title: CRISPRaX_Plasmid_Library

data_processing:
Alignment and read counting was performed using MAGeCK (0.5.9.3) with options [count --norm-method control] for all samples together (Li et al. 2014, Li et al. 2015).
Statistical analysis was performed using MAGeCK (0.5.9.3) with options [mle --norm-method control] (Li et al. 2014, Li et al. 2015)
Genome_build: -
Supplementary_files_format_and_content: char_library_dup.txt: Text file containing descriptions of the individual guides used for the screen. As some guides target multiple TSSs, they are duplicated within the file.
Supplementary_files_format_and_content: raw_counts_dup.txt: Raw counts assessed via MAGeCK count. Guides targeting multiple TSSs are duplicated.
Supplementary_files_format_and_content: mageck_mle_dup.txt: Results of the MAGeCK MLE analysis, showing enrichment of individual TSSs within the screen.

organism: Synthetic plasmid

source_name: Plasmid

growth_protocol: E14-STN-dTsixP cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)) at a density of 3.13*10^4 cells/cm2.

extract_protocol:
The PrimeFlow RNA assay (Thermofisher) was used according to the manufacturer’s recommendations. Specifically, the assay was performed in conical 96-well plates for a total of 200 million cells per replicate with 5 million cells per well  using Xist specific probes, labelled with Alexa-Fluor647 (VB1-14258). 20 million cells were snap-frozen after the two fixation steps to be used as the Unsorted fraction.  Samples were resuspended in PrimeFlow™ RNA Storage Buffer before flow cytometry. Here, four different populations were sorted according to Xist expression. In more detail, a Xist-negative population was taken from the bottom-15% of Xist-expressing cells. Three Xist-positive populations were taken in 15%-intervals from the top Xist-expressing cells (0-15% = High, 15-30% = Medium, 30-45% = Low). Around 11-15 million cells were recovered per fraction. After sorting, the cell pellets were snap-frozen and stored at -80°C.  DNA from frozen cell pellets was isolated through phenol/chloroform extraction. Cell pellets were thawed and resuspended in 250 µl of lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2 M NaCl and 5 mM DTT (Roth) in TE Buffer) and incubated overnight at 65°C. The next day 200 µg of RNAse A (Thermo Fisher Scientific) were added and the samples were incubated at 37°C for 1 h. 100 µg of Proteinase K (Sigma) were subsequently added, followed by a 1 h incubation at 50°C. Phenol/chloroform/isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed for 1 min and subsequently centrifuged at 16,000 x g for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 h. DNA was pelleted by centrifugation for 16,000 x g for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50 µl water.
Sequencing libraries were prepared from both sorted and unsorted cell populations for each of the three independent screen replicates. Genomic DNA from frozen cell pellets was isolated by Phenol/Chloroform extraction. Briefly, cell pellets were thawed and resuspended in 250 µl of Lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2 M NaCl and 5 mM DTT (Roth) in TE Buffer) and incubated overnight at 65 °C. 200 µg of RNAse A (Thermo Fisher Scientific) were added to the sample and incubated at 37 °C for 1 h. 100 µg of Proteinase K (Sigma) were subsequently added followed by a 1 h incubation at 50 °C. Phenol/Chloroform/Isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed at room temperature for 1 min and subsequently centrifuged at 16,000 x g for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 2 µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80 °C for 1 h. DNA was pelleted by centrifugation for 16,000 x g for 15 min at 4 °C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50 µl H2O.  The genomically integrated sgRNA cassette was PCR-amplified to attach sequencing adaptors and sample barcodes. To ensure proper library coverage (300x), a total of 20 µg of each sample were amplified using the ReadyMix Kapa polymerase (Roche) with a total of 25 cycles and an annealing temperature of 56 °C. A relatively low amount of 0.5 µg genomic DNA was amplified per 50 µl PCR reaction since in samples stained with Flow-FISH, PCR amplification was inhibited at higher DNA concentrations. PCR was performed with the primer LR175 in combination with a sample-specific primer which contains a distinct 6-nucleotide barcode to allow sample identification after multiplexed deep sequencing (Primer sequences in Suppl. Table 4, LR178/LR180). Successful amplification was verified on a 1% agarose gel and the reactions were pooled. 1 ml of each pooled PCR was purified using the QIAquick PCR Purification Kit (Qiagen) and the resulting amplicons were loaded on a 1% agarose gel and purified using the QIAquick Gel Extraction Kit (Qiagen).
CRISPR screen

treatment_protocol: E14-STN-dTsixP cells were passaged for two passages in Serum+LIF-containing medium before a total of 1.200.000 cells were transduced with viral supernatant of the sgRNA library (MOI = 0.3). Puromycin selection (1 ng/µl, Sigma) was started 48 h after transduction and kept until the end of the experiment. Four days after transduction, 7.200.000 cells were differentiated by LIF withdrawal for 2 days. Expression of CRISPRa-SunTag system was induced using doxycycline (Clontech, 1 µg/ml) one day before differentiation and kept throughout the rest of the protocol. Cells were harvested with trypsin to reach a single cell suspension for Flow-FISH after 2 days of differentiation.

value: PlasmidLibrary

value: CRISPRa-Screen


title: RNAseq_TX1072_XO_d4_r2

status: Public on Jan 26 2022

type: SRA

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

library_source: transcriptomic

data_processing:
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.4). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’.
The reads were aligned using STAR (2.7.5a) with options [–outSAMattributes NH HI NM MD] to the N-masked mm10 genome (Dobin et al. 2013).
SAM files were translated into BAM files, filtered for properly paired reads and sorted using samtools (1.10) with options [view -b -h -f 3 -q 7] and [sort] (Li et al. 2009)
RNA-seq counts were quantified on exons only with the options [featureCounts(isPairedEnd = TRUE, GTF.featureType = “exon”, strandSpecific = 2, allowMultiOverlap = FALSE)].  Transcripts Per Million (TPM) was then calculated as Fragments Per Kilobase (FPK) divided by the scaling factor. The scaling factor was calculated as the sum of all FPK values divided by a million.
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: TX1072 XO Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon).

extract_protocol:
RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research) following the manufacturer’s instructions.
RNA-seq libraries were generated using the Tru-Seq Stranded Total RNA library preparation kit (Illumina) with 1 μg starting material for rRNA-depletion and amplified with 15 Cycles of PCR.

treatment_protocol: Differentiation was induced for 0, 1, 2, 3 or 4 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol at a density of 1.56*10^4 cells/cm2 in fibronectin-coated (10 μg/ml) tissue culture plates.

tag: cell line

value: TX1072 XO

tag: condition

value: Day 4

tag: replicate

tag: strain background

value: CAST / C57BL/6

tag: assay

value: RNAseq


title: WT_Rep1

status: Public on Jan 27 2022

city: Reno

first: Pedro

last: Miura

state: Nevada

address: 1664 N VIRGINIA ST MS 0314

department: Biology

country: USA

institute: University of Nevada, Reno

data_processing:
Illumina’s bcl2fastq_v2.19 software
Sequenced reads were trimmed for adaptor sequence, then mapped to WBcel235 whole genome using STAR v2.7.5a
read counts for each gene per exon were obtained using featurecounts v1.5.0 (options: -t exon -g gene_id)
normalized abundance measurements and differential expression analysis were obtained using DESeq2 v1.26.0 with default parameters
Genome_build: WBcel235
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were age-synchronized by hypochlorite treatment and collected eggs were hatched overnight at 20°C in 1x M9 buffer. L1 larvae were then plated onto NGM plates seeded with 10x concentrated E. coli OP50 bacteria and allowed to develop to the L4 larval stage at 20°C. L4 larvae were then collected, washed, and re-plated onto NGM plates and seeded with 10x E. coli OP50 bacteria. Day-1 adult worms were collected by filtering through a 30 µM nylon mesh to remove bacteria

extract_protocol:
RNA-seq analysis, 1-day adult worms were collected in Lysis/Binding Buffer from the mirVana miRNA isolation kit (Ambion, Cat #AM1560). Worms were immediately lysed by bead beating them for 5 min using a Bullet Blender Pro Storm (Next Advance). Total RNA was then extracted following mirVana manufacturers protocol and treated with DNAse I (Invitrogen, Cat #AM1907). RNA were assessed by a Bioanalyzer (Agilent), and quantified using Quant-iT RiboGreen RNA Assay kit (ThermoFisher Scientific, Cat #R11490)
poly(A)-selected libraries were prepared by Novogene LTD., (Beijing, China) at UC Davis genomics center

tag: strain

tag: tissue

value: whole worm

tag: age

value: day-1 adult

tag: genotype

value: wild type


title: RNAseq_TX1072_XO_d3_r1

value: Day 3


title: siCon_3

type: RNA

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 5 ug fragmented and biotinylated ssDNA were hybridized for 16 hr at 45C to Affymetrix Clariom S human arrays according to standard protocol. Washing and staining were performed using Affymetrix Fluidics Station 450.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were analyzed with packages available from Bioconductor (http://www.bioconductor.org). Normalization and calculation of gene expression was performed with the Robust Multichip Average expression measure using the oligo package.

label: biotin

organism: Homo sapiens

source_name: hADSC

label_protocol: Biotinylated cRNA was prepared using the GeneChip WT Plus Reagent Kit according to the standard Affymetrix protocol from 150ng total RNA.

growth_protocol: hADSC cells were plated at a cell density of 20 000 cells/cm2 and incubated at 37°C with 5% CO2. Adipogenesis was induced two days post confluence using DMEM/F12  as well as the adipogenic cocktail; 5 mg/mL insulin, 0.25 mmol/l dexamethasone, 0.5 mmol/l 3-isobutyl-1-methylxanthine (IBMX) and 10 mmol/l rosiglitazone for two days after which the dexamethasone and IBMX were removed and the cells were allowed to undergo full adipogenic differentiation.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, cat. 740955.250) according to the manufacture's instructions. The concentration, purity and quality were measured using Nanodrop 2000 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Short interfering oligonucleotides (siRNAs) were introduced by electroporation using a Neon Transfection System (1300 V, 20 ms, 2 pulses) 100 µL Kit (Invitrogen) in human in vitro differentiated hADSCs at day eight of differentiation. All transfections were performed using a final concentration of 20 nmol/L siRNA oligonucleotides and were compared with non-silencing control RNAi.

