Assembly: hg19
Supplementary files format and content: bigwig, narrowPeak

value: Control


title: mtKeima_Veh_replicate_3


title: ET42

description: ro.m.results.csv.gz

value: roosevelti

value: tahd positive


title: ET43

description: ro.m.results.csv.gz

value: tahd negative

value: male


title: Control_1, input

description:
Control_1, input
m6Aseq_control12.bw
control12_merge.narrowPeak


title: ET41

description: ro.m.results.csv.gz

value: Tendon


title: ET40

description: ro.m.results.csv.gz


title: mtKeima_Veh_replicate_1


title: liver

description: liver

source_name: liver

value: liver


title: kidney

description: kidney

source_name: kidney

value: kidney


title: mtKeima_NR_replicate_5

value: Nicotinamide riboside

value: 10 months


title: ET39

description: ro.m.results.csv.gz


title: Control_1, ip

description:
Control_1, ip
m6Aseq_control12.bw
control12_merge.narrowPeak

value: Human PDAC cell lines


title: mtKeima_NR_replicate_4

value: Cochlea

value: mtKeima


title: KO METTL3_2, input

description:
KO METTL3_2, input
koMETTL3_12_merge.narrowPeak

value: KO METTL3


title: KO METTL3_2, ip

description:
KO METTL3_2, ip
koMETTL3_12_merge.narrowPeak


title: mtKeima_NR_replicate_3

value: Female

value: 12 months


title: KO METTL3_1, input

description:
KO METTL3_1, input
koMETTL3_12_merge.narrowPeak


title: bladder

description: bladder

source_name: bladder

value: bladder


title: mtKeima_NR_replicate_2


title: ET37

description: ro.m.results.csv.gz


title: ET36

description: ro.m.results.csv.gz


title: lung

description: lung

source_name: lung

value: lung


title: breast

description: breast

source_name: breast

value: breast


title: mtKeima_NR_replicate_1


title: adipose

description: adipose

source_name: adipose

value: adipose


title: T47D

growth_protocol: RPMI-1640 with 10% fetal bovine serum


title: KO CFL1_2, input

description:
KO CFL1_2, input
koCFL1_12_merge.narrowPeak

value: KO CFL1


title: Control_2, ip

description:
Control_2, ip
m6Aseq_control12.bw
control12_merge.narrowPeak

value: Control


title: mtKeima_Veh_replicate_2

value: Vehicle


title: MCF7

growth_protocol: DMEM with 10% fetal bovine serum and 10 µg/ml insulin


title: cervix

description: cervix

source_name: cervix

value: cervix


title: ET35

description: ro.m.results.csv.gz

value: roosevelti

value: tahd negative

value: male

value: Tendon


title: ET33

description: ro.f.results.csv.gz

value: tahd positive

value: female


title: KO CFL1_1, input

description:
KO CFL1_1, input
koCFL1_12_merge.narrowPeak

value: Human PDAC cell lines


title: BT-474


title: KO CFL1_2, ip

description:
KO CFL1_2, ip
koCFL1_12_merge.narrowPeak


title: Mouse chondrocytes stimulated with M-LPS EVs 3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

data_processing:
ILlumina NovaSeq 6000
Quality of libraries was examined by Bioanalyzer High sensitivity DNA kit (Agilent) and the paired-end reads (100 bp) were further obtained by ILlumina NovaSeq 6000
Reads were mapped by alignment to mouse genome (mm10) using STAR, gene expression level was quantified using RSEM
Differentially expressed genes (DEGs) were analyzed using DESeq2 Wald test (R software packages)
Assembly: mm10
Supplementary files format and content: tab-delimited test files include count, TPM and FPKM values for each Sample

source_name: mouse chondrocyte

growth_protocol: Mouse chondrocytes were suspended in DMEM-F12 supplemented with 10% heat-inactivated fetal bovine serum (FBS; Sigma-Aldrich), 2mM L-Glutamine, 25mg/L penicillin/streptomycin

extract_protocol:
The chondrocytes were lysed with TRIzol Reagent (Invitrogen carlsbad, CA, USA) for RNA purification perfumed according to the manufacturer’s instructions (NucleoSpin® RNA, TAKARA, Tokyo, Japan).
The high-quality DNA-free RNA assayed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) were used for libraries generation (TruSeq Stranded mRNA Sample Preparation Kit; Illumina, Inc., San Diego, CA, USA). Quality of libraries was examined by Bioanalyzer High sensitivity DNA kit (Agilent)

treatment_protocol: Mouse chondrocytes were stimulated by treatment with macrophage-derived EVs and LPS stimulated macrophage-derved EVs at a protein concentration of 10 µg/ml for 24 hours.

tag: strain background

value: knee cartilage

value: LPS stimulated macrophage-derved EVs


title: Mouse chondrocytes stimulated with M-LPS EVs 2


title: KO METTL3_1, ip

description:
KO METTL3_1, ip
koMETTL3_12_merge.narrowPeak

value: KO METTL3


title: ET32

value: tahd omit


title: MLECs, SA, laminar flow 4

city: Houston

first: Shengyu

state: TX

address: 6670 Bertner Ave, R10-109, floor 10

institute: Houston Methodist Research Insitute

description: Sample 17

data_processing:
Kallisto uses a bootstrapping technique to estimate transcript abundance and its uncertainties by resampling the sequence reads. In this study, we applied this bootstrapping technique to repeat the analysis 100 times.  We used DESeq2, a R package for differentially expressed gene (DEG) analysis, to estimate the significance of differential expression and calculate p value from transcript abundance data.
Assembly: mm10
Supplementary files format and content: csv file containing the TPM of each gene in each samples

extract_protocol:
Total RNA was extracted from SENP2 S344A KI and WT ECs using the RNeasy Plus Micro Kit (Cat. No. 74034, QIAGEN, Germantown, MD).
DNBSEQ Eukaryotic Strand-specific mRNA library

value: lung

value: laminar flow

value: Mouse-lung endothelial cells

value: SA


title: Mouse chondrocytes stimulated with M-LPS EVs 1


title: ET31


title: MLECs, SA, laminar flow 3

description: Sample 12


title: KO CFL1_1, ip

description:
KO CFL1_1, ip
koCFL1_12_merge.narrowPeak

value: KO CFL1


title: Mouse chondrocytes stimulated with M-EVs 3

value: macrophage-derived EVs


title: Non-Tg and Fgf18 Tg

city: Tokyo

first: Takao

last: Seki

state: Ota-ku

address: 5-21-16 Omori-Nishi

department: Department of Biochemistry

institute: Toho University School of Medicine

description:
BD Rhapsody
Non-Tg tags: mST01, mST02, mST03
Fgf18 Tg tags: mST04, mST05, mST06

