title: T-ALL-cell-from mouse240

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to mm10 using HISAT2 to generate bam files
Counts aligns reads per gene with HTSeq
Differentially expressed gene list was obtained by using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq-normalized read counts; DEseq2-differentially expressed genes

source_name: T-ALL cell from mouse, Testa lab

growth_protocol: primary thymic T cells were harvested and directed lysed with Trizol.

extract_protocol:
RNA was extract with Trizol, and purified via Qiagen RNeasy column
Illumina stranded mRNA library prep kit was used
mRNA was enriched by using polyT beads, heat fragmentated, then reverse transcribled to cDNA.  Illumina adapters were ligated to the cDNA and PCR was performed to get the final library.

tag: genotype

value: Lck-Akt2;Dlx5 transgenic

value: Acute T-cell lymphoblastic lymphoma


title: RPE1_single_MidS_10_scRepli-seq

status: Public on Oct 07 2020

type: SRA

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

library_source: genomic

data_processing:
Library strategy: scRepli-seq
Single-cell data (FACS sorted samples): sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. We performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.  Single-cell data (samples collected by the micromanupitator): sequence reads were trimmed to remove the WGA4 universal sequences using seqtk program ("seqtk trimfq -b 30 -e 30", trimming 30bp of both 5' and 3' ends) before mapping.
Trimmed reads were mapped into hg19 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). Duplicated reads mapped into hg19 were removed by using picard tool and the reads overlapped with hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. Sequence reads were saved as a GenomicRanges object (data can be loaded by R program).
For the analysis of single mid-S cell (sample collected by micromanupitator), we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on the M-phase control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
Please see our scRepli-seq pipeline (https://github.com/kuzobuta/scRepliseq-Pipeline) for the further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: GenomirRanges object files including the mapped reads (GenomicRange_Format_data_set.zip) and README.txt describes the information of each sample.
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
For single-cells samples collected by FACS, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu). For single-cell samples collected by the micromanipulator, sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a WGA4 kit (Sigma, WGA4).
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).

tag: cell line

tag: cell type

value: Epithelial cells immortalized with hTERT

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: single-cell collection method

value: FACS

tag: cell cycle phase

value: MidS


title: T-ALL-cell-from mouse242

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

country: USA

institute: Fox Chase Cancer Center

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus


title: T-ALL-cell-from mouse352


title: Wild-type-T-cell-from mouse3

description: wild type

source_name: Primary T-cell from mouse, Testa lab

value: Wild-type

value: Primary T-cells


title: RPE1_single_MidS_09_scRepli-seq


title: Wild-type-T-cell-from mouse2

description: wild type


title: 352-PKF_S27_L001

description: WNT inhibitor treated

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to mm10 using HISAT2 to generate bam files
Counts aligns reads per gene with HTSeq
Differentially expressed gene list was obtained by using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq-normalized read counts,EdgeR-differentially expressed genes

molecule: total RNA

source_name: WNT inhibitor treated

growth_protocol: LCK-Akt2; Dlx5 double positive T-ALL cells were maintained under IMDM with 20% FBS

treatment_protocol: Cells were treated with β-Catenin/Tcf Inhibitor II, PKF118-310 at the indicated time/concentrations in the manuscript

value: T-ALL

value: Akt2;Dlx5 double transgenic


title: RPE1_single_MidS_15_scRepli-seq


title: RPMs

type: RNA

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

institute: Kyoto University

description: Gene expression data from resident peritoneal macrophages in peritoneal exudate of 8 weeks of postnatal C57BL/6J mice

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

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

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: Resident peritoneal macrophages

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit（Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The cells were centrifuged at 200 × g for 5 min, seed cells on a 10 centimeters dish in plenty of warm complete RPMI 1940 media. Allow to sit for 2h at 37 degrees with 5% carbon dioxide and then wash with warm PBS to remove unwanted cells, macrophages were gently scraped for detachment.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cRNA.

treatment_protocol: Fill a 1cc syringe with 3 % thioglycollate. Attach a 7 needle and inject 1 mL of the solution into the peritoneal cavity of each mouse. Return mouse to its cage and allow the immune response to proceed for 3 days.

value: Macrophage

tag: background strain

tag: age

value: 8 weeks


title: 352-PKF_S27_L002

description: WNT inhibitor treated


title: 352-CON_S24_L001

description: control

source_name: control


title: 352-CON_S24_L002

description: control


title: TGPMs

description: Gene expression data from thioglycolate-elicited peritoneal macrophages in peritoneal exudate of 8 weeks of postnatal C57BL/6J mice


title: 242-PKF_S3_L002

description: WNT inhibitor treated


title: 242-PKF_S3_L001

description: WNT inhibitor treated


title: Wild-type-T-cell-from mouse4

description: wild type


title: RPE1_single_MidS_06_scRepli-seq


title: 240-PKF_S15_L001

description: WNT inhibitor treated


title: RPE1_single_MidS_03_scRepli-seq


title: RPE1_single_MidS_05_scRepli-seq


title: RPE1_single_MidS_02_scRepli-seq


title: RPE1_single_MidS_01_scRepli-seq


title: RPE1_single_MidS_04_scRepli-seq


title: 240-PKF_S15_L002

description: WNT inhibitor treated


title: Wild-type-T-cell-from mouse1

description: wild type

source_name: Primary T-cell from mouse


title: RPE1_single_MidS_08_scRepli-seq


title: 240-CON_S13_L002

description: control


title: TCF-antibody-ChIP

description: cells ChIP with TCF antibody

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to mm10 using bowtie2 to generate bam files
MACS2 was used for peak calling
Nearest genes around peaks were annotated
Genome_build: mm10
Supplementary_files_format_and_content: peaks.tsv, genes.tsv

source_name: Testa lab-made-cell line

extract_protocol:
Active Motif ChIP-it kit was used. ChIP grade TCF antibody was used to immunoprecipitate the bound DNA fragments.
ChIP seq library was made by using NEB DNA ultraII kit
10ng input or pulldown DNA was used to do end-repair, A-tailing, Adapter ligation and PCR amplification.

treatment_protocol: Cells were fixed using final 1% formaldehyde, neutralized with glycine buffer. DNA as sonicated to 150-800bp smear using Covaris S200.

tag: chip antibody

value: anti-TCF (cell signaling TCF1/TCF7 (C63D9) Rabbit mAb #2203)


title: Chd8_HET_6mo_cortex_RNA_REP6

city: Chapel Hill

first: Travis

last: Ptacek

state: NC

address: 5109 Neuroscience Research Building

institute: UNC Neuroscience Center Bioinformatics Core

data_processing:
Sequencing and base calling on the Illumina HiSeq 2500
Quality filtering was performed using FASTX v0.0.14 fastq_quality_filter for reads with 90% of bases having a quality of 20+
Reads aligned to reference genome using STAR v2.5.2b
Gene expression quantified using salmon v0.11.3
Differential gene expression tested using DESeq v1.22.2
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of VST normalized counts from DESeq2 for all genes and samples

source_name: dissected cortex

extract_protocol:
Rneasy Plus Mini Kit (Qiagen)
TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions

tag: time point

value: 6 months

tag: strain

tag: tissue

value: dissected cortex


title: sonicated-DNA-input

description: DNA sonicated as ChIP control

value: none (sonicated-DNA-input)


title: 240-CON_S13_L001

description: control


title: Chd8_HET_E14.5_cortex_RNA_REP6

value: Embryonic day 14.5


title: RPE1_single_G1_02_scRepli-seq


title: RPE1_single_G1_03_scRepli-seq


title: RPE1_single_MidS_07_scRepli-seq


title: Chd8_HET_1mo_cortex_RNA_REP6

value: 1 month


title: Chd8_HET_1mo_cortex_RNA_REP5


title: Chd8_HET_12mo_cortex_RNA_REP5

value: 12 months


title: RPE1_single_G1_01_scRepli-seq

value: Epithelial cells immortalized with hTERT

value: Single cell


title: Proband_2

type: genomic

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Furthermore, the copy number of altered regions (CNAs) were calculated, the data was normalized to reference model (Thermo Fisher) of baseline reference intensities NA 33 (hg19/CRCh37). The copy number states (CNS) and their breakpoints were determined with the use of the Hidden Markov Model (HMM) software package. The threshold level of log2 ratio ≥0.5 and ≤0.5 were used respectively for the categorization of the altered chromosomal regions as copy number variation (CNV) gains and losses. The minimal number of probes was applied to determine the CNAs: 50 probes for duplication (gain); 25 probes for deletion (loss). To further identify the genes involved in the CNVs two databases were applied: the UCSC database (http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org). MLPA tests were also performed on the parents of the sample to determine carrier status.

source_name: peripheral blood mononuclear cells

label_protocol: The 250 ng of the genomic DNA was analysed in accordance with the manufacturers' protocols. The study based on an analysis of scanned data files which was generated with the Chromosome Analysis Suite v 3.3 (ChAS, Thermo Fisher, Waltham, MA).

extract_protocol: The researched material was the genomic DNA extracted from peripheral blood (PB) samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The concentration and quality of isolates were determined by spectrophotometry (NanoDrop 8000, Thermo Scientific, Waltham, MA).