tag: cell type

value: Adipose Derived Stem Cells (hADSC)

tag: treatment

value: control


title: 18 mo-1

city: Guangzhou

first: Mingsheng

last: Zhu

address: 1838 North Guangzhou Avenue

country: China

institute: Nanfang hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In   this step, clean data (clean reads) were obtained by removing reads containing adapter, reads   0 containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC   content the clean data were calculated. All the downstream analyses were based on the clean   data with high quality
Reference genome and gene model annotation files were downloaded from genome website   directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean   reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the   mapping tool for that Hisat2 can generate a database of splice junctions based on the gene   model annotation file and thus a better mapping result than other non-splice mapping tools
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per   Millions base pairs sequenced, considers the effect of sequencing depth and gene length for   the reads count at the same time, and is currently the most commonly used method for   estimating gene expression levels
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2   R package (1.20.0). DESeq2 provide statistical routines for determining differential expression   in digital gene expression data using a model based on the negative binomial distribution. The   resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling   the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were   assigned as differentially expressed
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample

organism: Mus

source_name: Kidney

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mus kidney


title: RNAseq_TX1072_XO_d1_r2

value: Day 1


title: RNAseq_TX1072_XO_d3_r3


title: RNAseq_TX1072_XO_d3_r2


title: siCon_1


title: RNAseq_TX1072_XO_d0_r2

value: Day 0


title: Biopsy_before_NACT_4

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

description: Paired with surgery sample 3

hyb_protocol: Hybridization was performed according to manufacturer's instructions. nCounter uses a molecular barcode technology, where the RNA is directly tagged with a target-specific capture probe and target-specific reporter probe containing a labeled barcode. We used the PanCancer IO 360 gene expression panel which includes 770 immune-related genes and associated controls.

scan_protocol: Scanning and image acquisition using the nanoString Digital Analyzer.

data_processing: nanoString data were analyzed and normalized in nSolver software, correcting for the expression of technical controls and 30 housekeeping genes included in the panel.

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_4

label_protocol: Labeling was performed according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from cells using RNeasy FFPE Kit (Qiagen) according to the manufacturer's instructions and DNA was eliminated by means of Rnase-Free Dnase Set (Qiagen).

treatment_protocol: Biopsy samples were collected from primary lesions before EOC patients underwent carboplatin/paclitaxel-based neoadjuvant chemotherapy, according to availability. Surgery samples were extracted from residual lesions after treatment with chemotherapy, according to availability.

value: Epithelial Ovarian Cancer

tag: sample type

value: Biopsy sample

tag: response to nact

value: Responder

tag: crs score


title: RNAseq_TX1072_XO_d1_r3


title: RNAseq_TX1072_XO_d2_r3

value: Day 2


title: RNAseq_TX1072_XO_d2_r2

value: TX1072 XO


title: RNAseq_TX1072_XO_d2_r1


title: RNAseq_TX1072_XO_d0_r3


title: non-EC SNHG12 gapmer 4

city: Boston

first: Mark

last: Feinberg

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's

description: CD31 negative portion of mouse gastrocnemius, isolated as the flowthrough from CD31-conjugated magnetic beads separation

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCh38

source_name: Non-endothelial portion of mouse gastrocnemius

extract_protocol:
Total RNA was extracted with QIAzol reagent and miRNeasy micro kit (Qiagen)
RNA-Seq analysis was performed with polyA selection and standard library construction using Illumina HiSeq2500 V4 2x100 PE  (Genewiz, South Plainfield, NJ).

treatment_protocol: gapmer  knockdown of the SNHG12 in mouse muscle

value: diabetic (db/db) mice

value: CD31- non-EC

tag: cell isolated from tissue

value: primary

value: non-EC SNHG12 gapmer injection into gastrocnemius


title: non-EC SNHG12 gapmer 1


title: non-EC SNHG12 gapmer 2


title: non-EC Control gapmer 4

value: non-EC control gapmer injection into gastrocnemius


title: non-EC SNHG12 gapmer 5


title: siCon_2


title: RNAseq_TX1072_XO_d0_r1

value: CAST / C57BL/6

value: RNAseq


title: non-EC SNHG12 gapmer 3


title: non-EC Control gapmer 3


title: non-EC Control gapmer 1


title: non-EC Control gapmer 2


title: siCKB_1

value: Adipose Derived Stem Cells (hADSC)

value: siCKB


title: EC SNHG12 gapmer 5

description: CD31+ portion of mouse gastrocnemius, isolated by CD31-conjugated magnetic beads

source_name: Isolated Gastrocnemius Mouse Endothelial Cell

value: CD31+ Endothelial Cell

value: SNHG12 gapmer injection into gastrocnemius


title: EC SNHG12 gapmer 4


title: RNAseq_TX1072_XO_d4_r1

value: Day 4


title: EC SNHG12 gapmer 2


title: EC Control gapmer 3

value: control gapmer injection into gastrocnemius


title: chip_413_FCX_P3_H3K27ac_CTTGTA

city: Seattle

first: Christopher

middle: H

last: Seward

state: WA

address: Stubbs Lab, Rm 404, 720 Broadway

institute: Pacific Northwest Research Institute

library_source: genomic

data_processing:
Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software
Reads were mapped to the mm10 mouse genome with Bowtie2
HOMER v4.7 was used to generate Tag Directories and bigWig files for visualization
Genome_build: mm9 for RNA-seq, mm10 for ChIP-seq
Supplementary_files_format_and_content: Tab separated file of normalized CPM counts of all expressed transcripts
Supplementary_files_format_and_content: BigWig Pileup of read locations

molecule: genomic DNA

source_name: Frontal Cortex Tissue of Brain

growth_protocol: Mice were housed in a temperature-controlled room in a reverse 12h/ 12h light-dark cycle. Six-week-old female mice (C57BL/6J x C3HJ F1 hybrids, with an agouti coat to allow clear distinction with the black-coated virgins) purchased from the Jackson Laboratory were impregnated, and co-housed with age-matched virgin female C57BL/6J mice during pregnancy and through the early post-partum pregnancy.

extract_protocol:
Freshly dissected tissue from 3 animals was pooled together, disaggregated, lysed to nuclei, and frozen at -80 until ChIP was performed with Abcam ab4729 antibodies.  Input samples are background DNA that have not been immunoprecipitated.
Libraries were prepared from eluted DNA using KAPA LTP library kits (KK8230) using Bioo Scientific index adapters, size-selected using AmpureXP beads (Beckman Coulter, Brea, CA, USA) and quality checked by Qubit 2.0 and Bioanalyzer (Agilent 2100). Samples were sequenced to a depth of 20-30M reads per replicate on an Illumina HiSeq 2500 sequencer using a TruSeq SBS sequencing kit, version 4, in single-end format with fragment length of 100 bp.

tag: developmental stage

value: Frontal Cortex Tissue of Brain


title: chip_423_AMY_P3_H3K27ac_GGCTACAT

source_name: Amygdala Tissue of Brain

value: Amygdala Tissue of Brain


title: chip_425_AMY_E18_H3K27ac_AGTTCCGT


title: EC Control gapmer 4


title: chip_407_STR_P3_H3K27ac_TCGAAG

source_name: Striatum Tissue of Brain

value: Striatum Tissue of Brain


title: chip_405_STR_E18_H3K27ac_TCATTC


title: chip_427_AMY_E18_input_CCGTCCCG


title: EC SNHG12 gapmer 3


title: RNAseq_TX1072_XO_d1_r1

value: TX1072 XO

value: Day 1


title: chip_421_FCX_P3_input_GATCAG


title: EC SNHG12 gapmer 1

value: diabetic (db/db) mice


title: chip_402_HYP_P3_H3K27ac_CGTACG

source_name: Hypothalamus Tissue of Brain

value: Hypothalamus Tissue of Brain


title: EC Control gapmer 2

value: primary


title: EC Control gapmer 5


title: chip_439_HYP_E18_input_2_GTCCGCAC


title: chip_426_AMY_E18_H3K27ac_ATGTCAGA


title: EC Control gapmer 1


title: chip_424_AMY_P3_input_AGTCAACA


title: chip_422_AMY_P3_H3K27ac_TAGCTTAT


title: chip_412_FCX_E18_input_CAGATC


title: chip_420_STR_P3_input_ACTTGA


title: chip_414_FCX_P3_H3K27ac_ATCACG


title: chip_419_STR_E18_input_TCCCGA


title: chip_411_FCX_E18_H3K27ac_GCCAAT


title: chip_410_FCX_E18_H3K27ac_ACAGTG


title: chip_408_STR_P3_H3K27ac_CGATGT


title: rna_P3_8_FC_TAATGCGC-TAATCTTA [P3_FC_8]

data_processing:
Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software
Reads were aligned with Tophat 2.0.8 using default parameters and reads inside of exon features were counted in union mode using htseq version 0.6.1.
CPMs were calculated in R
Genome_build: mm9 for RNA-seq, mm10 for ChIP-seq
Supplementary_files_format_and_content: Tab separated file of normalized CPM counts of all expressed transcripts
Supplementary_files_format_and_content: BigWig Pileup of read locations

extract_protocol:
Freshly dissected tissue was flash-frozen in liquid nitrogen and frozen at -80° C until RNA could be extracted. Total RNA was disrupted in Trizol (Life Technologies, Carlsbad, CA, USA) with a mechanical pestle according manufacturer’s specifications. The aqueous phase was precipitated in isopropanol, resuspended in nuclease-free water, treated with DNase I (New England Biolabs, Ipswich, MA, USA), and cleaned up using a Zymo RNA Clean & Concentrator™-25 kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s specifications. Prior to library preparation, total RNA was checked for purity using a NanoDrop ND-1000 spectrophotometer, integrity using RNA Nano chips on an Agilent 2100 Bioanalyzer, and concentration using a Qubit fluormeter.
Illumina sequencing libraries were generated with the TruSeq Stranded mRNA HT kit (Illumina) using an Eppendorf ePMotion 5075 robot, and were sequenced to a depth 45-60 million reads per sample on Hi-Seq 2500 instruments at the Roy J. Carver Biotechnology Center at the University of Illinois.


