title: EVs-Infected, Rep 3

city: Riverside

first: Emma

middle: H

last: Wilson

state: California

address: 3401 Watkins Dr

department: Biomedical Sciences

institute: University of California, Riverside

data_processing:
CLC Genomics Workbench v 24.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence and UMIs (unique molecular identifiers) with the miRNA workbench in CLC.
UMI free reads were mapped to miRbase (v 22) for the mouse genome in CLC.
Analysis and read count normalization were performed by DESeq2 (v 1.20.0)
Assembly: Mouse GRCm38 (Gencode)
Supplementary files format and content: tab-deliminited text file includes raw counts for each Sample
Supplementary files format and content: tab-deliminited text file includes normalized counts for each Sample

source_name: C57BL/6 embryos (E18-20) cortex

extract_protocol:
Primary cortical murine neurons were maintained in neurobasal medium sypplemented with 2% B-27, 0.5 mM  L-glutamine, and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C. Half of the neuronal cultures were infected with T. gondii at an MOI (multiplicity of infection) of 0.50, 8 days after culture. Neuronal supernatant was collected and filtered 9 days and 11 days after culture. Cultures were filtered through a 0.8 um filter and then spun at 500 g for 15 minutes at 4C and then again at 15,000 g for 20 minutes at 4C. EV miRNA was isolated with the exoRNAeasy Midi Kit (Qiagen, 77144) according to the manufacturer's protocol. RNA was harvested using Rneasy mini kit (Qiagen). 25 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA prep following manufacturer's protocol.

value: C57BL/6 embryos (E18-20) cortex

value: Primary neurons

value: WT

value: T. gondii


title: C2C12 Cells, Cycling, PSME3, replicate 3

status: Public on Apr 22 2025

type: SRA

city: Klosterneuburg

first: Kenneth

middle: David

last: Kuhn

address: Am Campus

country: Austria

institute: Institute of Science and Technology Austria

description:
Library name: Cycling_PSME3_r3
Cycling_PSME3_Comp_Peaks.bed

library_source: genomic

data_processing:
Reads were first cleaned by Trim Galore using automated adapter sequence detection. Reads were then mapped using Bowtie2 and then filtered for a MAPQ score of greater than 20. Peaks were called using MACS2 with the IgG sample used as a negative control for each condition (MFOLD bounds 5-50; 300 basepair band width; peak detection with q value and minimum FDR 0.05). Treatments and negative controls were not pooled for individual peak files (those with replicate names) and were pooled for all "comp" peak files. All peak files included are Broad Peak files generated by MACS2.
Assembly: mm10
Supplementary files format and content: Peak files are .bed format with the following columns (in order): Chrom. Start, End, Name, Score, Strand, ThickStart, ThickEnd, ItemRGB, BlockCount, BlockSizes, BlockStarts
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

growth_protocol: C2C12 cells were maintained in DMEM with 20% FBS and split every 48 hours, never being allowed to exceed 70% confluency. Cells were either in the growth stage (cycling) or grown to confluency, switched to DMEM plus 2% horse serum, and collected 48 hours thereafter (day 2).

extract_protocol:
CUT&RUN was performed according to the manufacturer's instructions using the Cell Signaling Technology CUT&RUN kit (#86652), except that cells were incubated with the primary antibody at room temperature for thirty minutes instead of at 4 C for a longer duration to reduce cell death.
Libraries were constructed according to the manufacturer's instructions using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645L) using the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S) as primers

treatment_protocol: Cycling cells were resuspended upon collection in 10% DMSO in FBS and frozen at -80C prior to performing CUT&RUN. Day 2 cells were subjected to other conditions to test the lability of PSME3 at the DNA. These cells were either frozen as cycling cells were, or collected fresh the day of the assay. In addition to this, cells were either used in their native state or were treated for five minutes at room temperature with 0.1% formaldehyde, followed immediately by quenching by bringing the solution to 12.5 mM glycine. When both crosslinking and freezing were performed, crosslinking was performed prior to freezing.

tag: cell line

tag: cell type

value: Myoblast

tag: treatment

value: Frozen, native

tag: antibody


title: wild type rep3

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

country: China

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the GRCz11 reference genome using the hisat2 version 2.1.0.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 0.485 (fold change >1.4) were considered to represent significantly differentially expressed genes (DEGs).
The pathway analysis of DEGs was performed using the Metascape webtool (www.metascape.org)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: polyA RNA

organism: Danio rerio

source_name: heart

extract_protocol:
For each sample, 15 adult ventricles were collected and placed in ice-cold perfusion buffer (130 mM NaCl, 5 mM KCl, 0.5 mM NaH2PO4, 10 mM HEPES, 10 mM Glucose, 10 mM 2,3-butanedionemonoxime, 10 mM taurine, 5 mM MgCl2, adjusting pH to 7.8 with NaOH). The ventricles were gently torn up, transferred, and digested in the digestion buffer (10 mg/ml protease, 30 μg/ml DNase I in perfusion buffer) for 3 h at 4℃ with constant gentle agitation by using a rotator. The digestion was then neutralized with 10% FBS (fetal bone serum) and the disassociated cells were filtered through a 100 μm-strainer to remove large clumps and pelleted at 500 x g for 10 min at 4℃. The pellet was re-suspended in Hank’s balance salt solution (HBSS). The disassociated cells were  gone through a 70 μm-strainer, and loaded on a Beckman Coulter MoFlo XDP system to sort for eGFP+ or DsRed+ cells. Either 6,000 eGFP+ or DsRed+ cells were sorted into lysis buffer (0.5% Triton X-100, 1 U/μl RNase inhibitor, 2.5 μM Oligo dT primer, 2.5 mM dNTP) on a Beckman Coulter MoFlo XDP system. After vortex and incubation for 3 min at 72℃, total mRNA was reverse-transcribed to cDNA using SuperScript II Reverse Transcriptase (Invitrogen, 18064014). cDNA was then amplified using KAPA HiFi HotStart ReadyMix (Huaruikang, kk2602) and purified using VAHTS DNA Clean Beads (Vazyme, N411).
1 ng cDNA per sample was used to generate library using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer’s instructions. In brief, 1 ng cDNA was fragmented using TruePrep Tagment Enzyme and then ligated with specific indexes. After amplification using TruePrep Amplify Enzyme, the cDNA library was purified using VAHTS DNA Clean Beads.

tag: tissue

value: heart

value: isolated primary cells

value: platelets

tag: genotype

value: wild ype

value: 1 days post heart amputation


title: C2C12 Cells, Cycling, PSME3, replicate 2

description:
Library name: Cycling_PSME3_r2
Cycling_PSME3_Comp_Peaks.bed


title: P5 SVZ, snRNAseq

city: Daejeon

first: Jeong Ho

last: Lee

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
Library name: 2470-V
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: SVZ

extract_protocol:
Fresh frozen human brain tissue was minced, followed by addition of lysis buffer consisting of phosphate-buffered saline (PBS) containing 0.2% Triton X-100, 1X protease inhibitor cocktail (Roche), 1 mM DTT, 0.2 U/μl RNasin® ribonuclease inhibitor (Promega), and 2% BSA. After mechanical digestion, samples were incubated for 5 minutes on ice and centrifuged for 5 minutes at 500 x g at 4 °C. The resulting pellet, containing cell nuclei, was resuspended in PBS containing 1 mM EDTA, 0.2 U/μl RNasin®, and 2% BSA, and then filtered through a 20-μm pluriStrainer Mini (pluriSelect). DAPI was added and DAPI+ nuclei were collected by FACS in PBS containing 1 U/μl RNasin® and 5% BSA. The nuclei solution was concentrated by centrifugation for 15 minutes at 1000 x g at 4 °C and resuspended in PBS containing 0.2 U/μl RNasin® and 1% BSA, after which nuclei were counted.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: SVZ

value: brain cells

tag: age

value: 71 years old

tag: Sex

value: female


title: Infiltrated Tumor, snRNAseq

description:
Library name: 2449-Tu
10x Genomics

source_name: Tumor

value: Tumor

value: 56 years old


title: C2C12 Cells, Day 2, fresh, crosslinked, H3K4me3

description: Library name: Day2_Fresh_Crosslinked_H3K4me3

value: Fresh, crosslinked


title: C2C12 Cells, Cycling, PSME3, replicate 1

description:
Library name: Cycling_PSME3_r1
Cycling_PSME3_Comp_Peaks.bed


title: EVs-Infected, Rep 1

country: USA

growth_protocol: Primary cortical murine neurons were maintained in neurobasal medium sypplemented with 2% B-27, 0.5 mM  L-glutamine, and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.

treatment_protocol: Half of the neuronal cultures were infected with T. gondii at an MOI (multiplicity of infection) of 0.50, 8 days after culture. Neuronal supernatant was collected and filtered 9 days and 11 days after culture. Cultures were filtered through a 0.8 um filter and then spun at 500 g for 15 minutes at 4C and then again at 15,000 g for 20 minutes at 4C. EV miRNA was isolated with the exoRNAeasy Midi Kit (Qiagen, 77144) according to the manufacturer's protocol.

value: C57BL/6 embryos (E18-20) cortex

value: Primary neurons


title: Infiltrated SVZ, snRNAseq

description:
Library name: 2449-V
10x Genomics


title: wild type rep1

value: wild type


title: EVs-Infected, Rep 2

value: WT

value: T. gondii


title: PBMC_Pie_Pre_RNA

city: New York City

first: Andrew

middle: Wayne

last: Daman

state: NY

address: 1300 York Avenue

department: Pathology

institute: Weill Cornell Medical College

description: Library name: PBMC_Pie_Pre_RNA

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the cell ranger software.
Paired-end ATAC-seq reads were quality trimmed using Trimmomatic.
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the consensus peak set was generated using the R package DiffBind. The consensus peakset was generated per celltype.
Assembly: hg38
Supplementary files format and content: h5ad anndata files for RNA and .tsv fragment files for ATAC

source_name: PBMC enriched for CD34+ cells

extract_protocol:
Cells were sorted into FACS buffer  using a BD Aria II.
The library was performed according to the manufacturers inscrutions (single cell 3' protocol 10x genomics)

treatment_protocol: Patients pre or post BCG adminsitration in the bladder, after 5 consequentive weekly doses

value: PBMC enriched for CD34+ cells

value: Pre-BCG Treatment


title: EVs-Uninfected, Rep 3


title: wild type rep2

value: heart

value: isolated primary cells

value: platelets


title: EVs-Uninfected, Rep 2


title: H1975 WT_1

city: Boston

first: Atrayee

last: Bhattacharya

state: Massachusetts

address: 450 Brookline Avenue

department: Medical Oncology

institute: DFCI

description: Library name: Sample1

data_processing:
Sequencing reads from each replicate were aligned to the human genome (GRCh38) using bwa-mem to generate sorted and deduplicated BAM files. Accessible chromatin regions were identified for each replicate using MACS3 in paired-end mode with an FDR threshold of 0.01
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: were cultured in RPMI1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA).

