title: HaCaT_A20 cDNA-containing lentiviral vector_TNF treatment_replicate 2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

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

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

source_name: HaCaT immortalized human keratinocytes, transduced with A20 cDNA-containing lentiviral vector (PF 5x UAS MCS W SV40 Prom A20), treatment with 500 µg/ml TNF for 1h

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

growth_protocol: The generation and characterization of the HaCaT immortalized human keratinocytes has been previously described [PMID: 2450098]. Cells were transduced with lentiviral vector PF 5x UAS MCS W SV40 Prom either empty or containing human A20 cDNA. Murine keratinocytes were isolated from the skin of newborn C57BL/6 mice and spontaneously immortalized in CnT-07 medium (CELLnTEC). Murine keratinocytes were transduced with pCF G5 either empty or containing murine A20 cDNA.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol.

treatment_protocol: Cells were pre-stimulated with 100nM 4-Hydroxy-Tamoxifen 24h before experiment for A20 overexpression. Cells were starved 6h in medium without FSC medium 6h before experiment. Cells were treated with 500ng/ml HF-TNF for 1h.

value: HaCaT

tag: cell type

value: immortalized human keratinocytes

tag: cell culture medium

value: DMEM

tag: passage number of cells

value: treatment with 500 µg/ml TNF for 1h

tag: experiment


title: HaCaT_empty lentiviral vector_TNF treatment_replicate 2

status: Public on Feb 20 2020

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HaCaT immortalized human keratinocytes, transduced with empty lentiviral vector (5x UAS MCS W SV40 Prom), treatment with 500 µg/ml TNF for 1h

tag: cell line

tag: genotype/variation

tag: treatment


title: HaCaT_empty lentiviral vector_TNF treatment_replicate 1

value: transduced with empty lentiviral vector (5x UAS MCS W SV40 Prom)


title: HaCaT_A20 cDNA-containing lentiviral vector_control treatment_replicate 1

source_name: HaCaT immortalized human keratinocytes, transduced with A20 cDNA-containing lentiviral vector (PF 5x UAS MCS W SV40 Prom A20), control treatment (vehicle; PBS:DMEM ratio 1:1000)


title: G24.2_NAA50amiRNA 24 Hr

type: SRA

city: Bloomington

first: Roger

last: Innes

state: IN

address: Myers Hall 302

department: Biology

country: USA

institute: Indiana University

library_source: transcriptomic

data_processing:
Trimmomatic (1; version 0.33; non-default parameters = ILLUMINACLIP<adapter_file>:2:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35) was used to trim reads of adapter and low-quality bases
Reads were mapped to the Arabidopsis thaliana genome using STAR with the final parameters (4; version 2.5.2a; --outSAMattributes All --outSAMunmapped Within --outReadsUnmapped Fastx --outFilterMultimapNmax 1 --seedSearchStartLmax 25 --chimSegmentMin 20 --quantMode GeneCounts --twopassMode Basic --outWigType wiggle --outWigStrand Unstranded --outWigNorm None --sjdbGTFtagExonParentTranscript Parent --sjdbGTFtagExonParentGene ID --outSAMtype BAM SortedByCoordinate).
Read counts were determined using a custom perl script.
Differential expression comparisons of all features with 5 or more reads (in total across all samples) were carried out with DESeq2 (2; R package version 3.4.0) along with the IHW (3) package to adjust for multiple testing procedures.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files are tab-delimited files indicating the number of reads associated with a gene

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana rosette

growth_protocol: 8/16 hr day/night cycle.

extract_protocol:
For each sample,  0.4 g leaf tissue was taken from the 4th leaf of 4 unique plants. RNA was extracted from 4-week-old Arabidopsis leaves using the Spectrum plant total RNA kit (Sigma-Aldritch) according to manufacturer’s instructions.
Total RNA was prepared into equimolar pools for each sample submitted to Indiana University’s Center for Genomics and Bioinformatics for cDNA library construction using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) following the standard manufacturing protocol.

treatment_protocol: Samples were sprayed with 50 μM dexamethasone.

tag: genotype

tag: tissue

value: leaf

tag: time (hours)


title: HaCaT_empty lentiviral vector_control treatment_replicate 2

source_name: HaCaT immortalized human keratinocytes, transduced with empty lentiviral vector (5x UAS MCS W SV40 Prom), control treatment (vehicle; PBS:DMEM ratio 1:1000)


title: HaCaT_empty lentiviral vector_control treatment_replicate 1

value: control treatment (vehicle; PBS:DMEM ratio 1:1000)


title: HaCaT_A20 cDNA-containing lentiviral vector_control treatment_replicate 2

value: transduced with A20 cDNA-containing lentiviral vector (PF 5x UAS MCS W SV40 Prom A20)


title: HaCaT_A20 cDNA-containing lentiviral vector_TNF treatment_replicate 1


title: ChIP-seq_G1E-ER4_24hr_H3K27ac_rep2

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Raw reads were aligned to mouse (mm10) genome assembly using Bowtie2 with default parameters.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm.
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: mm10
Supplementary_files_format_and_content: wig file and peak bed file

molecule: genomic DNA

organism: Mus musculus

source_name: mouse G1E-ER4 cells

growth_protocol: G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 5 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

treatment_protocol: Cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.

value: Mouse G1E-ER4 cells

tag: chip antibody


title: S24.1_ScrambledamiRNA 24 Hr

value: ScrambledamiRNA


title: S24.2_ScrambledamiRNA 24 Hr


title: HCI010_470_H_LU_62

city: Irvine

first: Devon

middle: A

last: Lawson

state: CA

address: 839 Health Science Road, Sprague Hall 114

department: Physiology and Biophysics

institute: UC Irvine

data_processing:
Files from the HiSeq2500 were demultiplexed and converted to FASTQ files. Paired-end 100bp reads were aligned to the hg21 human transcriptome using Bowtie2 and quantified using RSEM with the following parameters: rsem-calculate-expression -p $CORES --bowtie2 --paired-end READ1 READ2 gencodehg21. Expression values were log-transformed into log(TPM+1) matrices and loaded into the Seurat analysis package with the following parameters: p10 <- CreateSeuratObject(raw.data = p10.mat, min.cells = 8, min.genes = 1000,  project = "HCI010").
Genome_build: hg21
Supplementary_files_format_and_content: genes.results.FPKM.txt

source_name: Patient Derived Xenograft Single Cells

extract_protocol:
Animals at endpoint were euthanized by asphyxiation with CO2 followed by cervical dislocation and perfusion with 10mM EDTA in D-PBS.  Prior to perfusion, Evan’s Blue (Sigma-Aldrich, Cat. No. E2129-10G) was injected into the footpads and ears of anesthetized mice to aid in lymph node visualization. Solid tissues from the mice, which includes the primary tumour, lung, and lymph nodes were processed for flow cytometry by mechanically chopping with blades, followed by Collagenase IV digest (Sigma-Aldrich Cat. No. C5138-1G) in media (DMEM/F12 with 5% FBS, 5µg/mL insulin, and 1% Penstrep/Ampho B) for 45 min at 37°C. Cell suspensions were washed with 2 µg/mL DNAseI for 5 min and further dissociated with 0.05% Trypsin for 10 min. Following a wash with HBBS/2% FBS, cells were passed through a 70µm filter. Lung and primary tumour cells were treated with 1X RBC lysis buffer, followed by resuspension in DMEM/F12 with 10% FBS for FACS. We used the human-specific antibody CD298 (PE, BioLegend, Cat. No. 341704) and the mouse-specific antibody MHCI (APC, ThermoFisher, Scientific Cat. No. 17-5957-80). Flow cytometry was performed using the BD FACSAria Fusion cell sorter. Cell viability was determined by negative staining for SYTOX Blue (ThermoFisher Scientific Cat. No. S34857). Forward scatter area by forward scatter width (FSC W x FSC A) and side scatter area by side scatter width (SSC W x SSC A) was used to discriminate single cells from doublet and multiplet cells. Mouse cells were excluded by gating out CD298-MHCI+. Human primary tumour cells and metastatic cells were selected by gating on Sytox-CD298+MHC-I-.
Single cells were sorted directly into each well of a skirted 96-well PCR plate (Fisher Scientific, Eppendorf, Cat. No. E951020443) containing lysis buffer (0.2% Triton X-100, 2 U/µL RNAseOUT, 10µM oligo-dT30VN, and 10µM dNTPs). The plates were snap frozen on dry ice and stored at -80°C until further processing. Total RNA was converted into cDNA using the SmartSeq2 protocol and prepared for Illumina sequencing with the Nextera XT DNA Library Preparation Kit (Illumina, Cat No. FC-131-1096). Cells were sequenced at a depth of 1 million reads/cell on the HiSeq2500.

tag: patient id

tag: status

value: Metastasis

tag: tissue source

value: Lung

tag: mouse


title: ChIP-seq_G1E-ER4_24hr_H3K27ac_rep1


title: ChIP-seq_G1E-ER4_12hr_H3K27ac_rep2


title: S0.3_ScrambledamiRNA 0 Hr


title: S1.1_ScrambledamiRNA 12 Hr


title: ChIP-seq_G1E-ER4_6hr_H3K27ac_rep2


title: S1.3_ScrambledamiRNA 12 Hr


title: ChIP-seq_G1E-ER4_6hr_H3K27ac_rep1


title: S0.2_ScrambledamiRNA 0 Hr


title: S0.1_ScrambledamiRNA 0 Hr


title: S1.2_ScrambledamiRNA 12 Hr


title: HCI010_470_H_LU_60


title: ChIP-seq_G1E-ER4_12hr_H3K27ac_rep1


title: HCI010_470_H_LU_59


title: HCI010_470_H_LU_61


title: HCI010_470_H_LU_58


title: M121

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline
Reads were mapped using Salmon [reference Patroet al 2017] to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm38.cdna.all.fa file
Estimated transcript abundances from Salmon were imported into R using the tximeta package and analyzed for differential gene expression with edgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts

source_name: Right lateral liver lobe

extract_protocol:
Two-month-old mice right lateral liver lobes were homogenized in TriPure Isolation Reagent (Roche, 11667165001) in lysing matrix tubes (Lysing Matrix D, MP Bio, 116913100). After guanidinium thiocyanate-phenol-chloroform extraction, RNA was further extracted on column (RNEasy, QuiaGEN, 74104) and treated with DNAse (DNAse-set, QuiaGEN, 79254) to reduce gDNA contamination. In total, RNA from 12 samples were quantified by Qubit RNA BR assay kit (Thermo Fisher Scientific, Q10211) on a Qubit 4 Fluorometer (Thermo Fisher Scientific). RNA integrity was evaluated on the Agilent 2100 Bioanalyzer using the RNA 6000 nano kit (Agilent, 5067-1511). All samples had RNA integrity number values ≥ 7.8. Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).
Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations. Libraries were equimolarly pooled and sequenced on a single lane on an Illumina NovaSeq 6000 platform.