data_processing:
Sequencing configurations was follows: read1 67 base-pair [bp], read2 151 bp, index1 8 bp, index2 8 bp. Adapter trimming, quality filtering, and mapping to the cell barcode and GRCm38-101 reference transcriptome or BD Sampletag reference of fastq files were performed by using a pipeline (https://github.com/s-shichino1989/TASSeq) as described previously. Demultipleing of scRNA-seq data by BD sampletag was performed by using a pipeline (https://github.com/s-shichino1989/TASSeq) as described previously.
Resulted gene-expression count matrix was processed to down-stream single-cell analyses (integration of six datasets, UMAP dimension reduction, cell cluster identification, conserved marker identification) using Seurat version 4.1.1 in R version 4.1.3. (Butler et al., 2018). Briefly, six scRNA-seq datasets were integrated with merge functions of Seurat. Cells that contained a percentage of mitochondrial transcripts > 25% were filtered out. PCA analysis was performed against 6885 of highly-variable genes identified by FindVariableFeatures (selection.method = mvp, mean.cutoff = c(0.1, Inf), dispersion.cutoff = c(0.5, Inf)) function in Seurat. 1:56 PCs were selected by Jackstraw analysis and used for clustering analysis. Resolution was set as 1.45 for the FindCluster function. Then, doublet cells were annotated by co-expression of cell lineage-defining marker genes, and removed from the datasets. Next, marker genes in each cell cluster were defined by FindAllMarkers function in Seurat (test method = wilcox, minimum expression in each cluster >= 10%).
Assembly: mm10
Supplementary files format and content: RDS
Supplementary files format and content: matrix

source_name: Liver

extract_protocol:
The livers from 6-week-old non-Tg and Hep-Fgf18 Tg mice were perfused with the liver perfusion medium (17701-038, ThermoFisher Scientific) at a flow rate of 3 ml/minute for 5 minutes. Then, the livers were perfused with the basic perfusion solution (136 mM NaCl, 5.4 mM KCl, 5 mM CaCl2, 0.5 mM NaH2PO3 2H2O, 0.42 mM Na2HPO3, 10 mM HEPES pH 7.5, 5 mM glucose and 4.2 mM NaHCO3) containing 0.5 mg/ml collagenase type IV (YK101, Yakult) and 0.06 mg/ml DNase I (DN25, Sigma-Aldrich) at a flow rate of 3 ml/minute for 8 minutes. The digested livers were transferred to a glass dish, and fibrous connective tissues were removed from the livers with a pair of tweezers. For Hep-Fgf18 Tg mice, perfusion of livers with the basic perfusion solution alone was not sufficient to isolate liver non-parenchymal cells from fibrotic livers. Thus, after perfusion, we further incubated the livers with the basic perfusion solution using a stirrer bar at 37℃ for 5 min. Cells were dispersed by pipetting and were passed through a 70 um cell strainer. After centrifugation at 500 rpm for 1 min, the supernatant was transferred to a new tube. The pellet was resuspended with DMEM and centrifuged at 500 rpm for 1 min. The new supernatant was combined with the former supernatant and then centrifuged at 700 rpm for 2 min several times until no cell pellet was visible. The final supernatant was centrifuged at 1800 rpm for 5 min, and the pellets were resuspended in RBC-lysis solution (0.17 mM NH4Cl, 0.01 mM EDTA, 0.1 M Tris, pH 7.3), and then washed twice in DMEM medium containing 10% FCS. To enrich HSCs and fibroblasts, we depleted lineage marker-positive cells using APC-conjugated antibodies that react with the following lineage markers (CD31, CD45.2, CD146, EpCAM, and Ter119), followed by anti-APC micro-beads and LS columns (Miltenyi, 130-042-401). Following depletion, approximately 5 x 104 cells were stained with different DNA barcode-conjugated MHC class 1 antibodies (BDTM Mouse Immune Single-Cell Multiplexing Kit (MHC H2 Class I), BD Biosciences) to identify each mouse. Then, lineage negative cells were sorted by BD FACSAriaTM III (BD Biosciences).
Mixture of 2.4 × 104 cells from 3 non Tg and 3 Fgf18 Tg mice (approximately 4 × 103 cells from each mouse) were subject to scRNA-seq using BD RhapsodyTM Single-Cell Analysis System (BD Biosciences), and resulted cDNA was amplified by TAS-Seq protocol as previously described. Briefly, on-beads cDNA was polyC tailed with stochastic termination condition by terminal transferase, deoxycytidine, and spiked-in dideoxycytidine. Then, second strand synthesis and whole-transcriptome amplification were performed by PCR reactions. Size distribution of cDNA and BD Sampletag libraries were analyzed by MultiNA system (Shimazu). Resulted cDNA library was processed to sequencing library by using NEBNext UltraII FS library prep kit for Illumina (New England Biolabs), and sequencing adapters were added to associated BD Sampletag libraries by PCR. Sequencing was performed by Illumina Novaseq 6000 sequencer (Illumina, San Diego, CA, USA) and NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles). Pooled library concentration was adjusted to 2.0 nM and 12% PhiX control library v3 (Illumina) was spiked into the library.

value: Liver

value: Hepatic non parenchimal cells

value: multiplexed sample:Non-Tg and Fgf18 Tg

value: 6 weeks-old


title: Liver, LEPTIN-/- 3

first: Tan

last: Tan

address: Yuanmingyuan West Road 2#, Haidian District

department: College of Biological Science

data_processing:
HISAT was used for sequence alignment with the reference genome  to obtain the information of the reference genes and   the Mapped reads were obtained
using the Cuffdiff component of Cufflinks software, the gene expression levels were quantified.
Pearson's correlation co-efficient (r2  ) was used as an indicator to evaluate the biological correlation of repetition.
FPKM was used to determine the expression abundance of transcripts
The absolute value of Log2 Fold Change ≥1, and the corrected P value (FDR) < 0.05
Genome_build: (Sus_scrofa.Sscrofa10.2.dna.chromosome)
Supplementary_files_format_and_content: gene expression  FPKMs

organism: Sus scrofa

growth_protocol: Both the experimental group and the control group were provided with unlimited commercial feed

extract_protocol:
Total RNA was isolated from pig  liver tissues by TRIzol or RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CEMP (Chinese experimental mini-pig)

value: 22-35 months

value: LEPTIN-/-


title: Mouse chondrocytes stimulated with M-EVs 2

value: knee cartilage


title: ET30

description: ro.f.results.csv.gz

value: roosevelti

value: tahd negative

value: female

value: Tendon


title: MLECs, SA, laminar flow 2

description: Sample 11

value: lung

value: laminar flow


title: Liver, LEPTIN-/- 2


title: ET34

description: ro.m.results.csv.gz

value: male


title: Liver, LEPTIN-/- 1


title: Mouse chondrocytes stimulated with M-EVs 1


title: MLECs, SA, static 4

description: Sample 16

value: static

value: Mouse-lung endothelial cells

value: SA


title: Liver, WT 3

value: Liver

value: wild type


title: ET28

description: ro.f.results.csv.gz


title: Vglut-Cre_410_Replicate_11

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_11_SIC0011

data_processing:
Library strategy: reporter assay
Barcode counting script can be found in bitbucket repository. Briefly, we search for a flanking sequence around the barcode and count and then count occurences of that specific barcode sequence. https://bitbucket.org/jdlabteam/asd_3utr_mpra_analysis/src/master/
Genome_build: hg19 derived sequences (120 bp context of 3' UTR)
Supplementary_files_format_and_content: tab-delimited text; barcode counts for each RNA and DNA sample.

