title: luminal breast tumor_rep3

city: chengdu

first: huang

last: liang

address: No.24, South First Section, First Ring Road, Wuhou District, Chengdu City

institute: sicuan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2
Stringtie were used to assembl lncRNA reads and Cuffmerge to merge transcript by sample,then select  :exon number>2 & length > 200nt transcript
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Stringtie software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: luminal breast tumor

extract_protocol:
Total RNA was extracted from breast cancer fresh tissues, including 3 TNBC tissues and 3 Luminal breast cancer tissues. Total RNA from each sample was quantified by NanoDrop ND-1000 (ThermoFisher) and the quality of the RNA was assessed with the Agilent Bioanalyzer 2100. Transcriptome libraries from the mRNA fractions were generated following the RNA-Seq protocol (Illumina). Each sample was sequenced in a single lane with the Illumina PE150 Analyzer (Illumina) on a 150-bp paired-end run.   For strand-specific library construction, dUTP method of second-strand marking was employed as described(64). For the data processing, the raw sequencing reads were aligned to human reference genome (hg19) using the splice-aware aligner HISAT2(65). Read counts for each gene were normalized into FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values(66). The cutoff of differential gene expression was FDR <0.05, normalized by the respective control group.
Transcriptome libraries from the mRNA fractions were generated following the RNA-Seq protocol (Illumina).
lncRNA

treatment_protocol: untreated

value: Breast Cancer

tag: subtype

value: Luminal Breast Cancer


title: C2-3

status: Public on Nov 29 2021

type: SRA

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

country: USA

institute: Boston Children's Hospital

description: diploid-and-auto-tetraploid_gene_counts.txt

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed for adapter sequences using cutadapt v1.8.1 and read quality was confirmed using fastqc v0.11.9.
Reads were aligned using STAR v2.7.1a with two-pass mapping to a concatenated human-chimpanzee genome (hg38 and pt6).
The number of uniquely-mapped reads (MAPQ = 255) that overlap each gene was counted with featurecounts from the subread v1.6.0 package using a curated annotation (hg38.pt6.gtf). To generate the annotations, GRCh38.94 human exon annotations from Ensembl were mapped from hg38 to pt6 using pslMap. After removing mappings where the number of bases that map is less than half of the query exon size, we retained only exons that uniquely mapped from humans to chimpanzees. We then removed genes for which exons map to opposite DNA strands, different scaffolded chromosomes, or where consecutive exons map more than 800kb apart. We further filtered out exons where more than 10% of reads from diploid or auto-tetraploid lines map to the incorrect species when mapped to the composite genome.
Genome_build: hg38 and pt6
Supplementary_files_format_and_content: Gene counts for each species are represented with the human ensembl ID in the processed files. For allo-tetraploid lines, each sample is represented twice in the associated processed file, once as human allele counts ("Hs" prefix) and once as chimpanzee allele counts ("Pt" prefix).

molecule: polyA RNA

organism: Pan troglodytes

source_name: induced pluripotent stem cells

growth_protocol: iPSC lines were grown in mTeSR1 or mTeSR Plus (StemCell Technologies).

extract_protocol:
RNA was isolated using the Direct-Zol RNA Miniprep kit (Zymo Research, cat #R2051) or by Genewiz.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep (Illumina) or by Genewiz and sequenced on a HiSeq 4000 (2x150bp).

treatment_protocol: iPSCs were collected using accutase and flash frozen for storage at -80C.

tag: cell type

value: induced pluripotent stem cells

tag: cell line


title: 4H_S4 het_hip

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ sequencing reads were adaptor-trimmed and quality-filtered with Trimmomatic (Bolger et al., 2014), prior to mapping to the mm10 mouse reference genome with STAR (Dobin and Gingeras, 2016).
Gene count normalization and differential gene expression havehas been done with DESeq2 (Love et al., 2014).
GeneSCF was employed for functional enrichment analysis and ontology (Subhash and Kanduri, 2016).
Low-dimensional embedding of high-dimensional data was done by t-Distributed Neighbor Embedding (t-SNE) machine learning algorithm.
Genome_build: mm10

organism: Mus musculus

source_name: Scn1a het  Hippocampus

extract_protocol:
Cerebral cortex and hippocampus from 4-5- month- old mice were dissected and total RNA has been extracted with TRIzolTM reagent (ThermoFisher Scientific). Only high-quality RNA with ana RNA integrity number (RIN) of 8 or higher was used.
Library preparation and sequencing havehas been performed with the TruSeq RNA Library Preparation Kit v2 kit (Illumina) by Genewiz.

tag: tissue

value: hippocampus


title: C1-1


title: SQT1_hiPSCCM_mimicCtrl_1

city: Munich

first: Dena

last: Esfandyari

state: Bavaria

address: Haus 607, Biedersteiner Str. 29, IPT

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technical University of Munich

data_processing:
bcl2fastq (v2.20) for basecalling, fastq conversion, adapter trimming (only for SQT1 samples) and demultiplexing
Trim Galore! (v0.4.2 in Galaxy) for adapter trimming in healthy hiPSC-CMs
RNA STAR (v2.6.0 in Galaxy) with default parameters for alignment
StringTie (v1.3.6 in Galaxy) was used for transcript assembly and quantification
DESeq2 (v2.11.40.2 in Galaxy) for differential expression analysis and normalizing the counts
Genome_build: GRCh38, Gencode annotation v34 for SQT1 and v28 for healthy cells
Supplementary_files_format_and_content: tabular raw gene counts; excel file of the normalized count generated by DESeq2, TPM and FPKM

organism: Homo sapiens

growth_protocol: the hiPSCs were maintained in Geltrex-coated plates (1 ml per 35 mm plate, 1 hour incubation at 37 °C) in E8-flex medium (2 ml per 35 mm plate, medium exchange every other day) and passaged with Versene (1 ml per 35 mm plate, incubation for 5-10 min at room temperature) when confluent. For cardiac differentiation, the cells were passaged into 12 well plates and cultured in cardio differentiation medium to reach 85-90% of confluency, the optimal cell density for starting the differentiation (d0). The differentiation carried out using Wnt signaling modulators, CHIR99021 and IWP2 (both from Merck Millipore). The yielded hiPSC-CMs were maintained in cardio culture medium and one round of metabolic selection was performed between d20-30 in order to enrich cardiomyocytes. After selection hiPSC-CMs were enzymatically dissociated (using Collagenase I and Trypsin), replated in lower densities and maintained in cardio culture medium for approximately 60 days for further maturation.

extract_protocol:
After transfection of hiPSC-CMs with mimics or antimiRs for 48 h, the cells were washed with PBS 3 times and total RNA was isolated using peqGOLD RNAPure (VWR). The integrity and quantity of RNA was determined using Agilent Bioanalyzer 2100 or Agilent TapeStation 4200.
For healthy hiPSC-CMs, libraries were prepared from 1 µg RNA using Illumina TruSeq Stranded mRNA kit and for SQT1 hiPSC-CMs Illumina mRNA ligation kit was used for library preparation.

treatment_protocol: To elevate the intracellular level of miR-365, the cells were transfected with synthetic mimic-365. Inhibition of endogenous miR-365 was achieved by transfection of LNA-antimiR-365 (Exiqon-Qiagen). Negative control oligonucleotides with the same chemistry were used in each case (mimic-Ctrl and antimir-Ctrl, respectively). Transfection was performed using Lipofectamine RNAiMAX to  reach a final concentration of 25 nM oligonucleotides. The medium was exchanged 15-24 hours after transfection and the cells were processed 48 hours post-transfection.

value: iPSC-derived cardiomyocyte

tag: treatment

value: mimic-Ctrl

tag: disease state

value: short QT syndrome type 1


title: AS-415988-LR-47252

city: Freiburg

first: Christopher

last: Berlin

address: Hugstetter Straße 55

institute: University Hospital Freiburg

description: plus TAM

data_processing:
The Cell Ranger Single Cell Software Suite 3.1 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting
Instrument model NOVASEQ6000
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

molecule: total RNA

extract_protocol:
10x Chromium 3´ scRNA-seq (v2 chemistry) was performed according to the manufacturer's instructions.
10x Sequencing libraries were generated according to the manufacturer's instructions.

value: AOM/DSS tumour organoids

tag: genotype

tag: passages


title: 3H_S3 het_hip


title: AS-415984-LR-47251

description: plus TAM


title: C2-1


title: C1-3


title: luminal breast tumor_rep2

country: China


title: 15C_S15 het_cx

source_name: Scn1a het Cortex

value: cortex


title: 16C_S16 het_cx


title: luminal breast tumor_rep1


title: AS-415982-LR-47251

description: minus TAM


title: Triple Negative Breast Cancer rep3

source_name: Triple Negative Breast Cancer

value: Triple Negative Breast Cancer


title: Triple Negative Breast Cancer rep2


title: AS-415980-LR-47251

description: minus TAM


title: RNA-seq Tet2Rank–/–; Tet3aRank+/– osteoclasts rep1

city: Kyotanabe

first: Keizo

last: Nishikawa

state: Kyoto

address: 1-3, Tatara Miyakodani

department: Medical Life Systems

country: Japan

institute: Graduate School of Life and Medical Sciences

description: RNA-seq

data_processing:
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: Tet2Rank–/–; Tet3aRank+/– osteoclasts

extract_protocol:
Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturers’ instructions.
The library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode. Illumina Casava1.8.2 software used for basecalling.

treatment_protocol: Bone marrow cells derived from mice were seeded and cultured in alpha-MEM with 10%FBS containing M-CSF. After 2 days, adherent cells were used as bone marrow-derived monocyte/macrophage precursor cells (BMMs). The BMMs were further cultured in the presence of RANKL and M-CSF to generate osteoclasts.

value: Bone marrow-derived osteoclasts

tag: gender

value: Female

tag: strain


title: 231_lung2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2
Stringtie were used to assemble lncRNA reads and Cuffmerge to merge transcript by sample,then select  :exon number>2 & length > 200nt transcript
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Stringtie software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: lung

growth_protocol: Cells were cultured according to the recommended protocols

extract_protocol:
Adherent cells were collected with trypsin-EDTA and suspended with PBS.total RNA was harvested using Trizol (Invitrogen) according to the manufacturer’s instructions. Total RNA from each sample was quantified by NanoDrop ND-1000 (ThermoFisher) and the quality of the RNA was assessed with the Agilent Bioanalyzer 2100. Transcriptome libraries from the mRNA fractions were generated following the RNA-Seq protocol (Illumina). Each sample was sequenced in a single lane with the Illumina PE150 Analyzer (Illumina) on a 150-bp paired-end run.   For strand-specific library construction, dUTP method of second-strand marking was employed as described(64). For the data processing, the raw sequencing reads were aligned to human reference genome (hg19) using the splice-aware aligner HISAT2(65). Read counts for each gene were normalized into FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values(66). The cutoff of differential gene expression was FDR <0.05, normalized by the respective control group.
Transcriptome libraries from the mRNA fractions were generated following the RNA-Seq protocol (Illumina).
lncRNA

treatment_protocol: To discover the potential drivers of TNBC metastasis, we established an in vivo model by injecting MDA-MB-231cells into the tail veins of mice. Then, the breast tumor cells that successfully grew into metastatic lung tumors were collected and expanded in vitro, followed by re-injected into the tail veins of mice for lung metastasis. After three rounds of selection, a highly metastatic subline, MDA-MB-231-P3, was established


title: 14C_S14 het_cx


title: Anoctamin5-Si (NUGC4)

type: RNA

city: Kyoto city

first: Tomoyuki

last: Fukami

state: (None)

