title: 18433X3 GM org 3

city: Salt Lake City

first: Yueqi

last: Wang

address: 20 South 2030 East

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 100 and a reference database was created using STAR version 2.7.3a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0
Assembly: hg38; H_sapiens_Dec_2013; GRCh38
Supplementary files format and content: FeatureCounts output files combined into a single tab-delimited text file

growth_protocol: The protocols used for generating organoids is described in the papers

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq of 18433R samples were prepared using Illumina Stranded Total RNA Library Prep w Ribo-Zero Plus following manufacturer's protocols.
RNA libraries for RNA-seq of 18128R samples were prepared using Nextera DNA Flex Library Prep kit (read 1 adapter:CTGTCTCTTATACACATCT, read 2 adapter: CTGTCTCTTATACACATCT) following manufacturer's protocols.

value: telencephalic organoid

value: WT

value: male

value: neural differentiation


title: v3.4.2

status: Public on Aug 11 2022

type: SRA

city: Bethesda

first: Daniel

middle: S

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

country: USA

institute: NIH

description: nuclear RNA

library_source: transcriptomic

data_processing:
Alignment: The raw sequencing reads were aligned to a marmoset genome assembly, ASM275486v1 (GCA_002754865.1). To build a reference package suitable for analyzing both unspliced pre-mRNA and mature mRNA in the nuclei, as well as to include sequences of mito-chondrial genome, marmoset DNA sequence (FASTA) and annotation (GTF) files were acquired from the Ensembl release-95 and modified as follows. The complete mitochondrial sequence (NC_025586.1, GenBank) and its annotation (Wang et al., 2016) were manually added to the FASTA and GTF files. Next, a pre-mRNA GTF was made by replacing “transcript” with “exon” as the feature-type entry in the original GTF before making a reference package with CellRanger software (v3.0.2, 10x Genomics). This custom-built reference package was then used in CellRanger (version 3.1.0, 10x Genomics) to align sequencing reads for all samples. The option to estimate cell number automatically was used for most of the samples, unless otherwise speci-fied (see Table S1 for details). A filtered cell barcode-to-gene feature matrix was generated from the software and used for downstream analysis (Figure S2A).
Preprocessing & general quality control: The matrix was loaded to create an object in Seurat v3 (Butler et al., 2018; Stuart et al., 2019). Cells with <200 genes, >5000 genes, or >5% of counts mapped to mitochondrial genome were excluded. Genes observed in <5 cells were excluded. The filtered raw count matrix was then log normalized (ln(counts*100,000+1)) within each cell and scaled to account for differences in sequencing depth with Seurat. Next, DoubletFinder (McGinnis et al., 2019) was used to esti-mate and remove putative doublets to mitigate technical confounding artifacts in droplet-based sequencing data analysis. The top 3000 variable genes calculated by Seurat were used in linear dimension reduction (principal components analysis, PCA), and the top 30 PCA were used for clustering at low resolution (parameter = 0.4) to define crude cell types. These unsupervised clusters were used to provide a quick cluster annotation for homotypic doublet probability model-ing in DoubletFinder. Doublet rate was estimated by fitting a linear equation over a multiplet rate table provided by 10x Genomics. The rate = (0.0008*cell.number + 0.0527)/100) was used to calculate a Poisson distribution with and without homotypic doublet proportion to generate low confidence (DF.found.1) and high confidence (DF.found.2) doublet annotation. Unless otherwise specified, pN = 0.25, pK = 0.005 and automatic doublet removal based on DF.found.2 annotation were used, as the first line of screening. In parallel, SoupX (Young and Behjati, 2020) was used for ambient RNA background correction. Taken from the output of the 10x pipeline (raw_feature_bc_matrix), the ambient RNA from empty droplets that contained <10 unique mo-lecular identifiers (UMI) were profiled, and the “soup” contamination fraction was calculated for each cluster. Given that the nuclear transcriptome was profiled, genes that mapped to the mito-chondrial genome could be considered as ambient input. Therefore, the top mitochondrial genes (species with >1000 accumulated counts across profiled empty droplets) were used to estimate the global contamination fraction and adjust the raw count matrix. Next, the cell barcode that passed the DoubletFinder was used as an index to subset the SoupX-corrected matrix to gener-ate a new matrix as our downstream input (Figure S2A). For individual samples, a Seurat object was created, and the index labels (IL01_uniqueID, IL02_species, IL03_source, IL04_sex, IL05_ageDays, IL06_tissue.1, IL06_tissue.2, IL06_tissue.3, IL07_location, IL08_condition, IL09_illumina, IL10_chemistry, IL11_batch, IL12_LMinDays, IL13_LMaxDays, IL14_dataset, IL15_annotation) were added to the metadata as cell attributes. For each sample, 90% of nuclei were randomly selected, then all 42 samples were merged together for downstream comparison. The remaining 10% of the nuclei were set aside for classification assessment and validation.
Level 1 quality control & clustering: To divide nuclei into classes and facilitate artifact identification, nuclei were first classified using a set of parameters that does not highlight granular detail. In this round of clustering, only 50 PC for Harmony were computed to perform linear correction over IL01_uniqueID, as the el-bow plot from the preliminary analysis showing the standard deviation stopped visually decreas-ing after top 50 PC. The top 5 Harmony-corrected embeddings (H5) were used for Seurat to learn the UMAP and find cell classes at a low resolution (0.2). Canonical cell-type markers (PTPRC for immune cells, PDGFRA for OPC, MAG for oligodendrocytes, GFAP and SLC1A2 for astrocytes, LEPR and CEMIP for vasculature and meningeal cells, and CNTN5 and NRG1 for neurons) annotated 6 of the classes unambiguously. One cluster in the middle of the H5 UMAP had mixed expression of canonical markers, which suggested artifact. The “low quality” cell bar-codes that were found from the H50 condition (defined above) were overlaid on the H5 UMAP, which exclusively highlighted the putative artifact cluster. These nuclei were removed from fur-ther analysis, although the original UMAP embeddings were maintained for plotting purposes (Figure 1 and S3).
Level2 quality control & clustering: Nuclei that passed Level 1 QC were divided into 5 partitions (MIC, OPC, OLI, VAS/AST, NEU) based on the H5 UMAP result. The astrocytes and vasculature/meningeal cells were pooled into a single class prior to subclustering to facilitate artifact identification. Shared features in this class of cells were potentially explainable by their close association at CNS barriers (blood–CSF interface, blood–brain interface, and the CSF–brain interface). For each class, log-normalization and scaling were repeated from the divided raw count matrix, the top 3000 variable genes were used for 50 PC computation, Harmony correction over IL01_uniqueID, UMAP learn-ing, and clustering, as described above. The clustering resolution was iteratively increased from low to high (0–1.2), and clustering stability was tracked with clustree (v0.4.3) (Zappia and Oshlack, 2018). Aided by the branch visualization provided by the clustree, a tentative resolution that was relatively stable was selected, then differentially expressed gene (DEG) analysis on the clusters found with this parameter set was performed. The expression pattern of the top-expressed genes for each cluster within and across classes were checked, and artifacts clus-ters were manually imputed. Doublets tended to form small distinct clusters on UMAP that branched early in the clustering tree analysis with low splitting resolution, had mixed canonical marker-gene expression, and had similar expression patterns to cells in other partitions; thus, these doublets could be easily spotted and removed. For putative doublets within each class, additional rounds of DEG analysis were performed as necessary. Each time nuclei were re-moved, basic normalization, scaling, Harmony, and UMAP learning were repeated. To control for over-splitting, for clusters that appeared to be a single pile in the 2D UMAP space but were anno-tated into >1 cluster, additional rounds of DEG analysis were performed to see if binary markers could be found to label them. In addition, clustering was projected onto a 3D UMAP space to en-sure effects were not masked due to overcrowding in 2D. This strategy also helped to further elucidate cluster associations, aid decision-making with respect to groups of clusters that should be tested further, and spot potential gradient changes among clusters. If unique and or binary patterns could not be found in the current splitting resolution after these steps were performed, a step lower in resolution on the clustering tree was examined, and the analysis process was re-peated. The following compound naming convention to la

molecule: total RNA

organism: Callithrix jacchus

extract_protocol:
Tissue dissection: On the day of tissue harvest, marmosets were deeply anesthetized with 5% isoflurane until all visible signs of breathing were no longer detected. Animals were transcardially perfused with ice-cold artificial cerebrospinal fluid (aCSF) for 5 min with a pump. Brains were removed from the skull and submerged into ice-cold aCSF, and after removal of meninges within the solu-tion, were positioned in a custom-designed brain holder within 10 min post-perfusion. The brain was sectioned at 3 mm into 12–13 slabs in one step with a homemade blade-separator set in the solution. Each brain slab was transferred into a 6-well plate, submerged into RNAlater (RNAlater™ Stabilization Solution, AM7021, Invitrogen) with a homemade brain trap, and stored at 4°C overnight. The following day, brain slabs were positioned in 25 x 20 x 5 mm molds (Tis-sue-Tek® Cryomold®, 4557, Sakura Finetek) on ice to facilitate target sampling. Slabs were matched to MRI for each animal, and tissue annotation for gray (Liu et al., 2018a) and white matter (Liu et al., 2020) was informed by marmoset 3D MRI atlases V1 and V2. A cylinder of tissue 2 mm in diameter and 3 mm in height for each region (Figure 1B and S1) was collected with a tissue punch (EMS-core sampling tool, 69039-20, EMS). There were 5 white matter sam-ples from temporal and parietal lobes that did not exactly match in the two animals, however they were paired in lobes of the brain and showed no significant differences in later analysis (Figure 1B, SS05, SS06, and SS08). The cylinders were ejected into PCR tubes filled with 100 µL of RNAlater and stored at −80°C. Single-nucleus dissociation: Nuclei preparation was carried out as described (Matson et al., 2018), with minor modifi-cations. Briefly, on the day of dissociation, tissue samples were thawed on ice, removed from solution, dabbed with Kimwipes to remove residual RNAlater, and placed in a 1 mL douncer tube (Dounce Tissue Grinder, 357538, Wheaton). Each tissue was homogenized in 500 μL of lysis buffer containing 0.1% Triton-X100 in low sucrose buffer (0.32 M sucrose, 10 mM HEPES, 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, and 1 mM DTT in ddH2O, pH8) with loose pestle 25 times and tight pestle 10 times. The homogenate was filtered through a 40-μm mesh (Falcon® 40 µm Cell Strainer, 352340, Corning) to a 50-mL Falcon tube on ice. An additional 5 mL of low sucrose buffer was used to rinse the douncer tube and cell strainer. The filtered homogenate was further mixed with a handheld homogenizer (VWR® 200 Homogenizer) at a speed of ~1000 rpm to brake nuclei clumps for 5 sec. After homogenization, a serological pipet filled with 12 mL of high sucrose buffer (1 M sucrose, 10 mM HEPES, 3 mM MgAc, and 1 mM DTT in ddH2O, pH8) was placed underneath the lysate and disconnected from the pipettor, and the buffer was released from the serological pipette by gravity and set on ice. When most of high sucrose buffer was re-leased to form a density layer underneath the homogenate, the serological pipet was retrieved along the wall of the Falcon tube gently, without disturbing the low-high sucrose interface. The Falcon tube was capped and placed in a swing bucket to be centrifuged at 3,200 rcf for 30 min at 4°C. At the end of spin, the supernatant was decanted quickly without tabbing, and 1 mL of re-suspension buffer (0.02% BSA in 1X PBS, pH7.4) was added to the Falcon tube. Slow pipetting was employed to resuspend nuclei along the Falcon tube wall below the 5-mL mark to preserve nuclei integrity. Specifically, nuclei were rinsed off the wall in courses of 2 sec per trituration for 20 times total per tube. The Falcon tube was then capped and spun at 3,200 rcf for 10 min at 4°C. At the end of spin, the supernatant was removed by gently tabbing the tube until no visible liquid drop was left behind, and 200 μL of resuspension buffer was added to each sample to collect the nuclei. The nuclei suspension was filtered through a 35-μm mesh (Cell Strainer Snap Cap, 352235, Corning) twice and counted on a hemocytometer by trypan blue staining. During count-ing, the size and quantity of myelin and other debris were visually inspected under the scope, and the suspension was filtered 1–3 more times through the 35-μm mesh if necessary. Only round and dark-blue stained nuclei were considered of good quality and included in the final count.
10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v2 and v3