title: rna_P3_8_H_TAATGCGC-CAGGACGT [P3_H_8]


title: chip_399_HYP_E18_H3K27ac_GTGAAA


title: chip_398_HYP_E18_H3K27ac_GTCCGC


title: chip_418_HYP_E18_input_1_GTGGCC


title: chip_404_STR_E18_H3K27ac_GGTAGC


title: chip_403_HYP_P3_input_GAGTGG


title: rna_P3_6_A_TAATGCGC-TATAGCCT [P3_A_6]


title: rna_P3_6_STR_TAATGCGC-GGCTCTGA [P3_STR_6]


title: rna_P3_6_H_TAATGCGC-CCTATCCT [P3_H_6]


title: rna_P3_8_A_TAATGCGC-AGGCGAAG [P3_A_8]


title: rna_P3_8_STR_TAATGCGC-GTACTGAC [P3_STR_8]


title: chip_401_HYP_P3_H3K27ac_GTTTCG


title: rna_P3_6_FC_TAATGCGC-ATAGAGGC [P3_FC_6]


title: rna_P3_5_STR_CTGAAGCT-GTACTGAC [P3_STR_5]


title: rna_P3_5_A_CTGAAGCT-AGGCGAAG [P3_A_5]


title: rna_P3_5_FC_CTGAAGCT-TAATCTTA [P3_FC_5]


title: rna_P3_5_H_CTGAAGCT-CAGGACGT [P3_H_5]


title: rna_P3_4_STR_CGGCTATG-GGCTCTGA [P3_STR_4]


title: rna_P3_4_FC_CGGCTATG-ATAGAGGC [P3_FC_4]


title: rna_P3_4_A_CGGCTATG-TATAGCCT [P3_A_4]


title: rna_P3_2_STR_CTGAAGCT-GGCTCTGA [P3_STR_2]


title: rna_P1_7_H_GAATTCGT-CCTATCCT [P1_H_7]


title: rna_P1_5_H_ATTCAGAA-CAGGACGT [P1_H_5]


title: rna_P1_5_FC_ATTCAGAA-TAATCTTA [P1_FC_5]


title: rna_P3_2_FC_CTGAAGCT-ATAGAGGC [P3_FC_2]


title: rna_P1_7_FC_GAATTCGT-ATAGAGGC [P1_FC_7]


title: rna_P3_2_H_CTGAAGCT-CCTATCCT [P3_H_2]


title: rna_P3_2_A_CTGAAGCT-TATAGCCT [P3_A_2]


title: rna_P1_5_A_ATTCAGAA-AGGCGAAG [P1_A_5]


title: rna_P1_4_H_ATTCAGAA-CCTATCCT [P1_H_4]


title: rna_P1_7_A_GAATTCGT-TATAGCCT [P1_A_7]


title: rna_P1_4_A_ATTCAGAA-TATAGCCT [P1_A_4]


title: rna_P1_4_STR_ATTCAGAA-GGCTCTGA [P1_STR_4]


title: rna_P1_5_STR_ATTCAGAA-GTACTGAC [P1_STR_5]


title: rna_P1_1_H_GAGATTCC-CAGGACGT [P1_H_1]


title: rna_P1_10_STR_GAATTCGT-GTACTGAC [P1_STR_10]


title: rna_P1_1_FC_GAGATTCC-TAATCTTA [P1_FC_1]


title: rna_P1_1_STR_GAGATTCC-GTACTGAC [P1_STR_1]


title: rna_P1_10_FC_SWP_GAATTCGT-TAATCTTA [P1_FC_10]


title: rna_E18_9_STR_GAGATTCC-GGCTCTGA [E18_STR_9]


title: rna_E18_9_H_GAGATTCC-CCTATCCT [E18_H_9]


title: rna_P1_10_H_SWP_GAATTCGT-CAGGACGT [P1_H_10]


title: rna_E18_9_A_GAGATTCC-TATAGCCT [E18_A_9]


title: rna_P3_4_H_CGGCTATG-CCTATCCT [P3_H_4]


title: rna_E18_8_H_TCCGGAGA-CAGGACGT [E18_H_8]


title: rna_P1_4_FC_ATTCAGAA-ATAGAGGC [P1_FC_4]


title: rna_P1_10_A_GAATTCGT-AGGCGAAG [P1_A_10]


title: rna_E18_7_STR_TCCGGAGA-GGCTCTGA [E18_STR_7]


title: rna_E18_8_STR_TCCGGAGA-GTACTGAC [E18_STR_8]


title: rna_E18_7_H_TCCGGAGA-CCTATCCT [E18_H_7]


title: rna_E18_8_FC_TCCGGAGA-TAATCTTA [E18_FC_8]


title: rna_E18_5_A_ATTACTCG-AGGCGAAG [E18_A_5]


title: rna_E18_5_STR_ATTACTCG-GTACTGAC [E18_STR_5]


title: rna_E18_5_H_ATTACTCG-CAGGACGT [E18_H_5]


title: rna_E18_5_FC_ATTACTCG-TAATCTTA [E18_FC_5]


title: rna_E18_7_A_TCCGGAGA-TATAGCCT [E18_A_7]


title: rna_E18_7_FC_TCCGGAGA-ATAGAGGC [E18_FC_7]


title: rna_E18_4_FC_ATTACTCG-ATAGAGGC [E18_FC_4]


title: rna_P1_1_A_GAGATTCC-AGGCGAAG [P1_A_1]


title: rna_E18_4_A_ATTACTCG-TATAGCCT [E18_A_4]


title: rna_E18_4_H_ATTACTCG-CCTATCCT [E18_H_4]


title: rna_E18_9_FC_GAGATTCC-ATAGAGGC [E18_FC_9]


title: rna_E18_4_STR_ATTACTCG-GGCTCTGA [E18_STR_4]


title: WL4

city: Houston

first: Zhongcheng

last: Shi

state: TEXAS

address: 1102 Bates

department: Pathology and Immunology

institute: Baylor College of Medicine

description:
WL4
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option

data_processing:
bcl2fastq2-v2.17.1.14
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: sample.counts.txt,  unique hit count for all the genes

source_name: neutrophils

extract_protocol:
low-density and high-density neutrophils were purified from mouse peritoneal cells elicited by Casein, and RNA was extracted using a Qiagen RNeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neutrophils

value: wildtype

tag: population

value: low density neutrophils


title: WL2

description:
WL2
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option


title: WH4

description:
WH4
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option

value: high density neutrophils


title: KL1

description:
KL1
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option

value: H2R deficient


title: WH2

description:
WH2
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option


title: KH1

description:
KH1
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option


title: KH2

description:
KH2
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option


title: EC64

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the mm10 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: mm10
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Endothelial Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, after MACS and FACS purification, a single PGC or gonadal somatic cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 25 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the PGCs of the same fetal sample were pooled together and the amplified cDNA of the gonadal somatic cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 2500 platform (sequenced by Novogene).

value: Endothelial Cells


title: EC51


title: EC52


title: EC63


title: EC53


title: EC49


title: EC50


title: EC48


title: EC44


title: KL2

description:
KL2
Sequencing instrument information not available. Illumina HiSeq 2500 used as a likely option


title: EC47


title: EC45


title: EC41


title: EC42


title: C666_1_streptoc

city: Nanning

first: Bo

last: Li

state: Guangxi

address: No. 22 Shuangyong road

department: Radiation oncology

institute: Guangxi Medical University

description: Gene expression data from C666-1 cells co-culture with streptoc

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Cartridge HG-U133 plus 2.0

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using RevertAid First Strand cDNA Synthesis Kit.

growth_protocol: All cells were incubated at 37℃ in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: NP69 cells co-culture with LPS, PGN, streptoc. C666-1 NPC cells co-culture with streptoc.

value: Nasopharyngeal carcinoma


title: NP69_LPS

description: Gene expression data from NP69 cells co-culture with LPS

value: Normal nasopharyngeal epithelium


title: C666_1_ctrl

description: Gene expression data from C666-1 cells


title: NP69_PGN

description: Gene expression data from NP69 cells co-culture with PGN


title: NP69_streptoc

description: Gene expression data from NP69 cells co-culture with streptoc


title: EC37


title: EC43


title: EC46


title: MDAMB203

city: Mitaka

first: Yamaga

last: Takashi

country: Japan

institute: Kyorin University

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: MDA-MB-231 and T-47D cells were purchased from ATCC and cultured in RPMI1640 complete medium (nacalai).

extract_protocol: total RNA was extracted with Isogen (Nippon Gene) according to manufacturer's protocol.

treatment_protocol: Cells were treated with 100μM of JPH203 for 24 hours. Same concentration of Captisol was used as control.

tag: cell line


title: SGC0946 THP1 H3K79me2 ChIP-seq

city: Shanghai

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Reads were aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: Hg38
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins).

source_name: THP1 cell line

growth_protocol: Human cells THP1 cells were cultured in RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin + 2 mM L-Glutamine + 55 μM β-mercaptoethanol.

extract_protocol:
For immunoprecipitation, on day 1 antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat. no. 10002D) by incubating at 4 °C for 3 hours. Afterwards, the bead-antibody complexes were washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4 °C overnight. On day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH 7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10 µg/ml RNase A for both elution and RNA digestion, and incubated at 55 °C for 1 hour. Then Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the temperature was increased to 65 °C for crosslink reversal. After incubation for 4 to 6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).
ChIP-seq libraries: The libraries were constructed with 2–10 ng immunoprecipitated DNA. After end-repair, A-tailing, and barcode ligation, barcoded DNA was amplified by 16-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

treatment_protocol: For fixation, cells were fixed initially  with 0.4% formaldehyde at room temperature for 10 min. For sonication, fixed cells were washed twice with PBS and resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH 7.4) supplemented with Protease Inhibitor Cocktail (Millipore, cat. no. 535140) at a concentration of 40 million cells/ml; genomic DNA was disrupted to a size range of 100 to 500 bp.

tag: genotype/variation

value: WT

tag: antibody

tag: fixation

value: EGS + FA


title: DMSO THP1 H3K79me2 ChIP-seq

value: DMSO


title: EC40


title: EC38


title: EC39


title: T47D203


title: EC33


title: EC34


title: EC SNHG12 gapmer 4

description: HUVEC Replicate 4

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.