tag: strain

value: NMRI (from Charles River Laboratories (Sulzfeld, Deutschland)

value: Liver (right lateral lobe)

tag: age

value: 2 months

tag: Sex

value: male

tag: time of euthanasia


title: ChIP-seq_G1E-ER4_2hr_H3K27ac_rep2


title: M131


title: sRNAs from Huh7.5.1 cells

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

data_processing:
Deep sequencing data analysis was performed as in (Girardi et al. 2013. Identification of RNase L-dependent, 3'-end-modified, viral small RNAs in Sindbis virus-infected mammalian cells. Mbio 4(6):e00698-00613) with slight modifications.
Briefly, FASTX-Toolkit was first applied to remove instances of the 3' adaptor.
Remaining reads between 18 and 32 nt in length were then mapped to the human genome using Bowtie 1.0.0. Up to 2 mismatches in total with no more than 1 mismatch in the first 15 nucleotides of each read were permitted. In addition, only alignments from the lowest mismatch-stratum were recorded and reads that could map to more than 50 loci were discarded.
Finally, expressed human miRNAs (miRBase Release 20) were identified and quantified using BEDTools 2.16.2 by comparing their genomic coordinates to those of the aligned reads.
During the quantification process, multiple mapped reads were weighted by the number of mapping sites in other miRNAs and the final counts were normalized per million miRNA reads (RPM).
Genome_build: hg19
Supplementary_files_format_and_content: An annotation file of the expressed cellular miRNAs is provided in tab-delimited format (Huh751_miR_annot.txt: miR, Abundance(RPM)).

source_name: Huh7.5.1 cell line

growth_protocol: Huh7.5.1 cells were maintained in Dulbecco’s modified Eagle medium (DMEM) 4.5 g/L glucose (Gibco) supplemented with 10% fetal bovine serum (FBS) (Clontech), 1% MEM Non-Essential Amino Acids Solution (NEAA 100X, Gibco) and 0.5% Gentamicin 10 mg/mL (Gibco) in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
RNA was extracted from Huh7.5.1 cells using Tri-reagent (Ambion) as per manufacturer’s instructions.
Small RNA libraries were prepared from 25 μg of total RNA as previously described (Pfeffer, S. 2007. Identification of virally encoded microRNAs. Methods Enzymol. 427:51-63), except that PCR products were not concatemerized but directly sent for large-scale sequencing.

tag: cell type


title: ChIP-seq_G1E-ER4_2hr_H3K27ac_rep1


title: ChIP-seq_G1E-ER4_0hr_H3K27ac_rep2


title: F96

value: female


title: M95


title: mGBM2-tumour-shSox10-18

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

country: Germany

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

data_processing:
Reads were aligned to the mouse genome (mm10 build) with the Gencode reference transcriptome (M2) using STAR (v2.3.0e).
Read counts for each gene were quantified as the total number of reads mapping to exons using featureCounts (Subread v1.5.3).
Gene expression values for each sample were quantified using the transcripts per million (TPM) metric.
Genome_build: mm10

molecule: polyA RNA

source_name: mouse glioblastoma tumour, of syngeneic transplant of glioblastoma cells generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53

growth_protocol: The primary mouse glioblastoma cell line (mGBM2) with Pten/Tp53 double knockout was established by the lab of Prof. Peter Angel in the German Cancer Research Center (DKFZ) (Costa et al. 2020, submitted). The cells used in these experiments are the result of two further in vivo passages of the cell line described previously (Costa et al., Blood Advances 2019). mGBM2 cells were characterized as the Proneural/RTK I subtype with high Sox10 expression based on RNA-seq profiling. mGBM2 cells were cultured at 37℃ in DMEM/F12 medium supplement with N2 supplement, EGF (20ng/ml), FGF (20ng/ml), Penicillin/Streptomycin and glutamine. The recipient C57/Bl6 mice were kept under standard conditions.

extract_protocol:
The tumour bulk was removed from the recipient animal, and cut into small pieces. Lysis was performed using the RLT buffer from, and total RNA was isolated using, the RNeasy kit (Qiagen) according to the manufacturer's protocol.
RNA-seq library preparation of each tumour (control, n=3; shSox10, n=5) was performed using the polyA-selected RNA-seq libraries preparation protocol with the TruSeq Stranded RNAseq Illumina kit by the DKFZ Genomics & Proteomics Core Facility. Libraries were multiplexed and sequenced in a single lane on a HiSeq 2000 v4, generating 50bp single-end reads.

treatment_protocol: Sox10 knockdown was carried out using lentivirus transduction of mGBM2 with the shSox10 (TRCN0000244290). All cells were Puromycin selected and Sox10 knockdown level was RT-PCR validated before injection. 200k cells (shNT and shSox10, in 1µl volume) were intracranially injected into adult C57/B6 mice (6 weeks age, female) brain under anesthesia with Isoflurane. Recipient mice were euthanised once severe symptoms became apparent.

value: syngeneic mouse glioblastoma consisting of transplanted mGBM2 cells and host normal cells


title: mGBM2-tumour-shSox10-17


title: ChIP-seq_G1E-ER4_0hr_H3K27ac_rep1


title: HCI010_470_H_LU_55


title: ChIP-seq_G1E-ER4_24hr_H3K4m3_rep2

value: H3K4m3, Millipore, 07-473


title: M83


title: mGBM2-tumour-shSox10-14


title: F84


title: HCI010_470_H_LU_53


title: mGBM2-tumour-shSox10-11


title: HCI010_470_H_LU_54


title: HCI010_470_H_LU_52


title: mGBM2-tumour-shSox10-15


title: ChIP-seq_G1E-ER4_12hr_H3K4m3_rep2


title: HCI010_470_H_LU_51


title: ChIP-seq_G1E-ER4_24hr_H3K4m3_rep1


title: mGBM2-tumour-NT-6


title: F118

value: Wild-type


title: mGBM2-tumour-NT-5


title: HCI010_470_H_LU_50


title: ChIP-seq_G1E-ER4_12hr_H3K4m3_rep1


title: F116


title: HCI010_470_H_LU_57


title: HCI010_470_H_LU_56


title: M124


title: mGBM2-tumour-NT-3


title: M123


title: HCI010_470_H_LU_49


title: ChIP-seq_G1E-ER4_6hr_H3K4m3_rep2


title: ChIP-seq_G1E-ER4_6hr_H3K4m3_rep1


title: mGBM2-cells-shSox10

source_name: mouse glioblastoma cells generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53

tag: subtype

value: RTK_I-like cell line

value: mouse glioblastoma cell line


title: F117


title: M122


title: mGBM2-cells-NT


title: ChIP-seq_G1E-ER4_2hr_H3K4m3_rep2


title: ChIP-seq_G1E-ER4_2hr_H3K4m3_rep1


title: R837+T rep3

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

country: China

institute: Renji Hospital

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 mm8 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample ...

source_name: plasmacytoid dendritic cell

growth_protocol: Cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco) at 37°C and 5% CO2 or collected directly for subsequent experiments.

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Mouse plasmacytoid dendritic cells were stimulated with R837, together with or without taurine for 12 hours.

value: spleen

value: R837+Taurine stimulated


title: HCI010_470_H_LU_47


title: SADay8(+)TGFb1_mRNA

city: Rochester

first: Edward

middle: B.

last: Leof

state: MN

address: 200 First Street SW

department: Thoracic Disease Research Unit

institute: Mayo Clinic

description:
messengerRNA (mRNA)
Day8_mRNA.txt

data_processing:
Base-calling was performed using Illumina’s RTA (version 1.17.21.3).
Mayo Clinic Division of Biomedical Statistics and Informatics used a comprehensive bioinformatics pipeline, MAP-RSeq, for mapping, gene expression counts, alignment to the reference genome for Mus musculus (mm10), and quality control.
Genes with raw counts lower than 30 reads were excluded.
Fold change of differentially expressed genes was determined by empirical analysis of RNA-seq gene expression profiles in R, using Bioconductor’s bioinformatics package edgeR (v3.9).
mRNA and miRNA with p-values <0.05 (adjusted for false discovery rate of 5%) were considered differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: txt file; Fold expression +TGFβ treatment, normalized to vehicle treated (-TGFβ).

source_name: AKR-2B Fibroblasts

growth_protocol: Using a CytoSelect Cell Transformation Assay (CBA-135; Cell Biolabs Inc., San Diego, CA, USA), cells were plated in top plugs at a concentration of 3x104 AKR-2B cells/well in a 6-well plate.

extract_protocol:
Colonies were recovered from agarose with Cel Biolab’s matrix solubilization solution, RNA was extracted with Trizol, and aqueous phase was purified with Qiagen RNeasy Kit (Qiagen, Redwood City, CA, USA). Total RNA concentration and purity were assessed by the NanodropeOneC Microvolume UV-Vis Spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA) with both A260/A230 and A260/A280 ratios.
Library preparation was completed by Mayo Clinic’s Genome Analysis Core (Rochester, MN, USA), using 100 ng -1 μg of total RNA with TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Cells were plated in soft agar in the presence or absence of 25 ng/mL TGFβ after 2, 4, and 8 days (n=1 per condition).

tag: cell line

value: fibroblasts

tag: stimulation

value: Cells Simulated with TGFBeta

tag: time point

value: 8 Days

tag: growth medium

value: Anchorage Independent Growth in Soft Agar


title: R837+T rep2

tag: tissue

tag: treatment


title: R837+T rep1


title: HCI010_470_H_LU_46

value: Metastasis

value: Lung


title: HCI010_470_H_LU_48


title: ChIP-seq_G1E-ER4_0hr_H3K4m3_rep1

value: Mouse G1E-ER4 cells

tag: chip antibody


title: SADay4(+)TGFb1_mRNA

description:
messengerRNA (mRNA)
Day4_mRNA.txt

value: 4 Days


title: R837 rep3

value: R837 stimulated


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_24hr_rep3

description: CAPTURE-3C-seq_G1E-ER4_sgPromoter_24hr_combined_interaction

data_processing:
Library strategy: 3C-seq
Sequencing reads were aligned to human genome assembly hg19  or mm10 using Bowtie2 v2.2.8 with default parameters. The reads with low mapping qualit and duplicate reads were removed after the aligment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (http://wiki.wubrowse.org/Long-range).
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Pairwise Interaction Format

source_name: Mouse G1E-ER4 cells

growth_protocol: Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS).  G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).

extract_protocol: For 3C-seq analysis using the Illumina NextSeq500, 10 ng of 3C DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

treatment_protocol: G1E-ER4 cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.

