title: si.LINC2.D14.4_S8

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

data_processing:
Human: Raw sequencing reads in the fastq files were mapped with STAR version 2.7.1a to the Gencode release 36 based on the GRCh38.p12 reference human genome with the corresponding GTF files.
Table counts was obtained with FeatureCounts function in the package subread, version 1.6.4
Assembly: GRCh38
Supplementary files format and content: txt files containing the table counts obtained with FeatureCounts

source_name: Cultures of in vitro differentiated primary subcutaneous human adipocytes

growth_protocol: To induce the adipogenic conversion of adipocyte progenitors, human preadipocytes (SP-F-1, Zen-Bio, Inc.) were led to grow as a monolayer in preadipocyte medium (PM-1) until reaching confluence, and then incubated with adipocyte differentiation medium (DM-2) for 7 days. This media is composed of DMEM / Ham’s F-12 (1:1), HEPES, FBS, biotin, pantothenate, insulin, dexamethasone, IBMX, PPARγ agonist, penicillin, streptomycin and amphotericin B. Thereafter, differentiating adipocytes were maintained in adipocyte maintenance medium (AM-1) for 7 additional days (DM-2 without dexamethasone, IBMX and PPARγ agonists). During this process, the shape of preadipocytes evolves from the flattened form to rounded cells containing abundant lipid droplets, and are thus considered differentiated, mature adipocytes (~12th day and thereafter).

extract_protocol:
Total RNA was purified from human adipose tissue and cells using RNeasy Mini Kit (QIAgen, 74104). Fat samples (~150 µg) and cell monolayers were homogenized in 0.6 mL of QIAzol® Lysis Reagent (QIAgen, 79306).
NGS libraries with polyA capture were prepared according to the manual Protocol for use with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) (versión 1.0, 4/17)

treatment_protocol: Once differentiated, we challenged these cultures of primary human adipocytes with the ectopic presence of synthetic small interfering (si-)RNAs directed against our lncRNA candidate or a non-targeting si-RNA control.

tag: condition


title: FACS gate A rep 2 bio rep 3

status: Public on Jan 31 2024

type: SRA

city: Copenhagen

first: Kristoffer

last: Johansson

address: Ole Maaløes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
Barcodes of 18 bases were mapped to variants using exact match. Normalized populations per FACS gate were used to calculate a protein stability index (PSI) and that was finally normalized to an abundance score where 1 is wildtype and 0 the median PSI of nonsence variants
A variant-barcode map was made from long-read sequencing of the plasmid before transfection. Reads were aligned to the synthetic barcode-gfp-parkin construct using BWA software
Assembly: NA
Supplementary files format and content: vamp_parkin.csv: Colon separated file format contaning abundance scores
Supplementary files format and content: barcode_map.csv.gz: Colon separated file format containing the map between barcodes and protein variants
Library strategy: VAMP-seq

molecule: genomic DNA

organism: synthetic construct

extract_protocol:
Genomic DNA was extracted from cells using the DNeasy blood & tissue Kit (Qiagen) following the manufacturer’s protocol titled “Protocol: Purification of Total DNA from Animal Blood or Cells (Spin-Column Protocol)”
A site-saturation library of codon optimized human parkin were custom synthesized and barcoded. Constructs of PRKN variants fused to GFP and an IRES-mCherry expression control were integrated into a HEK293T landing pad cell line

tag: cell line


title: si.LINC2.D14.3_S7

country: Spain

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

value: Cultures of in vitro differentiated primary subcutaneous human adipocytes


title: si.LINC2.D14.2_S6


title: si.LINC2.D14.1_S5


title: FACS gate D rep 1 bio rep 3


title: Pt115_Cancer

city: Baltimore

first: Angelo

last: De Marzo

state: Maryland

address: 1550 Orleans Street, CRB II RM 138

country: USA

institute: Johns Hopkins University School of Medicine

data_processing:
Trim galore v0.6.3 was used to trim the reads.
Bwa v0.7.7 (mem) was used to align to the hg19 and hg38 human genome builds.
Piccard-tools v1.119 & GATK v3.6.0 were used to create a recalibrated bam file.
Assembly: hg19 and hg38 human genome builds
Supplementary files format and content: Posterior mean estimate transcripts per million (pmeTPM) for each sample
Supplementary files format and content: Expected count for each sample

molecule: total RNA

source_name: Prostate

extract_protocol:
Tissue digestion and DNA/RNA extraction was performed using Allprep DNA/RNA Kits following the manufacturer’s recommendations (Qiagen, 802804)
Libraries were constructed according to the protocol provided in the Illumina Nano TruSeq Library prep guide. Assessment of the yield and size distribution of the amplified library was performed on the Agilent 2100 Bioanalyzer using the High Sensitivity Chip. Libraries were then pooled at equal molar concentrations for sequencing. Sequencing was performed using Illumina HiSeqX and NovaSeq6000 with Paired End 150 bp x 150 bp read configuration.

value: Prostate


title: Pt115_Benign


title: FACS gate C rep 1 bio rep 3


title: Pt114_Benign


title: CTRL3.D14_S3

value: CTRL


title: IMR90 cells, ER-RAS 3 days 4OHT, Replicate A

city: Montréal

first: Gerardo

last: Ferbeyre

state: Québec

address: 900 rue Saint-Denis

country: Canada

institute: Centre de recherche du CHUM (CRCHUM)

data_processing:
Trimmomatic version 0.35 - STAR version 2.5.1b - DESeq2 version 1.18.1
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35.
Trimmed sequences reads were mapped to GRCh38 using STAR version 2.5.1b.
Gene expressions were obtained as readcount directly from STAR and normalization of gene readcounts was performed using DESeq2 version 1.18.1.
Assembly: GRCh38/hg38
Supplementary files format and content: Excel file include normalize gene readcounts for all samples.

growth_protocol: IMR90 cells were maintained in DMEM supplemented with 10% premium fetal bovine serum (FBS), 1% penicillin/streptomycin sulfate and 2 mM L-glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested in TRIzol at the end of treatment and RNA was harvested according to the manufacturer’s instructions. Once at the precipitation step, RNA samples were loaded on a RNeasy column (Qiagen Mini Kit #74106). 1000 ng of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using the KAPA mRNAseq Hyperprep kit (KAPA, Cat no. KK8581) following manufacturer's protocols.

treatment_protocol: Uncommitted control cells were treated with for 30h and committed cells were treated for 72h with 100nM of 4OHT.

tag: cell type

value: Normal Human Diploid Fibroblasts

tag: genotype

value: ER-RAS

tag: treatment

tag: time

value: Day 3


title: CTRL2.D14_S2


title: Pt114_Cancer


title: Pt113_Benign


title: FACS gate A rep 1 bio rep 3


title: Pt112_Benign


title: Pt113_Cancer


title: CTRL1.D14_S1


title: Pt112_Cancer


title: FACS gate B rep 1 bio rep 3


title: CTRL4.D14_S4


title: FACS gate D rep 3 bio rep 2


title: IPhnRNPK_3

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

data_processing:
The standard workflow of the RNA-Seq data analysis was performed with an in-house pipeline embedded in the QuickNGS workflow management system . For instance, the generation of the fastq files and the subsequent adapter removal were completed using the Illumina software bcl2fastq (https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html). Subsequently, the reads were aligned to the hg38 reference genome sequence using STAR v2.5.2b  with default parameters. In the quantification step, reads were counted with featureCounts  from the subread package v1.5.1 available online (http://subread.sourceforge.net). Here we used the reverse stranded mode (-s 2) to account for the reverse stranded feature of the library preparation kit; otherwise, default parameters. PCA-analysis and sample similarity analysis (Supplementary Figure 1) for controlling clustering quality of the condition’s replicates, was performed with PlotPCA function from the DESeq2 package v1.10.1  and using the dist function from the R stats package, using the euclidean distance for the method parameter, respectively. Based on PCA-plot and sample similarity heatmap (Supplementary Figure 1), as well as low sequencing depth, high duplication level and high multimapping rate of one replicate of the control samples (Supplementary table 3), this sample was discarded from downstream analysis.
Differential expression analysis was performed in R using the DESeq2 package and selecting the local regression parameter and otherwise standard workflow. The final list of enriched targets was generated by selecting first all RNAs with a control mean > 100 in the Input sample and then RNAs being enriched in IPP hnRNP K with a fold change > 2 and p < 0,05. In a last step, only RNAs specifically enriched in IP hnRNP K and not in IP Ctrl were chosen.
Motif matching was performed as followed: we have used biomaRt (v2.38.0) to fetch metadata and sequences from ensembl database. Transcriptome-wide and biotype-specific matching of the hnRNP K motifs were performed with an own Java software build for this purpose (https://github.com/ATA82/MotifSearcher).
Genome_build: hg38
Supplementary_files_format_and_content: Table for each of the differential expression analyses of the all comparisons in excel format, containing a list of genes which respective Log Fold Change information and Significance values (p-values) as well as additional statistical information.
Supplementary_files_format_and_content: Motif matches tables
Supplementary_files_format_and_content: Identified target RNAs
Supplementary_files_format_and_content: All Motif Matching results are in Excel format, differential expression results are in tsv Format.

source_name: KG-1 cell line

growth_protocol: KG-1 cells cultured in RPMI 1640 media supplemented with 10 % fetal bovine serum (FBS) (Sigma) and 1 % Penicillin/Streptomycin (PS) (Thermo Fisher Scientific) and maintained at 37 °C and 5 % CO2. Passaged once to a density of 2x10^5 cells/ml and then grown to 5x10^5 cells/ml for harvest

extract_protocol:
Cytoplasmic extracts isolated by hypotonic lysis in a Dounce homogenisator. Cells washed twice in MOPS-buffered saline. Cell pellet resuspended in 1,5 ml hypotonic lysis buffer per gram cells and lysis in a Dounce homogenisator. Cell debris removed by centrifugation and supernatant was used for Co-immunoprecipitation (IPP). For IPP 1 mg of cytoplasmic extract was diluted in 500 µl IPP buffer (20 mM HEPES, pH 7.4, 100 mM KCl, 5 mM magnesium acetate, 1 mM dithiothreitol, 0.025% Triton X-100, and protease inhibitors) and incubated with 30 µl of Protein G Sepharose™ 4 Fast Flow beads (GE Healthcare Life Sciences) coupled to a-hnRNP K antibody (Naarmann-de Vries et al. 2016) or a non-related control for 1.5 h at 4°C. Beads were washed twice with IPP buffer. Subsequent RNA isolation with TRIzol. 100 µg of cytoplasmic extract were used as an Input control for RNA analysis
Quality checks of RNA samples were performed with the TapeStation 4200 using the Agilent RNA ScreenTape Assay kit. Quantification was performed using the Quantus RNA System (Promega). cDNA libraries were produced employing the TrueSeq Stranded Total RNA Library Preparation Kit with Ribo-Zero Gold Kit according to the manufacturer´s instructions (Illumina Inc., San Diego, CA, USA), using 500 ng input RNA or 10 µl for the immunoprecipitated samples, respectively. Quality and quantity of the cDNA libraries were assessed using the 4200 TapeStation (D1000 screen tape assay) and the Quantus dsDNA system, respectively.