extract_protocol:
Nuclear lysis buffer was used to isoltae nuclei
50,000 cells were subjected to tagmentation reactions with 2.5 μL Tn5 Transposase (Illumina), purified with Qiagen MinElute PCR Purification Kit (Qiagen) and PCR amplified for 8–9 cycles. Quality of ATAC-seq libraries was confirmed with Bioanalyzer prior to sequencing.

value: Non Small Cell Lung Cancer


title: U3

city: Wuxi

first: Yuzheng

last: Huang

state: Jiangsu

address: 117 Meiyuan Yangxiang

institute: Jiangsu Institute of Parasitic Diseases

description: Library name: Sample9

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 50M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Then about 48M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCh38.p13
Supplementary files format and content: fpkm, raw counts for each Sample

growth_protocol: lx-2 cells were maintained in DMEM supplemented with 10% fetal bovineserum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Hepatic stellate cells

value: wide type

value: Uridine&TGF-β(Day 1)


title: C2C12 Cells, Cycling, H3K4me3, replicate 2

description:
Library name: Cycling_H3K4me3_r2
Cycling_H3K4me3_Comp_Peaks.bed

value: Myoblast

value: Frozen, native


title: EVs-Uninfected, Rep 1


title: U2

description: Library name: Sample8


title: T11.1

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
pt_npe.vs.pt_pe.results.csv.gz
t_npe.vs.pt_pe.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: GRCh38
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: buccal

growth_protocol: The Indiana University Health (IUH) Hospitals (Riley Hospital for Children, IUH Methodist, IUH North) and Franciscan Health, Indianapolis, Indiana, USA provided samples for the current study. Informed consent and HIPAA authorization was obtained from all participants prior to the clinical sample collection. The study protocol was approved by the Indiana University Institutional Review Board (IRB) #1901985132 and the Franciscan Institutional Review Board (IRB), #1489434. Informed consent and HIPAA authorization were obtained from all participants prior to sample collection. All study samples were collected approximately nine days following birth and stored at -20 ºC.

extract_protocol:
Frozen human buccal samples were thawed for analysis. Genomic DNA from buccal samples was prepared as follows: The buccal brush was suspended in 750 μl of cell lysis solution and 3.5 µl of Proteinase K (20 mg/ml). This suspension was incubated at 55 ºC for 3 hours, then vortexed and centrifuged briefly. The lysis solution was then transferred to a new 1.5 µl microcentrifuge tube. The microcentrifuge tube with the buccal brush was centrifuged again to retain any remaining solution which was combined with the transferred lysis solution. The buccal brush was discarded and 300 µl of protein precipitation solution (Promega, A795A, Madison, WI) was added to the lysis solution. The sample was incubated on ice for 15 minutes, then centrifuged at 4 ºC for 30 minutes. The supernatant was transferred to a fresh 2 mL microcentrifuge tube and 1,000 µl ice cold isopropanol was added along with 2 µL glycoblue. This suspension was mixed thoroughly and incubated at -20 ºC overnight. The suspension was then centrifuged at 4 ºC for 20 minutes, the supernatant was discarded, and the pellet was washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed. Individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 ºC, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP (immunoprecipitation) buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 ºC. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50 μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 ºC. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2 μl of glycoblue (20 mg/ml), 20μl of 5M NaCl and 500 μl ethanol were added and mixed well, then precipitated in -20 ºC freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000 rpm for 20 min at 4 ºC and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500 μl cold 70% ethanol in -20 ºC freezer for 15 min then centrifuged again at 14,000 rpm for 5 min at 4 ºC and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20 μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: Maternal samples were categorized by gestation at delivery, hypertensive disorders of pregnancy, and maternal diabetes. The case group consisted of preterm deliveries (<37 weeks gestation) and maternal preeclampsia. The control groups consisted of term deliveries (≥37 weeks gestation) with no maternal preeclampsia, and preterm deliveries (<37 weeks gestation) with no preterm preeclampsia.

tag: sample number

tag: birth timing

value: preterm

tag: preeclampsia status

value: preeclampsia

value: buccal


title: C2C12 Cells, Cycling, H3K4me3, replicate 1

description:
Library name: Cycling_H3K4me3_r1
Cycling_H3K4me3_Comp_Peaks.bed


title: C2C12 Cells, Cycling, H3K4me3, replicate 3

description:
Library name: Cycling_H3K4me3_r3
Cycling_H3K4me3_Comp_Peaks.bed


title: T44.1

value: term

value: non-preeclampsia


title: T95.1


title: U1

description: Library name: Sample7


title: 786-O-LM ATAC Rep2

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
The data was analyzed as described previously (https://doi.org/10.1016/j.molcel.2020.01.009). GSEA analysis and GO analysis were performed by using the WebGestalt (WEB-based Gene SeT AnaLysis Toolkit).
Assembly: hg19
Supplementary files format and content: DESeq2 files show the direct output from DESeq2 between RNA-seq comparisons.
Supplementary files format and content: VST expression files contain the variance stabilizing transformation (VST)-corrected read counts for each gene.
Supplementary files format and content: ATAC-seq bigwigs contain the genome-wide, read-depth normalized ATAC-seq signal.

source_name: cell line

growth_protocol: The cell lines used in this study were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM,Gibco) high glucose medium supplemented with 10% fetal bovine serum (FBS) and 1%penicillin/streptomycin unless specifically indicated. The normal kidney cell line HK-2 was grownin keratinocyte serum-free medium (K-SFM, Gibco). The PDX cell lines, acquired from Dr. James Brugarolas’s lab at UT Southwestern, were grown in DMEM high glucose supplemented with 10% FBS, 1% Pen/Strep, 1X MEM Non-essential amino acids (Gibco, 11140050), 0.01µg/ml EGF (Bio-Techne, 236-EG), and 0.4µg/ml Hydrocortisone (STEMCELL, 07925). All cells werecultured in a humidified incubator at 37°C with 5% CO2. All cells were tested negative for mycoplasma by using the mycoplasma detection kit (Lonza, LT07–218) or mycoplasmaelimination reagent-plasmocin (Invivogen, ant-mpt).

extract_protocol:
Sample preparation for the assay of transposase-accessible chromatin with sequencing (ATAC-seq) was performed according to the Manual of the ATAC-seq Kit (Active Motif, 53150). Briefly, cells were collected, pelleted, and resuspended in ATAC lysis buffer.
Cells were pelleted again, followed by tagmentation reaction in the master mix and purification by applying DNA purification binding buffer and column. Tagmented DNA was amplified by PCR using the i5/i7 indexed primer, followed by sequencing at the Next Generation Sequencing core facility in UT Southwestern.

treatment_protocol: The mice with orthotopic injection of 786-O cells were sacrificed at week-8. Kidney primary tumors and lung mets tissue were collected, washed with cold PBS and chopped with sterile razor blade/scissors, followed by incubation with 1mg/ml collagenase (type 4) in serum-free DMEM media for 1~2h at 37°C with shaking. Tissues were pelleted (200g, 3min), washed with PBS, resuspended with trypsin EDTA for 5 min at 37°C, pelleted and rewashed, filtered through the 100µm EZFlow cell strainer, pelleted and resuspended in DMEM medium supplemented with 10% FBS and 2% pen/strep, and cultured in the incubator for several passages to yield purified 786-O cells. The cells isolated from primary tumor were indicated as 786-O-P, while the cells isolated from the lung were 786-O-LM.

value: cell line

tag: location

value: Lung metastasis


title: T3

description: Library name: Sample6

value: TGF-β(Day 1)


title: Tet3_cKO_RNAseq_rep2

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

institute: Albert Einstein College of Medicine

description: Library name: Tet3_cKO_RNAseq_rep2

data_processing:
Adaptors were trimmed using trim galore (v0.6.7) and trimmed reads were mapped to the mouse genome (mm39) using STAR (v2.7.9a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Assembly: mm39
Supplementary files format and content: CSV

source_name: Lin– bone marrow cells

extract_protocol:
RNA was extracted from Lin– using RNeasy micro kit.
Libraries were prepared by Novogene (https://en.novogene.com/).

value: Lin– bone marrow cells

value: Tie2+/cre; Tet3F/F


title: 786-O-LM ATAC Rep1


title: T4.1


title: Tet3_cKO_RNAseq_rep1

description: Library name: Tet3_cKO_RNAseq_rep1


title: P4 SVZ, snRNAseq

description:
Library name: 2459-V
10x Genomics

value: SVZ

value: brain cells

value: 76 years old

value: male


title: 786-O-P ATAC Rep2

value: Primary site


title: T73.1


title: T35.1


title: Tet3_control_RNAseq_rep1

description: Library name: Tet3_control_RNAseq_rep1


title: Tet3_control_RNAseq_rep2

description: Library name: Tet3_control_RNAseq_rep2


title: T2

description: Library name: Sample5

value: Hepatic stellate cells

value: wide type


title: 786-O-P ATAC Rep1


title: T22.1

value: preterm


title: C2

description: Library name: Sample2


title: MCHTB362 Section_C200_2Bb

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description: FFPE Spatial transcriptomic sequencing

data_processing:
FASTQ files were processed with 10x Genomics Spaceranger pipeline v.2.0.0
Spaceranger outputs were then processed using VR-Omics workflow
Assembly: GRCh38
Supplementary files format and content: h5: processed gene count matrix and metadata
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: VROmics.tar.gz: input directory for VR-Omics software
Library strategy: Spatial Transcriptomics

source_name: cardiac rhabdomyoma

extract_protocol:
Tissues were embedded in FFPE and sectioned to 10 micron thickness
Spatial transcriptomics sequencing libraries were prepared according to 10x Genomics Visium Spatial Gene Expression Slides & Reagents kit according to manufacturer's instructions

value: cardiac rhabdomyoma

tag: patient


title: C3

description: Library name: Sample3


title: C1

description: Library name: Sample1


title: PT416M

value: preeclampsia

value: buccal


title: MCHTB362 Section_C200_2C

description: FFPE Spatial transcriptomic sequencing


title: MCHTB302_C200_3

description: FFPE Spatial transcritpomic sequencing


title: MCHTB362 Section_C200_2Ba

description: FFPE Spatial transcriptomic sequencing


title: Tet3_cKO_EMseq_rep2

description: Library name: Tet3_cKO_EMseq_rep2

data_processing:
The negative control lambda DNA mapping rate was <1%. pUC19 mapping rate was >80% confirming reaction efficiency. Adaptors were trimmed using trim galore (v0.6.7) and trimmed reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine was extracted with bismark_methylation_extractor. DMR analysis was done using the methpipe package following the methpipe manual.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files for DNA methylation and hydroxymethylation were generated using bedGraphToBigWig, and used to generate line plots and heatmaps with plotProfile and plotHeatmap.Hyper DMR peaks were annotated with the R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bed files
Library strategy: EM-seq

extract_protocol:
DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit.
Libraries were prepped using the NEBNext EM-seq kit.