tag: b-estradiol time point

tag: streptavidin dynabeads

value: ThermoFisher 65602


title: SADay4(-)TGFb1_mRNA

description:
messengerRNA (mRNA)
Day4_mRNA.txt

value: Cells Simulated with Vehicle


title: HCI010_470_H_LU_44

tag: patient id

tag: status

tag: tissue source


title: HCI010_470_H_LU_43

tag: mouse


title: R837 rep2

tag: strain


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_24hr_rep2


title: SADay2(+)TGFb1_mRNA

description:
messengerRNA (mRNA)
Day2_mRNA.txt

value: 2 Days


title: R837 rep1


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_24hr_rep1


title: HCI010_470_H_LU_42


title: SADay2(-)TGFb1_mRNA

description:
messengerRNA (mRNA)
Day2_mRNA.txt


title: HCI010_470_H_LU_41


title: SADay8(+)TGFb1_miRNA

description:
microRNA (miRNA/smRNA)
miRNA_logFoldChange
Unique_mature_miRNA_expression


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_12hr_rep3

description: CAPTURE-3C-seq_G1E-ER4_sgPromoter_12hr_combined_interaction


title: HCI010_470_H_LU_45


title: HCI010_470_H_LU_40


title: SADay8(-)TGFb1_mRNA

description:
messengerRNA (mRNA)
Day8_mRNA.txt


title: SADay8(-)TGFb1_miRNA


title: ChIP-seq_G1E-ER4_0hr_H3K4m3_rep2

value: H3K4m3, Millipore, 07-473


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_12hr_rep2


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_12hr_rep1


title: HCI010_470_H_LU_38


title: HCI010_470_H_LU_39


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_6hr_rep3

description: CAPTURE-3C-seq_G1E-ER4_sgPromoter_6hr_combined_interaction


title: SADay4(+)TGFb1_miRNA


title: SADay4(-)TGFb1_miRNA


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_6hr_rep2


title: HCI010_470_H_LU_37


title: SADay2(+)TGFb1_miRNA


title: SADay2(-)TGFb1_miRNA


title: HCI010_470_H_LU_35


title: HCI010_470_H_LU_36


title: HCI010_470_H_LU_34


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_2hr_rep2

description: CAPTURE-3C-seq_G1E-ER4_sgPromoter_2hr_combined_interaction


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_2hr_rep1


title: HCI010_470_H_LU_33


title: 15051_SPL_OT_BN_EMM_MYC+

type: genomic

city: Scottsdale

first: Marta

last: Chesi

state: AZ

address: 13400 E Shea Blvd

hyb_protocol: Aliquots of Agilent dye-specific Oligo aCGH hybridization mixes were added to the samples as recommended by the manafacturer. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

scan_protocol: Scanned on DNA Microarray Scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.  The file 'Normalized data.txt' on the series record contains the normalized values with probe name, chromosome coordinates, and gene name.

label: AlexaFluor 5

label_protocol: 1.2 ug of tumor and reference DNA were independently labeled using the Bioprime Total for Agilent aCGH Kit as recommended by the manafacturer. Alexa Fluor 5 dye was used to label tumor DNA samples and Alexa Fluor 3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with PureLink spin columns.

extract_protocol: Genomic DNA was obtained from magnetically selected CD138+ myeloma cells or from splenocytes using the Puregene Core A kit (Qiagen) according to manufacturer’s recommendations.

tag: background strain

tag: donor/recipient

value: OT

tag: bortezomib treatment

value: BN

tag: genotype

value: MYC+

tag: diagnosis

value: EMM

tag: Sex

value: M

value: SPL

label: AlexaFluor 3

source_name: Pooled male splenocytes

value: splenocytes

value: male


title: 14660_SPL_OT_BN_EMM_MYC+

value: F

tag: cell type


title: HCI010_470_H_LU_32

value: Metastasis

value: Lung


title: 14246_BMSPL_OT_BN_EMM_MYC+BCL6+

tag: tissue

value: BM+SPL


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_0hr_rep3

description: CAPTURE-3C-seq_G1E-ER4_sgPromoter_0hr_combined_interaction

value: Mouse G1E-ER4 cells


title: HCI010_470_H_LU_31


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_6hr_rep1

value: ThermoFisher 65602


title: 14123_SPL_R_BN_EMM_MYC+

value: R


title: 14153_SPL_OT_BN_EMM_MYC+


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_2hr_rep3


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_0hr_rep1


title: Deep_neurons_control_male_1055

city: Toledo

first: Robert

last: McCullumsmith

state: OH

address: 3000 Arlington Ave.

institute: The University of Toledo

hyb_protocol: Arrays were washed and stained with phycoerythrein-conjugated streptavidin in a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures.

scan_protocol: Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner.

data_processing: AGEC QC outputs (ALE Box Plots, RLE Box Plots, and Pos_vs_Neg_AUC values) were used to identify potential outlier arrays; outlier evaluation was also performed by Principal Components Analysis in GeneMaths XT.

source_name: Deep neurons control_male

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA of 2000 pyramidal neurons of each subject.

growth_protocol: Frozen tissue

extract_protocol: Total unpooled RNA from the 2000 pyramidal neurons from each subject was purified with the QuickGene RNA Tissue kit SII in conjunction with the QuickGene Mini-80 semi-automated station.

treatment_protocol: Frozen tissue was sectioned at 14 μm on SuperFrost®/Plus 96 glass slides and stored at -80 °C until use. 2000 pyramidal neurons from each sample were collected by laser capture microdissection.

tag: disease state

value: control

value: Male

tag: pmi

tag: age

tag: ph

tag: meds

value: OFF

value: pyramidal neurons

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: HCI010_470_H_LU_30

tag: patient id

tag: status


title: HCI010_470_H_LU_29

tag: tissue source

tag: mouse


title: CAPTURE-3C-seq_G1E-ER4_sgPromoter_0hr_rep2

tag: b-estradiol time point

tag: streptavidin dynabeads


title: HCI010_470_H_LU_28


title: ATAC-seq_G1E-ER4_24hr_rep2

data_processing:
Sequencing reads were aligned to mouse genome assembly mm10 using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq 2 (MACS2) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Genome_build: mm10
Supplementary_files_format_and_content: wig file and peak bed file

extract_protocol: For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference mouse genome (mm10) were retained for downstream data analysis.

tag: time point


title: 13855_SPL_OT_BN_EMM_MYC+

tag: background strain

tag: donor/recipient

value: OT

tag: bortezomib treatment

value: BN

tag: genotype

value: MYC+

value: EMM


title: 14154_BM_R1_BN_MM_MYC+

tag: diagnosis

value: MM

tag: Sex

tag: tissue

value: BM

tag: cell type

value: splenocytes

value: male


title: Deep_neurons_schizophrenia_female_934

source_name: Deep neurons schizophrenia_female

tag: disease state

value: schizophrenia

value: Female

tag: pmi

tag: age

tag: ph

value: ON


title: 13801_TM_OT_BN_EMM_MYC+

value: F

value: TM


title: HCI010_470_H_LU_27

tag: patient id

tag: status

value: Metastasis

tag: tissue source

value: Lung


title: ATAC-seq_G1E-ER4_12hr_rep2

value: Mouse G1E-ER4 cells


title: Deep_neurons_control_male_1052

value: control

value: Male

tag: meds

value: OFF

value: pyramidal neurons

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: HCI010_470_H_LU_25

tag: mouse


title: Deep_neurons_control_male_2012


title: 13826_SPL_OT_BN_EMM_MYC+

tag: background strain

value: OT

value: BN

value: MYC+

value: EMM

value: SPL


title: ATAC-seq_G1E-ER4_24hr_rep1

tag: time point


title: 13795_BM_OT_BN_MM_MYC+

tag: donor/recipient

tag: bortezomib treatment

value: MM

value: M

value: BM

value: splenocytes

value: male


title: Deep_neurons_schizophrenia_male_998

source_name: Deep neurons schizophrenia_male

value: schizophrenia


title: ATAC-seq_G1E-ER4_12hr_rep1

value: Mouse G1E-ER4 cells


title: Deep_neurons_schizophrenia_female_971

value: Female

value: ON


title: Deep_neurons_schizophrenia_female_833


title: HCI010_470_H_LU_24

value: Metastasis

value: Lung


title: Deep_neurons_control_female_800

source_name: Deep neurons control_female

value: control

value: OFF

value: pyramidal neurons

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: ATAC-seq_G1E-ER4_6hr_rep1


title: 13769_BM_OT_BN_MM_MYC+FGFR3+

value: OT

value: BN

tag: genotype

tag: diagnosis


title: Deep_neurons_control_female_900

tag: Sex

tag: tissue


title: ATAC-seq_G1E-ER4_6hr_rep2


title: Deep_neurons_control_male_843

tag: disease state

value: Male


title: HCI010_470_H_LU_23


title: 13429_BM_OT_BN_MM_MYC+

value: MYC+

value: MM

value: M

tag: cell type


title: 13756_SPL_OT_BR_EMM_MYC+

value: BR

value: EMM

value: SPL

value: splenocytes

value: male


title: 13742_SPL_OT_BN_EMM_MYC+

value: F


title: HCI010_470_H_LU_26

value: Metastasis

value: Lung


title: ATAC-seq_G1E-ER4_2hr_rep2

value: Mouse G1E-ER4 cells


title: HCI010_470_H_LU_22


title: ATAC-seq_G1E-ER4_0hr_rep2


title: Deep_neurons_control_male_781

value: control

tag: pmi

tag: age

value: OFF

value: pyramidal neurons


title: HCI010_470_H_LU_21

tag: patient id


title: 13410_TM_OT_BN_EMM_MYC+

value: OT

value: BN

value: TM


title: ATAC-seq_G1E-ER4_0hr_rep1


title: 13045_SPL_R_BN_EMM_MYC+

value: R

value: MYC+


title: 13321_BM_R_BN_MM_MYC+

value: MM

value: M

value: BM


title: ATAC-seq_G1E-ER4_2hr_rep1


title: B15W70R2F_ADT

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

description: Single-cell epitope profiling

data_processing:
Sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants.
The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices. CITE-seq-Count (v1.2) was used to get ADT counts in the CITE-seq libraries
Bulk mRNA reads were mapped with STAR. Gene counts were computed with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Digital Gene Expression matrices contain UMI counts per cell and per gene. featureCounts measure gene abundances in mRNA samples (read counts). ADT files contain antibody-derived tag counts per cell and per antibody