source_name: excitatory neurons

growth_protocol: Cells were grown in basal medium (2% FBS in DMEM) with 1% penicillin-streptomycin at 37°C, 5% CO2.

extract_protocol:
N2a cells lifted in 250uL PBS and 750µL Trizol, followed by addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions. Vglut-cre brains were harvested at P21 and homogenized. Lysates were clarified and mixed 3:1 with Trizol, followed by addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from viral prep/cells was prepared simultaneously, starting with the first PCR step.

treatment_protocol: Cells were transfected (lipofectamine) with MPRA plasmid library in basal medium without antibiotic for ~12 hours and collected 48 hours post-transfection

value: excitatory neurons

value: post natal day 21

tag: molecule subtype

value: total RNA


title: Vglut-Cre_410_Replicate_10

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_10_SIC0010


title: MLECs, SA, static 2

description: Sample 8


title: ET26

description: ro.f.results.csv.gz

value: tahd positive


title: Vglut-Cre_410_Replicate_9

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_9_SIC0009


title: Liver, WT 1

value: CEMP (Chinese experimental mini-pig)

value: 22-35 months


title: ET29

description: ro.f.results.csv.gz

value: roosevelti


title: MLECs, SA, laminar flow 1

description: Sample 10


title: Vglut-Cre_410_Replicate_8

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_8_SIC0007


title: Vglut-Cre_410_Replicate_7

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_7_SIC0006


title: MLECs, WT, laminar flow 3

description: Sample 6

value: WT


title: MLECs, WT, laminar flow 4

description: Sample 14


title: Vglut-Cre_410_Replicate_6

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_6_SIC0005


title: ET38

description: ro.m.results.csv.gz

value: tahd negative

value: Tendon


title: ET23

value: tahd omit

value: female


title: MLECs, WT, laminar flow 2

description: Sample 5

value: lung

value: laminar flow


title: F6_CytoID_pos

city: Philadelphia

first: Kelly

middle: A

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

description: 10X Genomics

data_processing:
Deconvolution of scRNA-Seq reads followed 10X Genomics Cell Ranger (v6.0.0) pipeline. Massively parallel digital transcriptional profiling of single cells was performed using command ‘cellranger count’ with FASTQ files as input from each sample. For cellranger count, R1 and R2 were trimmed to 28 and 91 bp, respectively, to remove PCR adapters. The mouse genome mm10 (GENCODE vM23/Ensembl 98) was used as the reference for genome alignment and feature counting. From the output, the filtered matrices were used for downstream analyses. Matrices for each murine peeled epithelium sample were imported and transformed into Seurat (v4) objects for further processing. Cells with over 10% transcripts consisting of mitochondrial genes, under 1,500 unique genes, over 6,000 unique genes, or over 60,000 total UMIs were excluded to remove doublets or dead/dying cells. 13,667 cells passed this threshold. Analysis of the filtered matrices follows Seurat integration workflow using SCTransform function, which normalizes counts while accounting for read depth and subsequently searches for the top 2,000 most variable feature per sample with corrected counts for integration. Reciprocal PCA was then used to find integration transcript anchors between all matrices. Genes used for integration were ranked by the number of matrices they appear in. From this point on, dimensionality reduction used genes and values that were pre-processed using the integration workflow. However, raw and normalized counts were stored for downstream differential expression tests. The resulting dataset was then reduced via PCA, resulting in 30 principal components. An elbow plot was generated to examine the standard deviations of each component, which verified that the first 30 principal components contain most of the sources of variation in the dataset. To capture all the sources of variation in the dataset, all principal components were then used as input to the UMAP dimensionality reduction procedure (arXiv:1802.03426). Because of our interest in the relationship between cell cycle phases and cell fates, we opted not to regress cell cycle genes in our dimensionality reduction steps. A Shared Nearest Neighbor (SNN) graph was then constructed with the principal components of PCA by first determining the nearest neighbors for each cell and subsequently creating the SNN guided by neighborhood overlap between each cell and its nearest neighbors. Clusters were then determined by a modularity optimization algorithm by Waltman and van Eck.  To choose an optimal clustering resolution, a clustering tree was generated with the R package cluster which depicts movement of cells across clusters as resolution is increased from 0.1 to 1 with 0.1 increments. Resolution 0.4 was chosen, as it is the earliest resolution that created several clusters that were stable as the resolution was increased, as well as having a minimal number of clusters that were composed of multiple clusters from the next lowest resolution.  For each cluster, differentially expressed genes (DEGs) were calculated by comparing expression of genes within the cells of the cluster over the expression of the genes in all other clusters. The statistical workflow to determine differential expression was Seurat’s implementation of Wilcoxon’s signed-rank test. Significance cutoff for DEGs is a Bonferroni-adjusted p value of 0.05, and the fold change cutoff is below −0.25 or above 0.25 natural log fold change.
Assembly: GRCm38
Supplementary files format and content: Matrix files in comma-separated values

source_name: Esophageal epithelium organoids

growth_protocol: Esophageal epithelial cells were isolated from C57B6 animals, stained for integrin-b1, DAPI and Cyto-ID and sorted into two populations: (1) Integrin-b1 positive, DAPI negative, Cyto-ID Low (negative) and (2) Integrin-b1 positive, DAPI negative, Cyto-ID High (positive). Sorted Cyto-IDLow and Cyto-IDHigh murine esophageal basal cells were resuspended in mouse KSFM medium and mixed with 90-95% Matrigel (354234; Corning). Using 24 well plates, 500- 1000 cells were seeded per well in 50 μl Matrigel. After solidification, 500μlof Advanced DMEM/F12 (12634-101; Gibco) supplemented with 1XGlutamax (35050-061; Gibco), 1X HEPES (15630-080; Gibco),1% v/v penicillin-streptomycin (15140-122; Gibco), 1X N2 Supplement (17502-001; Gibco), 1X B27 Supplement (17504-044; Gibco), 0.1 mM N-acetyl-L-cysteine (616-91-1; Fisher Chemical), 50 ng/ml human recombinant EGF (10450-013; Gibco), 3.0% Noggin/R-Spondin-conditioned media, and 10μMY27632 (1254; Tocris Bioscience) was added to each well.