title: PT412M


title: Tet3_cKO_EMseq_rep1

description: Library name: Tet3_cKO_EMseq_rep1


title: Tet3_control_EMseq_rep2

description: Library name: Tet3_control_EMseq_rep2


title: H1975, Hypoxia, miRNA

city: Changchun

first: Kun

last: Liu

address: 1266 Fujin Road, Chaoyang District, Changchun City, Jilin Province, China

institute: Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University

description:
Library name: Sample 4
H1975-Hypoxia
miRNA-counts.txt
miRNA-TPM.txt

data_processing:
The libraries were sequenced on the Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. About RNA-seq raw reads for each sample were generated. Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads. About RNA-seq clean reads for each sample were retained for subsequent analyses.  The clean reads were mapped to the human genome (GRCh38) using HISAT2.FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq count.
The libraries were finally sequenced using the llumina NovaSeq 6000 platform. The small RNA sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China). The basic reads were converted into sequence data (also called raw data/reads) by base calling. Low quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt or longer than 41 nt from the raw data were filtered, and the clean reads were obtained.  For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and so on. These RNAs were aligned and then subjected to the Bowtie search against Rfam v.10.1 (http://www.sanger.ac.uk/software/Rfam). The known miRNAs were identified by aligning against miRBase v22 database (http://www.mirbase.org/), and the known miRNA expression patterns in different samples were analyzed. After that, unannotated reads were analyzed by mirdeep2 to predict novel miRNAs. Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence and miRNA mature sequence were also identified.
Assembly: the human genome (GRCh38) used for read alignment
Supplementary files format and content: "mRNA-counts.xls" include raw counts for each RNA-seq Sample
Supplementary files format and content: "miRNA-counts.xls" include raw counts for each miRNA-seq Sample
Supplementary files format and content: "mRNA-FPKM.xls" include FPKM values for each RNA-seq Sample
Supplementary files format and content: "miRNA-TPM.xls" include TPM values for each miRNA-seq Sample

growth_protocol: H1975 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
For RNA, total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. 4 μg total RNA of each sample was used for the RNA library construction. For miRNA, total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. 1 μg total RNA of each sample was used for the miRNA library construction.
RNA libraries for RNA-seq were prepared TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. And RNA libraries for miRNA-seq were prepared using TruSeq Small RNA Sample Prep Kits (Cat. No.RS-200-0012, Illumina, USA.) following the manufacturer’s recommendations.

treatment_protocol: For hypoxic culture, H1975 cells were transferred to a hypoxic incubator with mixed gas and cultured for 24 h (gas ratio was N2:O2:CO2 = 94:1:5)

value: lung adenocarcinoma cells

value: WT

value: Hypoxia


title: PT410M


title: PT426M

value: term

value: non-preeclampsia


title: H1975, NC, miRNA

description:
Library name: Sample 3
H1975-NC
miRNA-counts.txt
miRNA-TPM.txt

value: Normoxia


title: MCHTB362 Section_C200_2Ab

description: FFPE Spatial transcriptomic sequencing


title: Tet3_cKO_EhmCseq_rep2

description: Library name: Tet3_cKO_EhmCseq_rep2

data_processing:
The negative control lambda DNA mapping rate was <1%. T4 mapping rate was >80% confirming reaction efficiency. Adaptors were trimmed using trim galore (v0.6.7) and trimmed reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine was extracted with bismark_methylation_extractor. DhmR analysis was done using the methpipe package following the methpipe manual.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files for DNA methylation and hydroxymethylation were generated using bedGraphToBigWig, and used to generate line plots and heatmaps with plotProfile and plotHeatmap. HypoDhMR peaks were annotated with the R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bed files
Library strategy: E5hmC-seq

extract_protocol:
DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit.
Libraries were prepped using the NEBNext E5hmC-seq kit.

value: Lin– bone marrow cells

value: Tie2+/cre; Tet3F/F


title: MCHTB362 Section_C200_2Aa

description: FFPE Spatial transcriptomic sequencing


title: H1975, Hypoxia

description:
Library name: Sample 2
H1975-Hypoxia
mRNA-counts.txt
mRNA-FPKM.txt


title: PT433M


title: Tet3_cKO_EhmCseq_rep1

description: Library name: Tet3_cKO_EhmCseq_rep1


title: MCHTB361 Section C200_1C

description: FFPE Spatial transcriptomic sequencing


title: PT441M


title: MCHTB361 Section C200_1B

description: FFPE Spatial transcriptomic sequencing


title: MCHTB361 Section C200_1A

description: FFPE Spatial transcriptomic sequencing


title: EVs-Infected, Rep 3

data_processing:
R Studio v 4.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim galore (v 0.6.7) (parameters: --fastqc --gzip --trim-n  -j ${NUM_CORES} -o ${TRIMGALORE_DIR} --basename ${SAMPLENAME})
Trimmed sequence reads were mapped to GRCm39 vM34 using STAR (v 2.7.11a) (parameters: --runThreadN ${NUM_CORES} --runMode alignReads --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${STAR_DIR}/${SAMPLENAME}_ --genomeDir ${INDEX} --outFilterMismatchNmax 0 --outFilterMultimapNmax 1 --quantMode GeneCounts --outWigType wiggle)
Read count extraction were performed by featureCounts (v 1.5.0-p3) (parameters: -T ${NUM_CORES} -s ${STRANDED} -a ${GTF} -t exon -g gene_id --primary -o ${FEATURECOUNTS_DIR}/${SAMPLENAME}.fcnts.txt)
Analysis and read count normalization were performed by DESeq2 (v 1.20.0)
Assembly: Mouse GRCm39 (Gencode) vM34
Supplementary files format and content: tab-deliminited text file includes raw counts for each Sample
Supplementary files format and content: tab-deliminited text file includes normalized counts for each Sample

source_name: C57BL/6 pups (P0-3) cortex

growth_protocol: Primary cortical murine astrocytes were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids, 1% L-glutamine, 1% HEPES, and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 25 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA prep following manufacturer's protocol.

treatment_protocol: One day after plating 100 nM of dexamethasone was added to all the wells, except the no dexamethasone media control, for 24 hours before the addition of the experimental groups. For the EV groups 2ug/mL were added and 100 ng/mL and 100 U/mL for LPS/IFNy.

value: C57BL/6 pups (P0-3) cortex

value: Primary astrocytes

value: Dexamethasone


title: PT425M


title: H1975, NC

description:
Library name: Sample 1
H1975-NC
mRNA-counts.txt
mRNA-FPKM.txt


title: Tet3_control_EhmCseq_rep2

description: Library name: Tet3_control_EhmCseq_rep2


title: Tet3_control_EMseq_rep1

description: Library name: Tet3_control_EMseq_rep1


title: Tet3_control_EhmCseq_rep1

description: Library name: Tet3_control_EhmCseq_rep1


title: MCHTB302_C200_4

description:
FFPE Spatial transcriptomic sequencing
MCHTB302_joint.h5 and MCHTB302_Joint_Clustering_VROmics.tar.gz represent MCHTB302 Joint Clusters of Sections C200_2 and C200_4


title: RCC243-tdTomato, Capsule Tumour

city: Toronto

last: Ohh

state: Ontario

address: 661 University Avenue

department: Department of Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

description: RCC243-tdTomato Renal Capsule Tumour

data_processing:
The submitted samples were processed at the Princess Margaret Genomic Centre using the 10X Genomics Chromium Single Cell 3' Reagent Kit (v3.1) user guide.
Briefly, viability and cell count were first confirmed using a haemocytometer and then the Chromium Next GEM Chip G was used to generate the GEMs with the sample.
A thermal cycler was used to generate the sample cDNA and then subsequent purificaiton and amplification was used to construct the cDNA library.
The sample was then sequenced with the Micro Flow Cell and the Illumina MiSeq platform for an estimated cell count and targeted number of reads that would be used for sequencing with the S2 Flow Cell and Illumina NovaSeq 6000.
FASTQ files were then generated and processed using the GRCh38-2020-A reference transcriptome and Cell Ranger version 6.0.0.
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger pipeline files (processed tsv and mtx files) that includes the filtered feature-barcode matrices used for subsequent analysis

source_name: Mouse Kidney

growth_protocol: RCC243/RCC243-tdTomato cells were cultured in IMDM supplemented with 10% FBS on collagen-coated plates at 5% CO2, 2% O2, and at 37°C (from Huang, R. et al. 2021). These cells were used for the renal capsule injections (orthotopic models) and for the tail vein or intracardiac injections (metastatic models) in NOD/SCID-γ mice. One million RCC243 or RCC243-tdTomato cells were used for the renal capsule injection as a 1:1 PBS to Matrigel mixture. Whereas 500,000 or 100,000 RCC243-tdTomato cells in PBS were used for the tail vein or intracardiac injections, respectively.