tag: subject status

value: patient with 16p11.2 microdeletion syndrome

tag: gender

value: female

value: 2 years

value: peripheral blood mononuclear cells


title: Proband_3

value: male

value: 2 months


title: Chd8_HET_E14.5_cortex_RNA_REP5


title: 242-CON_S1_L001

description: control

value: T-ALL

value: Akt2;Dlx5 double transgenic


title: Chd8_HET_12mo_cortex_RNA_REP4


title: Chd8_HET_6mo_cortex_RNA_REP4


title: Chd8_HET_1mo_cortex_RNA_REP4


title: 242-CON_S1_L002

description: control


title: Chd8_HET_E14.5_cortex_RNA_REP2


title: Chd8_HET_E14.5_cortex_RNA_REP4


title: Proband_1

value: 5.5 years


title: Chd8_HET_6mo_cortex_RNA_REP5

value: 6 months


title: Chd8_HET_12mo_cortex_RNA_REP6

value: dissected cortex


title: Chd8_HET_6mo_cortex_RNA_REP3


title: Chd8_HET_1mo_cortex_RNA_REP3


title: WNT Dawn 23h Rep 3

city: RALEIGH

first: Montana

last: Knight

address: Campus Box 7566

department: Genomic Sciences Graduate Program

institute: North Carolina State University

data_processing:
Trimmed files were aligned using Hisat v2. MH63 (rigw.com). The resulting bam files were then piped to htseq count version 0.6.0. Using the options -f bam, -s reverse,and -m union counts per gene were generated for the annotated genes in MH63. Counts were than normilized to counts per million.
Genome_build: MH63RS1
Supplementary_files_format_and_content: http://rice.hzau.edu.cn/cgi-bin/gb2/gbrowse_details/
Supplementary_files_format_and_content: Raw Counts

organism: Oryza sativa Indica Group

source_name: Rice Leaf Tissue

growth_protocol: An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.

extract_protocol:
Tissue samples were stored at -80C until needed. The leaf tissue samples were first grinded. The tissue then lyophilized at -60C overnight before RNA extractions.Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) with the recommended RLT lysis buffer. The RNA extraction provided protocol was followed the inclusion of DNase step. RNA concentration was then measured with NANOdrop 2000. 2ug of RNA was used with NEBNext Poly(A) Magnetic mRNA isolation kit (NEB). Oligo(dT) attached to magnetic beads isolate mRNA by attaching to ploy(A) modified mRNA
RNA libraries were prepared for sequencing using NEB ultra directional library prep kit

treatment_protocol: Plants were grown in a field setting. WNT were treated with IR heater at night. 24C, 26C, 28C, and 30C rice were treated with field tents for increased night temperatures

tag: group

value: WNT

value: Leaf Tissue

value: Dawn 23h


title: Chd8_HET_E14.5_cortex_RNA_REP3

value: Embryonic day 14.5


title: Chd8_HET_6mo_cortex_RNA_REP1


title: Chd8_HET_E14.5_cortex_RNA_REP1


title: WNT Dawn 23h Rep 1


title: Chd8_HET_12mo_cortex_RNA_REP2

value: 12 months


title: Chd8_WT_12mo_cortex_RNA_REP6

value: WT


title: Chd8_HET_12mo_cortex_RNA_REP3


title: Chd8_HET_6mo_cortex_RNA_REP2


title: Chd8_WT_6mo_cortex_RNA_REP6


title: Chd8_HET_1mo_cortex_RNA_REP2

value: 1 month


title: WNT Dawn 23h Rep 4


title: WNT Dawn 17h Rep 4

value: Dawn 17h


title: Chd8_HET_12mo_cortex_RNA_REP1


title: WNT Dawn 17h Rep 2


title: WNT Dawn 17h Rep 1


title: Chd8_HET_1mo_cortex_RNA_REP1


title: WNT Dawn 23h Rep 2


title: WNT Dawn 14h Rep 4

value: Dawn 14h


title: Chd8_WT_E14.5_cortex_RNA_REP6


title: Chd8_WT_6mo_cortex_RNA_REP4


title: RME1_ChIP_Lower array

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

hyb_protocol: The labeled DNA was speed-vaced and the pellets were resuspended in 104 µl of H2O. 26 µl of Agilent 10X blocking agent and 130 µl of Agilent 2X Hybridization Buffer were added for a total of 260 µl hybridization mix. Samples were heated at 95ºC for 3 minutes and incubated immediately at 37ºC during 30 min. 245 µl were dispensed onto each of the 2x400k Agilent gaskets. The hybridization chambers were assembled and rotated overnight at 65ºC as per the manufecturer's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

data_processing: Data were normalized using Quantile normalization

organism: Candida albicans

source_name: Candida albicans untagged strains

label_protocol: The IP DNA (40 µl out of 50 µl) fragments were blunted with T4 DNA polymerase and ligated to unidirectional linkers. The DNA was amplified by ligation-mediated PCR in the presence of aminoallyl-modified dUTP. Labeling was carried out post-PCR using monoreactive Cy dye N-hydroxysuccinimide esters (Cy5/Cy3 monoreactive dye packs; Amersham Biosciences) that react specifically with the aminoallyl-modified dUTP [5-(3-aminoallyl)-2′ deoxyuridine-5′-triphosphate; Sigma-Aldrich]. Labeled IP DNA from the tagged strain (Cy5) and the untagged control strain (Cy3) were mixed and hybridized to C. albicans tiling arrays (platform GPL17892)

growth_protocol: Cells were grown overnight in YPD medium at 30°C, diluted to an OD600 nm of 0.2 in 50 ml YPD medium supplemented with 40 µg/ml doxycycline and re-grown for 4h at 30ºC.

extract_protocol: PTET-TAP-RME1 (Tagged) and PTET-RME1 (untagged control) were grown overnight in YPD at 30°C, diluted to an OD600 nm of 0.2 in 50 ml YPD medium supplemented with 40 g/ml doxycycline and grown during 4 hours at 30°C.  cultures were treated with 1% formaldehyde (cross-linking) and snap-frozen in liquid nitrogen. Total cell extracts were prepared by bead beating using a FastPrep-24 instrument (MP Biomedicals) with 10 runs during 40 seconds each at 5.5 m/sec and 1 minute on ice in between. Soluble chromatin fragments were prepared by sonicating the extracts 6 times during 20 sec at power 8 (knob position) for an output signal amplitude of 15 (Microns, Peak to Peak) using a probe sonicator (MSE), yielding a majority of ~200-500 bp DNA fragments. Immunoprecipitation was conducted overnight at 4ºC with 500 µl of clarified sonicated extracts and 40 µl of IgG-coated magnetic beads (Dynabeads Pan mouse IgG, Invitrogen), previously prehybed overnight with PBS-0.1% BSA at 4ºC.

tag: sample type

value: PTET-RME1 (untagged control)

tag: modification

value: Immunoprecipitated DNA

value: PTET-TAP-RME1 (Tagged)

source_name: Candida albicans strains expressing a TAP-tagged version of the RME1 gene placed under the control of a doxycycline-inducible promoter


title: RME1_ChIP_Upper array


title: elasatse7days

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

institute: University of Michigan

data_processing:
The Cell Ranger Single Cell Software Suite, version 3.0 was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.
Cloupe files were generated using the Cell Ranger 3.0 version. A description of the pipeline and instructions can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/cellranger
The CellRanger count command was run on the individual Fastq datasets to produce expression data
R package Seurat v3.0 was used for cell filtration, normalization, principal component analysis, variable genes finding, clustering analysis, and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction.Data were then log-normalized for the subsequent analyses. Principal component analysis (PCA) was used for dimension reduction, followed by clustering analysis in principal component analysis space using a graph-based clustering approach. UMAP was then used for the two-dimensional visualization of the identified clusters. The Seurat functions Vlnplot, FeaturePlot, DotPlot and DoHeatmap were used to visualize the gene expression with violin plot, feature plot, dot plot and heatmap, respectively. Markers for a specific cluster against all remaining cells were found by using the Seurat function FindAllMarkers.
Genome_build: Data were mapped to the pre-build mouse reference genome (mm10, version 1.2.0), and the mapping rate of the reads mapped to genome for the three samples was more than 93%.
Supplementary_files_format_and_content: UMAP was then used for the two-dimensional visualization of the identified clusters. The Seurat functions Vlnplot, FeaturePlot, DotPlot and DoHeatmap were used to visualize the gene expression with violin plot, feature plot, dot plot and heatmap, respectively.
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: mouse infrarenal abdominal aortic cells

extract_protocol:
The infrarenal abdominal aortas pooled from five mice in each group were digested with enzyme solution [450 U/ml collagenase type I (Gibco, cat# 17100-017), 125 U/ml collagenase type XI (Millipore Sigma, cat# C7657), 60 U/ml hyaluronidase type I-s (Millipore Sigma, cat# H3506), and 60 U/ml DNase I (Millipore Sigma, cat# DN25)] for 1.5 hours at 37oC. The cell suspension was strained through a 70 μm filter and washed thrice with PBS. The single cells were resuspended in opti-MEM with 10% FBS. The cell suspensions were loaded on a 10x Genomics Chromium instrument to generate single cell gel beads in emulsion (GEMs).
Libraries were prepared using the Chromium Single cell 3' Reagent Kits v2 (CG00052): Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3’ Chip Kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262). Libraries were sequenced on an Illumina HiSeq 4000 using paired-end sequencing with approximately >90% sequencing saturation.