treatment_protocol: Untreated

tag: original tissue

value: Bone marrow

value: acute myeloid leukemia


title: Pt111_Benign


title: FACS gate C rep 3 bio rep 2


title: Pt110_Benign


title: FACS gate B rep 3 bio rep 2


title: Pt109_Cancer


title: IPhnRNPK_2


title: FACS gate A rep 3 bio rep 2


title: Pt109_Benign


title: IPCtrl_3


title: FACS gate D rep 2 bio rep 2


title: Pt108_Benign


title: Pt108_Cancer


title: FACS gate C rep 2 bio rep 2


title: Pt107_Cancer


title: Pt106_Benign


title: InputKG1a_3


title: Pt111_Cancer


title: InputKG1a_2


title: Pt110_Cancer


title: Pt106_Cancer


title: IPhnRNPK


title: Pt105_Benign


title: FACS gate B rep 1 bio rep 2


title: FACS gate D rep 1 bio rep 2


title: IPCtrl_2


title: REH S3I-201 50uM 6 hours_3

city: London

first: Luca

last: Gasparoli

address: 30 Guilford Street, Location 1B

department: Developmental Biology and Cancer

country: United Kingdom

institute: UCL Great Ormond Institute of Child Health

description: S3I-201 treated REH (6 hours)

data_processing:
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
Fastq was demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poor quality sequences.
Pre-processed data were then aligned to the genome (UCSC hg38) with Bowtie 2 and deduplicated using Picard.
Reads-per-transcript were counted by FeatureCounts, before differential expresson analysis by SARTools, a DESeq2 wrapper.
hg38
Genome_build: tab-delimited text file including average count values for each sample.

source_name: REH

growth_protocol: REH cells (B precursor ALL cell line) (DSMZ, Braunschweig, Germany) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit according to manufacturers instructions
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols

treatment_protocol: REH cells were treated for 6 hours with DMSO or 50uM S3I-201

value: REH


title: FACS gate C rep 1 bio rep 2


title: REH S3I-201 50uM 6 hours_2

description: S3I-201 treated REH (6 hours)


title: FACS gate B rep 2 bio rep 2


title: Pt107_Benign


title: Pt105_Cancer


title: FACS gate A rep 1 bio rep 2


title: HH2 Input

city: Beijing

first: Peirong

last: Li

state: Beijing

address: Zhanghualu No.50

country: China

institute: Beijing Academy of Agricultural and Forestry Sciences

description: BrJMJ18Par overexpressing Par grown und 28℃. Input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: ZIP
Supplementary files format and content: annotation call_peak GO_KEGG motif

organism: Brassica rapa var. parachinensis

source_name: leaf

growth_protocol: Par plants grown under 21℃ for 5 weeks or 4 weeks following 1 weeks under 28℃ were used.

extract_protocol:
1.5 g samples were washed twice in cold phosphate-buffered saline (PBS), cross-linked with 1% formaldehyde for 10 minutes at room temperature, and then quenched by the addition of glycine (125 mmol/L final concentration). Afterwards, samples were lysed and chromatin was obtained on ice. Chromatin was sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: leaf

tag: chip antibody

value: none (input)

value: mesophyll cell

value: High temperature (28C)


title: LH2 IP

description: BrJMJ18Par overexpressing Par grown und 21℃. Anti-GFP IP

value: Anti-GFP antibody (ab290, Abcam)

value: Low temperature (21C)


title: LCK IP

description: Wild type Par plants grown under 21℃. Anti-GFP IP

value: Par WT


title: HCK IP

description: Wild type Par plants grown under 28℃.Anti-GFP IP


title: LH1 IP

description: BrJMJ18WT overexpressing Par grown und 21℃. Anti-GFP IP


title: IPCtrl


title: Pt104_Benign


title: FACS gate A rep 2 bio rep 2


title: REH S3I-201 50uM 6 hours_1

description: S3I-201 treated REH (6 hours)


title: Pt104_Cancer


title: HH2 IP

description: BrJMJ18Par overexpressing Par grown und 28℃. Anti-GFP IP


title: HH1 IP

description: BrJMJ18WT overexpressing Par grown und 28℃. Anti-GFP IP


title: InputKG1a


title: Pt103_Cancer


title: HH1 Input

description: BrJMJ18WT overexpressing Par grown und 28℃. Input


title: FACS gate C rep 3 bio rep 1


title: LH2 Input

description: BrJMJ18Par overexpressing Par grown und 21℃. Input


title: REH DMSO 6 hours_2

description: DMSO treated REH (6 hours)

value: DMSO


title: Pt103_Benign


title: LH1 Input

description: BrJMJ18WT overexpressing Par grown und 21℃. Input


title: REH DMSO 6 hours_1

description: DMSO treated REH (6 hours)


title: FACS gate B rep 3 bio rep 1


title: FACS gate A rep 3 bio rep 1


title: LCK Input

description: Wild type Par plants grown under 21℃. Input


title: Pt102_Benign


title: REH shSTAT3_3

treatment_protocol: REH cells were transduced with either scramble control or STAT3 specific shRNA, via lentiviral particles. Transduced cells were selected with puromycin for 3 days and then Dead Cell Removal was performed prior to total RNA extraction.

value: shSTAT3 transduced REH


title: FACS gate D rep 3 bio rep 1


title: Pt101_Benign

value: Prostate


title: Pt102_Cancer


title: REH shSTAT3_1


title: Pt101_Cancer


title: HCK Input

description: Wild type Par plants grown under 28℃.Input


title: high-phenolics, droughted, rep2

city: Shahin shar

first: Maryam

last: Salami

state: Mokhaberat

address: shahid beheshti

country: Iran

institute: Shiraz University

data_processing:
Clean reads were mapped in the reference genome of “Darmor-bzh” (http://www.genoscope.cns.fr/brassicanapus/). The obtained genes from the previous step were quantitatively analyzed using Cluffquant and Cluffnorm of Cufflinks 2.0.0. Gene expression levels were estimated by the FPKM (fragments per kilobase of exon per million mapped fragments), as well as an all by all differential expression analysis by combining replications.
Assembly: UCSC
Supplementary files format and content: Supplementary_files_format_and_content: ProcessedDataMatrix_Final.txt: Tab-delimited text file includes FPKMs (log2) for each sample.

organism: Brassica napus

source_name: Flower

growth_protocol: The plants were grown in pots in a greenhouse (26–28 °C) under short-day (12 hours of light and 12 hours of dark) conditions until the initial flower stage. When the flower was visible, half of the plants were exposed to drought stress conditions

extract_protocol:
Total RNA was isolated from each sample using a Plant RNA Mini Kit (Tiangen, Inc., China) according to the manufacturer’s protocol.
Four cDNA libraries were constructed and RNA-Seq was performed on a DNBSEQ-G400 platform.Low-quality reads were filtered out using NGS QC toolkit v2.2.3 (https://omictools.com/ngs-qc-toolkit-tool).

treatment_protocol: During irrigation, drought treated flower pots maintain a soil relative water content of 10% (irrigated with PEG6000 at a concentration of 20%), while adequately watered flower pots maintain a soil relative water content of 30% (irrigated with sterile water of equal volume)

value: Flower

value: genotype

value: Drought

tag: group

value: high-phenolics


title: REH DMSO 6 hours_3

description: DMSO treated REH (6 hours)


title: REH shSTAT3_2


title: high-phenolics, droughted, rep3


title: FACS gate C rep 2 bio rep 1


title: FACS gate B rep 2 bio rep 1


title: REH scramble control_3

value: scramble transduced REH


title: REH scramble control_2


title: Pt100_Cancer


title: low-phenolics, droughted, rep3

value: low-phenolics


title: FACS gate D rep 1 bio rep 1


title: Pt100_Benign


title: REH scramble control_1

value: REH


title: low-phenolics, droughted, rep2


title: Pt99_Benign


title: FACS gate C rep 1 bio rep 1


title: FACS gate D rep 2 bio rep 1


title: Pt99_Cancer


title: FACS gate B rep 1 bio rep 1


title: low-phenolics, droughted, rep1


title: FACS gate A rep 2 bio rep 1


title: FACS gate A rep 1 bio rep 1


title: Pt98_Benign


title: high-phenolics, control, rep3

value: Control


title: high-phenolics, droughted, rep1


title: high-phenolics, control, rep1


title: Pt98_Cancer


title: Pt97_Cancer


title: high-phenolics, control, rep2


title: Pt97_Benign


title: low-phenolics, control, rep2


title: low-phenolics, control, rep3


title: Injury NMDA 36hr, snRNA-seq

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The single-cell RNA sequencing files were processed for demultiplexing and analyzed using Cell Ranger ARC v2.0. The genes were mapped and referenced using the zebrafish reference genome DanRer11.
To address potential ambient RNA contamination in the cell-by-gene expression matrix, we employed SoupX R package with default parameters for further ambient RNA cleaning for each sample.
Assembly: DanRer11
Supplementary files format and content: Tab separated and matrix files

organism: Danio rerio

source_name: Retina

growth_protocol: All the zebrafish used in this study were adults between 6 and 12 months old. Prior to any experiments, the fish were anesthetized or euthanized using 1:1000 or 1:500 2-phenoxyethanol (Sigma), respectively.

extract_protocol:
Zebrafish retinas (4-6 retinas from 4-6 fish) were collected at different timepoints after NMDA and LD treatments, and flash-frozen in dry ice for ~15min before being transferred to a -80 ? freezer for storage.
Fixed cells were recovered and subjected to 10x Genomics Single Cell protocol as described previously. Libraries were prepared and sequenced on Illumina NovaSeq at ~500 million reads per library.

treatment_protocol: Phototoxic treatment that causes photoreceptor ablation was used to initiate a regenerative response in the zebrafish retina 2,53. All fish subjected to light damage were dark-adapted for two weeks and then placed adjacent to intense fluorescent lights for 96 hours. The temperature of the fish tanks was regularly monitored and maintained at 34ºC. After 96 hours, the fish were returned to the animal facility with a normal light/dark cycle and maintained for 7, 14, or 21 days recovery (DR). N-methyl-D-aspartate (NMDA, Sigma M3262) was administered to normal light/dark cycled fish via an intravitreal injection of 0.3µL 100mM NMDA solution in sterile PBS with a Hamilton syringe (Hamilton, 2.5µL Model 62 RN SYR, 87942), followed by placing the tanks in a dark incubator at 33ºC for 96 hours, after which the tanks were moved back into a normal light/dark cycle for 7 or 14 days recovery.  EdU (5-Ethynyl-2'-deoxyuridine, Life technologies A10044) was administered as previously described 53. Fish were anesthetized using 1:1000 2-phenoxyethanol and immobilized under a paper towel in a petri dish. Then, using an insulin syringe equipped with a 30-gauge needle, approximately 20 µL 1mg/mL EdU in water was injected intraperitoneally into each zebrafish at 60, 72, 84, 96 and 108 hours after damage. The retinal tissues were harvested at either 3, 7, 14, or 21 days recovery.