extract_protocol:
After 15 days of culture, single cells were isolated from organoids via incubation for 5 minutes with 1X Dispase (354235; Corning) in HBSS followed by incubation for 1 hour at 37°C with shaking at 1000 RPM in 0.25% Trypsin-EDTA (25-510; Genesee Scientific) supplemented with 10 μM Y27632. Cells were then forced through a cell strainer (70 μm) into a tube containing 4 ml 250 μg/ml soybean trypsin inhibitor (17975-209; Gibco) in PBS.  Cells were pelleted then resuspended in complete ‘mouse’ keratinocyte serum-free medium (KSFM): KSFM without calcium chloride (10725-018, Gibco, Waltham, MA, USA) with recombinant epidermal growth factor (1 ng/ml), bovine pituitary extract, (50 mg/ml), 1% penicillin/streptomycin (15140-122; Gibco, and 0.018 mM CaCl2 (349610025; Acros Organics). Single cell suspension was enriched for live cells using Dead Cell Removal kit (130-090-101; Miltenyi Biotec) according to the manufacturer’s protocol.
Single cell droplets were generated with chromium single-cell controller using Chromium Next GEM Single Cell 3’ Kit v3.1 (1000121; 10x Genomics). 5000–7000 cells were collected to make cDNA at the single cell level. Full-length cDNA with unique molecular identifiers (UMIs) was synthesized via reverse-transcription in the droplet. After PCR amplification and purification, cDNA was fragmented to around 270 bp and Illumina adapters with index were ligated to fragmented cDNA. After PCR, purification, and size selection, single cell RNA libraries were 450 bp in length and sequenced on Illumina sequencer at R1 = 28 bp, R2 = 91 bp.

value: Squamous cells

value: Esophageal epithelium organoids

value: 15 days

value: Cyto-ID High


title: F6_CytoID_neg

description: 10X Genomics

value: Cyto-ID Low


title: ET22

description: ro.f.results.csv.gz


title: ET27

description: ro.f.results.csv.gz


title: MLECs, SA, static 3

description: Sample 9

value: static

value: Mouse-lung endothelial cells

value: SA


title: M3_CytoID_pos

description: 10X Genomics


title: Liver, WT 2

value: CEMP (Chinese experimental mini-pig)

value: Liver

value: 22-35 months

value: wild type


title: M3_CytoID_neg

description: 10X Genomics


title: Vglut-Cre_410_Replicate_5

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_5_SIC0004

value: excitatory neurons

value: post natal day 21

value: total RNA


title: ET21

description: ro.f.results.csv.gz

value: roosevelti

value: tahd positive

value: female

value: Tendon


title: Vglut-Cre_410_Replicate_4

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_4_SIC0002


title: F2_CytoID_Pos

description: 10X Genomics

value: Squamous cells

value: Esophageal epithelium organoids

value: 15 days


title: ET20

description: ro.f.results.csv.gz


title: ET25

description: ro.f.results.csv.gz


title: MLECs, WT, static 4

description: Sample 13

value: lung

value: static

value: WT


title: MLECs, WT, laminar flow 1

description: Sample 4

value: laminar flow

value: Mouse-lung endothelial cells


title: ET24

description: ro.f.results.csv.gz


title: Vglut-Cre_410_ViralDNA_TechRep_2

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_vdna2_SIC0032

source_name: Adeno-associated virus 9

value: viral DNA


title: MLECs, SA, static 1

description: Sample 7

value: SA


title: ET19

description: ro.f.results.csv.gz


title: Vglut-Cre_410_ViralDNA_TechRep_1

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_vdna1_SIC0031


title: MLECs, WT, static 3

description: Sample 3


title: ET18

description: ro.f.results.csv.gz


title: MLECs, WT, static 2

description: Sample 2


title: Male2-CytoID-Positive

data_processing:
FASTQ files were obtained at Illumina Base Space. Sequencing reads were aligned to the mouse genome GRCm38 and gene counts were calculated using STAR v2.7.3 aligner.  Differential expression analysis was performed in R using the DESeq2 package. DESeq2 calculates differential expression by median of ratios method. DESeq2 calculated fold changes and significance. Sample-specific gene ratios are calculated as the gene count over the geometric mean for each specific gene. P-values are adjusted for multiple testing by Benjamin-Hochberg.
Assembly: GRCm38
Supplementary files format and content: Matrix files in comma-separated values

source_name: Esophageal epithelium

extract_protocol:
Esophageal epithelium-enriched tissue layer was peeled from muscle then incubated in 1 ml 1X Dispase I (354235; Corning; Bedford, MA, USA) diluted 1:4 in Hank’s Balanced Salt Solution (HBSS; 14025-076; Gibco; Grand Island, NY, USA) for 10 minutes at 37 °C with shaking at 1000 RPM (5384; Eppendorf F1.5 Thermomixer; Hamburg, Germany). Following removal from Dispase I, esophageal epithelium was minced with sharp scissors then incubated in 1 ml of 0.25% Trypsin-EDTA (25-053-CI; Corning; Manassas, VA, USA) for 10 min at 37 °C with shaking at 1000 RPM. Trypsin and tissue pieces were forced through 70 μm cell strainer into 50 ml conical tube containing 4 ml soybean trypsin inhibitor (STI; 9035-81-8; Grand Island, NY, USA). Cells were pelleted at 1300 RPM for 3 min then resuspended in 500 μl complete mouse keratinocyte–serum-free medium (37010022; Gibco; Carlsbad, CA, USA). Cell number and viability were measured using Automated Cell Count (AMQAX1000, Invitrogen Countess II, Bothell, WA, USA) by mixing 5 μl cell suspension with 5 μl 0.4% trypan blue solution (T10282; Invitrogen; Eugene, OR, USA). To isolate Cyto-ID Low and Cyto-ID High esophageal basal cells, the resulting single cell suspension was incubated at 37C for 30 minutes with Integrin-b1 antibody (APC anti-mouse/rat CD29; 102216; Biolegend) at 1:100 dilution. Cells were washed, pelleted at 1000 RPM for 5 minutes, and incubated at 37C for 30 minutes with Cyto-ID (ENZ-51031-K200; Enzo Life Sciences) at 1:1000 dilution. After washing, cells were resuspended in FACS buffer (1% of BSA in PBS) and 2 μg/ml DAPI (D1306; Invitrogen) was added immediately before sorting using FACS Aria Cell Sorter (BD Biosciences). Total live esophageal epithelium cell compartment (DAPI negative; Integrin-b1 positive) was sorted based upon Cyto-ID fluorescence into two populations: Cyto-ID Low (negative)  and Cyto-ID High (positive). RNA was isolated from sorted Cyto-ID Low and Cyto-ID High murine esophageal basal cells using RNeasy Mini Kit (74104; Qiagen) according to the manufacturer’s protocol.
To make stranded mRNA-Seq library: 500 ng total RNA from each sample were used to make library according to the product guide of stranded mRNA library kit (, E4720L; NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina). In short, mRNAs were enriched twice via poly-T based RNA purification beads and subjected to fragmentation at 94C for 15 minutes via divalent cation method. The 1st strand cDNA was synthesized by reverse transcriptase and random primers at 42C for 15 minutes, followed by 2nd strand synthesis at 16C for 1 hour.  A single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments at 37C for 30 minutes.  Adapters with IlluminaP5, P7 sequences as well as indices were ligated to the cDNA fragment at 30C for 10 minutes.  After purification using SPRIselect Beads (B23318;Beckman Coulter), a 13-cycle PCR reaction was used to enrich fragments. PCR was set at 98C for 10 seconds, 60C for 30 seconds, and extended at 72C for 30 seconds.  Libraries were again purified using SPRIselect Beads. Quality check was performed on Agilent 2100 bioanalyzer using Agilent high sensitive DNA kit (5067-4626). Quantification was performed with Qubit 3.0 fluorometer (Q33216, ThermoFisher Scientific) using Qubit 1X dsDNA HS Assay Kit (Q33230). Sample libraries were subsequently pooled and loaded to Nextseq 500.   Samples were sequenced 50-200 bases pair-end on Nextseq 500 machine with 30 million read depth.