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

label: biotin

source_name: Total RNA of NUGC4 cells

label_protocol: standard protocol

growth_protocol: Cells were cultured in RPMI-1640 (Nacalai Tesque, Kyoto, Japan) containing 100 μg/ml of streptomycin, 100 U/ml of penicillin, and 10% fetal bovine serum (FBS) at 37℃ in a 5% CO2 incubator.

extract_protocol: We extracted total RNA by using an RNeasy kit (Qiagen, Valencia, CA)

treatment_protocol: siRNA was transfected 24 h after seeding. All siRNA reverse transfection procedures were performed using Lipofectamine RNAiMAX reagent (Invitrogen, Carlsbad, CA, USA) with a final siRNA concentration of 20 nmol/l as described by the manufacturer. ANO5 siRNA (Stealth RNAiTM siRNA #HSS137119) and control siRNA (Stealth RNAiTM siRNA Negative Control) were obtained from Invitrogen.

tag: genotype/variation


title: 13C_S13 het_cx


title: AS-415978-LR-47251

description: minus TAM


title: AS-415980-LR-47252

description: minus TAM


title: 231_lung1

value: highly metastatic subline, MDA-MB-231-P3


title: AS-415976-LR-47252

description: minus TAM


title: 4'-BR 3

city: Madison

first: Nihal

last: Ahmad

state: Wisconsin

address: WIMR II, 1111 Highland Ave

department: Dermatology

institute: University of Wisconsin

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing: nSolver software with advanced analysis module (NanoString Technologies, Seattle, WA) was used for the QC, normalization, differential gene expression, and functional pathways score analyses in accordance with guidance provided by Nanostring. Principle component analysis (PCA) was performed to assess sample grouping.

label: Nanostring

source_name: BrafV600E/PtenNULL melanoma mice

label_protocol: standard NanoString protocol

extract_protocol: RNA was extracted from tumors obtained from control and 4'-BR-treated mice (n = 6), followed by determination of expression of 770 genes (730 immune genes and 40 housekeeping genes) via the Mouse PanCancer Immune Profiling Panel using the nCounter platform in the NanoString Technologies laboratories.

treatment_protocol: Tumors were induced by topical application of 4-hydroxy-tamoxifen on shaved backs of 10-week-old mice, and treated with 4′‐BR (30 mg/kg b.wt.; intraperitoneally; 3d/week for 5 weeks).

tag: cancer type

value: Melanoma


title: Control 2


title: Negative-Control (NUGC4)

value: Negative-Control


title: AS-415976-LR-47251

description: minus TAM


title: RNA-seq Tet2Rank–/–; Tet3aRank+/– osteoclasts rep3

description: RNA-seq

value: Male


title: RNA-seq Wild-type osteoclasts rep1

description: RNA-seq

source_name: Wild-type osteoclasts


title: 231_con_rep1

source_name: con

value: triple negative breast cancer cell line, MDA-MB-231


title: Triple Negative Breast Cancer rep1

value: Breast Cancer


title: 4'-BR 2


title: RNA-seq Tet2Rank–/–; Tet3aRank+/– osteoclasts rep2

description: RNA-seq


title: AS-415978-LR-47252

description: minus TAM


title: 4'-BR 1


title: Liver_BMALKO_DD_CT44_A

status: Public on Nov 28 2021

city: Rehovot

first: Gal

last: Manella

state: Israel

address: 234 Herzel St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
The rest of analysis was done through the UTAP pipline. Reads were trimmed using cutadapt
Reads were mapped to genome (/shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index) using STAR (default parameters)
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
Counting was done using htseq-count (union mode)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files containing the raw counts for each gene and sample

source_name: Liver

growth_protocol: 3mo mice were housed under standard light-dark conditions (12h/12h) for 2 weeks before the experiment, and during the experiment.

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissection and stored at -80°C till used. For RNA extraction, the tissues were soaked in TRI-reagent (Sigma) and were homogenized by bead beater (Bead Ruptor e24, OMNI), and then proceeded by a standard TRI-reagent based RNA extraction protocol. RNA concentration was determined using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific). RNA Integrity was validated using 2200 TapeStation (Agilent).
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.

treatment_protocol: Mice were kept in constant darkness, food served ad libitum

tag: ct


title: Liver_BMALKO_DD_CT44_B


title: Liver_BMALKO_DD_CT44_D


title: Liver_BMALKO_DD_CT44_C


title: Liver_BMALKO_DD_CT40_C


title: RNA-seq Wild-type osteoclasts rep3

description: RNA-seq


title: 231_con_rep2


title: RNA-seq Wild-type osteoclasts rep2

description: RNA-seq


title: Control 3


title: Liver_BMALKO_DD_CT36_C


title: Liver_BMALKO_DD_CT36_D


title: Liver_BMALKO_DD_CT32_C


title: Liver_BMALKO_DD_CT36_A


title: Liver_BMALKO_DD_CT28_D


title: Control 1


title: AS-415982-LR-47252

description: minus TAM


title: Liver_BMALKO_DD_CT24_B


title: Liver_BMALKO_DD_CT40_D


title: Liver_BMALKO_DD_CT40_A


title: Liver_BMALKO_DD_CT36_B


title: Liver_BMALKO_DD_CT32_D


title: Liver_BMALKO_DD_CT20_C


title: Liver_BMALKO_DD_CT28_C


title: Liver_BMALKO_DD_CT28_B


title: Liver_BMALKO_DD_CT28_A


title: Liver_BMALKO_DD_CT32_B


title: Liver_BMALKO_DD_CT24_D


title: Liver_BMALKO_DD_CT24_C


title: Liver_BMALKO_DD_CT24_A


title: Liver_BMALKO_DD_CT40_B


title: Liver_BMALKO_DD_CT12_A


title: Liver_BMALKO_DD_CT12_B


title: Liver_BMALKO_DD_CT8_A


title: Liver_BMALKO_DD_CT4_C


title: Liver_BMALKO_DD_CT4_B


title: Liver_BMALKO_DD_CT20_D


title: Liver_BMALKO_DD_CT16_B


title: Liver_BMALKO_DD_CT20_B


title: Liver_BMALKO_DD_CT16_C


title: Liver_BMALKO_DD_CT12_D


title: Liver_BMALKO_DD_CT12_C


title: Liver_BMALKO_DD_CT0_C


title: Liver_BMALKO_DD_CT0_A


title: Liver_BMALKO_DD_CT8_D


title: Liver_PerDKO_DD_CT8_A

description: processed data file: R389_Liver_PerDKO_reads.xlsx

data_processing:
Illumina bcl2fastq software used for basecalling.
The rest of analysis was done through the UTAP pipline. Reads were trimmed using cutadapt
Reads were mapped to genome (/shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index) using STAR (default parameters)
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
Counting was done using htseq-count (union mode)
Normalization of the counts was performed using DESeq2 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files containing for each gene and sample the raw counts and normalized counts

growth_protocol: 3mo mice were housed under standard light-dark conditions (12h/12h) for 2 weeks before the experiment, in standard conditions with food provided ad libitum.

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissection and stored at -80°C till used. For RNA extraction, the tissues were soaked in TRI-reagent (Sigma) and were homogenized by bead beater (Bead Ruptor e24, OMNI), and then proceeded by a standard TRI-reagent based RNA extraction protocol. RNA concentration was determined using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific). RNA Integrity was validated using 2200 TapeStation (Agilent).
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.
3' RNA-seq for digital gene expression quantitation

treatment_protocol: Mice were kept in constant darkness, and harvested in 4 h intervals, starting at CT0 (beginning of first subjective day) until CT44 h.

value: PerDKO

tag: time point

value: Liver


title: Liver_BMALKO_DD_CT8_C


title: Liver_BMALKO_DD_CT4_D


title: Liver_PerDKO_DD_CT8_B


title: Liver_PerDKO_DD_CT44_B


title: Liver_PerDKO_DD_CT44_C


title: Liver_BMALKO_DD_CT8_B


title: Liver_BMALKO_DD_CT32_A


title: Liver_PerDKO_DD_CT40_D


title: Liver_PerDKO_DD_CT44_A


title: Liver_BMALKO_DD_CT16_D


title: Liver_BMALKO_DD_CT4_A


title: Liver_PerDKO_DD_CT4_D


title: Liver_PerDKO_DD_CT4_C


title: Liver_BMALKO_DD_CT0_B


title: Liver_PerDKO_DD_CT4_B


title: Liver_BMALKO_DD_CT0_D


title: Liver_PerDKO_DD_CT36_D


title: Liver_PerDKO_DD_CT44_D


title: Liver_PerDKO_DD_CT8_C


title: Liver_PerDKO_DD_CT40_A


title: Liver_PerDKO_DD_CT4_A


title: Liver_PerDKO_DD_CT36_A


title: Liver_PerDKO_DD_CT32_D


title: Liver_PerDKO_DD_CT36_B


title: Liver_PerDKO_DD_CT32_C


title: Liver_PerDKO_DD_CT32_B


title: Liver_PerDKO_DD_CT40_B


title: Liver_PerDKO_DD_CT32_A


title: Liver_PerDKO_DD_CT40_C


title: Liver_PerDKO_DD_CT28_D


title: Liver_PerDKO_DD_CT28_C


title: Liver_PerDKO_DD_CT28_B


title: Liver_PerDKO_DD_CT28_A


title: Liver_PerDKO_DD_CT24_D


title: Liver_PerDKO_DD_CT36_C


title: Liver_PerDKO_DD_CT16_D


title: Liver_PerDKO_DD_CT24_C


title: Liver_PerDKO_DD_CT20_B


title: Liver_PerDKO_DD_CT20_C


title: Liver_PerDKO_DD_CT24_B


title: Liver_PerDKO_DD_CT16_C


title: Liver_PerDKO_DD_CT24_A


title: Liver_PerDKO_DD_CT16_B


title: Liver_PerDKO_DD_CT12_D


title: Liver_PerDKO_DD_CT16_A


title: Liver_PerDKO_DD_CT12_A


title: Liver_PerDKO_DD_CT12_C


title: Liver_PerDKO_DD_CT12_B


title: Liver_PerDKO_DD_CT0_C


title: Liver_PerDKO_DD_CT0_D


title: Liver_PerDKO_DD_CT0_B


title: Liver_PerDKO_DD_CT0_A


title: Liver_WT_DD_CT8_D

description: processed data file: R370_Liver_WT_reads.xlsx

value: WT


title: Liver_WT_DD_CT8_C


title: Liver_WT_DD_CT8_B


title: Liver_WT_DD_CT8_A


title: Liver_WT_DD_CT44_B


title: Liver_WT_DD_CT44_D


title: Liver_WT_DD_CT44_A


title: Liver_PerDKO_DD_CT20_A


title: Liver_WT_DD_CT44_C


title: Liver_WT_DD_CT40_D


title: Liver_WT_DD_CT40_B


title: Liver_WT_DD_CT4_C


title: Liver_WT_DD_CT4_D


title: Liver_WT_DD_CT36_D


title: Liver_WT_DD_CT36_C


title: Liver_WT_DD_CT40_A


title: Liver_WT_DD_CT4_B


title: Liver_WT_DD_CT4_A


title: Liver_WT_DD_CT32_C


title: Liver_WT_DD_CT36_A


title: Liver_WT_DD_CT32_D


title: Liver_WT_DD_CT24_C


title: Liver_WT_DD_CT28_B


title: Liver_WT_DD_CT28_C


title: Liver_WT_DD_CT32_B


title: Liver_WT_DD_CT24_B


title: Liver_WT_DD_CT28_A


title: Liver_WT_DD_CT24_D


title: G9gl B cells_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Splenic Fo B cells sorted by gating the B220+ CD93- CD21lo CD23hi fraction from 8-week-old G9gl homozygous mice