source_name: Drop-seq of mouse submandibular gland

extract_protocol:
Single-cell Drop-seq: submandibular glands were dissected, enzymatically dissociated, and single-cell suspensions obtained by FACS prior to methanol fixation and subsequent rehydration for single-cell RNA experiments; Bulk RNA-seq: RNA was extracted by Trizol from freshly dissected submandibular glands
Single-cell Drop-seq (Macosko et al., Cell 2015 + Drop-Seq laboratory protocol v.3.1. 2015. http:// mccarrolllab.com/dropseq/) ; Bulk RNA-seq: TruSeq Stranded mRNA LT Sample Prep Kit, Illumina

value: female

tag: Stage


title: B15W70R1M_ADT

description: Single-cell epitope profiling

value: male


title: Deep_neurons_schizophrenia_male_814

value: schizophrenia

value: Male

tag: ph

value: ON

tag: tissue source

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: Deep_neurons_control_female_756

value: control

value: Female

tag: meds


title: HCI010_470_H_LU_17

tag: status

value: Metastasis

value: Lung

tag: mouse


title: Deep_neurons_control_female_684

value: OFF

value: pyramidal neurons


title: Deep_neurons_schizophrenia_male_700


title: Deep_neurons_control_male_495


title: B15T70R2F_ADT

description: Single-cell epitope profiling

value: double mutant


title: HCI010_470_H_LU_20


title: HCI010_470_H_LU_16


title: Deep_neurons_schizophrenia_female_426


title: 12869_BM_R_BN_EMM_MYC+

tag: background strain

tag: donor/recipient

value: R

value: BN

value: MYC+

value: EMM

value: splenocytes


title: 12811_SPL_OT_BN_EMM_MYC+

value: OT

tag: bortezomib treatment

tag: genotype

value: F

value: SPL

value: male


title: 13051_SPL_R_BN_EMM_MYC+

tag: diagnosis

tag: Sex


title: HCI010_470_H_LU_19


title: 13044_BM_R_BN_MM_MYC+

value: MM

tag: tissue

value: BM


title: B15T70R1F_ADT

description: Single-cell epitope profiling

value: female


title: 12996_SPL_OT_BN_EMM_MYC+

value: M

tag: cell type


title: B15W70R2F_RNA

description: Single-cell transcriptomics

value: control


title: HCI010_470_H_LU_18

value: Metastasis

value: Lung


title: HCI010_470_H_LU_15


title: Deep_neurons_schizophrenia_male_331

tag: disease state

value: schizophrenia

value: Male

tag: pmi

value: ON

value: pyramidal neurons

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: HCI010_470_H_LU_14

tag: patient id


title: 12803_BM_OT_BN_EMM_MYC+

value: BN

value: MYC+

value: EMM

value: splenocytes


title: B15W70R1M_RNA

description: Single-cell transcriptomics

value: male

tag: Stage


title: B15T70R2F_RNA

description: Single-cell transcriptomics

value: double mutant


title: HCI010_470_H_LU_13


title: HCI010_470_H_LU_12


title: 12653_SPL_R2_BR_EMM_MYC+

value: BR

value: SPL


title: HCI010_470_H_LU_11


title: 12728_BM_OT_BN_MM_MYC+

value: OT

value: MM

value: M

value: BM


title: B15T70R1F_RNA

description: Single-cell transcriptomics

value: female


title: mouse BAT ATAC-seq cre-2

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
atactk (0.1.5) was used for adapator trimming.
bwa (0.7.17-r1188) was used for alignment to generate bam files.
Duplicates were marked by Picard (v.2.8.14).
Samtools was used to remove duplicates.
macs2 (2.1.1.20160309) was used for peak calling.
The treat_pileup.bedgraph files (generated by macs2) from each individual samples were normalized to its own library size and converted to bigwig file by bedGraphToBigWig (v.4).
Broad peaks were filtered against an mm10 blacklist (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz).
The master peaks list was generated from the union of all blacklist-filtered broad peaks, which were kept those overlapping with peak calls (FDR < 0.1) from at least 2 of 3 biological replicates
Bedtools (v.2.27.1) was used to count reads in each peak for each sample.
The R package DESeq2 (v.1.20.0) was used to perform the differential peak analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from ATAC-seq, bigwig file of ATAC-seq coverage.

source_name: brown adipose tissue

extract_protocol: Nuclei from frozen mouse brown fat were isolated by gradient centrifugation. 50000 isolated nuclei were used in each transposase reaction (Illumina). The sequencing libraries were barcoded and amplified by 2-step PCR. DNA sequencing were performed on Illumina NextSeq-500 instrument with 38-bp paired-end reads.

tag: strain

value: whole brown adipose tissue

tag: phenotype

value: AKO


title: HCI010_470_H_LU_10

value: Metastasis

tag: tissue source

value: Lung


title: mouse BAT ATAC-seq cre-1


title: ethanol-5

city: Indianapolis

first: James

last: Marrs

address: 723 West Michigan Street

institute: Indiana University-Purdue University Indianapolis

hyb_protocol: hybridized for 17h washed and stained on the Affymetrix Fluidics station

scan_protocol: Scanned using the Affymetrix 3000 scanner. Data was collected using GCOS software from Affymetrix.

data_processing: Affymetrix Gene Expression console was used to generate MAS5 signals, detection calls and detection p-values

organism: Danio rerio

source_name: embryos

label_protocol: Standard protocol for Affymetrix 3' IVT Express kit using 100ng of total RNA

growth_protocol: Both treatment groups were grown in embryo medium at 28.5 degrees C, but ethanol-treated zebrafish embryos that grown in 100 mM ethanol from 2 to 4.5 hours postfertilization.

extract_protocol: Total RNA was extracted from pools of 20 control and 20 ethanol-treated embryos using TRIzol reagent (Sigma, St Louis, MO, USA). Seven independent experiments were done. RNA samples were purified by passing through the Qiagen RNAeasy column (Cat. No. 74104).

treatment_protocol: Control vs. ethanol-treated zebrafish embryos that were treated from 2 to 4.5 hours postfertilization prior to total RNA being isolated at 4.5 hours postfertilization.

tag: treatment

value: ethanol

value: Danio rerio ABTL strain


title: Deep_neurons_schizophrenia_male_278

value: schizophrenia

value: Male

tag: age

tag: ph

tag: meds

value: Unknown

value: pyramidal neurons

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: ethanol-6


title: Deep_neurons_schizophrenia_female_106

value: Female

value: ON


title: HCI010_470_H_LU_8

tag: status

tag: mouse


title: Superficial_neurons_control_male_2012

source_name: Superficial neurons control_male

value: control

value: OFF

value: Neurons captured by LCM isolated from superficial (lamina II-III) layers


title: mouse BAT ATAC-seq lox-3

value: flox/flox


title: 12598_SPL_R2_BR_EMM_MYC+

tag: background strain

tag: donor/recipient

tag: bortezomib treatment

value: BR

tag: genotype

value: MYC+

tag: diagnosis

value: EMM

value: M

value: SPL

value: splenocytes

value: male


title: ethanol-4

value: ethanol

value: Danio rerio ABTL strain


title: ethanol-2


title: Superficial_neurons_schizophrenia_female_934

tag: disease state

value: schizophrenia

tag: Sex

tag: pmi

tag: tissue

value: pyramidal neurons


title: Superficial_neurons_control_male_1055

value: Male


title: Superficial_neurons_control_male_1052


title: Superficial_neurons_schizophrenia_male_998

source_name: Superficial neurons schizophrenia_male


title: control-5

tag: strain


title: HCI010_470_H_LU_7

source_name: Patient Derived Xenograft Single Cells

tag: patient id

value: Metastasis

tag: tissue source

value: Lung


title: ethanol-3

tag: treatment


title: HCI010_470_H_LU_9


title: mouse BAT ATAC-seq cre-3

value: whole brown adipose tissue

tag: phenotype

value: AKO


title: ethanol-1


title: HCI010_470_H_LU_6


title: HCI010_470_H_LU_5


title: control-6

value: control


title: Superficial_neurons_control_female_900

source_name: Superficial neurons control_female

value: Female

tag: age

tag: ph

tag: meds

value: OFF

value: Neurons captured by LCM isolated from superficial (lamina II-III) layers


title: Deep_neurons_schizophrenia_male_254

value: ON

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: bulk control

description: RNA-seq

data_processing:
Sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants.
The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices.
Bulk mRNA reads were mapped with STAR. Gene counts were computed with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Digital Gene Expression matrices contain UMI counts per cell and per gene. featureCounts measure gene abundances in mRNA samples (read counts)

source_name: RNA-seq of mouse submandibular gland

extract_protocol:
Single-cell Drop-seq: submandibular glands were dissected, enzymatically dissociated, and single-cell suspensions obtained by FACS prior to methanol fixation and subsequent rehydration for Drop-seq experiments; Bulk RNA-seq: RNA was extracted by Trizol from freshly dissected submandibular glands
Single-cell Drop-seq (Macosko et al., Cell 2015 + Drop-Seq laboratory protocol v.3.1. 2015. http:// mccarrolllab.com/dropseq/) ; Bulk RNA-seq: TruSeq Stranded mRNA LT Sample Prep Kit, Illumina
Single-cell RNA-seq + bulk RNA-seq

value: wildtype

value: female

tag: Stage


title: HCI010_470_H_LU_2

tag: status

tag: mouse


title: bulk double mutant

description: RNA-seq

tag: genotype

value: beta-catenin GOF; Bmpr1a LOF


title: HCI010_470_H_LU_3


title: B14W40R5M

description: Single-cell transcriptomics

value: male


title: HCI010_470_H_LU_1


title: B14T40R7F

description: Single-cell transcriptomics


title: mouse BAT ATAC-seq lox-1

value: flox/flox


title: T47D GFOGER_D3 replicate 3

city: Newark

first: Shawn

middle: William

last: Polson

state: DE

institute: University of Delaware

data_processing:
Analysis was performed by the University of Delaware Bioinformatics Core Facility using a modified MAPRseq pipeline implemented on the BioMix compute cluster at the Center for Bioinformatics and Computational Biology/Delaware Biotechnology Institute
Sequence quality was assessed using FASTQC
Sequences were end-trimmed (Q30) and filtered (no ambiguous nucleotides, 35bp minimum length after trimming) using Trim Galore (v0.4.4)
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Mapping quality was assessed using RSeQC v2.3.7 and metrics extracted from BedTools v2.17 and SamTools v1.4
Feature counts were extracted using HtSeq v0.6.1p1
Pairwise differential expression analysis was performed on features with >1 cpm in at least 2 samples using EdgeR v 3.16.5
Genome_build: Hg19-37.1
Supplementary_files_format_and_content: tab-delimited w/ the following columns: Chr, GeneID, Start, Stop, CodingLength, D3_MG_1_GeneCount, D3_MG_1_RPKM, D3_MG_2_GeneCount, D3_MG_2_RPKM, D3_MG_3_GeneCount, D3_MG_3_RPKM, D3_MI_1_GeneCount, D3_MI_1_RPKM, D3_MI_2_GeneCount, D3_MI_2_RPKM, D3_TG_1_GeneCount, D3_TG_1_RPKM, D3_TG_2_GeneCount, D3_TG_2_RPKM, D3_TG_3_GeneCount, D3_TG_3_RPKM, D3_TI_1_GeneCount, D3_TI_1_RPKM, D3_TI_2_GeneCount, D3_TI_2_RPKM, D3_TI_3_GeneCount, D3_TI_3_RPKM

source_name: T47D GFOGER_D3

growth_protocol: MDA-MB-231 and T47Ds were cultured in DMEM (Corning 10-013CV) + 10% FBS + Pen/strep + Fungizone. Media was replaced every 2-3 days. Cells encapsulated within hydrogels were cultured in 48-well plates with 500 µL of culture media.