value: Retina

value: NMDA


title: Plasma 4 Duplicate

type: RNA

city: Lebanon

first: Caitlin

middle: G

last: Howe

state: NH

address: 1 Medical Center Dr

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 58

hyb_protocol: NanoString recommended protocols were followed as described in the nCounter miRNA Expression Assay User's Manual

data_processing: We provide the RCC files here with the raw read counts including the sample-specific positive and negative controls. Counts from duplicate samples were averaged. We use the first sample number for duplicates in the matrix tab.

label: biotin

source_name: Plasma

extract_protocol: EVP miRNAs were extracted from from 500 μl of plasma, collected at approximately 24- to 28-weeks gestation, using the Qiagen Plasma/Serum exoRNeasy Kit (QIAGEN) according to the manufacturer's protocol. Eluted miRNAs were then further purified using Amicon Ultra Centrifugal Filters and concentrated using a speed vacuum concentrator

tag: gender

value: Female

tag: life stage

value: Prenatal

tag: days gestation at sample collection

tag: molecule subtype

value: miRNA


title: Injury LD 36hr, snRNA-seq

description: 10x Genomics

value: LD


title: Plasma 24 Duplicate

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 59

scan_protocol: NanoString recommended protocols were followed as described in the nCounter miRNA Expression Assay User's Manual


title: Injury LD 36hr, snATAC-seq

description: 10x Genomics


title: Plasma 9 Duplicate

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 56

label_protocol: NanoString recommended protocols were followed as described in the nCounter miRNA Expression Assay User's Manual


title: Plasma 55

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 55


title: Plasma 47 Duplicate

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 57


title: Pt96_Benign


title: low-phenolics, control, rep1


title: Pt96_Cancer


title: Control bio rep 7

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads from each sample's RNA-Seq fastq(.gz) file were mapped with STAR (Dobin, et. al) v2.7.1a to 26,150 indexed exemplar transcript sequences from the FHM genome (NCBI Accession WIOS00000000; BioSample SAMN12875914). Exemplar transcripts were defined as (one of) the transcripts from a given gene encoding (one of) the longest proteins from that gene. Two internally developed C programs were used to produce raw counts from the mapping output; reverse strand counts were used for further processing as dictated by sequencing protocol. Genomic gene and transcript coordinates and associated annotations are contained in files WIOS01.1.gbff.gz, WIOS01.2.gbff.gz and WIOS01.3.gbff.gz available at https://www.ncbi.nlm.nih.gov/Traces/wgs/WIOS01?display=contigs. Uniprot accessions associated with transcript/gene models are in the rawCountsGEO.txt file that is part of this GEO submission. That file also indicates which transcript models were selected from genes as exemplars for mapping. A gff version of the genome with gene/transcript model coordinates is available from the corresponding author upon request.
Raw counts from each sample were assessed with box plots, MDS plots, and density plots to screen for potential outlier samples. All samples remained for further processing.
Raw counts were normalized to log2 counts per million reads (CPM), using a combination of the edgerR and limma (voom) R packages. The normalized counts were not saved, but were used for downstream analysis steps (ranked DEG list production, classifier development and testing).
In each of the two treatment groups, five machine learing techinques (random forest, logistic regression with elastic net regularization (“glmnet”), naive Bayes, support vector machines with a Gaussian kernel, and gradient boosted decision trees) were applied to the normalized expression profiles. Each technique was tuned, trained, and made class predictions on each sample in a five-fold cross validation framework. Two learning methods, random forest and glmnet were used to test specifity in cross-chemical testing, and random forest was employed in a (leave-one-out-cross-validation) LOOCV scheme using all 32 samples to evaluate the success of  "three-way" classfication.
Genes with FDR <0.05 in each of the two treatment groups were imported into Qiagen's Ingenuity Pathway Analysis (IPA, version 49932394) with their (where applicable) associated Uniprot accessions and "core analysis" was performed on each treatment group, followed by a compartive analysis between the two groups.
Assembly: EPA_FHM_2.0.b
Supplementary files format and content: File rawCountsGEO.txt is tab delimited text file. The first three columns contain the internal IDs of the features (transcripts) mapped to, the features associated internal gene IDs, and their associated Uniprot identifiers, respectively. The rest of the columns contain the raw count data, derived from mapping, for each feature in each sample, where the first row of the remaining columns contains the sample IDs.

organism: Pimephales promelas

source_name: whole body

extract_protocol:
RNA was extracted from individual larvae using MagMAX™-96 Total RNA Isolation Kit (Thermo Fisher Scientific) following the manufacturer’s protocol. Samples were removed from -80 °C and immediately placed on ice. MagMax lysing/binding buffer (100 µl) was added to each tube. Samples were homogenized using a Bullet Blender Storm 24 homogenizer (Next Advance, Troy, NY).
RNA was quantified spectrophotometrically on a Synergy™ HTX Multi-Mode Microplate Reader using a Take3 Micro-Volume Plate (Biotek). RNA quality was assessed using a 4200 TapeStation (Agilent).
Sequencing libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen). Libraries were barcoded using the supplied i7 indices to allow multiplex sequencing of samples. Ten or eleven larvae (at least two from each beaker) from each treatment were used. All libraries were prepared from 250 ng total RNA according to the manufacturer’s protocol supplied with the kit.

treatment_protocol:
For two chemicals with different modes of action, 96h post-hatch individual fathead minnow (FHM) larvae were statically exposed to bifenthrin (3.2ug/L), CuSO4 (40 ug/L), or used as controls.
For treatment and controls, ten larvae were placed in each of five replicate 150 mL beakers containing 100 mL exposure solution. Beakers were arranged in a random manner on a tray, covered with an acrylic sheet to minimize evaporation, and placed in an incubator at 25 °C with a 16:8 h light:dark cycle. At 6 and 24 h, beakers were checked, and any dead larvae were removed. Three larvae from each beaker were removed at each of those time points as part of a separate experiment.
After 24 h, approximately 90 mL of the water was removed and replaced with fresh exposure solution for each beaker. At the end of the 48-h exposure, three larvae were removed from each beaker, and each larva was placed into a 1.5 ml microcentrifuge tube and frozen in liquid nitrogen. Each tube contained a 3.2 mm stainless steel bead to facilitate subsequent homogenization. Samples were transferred to -80 °C for storage.

value: whole body

value: larva

tag: age

value: 4 dpf/48 hr post hatch

tag: treatment vehicle

value: 100 mL MHRW, 0.002% DMSO

value: control

tag: concentration (ug/l)

tag: exposure duration

value: 48 hr


title: Pt95_Benign

value: Prostate


title: Control bio rep 5


title: Pt95_Cancer


title: Injury NMDA 36hr, snATAC-seq

description: 10x Genomics


title: Plasma 54

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 54


title: sample_27 PaTu-T - SAHA, 0.5 µM

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: matrix.txt

data_processing:
Reads were aligned to the human reference genome (GRCh38, Ensembl annotation release 100) and counted using STAR aligner (version 2.7.3a)
Assembly: GRCh38, Ensembl annotation release 100
Supplementary files format and content: tab-delimited table with read counts

source_name: PaTu-T

growth_protocol: The cell lines PaTu-S, Colo357, PaTu-T, PANC-1 and MIAPaCa-2 were cultivated in Dulbecco’s Modified Eagle Medium (DMEM, D5796), supplemented with 10% Fetal Bovine Serum (FBS, F9665) and 1% Penicillin/Streptomycin (PS, P0781), all from Sigma-Aldrich. The cell lines Capan-1 and Capan-2 were cultured in RPMI 1640 medium (21875091, Thermo Fisher Scientific) with 20% FBS and 1% PS. All cell lines were incubated at 37 °C in a humidified chamber with saturated atmosphere containing 5% CO2. Cell lines were passaged at a confluency of 80 - 90% with 1x Trypsin/EDTA (T3924, Sigma-Aldrich) in Dulbecco’s Phosphate-Buffered Saline (PBS). Cell lines were mycoplasma-negative as tested by PCR (ABM-G238, Biozol)

extract_protocol:
Total RNA was extracted using the RNeasy® Plus Mini Kit (74134, Qiagen).
PolyA-selected RNAseq libraries were prepared according to Illumina's instructions

treatment_protocol: A selective p300/CREB-binding protein (CBP) histone acetyltransferase (HAT) domain inhibitor A485 (6387, Tocris) and a pan-histone deacetylase (HDAC) inhibitor Vorinostat or suberoylanilide hydroxamic acid (SAHA, SML0061, Sigma-Aldrich) inhibiting class I and class II HDACs were used for short-term (24h or 96h) and long-term treatment (4-30 weeks) of seven PDAC cell lines, both dissolved in DMSO. For short-term treatment, all cell lines were treated with 10nM or 1µM A485 and 10nM or 0.5µM SAHA. For long-term treatment all cell lines were treated with 1µM A485 or 0.5µM SAHA, except MIAPaCa-2, which was treated with 0.05µM SAHA. Controls were treated with dissolvent DMSO. Cell lines under long-term conditions were treated Monday, Wednesday, Friday for a minimum of 4 weeks up to 30 weeks before used for experiments.