source_name: Human umbilical vein endothelial cells

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs, Lonza).

treatment_protocol: siRNA knockdown of the indicated genes

value: Endothelial Cell

value: SNHG12 gapmer treatment


title: MCF-7 shRNA control biological replicate 2

city: Baltimore

first: Rajini

last: Rao

state: MD

address: 725 N Wolfe St, WBSB 201

department: Physiology

institute: The Johns Hopkins University School of Medicine

hyb_protocol: 18hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform using their HG-U133_Plus_2.na36.annot.csv and HG-U133_Plus_2.cdf annotation files.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: MCF-7 Control

label_protocol: Biotinylated cRNAs were prepared with the GeneChip HT 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: MCF-7 cells were gown in DMEM (Thermo Fisher Scientific, Waltham, MA) containing antibiotic, and 10% FBS (Sigma Aldrich, St. Louis, MO)

extract_protocol: RNA was isolated using QIAGEN’s RNEasy Mini (Qiagen, Germantown, MD) manufacturer’s protocol.

treatment_protocol: A mixture of two shRNA constructs for SPCA2 was used. MCF-7 cells were transfected with virus for 48 hours, and selected with puromycin at varying concentrations according to kill curves performed  (2 µg/mL)

value: Control


title: MDAMBcont


title: Naïve replicate 2

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
RAN-seq reads were aligned to Mouse (Mus musculus) reference genome (version GRCm39 Gencode M26) and corresponding annotation were obtained from Gencode using STAR v2.7.8a
R package DESeq2 was used for data normalization and differentially expressed gene identification for each treatment vs. naïve samples. The expression value of each gene was expressed as read counts.   Differentially expressed genes (DEGs) were obtained by comparing treated samples with naïve samples (control) and all vaccinated samples compared with each other.  A q-value (adjusted p-value) of less than 0.05 and 2 fold change in ratio (abs (log2 fold-change) ≥1) were used to generate a DEGs list. KEGG pathway enrichment analyses were done using GOAL software; pathway enrichment p-values were computed using the Fisher’s exact test via the hypergeometric distribution and were BH corrected [71].
Genome_build: GRCm39 Gencode M26
Supplementary_files_format_and_content: In excel file format, including Raw read counts data;  Alignment summary

source_name: Naïve

extract_protocol:
Total RNA was isolated from the spleens of mice vaccinated ID with LVS or one of the SCHU S4 deletion mutants ΔclpB, ΔgplX and ΔlpcC, (4 spleens from each group treated individually throughout) using Tri reagent (Life Technologies). Genomic DNA contamination was removed by Turbo DNA-Free Kit (Life Technologies). RNA was processed for paired-end RNA sequencing using Illumina Hi-Seq2000 (Genome Quebec).
RNA-Seq Libraries were generated using the TruSeq strand RNA kit (Illumina). The RNA-Seq libraries were quantified by Qbit and qPCR according to the Illumina Sequencing Library qPCR Quantification Guide and the quality of the libraries was evaluated on Agilent Bioanalyzer 2100 using the Agilent DNA-100 chip.

treatment_protocol: Young adult female BALB/c mice (n=4 / group) were immunized ID with 105 CFU of one or other of the four vaccine strains . Immunization was performed by inoculation of 50µl of bacteria at a concentration of ~ 2x106 CFU /ml into the shaved mid-belly. The formation of an overt bleb at the site of inoculation was deemed to be indicative of successful ID administration. Four days after vaccination, mice were killed and serum was prepared from whole blood, and spleens were removed intact. Untreated mice were used as negative (naïve) controls.

value: spleens

value: BALB/c

tag: Sex

value: female


title: T47Dcont


title: WKY1

first: Xing

last: Tan

address: 880 Xiangyin Road

department: Department of Marine Biomedicine and Polar Medicine, Naval Medical Center

institute: Naval Medical University (Second Military Medical University)

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: RVLM from WKY rat

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Their weight was between 250-350 g, and were kept in 12h light and 12h dark animal room.

extract_protocol: RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: strain

value: Wistar-Kyoko (WKY) rats

value: rostral ventrolateral medulla (RVLM)


title: MCF-7 shSPCA2 biological replicate 2

source_name: MCF-7 ATP2C2 knockdown

value: ATP2C2 knockdown


title: MCF-7 shSPCA2 biological replicate 1


title: SHR3

source_name: RVLM from SHR

value: spontaneously hypertensive rats (SHR)

tag: tissue


title: WKY2


title: Naïve replicate 1


title: MCF-7 shRNA control biological replicate 1


title: SHR1


title: EC36


title: NP69_ctrl

description: Gene expression data from NP69  cells


title: WKY3


title: Naïve replicate 4


title: Naïve replicate 3


title: EC SNHG12 gapmer 2

description: HUVEC Replicate 2

value: primary


title: Live vaccine Strain (LVS) replicate 3

source_name: LVS


title: EC32

value: Endothelial Cells


title: EC35


title: Live vaccine Strain (LVS) replicate 4


title: SHR2


title: EC31


title: Live vaccine Strain (LVS) replicate 1


title: EC SNHG12 gapmer 3

description: HUVEC Replicate 3


title: EC Control gapmer 4

description: HUVEC Replicate 4

value: Control gapmer treatment


title: Live vaccine Strain (LVS) replicate 2


title: EC Control gapmer 2

description: HUVEC Replicate 2


title: mutant lpcC replicate 1

source_name: mutant lpcC


title: EC Control gapmer 1

description: HUVEC Replicate 1


title: mutant gplX replicate 3

source_name: mutant gplX


title: EC28


title: mutant lpcC replicate 4


title: EC30


title: EC29


title: YBX1 siRNA 4

description: HUVEC Replicate 4

value: YBX1 siRNA Knockdown


title: EC Control gapmer 3

description: HUVEC Replicate 3


title: EC22


title: mutant gplX replicate 1


title: mutant lpcC replicate 3


title: mutant lpcC replicate 2


title: EC SNHG12 gapmer 1

description: HUVEC Replicate 1


title: mutant gplX replicate 4


title: EC21


title: mutant clpB replicate 3

source_name: mutant clpB


title: mutant gplX replicate 2


title: mutant clpB replicate 4


title: YBX1 siRNA 3

description: HUVEC Replicate 3


title: mutant clpB replicate 2


title: YBX1 siRNA 2

description: HUVEC Replicate 2


title: EC19


title: IMP3 siRNA 4

description: HUVEC Replicate 4

value: IMP3 siRNA Knockdown


title: EC27


title: IMP3 siRNA 3

description: HUVEC Replicate 3


title: EC16


title: EC17


title: IMP3 siRNA 1

description: HUVEC Replicate 1


title: EC15


title: DNAPKcs siRNA 4

description: HUVEC Replicate 4

value: DNAPKcs siRNA Knockdown


title: EC20


title: DNAPKcs siRNA 3

description: HUVEC Replicate 3


title: YBX1 siRNA 1

description: HUVEC Replicate 1


title: DNAPKcs siRNA 2

description: HUVEC Replicate 2


title: EC18


title: IMP3 siRNA 2

description: HUVEC Replicate 2


title: EC12


title: EC14


title: mutant clpB replicate 1


title: EC13


title: DNAPKcs siRNA 1

description: HUVEC Replicate 1


title: EC11


title: DHX9 siRNA 3

description: HUVEC Replicate 3

value: DHX9 siRNA Knockdown


title: DHX9 siRNA 4

description: HUVEC Replicate 4

value: Endothelial Cell


title: DHX9 siRNA 2

description: HUVEC Replicate 2


title: EC10


title: EC8


title: EC9


title: DHX9 siRNA 1

description: HUVEC Replicate 1


title: Control siRNA 4

description: HUVEC Replicate 4

value: Control siRNA (Scramble) Knockdown


title: EC7


title: EC6


title: Control siRNA 2

description: HUVEC Replicate 2


title: EC5


title: U266_I3MO_rep2

city: Tianjin,China

first: Mu

last: Hao

address: 288 Nanjing Road, Heping District, Tianjin

institute: State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence trimmomatic v0.32 with parameters java -Xmx6000M -jar trimmomatic-0.36.jar PE -threads 4 -phred33 'SLIDINGWINDOW:4:20 MINLEN:30 LEADING:20 TRAILING:20', and then mapped to hg38 whole genome using star v.2.4.2a with parameters STAR \ --genomeDir /path/to/starIndex/GRCh38v22 \ --readFilesIn outdir/Sample1/clean/clean_1.fq.gz outdir/Sample1/clean/clean_2.fq.gz \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand zcat \ --outSAMattributes All \ --chimSegmentMin 10 \ --outSAMattrIHstart 0 \ --outSAMstrandField intronMotif \ --limitBAMsortRAM 2000000000 \ --runThreadN 4 \ --outWigType wiggle \ --outWigStrand Stranded \ --quantMode GeneCounts \ --outFileNamePrefix outdir/Sample1/align/ samtools index outdir/Sample1/align/Aligned.sortedByCoord.out.bam.
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using a protocol according to TCGA. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: Bone marrow

extract_protocol:
Total RNAs of 2 x 10^6  cells for each sample were extracted using the RNeasy Mini Kit (Qiagen). The RNA yield was determined by Nanodrop technology (Thermo Fisher Scientific), and quality was verified on the Agilent 2100 bioanalyzer (Agilent Technologies). cDNA libraries libraries were prepared for sequencing using standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: 10µM I3MO


title: Control siRNA 3

description: HUVEC Replicate 3


title: EC4


title: Control siRNA 1

description: HUVEC Replicate 1


title: M2_1

first: Yu-Tzu

last: Tai

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR with parameters (--outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000
Reads Per Kilobase of exon per Megabase of library size (RPKM) and ranscripts Per Kilobase Million (TPM) were calculated by using RSEM (Li et al, BMC bioinformatics, 2011)
Differential analysis was performed by DESeq2 (Love et al, Genome biology, 2018)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample ...