extract_protocol:
Briefly, the tumours were excised from the mouse models and mechanically and enzymatically dissociated using a mixture of IMDM, collagenase, protease, and DNase I. The cell suspension was then filtered and the enzymatic dissociation was stopped through the addition of cold 10% FBS in PBS. The cells were pelleted and ACK lysing buffer was added to lyse the red blood cells in the solution. The suspension was then washed, centrifuged, and re-suspended in cold 2% FBS in HBSS to check cell viability. Afterwards, the cell suspension was blocked and stained with mouse H2K-biotin, mouse CD45-biotin, and mouse CD31-biotin antibody. The cells were then washed and anti-biotin microbeads were added before being washed again. The cells were then labeled with Avidin-PE-Cy7 and then filtered for magnetic-activated cell sorting. The unlabeled human cells were acquired and checked for viability before sending the cells for single-cell RNA-sequencing.
The libraries were prepared based on the Single Cell 3' Reagent Kits v3.1 user guide

value: Mouse Kidney

value: Patient primary tumour derived ccRCC cells (from Lobo, N.C. et al. 2016) isolated after tumour dissociation using magentic-activated cell sorting

value: VHLmut (from Lobo, N.C. et al. 2016)


title: PT424M


title: EVs-Infected, Rep 2


title: MCHTB302_C200_2

value: cardiac rhabdomyoma


title: T1

description: Library name: Sample4

value: Hepatic stellate cells

value: wide type

value: TGF-β(Day 1)


title: RCC243, Patient-Derived Xenograft

description: RCC243 Patient-Derived Xenograft Renal Capsule Tumour

value: Patient-derived xenograft cells (from Lobo, N.C. et al. 2016)


title: RCC243-tdTomato, Lung Metastatic Tumour (Intracardiac Injection)

description: RCC243-tdTomato Metastatic Intracardiac Injection Tumour

source_name: Mouse Lungs

value: Mouse Lungs


title: PT437M

value: term

value: buccal


title: EVs-Infected, Rep 1

value: WT


title: MCHTB302_C200_1

description: FFPE Spatial transcriptomic sequencing


title: RCC243, Capsule Tumour

description: RCC243 Renal Capsule Tumour


title: PT421M

value: non-preeclampsia


title: 786-O sgHLF RNA Rep3

extract_protocol:
Total RNA was extracted by using the RNeasy® Mini Kit (Qiagen, 74106) according to corresponding handbook, and RNase-Free DNase Set (Qiagen, 79254) was applied for on-column digestion of DNA during RNA purification.
The library preparation, quality control, and sequencing were performed by the Novogene Corporation.

treatment_protocol: For lentiviral plasmids, 293T cells were used for virus production by co-transfection of the psPAX2 (Addgene, 12260) and pMD2.G (Addgene, 12259) in Opti-MEM with the addition of Lipofectamine 3000. 0.45 µm filters were then applied during the virus collection step. Cells were seeded in 6-well plates for 30-50% confluency, and 200 µl virus per well was added while 6-8µg/mL polybrene was used to increase infection efficiency. Media were replaced after 12-24h infection, and cells were cultured for another 1~2 days followed by an appropriate antibioticselection (Puromycin 2 µg/mL for sgRNA/shRNA plasmids, Blasticidin 10 µg/mL for pLX-304 backbone plasmids, G418 800 µg/mL for pInducer-20 backbone plasmids).

value: cell line

value: CRISPR-Cas9 treatment wih sgHLF (HLF targeting gRNA)

tag: hlf status

value: KO


title: EVs-Uninfected, Rep 2

value: C57BL/6 pups (P0-3) cortex

value: Primary astrocytes

value: Dexamethasone


title: PT436M


title: RCC243-tdTomato, Lung Metastatic Tumour (Tail Vein Injection)

description: RCC243-tdTomato Metastatic Tail Vein Injection Tumour

value: Patient primary tumour derived ccRCC cells (from Lobo, N.C. et al. 2016) isolated after tumour dissociation using magentic-activated cell sorting

value: VHLmut (from Lobo, N.C. et al. 2016)


title: PT440M


title: 786-O sgHLF RNA Rep1


title: PT432M


title: 786-O sgHLF RNA Rep2


title: PT417M

value: preterm


title: LPS/IFNy, Rep 3


title: EVs-Uninfected, Rep 1


title: LPS/IFNy, Rep 1


title: EVs-Uninfected, Rep 3


title: PT408M


title: 786-O sgCtrl RNA Rep2

value: CRISPR-Cas9 treatment wih sgCtrl (non-targeting gRNA)


title: HK-217 cells 0 Gy Control

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

description:
Library name: HK_217-MXC017_0Gy
10x Genomics

data_processing:
FASTQ files were aligned to a custom reference containing the human genome (GRCh38) and processed using the PIPseeker software, version 3.3.3 (Fluent Biosciences). Raw matrices were in processed in Seurat version 5 20. Cells with less than 500 genes were filtered out and cells with high mitochondrial gene count (>5%) were removed.
Assembly: human genome (hg38)
Supplementary files format and content: FASTQ and matrix files

source_name: patient-derived cell line

growth_protocol: Patient-derived HK-217 gliomaspheres were cultured in serum-free conditions in ultra-low adhesion plates in DMEM/F12, supplemented with SM1 Neuronal Supplement, EGF, bFGF and heparin.

extract_protocol:
At day 5, the gliomaspheres in the suspension culture were collected and dissociated with TrypLE (no phenol red), and the adherent differentiated cells were washed with HBSS and de-attached with Trypsin/EDTA. The cells were then pooled and filtered through a 40-µm strainer and counted with a hemacytometer. The samples were pelleted by centrifugation at 300 g for 5 minutes at 4°C, resuspended in the provided Cell Resuspension Buffer (Fluent Bioscience, Watertown, MA), and 50,000 cells were targeted for capture and processed for single-cell transcriptomics using the PIPseqTM T2 3’ Single Cell RNA Kit V5 (Fluent Biosciences).
Sequencing libraries were prepared according to PIPseq T2 instructions, with 12 cycles for cDNA amplification and 8 cycles for library amplification, depending on the DNA amount. The libraries were quantified using a Qubit 4 Fluorometer and a TapeStation 4200 and sequenced as per manufacturer recommendation on a NovaSeq X Plus – 25B 2 x150bp, with 3.25 billion reads in total for 8 samples.

treatment_protocol: HK-217 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.

value: Glioblastoma

value: control


title: 786-O sgCtrl RNA Rep3


title: HK-217 cells irradiated

description:
Library name: HK_217-MXC017_RT
10x Genomics


title: HK-217 cells RT + MXC-017 treated

description:
Library name: HK_217-MXC017_RT_MXC017
10x Genomics


title: Media, Rep 3


title: SW620 cells, activation screen, T20 0.38µM oxaliplatin

city: Bethesda

first: Robert

last: Robey

state: MD

address: 37 Convent Drive Rm 2112

institute: NCI

description:
Library name: Sample 13
Column name in SW620_oxaliplatin_Activation.count_normalized.txt: 0.38_OXAL
SW620_oxaliplatin_Activation.count.txt
SW620_oxaliplatin_Activation.count_normalized.txt

data_processing:
Sequencing reads were processed using Cutadapt v4.0. Low-quality bases (quality score <10) were trimmed from the 3′ end, and Illumina adapter sequences were removed from the 5′ end. Reads shorter than 20 bp after trimming were discarded. Downstream analysis was performed using the MAGeCK v0.5.7 algorithm. sgRNA reads were aligned to the respective pooled sgRNA library (Calabrese or Brunello) using the MAGeCK count function. Oxaliplatin-treated samples were compared to T0 or T20 untreated controls using the MAGeCK test function, with non-targeting sgRNAs used for count normalization, to generate ranked lists of gene hits.
Assembly: Calabrese or Brunello pooled sgRNA libraries
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

growth_protocol: SW620 cells were cultured in RPMI Medium + 10% FBS, 1% Pen/Strep, and 1% Glutamine. RKO cells were cultured in EMEM Medium + 10% FBS, 1% Pen/Strep, and 1% Glutamine. All cells were grown at 37oC with 5% CO2 in a humidified environment.

extract_protocol:
At least 1 × 10^9 cells were collected and genomic DNA was extracted using the QIAmp DNA blood Cell Maxi Kit (Qiagen).
sgRNA sequences were amplified using Taq polymerase (Takara Bio, Inc.) and adapted for sequencing. The desired DNA product was purified with 6% TBE gel (Invitrogen) and subjected to massive parallel amplicon sequencing carried out by an Illumina sequencer (Sanger/Illumina 1.9).

treatment_protocol: Cells were transduced with Cas9 or dCas9-VP64 and selected with blasticidin. Cells were transduced with either the Brunello and Calabrese libraries (MOI ~0.3), and selected with puromycin for 3 days. Cells were either left untreated or treated with oxaliplatin for 20 days.

value: colorectal cancer cells

value: dCas9-VP64, Calabrese sgRNA library

value: 0.38µM oxaliplatin

tag: time

value: Day 20


title: PT411M

value: non-preeclampsia

value: buccal


title: PT409M


title: LPS/IFNy, Rep 2

value: WT


title: SW620 cells, activation screen, T20 0.5µM oxaliplatin

description:
Library name: Sample 14
Column name in SW620_oxaliplatin_Activation.count_normalized.txt: 0.50_OXAL
SW620_oxaliplatin_Activation.count.txt
SW620_oxaliplatin_Activation.count_normalized.txt

value: 0.5µM oxaliplatin


title: HK-217 cells MXC-017 treated

description:
Library name: HK_217-MXC017_MXC017
10x Genomics


title: SW620 cells, activation screen, T20 untreated

description:
Library name: Sample 12
Column name in SW620_oxaliplatin_Activation.count_normalized.txt: T20
SW620_oxaliplatin_Activation.count.txt
SW620_oxaliplatin_Activation.count_normalized.txt


title: Media, Rep 2

value: C57BL/6 pups (P0-3) cortex


title: RKO cells, activation screen, T20 oxaliplatin

description:
Library name: Sample 11
Column name in RKO_oxaliplatin_Activation.count_normalized.txt: OXAL
RKO_oxaliplatin_Activation.count.txt
RKO_oxaliplatin_Activation.count_normalized.txt

source_name: RKO

value: RKO

value: 1.9µM oxaliplatin


title: PT402M


title: 786-O Lentivirus HLF (Overexpression) RNA Rep3

value: cell line

value: Lentiviral infection with pLX304-V5-HLF

value: Overexpression


title: Media, Rep 1

value: Primary astrocytes

value: Dexamethasone


title: 786-O sgCtrl RNA Rep1

value: CRISPR-Cas9 treatment wih sgCtrl (non-targeting gRNA)


title: 786-O Lentivirus HLF (Overexpression) RNA Rep1


title: RKO cells, activation screen, T20 untreated

description:
Library name: Sample 9
Column name in RKO_oxaliplatin_Activation.count_normalized.txt: T20
RKO_oxaliplatin_Activation.count.txt
RKO_oxaliplatin_Activation.count_normalized.txt

