title: MOLM14_shFLT3_n5_24

tag: transduction


title: 19128X12 Female Adrenal Gland, 9-week, Control, biol rep 4

status: Public on Apr 03 2023

type: SRA

city: Salt Lake City

first: Kaitlin

last: Basham

state: UT

address: 2000 Circle of Hope Dr.

department: Oncological Sciences

country: USA

institute: Huntsman Cancer Institute, University of Utah

library_source: transcriptomic

data_processing:
Mouse FASTA and GTF files were downloaded from Ensembl release 102 and a reference database was created using STAR version 2.7.6a.
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using RSEM version 1.6.3.
Expected gene counts were filtered to remove features with zero counts and features with fewer than 10 reads in any sample.
Assembly: Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1.
Supplementary files format and content: GRCm38
Supplementary files format and content: raw counts from featureCounts combined into a single tab-delimited matrix

molecule: total RNA

organism: Mus musculus

source_name: Adrenal Gland

growth_protocol: Adrenal glands were obtained from mice following rapid decapitation to mimize stress. Adrenals were places in ice-cold phosphate buffered saline, cleaned of excess fat and snap frozen in liquid nitrogen.

extract_protocol:
RLT lysis buffer (Qiagen, 74104) containing 1% b-mercaptoethanol was added to thawed adrenal tissue in high impact zirconium 1.5mm bead tubes (Benchmark Scientific, D1032-15). Samples were homogenized for 30 seconds using the Beadbug™ 3 (Benchmark Scientific, D1030), returned to ice, and homogenized for an additional 30 seconds. Total RNA isolation was completed using the RNeasy® Kit (Qiagen, 74104) according to manufacturer guidelines. DNases were removed using the RNase-Free DNase Set (Qiagen, 79254) and subsequently purified using the RNeasy MinElute Cleanup Kit (Qiagen, 74204) according to manufacturer guidelines
NEBNext Ultra II Directional RNA Library Prep with poly(A)mRNA Isolation

tag: tissue

value: Adrenal Gland

tag: strain

tag: Sex

value: Female

tag: genotype

value: SF1-Cre negative

tag: time


title: Sham5-cerebrospinal fluid

type: protein

city: Xinxiang

first: Han

last: Li

address: 601 Jinsui Road, Hongqi District, Xinxiang City, Henan Province

country: China

institute: Xinxiang Medical University

description: Secreted proteins

hyb_protocol: Centrifuge the Cy3-streptavidin tubule, then add 1.4 ml of sample diluent, mix well, and then quickly centrifuge again. Add 80 µ l of Cy3-streptavidin to each well, wrap the slide in aluminum foil and incubate it in a dark place. Incubate it on a shaking table at room temperature for 1 hour.

scan_protocol: The signals (532 nm excitation, 635 nm emission) were scanned and extracted using an InnoScan 300 scanner (Innopsys, Carbonne, France).

data_processing:
Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls.
QAR-INF-1 software was used to analyze the data

molecule: protein

organism: Rattus norvegicus

source_name: Cerebrospinal fluid of rat

label_protocol: Cy3-conjugated streptavidin

extract_protocol: none provided

value: Cerebrospinal fluid

tag: gender

value: Male

tag: treatment

value: Untreated


title: Wildtype megakaryocytes from male mice replicate #1

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Basecalling with NextSeq Control/RTA v2 and FastQ conversion with Bcl2fastq v2.20.0.422
Adapter clipping and trimming using Cutadapt version 2.1 with default parameters. In addition, Cutadapt was given the –nextseq-trim=20 switch to handle two color sequencing chemistry and reads that were trimmed to length 0 were discarded.
Mapping to mouse genome (GRCm38.p6) with  STAR v2.7.2b and raw read on counting gene level bases with featureCounts v1.6.4  using the RefSeq annotation.
Differential Expression analysis with DESeq2 (v1.24.0) with log fold change shrinkage using betaPrior
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: mRNA abundance measurements

source_name: Wildtype megakaryocytes from male mice

growth_protocol: native murine megakaryocytes isolated from bone marrow and purified by magnetic separation with anti-CD61-antibodies

extract_protocol:
Whole mRNA extraction using TRIzol reagent and the RNeasy Mini Extraction Kit (Qiagen) according to the manufacturers’ protocol.
DNA libraries suitable for sequencing were prepared from 50 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions

treatment_protocol: untreated

tag: strain background

value: wt

value: male

tag: cell type

value: bone marrow megakaryocytes


title: Sham4-cerebrospinal fluid

description: Secreted proteins


title: Sham3-cerebrospinal fluid

description: Secreted proteins


title: MOLM14_shCTL_n5_21

type: RNA

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

hyb_protocol: cDNA were hybridized to GeneChip® Clariom S Human (Affymetrix) at 45°C for 17 hours, then washed on the fluidic station FS450 (Affymetrix)

scan_protocol: GCS3000 7G (Thermo Fischer Scientific)

data_processing: Raw fluorescence intensity values were normalized using Robust Multiarray Average (RMA) algorithm in R to generate the normalized data matrix by performing background correction, quantile normalization and log2 transformation of raw fluorescence intensity values of each gene. All quality controls and statistics were performed using Partek® Genomics Suite software (Partek, St. Louis, MO, USA). Data were normalized using custom brainarray CDF files (v20 ENTREZG). To identify differentially expressed genes, we applied a classical analysis of variance (ANOVA) with a FDR permutation-base for each gene. We created a matrix with only the significant ANOVA site and performed Z-scoring of rows. Hierarchical clustering by Pearson's dissimilarity and average linkage and principal components analysis (PCA) were conducted in an unsupervised fashion to control for experimental bias or outlier samples.

label: biotin

organism: Homo sapiens

source_name: AML cell line

label_protocol: 100 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit

growth_protocol: AML cells were cultured in minimum essential medium (MEM)-α Glutamax (Life Technology, Carlsbad, CA, USA) supplemented with bovine serum albumin (BSA, Sigma-Aldrich, Saint Louis, MO, USA), 100 IU/mL penicillin and 100 µg/mL streptomycin (Life Technology) at 37°C under a 5% CO2 atmosphere.

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Redwood City, CA, USA) and quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit)

value: shCTL

tag: cell line

tag: disease

value: patient with AML


title: Mpig6b mutated megakaryocytes from male mice replicate #4


title: 19128X11 Female Adrenal Gland, 9-week, Control, biol rep 3


title: Mpig6b mutated megakaryocytes from male mice replicate #3


title: MOLM14_shFLT3_n3_23


title: MOLM14_shCTL_n3_20


title: MOLM14_shFLT3_n2_22


title: Sham2-cerebrospinal fluid

description: Secreted proteins


title: Mpig6b mutated megakaryocytes from male mice replicate #2


title: 19128X9 Female Adrenal Gland, 9-week, Control, biol rep 1


title: MOLM14_shCTL_n2_19


title: Mpig6b mutated megakaryocytes from male mice replicate #1


title: QUIZ__CEBPAOE_n3_12


title: Sham1-cerebrospinal fluid

description: Secreted proteins


title: 19128X8 Female, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 4

value: SF1-Cre+; Znrf3 Fx/Fx


title: WT Replicate 2

city: Toronto

first: Jeffrey

last: Fillingham

address: 350 Victoria Steet

country: Canada

institute: Toronto Metropolitan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (4.1)
Trimmed sequence reads were mapped to T_Thermophilia_MAC_2020 using STAR (ver 2.7.1)
Gene counts were extracted using the STAR aligner's quantMode
Assembly: T_Thermophillia_MAC_2020
Supplementary files format and content: tab-delimited text file include gene counts for each sample

molecule: polyA RNA

organism: Tetrahymena thermophila

source_name: growing Tetrahymena cells

growth_protocol: 30C; 100rpm; SPP liquid media

extract_protocol:
Total RNA was extracted from wildtype and H3.3 KO Tetrahymena during vegetative growth using the RNeasy extraction kit (Qiagen).
RNA was treated with DNase prior to library preparation. 1000 ng per sample was processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat # E7760L; New England Biolabs, Ipswich, USA; protocol v. v3.1_5/20) including PolyA selection.

treatment_protocol: H3.3 knockout cells in which HHT3 gene (MAC locus) has been replaced with the Neo drug resistance marker

value: growing Tetrahymena cells

tag: growth phase

value: vegetative growth

value: WT


title: Wildtype megakaryocytes from female mice replicate #4

value: female


title: CEBPAOE_n3_6

value: CEBPAOE


title: WT Replicate 1


title: 19128X6 Female, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 2

value: Adrenal Gland


title: 19128X7 Female, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 3

value: Female


title: QUIZ__CEBPAOE_n1_10


title: Wildtype megakaryocytes from female mice replicate #3


title: Wildtype megakaryocytes from female mice replicate #2


title: 19128X5 Female, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 1


title: H3.3 KO Replicate 1

value: H3.3 Knockout


title: 19128X4 Female Adrenal Gland, 6-week, Control, biol rep 4

value: SF1-Cre negative


title: H3.3 Input Replicate 2

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using cutadapt
ChIP-seq reads were aligned to T_Thermophilia_MAC_2020 genome using STAR (ver 2.7.1)
Peaks were called uing MACS (ver 2.2.7.1) with q-value cut-off <=0.05 and annotated using HOMER
Assembly: T_Thermophillia_MAC_2020
Supplementary files format and content: tab-delimited text file of significant peaks
Supplementary files format and content: bigWig file for each sample generated using bin size of 100 and RPKM normalization