value: Esophageal epithelium

value: 14-15 weeks old

value: Cyto-ID High

value: Male


title: Male2-CytoID-Negative

value: Cyto-ID Low


title: Vglut-Cre_410_Replicate_3_TechRep_2

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_3_2_SIC0030

value: excitatory neurons

value: post natal day 21

value: total RNA


title: MLECs, WT, static 1

description: Sample 1


title: ET17

description: ro.f.results.csv.gz

source_name: Tendon

value: roosevelti

value: tahd positive

value: female

value: Tendon


title: Male1-CytoID-Positive

value: Squamous cells


title: 14-16 weeks BAT KO rep2

city: Shenyang

first: Wei

last: Shen

state: Liaoning

address: No. 77 Puhe Road, Shenyang North New Area

department: School of Public Health

institute: China Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster.
Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Mus musculus from ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/ using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Brown adipose tissue

extract_protocol:
Total RNAs were extracted from BAT  using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Brown adipose tissue

value: KO

value: 14-16 weeks


title: ET16

description: ro.f.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the GCF_019320065.1 elk genome using Bowtie2.
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: GCF_019320065.1
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.
Library strategy: MeDIP-Seq


title: Vglut-Cre_410_Replicate_2_TechRep_2

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_2_2_SIC0028


title: ET15

description: ro.f.results.csv.gz


title: 14-16 weeks BAT KO rep3


title: 14-16 weeks BAT KO rep1


title: Female2-CytoID-Positive

value: Female


title: Vglut-Cre_410_Replicate_2_TechRep_1

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_2_1_SIC0027


title: ET14

description: ro.f.results.csv.gz


title: Female2-CytoID-Negative

value: Esophageal epithelium


title: Vglut-Cre_410__Replicate_1_TechRep_2

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_1_2_SIC0026


title: F2_CytoID_Neg

description: 10X Genomics

value: Esophageal epithelium organoids

value: 15 days


title: Vglut-Cre_410_Replicate_1_TechRep_1

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_1_1_SIC0025


title: Female1-CytoID-Positive

value: 14-15 weeks old

value: Cyto-ID High


title: ET12

description: ro.f.results.csv.gz

value: tahd negative


title: ET13

description: ro.f.results.csv.gz


title: 14-16 weeks BAT Flox rep3

value: Flox


title: 14-16 weeks BAT Flox rep2


title: Female1-CytoID-Negative

value: Cyto-ID Low


title: ET11

description: ro.f.results.csv.gz

value: roosevelti


title: N2a_410_DNA_Replicate_6

description:
NovaSeq_410_TRAP_Extracted_DNA_09092020_compiled_counts_10122020.csv
N2a_dna6_SIC0225

source_name: N2a cell line

value: neuroblastoma

value: genomic DNA


title: 14-16 weeks BAT Flox rep1


title: Vglut-Cre_410_Replicate_3_TechRep_1

description:
NovaSeq_05262020_Vglut_compiled_counts_06242020.csv
Vglut_3_1_SIC0029

value: excitatory neurons

value: post natal day 21

value: total RNA


title: N2a_410_DNA_Replicate_5

description:
NovaSeq_410_TRAP_Extracted_DNA_09092020_compiled_counts_10122020.csv
N2a_dna5_SIC0224


title: Male1-CytoID-Negative

value: Squamous cells

value: Male


title: Py_nonMIC_3

city: Lausanne

first: Candice Megan

last: Young

state: Vaud

address: Rue du Bugnon 25A

department: SV

institute: EPFL

data_processing:
Mapping was done with STAR (assembly mm10). Only reads uniquely mapped were conserved
Counts were obtained with HTSeq-counts
Assembly: GRCm38/mm10

source_name: Mammary

growth_protocol: Cells were grown in DMEM/F12 containing 2% FBS, 10 µg/ml insulin, 20 ng/ml hEGF, and 1% penstrep

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen)
The samples were subjected to library preparation by the TruSeq mRNA stranded method (Illumina).

treatment_protocol: Cells were FACs sorted one day after plating in vitro

value: Mammary

value: MMTV-PyMT

value: breast cancer

value: WT

value: Sorted for Lin-CD24+CD90-


title: 4 weeks BAT KO rep3

value: Brown adipose tissue

value: KO

value: 4 weeks


title: ET10

description: ro.f.results.csv.gz

extract_protocol:
Frozen elk tendon samples were thawed for analysis. Genomic DNA from tendon samples was prepared as follows: DNA was isolated from tendon samples by cutting a 2mm x 2mm x 2mm cube of tendon and rinsing twice in 1 ml PBS followed by centrifugation at 13,000g for 1 min to remove the Allprotect Tissue Reagent™. Each sample was minced and incubated with 1 mg/ml collagenase I in 1 ml PBS at 37° with rotation overnight.  Samples were then processed using the DNeasy Blood and Tissue Kit™ (Qiagen) to extract DNA, following the manufacturer’s protocols. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20 min at 4 C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min then centrifuged again at 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