data_processing:
Sequencing was performed on an Illumina HiSeq3000 platform in a 100 base paired-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: Splenic Fo B cells sorted by gating the B220+ CD93- CD21lo CD23hi from 8-w-old G9gl homozygous mice

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fisher) following the manufacturer’s instructions.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

value: B cells

value: G9gl homozygous


title: Liver_WT_DD_CT20_D


title: Liver_WT_DD_CT20_A


title: Liver_WT_DD_CT36_B


title: G9gl B cells_rep2


title: Liver_WT_DD_CT40_C


title: Liver_WT_DD_CT20_B


title: Liver_WT_DD_CT16_D


title: G9gl B cells_rep1


title: Liver_WT_DD_CT24_A


title: Liver_WT_DD_CT28_D


title: Liver_WT_DD_CT32_A


title: WT B cells_rep3

description: Splenic Fo B cells sorted by gating the B220+ CD93- CD21lo CD23hi fraction from 8-week-old B6 control mice

source_name: Splenic Fo B cells sorted by gating the B220+ CD93- CD21lo CD23hi from 8-w-old B6 ctrl mice

value: B6 control


title: Liver_WT_DD_CT16_B


title: WT B cells_rep2


title: WT B cells_rep1


title: totalRNA_2-cell_rep2

first: Yi

last: Zhang

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

data_processing: For paired-end sequencing reads of total RNA-seq, the first 3 nucleotides of read2 which were generated from TSO were firstly removed. For total RNA-seq and poly(A) RNA-seq, adaptors if presented in reads were trimmed with Trimmomatic (v0.39). The cleaned reads were mapped to mouse reference genome GRCm38 using STAR (v2.7.8a) with parameters: --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 and were converted to transcriptome alignments. RSEM (v1.3.1) was used to quantify the expression level of each gene. For total RNA-seq, the parameters for RSEM were --estimate-rspd --calc-ci --paired-end --strandedness reverse. For poly(A) RNA-seq, the parameters for RSEM were --estimate-rspd --calc-ci --paired-end --strandedness none.

source_name: 2 Cell

growth_protocol: MII oocytes were collected from superovulated female mice. For pre-implantation embryo collection, MII oocytes from WT B6D2F1/J female mice were fertilized with sperms from WT B6D2F1/J male in vitro. Oocytes and embryos were cultured at 37ºC under 5% CO2. The time when sperm were added to COCs was considered as 0-hour post fertilization (0 hpf). 1-cell, 2-cell, 4-cell, morula, and blastocyst embryos were collected at 12, 30, 48, 72, and 96 hpf, respectively.

extract_protocol: Total RNA-seq libraries were prepared using SMART-Seq® Stranded Kit (Clontech) following the manufacturer’s instructions. Poly(A) RNA-seq libraries were prepared using SMARTer ultralow input RNA cDNA preparation kit (Clontech). Nextera XT DNA library preparation kit (Illumina) was used for poly(A) RNA-seq cDNA fragmentation, adaptor ligation, and amplification according to the manufacturer’s instructions.

value: 2 Cell

value: untreated


title: Liver_WT_DD_CT16_A


title: liRiboseq_MII_rep1

data_processing: The first 3 nucleotides of each read which were generated from template switch oligo (TSO) from LiRibo-seq were removed and the poly(A) and adaptor sequences in each read were trimmed using Cutadapt (v2.10) with parameters: -m 20 -u 3 -a AAAAAAAA. Trimmed reads which were shorter than 20bp were discarded. To remove reads from rRNA and tRNA, we aligned the reads to sequences from SILVA rRNA database (https://www.arb-silva.de, release 138.1) and Genomic tRNA database (http://gtrnadb.ucsc.edu, mm10-tRNAs.fa), using bowtie2 (v2.4.2) with default parameters. Reads not mapped to rRNA and tRNA were used for further analysis. These reads were aligned to mouse reference genome GRCm38 using STAR (v2.7.8a) in end-to-end alignment mode and allowing 2 maximum mismatches per read. The genome alignments were converted to transcriptome alignments by STAR with Gencode M24 mouse gene annotations and only protein coding genes were used. To quantify the ribosome footprints for each protein coding gene, RSEM (v1.3.1) were employed with reads mapped to transcriptome as input and parameters: --estimate-rspd --calc-ci --strandedness forward.

molecule: cytoplasmic RNA

source_name: MII oocyte

extract_protocol: LiRibo-seq libraries were prepared using Active Ribo-Seq with RiboLace kit (IMMAGINA Biotechnology, RL001) and SMARTer® smRNA-Seq Kit (Takara, 635030) following the manufacturer’s instructions. Briefly, MII oocytes and embryos were cultured in KSOM with 10 g/ml of CHX and cultured at 37ºC under 5% CO2 for 15min. Then oocytes and embryos were briefly treated with Acidic Tyrode (Millipore) to remove zona pellucida, washed with M2 medium (Sigma-Aldrich), and finally washed with 0.2% BSA/PBS. 100-250 oocytes or embryos were collected and lysed with 100 ul of lysis buffer containing 1% of sodium deoxycholate, 5 U/ml DNase I, and 200 U/ml RiboLock RNase inhibitor. Oocytes and embryos were triturated with 30G needle and kept on ice for 15 min. After centrifugation at 20,000 g for 5 min, supernatant was transferred to a new tube and kept on ice for 20 min. Absorbance of lysate was checked at 260 nm with Nanodrop. Ribosome footprinting was generated with Nuclease treatment according to manufacturer’s instructions. Ribosome protected fragments (RPFs) were captured by functionalized RiboLace beads and purified by acid-phenol:chloroform following manufacturer’s instructions. Purified RPFs were dephosphorylated with T4 PNK diphosphatase and then used for library preparation with SMARTer® smRNA-Seq Kit (Takara, 635030). Artificial poly(A) tails were added to RPFs and cDNA were synthesized with 3’ smRNA dT primer. After amplification, 175-200 bp PCR products were purified with PAGE gel purification.

value: MII oocyte


title: Liver_WT_DD_CT12_D


title: Liver_WT_DD_CT12_C


title: Liver_WT_DD_CT20_C


title: totalRNA_MII_rep1


title: totalRNA_2-cell_rep1


title: Liver_WT_DD_CT16_C


title: Liver_WT_DD_CT0_C


title: Liver_WT_DD_CT12_B


title: ATAC_DMSO_rep2

library_source: genomic

data_processing: All the ATAC-seq reads were first trimmed of the adaptors with Cutadapt (v2.10), then aligned to the GRCm38 genomes using bowtie2 (v2.2.5) with the parameters: -X 800 -I 0 --no-mixed --no-discordant --no-unal. All the unmapped reads and duplicated reads were removed. The non-uniquely mapped reads were filtered by "XS:" flag in bam files. Reads with mapping quality (MAPQ) under 30 were removed by samtools (v1.11). bigwig files were generated using deeptools bamCoverage with parameters: --binSize 20 -e 250 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM. All the ATAC-seq peaks were called by macs2 with the parameters: -g mm --bdg --SPMR --nomodel -q 0.05 --nolambda --shift -100 --extsize 200.

molecule: genomic DNA

source_name: Zygote (paternal pronuclear)

extract_protocol: For ATAC-seq with paternal pronuclei (PPN), 1-cell embryos (12 hpf) were cultured in M2 medium containing 10 mg/ml cytochalasin B (Calbiochem) for 15 min. PPN were collected with minimal cytoplasm carryover using a Piezo-driven micromanipulator (Eppendorf). After washing with 1% BSA/PBS, 75-100 PPN were collected for ATAC-seq following the same protocol as previously described in Zhang et al., Genes & development, 2020.

treatment_protocol: For DMSO, cycloheximide (CHX), and alpa-Amanitin (AMA) treatment, MII oocytes were fertilized with sperms and treated with 20 ug/ml of CHX or AMA. For siRNA injection, GV oocytes were incubated in MEM + IBMX medium for 1 hour, and then oocytes were injected with 5 uM of siControl, siSmarcd2, or siCcnt2.

value: Zygote (paternal pronuclear)

value: treated with DMSO


title: totalRNA_1-cell_rep2

source_name: Zygote

value: Zygote


title: totalRNA_MII_rep2


title: RNA_Zygote_AMA_rep2

value: treated with α-amanitin


title: Liver_WT_DD_CT0_D


title: Coculture rep1

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

institute: The Weizmann Institute

data_processing:
Identification of human reads in the mouse RNA data was done as following: 1. Trimming of adapter and low quality bases with cutadapt v 2.8. 2. Alignment to hg38 with STAR (v 2.7.3a) using --alignEndsType EndToEnd and --outFilterMismatchNoverLmax 0. 3. Uniqly aligned reads with mapped mate were selected, and realigned to the mouse genome (mm10). 4. Reads which were aligned to hg38 with 0 mismatches and  with >2 mismatches with mm10 were considered as bonafide human reads. 5. HTseq was applied to count the number of reads par human gene.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: text, gene read count

organism:
Homo sapiens
Mus musculus

growth_protocol: All cell lines were cultured in DMEM (high glucose), supplemented with 10% Fetal Bovine Serum (FBS), 1 mM sodium pyruvate and antibiotics (0.1 mg/mL streptomycin and 10 U/mL penicillin) at 37 °C with 5% CO2