value: colorectal cancer cells


title: Media without Dexamethasone, Rep 3


title: PT403M

value: preterm


title: Media without Dexamethasone, Rep 2


title: 786-O Lentivirus Empty Vector RNA Rep3

value: Lentiviral infection with pLX304-V5


title: 786-O Lentivirus Empty Vector RNA Rep2


title: PT400M


title: Media without Dexamethasone, Rep 1


title: SW620 cells, KO screen, T20 untreated

description:
Library name: Sample 8
Column name in SW620_oxaliplatin_KO.count_normalized.txt: T20
SW620_oxaliplatin_KO.count.txt
SW620_oxaliplatin_KO.count_normalized.txt

value: Cas9, Brunello sgRNA library

value: Day 20


title: RKO cells, activation screen, T0 untreated

description:
Library name: Sample 7
Column name in RKO_oxaliplatin_Activation.count_normalized.txt: T0
RKO_oxaliplatin_Activation.count.txt
RKO_oxaliplatin_Activation.count_normalized.txt

value: dCas9-VP64, Calabrese sgRNA library

value: Day 0


title: PE485M

description:
pt_npe.vs.pt_pe.results.csv.gz
t_npe.vs.pt_pe.results.csv.gz

value: preeclampsia

value: buccal


title: CD3+ T cells isolated from tumor, treated with PBS, rep2

first: Xiaozhe

last: Yin

address: Room A305, Building Zhengyutong, Tsinghua University

institute: Tsinghua University

description:
T_gene_expression
T_C_1_R1.fastq.gz

data_processing:
The clean reads were mapped to the genome using HISAT2 (v2.0.4). The expression level of a gene was calculated by RSEM (v1.2.12). The RNA-Seq raw data were processed through the standard RNA-Seq analysis pipeline. Differential-expression analysis was carried out with DESeq2 version 1.24.0 (http://bioconductor.org/about/removed-packages/) in R v.3.3.1 (http://cran.r-project.org/).
Assembly: GRCm39
Supplementary files format and content: tab-delimited csv file includes RPKM values and raw counts for each Sample in DC group
Supplementary files format and content: tab-delimited csv file includes RPKM values and raw counts for each Sample in T group

source_name: MC38 tumor-bearing mice

extract_protocol:
Total RNA extraction, mRNA library construction, and sequencing were established by BGI.
Total RNA extraction, mRNA library construction, and sequencing were established by BGI.

treatment_protocol: DCs and TILs were isolated from MC38 tumor–bearing mice 72 h after the second treatment.

value: MC38 tumor

value: CD3+ T cells isolated from tumor

value: PBS


title: 786-O Lentivirus HLF (Overexpression) RNA Rep2

value: cell line

value: Lentiviral infection with pLX304-V5-HLF


title: PE483M


title: SW620 cells, KO screen, T20 0.38µM oxaliplatin

description:
Library name: Sample 4
Column name in SW620_oxaliplatin_KO.count_normalized.txt: OXAL038
SW620_oxaliplatin_KO.count.txt
SW620_oxaliplatin_KO.count_normalized.txt

value: 0.38µM oxaliplatin


title: SW620 cells, KO screen, T20 0.5µM oxaliplatin

description:
Library name: Sample 6
Column name in SW620_oxaliplatin_KO.count_normalized.txt: OXAL050
SW620_oxaliplatin_KO.count.txt
SW620_oxaliplatin_KO.count_normalized.txt

value: 0.5µM oxaliplatin


title: Pt79_24hr

city: Hampton

first: Eric

last: Lewallen

state: Virginia

address: 130 William R. Harvey Way

department: Biological Sciences

institute: Hampton University

description:
DEseq2_output_MO_24hr_vs_MO_3mo.txt
DEseq2 output_MO_0hr_vs_MO_24hr.txt

data_processing:
Raw data were uploaded to the Galaxy web platform (usegalaxy.org)
Cutadapt
RNA STAR
MultiQC
featureCounts
MultiQC
DESeq2
Assembly: hg_g1k_v37
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample
Supplementary files format and content: tab-delimited text file includes DESeq2 output for Monocyte 0hr versus T cell 0hr
Supplementary files format and content: tab-delimited text file includes DESeq2 output for Monocyte 0hr versus Monocyte 24hr
Supplementary files format and content: tab-delimited text file includes DESeq2 output for Monocyte 0hr versus Monocyte 3mo
Supplementary files format and content: tab-delimited text file includes DESeq2 output for Monocyte 24hr versus Monocyte 3mo

source_name: whole blood

extract_protocol:
Qiagen RNeasy
Whole blood was collected before the onset of surgery (t0), at 24 hours (t24hr), and during a final follow-up occurring at three months (t3m). Monocytes were separated from other peripheral blood cell types using a Ficoll-Hypaque density gradient. Monocytes were further purified by removal of B cells, NK cells and T cells using the negative separation technique. RNA was isolated from MO samples using commercial kits and protocols (Qiagen, Germantown, MD). The integrity of each RNA sample was validated using the Agilent 2100 Bioanalyser System (Agilent Technologies, Santa Clara, CA). The Next-Generation Sequencing Core at the University of Pennsylvania assisted with generating barcoded libraries. They also provided RNA-seq data using an Illumina NovaSeq 6000.

value: whole blood

value: Monocytes

tag: time point

value: 24 Hours


title: CD3+ T cells isolated from tumor, treated with X-Ray+ O-IMDQ, rep1

description:
T_gene_expression
T_I_1_R1.fastq.gz

value: X-Ray+O-IMDQ


title: RKO cells, KO screen, T20 untreated

description:
Library name: Sample 3
Column name in RKO_oxaliplatin_KO.count_normalized.txt: T20
RKO_oxaliplatin_KO.count.txt
RKO_oxaliplatin_KO.count_normalized.txt

value: RKO

value: colorectal cancer cells

value: Cas9, Brunello sgRNA library


title: PT407M

value: preterm

value: non-preeclampsia


title: Pt21_24hr


title: PE480M

value: buccal


title: PE484M

value: preeclampsia


title: RKO cells, KO screen, T20 oxaliplatin

description:
Library name: Sample 5
Column name in RKO_oxaliplatin_KO.count_normalized.txt: OXAL
RKO_oxaliplatin_KO.count.txt
RKO_oxaliplatin_KO.count_normalized.txt

value: 1.9µM oxaliplatin

value: Day 20


title: SW620 cells, activation screen, T0 untreated

description:
Library name: Sample 10
Column name in SW620_oxaliplatin_Activation.count_normalized.txt: T0
SW620_oxaliplatin_Activation.count.txt
SW620_oxaliplatin_Activation.count_normalized.txt

value: dCas9-VP64, Calabrese sgRNA library

value: Day 0


title: Pt44_24hr


title: DCs isolated from tumor, treated with X-Ray+ O-IMDQ, rep1

description:
DC_gene_expression
DC_I_4_R1.fastq.gz

value: MC38 tumor

value: DCs isolated from tumor


title: PE482M


title: Pt89_24hr

value: whole blood


title: DCs isolated from tumor, treated with PBS, rep2

description:
DC_gene_expression
DC_C_1_R1.fastq.gz

value: PBS


title: Mixture transcriptomic sequencing of young leaf, mature leaf, root, stem, flower

city: Kunming

first: Jindan

last: Wang

state: Yunnan

address: Lanhei road

institute: Kunming Institute of Botany, Chinese Academy of Sciences

description: Library name: S.br_transcriptome

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic  v 0.39
Aligning clean data to a reference genome using HISAT2 v 2.2.1
Assembling the aligned reads to obtain the assembled transcripts and FPKM values using Stringtie2 v 2.2.1 (parameter: -A)
The differentially expressed genes (DEGs) were identified by DESeq2  v 1.32.0
analysing AS events  using SUPPA2  v 2.3 (default)
analysing APA sites using LAPA v 0.0.5
Assembly: Sabra_v2
Supplementary files format and content: tab file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each organ
Supplementary files format and content: gtf files include annotation information for each Sample
Supplementary files format and content: csv files include FPKM values for DEGs
Supplementary files format and content: ioe files include different AS events
Supplementary files format and content: bed files include polyA sites

organism: Salix brachista

source_name: mix

extract_protocol:
Total RNA was extracted from 21 individual samples across seven organs using the Plant RNA Kit, and then reverse transcribed into cDNA, which was amplified by PCR to generate the cDNA libraries.
RNA libraries for RNA-seq were prepared in accordance with the specifications of the Illumina NovaSeq 6000 platform.

value: mix

value: tissue


title: 786-O Lentivirus Empty Vector RNA Rep1

value: cell line

value: Lentiviral infection with pLX304-V5

value: WT


title: SW620 cells, KO screen, T0 untreated

description:
Library name: Sample 2
Column name in SW620_oxaliplatin_KO.count_normalized.txt: T0
SW620_oxaliplatin_KO.count.txt
SW620_oxaliplatin_KO.count_normalized.txt

value: colorectal cancer cells

value: Cas9, Brunello sgRNA library


title: Pt74_24hr

value: Monocytes

value: 24 Hours


title: PE477M

value: preterm

value: non-preeclampsia

value: buccal


title: monoecious flower,rep3

description: Library name: S21G0304

source_name: flower

value: flower


title: RKO cells, KO screen, T0 untreated

description:
Library name: Sample 1
Column name in RKO_oxaliplatin_KO.count_normalized.txt:T0
RKO_oxaliplatin_KO.count.txt
RKO_oxaliplatin_KO.count_normalized.txt

value: RKO

value: Day 0


title: Pt21_3m

description:
DEseq2_output_MO_0hr_vs_MO_3mo.txt
DEseq2 output_MO_24hr_vs_MO_3mo.txt

value: whole blood

value: 3 Months


title: PE476M


title: monoecious flower,rep2

description: Library name: S21G0303


title: Pt79_3m


title: Pt49_3m


title: PE470M


title: Pt44_3m


title: PE479M

value: preeclampsia


title: Pt51_0hr

description:
DEseq2_output_MO_0hr_vs_MO_3mo.txt
DEseq2 output_MO_0hr_vs_MO_24hr.txt


title: male flower,rep2

description: Library name: S21G0300

value: tissue


title: male flower,rep3

description: Library name: S21G0301


title: PE471M


title: PE467M


title: PE474M


title: 14d, biological rep3

type: RNA

city: Fujisawa

first: Yoshinao

last: Oki

state: Kanagawa

address: 1866 Kameino

department: Department of Applied Biological Science

country: Japan

institute: Nihon University College of Bioresource Sciences

description: Gene expression data from DFAT grew to semiconfluence

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The data were analyzed with RMA using R/Bioconductor.