value: tahd negative

value: female

value: Tendon


title: N2a_410_DNA_Replicate_3

description:
NovaSeq_410_TRAP_Extracted_DNA_09092020_compiled_counts_10122020.csv
N2a_dna3_SIC0222

value: neuroblastoma

value: genomic DNA


title: N2a_410_DNA_Replicate_4

description:
NovaSeq_410_TRAP_Extracted_DNA_09092020_compiled_counts_10122020.csv
N2a_dna4_SIC0223


title: ET9

description: ro.f.results.csv.gz

value: roosevelti


title: N2a_410_DNA_Replicate_2

description:
NovaSeq_410_TRAP_Extracted_DNA_09092020_compiled_counts_10122020.csv
N2a_dna2_SIC0221


title: Py_MIC_3

value: Sorted for Lin-CD24+CD90+


title: ET8

description: ro.f.results.csv.gz


title: 4 weeks BAT Flox rep3

value: Flox


title: Py_nonMIC_1


title: N2a_410_DNA_Replicate_1

description:
NovaSeq_410_TRAP_Extracted_DNA_09092020_compiled_counts_10122020.csv
N2a_dna1_SIC0219


title: Py_nonMIC_2


title: 4 weeks BAT KO rep2


title: 4 weeks BAT Flox rep2


title: Py_MIC_2


title: ET6

value: tahd suspected positive


title: Py_MIC_1

value: Mammary


title: ET7

description: ro.f.results.csv.gz


title: N2a_410__TRAP_TRAP_Replicate_6

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_trap6_SIC0226

value: immunoprecipitated RNA


title: 4 weeks BAT Flox rep1


title: N2a_410__TRAP_TRAP_Replicate_5

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_trap5_SIC0225


title: 2_LoMMP

growth_protocol: Cells were grown in DMEM containing 10% FBS, 20 mM Hepes (pH 7.4), and 1% pen/strep

extract_protocol:
RNA was isolated from 100,000 cells using the Roche High Pure RNA Isolation Kit
Libraries were prepared using the Illumina stranded mRNA ligation preparation from 200 ng of RNA.

treatment_protocol: Cells were stained with 20 nM MitoSpy Red then sorted for the 5% high and 5% low populations

value: breast cancer

value: sorted for Low MMP


title: ET5

description: ro.f.results.csv.gz


title: N2a_410__TRAP_TRAP_Replicate_4

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_trap4_SIC0224


title: 2_HiMMP

value: WT

value: sorted for High MMP


title: N2a_410__TRAP_TRAP_Replicate_3

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_trap3_SIC0223


title: 1_LoMMP


title: N2a_410__TRAP_TRAP_Replicate_2

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_trap2_SIC0222


title: ET2

description: ro.f.results.csv.gz


title: ET3

description: ro.f.results.csv.gz


title: 1_HiMMP


title: ET1

description: ro.f.results.csv.gz


title: 4 weeks BAT KO rep1

value: Brown adipose tissue

value: KO


title: N2a_410__TRAP_TRAP_Replicate_1

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_trap1_SIC0221


title: N2a_410__TRAP_Input_Replicate_6

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_input6_SIC0219

value: total RNA


title: N2a_410__TRAP_Input_Replicate_5

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_input5_SIC0218


title: SCI surgery, PBS injection, D4

type: RNA

city: Clamart

first: Jules

last: GUEGUEN

address: 1 Rue Lieutenant Raoul Batany

country: France

institute: French Armed Forces Biomedical Research Institute (IRBA)

description:
Test D4
SCI PBS D4

data_processing:
Data were obtained on a LightCycler480 (Roche) and processed with LightCycler480 Software. The three most stable microRNAs were selected using Genorm software (v3.4). MiRNAs expressions were quantified using 2ΔCt method (ΔCt = Ctreference - Cttarget) with each reference. The final quantified value is the geometric mean of the 3 values obtained. For in vivo screening, the most stable miRNAs were hsa-miR-24-3p, hsa-miR-23b-3p, hsa-miR-125b-5p. "Matrix non-normalized Template" represents raw Ct values. "Matrix normalized Template" represents normalized values as previously described. "Fold Change Template" represents the ratio between "SHAM PBS D2" and subsequent conditions.
"Matrix non-normalized Template" represents raw Ct values. "Matrix normalized Template" represents normalized values as previously described. "Fold Change Template" represents the ratio between "SHAM PBS D2" and subsequent conditions.

label: Sybr Green

source_name: Gastrocnemius

label_protocol: Reverse transcriptions were performed with miRCURY LNA RT kit (339340, Qiagen). Post-RT cDNAs were diluted before microRNAs screening using miRNome Mouse&Rat panel I+II (V5, 339322, Qiagen).

extract_protocol: Total RNAs were extracted following a chloroform/isopropanol extraction/precipitation protocol

treatment_protocol: Total RNAs were extracted from NHOs mice gastrocnemius biopsy previously flash frozen in isopentane 2 or 4 days after SHAM/NHOs surgery.

tag: gender

value: Female

value: muscle

tag: sample

value: Pool of 3 independant samples


title: SCI surgery, CDTX injection, D4

description:
Test D4
SCI CDTX D4


title: SHAM surgery, PBS injection, D4

description:
Control D4
SHAM PBS D4


title: 4T1-Vehicle-48hr-4

description:
PE75
ME264_V

extract_protocol:
RNA was isolated from 500,000 to 1 million cells using the Roche High Pure RNA Isolation Kit
Libraries were prepared using the Illumina stranded mRNA ligation preparation from 200 ng of RNA.

treatment_protocol: Cells were treated for 48 hours in either Vehicle (H2O) or 5 mM Acetate prior to sample collection

tag: cell type

tag: genotype

value: Vehicle


title: SHAM surgery, CDTX injection, D4

description:
Test D4
SHAM CDTX D4

tag: strain


title: 4T1-Acetate-48hr-3

description:
PE75
ME370_A

tag: tissue

value: Acetate


title: 4T1-Acetate-48hr-4

description:
PE75
ME264_A


title: N2a_410__TRAP_Input_Replicate_4

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_input4_SIC0217

value: neuroblastoma


title: N2a_410__TRAP_Input_Replicate_3

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_input3_SIC0216


title: Col-0 seedling RNA-seq sample 6

city: East Lansing

first: Polly

last: Hsu

state: MI

address: 603 Wilson Road

department: Biochemistry and Molecular Biology

institute: Michigan State University

description:
Seedling RNA-seq sample 6
rRNA depleted RNA

data_processing:
For Ribo-seq libraries, adaptor (AGATCGGAAGAGCACACGTCT) was clipped with fastx_clipper (FASTX toolkit v0.0.14).
For both RNA-seq and Ribo-seq, we used Bowtie2 (v2.3.4.1) to remove the r/t/sn/sno sequences.
To calculate the translation efficiency, both RNA-seq and Ribo-seq reads were mapped to the CDS region of the transcriptome with STAR aligner (RNA-seq parameters: --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 2; Ribo-seq used the same parameter except --outFilterMismatchNmax 1).
The resulting bam files were merged and  used for quantifying the TPM (transcript per million) of each gene with RSEM (v1.3.1).
Genome_build: Araport11
Supplementary_files_format_and_content: RSEM output txt files for Ribo-seq and RNA-seq