tag: cell line

value: PaTu-T

value: Pancreatic ductal adenocarcinoma

value: SAHA, 0.5 µM


title: sample_26 PaTu-T - A485, 1µM

description: matrix.txt


title: Plasma 53

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 53


title: Plasma 52

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 52


title: Control bio rep 4

tag: tissue


title: Pt94_Cancer


title: sample_25 PaTu-T - con

description: matrix.txt

tag: cell type


title: Plasma 50

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 50


title: Control bio rep 3


title: Plasma 13 Duplicate

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 51


title: sample_24 PANC1 - SAHA, 0.5 µM

description: matrix.txt


title: Pt94_Benign


title: Pt93_Cancer


title: Control bio rep 2


title: sample_23 PANC1 - A485, 1 µM

description: matrix.txt


title: sample_22 PANC1 - con

description: matrix.txt


title: Pt93_Benign


title: Control bio rep 14


title: sample_21 MIA PaCa-2 - SAHA, 0.5 µM

description: matrix.txt

source_name: MIA PaCa-2

value: MIA PaCa-2


title: Plasma 49

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 49


title: Plasma 48

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 48


title: Plasma 46

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 46


title: Control bio rep 8


title: Plasma 47

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 47


title: Control bio rep 13


title: Pt92_Benign


title: Pt92_Cancer


title: Control bio rep 11


title: sample_20 MIA PaCa-2 - A485, 1 µM

description: matrix.txt


title: Pt91_Benign


title: Control bio rep 10


title: Plasma 45

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 45


title: Control bio rep 1


title: sample_15 PaTu-S - SAHA, 0.5 µM

description: matrix.txt

source_name: PaTu-S

value: PaTu-S


title: Pt91_Cancer


title: sample_19 MIA PaCa-2 - con

description: matrix.txt


title: sample_14 PaTu-S - A485, 1 µM

description: matrix.txt


title: Plasma 43

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 43


title: Copper sulfate bio rep 8

value: copper sulfate


title: Pt90_Cancer


title: sample_13 PaTu-S - con

description: matrix.txt


title: Pt90_Benign


title: Plasma 42

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 42

value: Female


title: Copper sulfate bio rep 7


title: Copper sulfate bio rep 6


title: sample_12 Colo357 - SAHA, 0.5 µM

description: matrix.txt


title: Pt89_Cancer


title: Pt89_Benign


title: Copper sulfate bio rep 5


title: sample_11 Colo357, A485, 1 µM

description: matrix.txt


title: Plasma 40

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 40

value: Prenatal


title: Plasma 44

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 44

value: miRNA


title: Copper sulfate bio rep 4


title: sample_10 Colo357, con

description: matrix.txt


title: Pt88_Benign


title: sample_6 Capan-2 - SAHA, 0.5 µM

description: matrix.txt


title: Plasma 39

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 39


title: Copper sulfate bio rep 2


title: Plasma 38

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 38


title: Pt88_Cancer


title: Pt87_Cancer


title: Copper sulfate bio rep 13


title: sample_5 Capan-2 - A485, 1 µM

description: matrix.txt


title: Plasma 37

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 37


title: Plasma 41

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 41


title: sample_3 Capan-1 - SAHA, 0.5 µM

description: matrix.txt


title: Pt86_Benign


title: Copper sulfate bio rep 11


title: Pt86_Cancer


title: Copper sulfate bio rep 10


title: sample_2 Capan-1 - A485,  1µM

description: matrix.txt


title: sample_1 Capan-1 - con

description: matrix.txt


title: Copper sulfate bio rep 1


title: Plasma 33

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 33


title: Plasma 35

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 35


title: Plasma 36

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 36


title: Pt85_Benign


title: Bifenthrin bio rep 8

value: bifenthrin


title: Plasma 32

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 32


title: Pt85_Cancer


title: Pt87_Benign


title: Pt84_Cancer


title: Plasma 31

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 31


title: Copper sulfate bio rep 14

value: whole body


title: sample_4 Capan-2 - con

description: matrix.txt


title: Plasma 30

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 30


title: Pt84_Benign


title: Pt83_Benign


title: Plasma 34

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 34


title: Bifenthrin bio rep 4

value: larva


title: Plasma 28

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 28


title: Bifenthrin bio rep 2

value: 4 dpf/48 hr post hatch


title: Plasma 29

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 29


title: Pt82_Cancer


title: non-syn-18

city: Shanghai

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

data_processing:
RNA-Seq reads untrimmed. Differential expression analysis was performed using the CPM (counts per million) function in the Bioconductor package edgeR (v 3.14.0). Low expression genes were excluded to make a simple correction for gene counts. Genes with P-value (instead of adjusted P-value) < 0.05 were assigned as differentially expressed.
Assembly: danRer11
Supplementary files format and content: Excel file include readcounts values for each Sample.

source_name: brain

growth_protocol: Tg(HuC:H2B-GCaMP6f) fish of 4-5 weeks old were used.

extract_protocol:
Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol (Invitrogen) and then purified on RNeasy columns (Qiagen).
Total RNA quality was assessed on a bioanalyzer (Thermofisher). RNA-Seq libraries (N=10) for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.

treatment_protocol: Tg(HuC:H2B-GCaMP6f) fish of 4-5 weeks old were fixed in a recording chamber containing extracellular fluid, and neurons with synchronized or non-synchronized calcium activity after CAS treatment were identified by two-photon imaging and collected separately with glass pipette.

value: brain

tag: strain

value: neurons in dorsal pallium

value: non-synchronized in response to CAS


title: non-syn-10-1

tag: treatment


title: non-syn-19-1


title: non-syn-15


title: non-syn-17


title: non-syn-22


title: Pt82_Benign

value: Prostate


title: Bifenthrin bio rep 7

value: 100 mL MHRW, 0.002% DMSO

value: 48 hr


title: Bifenthrin bio rep 13


title: non-syn-13


title: Pt81_Benign


title: Plasma 27

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 27


title: Bifenthrin bio rep 11


title: Bifenthrin bio rep 5


title: Plasma 25

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 25


title: non-syn-10


title: non-syn-6


title: Plasma 24

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 24


title: Bifenthrin bio rep 10


title: Pt81_Cancer


title: Pt83_Cancer


title: Plasma 23

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 23


title: Bifenthrin bio rep 14


title: non-syn-5


title: Bifenthrin bio rep 1


title: Pt80_Benign


title: Plasma 26

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 26


title: syn-22

value: synchronized in response to CAS


title: syn-21


title: Plasma 21

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 21


title: Pt80_Cancer


title: Plasma 22

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 22


title: Pt79_Cancer


title: Plasma 20

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 20


title: 5d-2

city: Anseong-si

first: Dasom

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero

country: South Korea

institute: Chung-Ang University

description:
replicate 2
Paired-end RNA sequencing

data_processing:
Quality of raw reads were pre-checked using the FastQC software.
Trimmed reads of each sample were aligned to the Arabidopsis TAIR10 genome using STAR aligner with default parameters.
Mapped reads were converted to digital counts using FeatureCounts and were analyzed using edgeR.
DEGs were identified based on an adjusted p-value <0.05 and an absolute log2 fold change ≥ 1.
Assembly: Arabidopsis thaliana reference genome (TAIR10) was downloaded via the TAIR database (https://www.arabidopsis.org/).
Supplementary files format and content: *.bw: bigWig files for individual samples.

organism: Arabidopsis thaliana

source_name: Whole plants

extract_protocol:
Total RNAs were isolated using the RNeasy Plant Mini Kit (QIAGEN, Valencia, CA) and treated with DNase I (NEB, USA).
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA).

value: Whole plants

tag: ecotype

value: Wounding

tag: time point


title: 5d-3

description:
replicate 3
Paired-end RNA sequencing


title: syn-20


title: 5d-1

description:
replicate 1
Paired-end RNA sequencing


title: Pt78_Benign


title: Plasma 19

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 19


title: 3d-3

description:
replicate 3
Paired-end RNA sequencing


title: syn-16


title: syn-14-1


title: Pt78_Cancer


title: 3d-2

description:
replicate 2
Paired-end RNA sequencing


title: Plasma 18

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 18


title: 3d-1

description:
replicate 1
Paired-end RNA sequencing


title: Pt77_Cancer


title: syn-9


title: Plasma 17

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 17


title: Plasma 16

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 16


title: Pt77_Benign


title: Pt79_Benign


title: syn-6


title: 24h-3

description:
replicate 3
Paired-end RNA sequencing


title: Plasma 15

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 15


title: syn-5


title: Plasma 14

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 14


title: 24h-2

description:
replicate 2
Paired-end RNA sequencing


title: Pt76_Cancer


title: syn-4-1


title: Pt76_Benign


title: Pt75_Benign


title: syn-4


title: Pt75_Cancer


title: 12h-2

description:
replicate 2
Paired-end RNA sequencing


title: Plasma 12

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 12


title: Plasma 11

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 11


title: Pt74_Cancer


title: 24h-1

description:
replicate 1
Paired-end RNA sequencing


title: Plasma 13

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 13


title: 12h-3

description:
replicate 3
Paired-end RNA sequencing


title: 12h-1

description:
replicate 1
Paired-end RNA sequencing


title: Pt73_Benign


title: 1M7+, biological replicate 2-3

city: Cambridge

first: Seungchan

last: Baek

state: Massachusetts

address: 22 Water St, Apt 326

institute: Broad Institute

description:
The replicates 2-3 contains a subset of the replicate 1.
SHAPE_reactivity.csv
SHAPE-based_pri-miRNA_structures.csv

library_source: other

data_processing:
Raw sequences were quality-filtered using the FASTX Toolkit (v. 0.0.13.2; http://hannonlab.cshl.edu/fastx_toolkit; fastq_quality_filter -q 25 -p 80). The filtered sequences were aligned to pri-miRNA construct sequences using bowtie2 with reduced mismatch and gap extension penalties (version 2.2.479; --end-to-end --mp 5,1 --rdg 5,1 --rfg 5,1 --no-mixed --no-unal --norc).
From the aligned sequences, mutations at each nucleotide position were counted using the ShapeMapper package (version 1.0). Ambiguously mapped reads were discarded, and consecutive mutations were merged during alignment parsing (parseAlignment -combine_strand -deletion_masking -remove_ambig_del -min_map_qual 2).
SHAPE reactivity was calculated by dividing the difference between mutation rates in the 1M7-treated and 1M7-untreated samples by mutation rates in the RNA-denatured sample, as described in the previous study. SHAPE reactivities were normalized by the 90th percentile of reactivities within each RNA species.
Secondary structures were modeled using the RNAstructure package (Fold, version 5.841).
Assembly: Hg38
Assembly: Pri-miRNA construct sequences (Table S2)
Supplementary files format and content: SHAPE reactivities and secondary structures were prepared as csv files.
Library strategy: SHAPE-Seq

molecule: other

source_name: In vitro

growth_protocol: The DNA constructs were pooled, purified (QIAquick PCR Purification Kit, QIAGEN), and treated with SurveyorⓇ Mutation Detection Kit (IDT) to remove DNA with mutations. Then, the DNAs were gel-purified and amplified by PCR using KAPA HiFi HotStart ReadyMix (Kapa Biosystems) with primers; 5′-TAATACGACTCACTATAGGGCCTATTCAGTTACAGCG-3′ (forward) and 5′-m(2′-O-Me)GmUTGCTAGCTTCAGTACG-3′ (reverse). Finally, pri-miRNAs were prepared by in vitro transcription using MEGAscript™ T7 Transcription Kit (Ambion).

extract_protocol:
After the modification, RNAs were precipitated by ethanol.
the SHAPE-modified RNAs were subjected to reverse transcription for 3 h at 42℃ using SuperScript II (Invitrogen). The RT primer (5′-CCTTGGCACCCGAGAATTCCANNNNNNGTTGCTAGCTTCAGTACG-3′) contains the sequence complementary to the 3′ custom adapter, which is followed by six random nucleotides and RNA 5′ adapter sequence of TruSeq Small RNA Library Preparation Kit (Illumina). Reverse transcriptase buffer contained 0.5 mM premixed dNTPs, 50 mM Tris-HCl pH 8.0, 75 mM KCl, 6 mM MnCl2 and 10 mM DTT.
After reverse transcription, cDNAs were purified by Agencourt RNAClean XP (Beckman). Sequencing libraries were generated using the one-step PCR approach. The PCR reactions were performed using Q5 Hot Start High-Fidelity DNA polymerase (NEB) with the forward PCR primer (5′-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATCNNNNNNGCCTATTCAGTTACAGCG-3′), which contains the P5 sequence for Illumina paired-end sequencing at the 5′ end, six random nucleotides, and the sequence complementary to the 5′ common sequence. RNA PCR Index Primers of Truseq Small RNA Library Preparation Kit were used as reverse primers. One-step PCR was performed for 3 cycles to tag cDNAs and generate the final library for sequencing. PCR products were purified using AMPure XP beads (Beckman). The library was sequenced on Illumina Hiseq X-10 (150x150 paired-end run) with 50% of the PhiX control library (Illumina).