growth_protocol: H929 cells were cultured in RPMI1640 with 10% FBS

extract_protocol:
Total RNA was extracted using TRIzol and purified using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer’s instructions. Concentration and quality of extracted RNA were measured and quality control (QC) were done following three main methods:  (1) Nanodrop: Preliminary quantitation  (2) Agarose Gel Electrophoresis: tests RNA degradation and potential contamination  (3) Agilent 2100: checks RNA integrity and quantitation
Libraries from mRNA were prepared using 1 μg of RNA starting material and NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Illumina, CA, USA) according to the manufacturer’s protocol. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.  The quality control of library consists of three steps:  (1) Qubit 2.0: tests the library concentration preliminarily.  (2) Agilent 2100: tests the insert size.  (3) Q-PCR: quantifies the library effective concentration precisely.

treatment_protocol: H929 cells were treated with M2 (0.5 uM) or control vehicle (solvent) for 1 day followed by RNA extraction.  Two biological replicates from independent treatment were used.

value: myeloma derived cell line


title: ctrl_2

value: solvent


title: U266_WT_rep1

value: DMSO


title: U266_WT_rep2


title: ctrl_1


title: Gastric mucosa_autoiimune gastritis_08

type: genomic

city: Tsukiji, Chuo-ku

first: Chihiro

last: Takeuchi

state: Tokyo

department: Division of Epigenomics

institute: National Cancer Center Research Institute

description: biopsy specimen, gastric mucosa

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the standard phenol/chloroform method.

tag: gender

value: Female

tag: age

tag: disease state

value: autoiimmune gastritis


title: M2_2

tag: cell type

tag: treatment


title: RPMI8226_I3MO_rep1

tag: genotype


title: U266_I3MO_rep1


title: Gastric mucosa_H-pylori-associated gastritis_08

description: biopsy specimen, gastric mucosa

value: Male

value: H. pylori-assocatited gastritis


title: Gastric mucosa_autoiimune gastritis_10

description: biopsy specimen, gastric mucosa


title: RPMI8226_WT_rep2


title: hNPC_vec_rep2

first: ping

last: li

state: Guangdong

address: No.74, zhongshan Road

institute: sun-yat sen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastp (version 0.12.4) software was use to do reads filtering, including adapter removing, low quality base removing (lower than 20),et. al.
HISAT2 (version 2.1.0)software were used to do alignmnet with reference genome with bwa algorithm
Reads count mapping to each chromosome were calculated using HTSeq (0.10.0) software and FPKM was used to measure gene expression
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include expression values for genes

growth_protocol: hNPCs were cultured in ReNcell NSC maintenance medium.

extract_protocol:
Total RNA was extracted using Trizol reagent (invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quntity and purity were analyzed by Life Invitrogen Qubit® 3.0 and NanoDrop™.
RNA libraries were prepared for sequencing using standard illunima protocols

treatment_protocol: hNPCs expreesing NS5 48 hours post infection by lentivirus.

value: human neural progenitor cells (hNPCs)

value: vector control


title: hNPC_NS5_rep2

value: overexpressed ZIKV-NS5


title: Gastric mucosa_H-pylori-associated gastritis_09

description: biopsy specimen, gastric mucosa


title: hNPC_vec_rep1


title: Gastric mucosa_autoiimune gastritis_11

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_normal_gastritis_03

description: biopsy specimen, gastric mucosa

value: normal


title: Gastric mucosa_autoiimune gastritis_07

description: biopsy specimen, gastric mucosa


title: RPMI8226_I3MO_rep2


title: Gastric mucosa_autoiimune gastritis_06

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_H-pylori-associated gastritis_05

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_normal_gastritis_04

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_normal_gastritis_02

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_autoiimune gastritis_09

description: biopsy specimen, gastric mucosa


title: WT-RNAseq-2

city: new york

first: clemence

last: claussin

state: New York

address: 1275 York Avenue

department: molecular biology

institute: Memorial sloan kettering cancer center

description: RNAs were pulsed labeled for 15min, 15min after released with

data_processing:
Base calling was performed using Guppy (Oxford Nanopore)
Reads were mapped to the genome using Minimap2
position and orientation of the reads primers were defined using LAST ( kielbasa et al, 2011)

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: yeast were grown at 25C in rich media

extract_protocol:
RNAs were extracted using invitrogen extraction kit and as described in Baptista and Devys, 2018; mRNA was enriched using NEB mRNA selection kit #E7490S
Library was constructed using SQK-DSC109 library kit (Oxford Nanopore)
Nanopore MinION FLO-MIN106 flow cells R9

treatment_protocol: Cells were arrested into G1 phase with alpha factor, 15min after release from G1, 4-thiouracil was added to the culture to labelled nascent RNAs, cells were collected 30min after alpha factor release.

value: 30min S-phase at 25C with 15min pulsed labelled of 4-thiouracil


title: Gastric mucosa_autoiimune gastritis_05

description: biopsy specimen, gastric mucosa


title: small RNA sequencing from Exosome RNA_Wharton's jelly #4

city: Faridabad

first: Arup

last: Banerjee

state: Haryana

address: NCR Biotech Science Cluster

country: India

institute: Regional Centre for Biotechnology

data_processing:
Inbuilt Illumina Casava 1.8.2 software used for basecalling.
QC of sequenced reads were done by FASTQC.
Adapter cutting were done by cutadapt.
The raw reads corresponding to Illumina RNA-seq FASTQ files were aligned in Strand NGS software v3.4 against the human reference genome (Build hg19, Gene feature: UCSC Genes, Library layout: single end). Differential expression analysis of miRNA from different groups were performed using the DESeq script 2 via the script editor in Strand NGS with a p-value ≤ 0.05 and fold change 1.5 or 2 fold.
Quantification was done to obtain the read  densities by Strand NGS software.
Genome_build: Build hg19, Gene feature: UCSC Genes, Library layout: single end

source_name: Wharton's jelly Exosome isolated from conditioned media

growth_protocol: MSCs were propagated in DMEM (LG) media (Life Technologies, USA) containing 10% FBS (HyClone, USA), 2mM L-glutamine,100 U/ml of penicillin and 100 U/ml of streptomycin (Life Technologies, USA).

extract_protocol:
Exosomes were processed for total RNA isolation using miRCURY RNA Exosome Isolation kit (Exiqon, Denmark, Europe) following manufacturer’s recommendations.
RNA-seq library preparation was performed using TruSeq® RNA library Prep Kit v2 (Illumina).

treatment_protocol: For enrichment of exosomes, the MSCs were cultured in serum free media -STEMPRO® MSC SFM CTS (Thermo Fisher Scientific, USA) for 48 hours. The conditioned media from MSCs cultured for 48 h was pooled together for exosome isolation by ultracentrifugation

value: Wharton's jelly Exosome


title: Gastric mucosa_normal_gastritis_01

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_H-pylori-associated gastritis_04

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_autoiimune gastritis_02

description: biopsy specimen, gastric mucosa


title: rrm3-rep1

description: cell were arrested with alpha factor, released in presence of 400ug/mL brdu at 25C, and collected at 30min after release for replicon-seq experiment

data_processing:
Base calling was performed using Guppy (Oxford Nanopore)
Reads were mapped to the genome using Minimap2
BrdU containing reads were call using DNAscent V2, reads were split into 250bp interval to assign as BrdU positive or negative reads, BrdU score was then calculated, and only reads with a BrdU > or = 0.5 were selected
Custom genome was constructed from Nanopre reads using Canu.

extract_protocol:
DNA was extracted as in Replicon-seq protocol after calcium induction of MNase
Library was constructed using SQK-SKL109 or SQK-SKL110 kit (Oxford Nanopore)
Nanopore MinION FLO-MIN106 flow cells R9

treatment_protocol: Cells are arrested in G1 with alpha factor; 400ug/mL of BrdU was added 30min before release from G1 , cells were released into pre-warmed media containing 400ug/mL BrdU.

value: 30min S-phase at 25C with 400ug/mL BrdU


title: Gastric mucosa_H-pylori-associated gastritis_06

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_H-pylori-associated gastritis_02

description: biopsy specimen, gastric mucosa


title: WT-rep2


title: WT-RNAseq-1


title: hNPC_NS5_rep1


title: Gastric mucosa_H-pylori-associated gastritis_07

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_H-pylori-associated gastritis_01

description: biopsy specimen, gastric mucosa


title: ANBL6_BR_I3MO_rep2

value: bortezomib resistant

value: 5µM I3MO


title: small RNA sequencing from Exosome RNA_Bone marrow #4

source_name: Bone marrow Exosome isolated from conditioned media

value: Bone marrow Exosome


title: small RNA sequencing from Exosome RNA_Wharton's jelly #2


title: Gastric mucosa_H-pylori-associated gastritis_03

description: biopsy specimen, gastric mucosa


title: Gastric mucosa_autoiimune gastritis_03

description: biopsy specimen, gastric mucosa


title: TBI_Thalamus_t52 [miRNA-seq]

city: Kuopio

first: Noora

last: Puhakka

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Adapters were trimmed off as part of the base calling. Subsequenctly the data was quality checked with FastQC.
Sequences were mapped against rat reference genome RGSC3.4 and annotated with mirBase 20.
Genome_build: RGSC3.4
Supplementary_files_format_and_content: Count tables (tsv).

extract_protocol:
RNA was extracted rom the perilesional cortex and ipsilateral thalamus using a mirVana miRNA isolation kit (#AM1560, Life Technologies (Ambion) Carlsbad, CA, USA), QIAshredder (#79654, Qiagen), and AllPrep DNA/RNA Mini Kit (#80204, Qiagen). Thereafter, RNA purification was performed using miRCURY™ RNA Isolation Kit (#300111, Exiqon, Vedbaek, Denmark).
300ng of total RNA was converted into microRNA NGS libraries using NEBNEXT library generation kit (New England Biolabs Inc.) according to the manufacturer’s instructions. Samples were sequenced on the Illumina NextSeq 500 system.