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Mini kit (Macharey Nagel) and RNA integrity was checked by Agilent Tapestation 2100, while the concentration was measured using a NanoDrop microvolume spectrophotometer and Qubit 2.0 BR assay
RNA-sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). 2 µg RNA of each sample were processed in two separate reactions. Libraries were amplified with 8 PCR cycles, and sequenced on a Novaseq 6000 SP1 flowcell with 2x150 bp paired-end reads.

treatment_protocol: MEF cells were either cultured alone (single culture) or in co-culture with MCF7 cells (co-culture) for 12 hours. After that, cells were trypisized and sorted by antigen-based magnetic sorting using CD326-magnetic microbeads. CD326 is specifically expressed on the surface of MCF7. CD326-depleted fraction is enriched with MEF cells. mRNAs from MCF7 in MEF cells are detected with RNA-Seq. For detailed protocol, see: 1. Dasgupta S, Gerst JE (2020) A protocol for non-biased identification of RNAs transferred between heterologous mammalian cell types using rna tagging, cell sorting, and sequencing. Methods in Mol.Biol. (Humana Press Inc.), pp 195–214

tag: sample type

value: Coculture

tag: biological replicate

value: rep 1

tag: technical replicate


title: ATAC_CHX_rep2

value: treated with CHX


title: Liver_WT_DD_CT0_B


title: totalRNA_1-cell_rep1


title: RNA_Zygote_AMA_rep1


title: Mix rep2

value: Mix

value: rep 2


title: Liver_WT_DD_CT0_A

value: Liver


title: RNA_Zygote_Control_rep1

value: WT


title: AMSC_Q39540_p4

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: Adipose-derived MSC_proliferating

growth_protocol: AMSCs were expanded in growth medium composed of Advanced MEM (Gibco) with 5% human platelet lysate (Mill Creek Life Sciences), 2 mM L-glutamine (Invitrogen), 2U/mL heparin (NovaPlus®) and antibiotics (100 U/ml penicillin, 100 g/ml streptomycin) and maintained at 37°C in 5 % CO2.

extract_protocol:
Total RNA was isolated from AMSCs using Trizol® Reagent (Thermo) and purified using the Direct-zol mini kit (Zymo).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD36-APC antibody (A87786, Beckman Coulter) with Anti-APC microbeads was utilized for labelling AMSCs for magnetic cell sorting.

value: Adipose-derived MSC

value: proliferating (~80% confluent)


title: RNA_Zygote_Control_rep2


title: Mix rep1


title: Liver_WT_DD_CT12_A


title: Coculture rep2


title: RNA_Zygote_CHX_rep2


title: AMSC_Q39536


title: RNA_Zygote_DMSO_rep1


title: RNA_Zygote_CHX_rep1


title: RNA_Zygote_DMSO_rep2


title: RNA_1-cell_rep2


title: RNA_MII_rep1


title: RNA_MII_rep2


title: AMSC_211p8_prolif_POS_B

tag: fraction/population

value: postive (enriched)


title: AMSC_211p8_prolif_UNSORT_C

tag: cell type

value: unsorted


title: RNA_1-cell_rep1

value: untreated


title: AMSC_211p8_conf_UNSORT_B

source_name: Adipose-derived MSC_confluent

value: 100% confluent.


title: AMSC_211p8_prolif_NEG_B

value: negative (depleted)


title: AMSC_211p8_conf_POS_C


title: lambda_D4

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

description: mislabelling during lib prep: day->IFN

data_processing:
RNA libraries were run on Illumina NovaSeq6000, basecalling was performed using Real-Time Analysis (RTA) v3.3.3
bcl files were converted to fastq files with bcl2fastq v2.20.0.422
Quality of fastq files was checked with CLC Genomics Workbench 20
FASTQ files of RNA sequencing files were imported into the Array Studio software v10.2.5.9 (QIAGEN, Cary, NC, USA) package for further data analysis.
All FASTQ files were aligned to the gene model Ensembl v96 and to the reference library Human B38 using the proprietary OmicSoft Aligner OSA62.
Genome_build: human NCBI genome build B38; Ensembl v96
Supplementary_files_format_and_content: xlsx

source_name: healthy tissue from explanted lungs

extract_protocol:
Total RNA was purified from hAECs using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions with preceding DNase I digestion with RNase-Free DNase Set (Qiagen). Quality and integrity of total RNA was controlled on 5200 Fragment Analyzer System (Agilent Technologies).
RNA sequencing library was generated from 50 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols.
The libraries were treated with Illumina Free Adapter Blocking and were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run 2x 50 bp) with an average of 3 x107 reads per RNA sample.

value: primary human airway epithelial cells

value: male

tag: donor

tag: virus strain

tag: ifn type


title: lambda_D2

description: mislabelling during lib prep: day->IFN

value: female


title: lambda_D1

description: mislabelling during lib prep: day->IFN


title: D4_mock


title: AMSC_211p8_conf_NEG_C


title: D4_inf


title: D4_day_8

description: mislabelling during lib prep: day->IFN


title: lambda_D3

description: mislabelling during lib prep: day->IFN


title: D4_day_6

description: mislabelling during lib prep: day->IFN


title: D4_day_2

description: mislabelling during lib prep: day->IFN


title: D4_day_7

description: mislabelling during lib prep: day->IFN


title: D4_day_4

description: mislabelling during lib prep: day->IFN


title: D4_day_17

description: mislabelling during lib prep: day->IFN


title: Ring1a/b 2KO lingual epithelium rep1

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm10) using the Tophat (v2.0.13)
Gene models of Refgene were downloaded from the UCSC genome browser on March 13, 2017. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using the cufflinks (v2.2.1). Lowly expressed genes (mean FPKM values < 1 in both groups under comparison) were excluded from differential expression analysis.
read counts from HTseq (v0.6.1)
DESeq2 (v1.6.3) was used to determine differentially expressed genes
genes with >2 fold change, false discovery rate (FDR) < 0.05, and FPKM>1 were identified as significantly differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene expression values (read counts from HTseq)

source_name: Lingual epithelium

extract_protocol:
Basal lingual epithelial cells were purified from E16 embryos. Tongues were removed from the mandible and cut to exclude the posterior circumvallate papillae. For RNA and RNA-Seq analysis of control, Krt14-Cre Ring1a-/- Ring1b flox/flox mice, E16 tongues were collected. Tissues were cut into small pieces and incubated with 1.26U/mL dispase (Invitrogen) and 0.3% type 1 collagenase (Worthington) for 45 minutes at 37ºC with 80 rpm shaking. Tissues were washed with 1xPBS, dissociated with 0.25% Trypsin with 2.21mM EDTA (Corning Cellgro; Manassas, VA, USA), and then washed twice with 1xPBS. Cells were stained with 1:200 EpCAM-APC antibodies (Biolegend; San Diego, CA, USA) for 30 min on ice and washed twice with 1x HBSS prior to cell sorting. For ChIP analysis, control newborn P0 mice were collected. All cell isolations were performed on a FACS Influx instrument (BD, Franklin Lakes, NJ, USA). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN). Complimentary DNA was reverse-transcribed from total RNA using qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, MD, USA) according to the manufacturer’s instructions.
15ng of RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (Nugen). Libraries were constructed from 50ng of sonicated cDNA (Covaris) using the Ovation Ultra Low DR Multiplex system (Nugen). The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced at GENEWIZ on the Illumina HiSeq platform, obtaining 100-nucleotide single reads.

value: Lingual cells

tag: tissue

value: Lingual epithelium

tag: age

value: Embryonic day 16

value: Ring1a-/- Ring1bfl/fl K14-Cre+


title: Ring1a/b 2KO lingual epithelium rep2

tag: genotype


title: D4_day_21

description: mislabelling during lib prep: day->IFN

tag: gender


title: N2_3

city: Tokyo

first: Yasuhiro

last: Nakano

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University (TMDU)

hyb_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent), according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

scan_protocol: Scaned using microarray scanner G2690D

data_processing: All scanned images were analyzed using Agilent feature extraction software (v11.5.1.1). Raw data were imported with GeneSpring GX software (v14.9, Agilent Technologies, CA, USA) with adapted by 75 percentile shift normalization

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using NucleoSpin RNA XS (Takara, Japan) and quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: liver

value: AAV8-NICD2 (3 x 10^11 vg/mouse) + AAV8-GFP (3 x 10^11 vg/mouse)

tag: strain

tag: Sex


title: D4_day_1

description: mislabelling during lib prep: day->IFN


title: D4_day_5

description: mislabelling during lib prep: day->IFN


title: G 96h repeat2

city: Xiamen

first: Yulin

last: Bai

address: Xiang'an South Road

institute: Xiamen University

description: G 96h repeat2

data_processing:
TrimGalore (https://github.com/FelixKrueger/TrimGalore) and FastQC were used to control the quality of sequencing data.
The clean reads were aligned to a reference genome of L. crocea by Hisat2 (v. 4.8.5).
Samtools (v. 1.10) was used to filt out the mapping reads which were de-novo assembled separately for each sample by StringTie (v. 2.1.4).
the assembled transcriptomes of each sample were merged to an integrated transcriptome of all tissues by StringTie (v. 2.1.4) using “--merge” option.
Based on the Hisat2 alignment BAM file, StringTie and Deseq2 were used to estimate and quantify gene expression separately for each RNA-seq data with default parameters
Genome_build: GenBank: RQIN00000000.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Larimichthys crocea

source_name: Gill

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, USA), according to the manufacturer's instructions. Genomic DNA was removed using DNase (New England Biolabs), and RNA purity was assessed using the NanoDrop 2000 (NanoDrop Technologies, USA). The integrity of each RNA sample was detected by agarose gel electrophoresis and had an A260:A280 ratio and A260:A230 ratio. The RNA samples were used for the subsequent library construction.
standard illumina protocols

value: Gill

tag: agent

value: Cryptocaryon irritans


title: Control rep2

value: Control


title: D4_day_16

description: mislabelling during lib prep: day->IFN


title: G 96h repeat1

description: G 96h repeat1


title: N1+2_2

source_name: NICD1- and NICD2-OE

value: AAV8-NICD1 (3 x 10^11 vg/mouse) + AAV8-NICD2 (3 x 10^11 vg/mouse)


title: N1+2_1


title: N2_1


title: 108057_NOD

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

data_processing:
Illumina RTA 2.2.68 Basecaller.
Cellranger 3 mkoutput with Bcl2Fastq 2.19.1.
Cellranger 3 Count against mm10 genome to produce count matrix.
scRNA Seurat 4.0.1 used for marker gene analysis and visualization.
Bulk-RNA Tophat v2.0.13, FeatureCounts, DESeq2 v1.30.1.
Genome_build: mm10 scRNA / mm9 bulk-RNA
Supplementary_files_format_and_content: H5 Matrix Files, TPM Measurements.

source_name: Salivary Gland

extract_protocol:
Chromium Single Cell 3' v2 (10x Genomics).
TruSeq Stranded RNA (Illumina).