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated Tetrahymena nuclei and H3.3-GFP in complex with DNA  was isolated with ANTI-GFP antibody (abcam ab290)
Illumina's  TruSeq ChIP Sample Preparation Kit (cat# IP-202-1012)

treatment_protocol: Growing Tetrahymena cells were crosslinked with 1% PFA (paraformaldehyde) in PBS


title: QUIZ__CEBPAOE_n2_11


title: 19128X3 Female Adrenal Gland, 6-week, Control, biol rep 3


title: Wildtype megakaryocytes from female mice replicate #1


title: CEBPAOE_n1_4


title: Mpig6b mutated megakaryocytes from female mice replicate #3


title: 19128X2 Female Adrenal Gland, 6-week, Control, biol rep 2


title: H3.3 Input Repliciate 1


title: H3.3 ChIP Replicate 2

tag: chip antibody

value: anti-GFP


title: Mpig6b mutated megakaryocytes from female mice replicate #2


title: CEBPAOE_n2_5


title: H3.3 ChIP Replicate 1


title: H3.3 KO Replicate 2


title: 19128X1 Female Adrenal Gland, 6-week, Control, biol rep 1


title: empty_n2_2

value: empty


title: Mpig6b mutated megakaryocytes from female mice replicate #1


title: DN1 + DN2 + DN3. + gammadelta thymocytes

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

data_processing:
Th Illumina sequencing files were demultiplexed and aligned to Mus musculus genome (mm10) using the CellRanger pipeline (10X Genomics) to generate a feature barcode matrix from the raw bcl file.
Using R software (v3.6.3 and v4.1.0 ) with Seurat (v2.3 and v3.2.2), low-quality cells were filtered with based on genes and mitochondria gene expression.
The data was then normalised using VST selection method
Downstream analysis was performed (Principal componennt analysis, DoubletFinder, Clustering, Trajectory inference and differential expression analysis)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for each Sample
Supplementary_files_format_and_content: tab-delimited text files for each Sample (compressed by the standard GNU Zip compression algorithm)
Supplementary_files_format_and_content: A matrix of counts per gene for every cell

source_name: Early T cell development

growth_protocol: C57BL/6 mice at 6-8-week of age were euthanised by asphyxiation with CO2 and the thymi were excised and placed in RPMI 1640 medium. Thymi were passed through a 70µm stainless steel mesh to produce single cell suspensions of thymocytes.

extract_protocol:
Library was generated by Chromium™ Single Cell 3’ Library Construction (10x Genomics).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four thymi were pooled for each sample and then depleted of CD4 or CD8 expression cells (DP, CD4SP and CD8SP) using anti-CD4 and CD8 MACS magnetic beads (Miltenyi Biotec). The depleted samples were then sorted for DN1 (CD4-CD8-CD25-CD44+), DN2 (CD4-CD8-CD25+CD44+), DN3 (CD4-CD8-CD25+CD44-), DN4 (CD4-CD8-CD25-CD44-), or gammadelta (CD4-CD8-TCRgd+) thymocytes on a FACSAria (BD Biosciences).

value: thymus

tag: age

value: week 6


title: QUIZ_empty_n2_8


title: empty_n3_3


title: Mpig6b mutated megakaryocytes from female mice replicate #4

value: bone marrow megakaryocytes


title: empty_n1_1


title: motorneuron tgfb2 , biological replicate # D

status: Public on Apr 02 2023

city: Stockholm

first: Caroline

last: Lindblad

address: BioClinicum J5:20

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
Pooled libraries were sequenced on Illumina NextSeq 550 using paired-end sequencing with 91 cycles. Samples were de-multiplexed and reads were mapped at the sequencing facility using STAR, run from a Linux server.
Assembly: Ensembl gene ID, version 102, accessed through biomaRt R package
Supplementary files format and content: ; separated csv file, including raw counts (that were further processed through the DESeq2)

source_name: differentiated embryonic stem cells

growth_protocol: Mouse embryonic stem cells (ES-cells) were differentiated in accordance with Wichterle et al (Cell, 2002). In brief, ES cells were seeded. Differentiation was induced following two days of expansion. Two days after initiation of differentiation, resulting free-floating embryoid bodies were supplemented with 1mM retinoic acid and 0.5 mM smoothened agonist. On day six, EBs were dissociated into single cell populations of neurons and glial progenitor cells using 0.05% trypsin and trituration. Cells were resuspended or as described below. ES-derived brainstem/rostroventral spinal astrocyte-like cells (ES-astrocytes) were differentiated using dissociated EBs that were plated at a density of 15 M cells on poly-L-ornithine/laminin coated dishes in astrocyte medium supplemented with basic fibroblast growth factor and epidermal growth factor. Cells were propagated in adherent monolayer cultures from passage (P) 0 until P3, without addition of differentiation factors. Astrocyte differentiation was initiated using a panel of differentiation factors, previously associated with astrocytic differentiation.

extract_protocol:
We lysed ~200 FACS-sorted cells/sample in a lysis buffer containing dNTP and oligo-dT primers. PolyA+ RNA was converted to cDNA using a reverse transcriptase reaction. For cDNA fragmentation and barcoding, we employed the Tn5-based tagmentation procedure. We used Illumina-compatible barcodes (8 base pairs, dual-index).
We lysed ~200 FACS-sorted cells/sample in a lysis buffer containing dNTP and oligo-dT primers. PolyA+ RNA was converted to cDNA using a reverse transcriptase reaction. For cDNA fragmentation and barcoding, we employed the Tn5-based tagmentation procedure. We used Illumina-compatible barcodes (8 base pairs, dual-index).

treatment_protocol: ES-astrocytes were stimulated with a neuroinflammatory mediator for 24 hours (see treatment groups above). IL-1α  and TNF-α were used as positive controls. Neuroinflammatory proteins assessed included: complement component 1Q (C1Q), complement component 5 (C5); IL1-β, IL-6, and transforming growth factor- (TGF-) β2. For co-cultures, ES-motor neuron homogeneity was ensured using fluorescence-activated cell sorting with gating optimized for eGFP+. ES-motor neurons were plated on top of ES-astrocytes. ES-motor neuron dissociation was conducted the same day as sorting and plating.

value: differentiated embryonic stem cells

value: non-commercial cell line derived from mouse strain B6.Cg-Tg(Hlxb9-GFP)1Tmj/J

value: motorneuron


title: QUIZ_empty_n3_9

value: patient with AML


title: QUIZ_empty_n1_7


title: astrocyte il1a+tnfa , biological replicate # D

value: astrocyte


title: motorneuron control , biological replicate # D

value: control


title: astrocyte c1q+c5 , biological replicate # D


title: motorneuron il1a+tnfa , biological replicate # D


title: astrocyte il1b+il6 , biological replicate # D


title: motorneuron c1q+c5 , biological replicate # D


title: astrocyte control , biological replicate # D


title: motorneuron il1b+il6 , biological replicate # C


title: astrocyte tgfb2 , biological replicate # C


title: motorneuron c1q+c5 , biological replicate # C


title: astrocyte c1q+c5 , biological replicate # C


title: astrocyte il1b+il6 , biological replicate # C


title: astrocyte il1a+tnfa , biological replicate # C


title: motorneuron il1a+tnfa , biological replicate # C


title: astrocyte tgfb2 , biological replicate # D


title: motorneuron il1b+il6 , biological replicate # D


title: motorneuron tgfb2 , biological replicate # B


title: astrocyte tgfb2 , biological replicate # B


title: motorneuron control , biological replicate # C


title: astrocyte il1b+il6 , biological replicate # B


title: astrocyte c1q+c5 , biological replicate # B


title: motorneuron c1q+c5 , biological replicate # B


title: motorneuron il1a+tnfa , biological replicate # B


title: motorneuron tgfb2 , biological replicate # C


title: astrocyte il1a+tnfa , biological replicate # B


title: astrocyte tgfb2 , biological replicate # A


title: astrocyte control , biological replicate # B


title: motorneuron tgfb2 , biological replicate # A


title: motorneuron c1q+c5 , biological replicate # A


title: astrocyte il1b+il6 , biological replicate # A


title: astrocyte c1q+c5 , biological replicate # A


title: motorneuron il1b+il6 , biological replicate # A


title: motorneuron il1a+tnfa , biological replicate # A


title: astrocyte control , biological replicate # C


title: motorneuron il1b+il6 , biological replicate # B


title: astrocyte control , biological replicate # A


title: Pre-pro-B_healthy2

city: Stanford

first: Jolanda

last: Sarno

state: California

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

description: VST data_healthy pops.xlsx

data_processing:
Sequence reads trimmed for adaptor sequence and mapped to GRCh38.
Read counts were extract and normalized to VST using DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: Excel files including VST (variance-stabilizing transformation) data

source_name: healthy donor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMARTER Ultra low kit (Takara Bio/Clonotech Laboratories) for sequencing of healthy populations and Illumina TruSeq mRNA stranded kit for sequencing human BCP-ALL cell lines.