value: M

value: GM

value: Telencephalon

value: fCTX

value: NaiveCtrl


title: oASC, ATAC Rep1

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

library_source: genomic

data_processing:
Adapters were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters‘PE CROP: 50.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with parameters ‘--minins 30 --maxins 2000 --dovetail -k 4 --very-sensitive-local’
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings.
Next, unmapped reads, duplicate reads, non-primary alignments, reads with their mate unmapped and read alignments with a mapping quality below 30 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1804 -f 2 -q 30 -b’.
Peak calling was performed on each individual replicate from the previous section using Genrich (v0.6, available at https://github.com/jsh58/Genrich) with the following parameters: -j -y -r -e chrM -v -f.
Genome_build: mm10
Supplementary_files_format_and_content: NarrowPeak files with blacklisted peaks removed; BigWig files of ATAC-seq signal along mm10 after downsampling step.

molecule: genomic DNA

organism: Mus musculus

source_name: 2.5days post-injured old satellite cells

extract_protocol:
Isolated satellite cells were lysed using ATAC-seq lysis buffer ( (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Library was constructed based on protocols from Buenrostro et al., (2015) and Chen et al., (2016). Briefly, lysates were tagmented with Tn5 (Vazyme), reverse-crosslinked,  and amplified using NEBNext High-Fidelity 2 x PCR Master Mix (NEB). Library was then sequenced using DNBSEQ-G400 sequencer (BGI).

treatment_protocol: Mouse hind limb was injured by BaCl2 injection. Mice were perfused with PFA before satellite cell isolation.

tag: strain

tag: tissue

value: Skeletal muscle

tag: cell type

value: Muscle stem cells

tag: treatment

value: BaCl2 injury

tag: time

value: 2.5 dpi


title: 18433X1 GM org 1

state: Utah

organism: Homo sapiens

tag: cell line

tag: genotype

tag: Sex


title: IMR90 cells, vehicle, biol rep 6

type: genomic

city: Providence

first: Calvin

last: Leung

state: RI

address: 70 Ship Street

department: MCB

institute: Brown University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to the  Infinium methylation EPIC array according to the standard Illumina protocol.

scan_protocol: Arrays were imaged using the BeadArray Reader.

data_processing: Based on standard quality control procedures, the following probes were removed: (i) previously identified cross-reactive and polymorphic probes; (ii) CpG probes with less than 3 beads or with a detection p-value over 1% in at least 1% of the samples assayed; (iii) CpG probes mapping to the Y chromosome; and (iv) probes containing SNPs with a minor allele frequency > 1% located within 10 bases of the CpG. Raw signal intensities were normalized with subset quantile normalization available in the minfi package.

label: Cy5 and Cy3

source_name: normal lung tissue

label_protocol: Labeling was performed according to the standard Illumina protocol.

extract_protocol: DNA was extracted using the GenFind V3 DNA extraction and purification kit (Beckman Coulter).

value: normal lung tissue

value: vehicle


title: v3.4.1

description: nuclear RNA

value: F


title: v3.3.8

description: nuclear RNA

value: WM

value: pWM


title: 18128X5 EYQ org 2

source_name: EYQ

value: EYQ

value: telencephalic organoid

value: female


title: 7dpi, ATAC Rep2

source_name: 7 days post-injured satellite cells followed by in situ fixation


title: 14dpi, ATAC Rep2

source_name: 14 dayspost-injured satellite cells followed by in situ fixation


title: v3.3.6

description: nuclear RNA


title: 14dpi, ATAC Rep1

source_name: 14 days post-injured satellite cells followed by in situ fixation


title: 18128X4 EYQ org 1

value: neural differentiation


title: v3.3.2

description: nuclear RNA

value: tWM


title: 60hpi, ATAC Rep2

source_name: 60 hours post-injured satellite cells followed by in situ fixation


title: 18433X2 GM org 2

value: WT

value: male


title: v3.2.8

description: nuclear RNA

value: M

value: other

value: Diencephalon

value: Thal

value: NaiveCtrl


title: 18128X1 H9 org 1


title: 18128X3 H9 org 3


title: v3.2.6

description: nuclear RNA

value: LGN


title: 60hpi, ATAC Rep1

value: Skeletal muscle

value: Muscle stem cells

value: BaCl2 injury


title: 18128X2 H9 org 2


title: v3.2.5

description: nuclear RNA

value: Telencephalon

value: Cd


title: 28dpi, ATAC Rep1

source_name: 28 days post-injured satellite cells followed by in situ fixation


title: 18128X6 EYQ org 3

value: EYQ

value: telencephalic organoid


title: GFP+NeuroD4-3

city: Wenzhou

first: hao

state: Zhejiang

address: Nanbaixiang, Ouhai District

country: China

institute: the First  Affiliated Hospital of Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Hisat2 software is used for the sequence alignment between Clean Reads and the reference genome to obtain the position information on the reference genome or gene, as well as the unique sequence characteristics of the sequenced sample.
The FPKM value of each sample is calculated as an index to measure the transcript or gene expression level.
Assembly: GRCh38
Supplementary files format and content: list include FPKM values for all samples

source_name: U-251 MG cell line human

extract_protocol:
TRIzol was used to extract total RNA from U251 glioma cells after infection.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human-derived U251 cell line

value: infected with GFP+NeuroD4 lentivirus for 5 days


title: v3.2.4

description: nuclear RNA

value: F


title: 32hpi, ATAC Rep1

source_name: 32 hours post-injured satellite cells followed by in situ fixation


title: 7dpi, ATAC Rep1


title: GFP+NeuroD4-2


title: 16hpi, ATAC Rep2

source_name: 16 hours post-injured satellite cells followed by in situ fixation


title: GFP+NeuroD4-1


title: GFP-3

value: infected with GFP lentivirus for 5 days


title: 16hpi, ATAC Rep1


title: v3.2.7

description: nuclear RNA

value: M

value: Hipp


title: v3.2.2

description: nuclear RNA

value: other

value: Diencephalon


title: v3.2.3

description: nuclear RNA

value: NaiveCtrl


title: v3.2.1

description: nuclear RNA


title: GFP-2


title: GFP-1


title: 32hpi, ATAC Rep2


title: 8hpi, ATAC Rep1

source_name: 8 hours post-injured satellite cells followed by in situ fixation


title: 4hpi, ATAC Rep2

source_name: 4 hours post-injured satellite cells followed by in situ fixation


title: 4hpi, ATAC Rep1


title: 2hpi, ATAC Rep2

source_name: 2 hours post-injured satellite cells followed by in situ fixation


title: 1hpi, ATAC Rep2

source_name: 1 hour post-injured satellite cells followed by in situ fixation


title: 2hpi, ATAC Rep1


title: 8hpi, ATAC Rep2


title: 1hpi, ATAC Rep1


title: 0.5hpi, ATAC Rep1

source_name: 0.5 hours post-injured satellite cells followed by in situ fixation


title: XY O - statin - 3

city: Los Angeles

first: Karen

last: Reue

state: CA

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
RNA-seq alignment was performed with STAR v2.4.1a to the mouse genome GRCm38.97.
The read-count per gene was quantified with HTSeq and Ensembl Mus_musculus.GRCm38.97 GTF file.
Differential gene analysis was performed with DESeq2 (v3.26.8). Significance was denoted as adjusted p value<0.05 and fold change>1.25 unless otherwise denoted.
Assembly: GRCm38.97
Supplementary files format and content: CPM.csv, this processed data file contains counts per million (CPM) for all 24 samples for all mapped genes.
Supplementary files format and content: DESeq2_normcounts.csv, this processed data file contains the DESeq2 normalized counts for all 24 samples.

source_name: Liver

extract_protocol:
Liver tissue was homogenized in trizol and RNA was isolated.
Strand-specific RNA-seq libraries were constructed with the Universal plus mRNA-Seq Kit (NuGEN Technologies).

value: 0.1g Simvastatin per kg chow diet (Research Diets D1001)

tag: gonadal sex

value: Ovaries

tag: sex chromosomes

value: XY


title: XY O - statin - 2


title: PRPF39 shRNA, Rep2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

data_processing:
Sequencing adapters were removed with Cutadapt v2.1
Reads were aligned to the hg38 genome (Gencode 28) using STAR v2.7.9a
Transcript abundances were calculated using salmon v0.11.1
Differentially expressed genes were identified using tximport v1.20.0 and DESeq2 v1.32.0
Alternative splicing calculations were done using rMATS v4.0.1
Assembly: hg38 Gencode 28
Supplementary files format and content: salmon-calculated transcript abundances

molecule: polyA RNA

extract_protocol:
RNA was extracted with the Quick-RNA microprep kit (Zymo)
Polyadenylated RNA was isolated, fragmented, and incorporated into high-throughput sequencing libraries.

treatment_protocol: HEK293 cells were treated with lentiviruses containing shRNAs against PRPF39 or scrambled control shRNAs. Cells containing integrated shRNA sequences were then selected using puromycin.

value: PRPF39 shRNA


title: Ctrl shRNA, Rep2

value: control shRNA


title: PRPF39 shRNA, Rep3


title: PRPF39 shRNA, Rep1


title: XY O - statin - 1


title: 6 month N40K (replicate 1)

city: Memphis

first: Yingxue

last: Fu

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: N40K-Tg littermates by crossing N40K-Tg and FAD mice

data_processing:
Basecalls performed using Illumina Casava software.
Fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
BAM files were converted to BED files using bedtools (bamToBed, v2.16.1). Table Browser program (http://genome.ucsc.edu) was used to generate three BED files: (i) RefSeq Genes (Whole Gene), (ii) RefSeq Genes (Exons) and (iii) RefSeq Genes (Introns).
intersectBed (v2.16.1) was used to define the intersections between mapped reads and the three RefSeq BED files.
A splicing deficiency (Sd) score was calculated for each gene as the ratio of length-corrected read counts aligned to introns and exons
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table of Sd scores for every gene and every sample

source_name: Cortex

extract_protocol:
Total RNA was extracted by RNAeasy Mini kit (Qiagen). For mouse hippocampus or cortex, total RNA was extracted by RNA-easy Lipid Tissue Kit (Qiagen) as described in the manual, including with DNAse I digestion to remove contaminated DNA.
RNA sequencing libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina), including poly(A) RNA purification. Libraries were then quantified using the Quant-iT PicoGreen dsDNA assay (Thermo Fisher) and MiSeq Reagent Kit Nano v2 (Illumina). One hundred cycle paired-end sequencing (100 bp) was performed on an Illumina HiSeq 2500.