value: Sprague-Dawley

value: Adult

value: traumatic brain injury

value: Thalamus

tag: molecule subtype

value: small RNA


title: ARP1_I3MO_rep1

value: wild type

value: 10µM I3MO


title: ARP1_I3MO_rep2


title: small RNA sequencing from Exosome RNA_Wharton's jelly #3


title: WT-rep1


title: small RNA sequencing from Exosome RNA_Bone marrow #3


title: ARP1_WT_rep2

value: DMSO


title: TBI_Thalamus_t56 [miRNA-seq]


title: ARP1_WT_rep1


title: ANBL6_BR_rep2


title: RPMI8226_WT_rep1


title: Control_Thalamus_t34 [miRNA-seq]

value: sham-operated control


title: small RNA sequencing from Exosome RNA_Wharton's jelly #1


title: ANBL6_BR_rep1


title: Control_Thalamus_t50 [miRNA-seq]


title: Control_Thalamus_t55 [miRNA-seq]


title: ANBL6_BR_I3MO_rep1


title: TBI_Thalamus_t24 [miRNA-seq]


title: small RNA sequencing from Exosome RNA_Adipose Tissue #4

source_name: Adipose Tissue Exosome isolated from conditioned media

value: Adipose Tissue Exosome


title: ANBL6_I3MO_rep1


title: TBI_Thalamus_t45 [miRNA-seq]


title: Control_Thalamus_t38 [miRNA-seq]


title: TBI_Cortex_c56 [miRNA-seq]

value: Cortex


title: TBI_Thalamus_t63 [miRNA-seq]


title: TBI_Cortex_c52 [miRNA-seq]


title: small RNA sequencing from Exosome RNA_Adipose Tissue #2


title: small RNA sequencing from Exosome RNA_Bone marrow #2


title: Control_Thalamus_t32 [miRNA-seq]


title: ANBL6_WT_rep1


title: Control_Thalamus_t26 [miRNA-seq]


title: Gastric mucosa_autoiimune gastritis_04

description: biopsy specimen, gastric mucosa

value: Male

value: autoiimmune gastritis


title: Gastric mucosa_autoiimune gastritis_01

description: biopsy specimen, gastric mucosa

value: Female


title: Control_Cortex_c38 [miRNA-seq]


title: ANBL6_I3MO_rep2


title: Control_Cortex_c32 [miRNA-seq]


title: TBI_Thalamus_t22 [miRNA-seq]


title: Control_Cortex_c34 [miRNA-seq]


title: TBI_Cortex_c63 [miRNA-seq]


title: m7G_Normoxia_IP

city: Zhan Jiang

first: Xiaoyu

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

data_processing:
Paired-end reads were harvested from an Illumina NovaSeq 6000 sequencer
Cutadapt (v1.9.3), command line software, was used to identify and trim 3’ adapter and low-quality bases for rawdata.
The clean data were mapped to the reference genome (GRCz11) using Hisat2 software (v2.0.4).
For RNA-seq: Guiding by the Ensembl GTF gene annotation file, Cuffdiff software (part of cufflinks) was used to obtain the gene level FPKM as the expression profiles of mRNA, fold change and p-value were calculated based on FPKM
For MeRIP-seq: To identify the methylated sites on RNAs (peaks), MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP-Seq data were performed by utilizing a Perl script, findMotifGenome.pl, from HOMER software.
Genome_build: GRCz11
Supplementary_files_format_and_content: Gene expression values(FPKM and Counts) and methylated sites

organism: Danio rerio

source_name: zebrafish brain tissue

extract_protocol:
Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA)
For RNA-seq : TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA)
For MeRIP-seq: GenSeqTM RNA IP Kit (GenSeq Inc., China) and NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA)
RNA-seq and MeRIP-seq

treatment_protocol: Adult wild-type zebrafish (Danio rerio) were bred according to standard methods. For hypoxia treatment, we followed settings established in a previously published protocol(Yu et,al 2011) with modified conditions. Briefly, zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water (O2: 0.3-0.4 mg/L). Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4-0.6 mg/L. Nitrogen (1 L/min) was used to maintain the dissolved oxygen level in the water. After approximately 5 minutes, when the fish became motionless, the zebrafish brain were dissected on ice after anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.

value: brain


title: ScACS-8-2_S45

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

institute: University of Alberta

data_processing:
Partek Flow: Trim bases Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Partek Flow: Alignment (STAR 2.7.3a) Default settings from Partek Flow
Partek Flow: Quantify to annotation model (Partek E/M) Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Partek Flow: Filter features Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts
Partek Flow: Normalize counts Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
Partek Flow: ANOVA for DEGs Factors: Treatment + Sex + Sex*Donor info(Random) + Treatment*Sex. Shrinkage of error term variance: Limma-trend

source_name: human engineered meniscus

growth_protocol: Meniscus cells (meniscus fibrochondrocytes) were isolated from partial meniscectomy tissue samples. They were expanded in normoxia (standard 5% CO2, 95% air incubator) to passage 2 (~3 population doublings) with supplementation of TGF-beta1 and FGF-2. They were then seeded onto cylindrical type I collagen scaffolds (6 mm diameter, 3.5 mm height) at a density of 5x10^6 million/cm^3 and cultured for 2 weeks in normoxia in a standard chondrogenic medium containing TGF-beta3 to form engineered meniscus tissues before treatment.

extract_protocol:
RNA was extracted using LunaNano PureSPIN columns with a DNAse digestion step. RNA concentrations were measured using a NanoDrop One. Equal masses of RNA from 4 replicate tissues from each donor in each condition were then pooled together to reduce inter-replicate variability (12 pools in total). These samples were then shipped to the UBC Biomedical Research Center for RNA sequencing.
Illumina NextSeq 500: PolyA selection, 20million paired reads

treatment_protocol: After preculture period, tissues were randomly allocated into treatments in Static, CHP or SMG for 3 weeks. On the last day, tissues were put into TRIzol reagent and frozen to preserve RNA level changes.

value: M

tag: mechanical condition

value: SMG


title: small RNA sequencing from Exosome RNA_Adipose Tissue #3


title: Control_Cortex_c55 [miRNA-seq]

value: Sprague-Dawley


title: ANBL6_WT_rep2


title: TBI_Cortex_c22 [miRNA-seq]

value: Adult


title: ScACS-7-3_S43

value: F

value: CHP


title: ScACS-8-1_S44

value: Static


title: TBI_Thalamus_t56 [RNA-seq]

data_processing:
Tophat (v2.0.11) was used to align the sequencing reads to the reference genome (RGSC3.4) with the sequence aligner Bowtie2 (v. 2.2.2).
Cufflinks (v2.2.1) was used to take the alignment results from Tophat to assemble the aligned sequences into transcripts, constructing a map or a snapshot of the transcriptome. Reference genome version RGSC3.4 was used. To guide the assembly process, an existing transcript annotation (Rnor_5.0 Ensembl) was used.
When comparing groups, Cuffdiff (Trapnell et al. 2013) was used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output.
Genome_build: RGSC3.4
Supplementary_files_format_and_content: Count table (count_table) and differential gene expression analysis (diff).

extract_protocol:
RNA was extracted rom the perilesional cortex and ipsilateral thalamus using a mirVana miRNA isolation kit (#AM1560, Life Technologies (Ambion) Carlsbad, CA, USA), QIAshredder (#79654, Qiagen), and AllPrep DNA/RNA Mini Kit (#80204, Qiagen). Thereafter, RNA purification was performed using miRCURY™ RNA Isolation Kit (#300111, Exiqon, Vedbaek, Denmark).
The library preparation was done using TruSeq® Stranded mRNA Sample preparation kit (Illumina inc). The starting material (300 ng) of total RNA was mRNA enriched using the oligodT bead system.
RNA-Seq. Nextseq500 instrument using High Output sequencing kit (75 cycles) according to the manufacturer instructions (Illumina Inc.).

value: traumatic brain injury

value: Thalamus


title: Control_Cortex_c50 [miRNA-seq]

value: small RNA


title: TBI_Cortex_c45 [miRNA-seq]


title: Control_Thalamus_t55 [RNA-seq]

value: sham-operated control


title: small RNA sequencing from Exosome RNA_Adipose Tissue #1

value: Adipose Tissue Exosome


title: ScACS-7-2_S42


title: m6A_Normoxia_IP


title: m6A_Normoxia_Input


title: TBI_Thalamus_t45 [RNA-seq]


title: ScACS-6-3B_S12


title: small RNA sequencing from Exosome RNA_Bone marrow #1

value: Bone marrow Exosome


title: Control_Thalamus_t34 [RNA-seq]


title: Control_Cortex_c26 [miRNA-seq]

value: Cortex


title: Control_Thalamus_t32 [RNA-seq]


title: m7G_Normoxia_Input


title: TBI_Cortex_c24 [miRNA-seq]


title: Control_Thalamus_t26 [RNA-seq]


title: ScACS-6-2B_S11


title: m7G_Hypoxia_IP


title: TBI_Thalamus_t24 [RNA-seq]


title: rrm3-rep2

value: 30min S-phase at 25C with 400ug/mL BrdU


title: ScACS-6-1B_S10


title: TBI_Thalamus_t63 [RNA-seq]


title: m7G_Hypoxia_Input


title: m5C_Normoxia_Input


title: TBI_Thalamus_t52 [RNA-seq]


title: ScACS-8-3_S46


title: Control_Thalamus_t50 [RNA-seq]


title: TBI_Cortex_c52 [RNA-seq]


title: ScACS-7-1_S41


title: Control_Thalamus_t38 [RNA-seq]


title: m5C_Hypoxia_Input


title: m6A_Hypoxia_IP


title: TBI_Thalamus_t22 [RNA-seq]


title: m6A_Hypoxia_Input


title: TBI_Cortex_c63 [RNA-seq]


title: Control_Cortex_c32 [RNA-seq]


title: Control_Cortex_c55 [RNA-seq]


title: ScACS-5-2B_S8


title: m5C_Hypoxia_IP


title: TBI_Cortex_c56 [RNA-seq]


title: ScACS-5-1B_S7


title: m1A_Normoxia_IP


title: ScACS-4-3B_S6


title: Control_Cortex_c38 [RNA-seq]


title: ScACS-4-1B_S4


title: Control_Cortex_c34 [RNA-seq]


title: ScACS-4-2B_S5


title: m1A_Hypoxia_Input


title: m5C_Normoxia_IP


title: ScACS-5-3B_S9


title: Control_Cortex_c50 [RNA-seq]


title: m1A_Normoxia_Input


title: TBI_Cortex_c45 [RNA-seq]


title: m1A_Hypoxia_IP


title: TBI_Cortex_c22 [RNA-seq]


title: TBI_Cortex_c24 [RNA-seq]


title: mRNA_Hypoxia


title: CRISPRaX_Screen_Top_r3

city: Berlin

first: Till

last: Schwämmle

address: Ihnestrasse 63

institute: Max Planck Institute for Molecular Genetics

data_processing:
Alignment and read counting was performed using MAGeCK (0.5.9.3) with options [count --norm-method control] for all samples together (Li et al. 2014, Li et al. 2015).
Statistical analysis was performed using MAGeCK (0.5.9.3) with options [mle --norm-method control] (Li et al. 2014, Li et al. 2015)
Genome_build: -
Supplementary_files_format_and_content: char_library_dup.txt: Text file containing descriptions of the individual guides used for the screen. As some guides target multiple TSSs, they are duplicated within the file.
Supplementary_files_format_and_content: raw_counts_dup.txt: Raw counts assessed via MAGeCK count. Guides targeting multiple TSSs are duplicated.
Supplementary_files_format_and_content: mageck_mle_dup.txt: Results of the MAGeCK MLE analysis, showing enrichment of individual TSSs within the screen.