label: biotin

source_name: Liver after 14-day 70% partial hepatectomy in mice.

label_protocol: 5 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: liver


title: PE475M


title: 7d, biological rep3

description: Gene expression data from AC derived from fat tissue

source_name: Liver after 7-day 70% partial hepatectomy in mice.


title: male flower,rep1

description: Library name: S21G0299


title: 14d, biological rep1


title: monoecious flower,rep1

description: Library name: S21G0302


title: 14d, biological rep2


title: female flower,rep3

description: Library name: S21G0297


title: 7d, biological rep1


title: stem,rep3

description: Library name: S21G0298

source_name: stem

value: stem


title: PE469M


title: M_Pt74_0hr

description:
DEseq2_output_MO_0hr_vs_T_0hr.txt
DEseq2_output_MO_0hr_vs_MO_3mo.txt
DEseq2 output_MO_0hr_vs_MO_24hr.txt


title: M_Pt70_0hr


title: PE465M


title: M_Pt89_0hr


title: PE464M


title: Pt51_3m


title: root,rep3

description: Library name: S21G0294

source_name: root

value: root


title: M_Pt79_0hr


title: Pt106_3mo_1

value: T cells


title: mature leaf,rep3

description: Library name: S21G0296

source_name: leaf

value: leaf


title: young leaf,rep3

description: Library name: S21G0295


title: PE462M

source_name: buccal


title: stem,rep2

description: Library name: S21G0293


title: 7d, biological rep2


title: PE463M


title: 4d, biological rep3

source_name: Liver after 4-day 70% partial hepatectomy in mice.


title: female flower, rep2

description: Library name: S21G0292


title: Pt104_3mo_1


title: Pt70_3mo


title: 4d, biological rep2


title: 4d, biological rep1


title: 3d, biological rep3

source_name: Liver after 3-day 70% partial hepatectomy in mice.


title: PE461M


title: 3d, biological rep2


title: PE459M


title: young leaf,rep2

description: Library name: S21G0290


title: PE460M


title: mature leaf,rep2

description: Library name: S21G0291


title: T_pt67_0hr


title: root,rep2

description: Library name: S21G0289


title: T_pt140_0hr


title: PE458M


title: 3d, biological rep1


title: T_pt104_0hr


title: 2d, biological rep3

source_name: Liver after 2-day 70% partial hepatectomy in mice.


title: stem,rep1

description: Library name: S21G0288


title: root,rep1

description: Library name: S21G0287


title: T_pt106_0hr


title: T_pt53_0hr


title: 2d, biological rep1


title: mature leaf,rep1

description: Library name: S21G0286


title: A87886

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS-UCD1.2) using the miRDeep2 package (version 2.00.8), the miRDeep2 quantifier module was used to quantify all expressed miRNAs in the sequence data, producing read counts for each individual sample.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Hypothalamic arcuate nucleus

growth_protocol: Holstein-Friesian bull calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-12 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.0 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
total RNA was  precipitated and purified from hypothalamic arcuate nucleus samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates.

value: Hypothalamic arcuate nucleus

value: Holstein-Friesian

value: Moderate


title: 1d, biological rep2

source_name: Liver after 1-day 70% partial hepatectomy in mice.


title: 1d, biological rep3


title: A73759


title: A97821


title: PC3_cell

city: Phoenix

first: Kendall

last: Van Keuren-Jensen

state: AZ

address: 445 N. 5th Street

institute: Translational Genomics Research Institute

description: EVs not isolated

data_processing:
fastq files were generated using bcl2fastq v2.19.1.403
Reads were trimmed with cutadapt v2.7
Trimmed fastqs were aligned to the GRCh38 genome with STAR v2.6.1d using the following parameters: --runMode alignReads --outSAMtype BAM Unsorted --outSAMmode Full --outSAMstrandField intronMotif --outFilterType BySJout --outSAMunmapped Within --outSAMmapqUnique 255 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignMatesGapMax 1000000 --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 18 --alignSJDBoverhangMin 18 --chimSegmentMin 18 --chimJunctionOverhangMin 18 --outSJfilterOverhangMin 18 18 18 18 --alignTranscriptsPerReadNmax 50000
Aligned reads were counted with featureCounts v1.6.3 using a genome annotation combined from GENCODE 29 and LNCipedia 5.2
.txt files produced for individual samples were aggregated into a single .txt file using python
Assembly: human genome GRCh38
Supplementary files format and content: A single tab delimited .txt file containing raw counts for each sample

source_name: Prostate

growth_protocol: PC3 cells were grown in Dulbecco's Modified Eagle Medium and supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 1% PenStrep.

extract_protocol:
RNA was extracted with Trizol and harvested using Clontech's SMARTer Stranded Total RNA-Seq Kit
RNA libraries were prepared using the SMARTerPicov2 kit

value: Prostate

value: prostate cancer epithelial cells


title: young leaf,rep1

description: Library name: S21G0285


title: PC3_100K_set3

description: 100K spin


title: 1d, biological rep1


title: A61973


title: female flower, rep1

description: Library name: S21G0284

value: flower


title: wKD_rep2, dme ovary, smallRNA-seq

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads. Small RNA reads that passed quality control and minimal length filter (>18 nt) were mapped to the reference genome (BDGP assembly R6/dm6), and miRNAs sequences of miRbase by bowtie2. To identify piRNAs, we used reads with a length from 24 to 29 nt. The Rsamtools package was used to process bam files. FeatureCounts was used to calculate the read counts.
Assembly: dme6
Supplementary files format and content: tab-delimited text files include counts for each Sample

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt).
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2013 PMID: 23665228). Sequencing was performed on the Illumina HiSeq1500 platform.

value: ovary

value: germline knockdown white_sh (#30033, VDRC)


title: PC3_10K_set3

description: 10K spin


title: A61965


title: wKD_rep1, dme ovary, smallRNA-seq


title: Calu-3 cells, SD, 100nM, 3rd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling. The raw reads were trimmed of low-quality bases using a FASTX-Toolkit (v.0.0.13;   http://hannonlab.cshl.edu/fastx_toolkit/).  Then the clean reads were evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Clean reads were aligned to the human GRch38 genome by tophat2 (Kim, Pertea et al. 2013) allowing 4 mismatches. Uniquely mapped reads were ultimately used to calculate read number and fragments per kilobase of exon model per pillion mapped fragments (FPKM) for each gene. The expression levels of genes were evaluated using FPKM.
The software edgeR (Robinson, McCarthy et al. 2010) , which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥1.5 or ≤0.37) and p-value (p-value ≤ 0.01) to determine whether a gene was differentially expressed.
To systematically analyze the lncRNA expression pattern, we used a pipeline for lncRNAs identification similar as previously reported (Liu, Wang et al. 2017), which was constructed based on the cufflinks software (Trapnell, Roberts et al. 2012).
We predicted circRNAs with our data by utilizing the find_circ (version 1.2) software with default parameters (Memczak, Jens et al. 2013). Differentially expressed genes and circRNAs between the paired groups were analyzed by using TCC (Sun, Nishiyama et al. 2013) in R packages. For each gene, significance p-value and FDR were obtained based on the model of negative binomial distribution. Fold changes of gene expression were also estimated within the edgeR statistical package. The criterion for DEcircR has been set as |fold change| > 2 and FDR < 0.05.  TCC parameters: norm.method = "tmm", test.method = "edger",iteration = 3, floorPDEG = 0.05
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes read counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: lung

growth_protocol: Calu-3 cells line (Procell Life Science & Technology Co., Ltd.,China) were cultured at 37℃ with 5% CO2 in MEM with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
The selected treatment Calu-3 cells were subjected to total RNA extraction using TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-Zero Gold rRNA Removal Kit (human/mouse/rat)(N406-01, Vazyme) and remained RNAs were fragmented and purified, and converted into double strand cDNA. After end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). After purification, ligation products corresponding to 200 ~ 500 BPS were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified, and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared for following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: Calu-3 cells treated with spike protein for 24h with different concentrations of 0nM, 1nM, 5nM, 10nM, 20nM, 50nM, 100nM, and 500nM.  Then we added 0.75 μM actinomycin D (A4262, sigma) for 12h, and detected apoptosis with flow cytometry (Cytoflex, Beckman) using double-stained with APC-conjugated Annexin V and 7-aminoactinomycin D (4A Biotech Co. Ltd., Beijing, China) according to the manufacturer's protocol.

value: lung

value: treated with spike protein at concentration of 100nM


title: A57826


title: PC3_100K_set2

description: 100K spin


title: PC3_10K_set2

description: 10K spin


title: Ars2KD_rep2, dme ovary, smallRNA-seq

value: germline knockdown Ars2_sh1 (#106344, VDRC)


title: Calu-3 cells, SD, 100nM, 2nd


title: Ars2KD_rep1, dme ovary, smallRNA-seq


title: A51980


title: Calu-3 cells, SD, 100nM, 1st


title: 0d, biological rep1

source_name: Liver after 0-day 70% partial hepatectomy in mice.


title: 0d, biological rep2


title: PC3_2_8K_set2

description: 2.8K spin


title: PC3_100K_set1

description: 100K spin


title: A57867


title: A47874


title: wKD_rep2, dme ovary, chromRNA-seq

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads.The STAR splice-aware aligner was used to map the reads to the reference genome (BDGP assembly R6/dm6). The Rsamtools package was used to process bam files. FeatureCounts was used to calculate the read counts for gene (Ensembl) and repeat databases (RepeatMasker) prepared by biomaRt package.
Assembly: dme6
Supplementary files format and content: tab-delimited text files include counts for each Sample
Library strategy: chromRNA-seq

extract_protocol:
Chromatin-associated RNA was extracted as descirbed in (Chen et al 2016, PMID: 27292797).
cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Reaction of tagmentation was performed in according to previously published protocol (Picelli et al. 2014 PMID: 25079858) using in-house produced Tn5 charged with oligonucleotides compatible with the Illumina system. Sequencing was performed on the Illumina HiSeq1500 platform.