organism: Arabidopsis thaliana

source_name: 7-day old Seedlings

growth_protocol: Arabidopsis Col seeds were surface sterilized with 70% ethanol for 5 minutes, followed by 33% bleach and 0.03% Tween 20 for 10 minutes, and rinsed with sterile water 5 times. The seeds were imbibed at 4°C in dark for 2 days, and then grown hydroponically with sterile liquid media (2.15 g/L Murashige and Skoog salt, 1% sucrose, 0.5 g/L MES, pH 5.7) shaken at 85 rpm under 16 hours light and 8 hours dark at 22 °C for one week.

extract_protocol:
Plant lysates were prepared as previously described. Briefly, per 0.1 g of grounded tissue power was resuspend in 400 µL of lysis buffer (100 mM Tris-HCl [pH 8], 40 mM KCl, 20 mM MgCl2, 2% [v/v] polyoxyethylene [10] tridecyl ether [Sigma, P2393], 1% [w/v] sodium deoxycholate [Sigma, D6750], 1 mM dithiothreitol, 100 µg/mL cycloheximide [Sigma, C4859], 100 µg/mL chloramphenicol [Sigma R4408], and 10 units/mL DNase I [Epicenter, D9905K]). The lysates were spined at 3,000 g for 3 min and the supernantant was transferred to new tube and subsequently centrifuged at 20,000 g for 10 min. The supernantant was transferred to new tube and the RNA concentration was determined using Qubit RNA HS assay (Thermo Fisher Scientific; Q32852). Aliquots of 100 µL and 200 µL of the lysates were made and flash frozen in liquid nitrogen and stored in -80°C freezer until further process
Ribo-seq library construction: Ribosome footprints were obtained using 200 µL of the lysates above and the sequencing libraries were constructed following our previous method with the following modifications: briefly, after RNase I digestion (50 unit nuclease per 40 µg of RNA, the nuclease was provided in TruSeq Mammalian Ribo Profile Kit, illumina, RPHMR12126) and size exclusion column step, RNA > 17 nt was isolated by RNA Clean & Concentrator-25 kit (Zymo Research, R1017) and separated in 15% Urea-TBE gels (Invitrogen, EC68852BOX). Gel slices between 28-30 nt were isolated and the RNAs were purified as previously described. Next, rRNA depletion was performed using RiboZero Plant Leaf kit (Illumina, MRZPL1224) with one quarter of recommended reaction volume. Ribo-seq libraries were then constructed using TruSeq Mammalian Ribo Profile Kit (illumina, RPHMR12126) as previously described with 9 cycles of PCR amplification. Equal molarity of libraries were pooled and sequenced on Hi-Seq 4000 using single end 50 bp sequencing. RNA-seq library construction: Total RNA greater than 200 nt was purified using 100 µL of the lysates above as previously described with RNA Clean & Concentrator-25 kit (Zymo Research, R1017). RNA integrity was evaluated using Bioanalyzer (Agilent) RNA pico chip and RNA integrity number (RIN) ranging from 7.2 to 7.7 were observed among the samples. A 4 µg of RNA per sample was subjected to rRNA depletion using RiboZero Plant Leaf kit (Illumina, MRZPL1224) following the manufacturer’s recommendation. Then, 100 ng of rRNA-depleted RNA was fragmented to around 200-nt long based on the RIN reported by Bioanalyzer, and strand-specific sequencing libraries were made using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) with 8 cycles of amplification. Equal molarity of libraries were pooled and sequenced on Hi-Seq 4000 using pair-end 100 bp sequencing.

treatment_protocol: At Zeitgeber time 3 (3 hours after light on), DMSO that corresponded to 0.1% of media volume was added to the media (these were mock samples of our large-scale experiment). After 20 and 60 minutes later, three biological replicates of each time point were harvested and immediately flash frozen in liquid nitrogen.

tag: organ

value: Seedlings

tag: cultivar


title: 4T1-Vehicle-48hr-3

description:
PE75
ME370_V


title: Col-0 seedling RNA-seq sample 5

description:
Seedling RNA-seq sample 5
rRNA depleted RNA


title: ET4

first: Michael

address: Abelson 507

description: ro.f.results.csv.gz

tag: subspecies

value: roosevelti

tag: group

value: tahd negative

tag: Sex

value: female

value: Tendon


title: SCI surgery, CDTX injection, D2

description:
Test D2
SCI CDTX D2


title: 4T1-Acetate-48hr-2

description:
PE75
ME379_A

value: Mammary

tag: cell line

value: breast cancer

tag: treatment


title: N2a_410__TRAP_Input_Replicate_2

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_input2_SIC0215

tag: age


title: 4T1-Vehicle-48hr-2

description:
PE75
ME379_V

value: WT


title: SCI surgery, PBS injection, D2

description:
Test D2
SCI PBS D2


title: Col-0 seedling RNA-seq sample 3

description:
Seedling RNA-seq sample 3
rRNA depleted RNA


title: N2a_410__TRAP_Input_Replicate_1

description:
NovaSeq_05262020_N2a_compiled_counts_06262020.csv
N2a_input1_SIC0214


title: 4T1-Acetate-48hr-1

description:
PE75
ME333_A


title: SHAM surgery, CDTX injection, D2

description:
Test D2
SHAM CDTX D2


title: Col-0 seedling RNA-seq sample 2

description:
Seedling RNA-seq sample 2
rRNA depleted RNA


title: SHAM surgery, PBS injection, D2

description:
Control D2
SHAM PBS D2


title: CD45+ IL10 Ctrl

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

data_processing:
Fastq Files were demutiplexed using Cellranger
Count tables were produced using cellranger
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: h5

source_name: Kidney CD45+ Cells

growth_protocol: Mice were housed in a SPF facility

extract_protocol:
10x protocoll
10x 3' v3

treatment_protocol: Kidenys were taken and a single cell suspsion created following digestion with liberase. CD45+ cells were then sorted