source_name: Mouse embryonic stem cells

extract_protocol:
The PrimeFlow RNA assay (Thermofisher) was used according to the manufacturer’s recommendations. Specifically, the assay was performed in conical 96-well plates for a total of 200 million cells per replicate with 5 million cells per well  using Xist specific probes, labelled with Alexa-Fluor647 (VB1-14258). 20 million cells were snap-frozen after the two fixation steps to be used as the Unsorted fraction.  Samples were resuspended in PrimeFlow™ RNA Storage Buffer before flow cytometry. Here, four different populations were sorted according to Xist expression. In more detail, a Xist-negative population was taken from the bottom-15% of Xist-expressing cells. Three Xist-positive populations were taken in 15%-intervals from the top Xist-expressing cells (0-15% = High, 15-30% = Medium, 30-45% = Low). Around 11-15 million cells were recovered per fraction. After sorting, the cell pellets were snap-frozen and stored at -80°C.  DNA from frozen cell pellets was isolated through phenol/chloroform extraction. Cell pellets were thawed and resuspended in 250 µl of lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2 M NaCl and 5 mM DTT (Roth) in TE Buffer) and incubated overnight at 65°C. The next day 200 µg of RNAse A (Thermo Fisher Scientific) were added and the samples were incubated at 37°C for 1 h. 100 µg of Proteinase K (Sigma) were subsequently added, followed by a 1 h incubation at 50°C. Phenol/chloroform/isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed for 1 min and subsequently centrifuged at 16,000 x g for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 h. DNA was pelleted by centrifugation for 16,000 x g for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50 µl water.
Sequencing libraries were prepared from both sorted and unsorted cell populations for each of the three independent screen replicates. Genomic DNA from frozen cell pellets was isolated by Phenol/Chloroform extraction. Briefly, cell pellets were thawed and resuspended in 250 µl of Lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2 M NaCl and 5 mM DTT (Roth) in TE Buffer) and incubated overnight at 65 °C. 200 µg of RNAse A (Thermo Fisher Scientific) were added to the sample and incubated at 37 °C for 1 h. 100 µg of Proteinase K (Sigma) were subsequently added followed by a 1 h incubation at 50 °C. Phenol/Chloroform/Isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed at room temperature for 1 min and subsequently centrifuged at 16,000 x g for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 2 µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80 °C for 1 h. DNA was pelleted by centrifugation for 16,000 x g for 15 min at 4 °C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50 µl H2O.  The genomically integrated sgRNA cassette was PCR-amplified to attach sequencing adaptors and sample barcodes. To ensure proper library coverage (300x), a total of 20 µg of each sample were amplified using the ReadyMix Kapa polymerase (Roche) with a total of 25 cycles and an annealing temperature of 56 °C. A relatively low amount of 0.5 µg genomic DNA was amplified per 50 µl PCR reaction since in samples stained with Flow-FISH, PCR amplification was inhibited at higher DNA concentrations. PCR was performed with the primer LR175 in combination with a sample-specific primer which contains a distinct 6-nucleotide barcode to allow sample identification after multiplexed deep sequencing (Primer sequences in Suppl. Table 4, LR178/LR180). Successful amplification was verified on a 1% agarose gel and the reactions were pooled. 1 ml of each pooled PCR was purified using the QIAquick PCR Purification Kit (Qiagen) and the resulting amplicons were loaded on a 1% agarose gel and purified using the QIAquick Gel Extraction Kit (Qiagen).
CRISPR screen

treatment_protocol: E14-STN-dTsixP cells were passaged for two passages in Serum+LIF-containing medium before a total of 1.200.000 cells were transduced with viral supernatant of the sgRNA library (MOI = 0.3). Puromycin selection (1 ng/µl, Sigma) was started 48 h after transduction and kept until the end of the experiment. Four days after transduction, 7.200.000 cells were differentiated by LIF withdrawal for 2 days. Expression of CRISPRa-SunTag system was induced using doxycycline (Clontech, 1 µg/ml) one day before differentiation and kept throughout the rest of the protocol. Cells were harvested with trypsin to reach a single cell suspension for Flow-FISH after 2 days of differentiation.

tag: condition

value: Top

tag: replicate

tag: strain background

tag: assay

value: CRISPRa-Screen


title: ScACS-3-3B_S3


title: HK-1 monolayer_20 uM Baicalein treatment_replicate 2

city: Bangkok

first: Pichamon

last: Kiatwuthinon

address: 50 Ngamwongwan Rd. Ladyao Jatujak

department: Biochemistry

country: Thailand

institute: Kasetsart University

hyb_protocol: The HumanArray (HOA 5.1) (PharynxBiotec) chips were first pre-warmed for 10 minutes in a 60 °C oven. Then, the arrays were pre-hybridized with prehybridization buffer for 1 hour at 42 °C. The arrays were rinsed with ultrapure water and spun to eliminate water residue. The chips were then hybridized with Cy3-labeled cDNA strands, covered with a cover glass slides, incubated in hybridization chambers saturated with 2x SSC buffer for 16-18 hours at 42 °C.

scan_protocol: The intensity of Cy3 hybridized arrays were subjected to be scanned by Tecan scanner LS Reloaded. The intensities of the image were processed and quantified with Array Pro Analyzer software. A laser 532 nm was used to scan with 6 µm resolution and 220 PMT gain. The raw data formats were stored in TIFF images and GPR data files.

data_processing: The results from scanning of all three biological replicate data were obtained in raw intensity format. The intensities of control and unknown genes were removed. The remaining obtained raw data on intensities were re-scaled by obtained log2 value, quantile normalized, and ranked, respectively. One-way ANOVA was performed for statistical tests.

source_name: nasopharyngeal cancer

label_protocol: Ten grams of total RNA from each sample were reverse-transcribed by reverse transcriptase enzyme (Thermo scientific) in the presence of seven grams of Cy3-labeled nonamer random primers, 3.33 mM dNTP, Ribolock nuclease inhibitor, and 5 mM DTT according to the typical reverse transcription protocol. The reaction mixture was incubated at 25 and 42°C for 5 and 180 minutes, respectively. Then, 200 mM NaOH and 20 mM EDTA were added at 1:1 ratio to remove the RNA template strands. The reaction was incubated at 65 °C for 10 minutes. One volume of 1 M HEPES buffer was added to stop the reaction. The Cy3-labeled cDNA strands were purified by Gene Jet DNA purification kit (Thermo scientific) according to the manual. The purified cDNA samples were stored at -80 °C until a hybridization step.

growth_protocol: NPC HK-1 cells were cultured in RPMI-1640 media supplemented with 10% FBS and 100 U/ml of penicillin/streptomycin, incubated at 37 °C with 5% CO2. On the day of cell plating, cells were trypsinized into single cell suspension. The cell pellets for RNA extraction were obtained by centrifugation at 3,000 rpm for 5 minutes.

extract_protocol: The cells were collected from the cultures and lysed using lysis buffer. Total RNA was then extracted using the RNA extraction kit according to the manual (E.Z.N.A.® Total RNA Kit I, Omega Biotek). Total RNA samples were treated with DNAse I (Omega Biotek) to remove contaminated DNA. Then, the RNA samples were spectrophotometrically quantified by measuring the absorbance at 260 and 280 nm using Nanodrop. The RNA samples with the absorbance ratio of 260/280 nm higher than 1.8 were carried to a labeling process.

treatment_protocol: A stock solution of baicalein was prepared at 100 mM in dimethyl sulfoxide (DMSO). The desired concentrations of baicalein, 10 and 20 uM were freshly prepared in serum-free medium prior use. The cells were plated on petri dishes overnight and incubated with the baicalein solution for 24 hours. After incubation, the fresh media was replaced, and the cells were collected for RNA extraction.

value: Nasopharyngeal carcinoma (NPC)

tag: cell line

tag: culture system

value: monolayer in Petri dish

tag: agent

value: Baicalein

tag: dose

value: 20 uM


title: ScACS-3-2B_S2

tag: Sex

value: F

value: SMG


title: CRISPRaX_Screen_Top_r2

growth_protocol: E14-STN-dTsixP cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)) at a density of 3.13*10^4 cells/cm2.


title: mRNA_Normoxia

tag: tissue

value: brain


title: Control_Cortex_c26 [RNA-seq]

tag: strain

value: Sprague-Dawley

tag: age

value: Adult


title: ScACS-1-3B_S20

value: CHP


title: ScACS-3-1B_S24

value: Static


title: HK-1 monolayer_20 uM Baicalein treatment_replicate 3

tag: disease state


title: ScACS-2-3B_S23

value: M


title: CRISPRaX_Screen_Unsorted_r3

value: Unsorted


title: ScACS-1-2B_S19


title: HK-1 monolayer_20 uM Baicalein treatment_replicate 1


title: HK-1 monolayer_non treatment_replicate 3

value: control


title: HK-1 monolayer_10 uM Baicalein treatment_replicate 2

value: 10 uM


title: HK-1 monolayer_non treatment_replicate 2


title: HK-1 monolayer_10 uM Baicalein treatment_replicate 3


title: ScACS-2-2B_S22


title: ScACS-2-1B_S21


title: CRISPRaX_Screen_Unsorted_r2


title: CRISPRaX_Screen_Top_r1

value: Top


title: HK-1 monolayer_10 uM Baicalein treatment_replicate 1


title: Caco-2 cells, grown in a microfluidic device, TiO2-control, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

source_name: Caco-2 cells, grown in a microfluidic device (seeding density of 75,000 cell per cm2; exposed to a continuous flow of 100 µL/h) for 21 days, then exposed to TiO2-control medium for 6 hrs