title: PC3_2_8K_set3

description: 2.8K spin


title: Calu-3 cells, SD, 0nM, 3rd

value: control plasmid


title: A47825


title: A97854


title: A41971


title: Ars2KD_rep2, dme ovary, chromRNA-seq

value: germline knockdown Ars2_sh2 (#22575, VDRC)


title: Calu-3 cells, SD, 0nM, 2nd


title: 2d, biological rep2

value: liver


title: PC3_10K_set1

description: 10K spin


title: Calu-3 cells, SD, 0nM, 1st


title: 0d, biological rep3


title: A38765


title: Ars2KD_rep1, dme ovary, chromRNA-seq


title: A21978


title: ptth,young-female,rep2

city: Ames

first: Ping

last: Kang

state: Iowa

address: 3266 Molecular Biology Building 2437 Pammel Drive

department: GDCB

institute: Iowa State University

data_processing:
The reference genome and gene model annotation files were downloaded from genome website. STAR (2.7.3a) was used to generate the index of the reference genome and the mapping of the raw sequencing reads
The gene expression level was quantify by htseq (0.11.2)
The differential expression analysis is performed by DESeq2(1.20.0)
Assembly: Drosophila_melanogaster.BDGP6.22.98
Supplementary files format and content: "Female_normalized_counts.xlsx" file includes the normalized reads count of each gene for each sample.

source_name: Whole body

extract_protocol:
For RNA extraction. using Trizol method and following by DNase treatment(Ambion). RNA concentration was quantified by Qubit RNA BR Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA Catalog number: Q10210). RNA-Seq libraries were constructed using 300 ng of total RNA and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA. Catalog number: E7420). RNA concentrations were measured using Qubit RNA BR Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA Catalog number: Q10210). Poly(A) mRNA was isolated using NEBNext Oligo d(T)25 beads and fragmented into 200 nt in size. After first strand and second strand cDNA synthesis, each cDNA library was ligated with a NEBNext adaptor and barcoded with an adaptor-specific index. Twelve libraries were pooled in equal concentrations, and sequenced using Illumina HiSeq 3000 platform (single-end, 50 bp reads format).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the cDNA was synthesized using random hexamer primers.  The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Whole body

value: female

value: young


title: ptth,young-female,rep1


title: A12937

value: Hypothalamic arcuate nucleus


title: WOB,young-female,rep3

value: wOB


title: wKD_rep1, dme ovary, chromRNA-seq


title: A93760

value: Holstein-Friesian

value: High


title: 158ABc

type: genomic

city: Zurich

first: Holger

last: Moch

address: Schmelzbergstrasse 12

department: Institute of Pathology and Molecular Pathology

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
EaCon, ASCAT
Merged Merged AT and GC data

source_name: FFPE Tumour

label_protocol: Affymetrix protocol

extract_protocol: Maxwell FFPE Tissue DNA Purification

value: Kidney (ccRCC)


title: 156ABc


title: WOB,young-female,rep1


title: A92928


title: 155ABc


title: 157ABc


title: WOB,young-female,rep2


title: ptth120BC2,1~3h hours after emerging ,rep2

data_processing:
The raw sequencing reads were processed through Novogene's in-house perl script to remove low quality reads
The reference genome and gene model annotation files were downloaded from genome website. Hisat2 (v2.0.5) was used to generate the index of the reference genome and the mapping of pair-end reads
The gene expression level was quantify by FeatureCounts (v1.5.0-p3)
The differential expression analysis is performed by DESeq2R package (1.20.0)
The clusterProfiler R package was used for the Gene Ontology (GO) and KEGG enrichment analysis of differential gene expression. The protein-protein interaction network is constructed
Assembly: Drosophila_melanogaster.BDGP6.46
Supplementary files format and content: "gene_fpkm.xls" is the excel table that includes the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene for each sample.

extract_protocol:
The samples were transferred to 1.7 ml centrifuge tube with a stainless-steel ball and 500ml Trizol. A0 was collected on the CO2 and transferred to a 1.7 ml centrifuge tube with a stainless-steel ball and 500ml Trizol. Tissuelyzer was used to smash the flies. About 15 pupa or flies were used in a biological replicate. Three biological replicates for each time points per genotype(wild type and Ptth mutants). RNA was sent to NOVOGENE for library and sequence after the total RNA was treated with DNase by the Turbo DNA-free kit (Invitrogen by Thermo Fisher Scitific, AM1907).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the cDNA was synthesized using random hexamer primers.  The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

tag: developmental stage

value: 1~3h hours after emerging


title: PC3_2_8K_set1

description: 2.8K spin

value: Prostate

tag: cell line

value: prostate cancer epithelial cells


title: ptth120BC2,1~3h hours after emerging ,rep3


title: 154ABc


title: 159ABc


title: ptth120BC2,1~3h hours after emerging ,rep1


title: A81983


title: 160ABc


title: A77860


title: A47858


title: A93744


title: ptth120BC2,4-day pupa(p4),rep3

value: 4-day pupa(p4)


title: 153ABc


title: A42931


title: 152ABc


title: ptth120BC2,4-day pupa(p4),rep2


title: ptth120BC2,4-day pupa(p4),rep1


title: 151ABc


title: A37840


title: A37824


title: 150AB


title: ptth120BC2,3-day pupa(p3),rep3

value: 3-day pupa(p3)


title: 149AB


title: A31979


title: ptth120BC2,3-day pupa(p3),rep2


title: A27864


title: ptth120BC2,3-day pupa(p3),rep1


title: 146AB


title: ptth120BC2,2-day pupa(p2),rep2

value: 2-day pupa(p2)


title: A27823


title: A27848


title: ptth120BC2,2-day pupa(p2),rep1


title: 148AB


title: A13745


title: 147AB


title: 143AB


title: ptth120BC2,2-day pupa(p2),rep3


title: 144AB


title: ptth120BC2,1-day pupa(p1),rep3

value: 1-day pupa(p1)


title: LL_M2_DG_ATAC

first: David

middle: A

last: Talmage

address: 35 Convent Dr, Room 3B-101

department: NINDS

institute: National Institutes of Health

description: 10x Multiome_ATAC

library_source: genomic single cell

data_processing:
Cell Ranger
Seurat - RNA (refer to manuscript for details)
Signac & Seurat - ATAC (refer to manuscript for details)
Assembly: Mm10
Supplementary files format and content: barcodes.tsv.gz- text file includes all barcodes from the experiment
Supplementary files format and content: features.tsv.gz- text file includes all Gene ID names
Supplementary files format and content: matrix.mtx.gz- raw feature barcode matrix file. The rows represent features, genes and peaks detected, while the columns consist of all barcodes that were detected in the experiment
Supplementary files format and content: atac_cut_sites.bigwig file contains a track of the smoothed transposition sites across the genome.

source_name: Brain

extract_protocol:
Fresh frozen microdissected DG tissue samples were processed according to the 10x Genomics nuclei extraction kit to obtain single nucleus suspensions.
Library construction was conduced according to manufacturer instructions using the snMultiome (snATAC-seq+snRNA-seq) kit.

value: Brain

tag: brain region

value: Dentate Gyrus

value: Male

value: LL

value: Homozygous V321L mutant


title: 141ABc


title: ptth120BC2,1-day pupa(p1),rep2

value: Whole body


title: LL_M1_DG_ATAC

description: 10x Multiome_ATAC

tag: treatment


title: LL_F2_DG_ATAC

description: 10x Multiome_ATAC

value: Female


title: 140ABc


title: A17855

value: Hypothalamic arcuate nucleus

value: Holstein-Friesian


title: 139ABc

value: Kidney (ccRCC)


title: ptth120BC2,white pupa(p0),rep3

value: white pupa(p0)


title: LL_F1_DG_ATAC

description: 10x Multiome_ATAC


title: ptth120BC2,white pupa(p0),rep2


title: 137ABc


title: VV_M2_DG_ATAC

description: 10x Multiome_ATAC

value: VV

value: Wild-type


title: 138AB


title: Autism patient (ASD) 29

city: Cairo

first: Amal

last: Mohamed

address: El-Bohooth

department: Human Cytogenetics

country: Egypt

institute: National Research Centre

description: Hybridization to SNP

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: We use Affymetrix fluidic station for wash and stain microchips.We used Affymetrix scanner 3000

data_processing: We use ChAS software to analyse the generated cell files

label: Biotin

source_name: Blood sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nano Quant instrumentation (Applied Biosystems), and agarose gel electrophoresis.

tag: disease state

value: ASD


title: ptth120BC2,white pupa(p0),rep1

tag: tissue


title: 135ABc


title: VV_M1_DG_ATAC

description: 10x Multiome_ATAC

tag: genotype


title: ptth120BC2,L3-120h-AEL,rep3


title: VV_F2_DG_ATAC

description: 10x Multiome_ATAC


title: 134ABc


title: ptth120BC2,1-day pupa(p1),rep1


title: ptth120BC2,L3-120h-AEL,rep2


title: VV_F1_DG_ATAC

description: 10x Multiome_ATAC


title: ptth120BC2,L3-120h-AEL,rep1


title: Autism patient (ASD) 20

description: Hybridization to SNP


title: 133ABc


title: Autism patient (ASD) 38

description: Hybridization to SNP


title: Autism patient (ASD) 34

description: Hybridization to SNP


title: ptth120BC2,L3-96h-AEL,rep3


title: LL_M2_DG_GEX

description: 10x Multiome_GEX


title: 132ABc


title: LL_M1_DG_GEX

description: 10x Multiome_GEX


title: 131ABc


title: Autism patient (ASD) 33

description: Hybridization to SNP


title: Autism patient (ASD) 28

description: Hybridization to SNP


title: LL_F2_DG_GEX

description: 10x Multiome_GEX


title: 129ABc


title: ptth120BC2,L3-96h-AEL,rep2


title: ptth120BC2,L3-96h-AEL,rep1


title: Autism patient (ASD) 35

description: Hybridization to SNP


title: Autism patient (ASD) 25

description: Hybridization to SNP


title: Autism patient (ASD) 30

description: Hybridization to SNP


title: 128ABc


title: LL_F1_DG_GEX

description: 10x Multiome_GEX


title: wOB,1~3h hours after emerging ,rep3

value: 1~3h hours after emerging

value: wOB


title: VV_M2_DG_GEX

description: 10x Multiome_GEX


title: Autism patient (ASD) 23

description: Hybridization to SNP


title: 123ABc


title: wOB,1~3h hours after emerging ,rep2


title: Autism patient (ASD) 27

description: Hybridization to SNP


title: VV_M1_DG_GEX

description: 10x Multiome_GEX


title: Autism patient (ASD) 24

description: Hybrisization to SNP


title: VV_F2_DG_GEX

description: 10x Multiome_GEX


title: 122ABc


title: Autism patient (ASD) 21

description: Hybridization to SNP


title: VV_F1_DG_GEX

description: 10x Multiome_GEX


title: 127ABc


title: 120ABc


title: wOB,4-day pupa(p4),rep2

value: 4-day pupa(p4)