tag: mating

value: Cortex


title: XY O - chow diet - 3

value: Chow diet (Research Diets D1001)


title: Nfkbiz_ff_epidermis

type: RNA

city: Sendai

first: Hitoshi

last: Terui

state: - - - International - - -

address: Seiryomachi 1-1, Aobaku

department: Dermatology

country: Japan

institute: Tohoku University School of Medicine

description: Gene expression of murine epidermis in stedy state

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) 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 (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring Software v14.9 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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 One Spectrophotometer.

extract_protocol: Total RNA from homogenized skin tissue was extracted with ISOGEN reagent (NIPPON GENE Co., Ltd., Toyama, Japan).

treatment_protocol: Murine skin was incubated for 30 min at 37°C with 3.8% ammonium thiocyanate in PBS. Epidermis was peeled off from dermis using forceps.

value: epidermis


title: XY O - chow diet - 2


title: Nfkbiz_ff_K5cre_epidermis


title: 17-3mo

city: Decatur

first: Akhilesh

last: Kaushal

state: GA

address: 1760 Haygood street

institute: Emory University

data_processing:
Reads were aligned to human reference sequence GRCh38/hg38, filtered, deduplicated and converted into a feature barcode matrix using Cell Ranger 6.0
Samples with low fraction reads (<70%), high reads mapped to antisense strand (>10%) and with problematic barcode rank plot were excluded. Final samples with feature barcode matrix containing data for genes and 55 surface proteins were analyzed using Seurat V3 (20).  Cells with fewer than 200 unique sequenced genes, more than 10% mitochondrial gene and more than 70,000 sequenced features were filtered to exclude dead cells and doublets. The data was batch corrected using canonical correlation analysis (CCA) method using Seurat V3 data integration pipeline.
Seurat V3 pipeline for multi-modal data was used for analysis. Batch correction was performed using CCA method in Seurat.
Assembly: GRCh38/hg38
Supplementary files format and content: HDF5
Library strategy: CITE-Seq

source_name: Multiple Myeloma Patient# 17 CITE-seq data at 3months after CAR T therapy

extract_protocol:
Cells were fixed, permeabilized and washed in accordance with the fluidigm`s cell surface and nuclear staining protocol as described.
Gene expression and cell surface libraries were prepared according to the protocol from 10X Genomics

tag: disease state

value: Multiple Myeloma (MM)

tag: subject id

value: Patient# 17

tag: treatment group

value: 3 months after CAR T therapy

value: Bone Marrow Mononuclear cells

tag: sequencing method

value: CITE-Seq


title: 01-pre

source_name: Multiple Myeloma Patient# 01 CITE-seq data before CAR T therapy

value: Patient# 01

value: before CAR T therapy


title: 08-pre

source_name: Multiple Myeloma Patient# 08 CITE-seq data before CAR T therapy

value: Patient# 08


title: 16-d28

source_name: Multiple Myeloma Patient# 16 CITE-seq data at Day 28 after CAR T therapy

value: Patient# 16

value: Day 28 after CAR T therapy


title: 16-pre

source_name: Multiple Myeloma Patient# 16 CITE-seq data before CAR T therapy


title: 03-3mo

source_name: Multiple Myeloma Patient# 03 CITE-seq data at 3 months after CAR T therapy

value: Patient# 03


title: 16-3mo

source_name: Multiple Myeloma Patient# 16 CITE-seq data at 3 months after CAR T therapy


title: Ctrl shRNA, Rep3


title: 01-d28

source_name: Multiple Myeloma Patient# 01 CITE-seq data at Day 28 after CAR T therapy


title: Ctrl shRNA, Rep1


title: Term-Seq dAGR-3

city: State College

first: Paul

last: Babitzke

state: PA

address: 203 Althouse Laboratory

institute: Pennsylvania State University

description:
dAGR-3
NusA depletion nusG deletion rho deletion - Termseq

data_processing:
Library strategy: Term-seq
base calling and quality scoring conducted via BaseSpace
adaptor trimming and low quality read removal via Trimmomatic v. 0.38 for RNA-seq .fastq dataset
all reads containing custom oligo were extracted via Cutadapt v. 1.16 for Term-seq .fastq dataset
both RNA-seq and Term-seq .fastq files were mapped to B. subtilis genome using bwa-mem v.0.7.12-r1034
sam -> bam, and bam files split by strand via samtools v. 0.1.19-44428cd
coverage files (.cov) for 3' end mapping and .bedgraph files to illustrate coverage were generated using bedtools v. 2.26.0
2 custom python (python v. 3.8.3) scripts were used to identify 3' ends from Term-seq .fastq derived .cov files (located at: https://github.com/zfmandell/Term-seq)
RNA-seq coverage files generated using bedtools v. 2.26.0
Genome_build: Refseq : NC_000964.3
Supplementary_files_format_and_content: bedgraph files, containing a list of called 3' ends with associated height values

organism: Bacillus subtilis

source_name: bacterial cell culture

growth_protocol: cells were plated on LB plates at 37°C w/ +2 mM IPTG when required and +20 µg/ml chloramphenicol -> single colonies isolated and grown O/N at 37°C standing culture in +0.4 mM IPTG when required and +20 µg/ml chloramphenicol -> next day, cells were grown at in LB at 37°C +20 µg/ml chloramphenicol

extract_protocol:
Total RNA was extracted from collected cell paste via RNeasy mini-kit (Qiagen, cat # 74104)
total RNA was dephosphorylated using CIP (NEB, discontinued), rRNA was depleted via ribo-zero Gram-positive rRNA depletion kits (Illumina, discontinued) or MICROBExpress (Thermo Fisher), remaining RNA was ligated to custom unique 2', 3’ dideoxy RNA oligonucleotide (IDT), Illumina sequencing libraries were generated from ligation products using TruSeq Stranded mRNA kit (Illumina, cat # 20020594) or NEBNext Ultra Directional (NEB, cat # E7760L)

value: rpoC-10His  amyE::Physpank-nusA lacIq -delta-nusA nusG::kan rho::tet Cmr Spr Emr Kmr Tetr


title: 0.5hpi, ATAC Rep2

value: Skeletal muscle

value: Muscle stem cells

value: BaCl2 injury


title: XY O - chow diet - 1

value: Chow diet (Research Diets D1001)

value: Ovaries

value: XY


title: Term-Seq dAGR-2

description:
dAGR-2
NusA depletion nusG deletion rho deletion - Termseq


title: XY T - statin - 3

value: 0.1g Simvastatin per kg chow diet (Research Diets D1001)

value: Testes


title: XY T - statin - 2


title: Term-Seq dAGR-1

description:
dAGR-1
NusA depletion nusG deletion rho deletion - Termseq


title: XY T - statin - 1


title: Term-Seq dGR-3

description:
dGR-3
nusG deletion rho deletion - Termseq

value: rpoC-10His nusG::kan rho::tet Cmr Kmr Tetr


title: 73SR_A_IAA_Rep2

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill

data_processing: Briefly, the raw reads were mapped to the Variovorax paradoxus CL14 genome (fasta file available on: https://github.com/isaisg/variovoraxRGI/blob/master/rawdata/2643221508.fna) using bowtie2 with the ‘very sensitive’ flag. Hits to each individual coding sequence were counted and annotated using the function featureCounts from the R package Rsubread , inputting the Variovorax paradoxus CL14 gff file (available on: https://github.com/isaisg/variovoraxRGI/blob/master/rawdata/2643221508.gff) and using the default parameters with the flag allowMultiOverlap = FALSE.

organism: Variovorax paradoxus

growth_protocol: V. paradoxus CL14 was grown in 5mL cultures of M9 minimal medium

extract_protocol:
Cells from all samples were harvested for RNA-Seq at 18 hours to ensure IAA was still present in the cultures of strains that degraded IAA most rapidly. Cells were pelleted by centrifuging the culture at 4,200 x g for 15 min and removing the supernatant. Cell pellets were frozen at -80°C prior to RNA extraction. To extract RNA, cells 27 were lysed in TRIzol Reagent (Invitrogen) according to the manufacturer instructions for lysis and phase separation.
After these steps RNA was purified from the aqueous phase using the RNeasy Mini kit (Qiagen) including the optional on-column DNase Digestion with RNase-Free DNase Set (Qiagen). Total RNA was quantified using the Qubit 2.0 fluorometer (Invitrogen) and RNA-seq libraries were prepared using the Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete kit (Tecan) according to the manufacturer instructions. The resulting libraries were pooled and sequenced on the Illumina HiSeq4000 to generate 50 bp single-end reads

treatment_protocol: Cultures were supplemented  with  15mM succinate and 0.5% (v/v) ethanol alone or containing IAA. IAA was at a final concentration  of 0.1 mg/mL in the medium to which it was added. Cultures were prepared at a starting OD600  of 0.02 and incubated at 28°C, shaking at 250rpm.

tag: bacteria

tag: iaa

value: Yes

tag: rep


title: 73SR_A_IAA_Rep1

tag: strain


title: XY T - chow diet - 2


title: 73SR_A_minus_Rep3

value: No


title: 73SR_A_minus_Rep2


title: XY T - chow diet - 1


title: d73_IAA_Rep2


title: Term-Seq dGR-2

description:
dGR-2
nusG deletion rho deletion - Termseq


title: Term-Seq dAG-3

description:
dAG-3
NusA depletion nusG deletion - Termseq

value: rpoC-10His  amyE::Physpank-nusA lacIq -delta-nusA nusG::kan Cmr Spr Emr Kmr


title: d73_IAA_Rep3


title: XX T - chow diet - 4

value: XX


title: Term-Seq dAR-3

description:
dAR-3
NusA depletion rho deletion - Termseq

value: rpoC-10His  amyE::Physpank-nusA lacIq -delta-nusA rho::tet Cmr Spr Emr Tetr


title: Term-Seq dGR-1

description:
dGR-1
nusG deletion rho deletion - Termseq


title: XX O - statin -2


title: XX O - statin -3


title: 73SR_A_minus_Rep1


title: d73_IAA_Rep1


title: 73SR_A_IAA_Rep3


title: Term-Seq dAR-1

description:
dAR-1
NusA depletion rho deletion - Termseq


title: d73_minus_Rep3


title: XX O - statin -1


title: Term-Seq dKR-3

description:
dKR-3
rho deletion KOW domain of NusG deletion - Termseq

value: rpoC-10His rho::tet nusG(-delta-KOW) Cmr Kmr Tetr


title: Term-Seq dKR-2

description:
dKR-2
rho deletion KOW domain of NusG deletion - Termseq


title: XX O - chow diet - 2


title: XX O - chow diet - 3


title: d73_minus_Rep2


title: Term-Seq dAR-2

description:
dAR-2
NusA depletion rho deletion - Termseq


title: d73_minus_Rep1


title: d50_IAA_Rep3


title: d50_IAA_Rep1


title: d50_IAA_Rep2


title: XX T - statin -2


title: XX O - chow diet - 1


title: Term-Seq dK-1

description:
dK-1
KOW domain of NusG deletion - Termseq

value: rpoC-10His nusG(-delta-KOW) Cmr Kmr


title: Term-Seq dK-2

description:
dK-2
KOW domain of NusG deletion - Termseq


title: Term-Seq dK-3

description:
dK-3
KOW domain of NusG deletion - Termseq


title: Term-Seq dR-3

description:
dR-3
rho deletion - Termseq

value: rpoC-10His rho::tet Cmr Tetr


title: XX T - chow diet - 3


title: XX T - statin -1


title: d50_minus_Rep2


title: XX T - chow diet - 2


title: Term-Seq dR-2

description:
dR-2
rho deletion - Termseq


title: d50_minus_Rep1


title: Term-Seq dR-1

description:
dR-1
rho deletion - Termseq


title: WT_A

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

data_processing:
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Robosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.5.2b)
Reads were counted using featureCounts from subreads package (v1.6.5) using strand specific mode.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were surface-sterilized by treatments with 70% EtOH and 5% hypochloryte-1% SDS, washed and stratified at 4°C for 2 days to obtain homogeneous germination. Seedlings were grown at 23°C on solid half-strength Murashige and Skoog (MS/2) medium (Duchefa), under long day conditions (16h light, 95μE.m-2.sec-1/8h dark).