value: 7 days

tag: agent

value: elastase exposure

tag: disease

value: aorta dilation

tag: genotype

value: wild type


title: WNT Dawn 14h Rep 2


title: Chd8_WT_1mo_cortex_RNA_REP4

value: dissected cortex


title: WNT Dawn 17h Rep 3

value: WNT


title: Chd8_WT_12mo_cortex_RNA_REP5


title: TRAP-seq of new OSNs, UNO - closed (R), rep2

city: Aurora

first: Stephen

middle: William

last: Santoro

state: Colorado

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado Denver - Anschutz Medical Campus

description: ribosome-bound RNA

data_processing:
Library strategy: TRAP-seq
FASTQ files were processed using FASTQ groomer.
Groomed FASTQ files were trimmed using Trim Galore! to remove adapters and Trimmomatic to remove low-quality sequences.
Trimmed FASTQ files were aligned to the mouse genome using HISAT2.
HISAT2-produced alignment files were quantified using featureCounts and normalized using Remove Unwanted Variation (RUV) based on control genes.
Gene-specific transcript levels were determined from variance-stabilizing transformation (VST)-normalized count files produced by Deseq2 using RUV-produced batch factors.
Genome_build: mm10
Supplementary_files_format_and_content: txt file contains normalized TRAP-seq transcript counts

source_name: Olfactory epithelium

extract_protocol:
Dissected OEs from UNO-treated, tamoxifen-injected, Ascl1-CreERT2/Ribotag mice were divided in half and homogenized. HA-tagged ribosome/RNA complexes were immunoprecipitated from homogenized half-OEs using anti-HA antibody-bound magnetic beads.
Following rRNA depletion, libraries were prepared from TRAP-isolated transcript samples corresponding to the open and closed sides of mouse OEs using the Ovation RNA-Seq System V2 kit (NuGEN). Libraries were paired-end sequenced (2 × 150 bases) to a depth of ~60 million fragments/sample.

treatment_protocol: Samples are from the open and closed sides of the olfactory epithelia of mice that were UNO-treated at PD14 and tamoxifen-treated at PD28 and 29.

value: Ascl1-CreERT2(+/-); Ribotag(+/+)

tag: Sex

value: female

tag: treatment

value: unilateral naris occlusion (PD14); tamoxifen (PD28, 29)

tag: side

value: open (R)

tag: cell type

value: new olfactory sensory neurons


title: heat-inactive elastase14days

value: 14 days

value: heat-inactive elastase exposure

value: no AAA


title: Chd8_WT_1mo_cortex_RNA_REP6

value: WT

value: 1 month


title: Chd8_WT_6mo_cortex_RNA_REP5

value: 6 months


title: Chd8_WT_1mo_cortex_RNA_REP5


title: TRAP-seq of new OSNs, UNO - closed (L), rep2

description: ribosome-bound RNA

tag: age

value: closed (L)


title: TRAP-seq of new OSNs, UNO - closed (R), rep1

description: ribosome-bound RNA

value: male


title: Chd8_WT_E14.5_cortex_RNA_REP5

value: Embryonic day 14.5


title: TRAP-seq of new OSNs, UNO - closed (L), rep1

description: ribosome-bound RNA


title: Chd8_WT_6mo_cortex_RNA_REP3


title: Chd8_WT_1mo_cortex_RNA_REP3


title: WNT Dusk Rep 2

value: Leaf Tissue

value: Dusk


title: WNT Dawn 14h Rep 3

value: WNT

value: Dawn 14h


title: WNT Dawn 10h Rep 4

value: Dawn 10h


title: WNT Dawn 10h Rep 3


title: elastase14days

value: elastase exposure

value: AAA

value: wild type


title: WNT Dawn 14h Rep 1


title: WNT Dusk Rep 4


title: Chd8_WT_12mo_cortex_RNA_REP4

value: 12 months

value: dissected cortex


title: Chd8_WT_12mo_cortex_RNA_REP2


title: Chd8_WT_E14.5_cortex_RNA_REP4


title: Female 1

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files for 10X V2 samples were generated and demultiplexed using Illumina bcl2fastq 2.18.0.12, and V3 samples were processed with bcl2fastq 2.20.0.422.
In V2 samples, R1 (26p) corresponds to a 16bp cell barcode + 10bp UMI barcode and R2 (98bp) contains the biological read.  For V3 samples, R1 (28bp) contains a 16bp cell barcode + 12bp UMI barcode, and R2 is only 91bp.
A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 3.0.0, GRCm38.93) using 10X Genomics Cellranger count version 3.0.2
Genome_build: GRCm38.93
Supplementary_files_format_and_content: Counts matrices are in Matrix Market CSR format and gzipped.  Rows correspond to genes in the associated features.tsv.gz and columns correspond to cell-barcodes in associated barcodes.tsv.gz

source_name: Ventroposterior hypothalamus

extract_protocol: Suspensions of dissociated cells were washed and suspended in PBS containing 0.04% BSA, and each suspension was processed as follows.  Cells were counted on Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded for capture onto an individual lane of a Chromium Controller (10X Genomics). Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform according to the manufacturer’s protocol (#CG00052) using version 2 (V2) chemistry for the first set of male and female samples and version 3 (V3) chemistry for the second set. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR.

value: Ventroposterior hypothalamus

value: female

tag: 10x chemistry

tag: harvest


title: WNT Dusk Rep 3

tag: time point


title: Mut8_PAX7_E18

city: PARIS

first: Pascal

last: Maire

address: 24 Rue du Fg St Jacques

department: Développement Reproduction et Cancer

institute: Institut Cochin. INSERM U1016, CNRS UMR 8104, U.Paris

hyb_protocol: The cDNA was then hybridized to GeneChip® Mouse Gene 1.0 or 2.0 ST (Affymetrix) at 45 °C for 17 h. After overnight hybridization, the ChIPs were washed using the fluidic station FS450 following specific protocols (Affymetrix).

scan_protocol: the ChIPs were  scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for quality controls

data_processing: Normalisation with R, by project  Project 1 :   WT1_Muscle_E15,WT2_Muscle_E15,WT3_Muscle_E15,Mut1_Muscle_E15,Mut2_Muscle_E15,Mut3_Muscle_E15 → mogene20st_Mm_ENTREZG from Brainarray, version 20, Matrix 3  WT1_Muscle_E18,WT2_Muscle_E18,Mut1_Muscle_E18,Mut2_Muscle_E18 →  mogene10st_Mm_ENTREZG from Brainarray, version 20, Matrix 2  Then we conserved only common genes between the two lists.    Project 2 :  WT1_PAX7_E15, WT2_PAX7_E15, WT3_PAX7_E15, Mut1_PAX7_E15, Mut2_PAX7_E15, Mut3_PAX7_E15, WT6_PAX7_E18, WT7_PAX7_E18, WT8_PAX7_E18, Mut6_PAX7_E18,Mut7_PAX7_E18,Mut8_PAX7_E18   mogene20st_Mm_ENTREZG from Brainarray, version 19, Matrix 1    We strictly follow the Brainrray recomandations for the normalisation by using the affy package they provide for each version of their custom CDF files.

source_name: myogenic stem cells

label_protocol: 50 ng (E18.5 whole back muscles), 2 ng (E15.5 FACS-sorted cells and whole back muscles) or 0.21 ng (E18.5 FACS-sorted cells) of total RNA were reverse-transcribed following the Ovation PicoSL or PicoV2 WTA System (Nugen). Briefly, the resulting double-strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 μg of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5 μg of Sens Target DNA were fragmented and labelled with biotin using Encore Biotin Module kit (Nugen).

growth_protocol: No growth protocol, the tissue is extracted directly from E15 or E18 embryos

extract_protocol: RNA extraction from Pax7-nGFP+ FACS-sorted cells was performed using the Qiagen RNeasy microkit directly after isolation. Whole back muscles required a tissue lyser lyse step in Trizol solution.

treatment_protocol: no treatment

tag: tissue

value: myogenic stem cells

tag: genotype/variation

value: SIX1/4 mutant


title: Chd8_WT_E14.5_cortex_RNA_REP2

value: WT

tag: strain


title: Mut7_PAX7_E18


title: Male 1

value: male


title: Chd8_WT_12mo_cortex_RNA_REP3


title: WNT Dawn 7h Rep 3

tag: group

value: Dawn 7h


title: WNT Dusk Rep 1

value: Leaf Tissue


title: Chd8_WT_12mo_cortex_RNA_REP1


title: Chd8_WT_E14.5_cortex_RNA_REP3

value: Embryonic day 14.5


title: Chd8_WT_1mo_cortex_RNA_REP1

value: 1 month


title: WNT Dawn 10h Rep 2

value: WNT


title: Chd8_WT_6mo_cortex_RNA_REP2

value: 6 months


title: Chd8_WT_E14.5_cortex_RNA_REP1


title: WNT Dawn 10h Rep 1

value: Dawn 10h


title: Chd8_WT_1mo_cortex_RNA_REP2


title: Mut6_PAX7_E18


title: Mut2_PAX7_E15


title: Leaf_replicate4

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
BS-seq reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1).
Reads with three or more consecutive methylated CHH sites were considered as “unconverted” and subsequently removed.
DNA methylation levels were calculated by #C/ (#C + #T).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: methylome profile