extract_protocol:
Hydrogels were degraded by incubating gels with 250 U collagenase for 20 minutes at 37 ℃ and 5% CO2. After gel degadation, cells were pelleted by centrifugation at 1000 RPM for 5 minutes, and PEG was removed. RNA was then extracted from cells by a Nucleospin miRNA kit (Takara), where cells were first placed into lysis buffer. Three gels of the same composition was used for one replicate of RNA. DNase treatment was performed duing RNA isolation.
RNA Indexed libraries were constructed from 100-500 ng of total RNA using the Universal Plus mRNA-seq Workflow Kit (Nugen)
Stranded Poly-A capture RNA-Seq

treatment_protocol: Cells were encapsulated in a hydrogel: 5 µL of the gel precusor solution with a single cell suspension of 5,000 cells/µL was polymersized on top of a pre-formed 15 µL base hydrogel without encapsulated cells (20 uL total hydrogel volume formed in 1-mL sterile syringe with end removed). Cells were formed by free-radical step growth-polymerization 'thiol-ene' click chemistry of a 4-arm PEG-SH and cell-degradable crosslinker (GPQGIWGQ) difunctional with allyloxycarbonyl groups. Two treatments per cell line were performed, consisting of a collagen (GFOGER peptide) or laminin (IKVAV peptide) environment.

tag: cell line

value: Mammary Gland/Breast; Derived From Metastatic Site:Pleural Effusion

tag: cell type

value: epithelial

value: Ductal Carcinoma

tag: time

value: 3 days

tag: growth matrix peptide

value: GFOGER


title: B14W40R4F

description: Single-cell transcriptomics

tag: Sex


title: Superficial_neurons_schizophrenia_female_890

tag: disease state

value: schizophrenia

tag: pmi

value: Unknown

tag: tissue

value: pyramidal neurons


title: T47D GFOGER_D3 replicate 2

department: Center for Bioinformatics and Computational Biology


title: control-2

tag: treatment

value: control

tag: strain

value: Danio rerio ABTL strain


title: control-1


title: Superficial_neurons_schizophrenia_female_833

value: Female

tag: age

value: ON

tag: tissue source

value: Neurons captured by LCM isolated from superficial (lamina II-III) layers


title: Superficial_neurons_control_male_843

value: Male

tag: ph

tag: meds

value: OFF


title: Superficial_neurons_control_female_800


title: B13T90R7F

description: Single-cell transcriptomics

value: beta-catenin GOF; Bmpr1a LOF

value: female

tag: Stage


title: control-4


title: Superficial_neurons_control_male_781


title: Superficial_neurons_schizophrenia_male_814


title: T47D IKVAV_D3 replicate 3

source_name: T47D IKVAV_D3

value: Mammary Gland/Breast; Derived From Metastatic Site:Pleural Effusion

value: IKVAV


title: Superficial_neurons_control_female_756


title: B13W40R3M

description: Single-cell transcriptomics

value: wildtype

value: male


title: T47D GFOGER_D3 replicate 1

value: epithelial

value: Ductal Carcinoma

value: 3 days

value: GFOGER


title: B13T40R6F

description: Single-cell transcriptomics


title: Superficial_neurons_schizophrenia_male_700

value: schizophrenia

value: pyramidal neurons


title: T47D IKVAV_D3 replicate 2


title: B13T40R5M

description: Single-cell transcriptomics


title: T47D IKVAV_D3 replicate 1


title: Superficial_neurons_control_female_684

value: control

value: Female


title: Superficial_neurons_control_female_659

value: Neurons captured by LCM isolated from superficial (lamina II-III) layers


title: control-3

value: Danio rerio ABTL strain


title: B12T90R6M

description: Single-cell transcriptomics


title: B12T40R4F

description: Single-cell transcriptomics


title: MDA-MB-231 GFOGER_D3 replicate 2

source_name: MDA-MB-231 GFOGER_D3

value: Adenocarcinoma


title: B12W40R2M

description: Single-cell transcriptomics


title: MDA-MB-231 GFOGER_D3 replicate 3


title: MDA-MB-231 GFOGER_D3 replicate 1


title: B12W40R1F

description: Single-cell transcriptomics


title: HCI010_470_H_LU_4

tag: patient id

tag: status

value: Metastasis

value: Lung

tag: mouse


title: Superficial_neurons_control_male_495

value: Male

value: OFF


title: MDA-MB-231 IKVAV_D3 replicate 1

source_name: MDA-MB-231 IKVAV_D3

tag: cell line

value: Mammary Gland/Breast; Derived From Metastatic Site:Pleural Effusion

tag: cell type

value: IKVAV


title: Deep_neurons_control_female_231

value: Neurons captured by LCM isolated from deep (lamina V-VI)  layers


title: B11T40R3M

description: Single-cell transcriptomics

tag: genotype

value: beta-catenin GOF; Bmpr1a LOF

value: male


title: B11T90R5F

description: Single-cell transcriptomics

tag: Sex

value: female


title: Superficial_neurons_schizophrenia_male_331

tag: disease state

value: schizophrenia

value: ON


title: Superficial_neurons_schizophrenia_female_426

tag: pmi

value: pyramidal neurons


title: Superficial_neurons_control_female_231

value: control

value: Female

tag: tissue


title: B11T40R1M

description: Single-cell transcriptomics


title: B11T40R2F

description: Single-cell transcriptomics


title: B9T90R4F

description: Single-cell transcriptomics


title: B9W90R6F

description: Single-cell transcriptomics

value: wildtype


title: B9W90R5M

description: Single-cell transcriptomics


title: Limb bud cells control

city: Suita

first: Yoshifumi

last: Takahata

state: Osaka

department: Dentistry

country: Japan

institute: Osaka University

description: Gene expression data from mouse Limb bud cells

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Limb bud cells control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Limb bud cells were cultured with α-ΜΕΜ containing 10% FBS.

extract_protocol: Total RNA was extracted with Nucleospin RNA kit

treatment_protocol: Limb bud cells were infected with control or Bmp2 adenovirus.

value: limb bud

tag: developmental stage

value: E12.5 day

value: ICR


title: Limb bud cells Bmp2

description: Gene expression data from mouse Lumb bud cells

source_name: Limb bud cells Bmp2

tag: strain


title: B8W90R4M

description: Single-cell transcriptomics


title: 0h giardia control rep3 (trophozoites)

city: Uppsala

first: Feifei

address: Husargatan 3

country: Sweden

institute: Uppsala University

data_processing:
Illumina HiSeq 2500, Demultiplexing and conversion to FASTQ performed using the bclfastq2
FASTQ files were mapped to combined Giardia WB genome and human GRCh38 using STAR v2.5.2b. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R using edgeR v3.26.8 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Genome_build: Giardia WB, AACB03000000
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts from STAR mapping for each sample, separated by host and parasite

organism: Giardia duodenalis

source_name: trophozoites

growth_protocol: Trophozoites were grown in TYI-S33 until 80% confluency after cells were detached and spun down. Giardia cells were resuspended in DMEM (HI-FBS) for 10 minutes and incubated with previously grown and differenatiated Caco2 cells for 1.5, 3 and 4.5 h. Prior interaction Giardia cells and Caco-2 cells were collected.

extract_protocol:
Performed according to the instructions provided with the Trizol reagent. RNA was then treated with DNaseI and extracted again by phenol chloroform extraction
Sequencing libraries were prepared from 250 ng total RNA using the TruSeq stranded mRNA library preparation kit (Cat# 20020594/5, Illumina Inc.) including polyA selection.The library preparation was performed according to the manufacturers’ protocol (#1000000040498).

treatment_protocol: Upon reaching 80% confluence, trophozoites were detached on ice (10m), pelleted and lysed in 1ml of Trizol and collected in Eppendorf tubes. Samples were frozen immediatedly in liquid nitrogen and kept at -80 until RNA extraction

value: WB

tag: growth medium

value: TYDK

tag: time

value: 0h giardia control


title: 0h giardia control rep2 (trophozoites)


title: B8T90R3F

description: Single-cell transcriptomics


title: MDA-MB-231 IKVAV_D3 replicate 2

value: Mammary Gland/Breast; Derived From Metastatic Site:Pleural Effusion

value: epithelial

value: Adenocarcinoma

value: 3 days

tag: growth matrix peptide

value: IKVAV


title: MDA-MB-231 IKVAV_D3 replicate 3

description:
D3_MI_3
This sample was determined to be an outlier that likely had RNA quality and/or library construction issues.  As such it was omitted from the analysis.


title: B8W90R3M

description: Single-cell transcriptomics

value: male


title: 0h giardia control rep1 (trophozoites)


title: B8T90R2M

description: Single-cell transcriptomics

value: beta-catenin GOF; Bmpr1a LOF


title: B7W90R2F

description: Single-cell transcriptomics

value: female


title: OE20 rep1

city: wuhan

first: wang

last: dujun

state: hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
filtered for quality control of the reads with the FastQC v0.11.8
filtered reads were pre-processed using the Trimmomatic-0.38;with parameters HEADCROP:12 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
reads mapping with Hisat2 v2.1.0
differentially-expressed genes(DEGs) were identified using the Cufflinks v2.2.1
Genome_build: RGAP 7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: root

growth_protocol: Seedlings of wild-type (WT) and  OsMYB305 overexpressed lines were growing in the culture solution (MS) containing 0.288 Mm NH4NO3 for 14 days.

extract_protocol:
Roots were harvested and frozen in liquid nitrogen,and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: 14 days

tag: cultivar

value: root

value: OsMYB305 overexpressed


title: B7W90R1F

description: Single-cell transcriptomics

value: wildtype

tag: Stage


title: OE20 rep2


title: OE15 rep2


title: NB4 cells-ATPR-72h-rep1

city: Hefei

first: Yu-bin

last: Feng

address: meishan street 81

institute: anhui medical university

description: Gene expression after 72h in ATPR-human NB4 cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data.