value: Kidney CD45+ Cells

tag: cre

value: CD19 Cre/+

value: IL10 wt/wt


title: 4T1-Vehicle-48hr-1

description:
PE75
ME333_V


title: Col-0 seedling RNA-seq sample 1

description:
Seedling RNA-seq sample 1
rRNA depleted RNA


title: CD45+ IL10 KO

value: IL10 fl/fl


title: Col-0 seedling RNA-seq sample 4

description:
Seedling RNA-seq sample 4
rRNA depleted RNA


title: Ophiostoma_piceae_FOH2_47h

status: Public on Sep 19 2023

city: Madrid

first: Jorge

last: Barriuso

address: C. Ramiro de Maeztu, 9

country: Spain

institute: CIB-CSIC

data_processing:
FASTQ read files were processed with Cutadapt and quality control was performed using MultiQC.
RNA reads were aligned to the genome of O. piceae CECT 20496 using STAR and the nf-core RNAseq pipeline allowing for unique mapping
Assembly: OphiostomapiceaeCECT20416v2.0
Supplementary files format and content: tab-delimited txt file with FPKM normalized counts

organism: Ophiostoma piceae

source_name: fungal cell

extract_protocol:
RNA was extracted using an RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions, followed by DNase treatment with TURBO DNA-free™ (Thermo Scientific).
RNA quality and quantity were determined using Experion™ (Bio-Rad) on-chip electrophoresis, where all samples met a RIN threshold >8. RNA sequencing (RNAseq) was performed on an Illumina NovaSeq 6000 platform by Novogene Co. Ltd, yielding 150 bp-long paired-end reads in FASTQ format.

value: fungal cell

value: FOH

tag: time


title: Ophiostoma_piceae_CTL1_68h

value: CTL


title: Ophiostoma_piceae_CTL1_47h


title: Ophiostoma_piceae_FOH1_68h


title: Ophiostoma_piceae_CTL2_68h


title: Ophiostoma_piceae_CTL2_22h


title: Ophiostoma_piceae_FOH1_47h


title: Ophiostoma_piceae_FOH1_22h


title: Ophiostoma_piceae_CTL1_22h


title: Ophiostoma_piceae_FOH2_22h


title: Helicobacter pylori, WT, rep3

city: Shen Zhen

first: Zhiyong

last: Zhai

state: Guang Dong

address: No.1333, XinAn Street, BaoAn District

institute: Shenzhen Hospital of Southern Medical University

data_processing:
www.genedenovo.com
Reads were filtered by fastp (version 0.18.0).The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample.

organism: Helicobacter pylori

source_name: Helicobacter pylori

growth_protocol: Helicobacter pylori were maintained in columbia blood agar medium at 37℃.GES-1 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)beads(Pronucleus：After total RNA was extracted, prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA)). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA)

value: Helicobacter pylori

tag: hp genotype


title: Helicobacter pylori, WT, rep2


title: Helicobacter pylori, CagA KO, rep3

value: CagA KO


title: Helicobacter pylori, WT, rep1


title: Helicobacter pylori, CagA KO, rep2


title: Helicobacter pylori, CagA KO, rep1


title: Ophiostoma_piceae_FOH2_68h


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_66-76_NAI_rep2

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Division of Genomic Medicine

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Standard icSHAPE bioinformatics pipeline was used (PMID:26766114).
After PCR duplicates removal and adapter (13 nt from 5ʹ end) trimming, sequencing reads were mapped to custom index of antisense Gadd45α SINEB2-a deletion mutants transcripts using Bowtie2. The mapping was focused on the region starting from 1 bp upstream of the SINE element till 88 bp downstream of it (to encompass all the reads with in SINE region). Following the icSHAPE pipeline, RT stops were calculated and normalized, and subsequently enrichment reactivity scores were calculated for each base by subtracting the background signal (DMSO data).
Assembly: Custom index:  >AS-Gadd45a-SINEB2a-del-27-36 GCAGCGACATCAGAAGAGGATATTGGAGATGGTTGAAGGCCACCATGTCGTTGCTGGGAATGAACTCAAGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG >AS-Gadd45a-SINEB2a-del-40-50 GCAGCGACATCAGAAGAGGATATTGGATCCCATTACAGATACCATGTCGTTGCTGGGAATGAACTCAAGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG >AS-Gadd45a-SINEB2a-del-66-76 GCAGCGACATCAGAAGAGGATATTGGATCCCATTACAGATGGTTGAAGGCCACCATGTCGTTGCTGAAGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG >AS-Gadd45a-SINEB2a-del-92-101 GCAGCGACATCAGAAGAGGATATTGGATCCCATTACAGATGGTTGAAGGCCACCATGTCGTTGCTGGGAATGAACTCAAGACCTCTGGAAGACTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG
Supplementary files format and content: Valid enrichment reactivity score for each base of SINEB2. Format: Each base position is represented by a different row. Columns 1-4 correspond to SINE-transcript name, position of each base, valid enrichment reactivity score for each modified base (bases with null values were not detected by icSHAPE), and sequence of the modified base.
Library strategy: icSHAPE

growth_protocol: HEK293T/17 cells were grown in 6-well culture dish in DMEM (1×) + GlutaMAX-1 supplemented with 10% fetal bovine serum and 1% penicillin streptomycin solution at 37°C, 5% CO2 until ~80% confluent.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and digested with DNaseI to remove DNA contamination. Purified RNA was ribo-depleted and used for further library construction.
icSHAPE library preparation protocol was followed (PMID:26766114). Briefly, ribo-depleted RNA was biotin-clicked, fragmented and end-repaired. Next, RNA was 3' end ligated followed by cDNA synthesis and circularization. Final library was PCR amplified.

treatment_protocol: Different antisense Gadd45α SINEB2-a deletion mutants in SINEUP-EGFP constructs were co-transfected with pEGFP-C2 in 10-cm plates. 24 h post-transfection, 20 million cells were treated with either NAI-N3 or DMSO (mock) following the icSHAPE protocol (PMID:26766114).

value: Human embryonic kidney cell line

value: Co-transfection with AS Gadd45a SINEB2a {delta}66-76 SINEUP-GFP and pEGFP-C2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_27-36_DMSO_rep2

value: Co-transfection with AS Gadd45a SINEB2a {delta}27-36 SINEUP-GFP and pEGFP-C2

value: DMSO (mock)


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_66-76_DMSO_rep2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_27-36_NAI_rep1


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_40-50_NAI_rep1

value: Co-transfection with AS Gadd45a SINEB2a {delta}40-50 SINEUP-GFP and pEGFP-C2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_27-36_DMSO_rep1


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_27-36_NAI_rep2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_40-50_NAI_rep2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_40-50_DMSO_rep2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_40-50_DMSO_rep1


title: Ophiostoma_piceae_CTL2_47h


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_66-76_NAI_rep1


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_92-101_NAI_rep2

value: Co-transfection with AS Gadd45a SINEB2a {delta}92-101 SINEUP-GFP and pEGFP-C2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_92-101_DMSO_rep2