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown at 22 °C in a long day (16 hour light, 8 hour dark) growth room. Flowers and leaves were collected from 4-5 week-old plants.

extract_protocol:
Genomic DNA from Arabidopsis flowers and leaves was extracted using DNeasy Plant Mini Kit (Qiagen). Concentration of the DNA was measured by Qubit dsDNA Broad-Range Assay kit (ThermoFisher). 50 μl aliquots containing 25, 50, 150, and 400 ng DNA were sheared by an S2 Focused-ultrasonicator (Covaris) to ~200 bp in average size using these parameters: intensity 5, duty cycle 10%, cycles per burst 200, and treatment time 120 sec.
EM-Seq libraries were prepared from sheared DNA using Enzymatic Methyl-seq kit following manufacturer instructions (New England BioLabs). For each input amount, three PCR conditions were used: 6, 12, and 18 cycles. Sheared DNA was end-repaired and ligated with TruSeq DNA single adapters (Illumina) using Kapa DNA HyperPrep kit (Roche). Adapter-ligated DNA was converted by EpiTect Bisulfite Kit (Qiagen). And converted DNA was amplified by MyTaq polymerase (Bioline) for 6, 12, or 18 cycles.

tag: ecotype

tag: developmental stage

value: 4 weeks

value: leaves


title: WNT Dawn 3h Rep 1

value: Dawn 3h


title: WNT Dawn 3h Rep 2


title: WT7_PAX7_E18


title: WNT Dawn 3h Rep 4


title: WNT Dawn 7h Rep 4


title: WNT Dawn 7h Rep 2


title: WT8_PAX7_E18


title: Chd8_WT_6mo_cortex_RNA_REP1

value: dissected cortex


title: WNT Dawn 7h Rep 1


title: WNT Dawn Rep 3

value: Dawn


title: 32D clone 3_pEGFP-N1_CXCL1/2 treated [C3]

city: Changchun

first: Xianlu

last: Zeng

address: No. 5268, Renmin Avenue

country: China

institute: Northeast Normal University

description: 32D clone 3 cells transfected with an empty vector

data_processing:
Library construction and sequencing on an Illumina HiSeq 2500 instrument
Bowtie2 v2.2.3 was used for building the genome index
Clean data was then aligned to the reference genome using HISAT2 v2.1.0
Gene expression levels were quantified using a software package called FPKM
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates
Genome_build: Mus musculus. GRCm38. 89
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

source_name: 32D clone 3_pEGFP-N1_CXCL1/2 treated

growth_protocol: 32D clone 3 cells were maintained in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 10% mouse interleukin(IL)-3 culture supplement.

extract_protocol:
The cellular RNA was extracted using Trizol reagent followed by a genomic DNA elimination step. RNA purity was checked using the kaiaoK5500® Spectrophotometer. RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 32D clone 3 cells transfected with PEGP-N1(an empty vector) or CXCR2 were cultured in complete medium supplemented with CXCL1 (50 ng/mL) and CXCL2 (50 ng/mL) for 4 h

value: bone marrow

tag: cell line

value: 32D clone 3 cells

value: transfected with an empty vector


title: Flower_replicate4

source_name: Flower

value: flowers


title: OV2

first: Zheng

last: Jin

address: Xinmin Street 126#

department: College of  Basic Medical Science

institute: Jilin 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 UCSC-hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Read counts data of each sample were calculated using featurecounts model of subread software (V1.6.5). Counts data of each sample were normalized using R package DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Read counts data for each sample

extract_protocol:
RNA was harvested using Trizol reagent. Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: macrophage cell line

value: Control of overexpression vector


title: WNT Dawn 3h Rep 3

value: Leaf Tissue


title: Mut3_PAX7_E15

value: myogenic stem cells

value: SIX1/4 mutant


title: OV1


title: Control Dawn 23h Rep 4

value: Control

value: Dawn 23h


title: 32D clone 3_pEGFP-N1-CXCR2_CXCL1/2 treated [T3]

description: 32D clone 3 cells transfected with CXCR2

value: transfected with CXCR2

value: CXCL1 (50 ng/mL) and CXCL2 (50 ng/mL) for 4 h


title: WT6_PAX7_E18

value: WT


title: WT2_PAX7_E15


title: 32D clone 3_pEGFP-N1-CXCR2_CXCL1/2 treated [T2]


title: WT3_PAX7_E15


title: Control Dawn 23h Rep 3


title: WT1_PAX7_E15


title: Leaf_replicate3

value: 4 weeks

value: leaves


title: OT1

value: TRIM59 overexpression


title: WNT Dawn Rep 2

value: WNT

value: Dawn


title: Leaf_replicate2


title: WNT Dawn Rep 1


title: Leaf_replicate1


title: Control Dawn 23h Rep 1


title: WNT Dawn Rep 4


title: 50ng-6PCR-WGBS_replicate2


title: 50ng-6PCR-EM_replicate2

data_processing:
library strategy: EM-seq
BS-seq reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1).
Reads with three or more consecutive methylated CHH sites were considered as “unconverted” and subsequently removed.
DNA methylation levels were calculated by #C/ (#C + #T).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: methylome profile


title: Flower_replicate3


title: 32D clone 3_pEGFP-N1_CXCL1/2 treated [C2]

value: bone marrow

value: 32D clone 3 cells

value: transfected with an empty vector


title: Control Dawn 17h Rep 3

value: Dawn 17h


title: OT2

value: macrophage cell line


title: OT3


title: Mut1_PAX7_E15

value: myogenic stem cells


title: 50ng-18PCR-EM_replicate2

value: flowers


title: Control Dawn 23h Rep 2

value: Control

value: Leaf Tissue


title: OV3

value: Control of overexpression vector


title: NC2

value: Control of shRNA


title: Control Dawn 17h Rep 4


title: NC3


title: Flower_replicate2


title: KD2

value: TRIM59 knock down


title: NC1


title: 50ng-18PCR-WGBS_replicate2

value: 4 weeks


title: Control Dawn 14h Rep 2

value: Dawn 14h


title: Control Dawn 17h Rep 2


title: KD3


title: Flower_replicate1


title: 400ng-6PCR-WGBS_replicate2


title: Control Dawn 17h Rep 1


title: MSCORS donor 30 3 Week

city: Leipzig

first: Hanluo

last: Li

address: Liebigstraße 12

department: Clinic and Policlinic for Oral-, Jaw- and Plastic Face Surgery

country: Germany

institute: University Hospital Leipzig

description: RNA integrity number (RIN): 9.50

data_processing:
Illumina Casava1.8 software used for basecalling.
Paired-end raw data (FASTQ pair files, R1.fq and R2.fq) from Illumina PE150 were pre-processed using previously described protocol from Chen et al., Bioinformatics, 2018, to filtere the interference information on adaptor, low quality and undetected bases. This pre-process includes: (A) adapter trimming; (B) base correction on the mismatched base (≤5bp) on R1 and R2; (C) sliding window quality pruning: low quality bases in a sliding window (4bp) were discarded; (D) elimination of the reads containing ≥40% bases with low quality (Quality Score≤20).
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) used for reference genome alignment.
HTSeq used to calculate Reads Count
FPKM (fragments per kilobase of exon model per million reads mapped) were calculated from HTSeq Reads counts.
Supplementary_files_format_and_content: summarized matrix excel file of Quality Report on pair-end fastq data
Supplementary_files_format_and_content: PDF files of raw data filter and preprocess for each Sample
Supplementary_files_format_and_content: tab-delimited excel files with raw gene counts for each Sample
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

source_name: Osteogenic differentiated mesenchymal stem cells from hair follicle outer root sheath

growth_protocol: Human anagen hair follicles were non-invasively plucked from scalp of healthy donors, washed and digested using 5mg/ml collagenase X, and seeded onto a Transwell membrane. After 3 weeks of cultivation on liquid-air interface, cell monolayers on Transwell membrane were trypsinized and subcultured onto normal culture flask. Attached and proliferating cells were characterized as MSCORS. MSCORS were cultivated in DMEM medium (low glucose) containing 10% Fetal Bovine Serum (FBS) at 37°C, 5% O2, 5% CO2. The cells attached and proliferated until confluence. This point was defined as passage 0 (P0). Analogously, cells were re-plated at the next growth confluence and labelled as as passage 1 (P1)-cells and passage 2 (P2)-cells.  MSCORS were cultivated until passage 2 were induced for osteogenic differentiation.