treatment_protocol: 1uM dexamethasone (Sigma) was used to treat cells for 48 hours. Ethanol was instead used as vehicle control

value: healthy donor

value: Bone marrow cells


title: Pro-B_healthy1

description: VST data_healthy pops.xlsx


title: Pre-pro-B_healthy3

description: VST data_healthy pops.xlsx


title: Pro-B_healthy3

description: VST data_healthy pops.xlsx


title: Pro-B_healthy2

description: VST data_healthy pops.xlsx


title: motorneuron control , biological replicate # A


title: Pre-B_healthy1

description: VST data_healthy pops.xlsx


title: Pre-B_healthy3

description: VST data_healthy pops.xlsx


title: motorneuron control , biological replicate # B


title: seminal plasma EVs, S188

city: Amherst

last: Pilsner

state: Massachusetts

address: 686 N PLEASANT

department: Environmental Health Sciences

institute: University of Massachusetts Amherst

description: non-coding RNA

data_processing:
Cutadapt was used for trimming reads <16 nts and filtering low quality reads (Phred score<20). The reads were then aligned to UniVec database to filter out potential sequencing contaminants using Bowtie2.
The unmapped reads were then sequentially aligned to transcriptome databases for ncRNA biotypes in the order miRNA>tRNA>piRNA>rRNA> “other” RNA>circRNA>lncRNA using STAR (v.2.7.6a) with the following parameters:  --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --outMultimapperOrder Random --runRNGseed 2021 --outSAMmultNmax 1 --seedSearchLmax 28 --seedSplitMin 9 --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outSAMattributes Standard. SAM/BAM data manipulation and counting of mapped reads was performed using samtools idxstats.
Biotype-specific counts were normalized using weighted trimmed mean of M-values TMM and species with normalized count (RPM) ≥ 1 in all samples were utilized for downstream diffrenetial expression analysis using EdgeR
Assembly: miRBase 22.1 (http://www.mirbase.org/); GtRNAdb (http://gtrnadb.ucsc.edu/) and RNAcentral v18 (https://rnacentral.org/); piRBase v.1.7.5 (http://www.regulatoryrna.org/database/piRNA/); circBase (http://www.circbase.org); Gencode (https://www.gencodegenes.org/)
Supplementary files format and content: Processed data are tab-delimited txt files and contain biotype-specific read count values for each sample.  The 4 columns per txt file represent (from left to right) biotype specific IDs, transcript length, reads mapped to forward strand, and reads mapped to the reverse strand, respectively.

source_name: seminal plasma extracellular vesicles

extract_protocol:
Seminal plasma extracellular vesicle total RNA isolation was perfomed using exoRNAeasy Midi Kit (Qiagen).
RNA libraries for small RNA-seq were prepared using Clontech SMARTER smRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Semen samples were collected from men of couples attending IVF treatment following a 2-3 days abstinence period. Male fertility diagnoses were based on semen quality parameters according to World Health Organization (WHO) reference values and Kruger strict morphology criteria. Semen samples were processed using a two-step (40% and 80%) gradient fractionation method and the resulting seminal plasma was stored in -80oC until subsequent analysis.

value: seminal plasma extracellular vesicles

tag: total motility_(%)

tag: morphology (%)

tag: volume (ml)

tag: count (10^6/ejaculates)

tag: status


title: Pre-pro-B_healthy1

description: VST data_healthy pops.xlsx


title: seminal plasma EVs, S187

description: non-coding RNA


title: astrocyte il1a+tnfa , biological replicate # A

tag: tissue


title: seminal plasma EVs, S183

description: non-coding RNA


title: Pre-B_healthy2

description: VST data_healthy pops.xlsx


title: seminal plasma EVs, S184

description: non-coding RNA


title: seminal plasma EVs, S176

description: non-coding RNA


title: seminal plasma EVs, S173

description: non-coding RNA


title: seminal plasma EVs, S168

description: non-coding RNA


title: seminal plasma EVs, S165

description: non-coding RNA


title: seminal plasma EVs, S164

description: non-coding RNA


title: seminal plasma EVs, S171

description: non-coding RNA


title: seminal plasma EVs, S166

description: non-coding RNA


title: seminal plasma EVs, S190

description: non-coding RNA


title: seminal plasma EVs, S162

description: non-coding RNA


title: seminal plasma EVs, S156

description: non-coding RNA


title: seminal plasma EVs, S153

description: non-coding RNA


title: seminal plasma EVs, S157

description: non-coding RNA


title: seminal plasma EVs, S154

description: non-coding RNA


title: seminal plasma EVs, S160

description: non-coding RNA


title: seminal plasma EVs, S152

description: non-coding RNA


title: 19128X15 Female, Adrenal Gland, 9-week SF1-Cre+;Znrf3Fx/Fx, biol rep 3

value: Adrenal Gland

tag: strain

tag: Sex

value: Female

tag: genotype

value: SF1-Cre+; Znrf3 Fx/Fx


title: seminal plasma EVs, S146

description: non-coding RNA


title: seminal plasma EVs, S180

description: non-coding RNA


title: seminal plasma EVs, S140

description: non-coding RNA


title: seminal plasma EVs, S161

description: non-coding RNA


title: 19128X10 Female Adrenal Gland, 9-week, Control, biol rep 2

value: SF1-Cre negative

tag: time


title: seminal plasma EVs, S172

description: non-coding RNA


title: seminal plasma EVs, S181

description: non-coding RNA


title: seminal plasma EVs, S143

description: non-coding RNA


title: seminal plasma EVs, S141

description: non-coding RNA


title: seminal plasma EVs, S137

description: non-coding RNA


title: seminal plasma EVs, S151

description: non-coding RNA


title: seminal plasma EVs, S135

description: non-coding RNA


title: seminal plasma EVs, S131

description: non-coding RNA


title: seminal plasma EVs, S134

description: non-coding RNA


title: seminal plasma EVs, S130

description: non-coding RNA


title: seminal plasma EVs, S129

description: non-coding RNA


title: seminal plasma EVs, S132

description: non-coding RNA


title: seminal plasma EVs, S128

description: non-coding RNA


title: seminal plasma EVs, S115

description: non-coding RNA


title: 2VO rats treated with tilianin-rep3

city: Beijing

first: Ting

last: Sun

address: Tiantanxili No.1

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Cutadapt V1.14 was used to remove adaptors (cutoff value Q lower than 20). The clean reads were obtained by using Trimmomatic V0.36 after removing low-quality bases at both ends. Reads were compared with the reference genome via miRBase database.
DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples. Genes were considered as significant differentially expressed if P<0.05 and |FoldChange| >1.
Assembly: the rats reference genome (http://asia.ensembl.org/ index.html)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: brain

growth_protocol: All the rats were housed under a 12-h light-dark cycle at room temprature and 60 ± 10% humidity and givenad libitumaccess to food and water.

extract_protocol:
Total RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon, China) according to the manufacturer’s protocol
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Next, sequencing libraries were constructed using TruSeq Small RNA Sample Prep Kits (RS-200-0024, Illumina, USA) following manufacturer’s recommendations. The library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: rats were anesthetized with pentobarbital sodium (30 mg/kg). We then separated the bilateral common carotid arteries and ligated them with a No.4–0 surgical suture. Rats in the tilianin treatment group received a daily dose of 40 mg/kg tilianin that was dissolved in 0.5% carboxymethylcellulose sodium (CMC-Na) (5 mL/kg/body weight) with a gastric tube for four weeks. Rats in the 2VO groups were given 0.5% CMC-Na vehicle (5 mL/kg/body weight) over the same period.