value: Salivary Gland

tag: model

value: Sjogrens Syndrome


title: N1_3

value: AAV8-NICD1 (3 x 10^11 vg/mouse) + AAV8-GFP (3 x 10^11 vg/mouse)


title: D4_day_14

description: mislabelling during lib prep: day->IFN


title: G 96h repeat3

description: G 96h repeat3

tag: time point


title: anti-Ago IP, rep3 [A549_3_IP]

first: Paulina

last: Pawlica

address: 295 Congress Avenue, BCMM Room 131

department: MBB

institute: Yale University

description:
processed data file:
miRNA_counts.xlsx

data_processing:
the reads were trimmed of adaptors using Cutadapt with the following settings -u 4 -O 7 -a N{4}TGGAATTCTCGGGTGCCAAGG -q 10 -m 18 -M
the reads were mapped with bowtie2 (--very-sensitive-local) to an index containing human and SARS-CoV-2 genomes
miRNAs were counted by using featureCounts and annotations obtained from miRbase (for Ago IP counts, viRNA-5p was added to the annotation file and treated as a host miRNA)
differential expression was determined using edgeR; because the series A,B and 1,2,3 were run separately, for differential expression analysis  we used mock samples from series A, B, 1 and 2; all other conditions had three replicates.
track visualization was performed using an IGV browser of generated with BEDtools bed files
Genome_build: Homo_sapiens.GRCh38.100.chr,NC_045512.2
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every miRNA and every sample (in different tabs)
Supplementary_files_format_and_content: Tables with differential expression (fold-change with P value)
Supplementary_files_format_and_content: Bed files for every sample at terminal time points

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: A549-hACE2_anti-Ago IP

growth_protocol: Calu-3cells were cultured in EMEM with 10% FBS and Pen/Strep, PC-9 cells were cultured in RPMI medium with 10% FBS and Pen/Strep. A549-hACE2 were cultured in F-12 medium with 10% FBS, Pen/Strep and 1 μg/ml of puromycin. Calu-3-Ago2 and Calu-3-EV cells were cultured in the presence of 1 μg/ml of puromycin.

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's protocol
1 mg of total RNA was used for library preparation using NEXTflex v2 kit (PerkinElemr) according to manufacture’s instructions

treatment_protocol: Cells were infected with SARS-CoV-2 at different MOIs and collected at different time points, some samples were subjected to either anti-Ago or anti-HA immunoprecipitation. The initial experiment was done in duplicate at high MOIs (series A and B). Subsequently we repeated the experiment for a third time and also adding a low MOI condition 24 hpi (series 1,2 and 3).

tag: cell line

tag: treatment/timepoint

value: anti-Ago IP

tag: molecule subtype

value: small RNA


title: anti-Ago IP, input, rep 3 [A549_3_IN]

description:
processed data file:
miRNA_counts.xlsx

source_name: A549-hACE2_anti-Ago IP, input

value: anti-Ago IP, input


title: N2_2

value: male


title: N1_2


title: GFP3

value: AAV8-GFP  (6 x 10^11 vg/mouse)


title: D4_day_10

description: mislabelling during lib prep: day->IFN

value: primary human airway epithelial cells


title: GFP1


title: N1_1


title: G 72h repeat3

description: G 72h repeat3


title: D3_mock

value: female


title: Control rep1

value: Lingual cells

value: Lingual epithelium

value: Embryonic day 16


title: anti-Ago IP, input, rep 2 [A549_2_IN]

description:
processed data file:
miRNA_counts.xlsx


title: anti-Ago IP, rep2 [A549_2_IP]

description:
processed data file:
miRNA_counts.xlsx


title: 108052_NOD


title: G 72h repeat2

description: G 72h repeat2

value: Gill


title: G 72h repeat1

description: G 72h repeat1

value: Cryptocaryon irritans


title: GFP2

value: liver


title: 108055_NOD


title: D3_day_8

description: mislabelling during lib prep: day->IFN


title: 105886_CONSG

value: Control


title: G 48h repeat3

description: G 48h repeat3


title: anti-Ago IP, input, rep 1 [A549_1_IN]

description:
processed data file:
miRNA_counts.xlsx


title: D3_day_7

description: mislabelling during lib prep: day->IFN


title: D3_day_6

description: mislabelling during lib prep: day->IFN


title: 105885_CONSG

value: Salivary Gland


title: D3_day_5

description: mislabelling during lib prep: day->IFN


title: NOD

description:
Sjogrens Syndrome Salivary
NOD-scRNA

value: Sjogrens Syndrome


title: G 48h repeat1

description: G 48h repeat1


title: anti-Ago IP, input, rep 3 [Calu3_3_IN]

description:
processed data file:
miRNA_counts.xlsx

source_name: Calu3_anti-Ago IP, input


title: D3_inf


title: G 48h repeat2

description: G 48h repeat2


title: D3_day_4

description: mislabelling during lib prep: day->IFN


title: G 24h repeat3

description: G 24h repeat3


title: G 24h repeat2

description: G 24h repeat2


title: anti-Ago IP, rep2 [Calu3_2_IP]

description:
processed data file:
miRNA_counts.xlsx

source_name: Calu3_anti-Ago IP


title: 105887_CONSG


title: anti-Ago IP, input, rep 2 [Calu3_2_IN]

description:
processed data file:
miRNA_counts.xlsx


title: anti-Ago IP, rep1 [A549_1_IP]

description:
processed data file:
miRNA_counts.xlsx


title: D3_day_21

description: mislabelling during lib prep: day->IFN


title: liRiboseq_Blastocyst_rep2

source_name: Blastocyst

value: Blastocyst

value: WT

tag: treatment

value: untreated


title: G 24h repeat1

description: G 24h repeat1


title: anti-Ago IP, rep1 [Calu3_1_IP]

description:
processed data file:
miRNA_counts.xlsx

value: anti-Ago IP

value: small RNA


title: liRiboseq_Blastocyst_rep1


title: anti-Ago IP, rep3 [Calu3_3_IP]

description:
processed data file:
miRNA_counts.xlsx


title: liRiboseq_Morula_rep2

source_name: Morula

value: Morula


title: G 0h repeat3

description: G 0h repeat3


title: D3_day_1

description: mislabelling during lib prep: day->IFN

tag: cell type

value: primary human airway epithelial cells


title: anti-Ago IP, input, rep 1 [Calu3_1_IN]

description:
processed data file:
miRNA_counts.xlsx

value: anti-Ago IP, input


title: D3_day_17

description: mislabelling during lib prep: day->IFN

value: female

tag: donor


title: liRiboseq_Morula_rep1


title: G 0h repeat2

description: G 0h repeat2


title: liRiboseq_4-cell_rep2

source_name: 4 Cell

value: 4 Cell


title: CTRL

description:
Normal Salivary Gland
CTRL-scRNA


title: D3_day_14

description: mislabelling during lib prep: day->IFN

tag: virus strain


title: D3_day_2

description: mislabelling during lib prep: day->IFN

tag: ifn type


title: G 0h repeat1

description: G 0h repeat1

tag: tissue


title: dental pulp stem cells-aging3

city: Tianjin

first: XIAOCAO

last: MA

address: Medical Collage of Nankai University

institute: Nankai University

description: F

data_processing:
BGISEQ-500 platform (BGI-Shenzhen, China) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,  aligned to reference genome and small RNA databases using Bowtie2, except for RFAM, which was aligned to Cmsearch.
All the expression of genes and transcripts were carried out using RSEM, and normalized by FPKM.
DEseq2 was applied to analysis differences in gene expression levels which were defined by default as those with P value<0.1 and absolute log fold change>2. At last, unified differential genes were analyzed using R-packet PHEATMAP for hierarchical clustering.
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: dental pulp stem cells

growth_protocol: The cells were maintained in MEM-alpha medium containing 15% fetal bovine serum and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from the DPSCs following the manual instructions, using Trizol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell style

value: dental pulp stem cells

tag: age stage

value: aging

value: dental pulp


title: D3_day_10

description: mislabelling during lib prep: day->IFN

tag: gender


title: 48hpi at MOI 0.05, rep 2 [A549_48h_2]

description:
processed data file:
miRNA_counts.xlsx
FC.csv

source_name: A549-hACE2_48hpi at MOI 0.05

value: 48hpi at MOI 0.05


title: 48hpi at MOI 0.05, rep 1 [A549_48h_1]


title: dental pulp stem cells-young3

description: E

value: young


title: liRiboseq_4-cell_rep1

tag: strain

tag: genotype


title: liRiboseq_2-cell_rep1

source_name: 2 Cell

value: 2 Cell


title: liRiboseq_2-cell_rep2


title: D2_mock


title: D2_inf


title: 24hpi at MOI 5, rep 3 [A549_24h_1]

source_name: A549-hACE2_24hpi at MOI 5

value: 24hpi at MOI 5


title: 24hpi at MOI 5, rep 2 [A549_24h_B]


title: liRiboseq_1-cell_rep2

source_name: Zygote

value: Zygote


title: dental pulp stem cells-aging2

description: C


title: D2_day_8

description: mislabelling during lib prep: day->IFN

source_name: healthy tissue from explanted lungs


title: liRiboseq_1-cell_rep1

value: WT


title: 24hpi at MOI 5, rep 1 [A549_24h_A]


title: dental pulp stem cells-aging1

description: B


title: 6hpi at MOI 5, rep 3 [A549_6h_1]

source_name: A549-hACE2_6hpi at MOI 5

value: 6hpi at MOI 5


title: 48hpi at MOI 0.05, rep 3 [A549_48h_3]


title: D2_day_7

description: mislabelling during lib prep: day->IFN


title: dental pulp stem cells-young1

description: A


title: liRiboseq_MII_rep2

source_name: MII oocyte

value: MII oocyte

value: untreated


title: D3_day_16

description: mislabelling during lib prep: day->IFN


title: 6hpi at MOI 5, rep 2 [A549_6h_B]

value: small RNA


title: D2_day_6

description: mislabelling during lib prep: day->IFN

value: primary human airway epithelial cells


title: liRiboseq_ESC_5k_rep2

source_name: mESC

value: mESC


title: dental pulp stem cells-young2

description: D


title: Single culture rep1

source_name: MEF

tag: sample type

value: Single culture

tag: biological replicate

value: rep 1

tag: technical replicate


title: 6hpi at MOI 5, rep 1 [A549_6h_A]

tag: cell line


title: mock, rep 4 [A549_m_2]

tag: treatment/timepoint

value: mock


title: Single culture rep2

value: rep 2


title: totalRNA_Blastocyst_rep2

value: Blastocyst


title: D2_day_4

description: mislabelling during lib prep: day->IFN

value: female


title: mock, rep 3 [A549_m_1]

tag: molecule subtype


title: D2_day_2

description: mislabelling during lib prep: day->IFN


title: liRiboseq_ESC_5k_rep1

tag: treatment


title: totalRNA_Blastocyst_rep1


title: mock, rep 2 [A549_m_B]


title: mock, rep 1 [A549_m_A]