extract_protocol:
Cultivation medium was removed, and cells were rinsed with PBS and harvested using QiazolTM (Qiagen, DE) reagent and isopropanol precipitation. RNA purity was measured using NanoDrop™One/OneC for ratios of OD260/280 and OD260/230. RNA was quantified using Qubit™RNA HS Assay Kit on Invitrogen Qubit® 3.0 Fluorometer. The integrity of RNA (RNA Integrity Number, RIN) was determined using Agilent 4200 TapeStation system
1 μg of total RNA for the construction of sequencing libraries. Poly-A-tailed mRNA was captured from the total RNA sample using oligo dT magnetic beads Dynabeads® Oligo(dT)25 (ThermoFisher, DE). As RNA template, selected RNA was heat fragmented, randomly primed using random primers (Invitrogen, CA) as RNA template, and complementary single-stranded cDNA was synthesized by M-MuLV (Biolabs, UK) reverse transcriptase. mRNA was degraded using RNaseH (2U/ml), and second strand of cDNA was synthesized by DNA polymerase I using dNTPs. Purified double strand cDNA was end-repaired using End Repair Buffer (Enzymatics, MA), and dA-tailed using DNA polymerase Klenow Fragment (3→5´exo-, Biolabs, UK) and dATP, adapter ligated of indexed adapters. cDNA of 200bp size was selected using AMPure XP beads (Beckman Coulter, US), and amplified via PCR. After purification, dscDNA library was quantified using Kapa qPCR, and the size of cDNA fragments was determined by Agilent 4200 TapeStation. After equimolar pooling, the samples were sequenced using Illumina PE150 kits.

treatment_protocol: MSCORS were seeded at 2x104 cells/cm2 density and incubated in Osteogenic Medium for 1 week, 2 week and 3 week. Osteogenic Medium contains basal DMEM (low glucose) containing 10% FBS, 2mM L-Glutamine, 200nM Dexamethasone, 50ug/ml Ascorbic Acid and 10mM β-glycerophosphate.

value: non-invasively plucked hair follicle outer root sheath

value: Osteogenic differentiation


title: MSCORS donor 30 1 Week

description: RNA integrity number (RIN): 9.50


title: KD1


title: Control Dawn 14h Rep 3


title: 400ng-18PCR-EM_replicate2


title: Control Dawn 14h Rep 4


title: Control Dusk Rep 4

value: Dusk


title: 50ng-12PCR-WGBS_replicate2


title: 50ng-12PCR-EM_replicate2


title: MSCORS donor 29 2 Week

description: RNA integrity number (RIN): 9.60


title: MSCORS donor 30 2 Week

description: RNA integrity number (RIN): 9.40


title: 400ng-6PCR-EM_replicate2


title: Control Dawn 14h Rep 1


title: 25ng-6PCR-WGBS_replicate2


title: Control Dusk Rep 1


title: MSCORS donor 29 3 Week

description: RNA integrity number (RIN): 9.90


title: Control Dusk Rep 3


title: 400ng-12PCR-WGBS_replicate2


title: 25ng-12PCR-EM_replicate2


title: Control Dawn 7h Rep 4

value: Dawn 7h


title: 25ng-18PCR-EM_replicate2


title: Control Dusk Rep 2


title: MSCORS donor 23 2 Week

description: RNA integrity number (RIN): 9.60


title: MSCORS donor 23 1 Week

description: RNA integrity number (RIN): 9.80


title: MSCORS donor 26 3 Week

description: RNA integrity number (RIN): 9.80


title: 400ng-18PCR-WGBS_replicate2


title: MSCORS donor 30 passage 2

description: RNA integrity number (RIN): 10.00

source_name: mesenchymal stem cells from hair follicle outer root sheath

growth_protocol: Human anagen hair follicles were non-invasively plucked from scalp of healthy donors, washed and digested using 5mg/ml collagenase X, and seeded onto a Transwell membrane. After 3 weeks of cultivation on air- liquid interface, cell monolayers on Transwell membrane were trypsinized and subcultured onto T25 cell culture flask. Attached and proliferating cells were characterized as Mesenchymal Stem Cells from the Outer Root Sheath of hair follicle (MSCORS). MSCORS were cultivated in DMEM medium (low glucose) containing 10% Fetal Bovine Serum (FBS) at 37°C, 5% O2, 5% CO2. The cells attached and proliferated until confluence. This point was defined as passage 0 (P0). Analogously, cells were re-plated at the next growth confluence and labelled as as passage 1 (P1)-cells and passage 2 (P2)-cells.

value: untreated


title: Control Dawn 10h Rep 4

value: Dawn 10h


title: 25ng-6PCR-EM_replicate2


title: 150ng-6PCR-EM_replicate2


title: MSCORS donor 26 2 Week

description: RNA integrity number (RIN): 9.40


title: Control Dawn 7h Rep 1


title: 400ng-12PCR-EM_replicate2


title: 25ng-18PCR-WGBS_replicate2


title: MSCORS donor 26 1 Week

description: RNA integrity number (RIN): 9.70


title: Control Dawn 10h Rep 3


title: Control Dawn 10h Rep 2


title: MSCORS donor 23 3 Week

description: RNA integrity number (RIN): 9.80


title: Control Dawn 10h Rep 1


title: 150ng-6PCR-WGBS_replicate2


title: Control Dawn 7h Rep 3


title: 150ng-12PCR-EM_replicate2


title: Control Dawn 3h Rep 3

value: Dawn 3h


title: MSCORS donor 29 passage 1

description: RNA integrity number (RIN): 9.80


title: Control Dawn 7h Rep 2


title: MSCORS donor 29 passage 0

description: RNA integrity number (RIN): 10.00


title: Control Dawn 3h Rep 4


title: MSCORS donor 29 1 Week

description: RNA integrity number (RIN): 9.90


title: MSCORS donor 30 passage 1

description: RNA integrity number (RIN): 9.80


title: MSCORS donor 30 passage 0

description: RNA integrity number (RIN): 10.00


title: 50ng-6PCR-EM_replicate1


title: 150ng-18PCR-EM_replicate2


title: 150ng-18PCR-WGBS_replicate2


title: 50ng-18PCR-WGBS_replicate1


title: 25ng-12PCR-WGBS_replicate2


title: MSCORS donor 26 passage 1

description: RNA integrity number (RIN): 9.50


title: MSCORS donor 29 passage 2

description: RNA integrity number (RIN): 9.80


title: 150ng-12PCR-WGBS_replicate2


title: 50ng-18PCR-EM_replicate1


title: 50ng-6PCR-WGBS_replicate1


title: Control Dawn 3h Rep 2


title: Control Dawn 3h Rep 1


title: MSCORS donor 23 passage 0

description: RNA integrity number (RIN): 10.00


title: MSCORS donor 23 passage 2

description: RNA integrity number (RIN): 9.90


title: Control Dawn Rep 4

value: Dawn


title: MSCORS donor 26 passage 2

description: RNA integrity number (RIN): 9.70


title: 400ng-6PCR-WGBS_replicate1


title: Control Dawn Rep 3


title: MSCORS donor 26 passage 0

description: RNA integrity number (RIN): 9.90


title: ADMSC donor 2 3 week

description: RNA integrity number (RIN): 9.40

data_processing:
Illumina Casava1.8 software used for basecalling.
Paired-end raw data (FASTQ pair files, R1.fq and R2.fq) from Illumina PE150 were pre-processed using previously described protocol from Chen et al., Bioinformatics, 2018, to filtere the interference information on adaptor, low quality and undetected bases. This pre-process includes: (A) adapter trimming; (B) base correction on the mismatched base (≤5bp) on R1 and R2; (C) sliding window quality pruning: low quality bases in a sliding window (4bp) were discarded; (D) elimination of the reads containing ≥40% bases with low quality (Quality Score≤20).
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) used for reference genome alignment.
HTSeq used to calculate Reads Count
FPKM (fragments per kilobase of exon model per million reads mapped) were calculated from HTSeq Reads counts.
Supplementary_files_format_and_content: summarized matrix excel file of Quality Report on pair-end fastq data
Supplementary_files_format_and_content: PDF files of raw data filter and pre-process for each Sample
Supplementary_files_format_and_content: tab-delimited excel files with raw gene counts for each Sample
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

source_name: Osteogenic differentiated adipose-derived mesenchymal stem cells

growth_protocol: ADMSC were isolated from human adipose tissue via 2mg/ml collagenase digestion, and seeded onto the cell culture flask with medium of DMEM (low glucose) containing 10% Fetal Bovine Serum (FBS) at 37°C, 5% O2, 5% CO2. ADMSC were cultivated until passage 2 and were then  osteogenically differentiated.

treatment_protocol: ADMSC were seeded at 2x104 cells/cm2 density and incubated in Osteogenic Medium for 1 week, 2 week and 3 week. Osteogenic Medium contains basal DMEM (low glucose) containing 10% FBS, 2mM L-Glutamine, 200nM Dexamethasone, 50ug/ml Ascorbic Acid and 10mM β-glycerophosphate.

value: Adipose Tissue


title: S10_CIE

city: Lubbock

first: Brent

middle: Romeo

last: Kisby

state: TX

address: 3601 4th Street

department: Pharmacology and Neuroscience

institute: TTUHSC

description:
Brain
CIE_amygdala_raw_counts.csv

data_processing:
Burrows-Wheeler Alignment to reference genome.
Aligned Sequencing reads were quantified using HTseq.
DESeq2 (v1.26) used for producing fold change, p values, and false discovery rate.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: CIE_amygdala_raw_counts.csv: Comma-separated matrix table with raw gene counts for every gene and every sample.