title: Autism patient (ASD) 26

description: Hybrisdization to SNP


title: Autism patient (ASD) 19

description: Hybridization to SNP


title: Autism patient (ASD) 17

description: Hybridization to SNP


title: Autism patient (ASD) 16

description: Hybridization to SNP


title: wOB,4-day pupa(p4),rep1


title: PEDV_Jejunum

city: Harbin

first: Yanan

address: 600 Changjiang Road, Xiangfang District, Harbin City

institute: Northeast Agricultural University

description: Library name: sample 2

data_processing:
Read Alignment
Quality Control
Normalization and Clustering
Differential Expression Analysis
Assembly: Sus scrofa reference genome (Sscrofa11.1)
Supplementary files format and content: Gene expression matrix in sparse Matrix Market format (.mtx.gz)
Supplementary files format and content: Gene annotation file (.tsv.gz)
Supplementary files format and content: Cell barcode file (.tsv.gz)

organism: Sus scrofa

source_name: Jejunum

extract_protocol:
Total RNA was extracted from pooled jejunum tissues using the TRIzol reagent (Invitrogen, USA) following the manufacturer's protocol.
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3.1 Kit according to the manufacturer's protocol. Briefly, high-quality total RNA was converted to cDNA, which was then fragmented and amplified. Gel beads containing barcoded oligonucleotides were used to capture and label single cells. After reverse transcription, barcoded cDNA was amplified by PCR, followed by library construction. The constructed libraries were assessed for quality using an Agilent 2100 Bioanalyzer and quantified by Qubit Fluorometer (Thermo Fisher Scientific). Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

value: Jejunum

value: PEDV-infected


title: 117ABc


title: Control_Jejunum

description: Library name: sample 1

value: control


title: Taproot and lateral roots, drought stress, degradome, biol rep 3

city: Poznań

first: Paulina

last: Kościelniak-Wawro

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology, Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

description: Library name: TR_LR-DS-D_rep3

data_processing:
Raw sequencing data underwent rigorous preprocessing, beginning with adapter trimming and quality filtering using Cutadapt, with minimum length thresholds set at 20 nucleotides for mRNA and 15 nucleotides for miRNA. Quality assessment was performed using FastQC, followed by alignment to the Quercus robur PM1N reference genome using HISAT2 for transcriptome data and Bowtie/ShortStack for miRNA analysis.
Assembly: Qrob_PM1N.fa.gz (https://urgi.versailles.inra.fr/download/oak/)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Quercus robur

source_name: root

growth_protocol: The study utilized Quercus robur L. seedlings grown from acorns obtained from the National State Forests' storage facility in Jarocin, Poland. Seedlings were cultivated using two distinct methods: in specialized rhizotron systems consisting of 30 × 50 cm transparent chambers with 2-3 cm spacing between plexiglass plates, and in conventional containers measuring 18 cm deep by 50 mm wide with a volume of 0.275 dm³. Both cultivation systems employed a standardized growth substrate composed of a 5:1 volumetric ratio of peat to perlite, supplemented with dolomite for pH adjustment and a slow-release fertilizer (Osmocote 15-9-12-2 N-P-K-Mg) at a concentration of 2.5 kg/m³. After one year of growth, container-grown seedlings were transplanted into rhizotrons to simulate natural field transplantation conditions. All plants were maintained in a semi-closed foil greenhouse at the Institute of Dendrology, Polish Academy of Sciences in Kórnik, Poland, with an automated irrigation system featuring drainage mechanisms to prevent waterlogging.

extract_protocol:
Meristematic zones from both taproots and lateral roots were collected from all experimental groups (control and drought-stressed plants from both cultivation methods). Total RNA was extracted using Total RNA Purification Kits from Norgen Biotek, followed by additional purification with RNA Clean-Up and Concentration Kits. RNA quality was rigorously assessed through three complementary methods: concentration measurement via Nanodrop spectrophotometry, integrity evaluation by agarose gel electrophoresis, and precise quality scoring using an Agilent 2100 Bioanalyzer, with only samples achieving RNA Integrity Numbers (RIN) greater than 8 proceeding to library construction.
High-quality RNA samples were processed into cDNA libraries using the TruSeq Stranded mRNA LT Sample Prep Kit, followed by sequencing on an Illumina NovaSeq platform configured for 150 bp paired-end reads for transcriptome, 50 bp single-end reads for miRNA and 50 bp single-end reads for degradome. The sequencing strategy encompassed comprehensive profiling of mRNA transcripts, miRNA molecules, and degradome fragments, with a minimum sequencing depth of 20 million reads per sample to ensure robust data acquisition. All library preparations and sequencing runs were performed in triplicate to guarantee experimental reproducibility.

treatment_protocol: Following an 8-week acclimatization period under optimal watering conditions from April to June, transplanted container seedlings were subjected to controlled drought stress for 4 weeks during the peak summer period. The treatment involved reducing soil moisture to 25% of control levels by restricting water availability to the lower quarter of the rhizotron depth, encouraging taproot growth into deeper soil layers. Environmental conditions were meticulously monitored using SM150 soil moisture sensors at 15 cm and 45 cm depths, with surface temperature recorded by HOBO Pro v2 monitoring systems (average temperatures: 23.44°C at soil surface, 20.48°C at 2m height). Plant physiological responses were tracked through daily chlorophyll fluorescence measurements using a Pocket PEA fluorimeter, with particular focus on PSII efficiency parameters (Fo/Fm, Fv/Fm, Fv/Fo) and the comprehensive Performance Index (PI) to determine the onset of severe photosynthetic stress.

value: root

value: wild-type

value: drought stress


title: Autism patient (ASD) 12

description: Hybridization to SNP


title: Autism patient (ASD) 18

description: Hybridization to SNP


title: wOB,3-day pupa(p3),rep3

value: Whole body

value: 3-day pupa(p3)


title: Taproot and lateral roots, drought stress, degradome, biol rep 2

description: Library name: TR_LR-DS-D_rep2


title: 112ABc


title: 118ABc


title: YS602_mH69_Control_rep1

city: Urbana

first: Hong

last: Jin

state: Illinois

address: 600 S Mathews Ave

department: Biochemistry

institute: University of Illinois at Urbana-Champaign

description: Library name: YS602_mH69_Control_rep1

data_processing:
Adapters were trimmed from sequenced reads using cutadapt v1.18 and barcodes were split using fastx barcode splitter in the Fastx-toolkit.
Unique molecular identifiers (UMI) were extracted and deduplicated using UMI tools v1.01.
Reads were aligned to the Saccharomyces cerevisiae.R64-1-1.107 reference genome (Ensemble) by STAR v2.7.3a.
BedGraph profiles and RNA content were separated by bedtools v2.29.2 and SAMtools v1.10.2, respectively.
Read counts were quantified for each gene using htseq-count v 0.11.3 and fivepseq 1.0.064 was employed to analysis 5 ends positions.
Assembly: Saccharomyces cerevisiae.R64-1-1.107 reference genome (Ensemble)
Supplementary files format and content: processed data in csv format, which is the raw count of sequencing reads for each transcripts

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Wildtype and mutant yeast cells were grown in 50 ml YEPD and harvested at an OD600 value of 0.6.

extract_protocol:
Cells were lysed using glass beads and total mRNA was extracted using phenol–chloroform. 50 ug of total mRNA was used as the starting material to perform 5PSeq.
Poly(A)-containing mRNA was enriched using 100 µl oligo(dT) beads (Dynabeads oligo (dT)25, Life Technologies) for 5P samples while randomly generated fragments of total RNA were prepared as controls. Both 5P and control RNAs were fragmented at 80˚C for 5 min. Following reverse transcription and second strand generation, overnight incubation at 4 °C with M-280 streptavidin beads (Life Technologies) was performed instead of 30 min at room temperature, as suggested for maximum capture of the cDNA. The final DNA adapter ligation reaction was carried out for 2hrs at 16˚C. Following PCR, each sample was purified separately with HighPrep beads (Magbio) as suggested and their quality was checked using Agilent 2100 Bioanalyzer. A Qubit 2.0 Fluorometer (Life Technologies) was used to determine the concentration of each library. Libraries were pooled in equal molar ratios and fragments were enriched between 300 and 500 nt for the library. The final libraries were sequenced using Illumina NovaSeq 6000.

treatment_protocol: Harvested cells were resuspended in a lysis buffer containing 50 mM Tris-HCl (pH 8.1), 130 mM NaCl, 5 mM EDTA, and 5% SDS.

tag: cell type

value: yeast cell

tag: strain

value: mRNA degradation intermediate


title: wOB,3-day pupa(p3),rep1


title: YS602_mH69_Control_rep2

description: Library name: YS602_mH69_Control_rep2


title: wOB,2-day pupa(p2),rep3

value: 2-day pupa(p2)


title: Taproot and lateral roots, drought stress, degradome, biol rep 1

description: Library name: TR_LR-DS-D_rep1


title: 116ABc

value: Kidney (ccRCC)


title: Autism patient (ASD) 36

description: Hybridization to SNP


title: 111ABc


title: wOB,4-day pupa(p4),rep3


title: Autism patient (ASD) 13

description: Hybridization to SNP


title: Taproot and lateral roots, control condition, degradome, biol rep 3

description: Library name: TR_LR-CT-D_rep3

value: control condition


title: YS602_mH69_5Pseq_rep2

description: Library name: YS602_mH69_5Pseq_rep2


title: YS602_mH69_5Pseq_rep1

description: Library name: YS602_mH69_5Pseq_rep1


title: 109AB


title: wOB,2-day pupa(p2),rep2


title: Autism patient (ASD) 8

description: Hybridization to SNP

value: ASD


title: 110AB


title: Taproot and lateral roots, control condition, degradome, biol rep 2

description: Library name: TR_LR-CT-D_rep2


title: wOB,1~3h hours after emerging ,rep1

value: 1~3h hours after emerging


title: wOB,2-day pupa(p2),rep1

value: wOB


title: Autism patient (ASD) 11

description: Hybridization to SNP