treatment_protocol: For each sample, 5 pmol of RNA mixture of pri-miRNAs and positive control RNAs (each pri-miRNA : each positive control RNA = 1 : 2) was refolded in 50 mM Tris-HCl pH 7.5, 100 mM NaCl, 2 mM MgCl2 in a final volume of 10 μL at 37℃ for 20 min. After folding, RNAs were modified in the presence of 10 mM 1M7 and incubated at 37℃ for 75 sec. The “No-reagent” control (Untreated), containing DMSO rather than SHAPE reagent, was performed in parallel. For the denatured sample, RNAs were modified using 1M7 (final 10 mM) under strongly denaturing conditions in 50 mM HEPES pH 8.0, 4 mM EDTA and 50% formamide at 95℃ for 1 min.

value: In vitro


title: Denatured, biological replicate 2-3


title: Denatured, biological replicate 2-2

description:
The replicates 2-2 contains a subset of the replicate 1.
SHAPE_reactivity.csv
SHAPE-based_pri-miRNA_structures.csv


title: 1M7-, biological replicate 2-3

value: DMSO


title: Plasma 9

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 9

value: Female

value: Prenatal


title: Plasma 10

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 10

value: miRNA


title: Pt73_Cancer


title: Pt72_Benign


title: Pt74_Benign


title: 6h-3

description:
replicate 3
Paired-end RNA sequencing


title: Denatured, biological replicate 2-1

description:
The replicates 2-1 contains a subset of the replicate 1.
SHAPE_reactivity.csv
SHAPE-based_pri-miRNA_structures.csv


title: 6h-2

description:
replicate 2
Paired-end RNA sequencing


title: 1M7+, biological replicate 2-2


title: Plasma 8

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 8


title: Plasma 7

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 7


title: Pt71_Cancer


title: 1M7-, biological replicate 2-2


title: 0h-3

description:
replicate 3
Paired-end RNA sequencing

value: Untreated


title: Plasma 6

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 6


title: Plasma 4

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 4


title: 0h-2

description:
replicate 2
Paired-end RNA sequencing


title: 1M7+, biological replicate 2-1


title: Pt72_Cancer


title: RLE-6TN cells, ChIP-1-IP

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

description:
Peak_Annotations.xlsx
Promoter_Peak_Annotation.xlsx

data_processing:
FastQC was used to assess the quality of raw sequencing reads.
Map the trimmed reads to a reference genome using alignment tools such as HISAT2.
Identify regions of enriched signal (peaks) representing DNA regions bound by the protein of interest.
Assembly: Rnor_6.0
Supplementary files format and content: xls files include peak annotations and promoter peak annotation

organism: Rattus norvegicus

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes to preserve the protein-DNA interactions.And lyse the cells to release the chromatin.Fragment the chromatin into smaller pieces using sonication or enzymatic digestion. This step is crucial to obtain DNA fragments of the appropriate size for sequencing.
ChIP-Seq libraries were prepared with the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bio Scientific.

value: alveolar Type II cells

value: transfected with LV-RUNX1

tag: chip antibody

value: Anti-RUNX1 antibody (abcam,#ab272456)


title: Pt70_Benign


title: Denatured, biological replicate 1

description:
SHAPE_reactivity.csv
SHAPE-based_pri-miRNA_structures.csv


title: 0h-1

description:
replicate 1
Paired-end RNA sequencing


title: RLE-6TN cells, ChIP-1-Input


title: 6h-1

description:
replicate 1
Paired-end RNA sequencing


title: Pt70_Cancer


title: CTN_50μM_rep2

city: Taipei

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

department: Graduate Institute of Toxicology

country: Taiwan

institute: National Taiwan University

data_processing:
Raw reads quality checked by fastqc
Raw reads trimmed by cutadapt
Trimmed raw reads aligned to rat reference genome by star
Alignment quality checked by rseqc
Read counts of gene normalized to CPM by edgeR
Assembly: Rattus norvegicus assembly mRatBN7.2 release 109
Supplementary files format and content: Tab-delimited TXT file containing read counts of each gene for each sample
Supplementary files format and content: CSV file containing log2CPM values of each gene for all the samples

growth_protocol: Rat cardiomyoblast H9c2 cells were maintained in DMEM medium containing 10% FBS and subcultured for every 3 days.

extract_protocol:
Total RNA extraction was performed with TRIzol reagent according to manufacturer’s instruction (Invitrogen, Waltham, MA). RNA quality assessment was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturer’s protocol.
cDNA library construction was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturer’s protocol.

treatment_protocol: Rat cardiomyoblast H9c2 cells were treated with 0 and 50 μM of CTN for 48 h in DMEM medium containing 10% FBS.

value: cardiomyoblast

value: CTN 50 μM

tag: time


title: 1M7-, biological replicate 1


title: CTN_50μM_rep1


title: Pt69_Benign

value: Prostate


title: Plasma 2

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 2

tag: gender


title: Plasma 3

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 3

tag: life stage


title: Pt71_Benign


title: CTN_0μM_rep1

value: CTN 0 μM


title: siSON_3

city: Xiamen

first: Mengjun

last: Zhang

address: State Key Laboratory of Cellular Stress Biology

department: Department of biochemistry

institute: Xiamen university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36).
Clean data were mapped to the reference genome of Homo sapiens from NCBI using STRA 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 RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: not provided
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 RPKM value for each sample.

source_name: HeLa

growth_protocol: All the cells were grown in DMEM (L120KJ), supplemented with 10% FBS (Moybio; 304 S450), penicillin/streptomycin (BasalMedia; S110JV), and Glutamax (BasalMedia; S210JV) at 37°C, 5% CO2.

extract_protocol:
Total RNAs were extracted from cells using TRIzol Reagent (Invitrogen, cat. NO 15596026). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210). 2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.
RNA library for RNA-seq were prepared using Stranded mRNA-seq Library Prep Kit following manufacture's protocols.

treatment_protocol: Knockdown experiments were performed with Lipofectamine RNAi Max (Life Technologies; 13778075) according to the manufacturer’s instructions. The following siRNAs synthesized by GenePharma (Shanghai, China): siSON: 5’-GCAUUUGGCCCAUCUGAGATT-3’; siSRRM2: 5’ GGUACGAGGAACAGCAAAUTT-3’

value: HeLa

value: cervical cancer cell

tag: genotype

value: SON knock down


title: Nkd_del_D6_rep2

city: Nanjing

first: Rui

last: Wang

state: Jiangsu

address: 2 Sipailou Road

department: School of Life Science and Technology

institute: Southeast University

description: The whole transcriptional profiles of wing discs expressing Nkd_del_D6_GFPC drived by MS1096-Gal4.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the fly reference genome (BDGP6) with HISAT2 (version 2.2.1).
The aligned reads were used to quantify mRNA expression by using featureCounts. The DESeq2 package in R was used to compute normalized fold-change and adjusted P value for each gene, comparing Nkd recombinant protein-expressing wing discs to the GFP-expressing controls.
Genome_build: BDGP6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: wing imaginal discs

growth_protocol: Experiments was carried out at 25 °C with standard medium

extract_protocol:
Each RNA sample was prepared from ~70 wing imaginal discs of late 3rd larvae, and RNA was harvested using Trizol reagent. RNA-seq libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wing imaginal discs

value: MS1096 > Nkd_del_D6_GFPC

tag: Stage

value: late third instar


title: Plasma 1

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 1

value: Female

tag: days gestation at sample collection

tag: molecule subtype


title: Nkd_del_30aa_rep1

description: The whole transcriptional profiles of wing discs expressing Nkd_del_30aa_GFPC drived by MS1096-Gal4.

value: MS1096 > Nkd_del_30aa_GFPC


title: Pt68_Cancer

first: Angelo

last: De Marzo

address: 1550 Orleans Street, CRB II RM 138

data_processing:
Trim galore v0.6.3 was used to trim the reads.
Bwa v0.7.7 (mem) was used to align to the hg19 and hg38 human genome builds.
Piccard-tools v1.119 & GATK v3.6.0 were used to create a recalibrated bam file.
Assembly: hg19 and hg38 human genome builds
Supplementary files format and content: Posterior mean estimate transcripts per million (pmeTPM) for each sample
Supplementary files format and content: Expected count for each sample

extract_protocol:
Tissue digestion and DNA/RNA extraction was performed using Allprep DNA/RNA Kits following the manufacturer’s recommendations (Qiagen, 802804)
Libraries were constructed according to the protocol provided in the Illumina Nano TruSeq Library prep guide. Assessment of the yield and size distribution of the amplified library was performed on the Agilent 2100 Bioanalyzer using the High Sensitivity Chip. Libraries were then pooled at equal molar concentrations for sequencing. Sequencing was performed using Illumina HiSeqX and NovaSeq6000 with Paired End 150 bp x 150 bp read configuration.


title: Pt69_Cancer


title: Choroid plexus Obese+TT 20

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

data_processing:
QC quality control and adapter removal was done by Novogene (UK) Company Limited.
Mapping to reference genome (rattus norvegicus Rnor_6.0.104) using STAR (v. 2.7.9a) (--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM)
Abundance quantified by RSEM (v. 1.3.3) (--bam --paired-end --forward-prob 0)
Differentially expressed genes are produced with standard procedure of DEseq2 (v. 3.16) using GeneCount output from STAR (--quantMode)
Assembly: Rnor_6.0 (rn6) v.104
Supplementary files format and content: tab-delimited text files for gene abundance for each samples in TPM and FPKM

source_name: Choroid plexus

extract_protocol:
Extraction was performed by Novogene (UK) Company Limited.
Done by Novogene (UK) Company using NEB Next® Ultra™ RNA Library Prep Kit, and sequenced on Illumina NovaSeq 6000, paired-end 150 bp, 12Gb output.

value: Choroid plexus

tag: age

value: 16 weeks

value: Zucker

tag: Sex

tag: phenotype

value: Obese

value: TT


title: Choroid plexus Obese+TT 19

tag: tissue


title: siSON_2

tag: cell line

tag: cell type


title: Nkd_del_R1S_rep1

description: The whole transcriptional profiles of wing discs expressing Nkd_del_R1S_GFPC drived by MS1096-Gal4.

value: MS1096 > Nkd_del_R1S_GFPC


title: Nkd_del_30aa_rep2


title: CTN_0μM_rep2

value: cardiomyoblast

tag: treatment


title: Pt68_Benign

city: Baltimore

source_name: Prostate

value: Prostate


title: siSRRM2_2

value: SRRM2 knock down


title: siSON_1

value: HeLa


title: 1M7-, biological replicate 2-1

value: In vitro

value: DMSO


title: Choroid plexus Obese+TT 18

tag: strain


title: 1M7+, biological replicate 1


title: Nkd_del_R1S_rep2

value: wing imaginal discs


title: siSRRM2_1

value: cervical cancer cell


title: Pt66_Benign


title: Choroid plexus Obese+TT 17


title: Nkd_del_D6_rep1

value: MS1096 > Nkd_del_D6_GFPC

value: late third instar


title: Nkd_rep1

description: The whole transcriptional profiles of wing discs expressing Nkd_GFPC drived by MS1096-Gal4.

value: MS1096 > Nkd_GFPC


title: Plasma 5

description:
miRNAs were isolated from extracellular vesicles and particles extracted from plasma
SAMPLE 5

value: Female

value: Prenatal

value: miRNA


title: siSRRM2_3


title: GFP_rep2

description: The whole transcriptional profiles of wing discs expressing GFP drived by MS1096-Gal4.