organism: Rattus norvegicus

source_name: Central Amygdala

extract_protocol:
CeA total RNA was isolated using the MagMAX™-96 Kit (Life Technologies, Carlsbad, CA) and checked for quality control (all RIN values were >8.6). RNA library preparation and sequencing occurred locally.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Sprague Dawley

value: Wild type

value: Central Amygdala

value: 14-16 weeks

value: Air Control

tag: timepoint

value: Immediately after last air exposure


title: MSCORS donor 23 passage 1

description: RNA integrity number (RIN): 9.80


title: Control Dawn Rep 1

value: Control

value: Leaf Tissue


title: ADMSC donor 1 3 week

description: RNA integrity number (RIN): 9.70


title: 50ng-12PCR-WGBS_replicate1

value: 4 weeks

value: flowers


title: S07_CIE

description:
Brain
CIE_amygdala_raw_counts.csv

tag: genotype


title: 400ng-12PCR-WGBS_replicate1


title: 50ng-12PCR-EM_replicate1


title: S11_CIE

description:
Brain
CIE_amygdala_raw_counts.csv


title: Control Dawn Rep 2


title: 400ng-6PCR-EM_replicate1


title: ADMSC donor 1 1 week

description: RNA integrity number (RIN): 9.70

value: Osteogenic differentiation


title: ADMSC donor 2 2 week

description: RNA integrity number (RIN): 9.40


title: 25ng-6PCR-WGBS_replicate1


title: S09_CIE

description:
Brain
CIE_amygdala_raw_counts.csv


title: 25ng-6PCR-EM_replicate1


title: 400ng-18PCR-WGBS_replicate1


title: ADMSC donor 2 passage 2

description: RNA integrity number (RIN): 9.70

source_name: Adipose-derived mesenchymal stem cells

growth_protocol: ADMSC were isolated from human adipose tissue via 2mg/ml collagenase digestion, and seeded onto the cell culture flask with medium of DMEM (low glucose) containing 10% Fetal Bovine Serum (FBS) at 37°C, 5% O2, 5% CO2. The cells attached and proliferated until confluence. This point was defined as passage 0 (P0). Analogously, cells were re-plated at the next growth confluence and labelled as as passage 1 (P1)-cells and passage 2 (P2)-cells.


title: S05_CIE

description:
Brain
CIE_amygdala_raw_counts.csv

value: Chronic Intermittent alcohol

value: Immediately after last alcohol exposure


title: ADMSC donor 2 passage 1

description: RNA integrity number (RIN): 9.60

value: untreated


title: 25ng-18PCR-WGBS_replicate1


title: 400ng-18PCR-EM_replicate1


title: S08_CIE

description:
Brain
CIE_amygdala_raw_counts.csv


title: ADMSC donor 1 2 week

description: RNA integrity number (RIN): 9.80


title: S03_CIE

description:
Brain
CIE_amygdala_raw_counts.csv


title: ADMSC donor 2 1 week

description: RNA integrity number (RIN): 9.70


title: 400ng-12PCR-EM_replicate1


title: S06_CIE

description:
Brain
CIE_amygdala_raw_counts.csv


title: 25ng-18PCR-EM_replicate1


title: ADMSC donor 1 passage 1

description: RNA integrity number (RIN): 9.80


title: ADMSC donor 1 passage 2

description: RNA integrity number (RIN): 9.80


title: ADMSC donor 1 passage 0

description: RNA integrity number (RIN): 10.00


title: S04_CIE

description:
Brain
CIE_amygdala_raw_counts.csv


title: 150ng-6PCR-WGBS_replicate1


title: ADMSC donor 2 passage 0

description: RNA integrity number (RIN): 9.90


title: S02_CIE

description:
Brain
CIE_amygdala_raw_counts.csv


title: Cell #14

city: Adelaide

first: Cedric

last: Bardy

state: SA

address: North Terrace

country: Australia

institute: South Australian Health and Medical Research Institute (SAHMRI)

data_processing:
Raw sequencing reads were mapped to the human reference transcriptome (GENCODE v19) using gapped-alignment strategies.
Alignment was performed by STAR (version 2.3.0).
Gene-level quantification was performed with HTseq (version 0.6.1).
Per-gene expression outputs were scaled to transcripts per million (TPM) units.
Genome_build: GENCODE v19
Supplementary_files_format_and_content: tab-delimited text file provides transcripts per million (TPM) expression values (rows = genes, columns = cells)

source_name: in vitro hPSC-derived neuron

growth_protocol: Human induced pluripotent stem cell cells (iPSCs) reprogrammed from dermal fibroblasts, and H9 embryonic stem cells (ESCs), were differentiated into neural progenitor cells (NPCs) using an embryoid body-based neural induction protocol (Bardy et al., 2016; Bardy et al., 2015; Boyer et al., 2012). NPCs were maintained and expanded in neural progenitor medium (DMEM/F12 supplemented with FGF8, Sonic Hedgehog, N2 and B27, without retinoic acid), and matured into neurons in neural maturation medium (BrainPhys™ basal supplemented with N2, B27, BDNF, GDNF, dibutyryl cyclic AMP, ascorbic acid and laminin). Half of the neuronal medium was gently replaced two to three times a week.

extract_protocol:
Following patch-clamp recording, each whole neuron (soma and neurites ≥150 μm away from the cell body) was collected and lysed in sample collection buffer as previously detailed in our Patch-seq protocol (van den Hurk et al., 2018). The SMARTer® Ultra® Low Input RNA for Illumina Sequencing kit (Clontech, Cat. No. 634828) was used for reverse transcription of single-cell RNA and subsequent amplification/purification of full-length cDNA.
Construction of Illumina sequencing libraries was performed using Nextera XT DNA Library Preparation Kit (Cat. No. FC-131-1096) and Indices (Cat. No. FC-131-1001) using 0.25 ng of full-length cDNA.

value: iPSC #1

value: in vitro hPSC-derived neuron

tag: action potential (ap) type

value: Type 5

tag: spontaneous synaptic activity

value: yes

tag: condition

value: healthy


title: 25ng-12PCR-WGBS_replicate1


title: S12_CIE

description:
Brain
CIE_amygdala_raw_counts.csv

value: Sprague Dawley

value: Wild type

value: Central Amygdala

tag: treatment


title: S01_CIE

description:
Brain
CIE_amygdala_raw_counts.csv

tag: age

value: 14-16 weeks


title: 150ng-18PCR-WGBS_replicate1


title: 25ng-12PCR-EM_replicate1


title: 150ng-12PCR-WGBS_replicate1


title: Mel+NAC_Replicate 3

city: Atlanta

first: Rui

last: Liu

state: GA

address: 2015 Uppergate Drive

department: Pediatrics

institute: Emory University

data_processing:
Illumina CASAVA base recognition software used for basecalling.
Indexes of the reference genome (GRCh38) was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
Data were filtered using the following specifications: remove reads with adaptor contamination; (2) remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%); (3) remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene, and then Fragments Per Kilobase Million (FPKM) was calculated to estimate gene abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows)

source_name: hiPSC-CMs

growth_protocol: The hiPSC line SCVI-273 (Stanford Cardiovascular Institute) was fed daily on Matrigel-coated plates with mTeSR™1-defined medium and passaged using Versene when compact colonies reached 90% confluence. For cardiomyocyte differentiation, hiPSCs were induced using a small molecule-guided differentiation protocol. At the day of induction (day 0), medium was replaced with RPMI 1640 medium supplemented with 2% B27 minus insulin and 6 µM CHIR99021. After 48 h (day 2), RPMI supplemented with 2% B27 minus insulin was used for 24 h. At day 3, 5 µM IWR1 was added to RPMI supplemented with 2% B27 minus insulin for another 48 h. From day 5, the small molecule-containing medium was replaced with RPMI supplemented with 2% regular B27 and the medium was changed every other day. hiPSC-CMs were further enriched by the metabolic selection method using RPMI without glucose supplemented with 2% B27 and 5 mM lactate from day 11 to 14. Alternatively, enriched hiPSC-CMs were generated by microscale generation of cardiospheres at day 6. Cells were observed under a microscope daily for beating cells, which typically appeared by day 7-9.

extract_protocol:
RNA was isolated from 1-1.5×106 hiPSC-CMs per sample using AurumTM total RNA mini kit per the manufacturer’s instructions. RNA quality and concentration were measured by Nanodrop Spectrophotometer. Total RNA quality was tested by Agarose Gel Electrophoresis and Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina TruSeq technology protocols.

treatment_protocol: At differentiation day 20, hiPSC-CMs were treated with DMSO, 20 µM melphalan, and 20 µM melphalan with 1 mM NAC, respectively, for 3 days.

tag: cell type

value: SCVI273 hiPSC derived cardiomyocytes

value: Day 23 differentiated cells

tag: agent

value: standard medium with melphalan treatment and NAC supplementation


title: Cell #4

value: ESC (H9)


title: Cell #3

value: Type 1

value: no


title: WT vs rme1_rep2

hyb_protocol: Gene Expression Hybridization Kit (Cat# 5188-5242) from Agilent Technologies was used to prepare 50 µl of purified labeled samples as recommended by the manufacturer, followed by hybridization to the GPL19289 platform.

scan_protocol: Images of Cy5 and Cy3 fluorescence were generated by scanning the expression arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).