title: D2_day_21

description: mislabelling during lib prep: day->IFN

tag: cell type


title: totalRNA_Morula_rep2

value: Morula


title: 48hpi at MOI 0.05, rep 3 [PC9_48h_3]

source_name: PC-9_48hpi at MOI 0.05

value: 48hpi at MOI 0.05


title: totalRNA_Morula_rep1


title: D2_day_1

description: mislabelling during lib prep: day->IFN

tag: donor


title: D2_day_17

description: mislabelling during lib prep: day->IFN

tag: virus strain


title: 48hpi at MOI 0.05, rep 2 [PC9_48h_2]


title: D2_day_16

description: mislabelling during lib prep: day->IFN

tag: ifn type


title: totalRNA_4-cell_rep2

tag: tissue

value: 4 Cell


title: male_left_DRG_Day1_axotomy_rep_3

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
FASTQ files were filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Trimmomatic (Version 0.39).
Transcript-level quantification was performed using Salmon (Version 1.3.0) in quasi-mapping mode using the Gencode mouse genome version M27. To correct for systematic biases commonly present in RNA-seq data, both -seqBias and -gcBias features were used.
Transcript- to gene-level conversion was done using Tximeta (Version 3.11).
RNA-seq quantification data quality was assessed using MultiQC (Version 1.9).
DEGs were determined in pairs of samples with SNA and the respective sham-operated controls using DESeq2 package. Datasets normalization was conducted using trimmed means of M-values (TMM) included in DESeq2 package. Statistical parameters for each DEG, including absolute expression, fold change (log2FC), p-values (by Wald test), and false discovery rates (FDR) were computed.
Genome_build: GENCODE M27 (05.05.21)
Supplementary_files_format_and_content: Salmon quant.sf format consisting Entrez IDs, Length, EffectiveLength, abundance measurements (TPM) and number of reads mapping to each transcript (NumReads).

source_name: ipsilateral Dorsal Root Ganglia

growth_protocol: Female and male C57BL6/J mice (6-8 weeks old, Jackson Labs) were randomly assigned to axotomy (n = 6/group) and sham (n = 4/group). The mice were housed in a temperature-controlled room (∼22 °C), on a 12-h light/dark cycle, and free access to food and water.

extract_protocol:
To minimize RNA degradation, all surgical and tissue harvesting instruments used were sterilized and further treated with RNase Away reagent and rinsed in RNase-free water. Tissues were immediately submerged in 500 µl RNAlater Stabilization Solution to preserve RNA integrity, placed at 4C overnight, then transferred for storage at -20C.
RNA purification. DRG from 2 animals were pooled to obtain at least 500 ng of total RNAs. Tissues were transferred in Trizol solution and disrupted by mechanical homogenization. Total RNAs were purified using RNeasy RNA purification reagents. RNA concentrations and quality were determined using Nanodrop absorbance ratios at 260/280nm and 260/230nm. RNA integrity was determined using Agilent Bioanalyzer Nano RNA chip. 500 ng of total RNA samples (3 replicates/group) with RIN≥7.0 were used for RNA-seq.
RNA-seq. mRNA libraries were generated following TruSeq Stranded mRNA library preparation protocol (Illumina). In brief, the Poly-A enriched mRNAs were purified using poly-T oligo coupled magnetic beads, followed by mRNA fragmentation, first and second strands synthesis, cleaning on AMPure XP beads, and 3’-adenylation. Barcoded libraries were constructed by ligation of TruSeq dual-index adapters. The quality of RNAseq libraries was validated using qPCR. Libraries were sized on Agilent Bioanalyzer DNA high sensitivity chip and normalized. RNA-seq was performed using the paired-end 100 cycle program on the NovaSeq 6000 system.
Base calls were recorded and converted to FASTQ files containing sequencing reads and the corresponding quality scores using Illumina software. Sequencing was conducted until we acquired at least 50 million paired-end reads per sample.

treatment_protocol: All procedures were conducted between 8 and 12 daytime. Under isoflurane anesthesia, the left sciatic nerve was exposed at the mid-thigh level. Axotomy was the entire width of the nerve using sterile microsurgery scissors. In a separate animal cohort, nerves were exposed using surgical scissors without transection (sham). The muscle was then sutured, and the skin stapled. At 24 h after surgery, lumbar (L) 4 and 5 DRG were collected for RNA isolation. All animal procedures were performed in agreement with the Policy on Humane Care and Use of Laboratory Animals and the protocol approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System.

value: Dorsal root ganglia

tag: Sex

value: male

value: axotomy surgery


title: male_left_DRG_Day1_axotomy_rep_2


title: D2_day_5

description: mislabelling during lib prep: day->IFN


title: female_left_DRG_Day1_axotomy_rep_1


title: female_left_DRG_Day1_axotomy_rep_2


title: male_left_DRG_Day1_axotomy_rep_1


title: totalRNA_4-cell_rep1

city: Boston

value: WT


title: female_left_DRG_Day1_axotomy_rep_3


title: 48hpi at MOI 0.05, rep 1 [PC9_48h_1]


title: D2_day_10

description: mislabelling during lib prep: day->IFN


title: 24hpi at MOI 5, rep 3 [PC9_24h_1]

source_name: PC-9_24hpi at MOI 5

value: 24hpi at MOI 5


title: ATAC_siSmarcd2_rep2

source_name: Zygote (paternal pronuclear)

value: Zygote (paternal pronuclear)

value: untreated


title: D2_day_14

description: mislabelling during lib prep: day->IFN

value: primary human airway epithelial cells


title: male_left_DRG_sham_rep_2

value: sham surgery


title: ATAC_siSmarcd2_rep1


title: ATAC_siControl_rep2

value: siControl


title: male_left_DRG_sham_rep_1


title: D1_inf


title: 24hpi at MOI 5, rep 1 [PC9_24h_A]

value: small RNA


title: D1_mock


title: ATAC_siControl_rep1


title: female_left_DRG_sham_rep_2


title: female_left_DRG_sham_rep_1


title: D1_day_8

description: mislabelling during lib prep: day->IFN


title: 6hpi at MOI 5, rep 2 [PC9_6h_B]

source_name: PC-9_6hpi at MOI 5

value: 6hpi at MOI 5


title: 6hpi at MOI 5, rep 3 [PC9_6h_1]


title: D1_day_7

description: mislabelling during lib prep: day->IFN


title: 6hpi at MOI 5, rep 1 [PC9_6h_A]


title: ATAC_DMSO_rep1

value: treated with DMSO


title: RNA_2-cell_siControl_rep2

value: 2 Cell


title: RNA_2-cell_siControl_rep1


title: mock, rep 3 [PC9_m_1]

value: mock


title: mock, rep 4 [PC9_m_2]


title: RNA_2-cell_siCcnt2_rep2


title: D1_day_5

description: mislabelling during lib prep: day->IFN

value: female


title: mock, rep 2 [PC9_m_B]


title: mock, rep 1 [PC9_m_A]


title: D1_day_6

description: mislabelling during lib prep: day->IFN


title: D1_day_21

description: mislabelling during lib prep: day->IFN


title: D1_day_2

description: mislabelling during lib prep: day->IFN


title: Non gustatory epithelium P0 control- Input

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using bowtie2 (v2.3.3, default parameters).
Duplicate reads were removed by the Samtools software v0.1.19 (Li et al. 2009).
Peaks (mostly broad) in  H2AK119ub1 ChIP samples were called as previously described (Goldberg et al. 2010) for the two replicates independently.
To visualize ChIP-seq signals, we used the Integrative Genomics Viewer (IGV; http://software.broadinstitute.org/software/igv/) and TDF files from the igvtools (v2.3.57; https://software.broadinstitute.org/software/igv/igvtools).
Genome_build: mm10
Supplementary_files_format_and_content: IGV tdf and peaks

source_name: Lingual epithelium

extract_protocol:
Basal lingual epithelial cells were purified from  P0 newborn mice. Tongues were removed from the mandible and cut to exclude the posterior circumvallate papillae. For ChIP, only control mice were collected. Tissues were cut into small pieces and incubated with 1.26U/mL dispase (Invitrogen) and 0.3% type 1 collagenase (Worthington) for 45 minutes at 37ºC with 80 rpm shaking. Tissues were washed with 1xPBS, dissociated with 0.25% Trypsin with 2.21mM EDTA (Corning Cellgro; Manassas, VA, USA), and then washed twice with 1xPBS. Cells were stained with 1:200 EpCAM-APC antibodies (Biolegend; San Diego, CA, USA) for 30 min on ice and washed twice with 1x HBSS prior to cell sorting.
For high-throughput ChIP sequencing, libraries were constructed from 4ng of Purified DNA using the DNA SMART ChIP-Seq Kit (Clontech; Palo Alto, CA, USA) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on the Illumina NextSeq 500 platform.  Two biological replicates were used for ChIP experiments.

value: Lingual cells

value: Lingual epithelium

tag: age

value: Postnatal day 0

value: Control

tag: chip antibody


title: D1_day_4

description: mislabelling during lib prep: day->IFN

tag: gender


title: D1_day_1

description: mislabelling during lib prep: day->IFN


title: 24hpi at MOI 5, rep 2 [PC9_24h_B]


title: D1_day_17

description: mislabelling during lib prep: day->IFN


title: Non gustatory epithelium P0 control- Rep2

value: postnatal day 0

tag: genotype

value: H2AK119ub (Cell Signaling, Cat# 8240S)


title: 48hpi at MOI 0.05, rep 2 [Calu3_48h_2]

source_name: Calu3_48hpi at MOI 0.05

value: 48hpi at MOI 0.05


title: 48hpi at MOI 0.05, rep 1 [Calu3_48h_1]


title: D1_day_16

description: mislabelling during lib prep: day->IFN


title: ATAC_CHX_rep1

value: Zygote (paternal pronuclear)

tag: strain

value: WT

value: treated with CHX


title: 24hpi at MOI 5, rep 3 [Calu3_24h_1]

source_name: Calu3_24hpi at MOI 5

value: 24hpi at MOI 5


title: D1_day_14

description: mislabelling during lib prep: day->IFN

value: primary human airway epithelial cells


title: 24hpi at MOI 5, rep 2 [Calu3_24h_B]

value: small RNA


title: CD19-D7-2_edited

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

data_processing:
No Trimmomatic-based adapter-trimming was performed as the sequencing facility had performed pre-cleaning on raw reads.
20~30 M paired-reads were recovered from each sample at the rate of ~350 M raw read-pairs per lane on an Illumina HiSeq 2000.
Raw files were subsequently mapped to human hg38 genome (GRCh38p7.13) using STAR v2.7.0 and GENCODE v35 annotation file.
Genome_build: GRCh38p7.13/hg38
Supplementary_files_format_and_content: tab-delimited txt file contains tabulated raw read count of genes from each sample