value: MS1096 > GFP


title: Ctr_2

value: WT


title: Ctr_3


title: Pt67_Benign


title: Pt65_Benign


title: Pt66_Cancer


title: GFP_rep1


title: Pt65_Cancer


title: Choroid plexus Lean+VEH 14

value: Choroid plexus

value: 16 weeks

value: Zucker

value: Lean

value: VEH


title: Ctr_1

value: HeLa


title: sgMIif2

city: hefei

first: linlin

last: yan

state: anhui

address: No. 96, Jinzhai Road

institute: University of Science and Technology of China

description: 10X Genomics

data_processing:
Alignment to GRCm38 reference genome, barcode, and unique molecular identifier (UMI) counting was performed using Cell Ranger (10X Genomics, v6.1.2). The Seurat package (version, 4.3.0) was used for downstream analysis.
UMI-1 and UMI-2 are sgcon group, UMI-3 and UMI-4 are sgMif group
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

organism: Mus musculus

source_name: Breast cancer

extract_protocol:
Three different tumors were dissociated to single-cell suspensions using collagenase I (2 mg/ml), collagenase IV (2 mg/ml), DNase I (1mg/ml) and a tissue dissociator. Cells filtered with a 40 μm filter were incubated with Red Blood Cell Lysis Buffer to remove red cells. Death cells were removed by Death Cell Removal Kit. Cells were resuspended in PBS and cell number was counted. Equal cells were collected for subsequent staining. Cells were then incubated with 20% FBS in PBS with 25 μg/mL of anti-mouse CD16/CD32 antibody  at 4°C for 10 minutes to minimize background antibody binding. Then cells were stained with FITC-anti-mouse CD45 at room temperature for 20 minutes, followed by PI staining for 5 minutes on ice. Cells after staining were sorted by the BD FACSAria II sorting system to harvest the FITC (CD45)-positive and PI-negative populations. Cells recovered were subjected to the 10X Genomics standard protocol for scRNA-seq.
RNA libraries were prepared for sequencing using standard protocols

value: Breast cancer

value: mouse breast cancer cell

value: Mif-depleted

tag: cell subtype

value: CD45+ immune cell population


title: Pt64_Benign

value: Prostate


title: sgMif1

description: 10X Genomics


title: Sperm, B2102S, summer

city: Pullman

first: Min

last: Du

state: WA

address: 1815 Ferdinand's Ln

department: Animal Science

institute: Washington State University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore program v 5.0
The Cattle reference genome ARS-UCD 1.2 (GCA 002263795.2) incorporated with Y chromosome (GenBank: CM011803.1) were used for paired end alignment by indexing with bowtie2 under bismark
Methylation information was extracted in CpG/CHG/CHH context by using bismark
Assembly: ARS-UCD 1.2
Supplementary files format and content: cov file containing methylation coverage count

organism: Bos taurus

source_name: Sperm

extract_protocol:
Sperm were collected after thawing the frozen semen straw at 37 ºC temperature
The genomic DNA spiked with lambda DNA were fragmented to 200-400bp with a Covaris s220 sonicator followed by terminal repair and adenylation. Lambda DNA was used as unmethylated control for bisulphite conversion rate calculation. Cytosine methylated barcodes were then ligated to the sonicated DNA and treated twice with an EZ DNA Methylation-Gold™ Kit (Zymo Research) for bisulfite conversion.

treatment_protocol: Frozen semen straw during winter were prepared  after an exposure to a cold period from January to February and during summer after exposure to high temperature during June and July.

tag: breed

value: Angus

value: Sperm

value: Male

value: high environmental temperature


title: Choroid plexus Obese 12

institute: University of Copenhagen

value: Female

value: Obese


title: Sperm, B2043S, summer


title: Nkd_rep2

value: wing imaginal discs

value: MS1096 > Nkd_GFPC

value: late third instar


title: Sperm, B2026S, summer


title: CON2

description: 10X Genomics

value: wild-type


title: Pt64_Cancer

institute: Johns Hopkins University School of Medicine


title: Pt63_Benign


title: Choroid plexus Lean+VEH 15

value: Choroid plexus

value: 16 weeks

value: Zucker

value: Lean

value: VEH


title: CON1

description: 10X Genomics

value: Breast cancer

value: mouse breast cancer cell

value: CD45+ immune cell population


title: Sperm, B2102W, winter

value: Angus

value: Sperm

value: Cold exposure durng winter


title: Pt63_Cancer

value: Prostate


title: Choroid plexus Obese 10

value: Female

value: Obese


title: Pt62_Benign


title: Pt62_Cancer


title: Choroid plexus Lean+VEH 13


title: eIF4E-BP1 TMEM119 cKO BL 2 IP

city: Montreal

first: Arkady

last: Khoutorsky

state: Quebec

address: 3655 Promenade Sir-William-Osler

institute: McGill University

description:
BP 2 IP
D11

data_processing:
RNA-seq read files (fastq files) were checked for quality by FastQC and read trimming was done based on the Phred score and per-base sequence content
Trimmed Reads were then mapped against the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR v2.2.1
Relative abundances in Transcripts Per Million (TPM) for every gene of every sample was quantified by stringtie v1.3.5
Assembly: Genome Reference Consortium Mouse Build 38 patch release 5
Supplementary files format and content: gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes

source_name: spinal cord

growth_protocol: Transgenic mice expressing Cre recombinase under the control of the TMEM119 promoter and reporter mouse line eGFPL10a were generated. Mice expressed egfp on l10a location of ribosomes. All experiments were carried out using male mice aged 8 to 12 weeks old.

extract_protocol:
Direct-zol RNA kit (Zymo Research)
rRNA-depleted stranded (HMR)

value: spinal cord

value: microglia

value: Immunoprecipitation (IP) with eGFP antibody


title: Sperm, B2026W, winter

value: Male


title: explants, stretched, rep3

city: Moscow

first: Fedor

middle: M

last: Eroshkin

address: 16/10 Miklukho-Maklaya str.

country: Russia

institute: IBCH RAS

data_processing:
fastq files were aligned to Xenopus laevis reference genome Xenla9.1 using TopHat2.
Non-normalized counts were obtained using HTseq software.
Statistics of differential expression (stretched vs control explants) were caluclated via DEseq R package.
Assembly: Xenla9.1
Supplementary files format and content: excel file (.xlsx) containing output from edgeR (for each transcript (gene))

organism: Xenopus laevis

source_name: embryonic tissue explants

growth_protocol: Xenopus laevis embryos were obtained, fertilized in vitro and dejellied in 2% cysteine in 0.1xMMR solution. Intact and treated embryos were grown up to stage 11.5 NF in 0.1xMMR solution.

extract_protocol:
All RNA purifications and RNA-seq analysis were made by Genoanalytica (Moscow, Russia). Briefly, total RNA was extracted from the samples with Trizol reagent according to the manufacturer’s protocol. Quality of RNA was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A) RNA was purified using Dynabeads® mRNA Purification Kit (Ambion).
Illumina library was made from poly(A) NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

treatment_protocol: At the stage 11.5 NF, neuroectodermal explants were cut off, combined in pairs, inner sides to each other (head to head), pinned them to an agarose substrate by thin glass needles and stretched within 3 hours. The procedure was adopted from (Beloussov et al., 1999). Control explants were pinned to agarose, but not stretched.

value: embryonic tissue explants

tag: developmental stage

value: wild type

value: stretched explants


title: Sperm, B2043W, winter


title: Pt61_Cancer


title: Pt61_Benign


title: eIF4E-BP1 TMEM119 cKO BL 3 IN

description:
BP 3 IN
G11


title: explants, stretched, rep2


title: eIF4E-BP1 TMEM119 cKO BL 1 IP

description:
BP 1 IP
B11


title: Choroid plexus Obese 11

value: Choroid plexus

value: 16 weeks

value: Zucker


title: Choroid plexus Lean 6

value: Lean


title: Choroid plexus Obese 7


title: eIF4E-BP1 TMEM119 cKO BL 2 IN

description:
BP 2 IN
E11


title: Choroid plexus Lean 5


title: Pt60_Benign


title: explants, control, rep3

value: control explants


title: Choroid plexus Obese 9


title: eIF4E-BP1 TMEM119 cKO BL 3 IP

description:
BP 3 IP
F11


title: eIF4E-BP1 TMEM119 cKO BL 1 IN

description:
BP 1 IN
C11


title: Choroid plexus Lean 4


title: Choroid plexus Lean 3


title: explants, control, rep1


title: Choroid plexus Obese 8


title: explants, control, rep2


title: Pt60_Cancer


title: TMEM119 Control BL 2 IP

description:
WT 2 IP
B12


title: HCT116_vector

first: yangfei

last: Xing

state: Shanghai

address: 197 Rui Jin Er Road

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The raw reads were initially processed using FastQC (v0.10.1) for quality control
Adapter sequences and poor-quality reads were removed using Cutadapt (v1.9.1)
Quality-filtered reads were aligned to the human genome (hg38) using HISAT2 (v2.0.1)
Gene-level read counts were generated from aligned reads by HTSeq (v0.6.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files including expression value (FPKM) for each gene

source_name: p53-null HCT116 cells

growth_protocol: p53-null HCT116 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco), L-glutamine, and appropriate antibiotics. Cell cultures were maintained in a 5% CO2 humidified incubator at 37℃.

extract_protocol: RNA was prepared using a total RNA purification kit (Sangon Biotech, B518651). The sequencing libraries were constructed from 1 μg of purified mRNA using TruSeq RNA Sample Prep Kit (Illumina, FC-122-1001) and paired-end sequencing was conducted on the Illumina HiSeq X Ten platform.

treatment_protocol: p53-null HCT116 cells were stably expressed wild-type p53 or mutant p53 followed by 24 h ATO treatment (PANDAs).

value: p53-null HCT116 cells

value: untreated


title: Pt58_Benign

value: Prostate


title: explants, stretched, rep1


title: Pt58_Cancer


title: TMEM119 Control BL 3 IP

description:
WT 3 IP
D12


title: Choroid plexus Lean 2

value: Female


title: TMEM119 Control BL 1 IP

description:
WT 1 IP
H11


title: Choroid plexus Lean 1


title: TMEM119 Control BL 2 IN

description:
WT 2 IN
C12


title: Pt57_Benign


title: HCT116_PANDAR282W

description: sourced from GSE151696 (GSM4588447)

value: treated with ATO for 24 hours


title: HCT116_p53WT


title: HCT116_PANDAM133T


title: sample39_striatum, 24 hour

city: Berkeley

first: Lynn

middle: T.