source_name: NB4 cells，ATPR，72h， replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: NB4 cells was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

value: NB4 cells

tag: treatment


title: NB4 cells-ATPR-72h-rep2

source_name: NB4 cells，ATPR，72h， replicate 2


title: NB4 cells-ATPR-72h-rep3

source_name: NB4 cells，ATPR，72h， replicate 3


title: B6T90R1M

description: Single-cell transcriptomics

source_name: Drop-seq of mouse submandibular gland


title: NB4 cells-Solvent-72h-rep3

description: Gene expression after 72h in Solvent-human NB4 cells

source_name: NB4 cells，Solvent，72h， replicate 3


title: NB4 cells-Solvent-72h-rep2

source_name: NB4 cells，Solvent，72h， replicate 2


title: OE15 rep1


title: WT rep2

value: WT


title: WT rep1


title: Combination_3 (circRNA)

city: Nanjing

first: Rong

address: 50 Zhongling Street

institute: Jiangsu Academy of Agricultural Sciences

description: circRNA sequencing

data_processing:
circRNA-Seq: Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
circRNA-Seq: We used Bowtie2 and Tophat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion
circRNA-Seq: CIRCExplorer was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer.
Genome_build: genome of species (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/115/GCF_000188115.3_SL2.50/GCF_000188115.3_SL2.50_genomic.fna.gz)
Supplementary_files_format_and_content: FPKMs

organism: Solanum lycopersicum

source_name: Combination, plants leaves

growth_protocol: Single seeds were sown in a plug tray and then cultured in climate chambers (RDN-560E-4, Dongnan Instrument Co, Ltd, Ningbo, China). The air temperature was 26/18°C (14 h/10 h, 6:00-20:00/20:00-6:00, day/night) with a light intensity of 300 μmol m–2 s–1 photosynthetic photon flux density (PPFD) (LED light source, Dongnan Instrument Co, Ltd, Ningbo, China) and 50-60% relative humidity (RH). The seedlings were irrigated by water every five days. Then, the 15-day-old seedlings were irrigated by nutrient solution according to the Japanese Garden test formula [Ca(NO3)2.4H2O, 945mg/L; KNO3, 809 mg/L; NH4H2PO4, 153 mg/L; MgSO4.7H2O, 493 mg/L; FeSO4.7H2O, 13.9 mg/L; Na2-EDTA, 18.6 mg/L; H3BO3, 2.86 mg/L; MnSO4.4H2O, 2.13 mg/L; ZnSO4.7H2O, 0.22 mg/L; CuSO4.5H2O, 0.08 mg/L; (NH4)6Mo7O24.4H2O, 0.02 mg/L] every three days. The 21-day-old healthy and uniform seedlings were transferred to plastic plots (11 cm diameter, 9 cm height) and then cultured in the climate chambers under the same conditions.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500/Hiseq 4000 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: The 24-day-old seedlings were divided into two groups with one group irrigated by water and another group without irrigation. After three days, half of the seedlings from the group with/without irrigation were treated at a normal temperature (26°C, 48 h, day) as a control and drought stress treatment. The rest half of the seedlings from the group with/without irrigation were treated at high temperature (38°C, 48 h, day) as a heat and combined stress treatment. The 24-day-old and 27-day-old seedlings at control and heat stress treatment were subjected to two additional irrigations with water as compared to that at drought and combined stress.

value: wild type

value: Combination

value: plants leaves


title: 3h infection rep3 (trophozoites)

organism:
Giardia duodenalis
Homo sapiens

source_name: trophozoites, Caco-2

value: WB

value: DMEM

value: 3h infection


title: 4.5h infection rep3 (trophozoites)

value: 4.5h infection


title: 1.5h infection rep3 (trophozoites)

value: 1.5h infection


title: Combination_2 (circRNA)

description: circRNA sequencing


title: 4.5h infection rep2 (trophozoites)


title: Sample 5 (KK-5)

city: Hyderabad

first: Rupinder

last: Kaur

state: Telangana

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

description: YPD grown; Replicate-1

data_processing:
RNA-seq reads were aligned to the Candida glabrata CBS138 genome and quantified using reference gene model in Kallisto (version 0.44.0).
Differential expression of the genes was estimated from aligned reads by using DESeq program.
Differentially expressed genes were filtered with the following setting: Fold change in expression (≥ 2) and p value (≤ 0.05).
Genome_build: Candida glabrata CBS138 genome
Supplementary_files_format_and_content: text files; File contain target_id, length, eff_length, est_counts and tpm

organism: Nakaseomyces glabratus

source_name: Cghhf1∆2∆ mutant cells

growth_protocol: C. glabrata wild-type and the Cghhf1Δhhf2Δ strains were inoculated in YPD medium and incubated for 16 h at 30⁰C under shaking conditions (200 rpm). These cultures were re-inoculated in the fresh YPD medium at an initial OD600 of 0.1, and grown for 3-4 h at 30⁰C to obtain logarithmic (log)-phase cultures.

extract_protocol:
Total RNA was extracted using acid-phenol method. Briefly, MMS-treated and untreated cultures of C. glabrata wild-type and Cghhf1Δ2Δ strains were pelleted down and washed twice with chilled DEPC-treated water. Cell pellets were suspended in 350 μl of chilled AE solution (50 mM NaOAc and 10 mM EDTA). Cells were lysed by adding 50 µl of 10% SDS and 400 µl of acid-phenol, followed by vortexing for 10 sec. Next, samples were incubated at 65°C and 800 rpm for 15 min on a Thermomixer. After 5 min incubation on ice, samples were centrifuged at 13000 rpm for 5 min at 4⁰C. The aqueous layer was transferred to a 2 ml micro-centrifuge tube and 400 µl chloroform was added, followed by centrifugation at 3000 rpm for 10 min at 4⁰C. The aqueous layer was transferred to a 1.5 ml micro-centrifuge tube, and RNA was precipitated with 40 µl of 3 M Na-Acetate (pH 5.3) and 400 µl of ethanol. Following incubation at -20°C for 2 h, RNA was pelleted down by centrifugation at 13000 rpm for 10 min at 4°C. The RNA pellet was washed twice with 70% ethanol, air dried and suspended in 50 μl of DEPC-treated water. To remove DNA contamination, 1 μl of DNase I (Invitrogen TM #18068015) was added to 1 µg of total RNA and incubated for 30 min at 37°C.
Library was prepared according to the Illumina TruSeq stranded mRNA sample preparation protocol. Briefly, poly-T oligo-attached magnetic beads were used for purification of poly-A containing mRNA molecules. After purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The first strand cDNA was synthesized from cleaved RNA fragments using reverse transcriptase and random primers. Strand specificity was achieved by having dUTP in the Second Strand Marking Mix (SMM) instead of dTTP, followed by the second strand cDNA synthesis using DNA polymerase I and RNase H. Additionally, Actinomycin D in the First Strand Synthesis Act D mix (FSA) improved strand specificity by preventing spurious DNA-dependent synthesis, while allowing RNA-dependent synthesis. Next, these cDNA fragments were subjected to addition of a single “A” base followed by adaptor ligation. Finally, adaptor-ligated products were purified and PCR enriched to create the final cDNA library. Quality control analysis and quantification of the cDNA library was performed before proceeding for sequencing.

treatment_protocol: Log-phase cultures of wild-type and Cghhf1Δ2Δ strains were either treated with 0.06% MMS for 45 min, or left untreated. During MMS treatment, cultures were incubated at 30⁰C under shaking conditions (200 rpm).

tag: growth phase

value: Log-phase

value: Untreated

value: Cghhf1{delta}2{delta} mutant


title: Sample 6 (KK-6)

description: YPD + 0.06% MMS grown; Replicate-1

value: MMS-treated


title: Sample 7 (KK-7)

description: YPD grown; Replicate-2


title: Sample 4 (KK-4)

description: YPD + 0.06% MMS grown; Replicate-2

source_name: wild-type cells


title: Sample 8 (KK-8)

description: YPD + 0.06% MMS grown; Replicate-2


title: Sample 2 (KK-2)

description: YPD + 0.06% MMS grown; Replicate-1


title: Combination_1 (circRNA)

description: circRNA sequencing


title: rBC BEGM-D8

city: New Haven

first: Allison

middle: M

last: Greaney

state: CT

address: 10 Amistad St

department: Biomedical Engineering

institute: Yale University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Samples were then processed at the Yale Center for Genome Analysis (YCGA) and analyzed using the Transcriptome Analysis Console (TAC) Software (ThermoFisher Scientific).

organism: Rattus norvegicus

source_name: rBC in BEGM, sample 3

label_protocol: Affymetrix protocol

growth_protocol: peBC were isolated from three groups of three native rats each (12wks, 370±39g, male WT Sprague Dawley) to generate three replicate lines of cells.

extract_protocol: After 8 days of culture, cells were harvested and mRNA samples isolated using the previously described RNA isolation kit (Qiagen), with added DNase digestion step.

treatment_protocol: On isolation, cells from each line were split into either BEGM or EpiX.