data_processing: GenePix Results (GPR) files were imported into the Arraypipe 2.0 for spot filtering, background subtraction (limma normexp BG correction) and Lowess global normalization of signal intensities

source_name: Wild-type clinical isolate grown in PCB at 25ºC in the dark and under microaerophilic conditions during 24h

label_protocol: First-strand cDNA synthesis and Cy5/Cy3 labeling from 20 µg total RNA was performed using the Superscript III indirect cDNA labeling system (Invitrogen).

growth_protocol: For the RME1_2h and RME1_4h microarray experiments (Samples 1-6), total RNA was extracted from 3 independently-generated crz2Δ/crz2Δ strains carrying the PTET-RME1 fusion, pre-grown overnight in 10 ml YPD at 30ºC then diluted in fresh YPD medium supplemented or not with 40 µg.mL−1 doxycycline to an OD600 nm of 0.2 and re-grown for 2 (samples 1-3) and 4 (samples 4-6) hours. For the CEC2018 WT vs. rme1 microarray experiments (samples 7-9), strains CEC2018 (wild-type) and the rme1-/- mutant derivative (rme1) were grown overnight at 30ºC in YPD medium, then diluted to an OD600 of 0.2 in 10 mL of PCB (10% potato/carrot extract and 1.5% dehydrated fresh bile) liquid medium and cultured at 25ºC in the dark and under microaerophilic conditions during 24h.

extract_protocol: Total RNA was extracted using the hot phenol method as decribed in Znaidi et al. (2013) PLoS Pathogens 9: e1003519.

value: wild-type clinical isolate CEC2018

source_name: CEC2018 rme1-/- mutant grown in PCB at 25ºC in the dark and under microaerophilic conditions during 24h

tag: genotype/variaton

value: CEC2018 clinical isolate carrying a homozygous rme1-/- deletion


title: WT vs rme1_rep3


title: 150ng-12PCR-EM_replicate1

value: 4 weeks

tag: tissue

value: flowers


title: NHLF_siFOXL1_2

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

institute: The University of Tokyo

description: siNC vs. siFOXL1_2.xlsx

data_processing:
CLC Genomics workbench software (Qiagen) was used to generate RPKM data.
Adapter sequences were removed, and read mapping was carried out using the default settings of RNA-Seq analysis package (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, and maximum number of hits for a read set to: 30).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel

source_name: NHLF

growth_protocol: Normal human lung fibroblasts (NHLFs) were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from NHLFs 48 h after siRNA transfection using the RNeasy Mini Kit (Qiagen).
The mRNA from eukaryotic organisms was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Small interfering RNAs (siRNAs) for human FOXL1 was purchased from Life technologies. NHLFs were transfected with 20 nM siRNA using Lipofectamine RNAiMAX.

tag: transfection

value: transfected with FOXL1 siRNAs


title: NHLF_siFOXL1_1

description: siNC vs. siFOXL1_1.xlsx


title: Mel+NAC_Replicate 1


title: Mel+NAC_Replicate 2


title: WT vs rme1_rep1

tag: genotype/variation


title: 150ng-6PCR-EM_replicate1


title: RME1_4h_rep3

source_name: Untreated control, grown in YPD medium during 4h

value: strain carrying CIp-PTET-RME1

value: untreated

source_name: Dox-treated at a concentration of 40 µg/mL in YPD medium for 4h

value: dox


title: At Col-0 -Pi

city: Irapuato

first: Luis

middle: Rafael

last: Herrera-Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Langebio

country: Mexico

institute: Cinvestav - Langebio

data_processing:
Basecalls for RNA-Seq were performed using illumina basecalling pipeline (SolexaPipeline 1.0). ShortRNA-Seq reads with 75-nt paired ends were generated by Illumina sequencing and aligned to the Arabidopsis thaliana reference genome from TAIR (www.arabidopsis.org).
Adapter sequences were removed using Trimmomatic (version 0.35). Alignment of RNA-Seq reads to the Arabidopsis thaliana Genome (TAIR10)  was performed using TopHat2 (version 2.0.9). Raw counts per gene were calculated using HTSeq (version 0.6.0).
Genome_build: TAIR 10
Supplementary_files_format_and_content: The count file has two columns that provide ID (Arabidopsis locus ID) and read number (the number of reads that were alligned to that locus). Raw files (.bam) contain the output of the alligned pairs (from right and left reads) to the reference genome (TAIR10).

source_name: Root tip

growth_protocol: Briefly, seeds were grown 4 days after germination under high phosphate(1mM Pi, +Pi) or low phosphate (5 µM, -Pi) conditions in petri dishes with 0.1X Modified MS media (0.5% w/v Sucrose, pH 5.7, and 1% w/v agar).

extract_protocol:
For RNA-Seq total RNA was isolated using the TRIZOL reagent (Invitrogen) according to the manufacturer's instructions and further purificated using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions.
For preparation of mRNA-Seq Libraries, total RNA was isolated from frozen root tip powder using the TRIzol® reagent (Invitrogen) according to the manufacturer’s instructions for isolation of total RNA from plant tissue and further purified using Plant RNeasy kit (Qiagen) according to the manufacturer’s instructions for RNA purification. Non–strand-specific mRNA-seq libraries were generated from 5 μg of total RNA (Plant RNeasy kit) and prepared by using the TruSeq RNA Sample Prep kit (Illumina) according to the manufacturer’s instructions.

value: Root tip

value: Low Phosphate

value: 4 days after germination


title: At med16-2 +Pi

value: med16-2 mutant

value: High Phosphate


title: At Col-0 +Pi


title: 150ng-18PCR-EM_replicate1


title: Control_Replicate 3

value: SCVI273 hiPSC derived cardiomyocytes

value: Day 23 differentiated cells

value: standard medium with DMSO


title: Mel_Replicate 1

value: standard medium with melphalan treatment


title: Control_Replicate 2


title: NHLF_siNC

description: siNC vs. siFOXL1_1.xlsx

value: transfected with control siRNAs


title: RME1_2h_rep1

source_name: Untreated control, grown in YPD medium during 2h

source_name: Dox-treated at a concentration of 40 µg/mL in YPD medium for 2h


title: RME1_2h_rep2


title: Cell #13

value: iPSC #1

value: in vitro hPSC-derived neuron

value: Type 4

value: yes

value: healthy


title: At med16-2 -Pi


title: RME1_4h_rep2

value: strain carrying CIp-PTET-RME1

value: untreated


title: Mel_Replicate 2


title: RME1_4h_rep1

value: dox


title: mouse_liver_AdVEGFA_rep2

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description:
ribosomal-depleted RNA
VEGFA2
AdVEGFA - treatment sample - replicate 2

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the mm9 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression values (RPKM, log2 fold changes and FDRs) and UCSC Bedgraphs are provided

source_name: liver tissue

extract_protocol:
RNA was purified using Trizol extraction, RNeasy Mini Kit and Ribo-Zero gold rRNA removal kit.
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: AdVEGF-A treatment via tail vein injections. Time point 6d after gene transfer.

tag: strain

value: liver

tag: replicate

value: biological replicate #2


title: mouse_liver_AdCMV_rep5

description:
ribosomal-depleted RNA
CMV5
AdCMV - control sample - replicate 5

value: biological replicate #5


title: mouse_liver_AdVEGFA_rep1

description:
ribosomal-depleted RNA
VEGFA1
AdVEGFA - treatment sample - replicate 1

value: biological replicate #1


title: mouse_liver_AdVEGFA_rep4

description:
ribosomal-depleted RNA
VEGFA4
AdVEGFA - treatment sample - replicate 4

value: biological replicate #4


title: RME1_2h_rep3


title: mouse_liver_AdVEGFA_rep3

description:
ribosomal-depleted RNA
VEGFA3
AdVEGFA - treatment sample - replicate 3

value: biological replicate #3


title: Mel_Replicate 3

value: SCVI273 hiPSC derived cardiomyocytes

tag: developmental stage

value: Day 23 differentiated cells


title: mouse_liver_AdCMV_rep2

description:
ribosomal-depleted RNA
CMV2
AdCMV - control sample - replicate 2


title: mouse_liver_AdCMV_rep3

description:
ribosomal-depleted RNA
CMV3
AdCMV - control sample - replicate 3


title: Pat_10_Treg-A

city: london

first: syed

last: mian

address: 123 Coldharbour Lane

country: United Kingdom

institute: King's College London

data_processing:
Reads were trimmed for adapters using cutadapt and aligned to hg19 genome using STAR
Quantification in expected counts from genes and isoforms were computed by RSEM4 using genecode annotation v.26
We used TMM method to estimate scale factors between samples followed by the voom function in limma to convert them into log2counts per million (logCPM) and quantile normalization
Differential expression between groups were evaluated by LIMMA bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: GeneLevelQuantification

source_name: T Regulatory Cells

growth_protocol: CD4+ cells were first pre-enriched from the live cell fraction from PBMCs using CD4+ T cell isolation kit (Miltenyi Biotec). Then CD4+ cells were sorted on BD FACSAria (BD Biosciences) for Treg-A and B subpopulation. Total Tregs, Treg-A and Treg-B were cultured in Prime XV T cell expansion XSFM (Irvine Scientific, Santa Ana, CA), supplemented with 5% human AB serum (Sigma Aldrich, St. Louis, MO) in the presence of 2 M all-trans-retinoic acid (ATRA; Sigma Aldrich) and 100 nM rapamycin (LC Laboratories, Woburn, MA) for 4 to 6 weeks. Tregs were stimulated with Dynabeads human T-activator CD3/CD28 (cell:bead ratio = 1:1) (Thermo Fisher Scientific, Waltham, MA) and 1000 IU/mL of human IL-2 (Proleukin; Novartis, Basel, Switzerland).