value: brain

tag: treatment

value: 2VO with tilianin


title: seminal plasma EVs, S112

description: non-coding RNA

tag: cell type


title: seminal plasma EVs, S113

description: non-coding RNA


title: seminal plasma EVs, S123

description: non-coding RNA


title: seminal plasma EVs, S102

description: non-coding RNA


title: 2VO rats treated with tilianin-rep1


title: 2VO rats-rep3


title: seminal plasma EVs, S103

description: non-coding RNA


title: seminal plasma EVs, S108

description: non-coding RNA


title: 2VO rats-rep2


title: 2VO rats-rep1


title: CML TKI LSK

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

description: inDrop on sorted LSK from CML mice treated with TKI

data_processing:
Basecalls performed using Partek Flow software, version 8.0
For scRNA-seq: Bowtie v.1.1.1 was used with parameter -e 80 and reads were aligned to the Ensembl release 85 Mus musculus GRCm38 reference as described earlier (Wolock et al., 2019a). Each library was initially filtered to include only abundant barcodes (> 500 total counts for all in vivo libraries; > 800 counts for cultured sample 1; > 1,000 counts for cultured samples 2 and 3), based on visual inspection of the histograms of total transcript counts per cell barcode. Next, we excluded putatively stressed or dying cells with > 30% (in vivo samples) or > 20% (cultured samples) of their transcripts coming from mitochondrial genes. Normalization of data was carried out as described earlier (Wolock et al., 2019a). For the in vivo samples, we also used Scrublet (Wolock et al., 2019b) to identify two clusters of cell doublets that co-expressed marker genes of distinct cell types
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for each Sample are provided

source_name: Sorted Lin-Sca1+cKti+

extract_protocol: Libraries were prepared according to inDrop's instructions

treatment_protocol: mice were treated with 400mg/kg of imatinib was administered by gavage every alternate day for 30 days

value: Stem and progenitor cells

tag: organ

value: Bone marrow

tag: murine strain

tag: treatement

value: 400mg/kg imatinib every alternate days for 4 weeks


title: Leaf_elf18_3

city: Durham

first: Paul

last: Zwack

state: NC

address: Campus Box 90338

institute: Duke University

data_processing:
read trimming with Trimmomatic
mapping, counting, normalization and differential expression using ARM-seq pipeline (Cozen et al., 2015 Nat. Methods)
Genome_build: Tair-10
Supplementary_files_format_and_content: tab-delimited files of normalized counts and differential expression

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Plants were grown in 12h:12h light:dark cycle on soil for 4 weeks at 22C

extract_protocol:
Tissue was ground in liquid nitrogen and small RNA was isolated using the Zymo Direct-zol kit
RNA was incubated in 0.1M Tris pH 9.0 for 45 min at 37°C for deacylation. Demethylation was perfomed as described (Zheng et al., 2015): RNA was incubated at room temperature for 2 hours with 160 pmol of wt AlkB and 200 pmol of D135S AlkB in abuffer containing 300 nM KCl, 2mM MgCl2, 50mM (NH4)2Fe(SO4)2×6H2O, 300mM 2-ketoglutarate, 2mM L-ascorbic acid, 50mg/mL nuclease free BSA, and 50 mM MES pH 5.0. RNA was then separated on a 10% TBE-Urea gel (Novex), the region of each lane corresponding to 55 – 100 nt was isolated and RNA was recovered by passive elution into 300mM sodium acetate pH 5.2 followed by ethanol precipitation. Libraries for Illumina® sequencing were prepared using the NEBNextÒ Multiplex Small RNA Library Prep Set for Illumina® (Set1) according to the manufacturer’s instructions.

treatment_protocol: The 4th and 5th leaves of 3 plants/rep were pressure-infiltrated with either water of 1µM elf18 in water then held for 1 hour before sample collection and freezing.

value: Col-0 (35S:5-LSTBF1-LUC)

value: Leaf

value: 1µM elf18


title: seminal plasma EVs, S090

description: non-coding RNA


title: Leaf_elf18_2


title: seminal plasma EVs, S084

description: non-coding RNA


title: seminal plasma EVs, S096

description: non-coding RNA


title: seminal plasma EVs, S97

description: non-coding RNA


title: Leaf_elf18_1


title: seminal plasma EVs, S119

description: non-coding RNA


title: CML LSK

description: inDrop on sorted LSK from CML mice

value: Untreated


title: WT TKI LSK

description: inDrop on sorted LSK from WT mice treated with TKI


title: seminal plasma EVs, S107

description: non-coding RNA


title: Leaf_Mock_3

value: mock (water)


title: 2VO rats treated with tilianin-rep2


title: Leaf_Mock_1


title: WT LSK

description: inDrop on sorted LSK from WT mice


title: seminal plasma EVs, S082

description: non-coding RNA


title: seminal plasma EVs, S080

description: non-coding RNA


title: seminal plasma EVs, S092

description: non-coding RNA


title: C31 , HCC , tumor , TB-neg

city: Jinan

first: Shaoshao

last: Xu

state: Shandong

address: 44 Wenhua Xi Road

department: Cheeloo College of Medicine

institute: shandong university

data_processing:
After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing.
Clean data (clean reads) were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated. Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes normalized FPKM and counts values for each Sample

source_name: tumor

extract_protocol:
RNA was harvested from a small tissue collected from HCC pantients in tumor budding positive and negative.
RNA libraries for RNA-seq were prepared using the NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

tag: individual

tag: disease

value: HCC

value: tumor

tag: tumor budding_state

value: TB-neg


title: seminal plasma EVs, S79

description: non-coding RNA

value: seminal plasma extracellular vesicles

tag: total motility_(%)

tag: morphology (%)


title: C29 , HCC , tumor , TB-neg


title: WT ex vivo 3

description: Bulk RNA-seq on ex vivo expanded WT HSCs using Nextera library prep

data_processing:
Basecalls performed using Partek Flow software, version 8.0
For Bulk RNA-seq: double-ended sequencing reads were aligned to the mouse (mm10) using Spliced Transcripts Alignment to a Reference (STAR 2.7.3a). Aligned reads were then quantified to the transcriptome (Ensembl Transcripts release 101) and normalized based on count per million
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for each Sample are provided

source_name: Sorted Lin-Sca1+cKit+CD150+

extract_protocol:
RNA was isolated using the RNeasy Plus mini kit (Qiagen) for bulk RNA-seq
Libraries were prepared according to Illumina's Nextera XT instructions

value: Stem cells

tag: background strain


title: WT ex vivo 2


title: C20 , HCC , tumor , TB-neg


title: C26 , HCC , tumor , TB-pos

value: TB-pos


title: C19 , HCC , tumor , TB-neg


title: seminal plasma EVs, S078

description: non-coding RNA

tag: volume (ml)

tag: count (10^6/ejaculates)

tag: status


title: WT ex vivo 1


title: C18 , HCC , tumor , TB-pos

tag: tissue


title: C15 , HCC , tumor , TB-pos


title: Leaf_Mock_2

tag: genotype


title: C10 , HCC , tumor , TB-neg


title: CML ex vivo 3

description: Bulk RNA-seq on ex vivo expanded CML LSCs using Nextera library prep


title: seminal plasma EVs, S74

description: non-coding RNA


title: C8 , HCC , tumor , TB-neg


title: C4 , HCC , tumor , TB-pos


title: CML ex vivo 2


title: C3 , HCC , tumor , TB-pos


title: C2 , HCC , tumor , TB-neg


title: C28 , HCC , tumor , TB-pos


title: CML ex vivo 1


title: seminal plasma EVs, S71

description: non-coding RNA


title: seminal plasma EVs, S072

description: non-coding RNA


title: C1 , HCC , tumor , TB-pos


title: WTVero3-2

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of adapters using Trimmomatic v0.32
Trimmed reads were aligned to reference genome chlSab2, NCBI annotation release 100 using STAR aligner v2.7.3a with parameters –winAnchorMultimapNmax 200 –outFilterMultimapNmax 100 –quantMode GeneCounts
DEseq2 was used to determine differential gene expression using counts.
Assembly: chlSab2
Supplementary files format and content: tab (raw counts)

organism: Chlorocebus sabaeus

source_name: Vero-E6 cell line

growth_protocol: WT Vero-E6 cells, DYRK1A KO#1 + vector, and DYRK1A KO#1 + complements were seeded at 3 x 105 cells/well in a 6-well plate and were treated with doxycycline for 72 hours to enable rescue of ACE2 and DPP4

extract_protocol:
Samples were performed in biological duplicate and harvested by scraping. Total cellular RNA was extracted using the Direct-zol RNA MiniPrep Plus (Zymo Research)
Libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina)