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase (Fermentas) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA

tag: tissue

value: seedlings

tag: developmental stage

value: wild type


title: XX T - chow diet - 1

tag: treatment


title: Term-Seq dA-3

description:
dA-3
NusA depletion - Termseq

value: rpoC-10His  amyE::Physpank-nusA lacIq -delta-nusA Cmr Spr Emr


title: SJMMALZ015843_G1: WT-12M-2

first: Ping-Chung

last: Chen

address: 262 Danny Thomas PL

department: Structural Biology

institute: St Jude Children's Research Hospital

description: Total RNA was extracted from hippocampus of the  non-transgenic wild type littermates at 12 months old of age.

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using an internal perl script and converted to FPKM using mm9
Genome_build: mm9

source_name: Non-transgenic wild type mice

extract_protocol:
RNAs were extracted by Trizol (Invitrogen) from about 20 mg aliquots of the same tumor samples for proteomics analyses.
For RNAseq, poly-A selected mRNA libraries were generated from ~1 µg total RNA using the Illumina TruSeq RNA Library Prep Kit. Libraries were sequenced on an Illumina HiSeq 2500 using paired-end 100 bp sequencing chemistry

value: hippocampus

value: Non transgenic control


title: SJMMALZ015844_G1: WT-12M-3


title: Term-Seq dKR-1

description:
dKR-1
rho deletion KOW domain of NusG deletion - Termseq


title: d6869_IAA_Rep3


title: G2 RNA rep2

city: Hefei

first: Ran

last: Zhang

address: No.96 Jinzhai road

institute: University of Science and Technology of China

data_processing:
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.5 with the following configurations: -3 120. Data were filtered using the following specifications: Samtools v1.7 was used to remove duplicate reads and chromosome M. peaks were called using Genrich version 0.5 with the following setting: -v -j.
For RNA-seq, reads were aligned to the mm9 genome assembly using hisat2 version 2.1.0. Data were sorted using Samtools v1.7. Counts were getting using featureCounts v1.5.0-p1.
Genome_build: mm9
Supplementary_files_format_and_content: narrowpeak files of peaks
Supplementary_files_format_and_content: bigwig files were generated using  the bamCoverage function of deepTools

growth_protocol: HeLa cells cells were grown in DMEM medium containing 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin (PS) at 37°C and 5% CO2. NIH3T3 cells cells were grown in DMEM medium containing 10% Newborn Calf Serum (NCS) at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. For ATAC-seq, Tn5 digest cells and then PCR for sequencing

treatment_protocol: Cell were culturing on G128 or G2 for 24h

value: cultured on G2 for 24h

tag: cell line


title: XX T - statin -3

value: 0.1g Simvastatin per kg chow diet (Research Diets D1001)


title: SJMMALZ015842_G1: WT-12M-1

tag: genotype


title: d6869_IAA_Rep2


title: Term-Seq dG-3

description:
dG-3
nusG deletion - Termseq

value: rpoC-10His nusG::kan Cmr Kmr


title: d50_minus_Rep3


title: SJMMALZ015841_G1: TG-12M-3

description: Total RNA was extracted from hippocampus of the N40K-Tg mice from Tg396 line at 12 months old of age.  The transgenic mice express N40K specifically in neurons through a modified CaMKIIa promoter.

source_name: N40K transgenic mice

value: SNRNP70 trunction to N40K


title: d6869_minus_Rep3


title: G2 RNA rep1


title: Term-Seq dG-2

description:
dG-2
nusG deletion - Termseq


title: G128 RNA rep2

value: cultured on G128 for 24h


title: SJMMALZ015839_G1: TG-12M-1


title: Term-Seq dG-1

description:
dG-1
nusG deletion - Termseq


title: SJMMALZ015840_G1: TG-12M-2


title: G128 RNA rep1


title: d6869_minus_Rep2

value: No


title: Term-Seq WT-3

description:
WT-3
Wild Type - Termseq

value: rpoC-10His Cmr


title: G2 ATAC rep2


title: d6869_minus_Rep1


title: SJMMALZ011838_G1: WT-3M-3

description: Total RNA was extracted from hippocampus of the  non-transgenic wild type littermates at 3 months old of age.


title: Term-Seq WT-2

description:
WT-2
Wild Type - Termseq


title: G2 ATAC rep1


title: G128 ATAC rep2


title: SJMMALZ011837_G1: WT-3M-2


title: SJMMALZ011836_G1: WT-3M-1


title: CL14wt_IAA_Rep3

value: Yes


title: Term-Seq WT-1

description:
WT-1
Wild Type - Termseq


title: d6869_IAA_Rep1


title: CL14wt_IAA_Rep1


title: G128 ATAC rep1


title: CL14wt_minus_Rep4


title: CD4+CD8+ DP cells (Thymus), KO2

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
The quality of RNA-Seq libraries was assessed by FastQC (v0.11.5). Cutadapt (version 1.17) was used to filter poor quality sequences.
RNA-Seq reads were aligned  to mouse genome GRCm38  using STAR (v2.6.0a).
Count files of all genes were calculated by Htseq-count (v0.6.1), and Reads Per Kilobase per Million mapped reads (RPKM) were calculated using R pakages.
Differential Gene Expression analysis was performed using DEseq2 (v1.24.0) from the counts.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file includes RPKMs for each sample
Supplementary_files_format_and_content: Tab-delimited text read counts

source_name: CD4+CD8+ DP cells (Thymus)

extract_protocol:
Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 6~8 weeks

value: thymus

value: LCKCre/+ Srsf1fl/fl


title: CL14wt_minus_Rep3


title: CD4+CD8+ DP cells (Thymus), KO1


title: SJMMALZ011840_G1: TG-3M-2

description: Total RNA was extracted from hippocampus of the N40K-Tg mice from Tg396 line at 3 months old of age.  The transgenic mice express N40K specifically in neurons through a modified CaMKIIa promoter.


title: SJMMALZ011839_G1: TG-3M-1


title: ICOS_3

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

data_processing:
Reads were mapped to the Homo Sapiens hg19 reference assembly using TopHat v2.0.10
Gene counts were computed using htseq-count and the GENCODE v24 gene annotation.
Genome_build: human GRCh37 / hg19
Supplementary_files_format_and_content: all.data.matrix.TPM.xlsx = File containing the normalized counts expressed in TPM in all samples.

source_name: PBMC

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from buffy coats provided by the local Blood Transfusion Service. Naïve CD4+ T cells from PBMC were purified with the EasySep™ Human naïve CD4+ T cells Negative Selection Kit.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen), following manufacturer instructions
Libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following manufacturer’s instructions.

treatment_protocol: 100.000 Naïve CD4+ T cells were plated on round-bottom 96-well plates; cells were stimulated with anti-CD3 mAb (OKT3, 10 ug/ml)+ B7h-Fc (5 ug/ml) or anti-CD3 mAb (OKT3, 10 ug/ml)+ B7.1-Fc (5 ug/ml)

tag: cell type

value: Naive CD4+ T cells

value: ICOS


title: CL14wt_minus_Rep2


title: CL14wt_IAA_Rep2


title: CD3_3


title: CD4+CD8+ DP cells (Thymus), WT2

value: WT


title: CD4+CD8+ DP cells (Thymus), WT1


title: SJMMALZ011841_G1: TG-3M-3


title: CL14wt_minus_Rep1


title: NP1CRTC-2

status: Public on Aug 10 2022

first: HANSONG

last: DENG

address: RM 5O1, BLDG 1, # 817 ZHENGLI RD, YANGPU DISTRICT

institute: Tongji University

data_processing:
Bcl2fastq (v2.17.1.14) software used for basecalling.
Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: Drosophila melanogaster .BDGP6.95
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Drosophila melanogaster

source_name: gut

extract_protocol:
For RNAseq in fly guts, around 20 guts of each sample were dissected in RNase-free PBS.  RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: post natal day 3-5

value: gut


title: NP1CRTC-3


title: NP1-3


title: NP1CRTC-1


title: NP1-1


title: NP1-2


title: Gr6H_6H3.300

city: Caparica

first: Patricia

middle: H.

last: Brito

address: Rua Câmara Pestana

country: Portugal

institute: NOVA School of Science and Technology

description: caudal fin 6hpa biological replicate 3

hyb_protocol: For hybridisation, the Agilent's Oligo aCGH/ChIP-on-Chip Hybridisation Kit (Agilent Technologies) was used. For example, each cRNA is hybridised on 8x60K microarrays at 65 ◦C for 17 h using Agilent’s recommended hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37◦C) Gene Expression Wash Buffer 2  for one minute.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 µm for SurePrint G3 Gene Expression Microarrays, and 5 µm for HD Microarray formats. This resulted in a raw data output of 1-colour hybridisation using the Agilent’s Feature Extraction software version 11, generating a 20 bit TIFF file

data_processing: Prior to data normalisation of the background substracted signals, the following processing steps are performed:removal of signals from control probes;mean of signals from replicate probes; and mean of signals from all probes of a target. Data Normalization: Background signals were subtracted and then normalized prior to the statistical analysis. For that, the arrays were quantile normalised using the ranked mean quantiles (Bolstad et al. 2003). Briefly, the mean signal of each target was ranked relative to all other targets and the ranked signal value replaced with the mean quantile value of the same rank.Thus, the highest value in all samples becomes the mean of the highest values, the second highest value becomes the mean of the second highest values, and so on. Quality Assurance: For data quality control and to identify potential outlier samples hierarchical clustering and a principal component analysis were performed.

organism: Danio rerio

source_name: Osteoblast

label_protocol: For genome-wide gene expression analysis on OakLabs’ ArrayXS Agilent microarrays as well as on Agilent’s catalogue microarrays, OakLabs fulfills the requirements for certified service providers and follows strictly the relevant protocols. For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate fluorescent cRNA (complementary  RNA). For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesisof cRNA labelled with cyanine 3-CTP is performed. Please refer the summary file for details regarding the used primer, yield of cRNA as well as cy3 incorporation rate

growth_protocol: Fish in homeostasis (not subjected to amputation) and fish subjected to caudal fin amputation were maintaned in a water tank in an incubator during 6 hours at 33ºC and divided in 2 groups for the control condition and in 3 groups for the 6 hours post-amputation condition

extract_protocol: The equivalent to one segment and a half of the uninjured caudal fins (not subjected to caudal fin amputation) was colleted and correponded to control condition. The equivalent of one segment and a half bellow the amputation zone of 6 hours post-amputated caudal fins was collected. Colleted caudal fins from control and from 6 hous post-amputation were subjected to tissue processing for Fluorescent activated cell sorting and 300 osteoblasts (GFP-positive) were isolated per contition directly into a lysis and RNA stabilization buffer   (provided by OakLabs GmbH).