last: Yang

state: CA

address: 1951 Oxford Street, 430E

department: Integrative Biology, Helen Wills Neuroscience Institute

institute: UC Berkeley

data_processing:
Fastq files were generated and demultiplexed using Illumina bcl2fastq2 v2.20 and default settings, on a server running CentOS Linux 7. No other processing, trimming, or filtering was conducted.
RNA-seq reads were aligned using STAR v2.9.1a against UCSC rat genome rn6.
Quality control check was performed using FastQC v0.11.9, MultiQC v1.11, and raw counts generated with featureCounts.
R studio was used for normalization and data analysis, R v4.0.2. with the packages tidyverse v1.3.1, IHW, DESeq2.
Assembly: UCSC rat genome rn6
Supplementary files format and content: tab-delimited text files include raw featureCounts values and DESeq2 normalized values for each sample

source_name: striatum, 24 hour

extract_protocol:
Total RNA was extracted from 100-150 mg of flash-frozen rat somatosensory cortex and striatum tissue. Glycoblue (Invitrogen #AM9515) was added to assist with RNA pellet isolation. Pellets were washed with 75% ethanol and allowed to dry before being dissolved in 20 μL of RNase-DNase free water. 2 μL of 10x DNase I Buffer (New England Biolabs, #m0303s), 1 μL of rDNase I (ThermoFisher Scientific, AM2235), and DNase Inactivation Reagent (ThermoFisher Scientific, AM1907) were added to each RNA sample for purification.
Library preparation was performed by the QB3-Berkeley Functional Genomics Laboratory at UC Berkeley. mRNA selection was done with the oligo-dT beads. Both total RNA and oligo dT bead selected mRNA quality was assessed on an Agilent 2100 Bioanalyzer. Libraries were prepared using the KAPA RNA Hyper Prep kit (Roche KK8540). Truncated universal stub adapters were ligated to cDNA fragments, which were then extended via PCR using unique dual indexing primers into full length Illumina adapters. Library quality was checked on an AATI (now Agilent) Fragment Analyzer. Libraries were then transferred to the QB3-Berkeley Vincent J. Coates Genomics Sequencing Laboratory, also at UC Berkeley. Library molarity was measured via quantitative PCR with the KAPA Library Quantification Kit (Roche KK4824) on a BioRad CFX Connect thermal cycler. Libraries were then pooled by molarity and sequenced on an Illumina NovaSeq 6000 S4 flowcell for 2 x 150 cycles, targeting at least 25M reads per sample.

value: striatum

tag: time

value: 24 hour


title: Pt67_Cancer


title: Pt59_Benign


title: TMEM119 Control BL 3 IN

description:
WT 3 IN
E12

value: spinal cord

value: microglia


title: sample40_striatum, 24 hour


title: Pt59_Cancer


title: Pt57_Cancer


title: TMEM119 Control BL 1 IN

description:
WT 1 IN
A12


title: Choroid plexus Lean+VEH 16

value: VEH


title: sample37_striatum, 24 hour


title: sample38_striatum, 24 hour


title: Pt56_Cancer


title: Pt56_Benign


title: sample36_ipsilateral sensorimotor cortex, 24 hour

value: ipsilateral sensorimotor cortex


title: Pt55_Benign


title: scRNA-seq of KO-CML-PBMC

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-mm10-1.2.0 genome assembly using cellranger v5.0.0
Counting data of reference gene expression levels were generated by cellranger v5.0.0 (automatic identification of chemistry properties)
Assembly: mm10
Supplementary files format and content: Tab separated values; MatrixMarket

source_name: PBMC from Mir142-/- BCR-ABL mice

growth_protocol: The cells were collected from the mice and sorted by flow cytometry before performing scRNA-seq. The cells have not been cultured or growed in vitro.

extract_protocol:
Single cells were captured on a 10xGenomics Chromium Controller using a 10X V3 Single Cell 3’ Solution kit (10xGenomics, Chromium Single Cell 3’ Reagent kit V3, Cat. PN-1000092). All protocols were performed following the manufacturer’s instructions.
Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat. 5067-4626). The library concentration was determined with a Qubit High Sensitivity DNA Assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired-end setting of 28 cycles of read (R) 1, 101 cycles of R2, and 8 cycles of index reads on Illumina NovaSeq 6000 platform, with sequencing depth of ~0.1 million reads per cell.

treatment_protocol: The cells were not treated.

value: PB

value: PBMC


title: scRNA-seq of KO-CML-SPLEEN-T cells

source_name: Spleen-T from Mir142-/- BCR-ABL mice

value: Spleen

value: T cells


title: scRNA-seq of KO-CML-BM cells

source_name: BM-T from Mir142-/- BCR-ABL mice

value: BM


title: Pt55_Cancer


title: sample34_ipsilateral sensorimotor cortex, 24 hour


title: sample35_ipsilateral sensorimotor cortex, 24 hour


title: sample33_ipsilateral sensorimotor cortex, 24 hour


title: scRNA-seq of WT-CML-SPLEEN-T cells

source_name: Spleen-T from Mir142+/+ BCR-ABL mice


title: scRNA-seq of WT-CML-BM cells

source_name: BM-T from Mir142+/+ BCR-ABL mice


title: Pt54_Benign


title: sample32_ipsilateral sensorimotor cortex, 24 hour


title: scRNA-seq of KO-CML-LMPP

source_name: BM LMPP from Mir142-/- BCR-ABL mice

value: LMPP


title: Pt54_Cancer


title: Pt53_Cancer


title: scRNA-seq of WT-CML-LMPP

source_name: BM LMPP from Mir142+/+ BCR-ABL mice


title: Pt53_Benign


title: sample30_ipsilateral sensorimotor cortex, 24 hour


title: sample31_ipsilateral sensorimotor cortex, 24 hour


title: scRNA-seq of KO-LMPP

source_name: BM LMPP from Mir142-/- mice


title: Pt52_Benign


title: sample28_contralateral sensorimotor cortex, 24 hour

value: contralateral sensorimotor cortex


title: sample29_ipsilateral sensorimotor cortex, 24 hour


title: Pt52_Cancer


title: PTH-pretreated, vehicle, 2wks of daily loading, rep9,cancellous bone,Right [D12]

city: Ithaca

first: Marjolein

last: van der Meulen

state: NY

address: Weill Hall

department: BME

institute: Cornell University

data_processing:
Computational was performed in a Unix environment
12bp were trimmed from 5’ end of sequenc reads using fastx_trimmer
Sequence reads were trimmed using trimmomatic(v0.39)
Trimmed sequences were mapped to mm10 using STAR
Each sample contained over 1 million of uniquely mapped reads to the mouse genome. Genes with less than 3 counts per million were not included for analysis.
Assembly: mm10
Supplementary files format and content: normalizedcounts.xls file includes normalized value from edgeR for each sample

source_name: cancellous bone

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen). 20uL of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq (Illumina) – 3’ RNAseq Kit following maufacturer’s protocols

value: cancellous bone

tag: limb

value: Right

value: 28 wks


title: PTH-pretreated, vehicle, 2wks of daily loading, rep8,cancellous bone,Right [D04]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep11,cortical bone,Right [D13]

source_name: cortical bone

value: cortical bone


title: PTH-pretreated, vehicle, 2wks of daily loading, rep6,cortical bone,L [D01]

value: L


title: PTH-pretreated, vehicle, 2wks of daily loading, rep10,cortical bone,Right [D21]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep10,cancellous bone,Right [D20]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep8,cortical bone,Right [C96]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep8,cortical bone,L [D17]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep7,cortical bone,L [D09]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,cancellous bone,L [C99]


title: scRNA-seq of WT-CML-PBMC

source_name: PBMC from Mir142+/+ BCR-ABL mice

tag: genotype


title: scRNA-seq of WT-LMPP

source_name: BM LMPP from Mir142+/+ mice


title: PTH-pretreated, vehicle, 2wks of daily loading, rep9,cortical bone,Right [D05]


title: Pt51_Benign

source_name: Prostate

value: Prostate


title: PTH-pretreated, vehicle, 2wks of daily loading, rep11,cancellous bone,Right [C95]


title: Pt51_Cancer


title: PTH-pretreated, vehicle, 2wks of daily loading, rep5,cortical bone,L [C92]


title: Pt50_Benign


title: sample26_contralateral sensorimotor cortex, 24 hour

value: 24 hour


title: sample27_contralateral sensorimotor cortex, 24 hour


title: sample25_contralateral sensorimotor cortex, 24 hour


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,cancellous bone,L [C91]


title: sample24_contralateral sensorimotor cortex, 24 hour


title: klf15 IP heart+pred single shot 2

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
A quality control check on the generated fastq ﬁles was performed using FastQC.
Peak analysis was conducted using HOMER software (v4.10, 70; standard commands) after aligning fastq files to the mm10 mouse genome using bowtie2 71.
Assembly: mm10
Supplementary files format and content: bedgraph file of peaks (raw counts)

source_name: heart

extract_protocol:
Atria- and blood-deprived hearts were cryopowdered using a liquid nitrogen-cooled Retsch Cryomill. The cryopow-dered tissue was then fixed in 10 ml 1% PFA for 30 minutes at room temperature with gentle nutation. Fixation was quenched 1ml of 1.375M glycine (Cat # BP381-5, Fisher Scientific, Waltham, MA) with gentle nutation for 5 minutes at room temperature. After centrifugation at 3000g for 5 minutes at 4°C, the pellet was resuspended in cell lysis buffer as per reported conditions 69, supplementing the cell lysis buffer with 3mg/ml cytochalasin B and rotating for 10 minutes at 4°C.  Nuclei were pelleted at 300g for 10 min at 4°C, and subsequently processed fol-lowing the reported protocol with the adjustment of adding 3µg/ml cytochalasin B into all solutions for chromatin preparation and sonication, antibody incubation, and wash steps.  Chromatin was then sonicated for 15 cycles (30 sec, high power; 30 sec pause; 500µl volume) in a water bath sonicator set at 4°C (Bioruptor 300; Dia-genode, Denville, NJ).  After centrifuging at 10000g for 10 minutes at 4°C, sheared chromatin was checked on agarose gel for a shear band comprised between ~150 and ~600bp. Two µg of chromatin was kept for pooled input controls, whereas ~50µg chromatin were used for each pull-down reaction in a final volume of 2ml rotating at 4°C overnight. Primary antibody: mouse monoclonal ANTI-FLAG M2 (#F1804, Sigma-Aldrich, St. Louis, MO). Chromatin complexes were precipitated with 100µl Dynabeads M-280 (sheep anti-mouse #11202D; Thermo Scientific, Waltham, MA).  After washes and elution, samples were treated with proteinase K (cat #19131; Qiagen, Hilden, Germany) at 55°C and cross-linking was reversed through overnight incubation at 65°C. DNA was purified using the MinElute puri-fication kit (cat #28004; Qiagen, Hilden, Germany), quantitated using Qubit reader and reagents.
Library preparation and sequencing were conducted at the CCHMC DNA sequencing Core. Up to 30 ng of post-Immunoprecipitation dsDNA as measured by Invitrogen™ Qubit™ high- sensitivity spectroﬂuorometric measurement was made into Illumina-compatible NGS libraries using the ThruPLEX® DNA-Seq kit from Takara Bio Inc.
Each created library was dual-indexed with 8-base molecular barcodes for high level mul5plexing. Libraries were made with 13 cycles of PCR ampliﬁcation.