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: A Caco-2 cell line (HTB-37), derived from a human colorectal adenocarcinoma, was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cells were grown (at passage number 29-45) in DMEM supplemented with 10 % FBS, 1 % penicillin-streptomycin, and 1 % MEM non-essential amino acid, further referred to as DMEM+. The cells were seeded at a density of ~75,000 cells per cm2 on 12-well Transwell PET inserts (0.4 µm pore size, 1.12 cm2 surface area, Corning Amsterdam, The Netherlands) and cultured in DMEM+ for 21 days. The medium was changed every two to three days. In the microfluidic device, the cells were seeded at a density of 75,000 cell per cm2 and were allowed to attach to the membrane for 24 h, without the fluid flow. The membrane was then inserted in the microfluidic chip and cells were exposed to a continuous flow of 100 µL/h DMEM+ until day 21 of culturing . By doing so, the shear stress in the AP compartment was ~0.002 dyne/cm2 at the cell membrane area, where the cells were grown. The DMEM+ medium contained sodium bicarbonate (10 mM) to optimize the pH buffering capacity.

extract_protocol: Cells were first washed with PBS. RNA was then isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: The metal-oxide nanomaterials were prepared and dispersed according to the Nanogenotox dispersion protocol (https://www.anses.fr/en/system/files/nanogenotox_deliverable_5.pdf). At day 21 post-seeding Caco-2 cells in either the gut-on-chip or Transwell were exposed to equal deposited doses based on the in vitro sedimentation, diffusion and dosimetry (ISDD) modelling. For the gut-on-chip, suspensions of 100 µg/mL TiO2 and 80 µg/mL ZnO were prepared in DMEM+. For each nanomaterial a dispersion solution in DMEM+ without metal served as control group. Solutions were perfused via the upper channel with a flow rate of 100 µL/h. DMEM+ without nanomaterials was pumped through the basolateral channel with an equal flow rate. After about 42 min the upper chamber was fully filled with the solution and the flow was stopped for 6 h in order to exclude the possible influence of laminar flow in gut-on-chip system resulting in the different exposure doses. This enabler the best comparison of the cellular response by cells grown in the two systems. In the Transwells, the cell culture medium of the AP side was replaced with 500 uL nanomaterial suspension of 50 µg/mL for TiO2 or 10 µg/mL ZnO and the medium of the basolateral side was refreshed with DMEM+ without nanomaterial culture medium followed by 6 h incubation.

value: Caco-2 (HTB-37)

tag: passage number

value: between 29-45

tag: growing condition

value: dynamic

tag: treatment

value: TiO2-control medium


title: Caco-2 cells, grown in a microfluidic device, ZnO, replicate 4

source_name: Caco-2 cells, grown in a microfluidic device (seeding density of 75,000 cell per cm2; exposed to a continuous flow of 100 µL/h) for 21 days, then exposed to a suspension of 80 µg/mL ZnO  in medium for 6 hrs

value: a suspension of 80 µg/mL ZnO in medium


title: HK-1 monolayer_non treatment_replicate 1

value: Nasopharyngeal carcinoma (NPC)

value: monolayer in Petri dish


title: Caco-2 cells, grown on Transwell inserts, ZnO, replicate 3

source_name: Caco-2 cells, grown on a Transwell PET insert (0.4 µm pore size, 1.12 cm2 surface area) for 21 days, then exposed to a suspension of 10 µg/mL ZnO  in medium for 6 hrs

value: static

value: a suspension of 10 µg/mL ZnO in medium


title: Fat1-TAC2

city: Guangzhou

first: Xiang

last: Li

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Original data were filtered to remove reads with joints, indeterminate base information and low quality, followed by sequencing error rate check and GC content distribution check to obtain clean reads used in subsequent analysis.
Clean reads were then mapped to mm10 genome with HISAT2 compares software.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Expression_Gene.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Heart

extract_protocol:
Total RNAs from the ventricular tissues of the sham group and the pressure overload group were isolated using TRIzol® Reagent (Thermo Fisher Scientific, USA). Each group contains two independent samples.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: group

value: Ventricular tissue


title: Caco-2 cells, grown on Transwell inserts, TiO2-control, replicate 1

source_name: Caco-2 cells, grown on a Transwell PET insert (0.4 µm pore size, 1.12 cm2 surface area) for 21 days, then exposed to TiO2-control medium for 6 hrs


title: Caco-2 cells, grown in a microfluidic device, TiO2, replicate 4

source_name: Caco-2 cells, grown in a microfluidic device (seeding density of 75,000 cell per cm2; exposed to a continuous flow of 100 µL/h) for 21 days, then exposed to a suspension of 100 µg/mL TiO2  in medium for 6 hrs


title: Caco-2 cells, grown on Transwell inserts, ZnO-control, replicate 4

source_name: Caco-2 cells, grown on a Transwell PET insert (0.4 µm pore size, 1.12 cm2 surface area) for 21 days, then exposed to ZnO-control medium for 6 hrs

value: ZnO-control medium


title: Caco-2 cells, grown in a microfluidic device, ZnO-control, replicate 2

source_name: Caco-2 cells, grown in a microfluidic device (seeding density of 75,000 cell per cm2; exposed to a continuous flow of 100 µL/h) for 21 days, then exposed to ZnO-control medium for 6 hrs


title: Caco-2 cells, grown in a microfluidic device, ZnO, replicate 3


title: HEALTHY CTRL sample 11

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using GRCh38 (Gencode release 27) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19
Supplementary_files_format_and_content: counts, FPKMs, TPMs

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 500-ng total RNA (Illumina). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

value: Blood

tag: cell type

value: Healthy Control


title: HEALTHY CTRL sample 10

value: Peripheral blood mononuclear cells (PBMCs)


title: Fat1-Sham2


title: ScACS-1-1B_S18

value: F

tag: mechanical condition

value: Static


title: HEALTHY CTRL sample 9


title: Fat1-Sham1


title: HEALTHY CTRL sample 12


title: HEALTHY CTRL sample 8


title: WT-TAC2

value: WT-TAC


title: Fat1-TAC1


title: HEALTHY CTRL sample 5


title: Caco-2 cells, grown in a microfluidic device, ZnO-control, replicate 3

value: Caco-2 (HTB-37)


title: Caco-2 cells, grown on Transwell inserts, ZnO, replicate 1

value: between 29-45


title: Caco-2 cells, grown in a microfluidic device, ZnO-control, replicate 4

value: dynamic


title: Caco-2 cells, grown in a microfluidic device, ZnO-control, replicate 1


title: Caco-2 cells, grown on Transwell inserts, ZnO-control, replicate 3


title: Caco-2 cells, grown in a microfluidic device, ZnO, replicate 2


title: CRISPRaX_Screen_Unsorted_r1

tag: condition

value: Unsorted

tag: replicate

tag: strain background

value: CRISPRa-Screen


title: KO2

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to mm10 mouse transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include UMI values for each cell

source_name: mouse embryonic cells

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq 4000 platform in 150 bp pair-ended manner

value: Endothelial Cells

tag: development stage

tag: genotype

value: Cdh5-Cre;Notch1fl/fl embryos (KO)


title: Caco-2 cells, grown on Transwell inserts, ZnO, replicate 2

tag: cell line

value: static


title: HEALTHY CTRL sample 2


title: Caco-2 cells, grown on Transwell inserts, ZnO, replicate 4

value: a suspension of 10 µg/mL ZnO in medium


title: WT

value: Cdh5-Cre;Notch1fl/+ littermate controls (Ctrl)


title: Caco-2 cells, grown on Transwell inserts, TiO2, replicate 3

source_name: Caco-2 cells, grown on a Transwell PET insert (0.4 µm pore size, 1.12 cm2 surface area) for 21 days, then exposed to a suspension of 50 µg/mL TiO2  in medium for 6 hrs

value: a suspension of 50 µg/mL TiO2 in medium


title: Caco-2 cells, grown in a microfluidic device, TiO2-control, replicate 2

value: TiO2-control medium


title: Caco-2 cells, grown in a microfluidic device, ZnO, replicate 1

value: a suspension of 80 µg/mL ZnO in medium


title: Caco-2 cells, grown on Transwell inserts, ZnO-control, replicate 2

value: ZnO-control medium


title: Caco-2 cells, grown on Transwell inserts, TiO2, replicate 1


title: Caco-2 cells, grown on Transwell inserts, ZnO-control, replicate 1


title: Caco-2 cells, grown on Transwell inserts, TiO2, replicate 2


title: EC115

value: Tie2-Dre;Nr2f2-CrexER X Unc5b-tdTomato


title: Caco-2 cells, grown on Transwell inserts, TiO2-control, replicate 4


title: Caco-2 cells, grown in a microfluidic device, TiO2, replicate 2

value: a suspension of 100 µg/mL TiO2 in medium


title: WT-TAC1

value: WT-TAC

value: Ventricular tissue


title: ALS sample 18

value: Blood

value: Peripheral blood mononuclear cells (PBMCs)

value: Amyotrophic Lateral Sclerosis


title: HEALTHY CTRL sample 7

value: Healthy Control


title: HEALTHY CTRL sample 6


title: HEALTHY CTRL sample 4


title: WT-Sham2

value: WT-Sham


title: Caco-2 cells, grown in a microfluidic device, TiO2, replicate 3

value: Caco-2 (HTB-37)

value: between 29-45

value: dynamic


title: Caco-2 cells, grown in a microfluidic device, TiO2, replicate 1


title: Caco-2 cells, grown in a microfluidic device, TiO2-control, replicate 4


title: ALS sample 17


title: Caco-2 cells, grown in a microfluidic device, TiO2-control, replicate 1


title: HEALTHY CTRL sample 3


title: ALS sample 16


title: EC111

value: Endothelial Cells

value: Unc5b-tdTomato reporter mouse lines