tag: transgenic line

value: Tg(ola.Bglap:EGFP)  hu4008

tag: genotype/variation

value: AB background

value: 3-5 months old adult

value: regeenrating caudal fin tissue

tag: time point

value: 6 hour post-amputation


title: Gr6H_6H1.300

description: caudal fin 6hpa biological replicate 1


title: Gr6H_6H2.300

description: caudal fin 6hpa biological replicate 2


title: GrU_U2.300

description: uninjured caudal fin 0hpa biological replicate 2

value: uninjured caudal fin tissue

value: 0 hour post-amputation


title: GrU_U3.300

description: uninjured caudal fin 0hpa biological replicate 3


title: neural retina, Wt, 17 months, 9-5

city: Cambridge

first: Angela

middle: Mae

last: Banks

state: MA

address: 22 Windsor St.

department: Ophthalmology

institute: Novartis Institutes for Biomedical Research

data_processing:
PISCES 2018.04.01
Sequence reads were mapped to GRCm38.p4 using the PISCES alignment pipeline
Read count extraction and normalization were performed using the PISCES alignment pipeline
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample

source_name: neural retina

extract_protocol:
RNA was harvested using RNeasy micro columns (Qiagen) including a DNase I treatment step. 200 ng of total RNA per sample was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using Illumina TruSeq® Stranded mRNA Sample Preparation kit on Hamilton STAR following manufacturer's protocols.

value: neural retina

value: female

value: Wt

tag: time

value: 17 months


title: neural retina, Wt, 17 months, 9-7


title: neural retina, Wt, 17 months, 9-4


title: neural retina, Wt, 17 months, 9-8


title: neural retina, Wt, 17 months, 9-2


title: neural retina, Wt, 17 months, 9-3


title: neural retina, Wt, 17 months, 9-6


title: posterior eyecup, Efemp1ki/ki, 17 months, 8-6

source_name: posterior eyecup

value: posterior eyecup


title: neural retina, Wt, 17 months, 9-1


title: posterior eyecup, Efemp1ki/ki, 17 months, 8-8


title: posterior eyecup, Efemp1ki/ki, 17 months, 8-5


title: posterior eyecup, Efemp1ki/ki, 17 months, 8-1


title: posterior eyecup, Wt, 17 months, 7-7


title: posterior eyecup, Wt, 17 months, 7-1


title: posterior eyecup, Wt, 17 months, 7-8


title: posterior eyecup, Wt, 17 months, 7-3


title: posterior eyecup, Wt, 17 months, 7-6


title: posterior eyecup, Wt, 17 months, 7-2


title: posterior eyecup, Wt, 17 months, 7-5


title: posterior eyecup, Wt, 17 months, 7-4


title: posterior eyecup, Efemp1ki/ki, 17 months, 8-7


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-9

value: 3 months


title: posterior eyecup, Efemp1ki/ki, 17 months, 8-2


title: posterior eyecup, Efemp1ki/ki, 17 months, 8-4


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-5


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-6


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-1


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-8


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-3


title: posterior eyecup, Wt, 3 months, 5-5


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-2


title: posterior eyecup, Efemp1ki/ki, 3 months, 6-4


title: posterior eyecup, Wt, 3 months, 5-9


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-8

value: 9 months


title: posterior eyecup, Wt, 3 months, 5-6


title: posterior eyecup, Wt, 3 months, 5-3


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-6


title: posterior eyecup, Wt, 3 months, 5-2


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-7


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-5


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-2


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-4


title: posterior eyecup, Wt, 9 months, 3-7


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-3


title: posterior eyecup, Wt, 9 months, 3-9


title: posterior eyecup, Efemp1ki/ki, 9 months, 4-1


title: posterior eyecup, Wt, 9 months, 3-6


title: posterior eyecup, Wt, 9 months, 3-5


title: posterior eyecup, Wt, 9 months, 3-4


title: posterior eyecup, Wt, 3 months, 5-7


title: posterior eyecup, Wt, 9 months, 3-3


title: neural retina, Efemp1ki/ki, 3 months, 14-8


title: posterior eyecup, Wt, 9 months, 3-1


title: neural retina, Efemp1ki/ki, 3 months, 14-7


title: neural retina, Efemp1ki/ki, 3 months, 14-3


title: neural retina, Efemp1ki/ki, 3 months, 14-2


title: posterior eyecup, Wt, 9 months, 3-8


title: neural retina, Efemp1ki/ki, 3 months, 14-5


title: neural retina, Efemp1ki/ki, 3 months, 14-4


title: neural retina, Wt, 3 months, 13-8


title: neural retina, Efemp1ki/ki, 3 months, 14-1


title: neural retina, Wt, 3 months, 13-7


title: neural retina, Wt, 3 months, 13-4


title: neural retina, Wt, 3 months, 13-6


title: neural retina, Wt, 3 months, 13-3


title: neural retina, Wt, 3 months, 13-5


title: neural retina, Efemp1ki/ki, 9 months, 12-7


title: neural retina, Efemp1ki/ki, 9 months, 12-9


title: neural retina, Efemp1ki/ki, 9 months, 12-8


title: neural retina, Wt, 3 months, 13-1


title: neural retina, Efemp1ki/ki, 9 months, 12-5


title: neural retina, Efemp1ki/ki, 9 months, 12-4


title: neural retina, Efemp1ki/ki, 9 months, 12-6


title: neural retina, Efemp1ki/ki, 3 months, 14-6


title: neural retina, Efemp1ki/ki, 9 months, 12-2


title: neural retina, Wt, 9 months, 11-8


title: neural retina, Efemp1ki/ki, 9 months, 12-3


title: neural retina, Wt, 9 months, 11-7


title: neural retina, Wt, 9 months, 11-6


title: neural retina, Wt, 9 months, 11-4


title: neural retina, Wt, 9 months, 11-5


title: neural retina, Wt, 9 months, 11-3


title: neural retina, Wt, 3 months, 13-2


title: neural retina, Wt, 9 months, 11-1


title: neural retina, Efemp1ki/ki, 17 months, 10-8


title: neural retina, Efemp1ki/ki, 17 months, 10-6


title: neural retina, Efemp1ki/ki, 17 months, 10-5


title: neural retina, Efemp1ki/ki, 17 months, 10-4


title: neural retina, Efemp1ki/ki, 17 months, 10-2


title: neural retina, Efemp1ki/ki, 17 months, 10-7


title: neural retina, Efemp1ki/ki, 17 months, 10-1


title: Ground Control_G14_RR9_B

city: Loma Linda

first: Xiao Wen

last: Mao

address: 11175 Campus Street

institute: Loma Linda University

hyb_protocol: nCounter CodeSet  utilizes target-specific Capture Probes and color-coded Reporter  Probes (CodeSet), which hybridize directly with a target-specific sequences of the single-stranded RNA in solution. Codeset hybridization is carried out overnight (MANUAL-10083-01,nCounter®Gene Expression Panels Overview)

scan_protocol: nCounter technology digitally detects barcoded individual target molecules through unique probe pair for each target molecule. Digital images are then  processed by the nCounter instrument, and the Reporter Probe counts are received tabulated for further analysis (MANUAL-10083-01,nCounter®Gene Expression Panels Overview).

data_processing: The Neuroflammation Panel includes 757 genes covering the core pathways and processes that define neuroimmune interactions and 13 potential housekeeping genes for normalization. Raw RCC data files generated from nCounter system were analyzed using nSolver 4.0 software with the Advanced Analysis module for downstream pathway analysis.

source_name: Brain Tissue

label_protocol:
Homogenization of Brain tissues was performed using 1.5 mm beads (Benchmark, # 1032-15) on Minilys homogenizer (Bertin Technologies) in RLT Plus buffer. The purity and concentration of the eluted RNA were measured using Nanodrop 2000 (Thermo Fisher Scientific, Waltham, MA) and stored at -80°C until further analysis. RNA samples (20 ng/ul) were shipped to Nanostring (Technologies Seattle, WA) and gene expression profiling of brain tissues was conducted using the nCounter® Neuroflammation Gene Expression panel.
n.a.

extract_protocol: Isolation of total RNA from the brain tissues was performed using DNA/RNA/miRNA Universal Kit (Qiagen, # 80224) according to the manufacturer’s instruction.

value: 10-week old

tag: Sex

value: Male

tag: sample type

value: GC


title: neural retina, Efemp1ki/ki, 17 months, 10-3


title: neural retina, Wt, 9 months, 11-2


title: Wild type B-Control 2

first: John

last: Wrobel

state: NC

address: 120 Mason Farm Rd

department: Department of Biochemistry and Biophysics

institute: University of North Carolina

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from the raw data. Q20, Q30 and GC content of the clean data were also calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome browser website (NCBI/UCSC/Ensembl). Paired-end clean reads were aligned to the GRCm38/mm10 genome assembly of the Mus Musculus reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
Quantification: featureCounts was used to count the number of reads mapped to each gene. Next, RPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of both sequencing depth and gene length for the read counts.
Assembly: GRCm38/mm10

source_name: B lymphocytes

growth_protocol: B lymphocytes were sorted from three Wild type mice and  three Tmem173-/- mice. 1x10e6 B cells were seeded wells of 96 well flat bottom plates.

extract_protocol:
Total RNA was extracted from B cells using the RNeasy Mini Kit (Qiagen, 74106).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: B lymphocytes were treated with 3'3'-cGAMP for 12 hours.

value: B lymphocytes

value: wild type

value: control


title: Wild type B-Control 1


title: Wild type B-cGAMP 3

value: cGAMP


title: Wild type B-cGAMP 2


title: Wild type B-Control 3


title: Tmem173-/- B-Control 3


title: Wild type B-cGAMP 1


title: Ground Control_G10_RR9_B


title: Ground Control_G9_RR9_B


title: Ground Control_G8_RR9_B


title: Ground Control_G12_RR9_B


title: FLIGHT_F14_RR9_B

value: FLT


title: Ground Control_G13_RR9_B


title: Tmem173-/- B-Control 1


title: Tmem173-/- B-cGAMP 3


title: FLIGHT_F13_RR9_B


title: FLIGHT_F10_RR9_B


title: FLIGHT_F12_RR9_B


title: Tmem173-/- B-cGAMP 2


title: Tmem173-/- B-cGAMP 1


title: Mouse spleen iNKT cell sample 2

city: Detroit

first: Indra

last: Adrianto

state: MI

address: 1 Ford Place

department: Public Health Sciences

institute: Henry Ford Health System

description: iNKT cells from mouse spleen (sample 2)

data_processing:
Sequencing read demultiplexing, aligning to the mm10 mouse reference genome, barcode processing, and UMI counting were performed using the 10X Genomics Cell Ranger (v3.1.0) pipeline.
Estimated number of cells captured per sample were between 2,646-2,867 with 60,622-70,044 mean reads per cell, 788-1,388 median genes per cell, and 1,468-3,597 median UMI counts per cell.
A filtered gene-barcode matrix for each sample containing only detected cellular barcodes was generated and subsequently analyzed using the R Seurat package.
Samples have 3 fastq files associated with them with a tag in the filename, namely I1, R1, and R2. The I1 contains the sample index. The R1 contains the 10x barcode (16 base pairs) followed by UMI (10 bp). The R2 contains the transcript reads.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger filtered gene-barcode matrix outputs of cell barcode, gene name, and UMI count matrix files.