tag: cell line

value: Epithelial cell

value: Wildtype


title: B8938 , HCC , tumor , TB-neg


title: B8940 , HCC , tumor , TB-pos


title: B8939 , HCC , tumor , TB-pos


title: B8936 , HCC , tumor , TB-pos


title: KO_Y33-2

tag: treatment

value: DYRK1A knockout + Mutant DYRK1A vector


title: B8937 , HCC , tumor , TB-neg


title: B08935 , HCC , tumor , TB-pos


title: KO_Y32-1

tag: cell type


title: seminal plasma EVs, S069

description: non-coding RNA


title: WTVero-1


title: B8931 , HCC , tumor , TB-pos


title: seminal plasma EVs, S067

description: non-coding RNA


title: B8928 , HCC , tumor , TB-neg


title: B14 , HCC , tumor , TB-neg


title: B12 , HCC , tumor , TB-pos


title: B13 , HCC , tumor , TB-pos


title: B11 , HCC , tumor , TB-pos


title: KO_WT3-2

value: DYRK1A knockout + WT DYRK1A vector


title: seminal plasma EVs, S070

description: non-coding RNA


title: KO_Vec3-2

value: DYRK1A knockout + empty vector


title: seminal plasma EVs, S062

description: non-coding RNA


title: seminal plasma EVs, S063

description: non-coding RNA


title: seminal plasma EVs, S068

description: non-coding RNA


title: KO_vec-1


title: KO_WT-1


title: seminal plasma EVs, S73

description: non-coding RNA


title: B9 , HCC , tumor , TB-pos


title: B4 , HCC , tumor , TB-neg


title: B10 , HCC , tumor , TB-neg


title: seminal plasma EVs, S059

description: non-coding RNA


title: B3-2 , HCC , tumor , TB-neg


title: B5 , HCC , tumor , TB-pos


title: WTVero-E6_2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of Nextera adaptor sequences using Trimmomatic v0.39
Trimmed reads were aligned to chlSab2 using Bowtie2 v2.2.9 with parameter -X2000
Duplicated, unpaired, and mitochondrial reads were removed using SAMTools v1.9
Reads were shifted +4 bp and −5 bp for forward and reverse strands, respectively
Peaks were called using MACS2 v2.2.6 with parameters –nomodel –keep-dup all -s 1 –shift 75 –extsize 150
Reads that fell inside peaks were counted using featureCounts v1.6.2
Differential accessibility analysis was performed using DESeq2 v1.32
Assembly: chlSab2
Supplementary files format and content: bigwig (Merged), txt (raw counts)

growth_protocol: Vero-E6 (ATCC) cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) with 5% heat-inactivated fetal bovine serum (FBS, VWR) and 1% Penicillin/Streptomycin (Gibco)

extract_protocol:
WT Vero-E6 cells, DYRK1A KO#1 + vector, and DYRK1A KO#1 + complement were seeded at 3 x 105 cells/well in a 6-well plate and were treated with doxycycline for 72 hours to enable rescue of ACE2 and DPP4. Samples were performed in biological duplicate and were harvested by scraping.
Samples were submitted to Yale Center for Genome Analysis for library generation and were sequenced on an Illumina NovaSeq S4 instrument as 101 nt long paired-end reads with goal of at least 45 x 105 reads per replicate


title: B8 , HCC , tumor , TB-pos


title: seminal plasma EVs, S060

description: non-coding RNA


title: seminal plasma EVs, S065

description: non-coding RNA


title: seminal plasma EVs, S058

description: non-coding RNA


title: B3-1 , HCC , tumor , TB-pos


title: B2-1 , HCC , tumor , TB-neg


title: A6KO_plus_WTDYRK1A_2

value: DYRK1A knock out + WT DYRK1A vector


title: WTVero-E6_1


title: seminal plasma EVs, S057

description: non-coding RNA


title: B2-3 , HCC , tumor , TB-neg


title: B2-2 , HCC , tumor , TB-neg


title: A6KO_plus_WTDYRK1A_1


title: B1-3 , HCC , tumor , TB-neg


title: A6KO_plus_vec_2

value: DYRK1A knock out + control vector


title: seminal plasma EVs, S056

description: non-coding RNA


title: B7 , HCC , tumor , TB-neg


title: seminal plasma EVs, S055

description: non-coding RNA


title: B1-2 , HCC , tumor , TB-pos


title: seminal plasma EVs, S054

description: non-coding RNA


title: A6KO_plus_vec_1


title: WT_compoundC

city: Hefei

first: Yucong

last: Wang

state: Anhui

address: 443 Huangshan Road

institute: USTC

description: RNA.txt.gz

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the human reference genome (hg19) with Bowtie2 (-v 1). For linear RNAs including lncRNAs and mRNAs, the corresponding reads were counted with BEDtools
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes reads for each RNA-seq Sample

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

value: HCC cell

value: WT

value: compoundC


title: KO_DMSO

description: RNA.txt.gz

value: circLARP2 KO

value: DMSO


title: seminal plasma EVs, S053

description: non-coding RNA


title: seminal plasma EVs, S052

description: non-coding RNA


title: WT_DMSO

description: RNA.txt.gz


title: seminal plasma EVs, S051

description: non-coding RNA


title: KO_IP

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
For circRNA prediction, CIRI2 were applied to identify high-confidence back-spliced junctions (BSJs). and the human reference genome we used was hg19
The adapters were first trimmed to obtain clean reads, and the left reads were then aligned to the human genome (hg19) with bowtie2. After the alignment, the Sam file was converted to the Bam file, duplicate reads due to amplification were removed and sorted, and finally, peak calling is performed using MACS2.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads for each RNA-seq Sample
Supplementary files format and content: tab-delimited bed files for each RIP-seq sample

value: HCC cellline

tag: molecule type

value: RNA IP RNA


title: WT_Input


title: WT_IP


title: KO_Input


title: OE_Input

value: circLARP2 OE


title: EV_IP

value: pcDNA3.0 EV


title: OE_IP


title: seminal plasma EVs, S049

description: non-coding RNA

value: seminal plasma extracellular vesicles


title: EV_Input


title: LM3

description: RNA-seq.txt.gz

source_name: non-metastatic HCC

value: non-metastatic HCC


title: LM2

description: RNA-seq.txt.gz


title: seminal plasma EVs, S050

description: non-coding RNA


title: seminal plasma EVs, S048

description: non-coding RNA


title: B1-1 , HCC , tumor , TB-pos

value: HCC

value: tumor

value: TB-pos


title: LM1

description: RNA-seq.txt.gz


title: seminal plasma EVs, S045

description: non-coding RNA


title: HM3

description: RNA-seq.txt.gz

source_name: metastatic HCC

value: metastatic HCC


title: REH wt dex_Biol rep2

description:
100bp 30M
VST data_cell lines.xlsx

source_name: REH wt

value: REH wt

value: BCP-ALL

value: dexamethasone

tag: time

value: 48 hrs


title: REH wt veh_Biol rep2

description:
100bp 30M
VST data_cell lines.xlsx

value: WT

value: vehicle (ethanol)


title: HM1

description: RNA-seq.txt.gz


title: HM2

description: RNA-seq.txt.gz


title: Meta-Positive-19

city: Kanazawa

first: Naohiro

last: Wakisaka

state: Ishikawa

country: Japan

institute: National Hospital Organization Kanazawa Medical Center

description: Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue

hyb_protocol: Hybridization was performed using GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: The array was scanned using GeneChip Scanner 3000 7G, Affymetrix,.

data_processing: The data were analyzed with Transcriptome Analysis Console T hermo Fisher Scientific Inc.using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Tonsil

label_protocol: cDNA synthesis, amplification and labeling were performed with WT Pico Reagent, and according to the standard Affymetrix protocol using Veriti 200, Life Technologies, Inc.

extract_protocol: Total RNA from FFPE block was isolated using RNeasyⓇ FFPE Kit.

tag: cancer

value: Oropharynx


title: Meta-Negative-7


title: REH wt dex_Biol rep1

description:
100bp 30M
VST data_cell lines.xlsx


title: REH wt veh_Biol rep1

description:
100bp 30M
VST data_cell lines.xlsx


title: Meta-Positive-16


title: Meta-Positive-20


title: seminal plasma EVs, S042

description: non-coding RNA


title: Meta-Positive-18


title: REH GCR veh_Biol rep2

description:
100bp 30M
VST data_cell lines.xlsx

source_name: REH GCR (overexpressing NR3C1)

value: REH GCR (overexpressing NR3C1)