growth_protocol: iPSCs were dissociated into single cells by accutase and replated at 5 × 105 cells per well on 6-well plate using mTeSR plus media with 5 μM ROCK inhibitor on Day (−1). On Day 0, cells were infected by 200 μl/well lentivirus cocktail containing 100 μl NGN2 virus and 100 μl rtTA virus (Zhang et al., 2013). The virus cocktail was prepared in mTeSR plus with 5 μM ROCK inhibitor. mTeSR plus media was switched to neuronal media consisting of Neurobasal media (Thermofisher), B27 supplement (Thermofisher), Glutamax (Thermofisher) and 2 μg/ml doxycycline (Sigma) on Day 1. After a two-day puromycin selection at 1 μg/ml on Day 2 and Day 3, it was withdrawn on Day 4. Cells were dissociated into single cells by accutase on Day 5 and replated on 6-well plates into 2 ml of neuronal culture media containing Neurobasal media, Glutamax, B27 supplement, 2 μg/ml doxycycline, 10 ng/ml BDNF (PeproTech), 10 ng/ml GDNF (PeproTech) and 10 ng/ml NT3 (PeproTech). Plates were coated with 0.1% PEI (Sigma) in 2 x Borate buffer (Thermofisher) on Day 3 overnight, washed four times with sterile ddH2O on Day 4 and dried overnight. On day 6, 2 ml of neuronal media were added into each well. Total in each well was 4 ml. Neurons were fed every 3 days with neuronal culture media by removing 2 ml and adding 2 ml of fresh media. Doxycycline was withdrawn on Day 21. Cells were collected on Day 30

extract_protocol:
Cells from iPSCs and iNs cultures were dissociated with accutase and washed with PBS. Then, cells were lysed in RLT plus buffer, and total RNA extracted with the RNeasy Plus Kit (Qiagen). cDNA was reverse transcribed from RNA with a high-capacity cDNA reverse transcription kit (Applied Biosystems).
The RNA sample was then cleaned with RNeasy MinElute Cleanup Kit (Qiagen), and subjected to RNA-seq at GENEWIZ (San Diego, CA). RNA-seq files were provided in the format of 2x150 bp paired-end (~25 M reads per sample) fastq files from GENEWIZ.
cDNA libraries were prepared using the polyA selection method with Illumina HiSeq kit and customized adapters.

treatment_protocol: For immunofluorescence staining rat astrocytes (Sigma) were plated in a DMEM media (Thermofisher) with 10% FBS (Thermofisher) as a 100 μl blob on glass cover slips at 0.5 × 104 cells per well on Day 4. On day 5, 100 μl were carefully removed and cells were plated as a 100 μl blob onto rat astrocytes at 0.5 × 104 cells per well in neuronal culture media containing Neurobasal media, Glutamax, B27 supplement, 2 μg/ml doxycycline, 10 ng/ml BDNF, 10 ng/ml GDNF and 10 ng/ml NT3 and 5% FBS. On day 6, cells were fed with 400 μl of neuronal media. On day 6, 500 μl of neuronal culture media were added into each well with half-volume of medium change every 3 days for continuous culturing. Total in each well was 1 ml. FBS concentration in neuronal culture media was reduced to 1 % on day 14. Doxycycline was withdrawn on Day 21.

value: edited

value: Glutamatergic, NGN2-induced, day-30 neuron


title: CD19-C12_edited


title: CD19-C7_unedited

value: unedited


title: D1_day_10

description: mislabelling during lib prep: day->IFN

value: female


title: CD19-D7-1_unedited


title: 6hpi at MOI 5, rep 3 [Calu3_6h_1]

source_name: Calu3_6hpi at MOI 5

value: 6hpi at MOI 5


title: RNA_2-cell_siCcnt2_rep1

source_name: 2 Cell

value: 2 Cell

value: untreated


title: 24hpi at MOI 5, rep 1 [Calu3_24h_A]


title: siMLK4_t24_3

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
hisat2
htseq-count, version 0.6.0, parameters: --stranded=reverse --secondary-alignments=ignore
removal of features with less then 32 counts based on the sum of normalized counts across all samples
DESeq2, version 1.26.0, vst normalization
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix

source_name: HCC1806_siMLK4_Doxorubicin 1 μM

growth_protocol: HCC1806 cell lines were culture in RPMIHCC1806 cells were cultured in RPMI-1640 supplemented with 10% FCS, 1% penicillin/streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate.

extract_protocol:
Total RNA was isolated using RNAeasy Kit (Qiagen)
KAPA RNA HyperPrep Kit, KAPA Dual-Indexed adapters

treatment_protocol: Cells were treated with doxorubicin at concentration of 1 μM for 24 hours

value: human triple-negative breast cancer cell line

tag: sirna

value: Doxorubicin 1 μM


title: siMLK4_t24_2


title: siMLK4_t24_1


title: 48hpi at MOI 0.05, rep 3 [Calu3_48h_3]


title: CD19-A7_unedited


title: 6hpi at MOI 5, rep 2 [Calu3_6h_B]


title: 6hpi at MOI 5, rep 1 [Calu3_6h_A]


title: siMLK4_t0_3

value: DMSO


title: CD07-F6_edited


title: Non gustatory epithelium P0 control- Rep1

value: Lingual cells

value: Lingual epithelium

value: Postnatal day 0

value: Control

value: H2AK119ub (Cell Signaling, Cat# 8240S)


title: CD07-D3_unedited


title: siMLK4_t0_2


title: CD07-G2_unedited


title: mock, rep 2 [Calu3_m_B]

value: mock


title: mock, rep 3 [Calu3_m_1]

value: small RNA


title: siNT_t24_3

source_name: HCC1806_siNT_Doxorubicin 1 μM

value: siNT


title: mock, rep 4 [Calu3_m_2]


title: mock, rep 1 [Calu3_m_A]


title: CD07-C1_unedited

value: Glutamatergic, NGN2-induced, day-30 neuron


title: siNT_t24_2


title: siMLK4_t0_1


title: siNT_t0_3


title: siNT_t24_1


title: siNT_t0_2


title: CD07-C3_edited

value: edited


title: Individual #14, EtOH, rep3

status: Public on Nov 27 2021

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
Doseresponse_Individual14_EtOH_24h_0.1pct_Sept2020
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH19

data_processing:
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183)
Read counts normalization via EdgeR 3.21.1 (TMM)
Differential gene expression analysis via EdgeR 3.21.1
Genome_build: hg38, Ensembl annotation version 103
Supplementary_files_format_and_content: Excel tables of normalized read counts and statistical metrics

source_name: Individual #14_EtOH_PBMC

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 24 h with either 100 nM, 250 nM, 1000 nM, 10.000 nM 25(OH)D3 (Sigma-Aldrich), 250 nM D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

tag: subject id

value: Individual #14

value: peripheral blood mononuclear cells (PBMC)

value: 0.1% ethanol for 24 h


title: siNT_t0_1

tag: cell line


title: Empa 3

city: Hannover

first: Lena

middle: Marie

last: Bode

address: Carl-Neuberg-Str. 1

department: Dept. of Cardiology and Angiology

institute: Hannover Medical School

data_processing:
Constructed RNA sequence libraries were delivered into HiSeq Machines (Illumina). Original raw data was converted to Sequenced Reads by base calling.
RNA-Seq reads were aligned to Ensembl reference using TopHat2 algorithm.
Raw count data per gene was analysed using HTSeq software.
Quantification of gene expression level as normalized counts was performed by DESeq by novogene.
The data was further analysed with Gene Set Enrichment Analysis (GSEA) software, C5 gene ontology sets were acquired from MSigDB.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed data files were generated by Novogene.
Supplementary_files_format_and_content: readcount.txt: Tab-delimited text file includes the read counts for each Sample.
Supplementary_files_format_and_content: DEG_Results.tar: Tar archive includes DEG results files. DEGsList.README.txt describes the files.

source_name: smooth muscle cells

growth_protocol: For each sample 4x 1 Mio. DHCASMCs per well were cultured to subconfluence.

extract_protocol:
Cells were washed twice with PBS and lysed with RLT-Buffer. RNA was isolated. RNA of 4 replicates of the same condition was pooled.
RNA pooled samples were diluted with H2O to 2µg of total RNA for the construction of treatment libraries.

treatment_protocol: Wells of the treatment group were stimulated with 750nM empagliflozin and growth medium and wells of the Control Group were stimulated with growth medium for 24h.

value: D-HCASMC-Diab. Type II

value: diabetic coronary artery smooth muscle cells

value: 750nM Empagliflozin in growth medium for 24h

tag: passages


title: CTRL 1

value: growth medium for 24h


title: CTRL 3


title: MCF7_hMeDIP_E2_10d

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

data_processing:
Low-quality bases and adapter-containing reads were also trimmed from raw data using trim-galore package under default parameters.
Trimmed reads were mapped to reference genome (hg19) using bowtie2 (v2.3.3.1) under default parameters. Duplicate reads were removed with samtools rmdup (v1.9) to get the unique mapped reads, then the mapped unique and monoclonal reads were extended to 150bp to match the average length of insert DNA fragments of the ChIP-seq libraries.
Extended mapped unique and monoclonal reads were transformed to bedGraph files and bigWig files using genomeCoverageBed script in bedtools, which were used to calculate tag density under 50-bp resolution.
hMeDIP peaks were called using MACS using default parameters, except for p value=0.05.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, reads density of hMeDIP signals

source_name: Beast cancer cell line

growth_protocol: MCF-7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco) and 100 U/ml penicillin/streptomycin (Invitrogen).

extract_protocol:
gDNA was sonicated to 200–500 bp fragments, denatured in boiling water and immediately cooled on ice. Fragmented DNA was added to IP buffer (10 mM Na-Phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100). 5hmC/ 5mC antibody (5hmC antibody, Active Motif #39769; 5mC antibody, Active Motif #39649) was added to the sample and incubated at 4°C for 4 h. Protein A/G beads were added to each reaction and incubated at 4°C for 2 h. The beads were washed using IP buffer for three times. The sample was resuspended in Proteinase K digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS, included 2 μl protease K) and incubated at 50°C for 2 h. The final sample was extracted using QIAquick PCR Purification Kit.
hMeDIP libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For estrogen stimulation, MCF-7 cells were cultured in phenol red-free RPMI 1640 medium (HyClone) plus 10% charcoal-depleted FBS (Biological Industries) for 5 days and followed by EtOH or E2 (1nM) treatment for 10 days.