molecule: nuclear RNA

source_name: Spleen

extract_protocol:
Murine peripheral organs, including spleen, liver and lymph nodes, were harvested from 5 weeks old C57BL/6 mice. For the enrichment of iNKT cells, total cells were stained with biotin-conjugated anti-mouse CD8 Ab, anti-mouse B220 Ab and anti-biotin magnetic beads (eBioscience). Negatively selected CD8- and B220- cells were then stained with anti-mouse TCR-b, CD1d-Tetramer Abs. iNKT cells of whole population were further sorted from C57BL/6 mouse peripheral organs using FACSAria II Usage, cells collected with purity greater than 97%.
Single cell sequencing libraries were generated using the 10X Genomics Chromium Single Cell 3’ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller. Reverse transcription of the GEM (GEM-RT) was performed in a Thermocycler (Veriti™ 96-Well Fast Thermal Cycler, Applied Biosynthesis; 53 °C 45 min, 85 °C 5 min, 4 °C hold). cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) with the same Thermocycler (98 °C 3 min; 98 °C 15 sec, 67 °C 20 sec, 72 °C 1 min, repeat 12 cycles; 72 °C 1 min, 4 °C hold). Amplified cDNA is cleaned up with SPRIselect Reagent Kit (Beckman Coulter) and followed by library construction procedure, including fragmentation, end repaired, adaptor ligation, and library amplification. A Bioanalyzer (Agilent) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using paired-end flow cell: Read 1, 26 cycles, i7 index 8 cycles; Read 2: 110 cycles.
Single-cell RNA-Seq

value: Spleen

value: iNKT cells

value: 5 weeks

value: WT


title: FLIGHT_F8_RR9_B


title: Tmem173-/- B-Control 2


title: Mouse liver iNKT cell sample 2

description: iNKT cells from mouse liver (sample 2)

source_name: Liver

value: Liver


title: Mouse lymph node iNKT cell sample 1

description: iNKT cells from mouse lymph node (sample 1)

source_name: Lymph Node

value: Lymph Node


title: JM20 plasma_Control OA adv

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

description: plasma_Control OA adv

data_processing: text files were downloaded from the QuantStudio 12K Flex and were imported in R as data tables. Expression matrices in qPCRset format were created for every dataset using the HTqPCR R package

label: FAM

extract_protocol: Total RNA was extracted from 200 μl of plasma using the automatic nucleic acid extractor Maxwell 48 (Promega, Madison, WI, USA)

tag: gender

value: Female

tag: msc status


title: JM21 plasma_Control OA adv

description: plasma_Control OA adv


title: Mouse liver iNKT cell sample 1

description: iNKT cells from mouse liver (sample 1)


title: GPA_Dox_Rep2

city: Edinburgh

first: Aida

last: Santos da Costa

state: Edinburgh

address: Old College, South Bridge

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads were pre-processed by trimming contaminants adapters using cutadapt. The trimmed reads were pseudo-aligned to cDNA sequences from UCSC’s knownGene transcriptome (mm9 assembly) using Kallisto with default settings. For differential expression analyses, transcript abundances were imported into R and summarised to the gene-level using the tximport workflow. Read counts were normalised and processed for differential expression with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: A single comma-separated table file shows the normalized counts for each sample

source_name: iGPA ESC line

growth_protocol: For embryoid bodies differentiation, mouse embryonic fibroblasts (MEFs) were first depleted from the mESCs by using 0.25% trypsin-EDTA (Life Technologies) to dissociate MEFs-coated mESCs culture dishes into a single cell suspension which was incubated on gelatin-coated (0.1%) dishes for 45 minutes at 37C. After removing the medium containing unattached mESCs suspension, mESCs were seeded on 60-mm bacterial-grade Petri dishes at 3×104 cells/cm2 in Dulbecco's Modified Eagle’s Medium (DMEM), supplemented with 10% fetal bovine serum (FBS) (ES-qualified), 2 mM L-Glutamine, 1 mM sodium pyruvate, 1 mM 2-mercaptoethanol,1% of penicillin-streptomycin and 1x non-essential amino acids (all from Life Technologies), but in the absence of LIF. Embryoid bodies formed within 24 hours, and medium was changed every 2 days.

extract_protocol:
Total RNA was extracted using Absolutely RNA Miniprep Kit (#400800, Agilent Technologies) from untreated embryoid bodies at day 6 and from FACS sorted embryoid bodies at day 6 previously treated with doxycycline for 48h. Cell sorting of Venus+ populations were done on a FACS Aria cell sorter (Becton Dickinson).
RNA-seq libraries were generated with 1ug of total RNA using KAPA mRNA HyperPrep Kit (KK8580, Kapa Biosystems) following manufacturer's instructions

treatment_protocol: 2 µg/ml of doxycycline for 48h (added to culture media on day 4 of of embryoid body differentiation)

value: iGPA-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Atoh1+Venus transgenes

tag: age of differentiation

value: EBs at day 6

tag: parental cell line

tag: dox treatment

value: 2 µg/ml doxycycline for 48h


title: JM19 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv

value: Male


title: JM18 plasma_Control OA adv

description: plasma_Control OA adv


title: JM17 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: FLIGHT_F9_RR9_B

tag: strain

value: 10-week old


title: JM16 plasma_Control OA adv

description: plasma_Control OA adv


title: JM15 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: JM14 plasma_Control OA adv

description: plasma_Control OA adv


title: P+A_Ctrl_Rep2

source_name: iP+A ESC line

value: iP+A-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Atoh1+Venus transgenes

value: No treatment


title: JM11 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: JM09 plasma_NSCLC_rep2b OA adv

description: plasma_NSCLC_rep2b OA adv


title: JM13 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: JM12 plasma_Control OA adv

description: plasma_Control OA adv


title: P+A_Ctrl_Rep1


title: P+A_Dox_Rep2


title: GPA_Dox_Rep1


title: GPA_Ctrl_Rep1


title: P+A_Dox_Rep1


title: G+P_Dox_Rep2

source_name: iG+P ESC line

value: iG+P-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Venus transgenes


title: Mouse spleen iNKT cell sample 1

description: iNKT cells from mouse spleen (sample 1)

tag: tissue

value: Spleen

value: iNKT cells


title: Mouse lymph node iNKT cell sample 2

description: iNKT cells from mouse lymph node (sample 2)

value: 5 weeks

value: WT


title: G+P_Ctrl_Rep2

tag: cell line


title: GPA_Ctrl_Rep2


title: JM07 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: G+P_Ctrl_Rep1


title: G+P_Dox_Rep1


title: JM05 plasma_NSCLC_rep1b OA adv

description: plasma_NSCLC_rep1b OA adv


title: G+A_Dox_Rep1

source_name: iG+A ESC line

value: iG+A-derived EB cells

value: Dox-inducible mESCs with Gfi1+Atoh1+Venus transgenes


title: JM08 plasma_Control-rep2a OA adv

description: plasma_Control-rep2a OA adv

value: Female


title: G+A_Dox_Rep2


title: JM10 plasma_Control_rep2c OA adv

description: plasma_Control_rep2c OA adv


title: G+A_Ctrl_Rep2


title: JM04 plasma_Control_rep1a OA adv

description: plasma_Control_rep1a OA adv


title: G+A_Ctrl_Rep1


title: JM03 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: JM02 plasma_Control OA adv

description: plasma_Control OA adv


title: Pou4f3_Dox_Rep2

source_name: iPou4f3 ESC line

value: iPou4f3-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Venus transgenes


title: JM01 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: JL99 plasma_NSCLC OA adv

description: plasma_NSCLC OA adv


title: SAMPLE 32_Chondrocyte, Rot/A, physioxia, euglycemia (rep4)

city: Ithaca

first: Michelle

middle: L

last: Delco

state: NY

address: 930 Campus Road C3-117 VMC

department: Clinical Sciences

institute: Cornell University College of Veterinary Medicine

data_processing:
Raw data from each experiment was downloaded from the ViiA 7 Real-Time PCR System as an .xlsx file. Raw CT values greater than that of the non-template controls were ommitted at this step and appear as blank cells. The values reported in the Matrix non-normalized (raw CT) sheet were calculated by veraging the three raw CT values to get mean CT per target. The values reported in the Matrix normalized sheet (ΔCT(GAPDH)) were calcuated by subtracting the mean CT of the target gene from the mean CT of GAPDH. The values reported in Fold Change 2^-(ΔΔCT(GAPDH)) sheet were calculated by subtracting the ΔCT(experimental) from the ΔCT(control). Control conditions were non-stimulated chondrocytes cultured in physioxia and euglycemia (samples 8,10, 23, 31 for replicates 1,2,3,4 respectively). *Samples 1,2,3,4 were removed from statistical anaylses because it was later determined that these chondrocytes were not cultured at hyperglycemia- this was due to a techincal mistake in making the media for this experiment and the actual concentration of glucose is unkown for these samples.
Matrix normalized ΔCT(GAPDH) compares the target gene signal to that of the housekeeping gene (GAPDH) in the same conditions. Fold Change 2^-(ΔΔCT(GAPDH)) is the log transformed comparison of the target gene signal in experimental vs. control conditions.

organism: Mus

label_protocol: The High-Capacity cDNA Reverse Transcription Kt (ThermoFisher, Catalog Number: 4368814) was used to generate cDNA according to manufactuer protocol. Sample RNA concentration was determined by Nanodrop. Three reactions (10 uL 2x RT Master mix + 10 uL sample) were performed for each sample. Thermocycler conditions: Step 1- 25C, 10 min Step 2- 37C, 120 min Step 3- 85C, 5 min Step 4: 4C, until samples were removed. For RT-qPCR,  sample cDNA was combined with TaqMan Fast Advanced Master Mix (ThermoFisher Catalog #: 4444557) according to manufactuer protocol and added to our custom TaqMan Array Plate. The plates were loaded into the ViiA 7 Real-Time PCR system and a Fast Block 96-well experiment was run according to the ViiA instrument user guide.

growth_protocol: Cartilage were harvested from the acetabulofemoral joints of 5-day-old UBC mCherry mice according to standard protocol (see https://doi.org/10.1038/nprot.2008.95). Briefly, cartilage was digested in a Collagenase D (0.5 mg/ml) solution overnight and then seeded at a density of 8 x 10^3 cells per cm. Isolated chondrocytes were incubated at 37C, 5% CO2 and either 5% O2 or 21% CO2. Prior to total RNA extraction, passage 3 chondrocytes were plated on a 12-well plate at a density of ~120,000 chondrocytes/well.

extract_protocol: Total RNA was isolated with the RNeasy Mini Kit (Qiagen Cat. No. / ID: 74104) according to manufactuer protocol.

treatment_protocol: Twelve-72 hours (at ~85% confluence) after plating the chondrocytes for experimentation, chondrocytes were either cultured in serum-free media for 12 hours (no stim) or stimulated with rotenone/antimycin A (0.5 µM/0.5µM) in serum-free media for 12 hours. All wells were aspirated of media, rinsed gently with PBS three times, and then trypsinized to remove cells for RNA isolation.