value: overexpress NR3C1


title: Meta-Positive-17


title: Meta-Positive-15


title: seminal plasma EVs, S043

description: non-coding RNA


title: Meta-Positive-14


title: REH GCR dex_Biol rep2

description:
100bp 30M
VST data_cell lines.xlsx


title: REH GCR dex_Biol rep1

description:
100bp 30M
VST data_cell lines.xlsx


title: seminal plasma EVs, S035

description: non-coding RNA


title: REH GCR veh_Biol rep1

description:
100bp 30M
VST data_cell lines.xlsx


title: seminal plasma EVs, S036

description: non-coding RNA


title: seminal plasma EVs, S032

description: non-coding RNA


title: NALM6 dex_Biol rep2

description:
100bp 30M
VST data_cell lines.xlsx


title: NALM6 veh_Biol rep2

description:
100bp 30M
VST data_cell lines.xlsx


title: seminal plasma EVs, S044

description: non-coding RNA


title: NALM6 veh_Biol rep1

description:
100bp 30M
VST data_cell lines.xlsx


title: Meta-Negative-6


title: Meta-Positive-11


title: Meta-Positive-13


title: seminal plasma EVs, S026

description: non-coding RNA


title: NALM6 dex_Biol rep1

description:
100bp 30M
VST data_cell lines.xlsx


title: 2VO treatment rep2

city: Zhanjiang

first: Tao

last: Tao

state: Guangdong

address: 236 Yuanzhu Road, Guangdong

department: Department of Anesthesiology

institute: Central People’s Hospital of Zhanjiang

description: total RNA in single cell level

data_processing:
Raw sequencing data from the Illumina platform were converted into Fastq files and aligned to the reference genome mm10 using the 10X Genomics Cell Ranger Pipeline.
After the alignment, a matrix file containing the cell barcode identity and gene values was exported by the 10X Genomics Cell Ranger Pipeline.
Matrix files for the samples were then processed and analyzed by Seurat R software 3.2.2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hippocampus

extract_protocol:
The hippocampus were cut into pieces and transferred it to a 1.5 mL microcentrifuge tube with 2 mg/mL isolation solution, containing pronase (Sigma, Cat# P6911-1G) and 50 μg/mL DNaseІ (Sigma, cat. no. D5025) in 1 mL Hibernate A (Invitrogen, cat. no. A1247501)/B27 (Invitrogen, cat. no. 17504) medium (HABG). The tissue and solution were mixed for 30 min at 37℃ in a horizontal shaker at 200 rpm. After incubation, the tissue was gently triturated by polished tips, and the single cells were released. The purified cells were obtained by density gradient centrifugation at 800 g for 15 min, resuspended in 1x PBS (calcium and magnesium-free) containing 1% BSA, and then centrifuged at 200 g for 2 min. Single cells were concentrated and resuspended in the desired medium.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 12 weeks

tag: strain

value: treatment

value: hippocampus


title: sham treatment rep2

description: total RNA in single cell level

value: control


title: seminal plasma EVs, S020

description: non-coding RNA

value: seminal plasma extracellular vesicles


title: seminal plasma EVs, S021

description: non-coding RNA


title: sham treatment rep1

description: total RNA in single cell level


title: HSIL_HPV, replicate 1, Spatial Transcriptomics

city: Shanghai

first: Chenyan

last: Guo

address: 419 Fangxie Road, Shanghai, China

institute: Fudan University Obstetrics and Gynecology Hospital

description: 10X Genomics

data_processing:
library strategy: spatial transcriptomics
Basecalls performed using CASAVA version 1.8
Read alignment and count summarization were performed using SpaceRanger
Seurat package was used for spot normalization and regression. PCA was constructed based on the scaled data with all high variable genes and top 30 principals were used for tSNE construction. Utilizing graph-based cluster method, we acquired the unsupervised the cell cluster result based the PCA top 30 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. logFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1. Spatial feature expression plots were generated with the SpatialFeaturePlot function in Seurat (version 3.1.3) and the STUtility R package (version 1.0.0).
Assembly: GRCh38Ensembl100
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: cervical tissue

extract_protocol:
ST transcriptomes were collected using 10X Chromium Spatial Gene Expression Slide & Reagent Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cervical tissue

value: cervical cells

tag: disease state

value: NO


title: CA_HPV, replicate 2, Spatial Transcriptomics

description: 10X Genomics


title: seminal plasma EVs, S019

description: non-coding RNA

tag: total motility_(%)


title: N_HPV, replicate 1, Spatial Transcriptomics

description: 10X Genomics


title: TIL_E_Tim3Pos

city: Suwon-si

first: Se Jin

last: Im

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

department: Department of Immunology

country: South Korea

institute: Sungkyunkwan University School of Medicine

data_processing:
Sequence data was aligned using HiSat2, and differential gene expression was determined using DeSeq2.
Assembly: Hg38
Supplementary files format and content: Excel file include raw counts that come from the RNAseq for all samples.

source_name: Exhausted (Tim-3+ PD-1+) CD8 TILs

extract_protocol:
Tumors were harvested in cold L-15 Leibovitz media (Hyclone), cut into small pieces and digested for 1hour with an enzyme cocktail of Collagenase I (125mg/L), Collagenase II (125mg/L), Collagenase IV (125mg/L), DNase I (50mg/L), and Elastase (50mg/L) (Worthington) at 37ºC with shaking. Lymphocytes were isolated by 44%/67% Percoll gradient centrifugation. Peripheral blood mononuclear cells were isolated according to standard protocol.
RNA libraries for RNA-seq were prepared using the Illumnia Nextera kit following manufacturer's protocols.

value: Primary and metastatic tumors in lung tissues (NSCLC Tumor)

value: CD8 Tumor-infiltrating lymphocytes (TILs)

tag: tumor stage

value: stage I-IV disease


title: seminal plasma EVs, S016

description: non-coding RNA

tag: morphology (%)


title: 2VO treatment rep1

description: total RNA in single cell level


title: Meta-Positive-10


title: TIL_E_CD28Pos

source_name: Stem-like (Tim-3-CD28+ PD-1+) CD8 TILs


title: CA_HPV, replicate 3,scRNAseq

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v5.0.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. log2FC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCh38Ensembl100
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols


title: seminal plasma EVs, S015

description: non-coding RNA

tag: volume (ml)


title: Meta-Positive-12


title: TIL_D_Tim3Pos


title: Meta-Positive-9


title: CA_HPV, replicate 2,scRNAseq

description: 10X Genomics


title: seminal plasma EVs, S012

description: non-coding RNA

tag: count (10^6/ejaculates)


title: Meta-Positive-6


title: CA_HPV, replicate 1,scRNAseq

description: 10X Genomics


title: seminal plasma EVs, S008

description: non-coding RNA

tag: status


title: TIL_C_Tim3Pos

tag: tissue


title: HSIL_HPV, replicate 2,scRNAseq

description: 10X Genomics


title: seminal plasma EVs, S006

description: non-coding RNA


title: Meta-Positive-8


title: CA_HPV, replicate 1, Spatial Transcriptomics

description: 10X Genomics


title: TIL_B_Tim3Pos


title: seminal plasma EVs, S004

description: non-coding RNA


title: TIL_D_CD28Pos


title: Meta-Negative-5


title: Meta-Positive-4


title: TIL_B_CD28Pos


title: N_HPV, replicate 2,scRNAseq

description: 10X Genomics


title: N_HPV, replicate 1,scRNAseq

description: 10X Genomics


title: TIL_C_CD28Pos


title: seminal plasma EVs, S014

description: non-coding RNA


title: NO_HPV, replicate 2,scRNAseq

description: 10X Genomics


title: naïve_A

source_name: naive (CCR7+CD45RA+CD58-CD95-) CD8 T cells

value: PBMCs

value: CD8 T lymphocytes

value: None (healthy subject)


title: HSIL_HPV, replicate 1,scRNAseq

description: 10X Genomics


title: NO_HPV, replicate 1,scRNAseq

description: 10X Genomics


title: HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium_rep2

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

description: Gene expression data from HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium for 7 days

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space)

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: hAESCs were isolated from the term placenta. Firstly, the amnion was aseptically separated from the chorion and then washed with 200 mL of Hank's Basic Salt Solution - Calcium and Magnesium Free (CMF-HBSS). The amnion was cut into smaller pieces using surgical scissors and placed in 50 mL conical tubes. A total of 20 mL pre-digestion buffer containing CMF-HBSS and 0.5 mM EGTA was added to the tubes. The amnion was gently rocked in the solution for 30 seconds and then transferred to new 50 mL conical tubes. Again 20 mL pre-digestion buffer was added to the tubes and was incubated at 37oC for 10 minutes. Next, the pre-digestion buffer was discarded, and 20 mL of 0.05% trypsin-EDTA was added to the tubes, incubated for 40 minutes at 37oC, and then placed on ice. Next, Dulbecco's Modified Eagle Medium (DMEM, 10% FBS, 1% Penn-Strep) was added to the trypsin digest and centrifuged at 200 g for 10 minutes at 4oC. After discarding the supernatant, the pellet was resuspended in 10 mL of DMEM and filtered through a 100 μm filter.   Cells were maintained in Placental Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) and were constantly monitored with media change every 2-4 days. The cells were cultured in 3D culture plates (ElplasiaTM, Kuraray Co., Ltd., Cat # RB 500 400 NA 24) coated with LipidureTM solution (NOF Corporation, Cat. # CMS206; 400 μL) (50 mg in 10 mL absolute ethanol) as described previously. hAESC spheroids were formed by seeding 1 × 106 cells into each well of the 24-well plates. Cells were seeded in the Placental Basal Epithelial Cell Medium and cultured for 24 h.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: After 24 h of initial culture, cells were treated with 20 μM of carnosic acid. Control samples were maintained in the Placental medium. The medium was changed every 48 hours, three times during the 7 d treatment duration. Finally, we collected the treatment and control samples from the one-week culture.