tag: media

value: BEGM


title: 1E_EpiX1

source_name: rBC in EpiX, sample 1

value: EpiX


title: Heat_2 (circRNA)

description: circRNA sequencing

source_name: Heat, plants leaves

value: Heat


title: Sample 3 (KK-3)

description: YPD grown; Replicate-2


title: 1.5h infection rep2 (trophozoites)

last: Xu

tag: cell line


title: NB4 cells-Solvent-72h-rep1

source_name: NB4 cells，Solvent，72h， replicate 1

value: NB4 cells


title: Sample 1 (KK-1)

description: YPD grown; Replicate-1

tag: genotype


title: 1B_BEGM1

source_name: rBC in BEGM, sample 1


title: rBC Epix-D8

source_name: rBC in EpiX, sample 3


title: 3E_EpiX3

source_name: rBC in EpiX, sample 2


title: 3B_BEGM3

source_name: rBC in BEGM, sample 2


title: Superficial_neurons_schizophrenia_female_971

value: schizophrenia

tag: Sex

value: Female

tag: ph

tag: meds

value: ON

value: pyramidal neurons

tag: tissue source

value: Neurons captured by LCM isolated from superficial (lamina II-III) layers


title: Heat_3 (circRNA)

description: circRNA sequencing

value: wild type

tag: tissue

value: plants leaves


title: 3h infection rep2 (trophozoites)

tag: strain

value: WB

value: DMEM

value: 3h infection


title: B14W40R6F

description: Single-cell transcriptomics

value: wildtype

value: female


title: 3h infection rep1 (trophozoites)

tag: growth medium


title: 4.5h infection rep1 (trophozoites)

tag: time

value: 4.5h infection


title: mouse BAT ATAC-seq lox-2

source_name: brown adipose tissue

value: whole brown adipose tissue

tag: phenotype

value: flox/flox


title: Drought_1 (circRNA)

description: circRNA sequencing

source_name: Drought, plants leaves

value: Drought


title: Drought_2 (circRNA)

description: circRNA sequencing


title: Drought_3 (circRNA)

description: circRNA sequencing


title: 1.5h infection rep1 (trophozoites)

value: 1.5h infection


title: Heat_1 (circRNA)

description: circRNA sequencing

value: Heat


title: Combination_2 (Degradome)

description: Degradome sequencing

data_processing:
Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were mapped to the mRNA database. Only the perfect matching alignment(s) for the given read would be kept for degradation analysis.
Degradome-Seq: All resulting reads (t-signature) were reverse- complemented and aligned to the miRNA identified in our study. No more than four alignment scores were allowed. Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored. The target was selected and categorized as 0, 1, 2，3，or 4. category 0—over one raw read at the position, abundance at the position is equal to the maximum on the transcript, and there is only one maximum on the transcript; category 1—over one raw read at theposition, abundance at the position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; category 2—over one raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; category 3—over one raw read at the position, abundance at the position is equal to or less than the median for the transcript; and category 4—only one raw read at the position.
Genome_build: mRNA database (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/ITAG3.2_cDNA.fasta)
Supplementary_files_format_and_content: normalized counts

value: Combination


title: csr-1_WT_piwi_CRISPR_line2_F8_sRNA-seq

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.15)
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.15) with options -u 4 and -u -4
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.1) with options -L 6 -i S,1,0.8 -N 0
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.5.2) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.1) with options -L 6 -i S,1,0.8 -N 0
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.26) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs along the genome

organism: Caenorhabditis elegans

source_name: nematodes

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching. The harvested animals were washed three times with M9 buffer and 40 µl of worm pellet was frozen in dry ice with TRI Reagent (MRC, Inc.). After five repetitions of freeze and thaw, total RNA was isolated according to the TRI Reagent protocol. Ten micrograms of RNA were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by phenol-extraction and isopropanol precipitation. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. 10 µg of total DNase treated RNAs with RIN > 8 was size seleceted from 15% UREA PAGE gel and used to generate small RNA libraries.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005) or Illumina MiniSeq platform using MiniSeq High Output Reagent Kit 75-cycles (FC-420-1001).

treatment_protocol: RNAi treatment was performed using worms grown on 15 cm Petri dishes seeded with concentrated RNAi food. The Arhinger RNAi library was used to pick the selected bacteria clones.

value: CRISPR-cas9 piwi mutant line 2

value: whole worm

tag: developmental stage

value: young adult, 48 hours post hatching


title: Combination_3 (Degradome)

description: Degradome sequencing

value: wild type


title: dhsc15

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

description:
Raw_counts_CCI_SHAM.txt
Normalized_gene_expression_TPM_CCI_SHAM.txt

data_processing:
Base-calling performed with Illumina analysis pipeline.
The RNA-Seq reads were directly aligned to the rn6 transcriptome index and the raw count matrix was generated using Kallisto (version 0.44.0).
Following TMM normalization, differential gene expression analysis was performed using the edgeR R package following the instructions.
Genome_build: rn6
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files showing raw gene counts and normalized TPM values for all samples.

source_name: DHSC

extract_protocol:
The dorsal horn of the spinal cord (lumbar L4-L6) was harvested on d9 post CCI or SHAM surgery. Tissues were immediately preserved in RNALater® overnight at 4°C. Total RNA was isolated the next day using RNeasy® Plus Universal Mini Kit (Qiagen, Germantown, MD USA) and quantitated by NanoDropTM (ThermoFisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Sprague Dawley

value: DHSC

value: SHAM


title: dhsc05

treatment_protocol: The dorsal horn of the spinal cord (lumbar L4-L6) was harvested on d9 post CCI or SHAM surgery.

value: CCI


title: csr-1_ADH_piwi_CRISPR_line2_F8_sRNA-seq

value: CRISPR-cas9 piwi mutant line 2; CRISPR-cas9 ADH csr-1


title: Control_3 (circRNA)

description: circRNA sequencing

source_name: Control, plants leaves

value: Control

value: plants leaves


title: dhsc13


title: Combination_1 (Degradome)

description: Degradome sequencing

source_name: Combination, plants leaves


title: Control_2 (circRNA)

description: circRNA sequencing


title: Heat_3 (Degradome)

description: Degradome sequencing


title: dhsc03


title: Control_1 (circRNA)

description: circRNA sequencing


title: dhsc01


title: MADM-CELL#4-H3K27me3

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

institute: Nagoya City University Graduate School of Medical Sciences

hyb_protocol: Labeled samples were then hybridized to the 2×400K mouse promoter array in the presence of mouse Cot-1 DNA for 48 hrs at 65°C.

scan_protocol: After washing the array according to the manufacturer’s protocol, arrays were scanned on an Agilent scanner.

data_processing: Obtained data is analyzed using Feature Extraction software (Agilent Technologies) and analyzed with GeneSpring GX 13.1.1

source_name: H3K27me3 ChIP DNA from MADM-CELL#4

label_protocol: ChIP sample and input DNA is amplified with GenomePlex® Complete Whole Genome Amplification (WGA) Kit (Sigma Aldrich) as the manufacturer’s protocol. ChIP products were labeled with Cy5 (red) and input and IP DNA with anti-pan H3 antibody with Cy3 (green) using a random primed Klenow polymerase reaction (Thermo Fisher Scientific) at 37°C for 2 h.

growth_protocol: Cells were isolated with immuno-panning method from P8 mouse.

extract_protocol: 1 x 10E6 cells were treated with 1% formaldehyde for 8 min to crosslink histones to DNA. After washing with cold PBS, the cell pellets were resuspended in lysis buffer (1% SDS, 10mM EDTA, 50 mM Tris-HCl pH 8.1 and Protease inhibitor) and sonicated for 10 minutes, using Covaris S220 (Covaris, Woburn, MA, USA). After diluting cell lysate 1:10 with the Dilution buffer (1% Triton, 2mM EDTA, 150mM NaCl, 20 mM Tris-HCl pH 8.1), diluted cell lysates were incubated for 16 hours at 4°C with Dynabeads, which were pre-coated with 3 μl of anti-K4 trimethylated histone H3 antibody and anti-K27 trimethylated histone H3 antibody and anti-pan histone H3 antibody. After washing, the beads were treated with 100 ul of Elution buffer (1% SDS and 0.1M NaHCO3) for 30 minutes at room temperature. The crosslinks were then reversed by heating the sample at 65°C for 4 hrs. DNA is extracted with AMPure XP beads (A63881, Beckman Coulter, Brea, CA) according to manufacturer’s instructions. We analyzed ChIP products as probes on the SurePrint G3 mouse promoter array 2x400K (G4858A; Agilent Technologies, Santa Clara, CA, USA).

tag: strain background

value: Mosaic Analysis with Double Markers (MADM) mouse [PMID:21737130]

tag: genotype/variation

tag: age

value: post-natal 8 days

tag: cell type

value: brain premaligmnant tumor cells

tag: chip antibody

value: Histone H3K27me3 antibody [PMID:18227620]

value: none, input DNA


title: ASTROCYTE-H3K27me3

source_name: H3K27me3 ChIP DNA from ASTROCYTE

growth_protocol: Cells were obtained  from embryonal normal mouse brain.

value: WT

value: normal astrocyte cells


title: NSC-H3K27me3

source_name: H3K27me3 ChIP DNA from NSC

growth_protocol: Cells were obtained  from normal mouse glial cells.

value: neural stem cells


title: RI_2

status: Public on Feb 19 2020

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing:
The processed fastq files were mapped to the mouse transcriptome and genome using TopHat (v2.0.13).
The genome version was GRCm38, with annotations from Ensembl release 84.
Quantification was done using htseq-count (version 0.6.0, http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
Normalization and differential expression were done with the DESeq2 package (version 1.12.4)
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression data matrix

source_name: Resistant-infected (CC Line 111)

growth_protocol: Experimental CC-RILs mice at age 8 to 12 wk of the International Livestock (IL) cohort, were provided by the Small Animal Facility, Faculty of Medicine, Tel Aviv University, Israel

extract_protocol:
Total high molecular weight genomic RNA was purified using the RNeasy kit (Qiagen, Hilden, Germany).
The mRNA was sequenced with a single-end technology (read length of 75) on NextSeq 500 platform (Illumina, San Diego, USA).

treatment_protocol: The mice were treated with Sulfamethoxazole (0.8 mg/ml) in drinking water for a continuous period of ten days, followed by an antibiotic-free period of three days, before oral application of mixed culture of P.g. (strain 381) and F.n. (strain PK1594) (control groups were treated with PBS and 2% Carboxymethycellulose).42 days after the last infection, the mice were sacrificed and the alveolar bone volume at the second molar of the left hemi-maxilla was evaluated by micro–computed tomography (µCT).

tag: line

value: CC Line 111

tag: infection

value: infected with P.g. (strain 381) and F.n. (strain PK1594)

value: Resistant

value: periodontal tissue


title: RC_2

source_name: Resistant-control (CC Line 111)

value: control


title: RI_4

source_name: Resistant-infected (CC Line 188)

value: CC Line 188


title: MADM-CELL#3-H3K27me3

source_name: H3K27me3 ChIP DNA from MADM-CELL#3

growth_protocol: Cells were isolated with immuno-panning method from P150 mouse.