value: Chondrocyte

tag: stimulation condition

value: rotenone/antimycin (0.5 μM/0.5 μM)

tag: oxygen concentration

value: physioxia

tag: glucose concentration

value: euglycemia

tag: condition

value: 5% oxygen, 0.45 g/L glucose


title: Pou4f3_Ctrl_Rep2

tag: cell type

value: EBs at day 6

value: No treatment


title: Pou4f3_Dox_Rep1

value: 2 µg/ml doxycycline for 48h


title: Gfi1_Dox_Rep2

source_name: iGfi1 ESC line

value: iGfi1-derived EB cells

value: Dox-inducible mESCs with Gfi1+Venus transgenes


title: JM06 plasma_Control_rep1c OA adv

description: plasma_Control_rep1c OA adv

value: Male


title: Gfi1_Dox_Rep1


title: SAMPLE 31_Chondrocyte, no stim, physioxia, euglycemia (rep4)

value: no stim


title: SAMPLE 29_Chondrocyte, no stim, hyperoxia, euglycemia (rep4)

value: hyperoxia

value: 21% oxygen, 0.45 g/L glucose


title: SAMPLE 30_Chondrocyte, Rot/A, hyperoxia, euglycemia (rep4)


title: Gfi1_Ctrl_Rep2


title: SAMPLE 28_Chondrocyte, no stim, hyperoxia, hyperglycemia (rep4)

value: hyperglycemia

value: 21% oxygen, 1 g/L glucose


title: Gfi1_Ctrl_Rep1


title: SAMPLE 27_Chondrocyte, no stim, physioxia, hyperglycemia (rep4)

value: 5% oxygen, 1 g/L glucose


title: JM00 plasma_Control OA adv

description: plasma_Control OA adv


title: SAMPLE 25_Chondrocyte, Rot/A, physioxia, hyperglycemia (rep4)

value: Chondrocyte


title: SAMPLE 26_Chondrocyte, Rot/A, hyperoxia, hyperglycemia (rep4)

value: rotenone/antimycin (0.5 μM/0.5 μM)


title: Atoh1_Dox_Rep1

source_name: iAtoh1 ESC line

value: iAtoh1-derived EB cells

value: Dox-inducible mESCs with Atoh1+Venus transgenes


title: Atoh1_Ctrl_Rep2


title: Atoh1_Ctrl_Rep1


title: G+A_ChIPAtoh1_Rep1

data_processing:
For quality analyses, reads were checked using using FastQC and MultiQC. Illumina contaminant adapter sequences were removed using Trimmomatic.
Reads were aligned to the UCSC mm9 assembly of the mouse genome using Bowtie 2 with the very-sensitive option.
For data filtering steps, PCR duplicates reads were removed using Picard Tool’s MarkDuplicates command (Broad Institute) and were filtered for MAPQ > = 40 using SAMtools. Reads aligned to ENCODE blacklist regions regions (Consortium 2012) were removed using BEDTools. Unmapped, secondary, and supplemental read alignments were filtered using SAMtools.
Peak calling was performed by first estimating the fragment size using cross-correlation analysis from the phantompeakqualtools software package. Peaks were called using MACS 2 on merged sample replicates against merged control replicates. The following arguments were used: --g mm --keep-dup all -s <read length> --nomodel --shift 0 --extsize <fragment size> -p 0.05 -B --SPMR.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include: 1) narrowPeak files that were generated using MACS2 at the peak-calling step. Please note that authors combined all reads from biological replicates for the analyses shown in the paper. 2) BigWig files containing the Input-subtracted ChIP-factor read counts / density that were generated using BamCompare from DeepTools. 3) Bed files containing the ChIP-Seq peak summit position only for peaks that shown a normalise read count over input higher than 0,05. Please note that authors only used these filtered peaks for downstream analyses shown in the paper.

extract_protocol:
6 days old EBs treated with 2 µg/ml doxycycline at day 4 were dissociated using 0.25% trypsin-EDTA (Invitrogen) in PBS and around 15x10^6 to 20x10^6 of cells were aliquoted into 15ml falcon tubes for fixation. Cells in each aliquot were fixed at room temperature for 12 minutes on 1% of formaldehyde solution (37% formaldehyde, Sigma-Aldrich). Formaldehyde was quenched with glycine (final 0.125 M) for 5 minutes at room temperature. Samples where then washed once with cold PBS containing protease inhibitors (cOmplete protease inhibitor cocktail, Roche). After, cells were centrifuged at 500 g and pellets were snap frozen on dry ice followed by storage at -80C until further use. The pellet for each sample (~20x10^6 of cells) was thawed and nuclei were isolated by re-suspension in lysis buffer (5 mM Pipes pH 8.0, 85 mM KCl, 1% NP40) with fresh protease inhibitors (cOmplete protease inhibitor cocktail, Roche) for 20 minutes on ice followed by brief vortexing and centrifugation at 500 g for 10 minutes at 4C. The nuclear pellet was re-suspended in 300 ul IP buffer (0.5% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, fresh protease inhibitors) and sheared by sonication (BioRuptor Pico, Diagenode) down to ~200-300 bp fragments using a total of 5-14 cycles of: 10 pulses of sonication on the ‘‘high’’ setting, each followed by 30 s off. Samples were then diluted in IP buffer without SDS, then 10 mg of the following antibodies was added for overnight incubation at 4C on a rotator: Monoclonal anti-flag M2 antibody (F1804, Sigma); Myc tag antibody-ChIP Grade (ab9132, Abcam); Anti-Gfi1 antibody (ab21061, Abcam). Dynabeads-ProteinG (Life Technologies) were blocked for 1-hour in 0.5% BSA in IP buffer with protease inhibitors, prior to incubation with the sonicated antibody bound chromatin suspensions. Bead-chromatin complexes were then serially washed for 5 minutes each with the following solutions: IP buffer (150 mM NaCl), followed by IP buffer with high salt concentration (500 mM NaCl), then 1 wash with washing-buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate, 1 mM EDTA), followed by 2 washes with TE (10 mM Tris, 1 mM EDTA). The DNA-protein complex was then eluted from beads by incubation with 100 ml of elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0) for 30 minutes at 65C, vortexing every 10 minutes, followed by magnet extraction of beads. The beads were re-washed with 150 ml TE with 1% SDS, magnet extracted, and the TE with remaining DNA solution was added to the eluted samples, followed by 65C overnight incubation to reverse crosslink the DNA-protein complexes. The dissociated DNA and protein solution was then treated with 4U of proteinase K (NEB) at 37C for 2 hours. DNA was isolated with SeraMag beads, using 450 ml SeraMag bead solution and 225 ml of 30% PEG in 1.25 M NaCl. After bead purification, DNA was re-suspended in 30 µl of ddH2O (DNase/RNase free) and for each ChIP sample, DNA concentration was estimated using Qubit fluorometric quantification (Invitrogen) before being stored at 80C.
8-10 ng of ChIP DNA was used for each sample. DNA ends were blunted by treatment with 5 µl T4 DNA ligase buffer (NEB), 2 µL 10 mM dNTP’s, 0.5 µl end repair mix (0.72 U T4 DNA polymerase, 0.24 U Klenow Fragment, 2.4 U T4 DNA Polynucleotide Kinase), up to 50 µl with ddH2O (DNase/RNase free). Samples were incubated for 30 minutes at 20C, and then purified with addition of 50ul SeraMag bead solution and 50 µl 30% PEG solution (in 1.25 M NaCl). DNA was eluted in 16.5 ul of TE/10 (10 mM TrisCl pH 8.0, 0.1 mM EDTA). DNA was then A-tailed at the 3’ ends by treating the eluate with 2 µl 10X NEB Buffer 2, 1 µl 4 mM dATP, 0.5 µl Klenow 3’ to 5’ exonuclease minus (NEB) in a total volume of 20 µl. Reaction was incubated at 37C for 30 minutes. Before adapter ligation, TruSeq adapters (Illumina) were first annealed by re-suspending each adapter at 100 mM (in 10 mM Tris-HCl pH7.8, 0.1 mM EDTA pH 8.0, 50 mM NaCl) and mixing them at a 1:1 ratio. Adaptor annealing occurred using a program of 2 min at 95C, 70 cycles of 30 s (95C decreasing by 1C each cycle). Annealed adaptors were diluted 1:200 (0.25 mM final) and then 1 µl was used for ligation reaction containing 20 µl of the A-tailed DNA, 1.5 µl Quick Ligase (2,000 U/ml NEB) and 2.5 µl of H2O. The reaction was incubated 20 minutes at room temperature and stopped by addition of 5 µL of 0.5 M EDTA pH 8.0. Next, DNA was purified using 50 µl SeraMag bead mix and 50 µl 30% PEG (in 1.25 M NaCl) and eluted in 15.5 µl of TE/10. Next, the adapter ligated DNA was amplified using the following protocol: 15 µl adaptor-ligated DNA, 1 µl TruSeq primer cocktail (0.25 mM), 15 µl 2X Kapa HiFi HotStart ready mix. The Libraries were amplified with the following protocol: 45 s at 98C, 5 cycles of (15 s at 98C, 30 s at 63C, 30 s at 72C), 1 minute of 72C, hold at 4C. After pre-amplification of the library, a size selection step was performed to obtain DNA fragments between 300 and 500 bp using the following procedure: 0.9X beads were added to ChIP DNA After 15 minutes incubation and 10 minutes magnet extraction, the supernatant was transferred to new tube and beads discarded. Then 0.2X beads were added to the solution, incubated 15 minutes followed by 10 minutes magnet extraction and beads re-suspension in 11.5 µl TE/10. 11 µl of pre-amplified and size selected DNA was further amplified with 1 µl TruSeq primer cocktail, 20 µl 2X Kapa HiFi HotStart ready mix, and 8 µl H2O using a PCR program of 45 s at 98C, 9-11 cycles of (15 s 98C, 30 s 63C, 30 s 72C), 1-minute 72C. After amplification, the DNA was isolated using SeraMag bead purification. Libraries were assessed using Agilent High Sensitivity D1000 ScreenTape System on an Agilent 2200 TapeStation. Finally, libraries were pooled at equal concentration and sequenced on the Illumina HiSeq 4000 platform.

treatment_protocol: 2 µg/ml doxycycline for 48h

tag: chip antibody

value: Flag

value: iG+A-derived EB cells

value: Dox-inducible mESCs with Gfi1+Atoh1+Venus transgenes


title: Pou4f3_Ctrl_Rep1

value: iPou4f3-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Venus transgenes

value: EBs at day 6

value: No treatment


title: P+A_ChIPPou4f3_Rep1

value: Myc

value: iP+A-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Atoh1+Venus transgenes

value: 2 µg/ml doxycycline for 48h


title: SAMPLE 23_Chondrocyte, no stim, physioxia, euglycemia (rep3)

value: no stim

value: physioxia

value: euglycemia

value: 5% oxygen, 0.45 g/L glucose


title: SAMPLE 24_Chondrocyte, Rot/A, physioxia, euglycemia (rep3)

value: Chondrocyte

value: rotenone/antimycin (0.5 μM/0.5 μM)


title: SAMPLE 21_Chondrocyte, Rot/A, physioxia, hyperglycemia (rep3)

value: hyperglycemia

value: 5% oxygen, 1 g/L glucose


title: SAMPLE 20_Chondrocyte, no stim, hyperoxia, hyperglycemia (rep3)

value: hyperoxia

value: 21% oxygen, 1 g/L glucose


title: P+A_ChIPAtoh1_Rep1

value: Flag


title: SAMPLE 19_Chondrocyte, Rot/A, hyperoxia, hyperglycemia (rep3)


title: SAMPLE 18_Chondrocyte, no stim, hyperoxia, euglycemia (rep3)

value: 21% oxygen, 0.45 g/L glucose


title: Atoh1_ChIPAtoh1_Rep1

value: iAtoh1-derived EB cells

value: Dox-inducible mESCs with Atoh1+Venus transgenes

value: EBs at day 6


title: Pou4f3_ChIPPou4f3_Rep1

value: Myc

value: iPou4f3-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Venus transgenes


title: GPA_ChIPGfi1_Rep1

value: iGPA-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Atoh1+Venus transgenes

value: 2 µg/ml doxycycline for 48h


title: Atoh1_Dox_Rep2


title: SAMPLE 17_Chondrocyte, Rot/A, hyperoxia, euglycemia (rep3)