value: Human Amniotic Epithelial Stem Cells

value: Control


title: Meta-Positive-7

value: Oropharynx


title: Meta-Negative-3


title: Meta-Positive-2


title: Meta-Negative-1


title: Meta-Positive-3


title: Meta-Negative-4


title: naïve_C


title: HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium_rep1

source_name: HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium for 7 days


title: Meta-Negative-2


title: HAESC 3D spheroids treated with carnosic acid_rep1

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Carnosic Acid for 7 days

source_name: HAESC 3D spheroids were treated with 20 uM Carnosic Acid for 7 days

value: Carnosic Acid


title: HAESC 3D spheroids treated with carnosic acid_rep2


title: Meta-Positive-1


title: 2H Group

status: Public on Apr 01 2023

city: RICHMOND

first: Jizhong

last: Han

state: VA - Virginia

address: 1220 E. Broad St.

institute: Virginia Commonwealth University

data_processing:
The libraries were sequenced using the Illumina HiSeq 2500 platform (Illumina) at Novogene Bioinformatics Technology Co., Ltd (Beijing, China).
The sequencing data were deposited in the NCBI database
Assembly: 56
Supplementary files format and content: tab-delimited text files include FPKM Values for each sample

organism: Candida albicans SC5314

source_name: cells

growth_protocol: Grown statically in 6mL Sabouraud medium at 30℃ overnight for activating strain. Spun down and then the pellet resuspended and adjusted with YNB medium.

extract_protocol:
Total RNA extraction using an TRNzol Universal Reagent (TianGen Biotechnology, Beijing, China).
RNA libraries for RNA-seq were prepared using QIAquick PCR purification kit.

treatment_protocol: Taken 2 tubes (50mL), aliquot a volume of 10mL freshly prepared OD600=0.2 Candida albicans and incubated for 2h at 30℃, added 50μL DMSO as control group, and treated group was added 50μL 2H (20mM).

value: cells

tag: genotype


title: pig #1 macrophages infected with VSV VSIV-ΔING-NJG

city: Orient Point

first: James

middle: Jiangtao

last: Zhu

state: NY

department: Plum Island Animal Disease Center

institute: USDA-ARS

description: pig DNA expression microarray

hyb_protocol: One Cy3 labled sample was cohybrided with the Cy5 labled control in one hybridization chamber (Agilent) containing an Agilent microarray (Array design #:Agilent-069270; 4 X 44k per slide). The chambers were incubated in a incubator at 65 C in a rotating cartridge overnight. After incubation, the arrays were washed with Agilent washing buffers according to amnufacturer's protocol.

scan_protocol: After hybridization and washing, the arrays were scanned at 5 micrometer per pixel with a Cy3 to Cy5 ratio of approximately 1 using a GenPix 4000B scanner (Molecular Devices) and the images were saved as tiff files.

data_processing:
The expression data were extracted from the tiff files using Agilent Genpix 7.0 software and the raw data were saved as gpr files for statisitcal analysis using R with librarys(limma, MASS, statmod, splines). LOESS method was applied to normalize interarray variation with a background subtraction of 40.
The gpr files were named based on the Agilent array serial number followed by the array number of the slide such as 256927010021-1.  The normalized Cy3 results of each sample were used as gene expression levels (photon per pixel) (provided in the Matrix). Gene expression levels of Sample 256927010021-1 were collected from pig #1 macrophages infected with VSV NJ0612NME6. Averaged Expression is the mean expression of each probe. Fold Change is the difference in expression level (fold) between VSV infections.  adj.P.Val is false discover rate. WT, M51R and Mock denote VSV NJ0612NME6, NJ0612NME6-M51R and mock infection, respectively.

organism: Sus scrofa

source_name: universal control

label_protocol: Low input RNA two color labeling kit (Agilent Technologies) was used to lable cRNA according to the manufacturer's protocol. Total RNA isolated from mock-infection was labeled with Cy5 as universal control. All samples including mock-infection were individually labeled with Cy3.

growth_protocol: Cultures of primary swine macrophages were prepared from defibrinated blood as previously described (Borca, M.V., Berggren, K.A., Ramirez-Medina, E., Vuono, E.A., Gladue, D.P., 2018. CRISPR/Cas Gene Editing of a Large DNA Virus: African Swine Fever Virus. Bio-protocol 8, e2978).

extract_protocol: Total RNA was extracted from each cell culture well using the RNeasy mini kit (Qiagen) following the manufacturer instructions. RNA quality was assessed using the Agilent 2100 bioanalyzer (Santa Clara, CA, USA) using an RNA nanochip. Quantification of RNA was conducted on a Nanodrop 1000 (Thermo Scientific).

treatment_protocol: The primary swine porcine macrophages cultured in six well plates containing 1x10^7 cells per well were infected with recombinant vesicular stomatitis viruses (VSV) at MOI of 10 TCID50 or mock-infected. After infection, the cells were incubated for five hours at 37 °C under 5% of CO2.

value: non-infected

value: primary macrophages

source_name: VSV-infected (VSIV-ΔING-NJG)

value: VSV-infected (VSIV-ΔING-NJG)


title: pig #1 macrophages infected with VSV NJ95COB

description: pig DNA expression microarray

source_name: VSV-infected (NJ95COB)

value: VSV-infected (NJ95COB)


title: pig #3 macrophages infected with VSV VSIV-ΔING-NJG

description: pig DNA expression microarray


title: DMSO Group

description: DMSO

value: WT

value: DMSO


title: pig #2 macrophages infected with VSV VSIV

description: pig DNA expression microarray

source_name: VSV-infected (VSIV)

value: VSV-infected (VSIV)


title: pig #2 macrophages infected with VSV NJ95COB

description: pig DNA expression microarray


title: Pig #1 macrophages not infected (Mock infection)

description: pig DNA expression microarray

source_name: Non-infected (mock)

value: Non-infected (mock)


title: pig #3 macrophages infected with VSV NJ0806VCB

description: pig DNA expression microarray

source_name: VSV-infected (NJ0806VCB)

value: VSV-infected (NJ0806VCB)


title: pig #2 macrophages infected with VSV NJ0612NME6-M51R

description: pig DNA expression microarray

source_name: VSV-infected (NJ0612NME6-M51R)

value: VSV-infected (NJ0612NME6-M51R)


title: pig #2 macrophages infected with VSV VSIV-ΔING-NJG

description: pig DNA expression microarray


title: pig #3 macrophages infected with VSV NJ0612NME6-M51R

description: pig DNA expression microarray


title: pig #1 macrophages infected with VSV NJ0612NME6-M51R

description: pig DNA expression microarray


title: Pig #2 macrophages not infected (Mock infection)

description: pig DNA expression microarray


title: pig #1 macrophages infected with VSV NJ0806VCB

description: pig DNA expression microarray


title: pig #3 macrophages infected with VSV VSIV

description: pig DNA expression microarray


title: pig #1 macrophages infected with VSV VSIV

description: pig DNA expression microarray


title: Meta-Positive-5

source_name: Tonsil


title: pig #3 macrophages infected with VSV NJ0612NME6

description: pig DNA expression microarray

source_name: VSV-infected (NJ0612NME6)

value: VSV-infected (NJ0612NME6)


title: 24D_Endurance_Post

city: Melbourne

first: Baubak

last: Shamim

state: VIC

address: Level 5, 215 Spring Street

department: Mary MacKillop Institute for Health Research

institute: Australian Catholic University

data_processing:
Base-calling was performed on Torrent Suite Software v5.8 (Life Technologies)
Reads were aligned using Tmap package for Torrent Suite™ software v5.8 (Life Technologies) with default parameters
Data were filtered using the following specifications…
Differentially Expressed Genes were obtained using R/Bioconductor package DESeq2 (v1.22.2)
Genome_build: GRCh37.hg19
Supplementary_files_format_and_content: txt files for Pre-to-Post intervention differentially expressed genes in each condition

source_name: Vastus lateralis muscle

extract_protocol:
RNA was isolated according to Life Technologies instructions accompanying the mirVana PARIS Kit (Part #AM1556)
Libraries were prepared according to Life Technologies instructions accompanying the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Part #A26325). Briefly, 50 ng of total RNA was reverse-transcribed to generate first strand cDNA using SuperScript™ VILO™ (Invitrogen) reverse transcriptase and random primers. Following reverse transcription, target genes were amplified using Ion AmpliSeq™ Transcriptome Human Gene Expression Core Panel. After target amplification, primer sequences were partially digested and amplicons were phosphorylated. The amplicons were then ligated to unique Ion Xpress™ barcodes (Life Technologies) and the resulting constructs were purified using Agencourt™ AMPure™ XP Magnetic Beads (Beckman Coulter). Libraries were quantified by qPCR against a standard curve of E. Coli DH10B, and normalized to 100 pM. Six libraries were pooled equally and 25 μL of the pooled mixture was used on one Ion 540™ Chip (Life Technologies) for template preparation using the Ion Chef™ Instrument (Life Technologies). Ion semiconductor sequencing was performed on the Ion S5 XL system (Life Technologies).