value: post-natal 150 days

value: brain tumor cells

value: Histone H3K27me3 antibody (pAb) (Abcam, 39155)

value: Anti-Histone H3 antibody (Abcam, ab1791)


title: OI_4

source_name: Over resistant-Infected (CC line 2126)

value: CC Line 2126

value: Over-resistant


title: OC_4

source_name: Over resistant-Control (CC line 2126)


title: OI_2

source_name: Over resistant-infected (CC line 2124)

value: CC Line 2124


title: SC_4

source_name: Susceptible-control (CC line 551)

value: CC Line 551

value: Susceptible


title: OC_2

source_name: Over resistant-control (CC line 2124)


title: SI_4

source_name: Susceptible-infected (CC line 551 )


title: RC_4

source_name: Resistant-control (CC Line 188)


title: SC_2

source_name: Susceptible-control (CC Line 785)

value: CC Line 785


title: SI_2

source_name: Susceptible-infected (CC line 785)


title: RC_1


title: RI_3


title: RC_3


title: OC_3

source_name: Over resistant-control (CC line 2126)


title: RI_1


title: OI_3

source_name: Over resistant-infected (CC line 2126)


title: NSC-H3K4me3

source_name: H3K4me3 ChIP DNA from NSC

value: WT

value: neural stem cells

value: Histone H3K4me3 antibody [PMID:18227620]

value: none, input DNA


title: OC_1

value: periodontal tissue


title: MADM-CELL#2-H3K27me3

source_name: H3K27me3 ChIP DNA from MADM-CELL#2

value: Mosaic Analysis with Double Markers (MADM) mouse [PMID:21737130]


title: OI_1

value: infected with P.g. (strain 381) and F.n. (strain PK1594)


title: SI_3

source_name: Susceptible-infected (CC line 551)


title: SC_3

value: control


title: SI_1

source_name: Susceptible-infected (CC Line 785)


title: SC_1


title: Corpus

city: Worcester

first: Elisa

last: Donnard

state: MA

address: 368 Plantation St

department: Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description: Single-cell RNA-Seq

data_processing:
Sequencing reads were processed as previously described (Derr et al., 2016), using the graphical interface DolphinNext [doi: https://doi.org/10.1101/689539]. Scripts and the full pipeline can be accessed through GitHub (github.com/garber-lab/inDrop_Processing). Briefly, fastq files were generated using bcl2fastq and default parameters. Valid reads were extracted using umitools [doi:10.1101/gr.209601.116] and valid barcode indices supplied by 10X Genomics. Reads where the UMI contains a base assigned as N were discarded. Remaining reads were aligned to the mm10 genome using HISAT2 v2.0.4 (Kim et al., 2019) with default parameters and the reference transcriptome RefSeq v69.
Alignment files were filtered to contain only reads from cell barcodes with at least 100 aligned reads and were submitted through ESAT (github.com/garber-lab/ESAT) for gene-level quantification of unique molecule identifiers (UMIs) with parameters -wLen 100 -wOlap 50 -wExt 1000 -sigTest .01 -multimap ignore -scPrep. Finally, we identify and correct UMIs that are likely a result of sequencing errors, by merging the UMIs observed only once that display hamming distance of 1 from a UMI detected by two or more aligned reads
Barcodes with at least 350 and no more than 15,000 unique molecular identifiers (UMIs) mapped to known genes were considered valid cells.
Background RNA contamination was removed from the gene expression matrix using a modified version of the algorithm SoupX v0.3.1 [https://doi.org/10.1101/303727]. Briefly, barcodes corresponding to empty droplets were selected per sample according to their distribution of UMIs per barcode (caput: 20=<x=<175, corpus: 20=<x=<150, cauda: 20=<x=<150, vas: 20=<x=<115; where x=total UMIs for a given barcode). UMI counts for empty droplets were used as input for the SoupX algorithm to infer the expression profile from the ambient contamination per sample. The main alteration consisted in the selection of the fraction of contamination per cell (rho), which was determined by the most frequent number of UMIs for the empty droplets in each sample (caput=139; corpus=114; cauda=109; vas=84), under the assumption that the same contamination level could be expected from valid cell containing droplets. Using these estimated contamination fractions, the SoupX algorithm was used to remove counts from genes that had a high probability of resulting from ambient RNA contamination for each cell with the function adjustCounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of unique molecular identifier (UMI) counts per gene for each cell
Supplementary_files_format_and_content: Metadata for each cell barcode in the quantification matrix file

source_name: epididymis

extract_protocol:
To obtain a sperm-depleted single cell suspension, eight epididymides explanted from four 10-12 weeks old FVB mice, euthanized according to IACUC protocol, were dissected into a 10cm plate containing 10ml of Krebs media pre-warmed to 35C. Using a dissection microscope with warm stage set to 35C, the organ was cleared from any fat and excessive connective tissue. In a clean 10cm dish containing 10 ml of Krebs media the organ was cut into four segments that roughly corresponded to caput, corpus, cauda, and vas. Each group of eight segment was placed into different 5 cm petri dishes with about 2 ml of Krebs media. Using curved scissors each group was further cut into roughly one to five-millimeter pieces and transferred to a 15ml conical tube. Media was added to a final volume of 10 ml, and samples allowed to decant while in an upright position at a 35C incubator for three to five minutes. Supernatant was discarded and this wash step repeated for two more times. In order to further remove sperm, the tubules were transferred to a 50ml conical tube containing 25 ml pre-warmed RPMI-1640 media. After ten minutes incubation at 35C under mild agitation, sample was allowed to settle for three to five minutes and supernatant discarded. These steps were repeated until supernatant looked clear.Tissue dissociation was optimized to obtain a single cell suspension free of sperm. Once dissected samples were cleared of any visible sperm, 3 ml of the RPMI-1640 sample mixture was transferred to a small 25ml glass Erlenmeyer flask containing 7 ml of dissociation media (Collagenase IV 4mg/ml, DNAse I 0.05 mg/ml) and placed in a 35C water bath with rotations of 200 rpm for 30 to 45 minutes. Afterwards, samples were transferred to a conical tube and allowed to settle. Supernatant was removed, leaving four to five ml of sample solution to be returned to the Erlenmeyer flask, were 10 ml of 0.25% trypsin-EDTA and 0.05 mg/ml DNAse and returned to the water bath. After 35 minutes the samples were pipetted up and down until there were no observable pieces of tissue, and allowed to incubate in the water bath for 20 more minutes. Once cell disaggregation was achieved 1 ml of FBS was added to inactivate the trypsin. Sample was transferred to falcon tube by passing the cell solution through a series of 100um, 70um, and 40um cell strainers, and adding media (RPMI-1640 supplemented with 10% FBS and antibiotic and anti-mycotic - 100 units/mL of penicillin, 100 µg/mL of streptomycin, and 0.025 µg/mL of Amphotericin B) to a final volume of 30 ml. Centrifuge for 15 minutes at 400 rcf (g) at RT. Discard supernatant and add 25 ml media and centrifuge for 5 minutes at 800 rcf (g) at RT. Discard supernatant and add 2ml of PBS, transfer cells to a 2 ml microfuge tube, centrifuge at 900rcf (g) for 3 minutes, discard supernatant, resuspend in 600ul PBS and count cells (tryphan blue) put them on ice and if good (>85% survival) proceed with the 10X protocol/dilutions.
Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics), as per the manual.

value: FVB/NJ

value: Corpus epididymis

tag: gender

value: male

value: 10-12 weeks old - adult


title: Caput

description: Single-cell RNA-Seq

value: Caput epididymis


title: Vas

description: Single-cell RNA-Seq

value: Vas deferens


title: MADM-CELL#4-H3K4me3

source_name: H3K4me3 ChIP DNA from MADM-CELL#4

value: post-natal 8 days

value: brain premaligmnant tumor cells


title: GRL20589: control sample 4

city: Blacksburg

first: Song

last: Li

state: VA

institute: Virginia Tech

data_processing:
read mapping was performed using STAR v2.5.2b
read counting was performed using featureCounts 1.5.1
differential expression analysis was performed using DESeq2 (1.26.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files for read counts and DESeq2 output

source_name: total splenocytes

extract_protocol: all the library preps were performed according to Illumina TruSeq v2 RNA Sample Preparation protocol. Quality of total RNA and cDNA libraries were checked on an Agilent BioAnalyzer 2100 (Agilent Technologies).Samples with RNA integrity scores > 8.0 were selected for RNA-Seq library preps. The cDNA sheared to an average of 300 bp. Individually indexed cDNA libraries were sequenced on one lane of Illumina HiSeq2500

treatment_protocol: Balb/c mice received tRA ( low dose of tRA treatment, 1 mg/kg body weight) daily from weaning till euthanasia at 3 months of age without the injection of pristane.

value: BALB/c mice

value: splenocytes

value: 3 month of age


title: GRL20587: control sample 2


title: Cauda

description: Single-cell RNA-Seq

value: Cauda epididymis


title: GRL20586: control sample 1


title: GRL20588: control sample 3


title: GRL20594: tRA treated sample 4


title: MADM-CELL#1-H3K27me3

source_name: H3K27me3 ChIP DNA from MADM-CELL#1

value: post-natal 150 days

value: brain tumor cells

value: Histone H3K27me3 antibody (pAb) (Abcam, 39155)

value: Anti-Histone H3 antibody (Abcam, ab1791)


title: GRL20593: tRA treated sample 3


title: GRL20591: tRA treated sample 1


title: MADM-CELL#2-H3K4me3

source_name: H3K4me3 ChIP DNA from MADM-CELL#2

value: Mosaic Analysis with Double Markers (MADM) mouse [PMID:21737130]

value: Anti-Histone H3 (tri methyl K4) (Abcam, ab8580)


title: H_F2

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: P21_lymphatic endothelial cells

extract_protocol:
Single lymphatic endothelial cells were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Revers transcritpion reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with 38/37 cycles paried-end high-output mode.

tag: Sex

value: Male

value: mouse back skin

value: lymphatic endothelial cells

tag: sorting markers

value: CD31+, LYVE1-, Podoplanin+


title: H_D3


title: H_F10


title: H_E4


title: H_D6


title: MADM-CELL#3-H3K4me3

source_name: H3K4me3 ChIP DNA from MADM-CELL#3


title: MADM-CELL#1-H3K4me3

source_name: H3K4me3 ChIP DNA from MADM-CELL#1


title: H_B9


title: ASTROCYTE-H3K4me3

source_name: H3K4me3 ChIP DNA from ASTROCYTE

value: WT

value: normal astrocyte cells

value: Histone H3K4me3 antibody [PMID:18227620]

value: none, input DNA


title: GRL20592: tRA treated sample 2

value: BALB/c mice

value: splenocytes


title: G_G6


title: H_A5


title: H_A6


title: H_E5


title: G_E12


title: G_D5


title: G_D12


title: G_E11


title: G_D2


title: G_C2


title: H_B2


title: F_C8


title: F_E9


title: G_A1


title: F_D3


title: G_B8


title: F_C10


title: G_B10


title: F_B8


title: E_A3


title: E_A9


title: E_B12


title: F_B11


title: F_A12


title: F_A10


title: E_C10


title: E_C8


title: F_B1


title: D_H5


title: E_A12


title: F_B12


title: F_C7


title: D_G6


title: D_G11


title: D_F5


title: D_E1


title: E_A6


title: E_B7


title: E_A4


title: D_D7


title: D_C3


title: D_C12


title: D_C7


title: D_B1


title: D_A4


title: D_E5


title: C_E8


title: C_C4


title: C_D1


title: C_D3


title: C_D11


title: C_B8


title: C_E12


title: G_B5


title: C_B7


title: C_E2


title: C_A9


title: C_A5


title: C_A8