value: Beast cancer cell line

value: 10d treatment with 100nM E2

tag: antibody

value: 5hmC Active Motif, #39769


title: MCF7_Input_E2_10d

tag: treatment


title: CTRL 2

tag: cell type


title: MCF7_Input_ETOH_10d

value: 10d treatment with 100nM ETOH


title: MCF7_hMeDIP_ETOH_10d


title: Empa 1


title: Individual #14, EtOH, rep1

description:
Doseresponse_Individual14_EtOH_24h_0.1pct_Sept2020
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH10


title: Individual #14, 250 nM 25D, rep3

description:
VitDHiD_Individual14_Vit25D3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual14-Vit25D3-rep3

source_name: Individual #14_250 nM 25D_PBMC


title: Individual #14, 250 nM D3, rep3

description:
VitDHiD_Individual14_VitD3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual14-VitD3-rep3

source_name: Individual #14_250 nM D3_PBMC

value: 250 nM D3 for 24 h


title: Individual #14, 250 nM 25D, rep2

description:
VitDHiD_Individual14_Vit25D3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual14-Vit25D3-rep2


title: Individual #14, 250 nM D3, rep2

description:
VitDHiD_Individual14_VitD3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual14-VitD3-rep2


title: Individual #14, 10000 nM 25D, rep2

description:
Doseresponse_Individual14_Vit25D3_24h_10000nM_Sept2020
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH02

source_name: Individual #14_10000 nM 25D_PBMC


title: Individual #14, 10000 nM 25D, rep3

description:
Doseresponse_Individual14_Vit25D3_24h_10000nM_Sept2020
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH03


title: Individual #14, 250 nM D3, rep1

description:
VitDHiD_Individual14_VitD3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual14-VitD3-rep1


title: Individual #14, 1000 nM 25D, rep3

description:
Doseresponse_Individual14_Vit25D3_24h_1000nM_Sept2020
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH06

source_name: Individual #14_1000 nM 25D_PBMC


title: Individual #14, 1000 nM 25D, rep2

description:
Doseresponse_Individual14_Vit25D3_24h_1000nM_Sept2020
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH05


title: Individual #14, 1000 nM 25D, rep1

description:
Doseresponse_Individual14_Vit25D3_24h_1000nM_Sept2020
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH04


title: Empa 2


title: ino80_27°C_12h_rep2

city: beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

institute: Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1.
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10.
Reads per gene were counted by HTseq version 0.11.2.
Transcripts per million (TPM) values were generated using R.
Differential gene expression analysis was performed using DESeq2 version 1.26.0.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.txt, TPM values for all samples.

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings

growth_protocol: Seedlings grown at 21°C under short-day conditions for 7 days.

extract_protocol:
Seedlings were collected and total RNA was extracted with Minibest plant RNA extraction kit (Takara).
Library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction.

treatment_protocol: 7-day-old seedlings were further grown at 21°C or 27°C for 1h and 12h.

tag: ecotype

value: Col

value: seedling

value: 7 days

value: 27oC for 12 hours


title: ino80_27°C_12h_rep3


title: Individual #14, EtOH, rep2

description:
Doseresponse_Individual14_EtOH_24h_0.1pct_Sept2020
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH11


title: ino80_27°C_12h_rep1


title: Individual #14, 100 nM 25D, rep3

description:
Doseresponse_Individual14_Vit25D3_24h_100nM_Sept2020
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH09

source_name: Individual #14_100 nM 25D_PBMC


title: ino80_21°C_12h_rep1

value: 21oC for 12 hours


title: ino80_21°C_12h_rep2


title: ino80_21°C_12h_rep3


title: Individual #14, 100 nM 25D, rep1

description:
Doseresponse_Individual14_Vit25D3_24h_100nM_Sept2020
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH07

value: Individual #14


title: Individual #14, 100 nM 25D, rep2

description:
Doseresponse_Individual14_Vit25D3_24h_100nM_Sept2020
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH08

value: peripheral blood mononuclear cells (PBMC)


title: Col_27°C_12h_rep3

value: wild type


title: Individual #14, 250 nM 25D, rep1

description:
VitDHiD_Individual14_Vit25D3_24h_250nM_Jan-Feb2019
HFLWNBGXC_1-3_19s003938-1-1_Carlberg_lane1-Individual14-Vit25D3-rep1


title: Individual #13, 250 nM D3, rep2

description:
VitDHiD_Individual13_VitD3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual13-VitD3-rep2

source_name: Individual #13_250 nM D3_PBMC

value: Individual #13


title: Individual #13, 250 nM D3, rep1

description:
VitDHiD_Individual13_VitD3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual13-VitD3-rep1


title: Col_27°C_12h_rep1


title: Col_21°C_12h_rep3


title: Individual #14, 10000 nM 25D, rep1

description:
Doseresponse_Individual14_Vit25D3_24h_10000nM_Sept2020
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH01


title: Individual #13, 250 nM 25D, rep3

description:
VitDHiD_Individual13_Vit25D3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual13-Vit25D3-rep3

source_name: Individual #13_250 nM 25D_PBMC


title: Individual #13, 250 nM 25D, rep2

description:
VitDHiD_Individual13_Vit25D3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual13-Vit25D3-rep2


title: Individual #13, 250 nM 25D, rep1

description:
VitDHiD_Individual13_Vit25D3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual13-Vit25D3-rep1


title: Col_21°C_12h_rep1


title: ino80_27°C_1h_rep3

value: 27oC for 1 hour


title: Individual #12, EtOH, rep2

description:
Doseresponse_Individual12_EtOH_24h_0.1pct_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH35

source_name: Individual #12_EtOH_PBMC

value: Individual #12

value: 0.1% ethanol for 24 h


title: ino80_27°C_1h_rep2


title: Individual #12, EtOH, rep1

description:
Doseresponse_Individual12_EtOH_24h_0.1pct_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH34


title: Col_27°C_12h_rep2


title: ino80_27°C_1h_rep1


title: Individual #12, 250 nM D3, rep2

description:
VitDHiD_Individual12_VitD3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual12-VitD3-rep2

source_name: Individual #12_250 nM D3_PBMC


title: Col_21°C_12h_rep2


title: Individual #12, 250 nM D3, rep3

description:
VitDHiD_Individual12_VitD3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual12-VitD3-rep3


title: ino80_21°C_1h_rep2

value: 21oC for 1 hour


title: ino80_21°C_1h_rep3


title: Individual #13, 250 nM D3, rep3

description:
VitDHiD_Individual13_VitD3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual13-VitD3-rep3


title: ino80_21°C_1h_rep1


title: Individual #12, 250 nM D3, rep1

description:
VitDHiD_Individual12_VitD3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual12-VitD3-rep1


title: Individual #12, 250 nM 25D, rep3

description:
VitDHiD_Individual12_Vit25D3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual12-Vit25D3-rep3

source_name: Individual #12_250 nM 25D_PBMC


title: gene_expression_K1

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level  3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

description: Gene expression data from Homo sapiens EBV+ PTCL (nodal TNKL) sample

hyb_protocol: cRNA samples were hybridized for 16 hr on GeneChip® Clariom D Assay (Human) Array according to the manufacturer's instruction. GeneChips were washed and stained in using the FS450_0001 fluidics protocol.

scan_protocol: Arrays were scanned using an Affymetrix 3000 7G scanner.

data_processing: Gene expression data were normalized with the robust multi-array average (RMA) algorithm through the “oligo” package (1.48.0) in R (ver 3.6)

source_name: EBV+ PTCL (nodal TNKL),K1,FFPE Preparation

label_protocol: Sample labeling was performed using GeneChip® Clariom D Assay (Human) Array according to the manufacturer's instruction.

extract_protocol: Total RNA from FFPE tissue samples were extracted by using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Invitrogen™.

treatment_protocol: Tissues were formalin fixed and embeded in paraffin to make FFPE tissue samples.

value: EBV+ PTCL (nodal TNKL)

tag: tissue preparation

value: FFPE


title: gene_expression_TNK04

source_name: EBV+ PTCL (nodal TNKL),TNK04,FFPE Preparation


title: gene_expression_TNK06

source_name: EBV+ PTCL (nodal TNKL),TNK06,FFPE Preparation


title: gene_expression_MD11

description: Gene expression data from Homo sapiens extranodal NKTL sample

source_name: extranodal NKTL,MD11,FFPE Preparation

value: extranodal NKTL


title: Individual #12, EtOH, rep3

description:
Doseresponse_Individual12_EtOH_24h_0.1pct_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH36


title: gene_expression_TNK10

source_name: EBV+ PTCL (nodal TNKL),TNK10,FFPE Preparation


title: Individual #12, 250 nM 25D, rep1

description:
VitDHiD_Individual12_Vit25D3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual12-Vit25D3-rep1


title: Col_27°C_1h_rep3


title: Col_27°C_1h_rep2


title: gene_expression_NKTL36

source_name: extranodal NKTL,NKTL36,FFPE Preparation


title: gene_expression_NKTL69

source_name: EBV+ PTCL (nodal TNKL),NKTL69,FFPE Preparation


title: Individual #12, 250 nM 25D, rep2

description:
VitDHiD_Individual12_Vit25D3_24h_250nM_Jan-Feb2019
HFLKWBGXC_1-2_19s003937-1-1_Carlberg_lane1-Individual12-Vit25D3-rep2


title: gene_expression_NKTL40

source_name: EBV+ PTCL (nodal TNKL),NKTL40,FFPE Preparation


title: gene_expression_NKTL23A


title: Col_27°C_1h_rep1


title: gene_expression_NKTL60

source_name: extranodal NKTL,NKTL60,FFPE Preparation


title: gene_expression_HKU-PTCL21

description: Gene expression data from Homo sapiens PTCL NOS sample

source_name: PTCL NOS,HKU-PTCL21,FFPE Preparation

value: PTCL NOS


title: gene_expression_NKTL22

source_name: extranodal NKTL,NKTL22,FFPE Preparation


title: gene_expression_NKTL16A


title: gene_expression_LN Control-2

description: Gene expression data from Homo sapiens LN Control-2 sample

source_name: LN Control-2,LN Control-2,FFPE Preparation

value: normal lymph node


title: gene_expression_MD07

source_name: extranodal NKTL,MD07,FFPE Preparation


title: Col_21°C_1h_rep3

source_name: 7-day-old seedlings

value: Col

value: seedling


title: Col_21°C_1h_rep2

value: 7 days


title: Individual #12, 10000 nM 25D, rep3

description:
Doseresponse_Individual12_Vit25D3_24h_10000nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH27

source_name: Individual #12_10000 nM 25D_PBMC


title: gene_expression_HKU-PTCL11

source_name: PTCL NOS,HKU-PTCL11,FFPE Preparation


title: Individual #12, 10000 nM 25D, rep2

description:
Doseresponse_Individual12_Vit25D3_24h_10000nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH26


title: Individual #12, 1000 nM 25D, rep3

description:
Doseresponse_Individual12_Vit25D3_24h_1000nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH30

source_name: Individual #12_1000 nM 25D_PBMC


title: Individual #12, 10000 nM 25D, rep1

description:
Doseresponse_Individual12_Vit25D3_24h_10000nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH25


title: Col_21°C_1h_rep1


title: Individual #12, 1000 nM 25D, rep2

description:
Doseresponse_Individual12_Vit25D3_24h_1000nM_Jan-Feb2019
HKWNYBGXG_Pool2_20s003469-1-1_Carlberg_lane125OH29