value: Chondrocyte

value: euglycemia


title: G+P_Input_Rep2

value: iG+P-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Venus transgenes


title: GPA_ChIPPou4f3_Rep1


title: G+A_Input_Rep2

value: iG+A-derived EB cells

value: Dox-inducible mESCs with Gfi1+Atoh1+Venus transgenes


title: SAMPLE 15_Chondrocyte, Rot/A, hyperoxia, hyperglycemia (rep2)

value: rotenone/antimycin (0.5 μM/0.5 μM)

value: hyperoxia

value: hyperglycemia

value: 21% oxygen, 1 g/L glucose


title: SAMPLE 16_Chondrocyte, no stim, hyperoxia, euglycemia (rep2)

value: no stim

value: 21% oxygen, 0.45 g/L glucose


title: P+A_Input_Rep2

value: iP+A-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Atoh1+Venus transgenes

value: EBs at day 6


title: SAMPLE 22_Chondrocyte, no stim, physioxia, hyperglycemia (rep3)

value: physioxia

value: 5% oxygen, 1 g/L glucose


title: SAMPLE 14_Chondrocyte, Rot/A, hyperoxia, euglycemia (rep2)

value: Chondrocyte


title: Pou4f3_Input_Rep2

value: iPou4f3-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Venus transgenes

value: 2 µg/ml doxycycline for 48h


title: SAMPLE 13_Chondrocyte, no stim, hyperoxia, hyperglycemia (rep2)


title: Atoh1_Input_Rep2

value: iAtoh1-derived EB cells

value: Dox-inducible mESCs with Atoh1+Venus transgenes


title: G+P_Input_Rep1

value: iG+P-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Venus transgenes


title: GPA_Input_Rep2

value: iGPA-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Atoh1+Venus transgenes


title: SAMPLE 9_Chondrocyte, no stim, physioxia, hyperglycemia (rep2)

value: no stim

value: hyperglycemia


title: P+A_Input_Rep1

value: iP+A-derived EB cells


title: SAMPLE 10_Chondrocyte, no stim, physioxia, euglycemia (rep2)

value: euglycemia

value: 5% oxygen, 0.45 g/L glucose


title: G+A_Input_Rep1

value: iG+A-derived EB cells

value: Dox-inducible mESCs with Gfi1+Atoh1+Venus transgenes

value: EBs at day 6


title: SAMPLE 12_Chondrocyte, Rot/A, physioxia, euglycemia (rep2)

value: Chondrocyte

value: rotenone/antimycin (0.5 μM/0.5 μM)

value: physioxia


title: Atoh1_Input_Rep1

value: iAtoh1-derived EB cells

value: 2 µg/ml doxycycline for 48h


title: SAMPLE 8_Chondrocyte, no stim, physioxia, euglycemia (rep1)


title: SAMPLE 11_Chondrocyte, Rot/A, physioxia, hyperglycemia (rep2)

value: 5% oxygen, 1 g/L glucose


title: SAMPLE 7_Chondrocyte, no stim, hyperoxia, euglycemia (rep1)

value: hyperoxia

value: 21% oxygen, 0.45 g/L glucose


title: GPA_ChIPAtoh1_Rep1

value: Flag

value: iGPA-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Atoh1+Venus transgenes


title: SAMPLE 4*_Chondrocyte, Rot/A, physioxia, hyperglycemia (rep1)

value: hyperglycemia


title: Pou4f3_Input_Rep1

value: iPou4f3-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Venus transgenes


title: SAMPLE 5_Chondrocyte, Rot/A, hyperoxia, euglycemia (rep1)

value: euglycemia


title: SAMPLE 3*_Chondrocyte, Rot/A, hyperoxia, hyperglycemia (rep1)

value: 21% oxygen, 1 g/L glucose


title: SAMPLE 6_Chondrocyte, Rot/A, physioxia, euglycemia (rep1)

value: 5% oxygen, 0.45 g/L glucose


title: GPA_Input_Rep1

value: EBs at day 6


title: G+P_ChIPPou4f3_Rep2

value: Myc

value: iG+P-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Venus transgenes


title: P+A_ChIPPou4f3_Rep2

value: iP+A-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Atoh1+Venus transgenes

value: 2 µg/ml doxycycline for 48h


title: Symptomatic5

city: New Orleans

middle: Cooper

last: Woods

state: LA

address: 1430 Tulane Avenue

department: Physiology

institute: Tulan

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
For abundance measurements, single-end reads were aligned to Homo_sapiens.GRch38.76 transcriptome with RSEM(v.1.1.0)
Assembly: Homo_sapiens.GRCh38.76
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Carotid

extract_protocol:
Carotids obtained from patients undergoing carotid endarterectomy and flash frozen in liquid nitrogen.  RNA was harvested using the Qiagen miReasy Mini Kit (Cat#217004). rRNA was removed using Ribo-Zero rRNA removal mix.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

value: carotid

tag: symptomatic status

value: symptomatic

tag: molecule subtype

value: Ribosome-depleted RNA


title: Symptomatic6


title: SAMPLE 1*_Chondrocyte, no stim, hyperoxia, hyperglycemia (rep1)

value: Chondrocyte

value: no stim

value: hyperoxia


title: P+A_ChIPAtoh1_Rep2

value: Flag


title: Symptomatic4


title: Symptomatic3


title: Pou4f3_ChIPPou4f3_Rep2

value: iPou4f3-derived EB cells

value: Dox-inducible mESCs with Pou4f3+Venus transgenes


title: Symptomatic2


title: Atoh1_ChIPAtoh1_Rep2

value: iAtoh1-derived EB cells

value: Dox-inducible mESCs with Atoh1+Venus transgenes


title: Symptomatic1


title: GPA_ChIPPou4f3_Rep2

value: Myc

value: iGPA-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Atoh1+Venus transgenes

value: EBs at day 6


title: Asymp5

value: asymptomatic


title: GPA_ChIPAtoh1_Rep2

value: 2 µg/ml doxycycline for 48h


title: Asymp4

value: carotid


title: G+P_ChIPPou4f3_Rep1

value: iG+P-derived EB cells

value: Dox-inducible mESCs with Gfi1+Pou4f3+Venus transgenes


title: Asymp2

value: Ribosome-depleted RNA


title: Asymp3


title: SAMPLE 2*_Chondrocyte, no stim, physioxia, hyperglycemia (rep1)

value: Chondrocyte

value: no stim

value: physioxia

value: hyperglycemia

value: 5% oxygen, 1 g/L glucose


title: Asymp1


title: leukemia cell-THP1-NC

city: wenzou

first: zhou

last: bin

address: Xuefubei Street, Ouhai District, Wenzhou

institute: The First Afliated Hospital of Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37
Supplementary_files_format_and_content: counts and FPKM values for each Sample

source_name: leukemia cell

extract_protocol:
cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: THP-1 monocytic leukemia cell line

tag: treatment

value: untreated


title: G+A_ChIPAtoh1_Rep2

value: Flag

value: iG+A-derived EB cells

value: Dox-inducible mESCs with Gfi1+Atoh1+Venus transgenes


title: NKT_mm_Thymus_St3_1: Mouse thymus stage 3 iNKT cell sample 1

description: Stage 3 iNKT cells from mouse thymus (sample 1)

data_processing:
Sequencing read demultiplexing, aligning to the mm10 mouse reference genome, barcode processing, and UMI counting were performed using the 10X Genomics Cell Ranger (v2.0.1) pipeline.
Estimated number of cells captured per sample were between 1,296-3,290 with 34,258-95,264 mean reads per cell, 764-1,892 median genes per cell, and 1,266-6,412 median UMI counts per cell.
A filtered gene-barcode matrix for each sample containing only detected cellular barcodes was generated and subsequently analyzed using the R Seurat package.
Samples have 3 fastq files associated with them with a tag in the filename, namely I1, R1, and R2. The I1 contains the sample index. The R1 contains the 10x barcode (16 base pairs) followed by UMI (10 bp). The R2 contains the transcript reads.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger filtered gene-barcode matrix outputs of cell barcode, gene name, and UMI count matrix files.

source_name: Thymus

extract_protocol:
Murine thymi were harvested from 5 weeks old C57BL/6 mice or Vα14 transgenic mice. The thymus iNKT cells were enriched by positive selection using biotinylated antibodies against PE. Stage 1(CD24-CD44-NK1.1-), stage 2(CD24-CD44+NK1.1-) and stage 3(CD24-CD44+NK1.1+) were sorted  from 5 weeks C57BL/6 mouse thymus, and Stage 0 iNKT cells (CD24+NK1.1-) were sorted from 5 weeks old Vα14 transgenic mouse thymus through BD FACS AriaII.
Single cell sequencing libraries were generated using the 10X Genomics Chromium Single Cell 3’ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller. Reverse transcription of the GEM (GEM-RT) was performed in a Thermocycler (Veriti™ 96-Well Fast Thermal Cycler, Applied Biosynthesis; 53 °C 45 min, 85 °C 5 min, 4 °C hold). cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) with the same Thermocycler (98 °C 3 min; 98 °C 15 sec, 67 °C 20 sec, 72 °C 1 min, repeat 12 cycles; 72 °C 1 min, 4 °C hold). Amplified cDNA is cleaned up with SPRIselect Reagent Kit (Beckman Coulter) and followed by library construction procedure, including fragmentation, end repaired, adaptor ligation, and library amplification. A Bioanalyzer (Agilent) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using paired-end flow cell: Read 1, 26 cycles, i7 index 8 cycles; Read 2: 110 cycles.

value: Thymus

tag: age

value: 5 weeks

value: Invariant natural killer T cells (iNKT) cells


title: NKT_mm_Thymus_St2_2: Mouse thymus stage 2 iNKT cell sample 2

description: Stage 2 iNKT cells from mouse thymus (sample 2)


title: NKT_mm_Thymus_St0_2: Mouse thymus stage 0 iNKT cell sample 2

description: Stage 0 iNKT cells from mouse thymus (sample 2)

value: Va14 transgenic (C57BL/6 background)

value: Invariant natural killer T cells (iNKT)


title: NKT_mm_Thymus_St1_1: Mouse thymus stage 1 iNKT cell sample 1

description: Stage 1 iNKT cells from mouse thymus (sample 1)


title: NKT_mm_Thymus_St1_2: Mouse thymus stage 1 iNKT cell sample 2

description: Stage 1 iNKT cells from mouse thymus (sample 2)


title: NKT_mm_Thymus_St2_1: Mouse thymus stage 2 iNKT cell sample 1

description: Stage 2 iNKT cells from mouse thymus (sample 1)


title: NKT_mm_Thymus_St0_1: Mouse thymus stage 0 iNKT cell sample 1

description: Stage 0 iNKT cells from mouse thymus (sample 1)


title: S6

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the bovine reference genome ARS-UCD1.2 using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Assembly: Bovine genome assembly: (ARS-UCD1.2)
Supplementary files format and content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Bos taurus

source_name: peripheral white blood cells

extract_protocol:
Total RNA was isolated and purified using TRIzol™ LS Reagent. RNA quantiy and quality were determined using Nanodrop One and Agilent Bioanalyzer. All samples had RNA integrity number (RIN) values > 8.
All the RNA-sequencing procedures were performed by Macrogen (Korea). Libraries were sequenced using Illumina’s HiSeq 2000.

value: peripheral white blood cells

tag: breed

value: Holstein

value: non-pregnant


title: S9


title: S5

value: pregnant


title: S7


title: S8


title: S10


title: S4