value: heart

value: male

value: prednisone


title: klf15 IP heart+pred single shot 3


title: klf15 IP heart+veh 3

value: vehicle


title: Pt48_Cancer

state: Maryland


title: Pt49_Cancer


title: vehicle, vehicle, 2wks of daily loading, rep7,cancellous bone,L [C83]


title: vehicle, vehicle, 2wks of daily loading, rep10,cancellous bone,Right [C87]


title: vehicle, vehicle, 2wks of daily loading, rep8,cortical bone,L [C84]


title: input IP heart+veh

value: pooled


title: klf15 IP heart+veh 1


title: klf15 IP heart+pred single shot 1


title: sample20_striatum, 1 hour

source_name: striatum, 1 hour

value: striatum

value: 1 hour


title: sample23_contralateral sensorimotor cortex, 24 hour


title: sample21_contralateral sensorimotor cortex, 24 hour


title: sample19_striatum, 1 hour


title: Pt47_Benign


title: Pt48_Benign


title: sample22_contralateral sensorimotor cortex, 24 hour


title: Pt47_Cancer


title: vehicle, vehicle, 2wks of daily loading, rep9,cancellous bone,Right [C79]


title: T_WT_3

city: Hefei

first: Shi

last: Yongjing

address: Jinzhai

data_processing:
TopHat v2.0.6.
The cDNA library was constructed using the SuperScript double‐stranded cDNA synthesis kit (Invitrogen, CA).
Trimmed reads were aligned to the mouse genome using TopHat v2.0.6.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Samples
Supplementary files format and content: tab-delimited text file includes RPKM values for each Samples

source_name: Tumor

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific, MA, USA).
RNA-seq library preparation and high-throughput sequencing were performed by Seqhealth Co., (Wuhan, China) using Novaseq 6000 sequencer (Illumina).

value: Tumor

value: NK cells

value: WT


title: klf15 IP heart+veh 2


title: Pt50_Cancer


title: sample18_striatum, 1 hour


title: vehicle, vehicle, 2wks of daily loading, rep7,cortical bone,L [C76]


title: Pt49_Benign


title: vehicle, vehicle, 2wks of daily loading, rep9,cortical bone,Right [C88]


title: Pt46_Benign


title: vehicle, vehicle, 2wks of daily loading, rep6,cancellous bone,L [C75]

value: cancellous bone


title: T_cKO_2

value: Conditional knock-out (cKO) of FBXO38


title: vehicle, vehicle, 2wks of daily loading, rep8,cortical bone,Right [C80]

value: Right

value: 28 wks


title: T_cKO_3


title: Pt46_Cancer


title: T_WT_2


title: sample16_ipsilateral sensorimotor cortex, 1 hour

source_name: ipsilateral sensorimotor cortex, 1 hour

value: ipsilateral sensorimotor cortex


title: Pt45_Cancer

value: Prostate


title: vehicle, vehicle, 2wks of daily loading, rep8,cancellous bone,Right [C71]


title: T_WT_1


title: sample15_ipsilateral sensorimotor cortex, 1 hour


title: Pt45_Benign


title: S_WT_3

source_name: Spleen

value: Spleen


title: Pt44_Cancer


title: vehicle, vehicle, 2wks of daily loading, rep6,cortical bone,L [C68]

value: cortical bone

value: L


title: sample14_ipsilateral sensorimotor cortex, 1 hour


title: S_WT_2


title: sample12_ipsilateral sensorimotor cortex, 1 hour


title: Pt44_Benign


title: vehicle, vehicle, 2wks of daily loading, rep5,cancellous bone,L [C67]


title: S_WT_1


title: sample11_ipsilateral sensorimotor cortex, 1 hour


title: sample17_striatum, 1 hour


title: vehicle, vehicle, 2wks of daily loading, rep6,cortical bone,Right [C64]


title: sample13_ipsilateral sensorimotor cortex, 1 hour


title: vehicle, vehicle, 2wks of daily loading, rep7,cortical bone,Right [C72]


title: S_cKO_3


title: S_cKO_2


title: T_cKO_1


title: Pt43_Cancer


title: vehicle, vehicle, 2wks of daily loading, rep7,cancellous bone,Right [C63]


title: Pt43_Benign


title: sample9_ipsilateral sensorimotor cortex, 1 hour


title: Pt42_Benign


title: S_cKO_1


title: sample10_ipsilateral sensorimotor cortex, 1 hour


title: vehicle, ALN-treated, 1wk of daily loading, rep5,cortical bone,Right [C56]

value: 27 wks


title: Pt42_Cancer


title: sample8_contralateral sensorimotor cortex, 1 hour

value: contralateral sensorimotor cortex


title: sample7_contralateral sensorimotor cortex, 1 hour


title: Pt41_Benign


title: vehicle, ALN-treated, 1wk of daily loading, rep7,cancellous bone,Right [C55]


title: Pt41_Cancer


title: Lvr_26_KD_9

city: California

first: Natalia

middle: Faraj

last: Murad

address: 500 Parnassus Ave

department: HemOnc

institute: University of California, San Francisco

description: liver keto diet 26 months

data_processing:
Data trimmed with trimmomatic, mapped to the reference genome with STAR and count matrix generated with RSEM.
Assembly: GRCm38
Supplementary files format and content: Normalized counts in a tab delimited file.

source_name: liver

extract_protocol:
For in vivo sequencing, RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research) following the manufacturer’s protocol.
RNA integrity and concentrations were assessed using an Agilent Bioanalyzer. The library was prepared using the KAPA RNA HyperPrep Kit (Roche) and QIAseq FastSelect RNA Removal Kit (QIAGEN)

value: liver

value: keto diet - 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep9,cortical bone,L [C52]


title: sample6_contralateral sensorimotor cortex, 1 hour

value: 1 hour


title: Lvr_26_KD_16

description: liver keto diet 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep7,cancellous bone,L [C51]


title: vehicle, vehicle, 2wks of daily loading, rep5,cortical bone,L [C60]


title: Pt40_Cancer


title: sample5_contralateral sensorimotor cortex, 1 hour


title: Lvr_26_KD_12

description: liver keto diet 26 months


title: vehicle, vehicle, 2wks of daily loading, rep4,cancellous bone,L [C59]


title: sample3_contralateral sensorimotor cortex, 1 hour


title: Pt39_Benign


title: sample4_contralateral sensorimotor cortex, 1 hour


title: Lvr_26_KD_13

description: liver keto diet 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep4,cortical bone,Right [C48]


title: sample2_contralateral sensorimotor cortex, 1 hour


title: Pt39_Cancer


title: vehicle, ALN-treated, 1wk of daily loading, rep6,cancellous bone,Right [C47]


title: vehicle, ALN-treated, 1wk of daily loading, rep8,cortical bone,L [C44]


title: Lvr_26_KD_15

description: liver keto diet 26 months


title: Pt38_Cancer


title: Lvr_26_KD_11

description: liver keto diet 26 months


title: Lvr_26_CD_8

description: liver control diet 26 months

value: control diet - 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep6,cancellous bone,L [C43]


title: Lvr_26_KD_10

description: liver keto diet 26 months


title: Pt38_Benign


title: Pt37_Benign


title: Lvr_26_CD_7

description: liver control diet 26 months


title: Lvr_26_CD_6

description: liver control diet 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep5,cancellous bone,Right [C39]


title: Lvr_26_KD_14

description: liver keto diet 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep3,cortical bone,Right [C40]


title: Pt37_Cancer


title: Pt36_Cancer


title: Lvr_26_CD_5

description: liver control diet 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep7,cortical bone,L [C36]


title: sample1_contralateral sensorimotor cortex, 1 hour


title: vehicle, ALN-treated, 1wk of daily loading, rep5,cancellous bone,L [C35]


title: vehicle, ALN-treated, 1wk of daily loading, rep4,cancellous bone,Right [C31]


title: Pt35_Cancer


title: Lvr_26_CD_4

description: liver control diet 26 months


title: Pt35_Benign


title: Pt36_Benign


title: vehicle, ALN-treated, 1wk of daily loading, rep10,cortical bone,L [C28]


title: Lvr_26_CD_3

description: liver control diet 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep2,cortical bone,Right [C32]


title: Pt34_Cancer


title: neurons_bhb_lps_2

data_processing:
Adapters removal and QC with trimmomatic (standard options)
Mapping to the genome GRch38 ensembl with STAR aligner
Count matrix generated with RSEM
Assembly: GRch38
Supplementary files format and content: Tab delimited text file with raw counts

source_name: brain

extract_protocol:
RNA was isolated using the Quick-RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s protocol.
The library was prepared with the KAPA RNA HyperPrep Kit (Roche) and sequenced on a HiSeq 4000 (Illumina).

value: brain

value: primary

value: neurons


title: neurons_bhb_lps_3


title: MM.1S miR-7

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

country: Japan

institute: Akita univ.

hyb_protocol: As materials and methods for DNA microarray protocol version 6.7 (Agilent).

scan_protocol: Agilent G2600D SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intencity with 75%tile normalization.

source_name: MM.1S miR-7

growth_protocol: 48 h culture

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: RPMI1640 plus 10% FCS.

tag: cellline

tag: miRNA


title: Lvr_26_CD_2

description: liver control diet 26 months


title: Pt34_Benign


title: neurons_bhb_lps_1


title: Pt33_Benign


title: Br_26_KD_15

description: brain keto diet 26 months


title: Lvr_26_CD_1

description: liver control diet 26 months


title: PTH-pretreated, non-loaded, replicate 9,cortical bone,L [864]

value: 26 wks


title: neurons_lps_3

value: lps


title: neurons_lps_1


title: KMS-11 Scr

source_name: KMS-11 Scr

label_protocol: As materials and methods for DNA microarray protocol version 6.7 (Agilent).

value: Scr


title: MM.1S Scr

source_name: MM.1S Scr


title: KMS-11 miR-7

source_name: KMS-11 miR-7


title: Pt33_Cancer


title: neurons_bhb_3

value: bhb


title: Br_26_KD_14

description: brain keto diet 26 months


title: Br_26_KD_13

description: brain keto diet 26 months


title: vehicle, ALN-treated, 1wk of daily loading, rep4,cancellous bone,L [C27]

value: cancellous bone


title: Br_26_KD_168

description: brain keto diet 26 months


title: PTH-pretreated, non-loaded, replicate 8,cortical bone,Right [857]

value: Right


title: neurons_lps_2


title: neurons_bhb_1


title: neurons_bhb_2


title: PTH-pretreated, non-loaded, replicate 7,cortical bone,L [850]

value: cortical bone


title: Pt31_Cancer

value: Prostate


title: Pt32_Benign


title: Br_26_KD_10

description: brain keto diet 26 months


title: PTH-pretreated, non-loaded, replicate 8,cancellous bone,Right [856]


title: Pt31_Benign


title: Pt32_Cancer


title: PTH-pretreated, non-loaded, replicate 7,cancellous bone,l [849]

value: l


title: neurons_control_2

value: control


title: Br_26_KD_11

description: brain keto diet 26 months


title: PTH-pretreated, non-loaded, replicate 6,cortical bone,Right [843]


title: Br_26_KD_9

description: brain keto diet 26 months


title: Pt30_Cancer


title: neurons_control_1


title: PTH-pretreated, non-loaded, replicate 6,cancellous bone,Right [842]


title: Br_26_CD_8

description: brain control diet 26 months