value: Vastus lateralis muscle

tag: condition

value: Endurance

value: Post


title: 24A_Endurance_Pre

value: Pre


title: 30A_Endurance_Pre


title: 8D_Endurance_Post


title: Sofleaf_sRNA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Saccharum officinarum

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the sorghum genome (JGI database).
PARE: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 20 nucleotides. PARE reads were mapped to the sorghum genome (JGI database).
Genome_build: Sorghum bicolor (JGI database)
Supplementary_files_format_and_content: Tag count file

organism: Saccharum hybrid cultivar

source_name: young leaf

extract_protocol: Small RNA libraries and PARE libraries were constructed from total RNA isolated from young leaves of sugarcane using Trizol Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). And the PARE library preparation protocol is based on Illumina’s TruSeq RNA  Sequencing Sample Preparation Guide (Illumina, San Diego, CA) The libraries were sequenced on an Illumina GAII at the Delaware Biotechnology Institute (Newark, DE).

value: young leaf

tag: cultivar

value: Banjarmasin Hitam

value: mature plants


title: Sofleaf_PARE

description: Saccharum officinarum

data_processing:
Library strategy: PARE-Seq
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the sorghum genome (JGI database).
PARE: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 20 nucleotides. PARE reads were mapped to the sorghum genome (JGI database).
Genome_build: Sorghum bicolor (JGI database)
Supplementary_files_format_and_content: Tag count file


title: pig #2 macrophages infected with VSV NJ0612NME6

description: pig DNA expression microarray

tag: treatment

value: non-infected

tag: cell type

value: primary macrophages


title: pig #3 macrophages infected with VSV NJ95COB

description: pig DNA expression microarray

value: VSV-infected (NJ95COB)


title: pig #2 macrophages infected with VSV NJ0806VCB

description: pig DNA expression microarray


title: 8A_Endurance_Pre

tag: time


title: 30D_Endurance_Post


title: 25D_Endurance_Post


title: 20A_Endurance_Pre


title: 20D_Endurance_Post


title: pig #1 macrophages infected with VSV NJ0612NME6

description: pig DNA expression microarray


title: 13D_Endurance_Post


title: 31D_Resistance_Post

value: Resistance


title: 31A_Resistance_Pre


title: 32D_Resistance_Post


title: 32A_Resistance_Pre


title: 27D_Resistance_Post


title: 27A_Resistance_Pre


title: 16D_Resistance_Post


title: 19D_Resistance_Post


title: 29D_Concurrent_Post

value: Concurrent


title: 2A_Resistance_Pre


title: 2D_Resistance_Post


title: 19A_Resistance_Pre


title: 28D_Concurrent_Post


title: 28A_Concurrent_Pre


title: 9D_Concurrent_Post


title: 26D_Concurrent_Post


title: 9A_Concurrent_Pre


title: 26A_Concurrent_Pre


title: 25A_Endurance_Pre


title: 14D_Concurrent_Post


title: 14A_Concurrent_Pre


title: 13A_Endurance_Pre


title: 4MOSC1-TNF-α+IFN-γ-rep3

city: wuhan

first: wang

last: shuo

state: HuBei

address: 237 Luoyu Road

institute: Wuhan University

data_processing:
BGISEQ-500 sequencer
Clean reads were mapped to the reference genome using HISAT/Bowtie2 tools.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The 4MOSC1  cells were grown in keratinocyte serum-free medium (K-SFM, Gibco-BRL).

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNAin total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA

treatment_protocol: For 4MOSC1 cells,TNF-α (25 ng/mL, Peprotech, 315-01A) and IFN-γ (25 ng/mL, Peprotech, 315-05) were utilized for 48h.

tag: cell line

value: stimulation with TNF-α and IFN-γ


title: 6D_Concurrent_Post


title: 4MOSC1-Control-rep3

value: No cytokines were added.


title: 4MOSC1-TNF-α+IFN-γ-rep1


title: 4MOSC1-TNF-α+IFN-γ-rep2


title: 16A_Resistance_Pre


title: 4MOSC1-Control-rep1


title: 29A_Concurrent_Pre


title: siOTUD6B_2 rep1

city: beijing

first: li

last: lei

address: 17 Panjiayuan Nanli

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: KYSE450 cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: esophageal squamous cell carcinoma cells

value: transfected with siOTUD6B


title: siOTUD6B_2 rep3


title: NC_2 rep2

value: transfected with negative control


title: siOTUD6B_2 rep2


title: NC_2 rep1


title: NC_2 rep3


title: IIHR-1939

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

data_processing:
Illumina platform used for base calling
TASSEL5 GBSv2 pipeline was used for identification of tags at cut sites and SNPs located across reference genome.
The fastq files were aligned against the tomato reference genome using the Bowtie2 tool version 2.2.9. The .sam file created from the Bowtie2 aligner program was used through SAMToGBSdbPlugin()
DiscoverySNPCallerPluginV2 took a GBSv2 database file as input and identified SNPs from the aligned tags.
Assembly: mm9
Supplementary files format and content: The VCF file generated from tassel pipeline was generated.
Supplementary files format and content: After filtration SNPs were retained provided in hapmap (hmp) format.

organism: Solanum pimpinellifolium

source_name: Leaf

extract_protocol:
gDNA was isolated from leaf samples by using Xcelgen Plant gDNA Isolation Kit (XG2611-01) as per the protocol described. The DNA was eluted in 50µl Nuclease-Free Water. The samples were quantified using Qubit Fluorometer. For determining A260/280 ratio, 1µl of sample was loaded in Nanodrop8000 spectrophotometer. The quality of samples was checked in 0.8% Agarose gel electrophoresis along with Hind III marker for the presence of intact bands.
To 100ng of gDNA, barcoded adapters (~0.1pM) were added and digested with Apek1 enzyme for 12h at 75oC. The barcoded and common adapters were ligated to the sticky ends of the digested DNA with T4 DNA Ligase enzyme at 22oC for 180 mins, followed by heat inactivation. The ligated products were pooled into 12 groups of 12 samples each group. The pool was PCR amplified to generate the final library pool.
High Sensitivity (HS) DNA chip and library pool was sequenced on Illumina platform to generate ~ 3 million reads/sample.

tag: domestication

value: Wild

value: Leaf


title: siOTUD6B_1 rep2

source_name: KYSE30 cells


title: WIR-5032

organism: Solanum chilense


title: 6A_Concurrent_Pre

value: Vastus lateralis muscle


title: NC_1 rep1


title: EC-528360


title: Sspoleaf-PARE

organism: Saccharum spontaneum

tag: age


title: NC_1 rep2


title: NC_1 rep3


title: Sspoleaf-sRNA


title: 4MOSC1-Control-rep2


title: Adult_nphx_1191

city: Daejeon

first: Myung Jin

last: Yang

institute: Institute for Basic Science

description:
Adult_nphx_lec
Adult_nphx_normalized_expression_matrix.csv

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

tag: strain

value: FACS sorted


title: siOTUD6B_1 rep1


title: Adult_nphx_1190


title: Adult_nphx_1193


title: siOTUD6B_1 rep3


title: Adult_nphx_1194


title: Adult_nphx_1196


title: Adult_nphx_1192


title: EC-521078


title: Adult_nphx_1189


title: Adult_nphx_1188


title: Adult_nphx_1185


title: Adult_nphx_1187


title: Adult_nphx_1195


title: Adult_nphx_1183


title: Adult_nphx_1184


title: Adult_nphx_1182


title: Adult_nphx_1186


title: Adult_nphx_1181


title: Adult_nphx_1175


title: Adult_nphx_1197


title: Adult_nphx_1180


title: Adult_nphx_1178


title: Adult_nphx_1174


title: Adult_nphx_1179


title: Adult_nphx_1176


title: Adult_nphx_1173


title: Adult_nphx_1172


title: Adult_nphx_1171


title: Adult_nphx_1166


title: Adult_nphx_1168


title: Adult_nphx_1159


title: Adult_nphx_1162


title: Adult_nphx_1167


title: Adult_nphx_1163


title: Adult_nphx_1165


title: Adult_nphx_1169


title: Adult_nphx_1164


title: Adult_nphx_1157


title: Adult_nphx_1156


title: Adult_nphx_1155


title: Adult_nphx_1158


title: Adult_nphx_1153


title: Adult_nphx_1152


title: Adult_nphx_1160


title: Adult_nphx_1154


title: Adult_nphx_1151


title: Adult_nphx_1177


title: Adult_nphx_1150


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