extract_protocol: RNA was isolated using DNeasy Blood & Tissue kit (Qiagen)

value: T Regulatory Cells

tag: disease

value: Aplastic anaemia


title: mouse_liver_AdCMV_rep4

description:
ribosomal-depleted RNA
CMV4
AdCMV - control sample - replicate 4


title: Pat_8_Treg-B


title: Pat_9_Treg-A


title: Pat_7_Treg-A


title: Control_Replicate 1

tag: cell line

value: standard medium with DMSO


title: Pat_6_Treg-A


title: Pat_6_Treg-B


title: mouse_liver_AdCMV_rep1

description:
ribosomal-depleted RNA
CMV1
AdCMV - control sample - replicate 1


title: palatal tonsils_CT_S04_rep1

city: Changsha

first: Chan

state: Hunan

address: NO.139 of Renmin road

institute: The Second Xiangya Hospital

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: palatal tonsils,CT,S04,replicate1

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: palatal tonsils were removed from sugery and then placed in liquid nitrogen for preservation

extract_protocol: Total RNA of palatal tonsils was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

value: palatal tonsils

tag: gender

value: male

tag: disease state

value: chronic tonsillitis


title: Pat_9_Treg-B


title: palatal tonsils_CT_S03_rep1

source_name: palatal tonsils,CT,S03,replicate1


title: palatal tonsils_IgAN_S02_rep1

source_name: palatal tonsils,IgAN,S02,replicate1

value: IgA nephropathy


title: Pat_5_Treg-B


title: Pat_5_Treg-A


title: Pat_8_Treg-A


title: Norm3 (circRNA-seq)

city: Shanghai

first: Niu

last: Qiao

address: 197 Rui Jin Er Road

department: National Research Center for Translational Medicine (Shanghai)

institute: Shanghai Jiao Tong University

data_processing:
Quality control:    Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
Reads mapping to the reference sequence:    The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using Bowtie (Langmead, B.et al)
circRNA identification:    The circRNA were detected and identified using find_circ (Sebastian Memczak et al., 2013) and CIRI2 (Gao et al., 2017). Circos software was used to construct the circos figure.
Known miRNA alignment:    Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary  structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.  Novel miRNA prediction The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA  through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively
Quantification of miRNA:  miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Quantification of gene expression level:  The raw counts were first normalized using TPM (Zhou et al., 2010) Normalized expression level = (readCount*1,000,000)/libsize (libsize is the sum of circRNA readcount)
Differential expression of miRNA:    For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
GO and KEGG enrichment analysis  Gene Ontology (GO) enrichment analysis for host genes of differentially expressed circRNAs were implemented by the GOseq R package, in which gene length bias was corrected (Young et al., 2010). GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system (Kanehisa et al., 2008), such as the cell, the organism and the ecosystem, from molecular-level information, especially largescale molecular datasets generated by genome sequencing and other highthroughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways (Mao, X.et al.1995).
Genome_build: hg19
Supplementary_files_format_and_content: TPMs

source_name: Peripheral vein blood

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 5 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per µg of RNA. The sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, 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 (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. 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, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: healthy controls

tag: Sex

value: peripheral blood


title: Pat_7_Treg-B


title: Norm2 (circRNA-seq)


title: HD_4_Treg-A

value: healthy


title: HD_4_Treg-B


title: palatal tonsils_IgAN_S01_rep1

source_name: palatal tonsils,IgAN,S01,replicate1


title: HD_3_Treg-B


title: OP3 (circRNA-seq)

value: patients with osteoporosis diagnosed


title: Norm1 (circRNA-seq)


title: mouse_liver_AdVEGFA_rep5

description:
ribosomal-depleted RNA
VEGFA5
AdVEGFA - treatment sample - replicate 5

value: liver

value: biological replicate #5


title: HD_3_Treg-A


title: OP2 (circRNA-seq)


title: OP1 (circRNA-seq)


title: HD_2_Treg-B


title: Norm3 (miRNA-seq)


title: HD_2_Treg-A


title: Pat_10_Treg-B


title: CL1-5(TO-ERα)#18 [D+E+T+1]

city: Zhunan, Miaoli

first: Lih-Ann

state: Taiwan

address: R1-5034, 35 Keyan Road

department: National Institute of Environmental Health Sciences

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data analysis was performed with GeneSpring GX software (Agilent Technologies). Arrays with less than 50% detected probes were excluded. Quantile normalisation was performed.

source_name: ERα-inducible derivative of the CL1-5 cell line

label_protocol: 500ng total RNA was converted into cDNA using biotinylated random nonamers, oligodeoxythymidine 18 primers and Illumina-supplied reagents, according to Illumina manufacturer's instructions.

growth_protocol: CL1-5(TO-ERα)#18 cells were seeded in phenol red-free RPMI  medium containing 10% charcoal-treated fetal bovine serum. After 24 h of attachment, cells were given doxycycline, TNFα, 17β-estradiol, and cigarette sidestream smoke particulates  as described in the treatment protocol.  During treatment, the concentration of  fetal bovine serum was reduced to 3%.

extract_protocol: RNA was extracted using Roche High Pure RNA isolation kit (Roche Applied Science, Basel, Switzerland). NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA) and Experion Automated Electrophoresis Station (Bio-Rad Laboratories, Hercules, CA, USA) were employed to check RNA quality and integrity.

treatment_protocol: CL1-5(TO-ERα)#18 cells were divided into two groups. One group was pretreated with 1 μg/ml doxycycline (D) for 24 h to induce ERα expression, while the other group remained in D-free medium. The D- group was then divided into 4 subgroups for separate treatments with none,  45 U/ml TNFα (T), 1 nM 17β-estradiol (E), and 20 μg/ml cigarette sidestream particulates (C) for 24 h. Similar treatments were given to the D+ group except there was one additional subgroup for cotreatment with 1 nM 17β-estradiol plus 45 U/ml TNFα. There were total 9 subgroups: D-E-T-, D-E-T+, D-E+T-, D-C+T-,  D+E-T-, D+E-T+, D+E+T-, D+E+T+, and D+C+T-. Each subgroup contained two independent samples (n=2).

value: Lung

tag: morphology

value: epithelial

value: adenocarcinoma

value: Doxycycline (1μg/ml)

value: TNFα (45U/ml)

value: 17β-estradiol (1nM)

tag: cigarette sidestream smoke particulates (20μg/ml)

tag: duplication


title: CL1-5(TO-ERα)#18 [D+C+T-1]

tag: treatment


title: Norm2 (miRNA-seq)

tag: age


title: CL1-5(TO-ERα)#18 [D+C+T-2]


title: CL1-5(TO-ERα)#18 [D+E+T-2]


title: CL1-5(TO-ERα)#18 [D+E+T-1]


title: CL1-5(TO-ERα)#18 [D+E-T+2]


title: HD_1_Treg-A

tag: cell type

value: T Regulatory Cells


title: CL1-5(TO-ERα)#18 [D+E+T+2]

tag: tissue


title: HD_1_Treg-B


title: Norm1 (miRNA-seq)


title: OP3 (miRNA-seq)


title: Experiment 2 uninfected (scRNA-seq)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: TNBC

data_processing:
The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Sample demultiplexing and analyses were performed using Seurat toolkit V3.
Genome_build: CanFam3 + vaccinia virus genome (NC_006998)
Supplementary_files_format_and_content: Cellranger v2.0 filtered gene barcodes matrix.

organism: Canis lupus familiaris

source_name: dog breast cancer (TNBC) biopsy 2

growth_protocol: Around 35 000 cells were seeded in a 6 well plate. Three days later, the medium was removed and 1 mL of virus or vehicle was added. Cells were left in an incubator at 37°C for an hour and 3 mL of fresh medium was added (time 0).

extract_protocol:
10x Genomics single-cell 3' V2 chemistry was used to generate single-cell emulsion.
Single-cell RNA-seq was performed following manufacturer’s protocol (Chromium™ Single Cell 3' Reagent Kit, V2 Chemistry) to obtain single cell 3’ libraries for Illumina sequencing.

treatment_protocol: Six hours after infection, cells were trypsinized using a standard protocol. Cells were then collected, washed in PBS and the pellet was resuspended in 100 µL. Cells were then counted and the viability of the cells was verified.

value: dog breast cancer (TNBC) biopsy 2

tag: infection

value: No treatment

tag: dose


title: OP1 (miRNA-seq)

value: male


title: Experiment 1 infected (scRNA-seq)

description: TNBC vaccinia infected

source_name: dog breast cancer (TNBC) biopsy 1

value: dog breast cancer (TNBC) biopsy 1

value: vaccinia infected


title: Experiment 2 Infected (scRNA-seq)

description: TNBC vaccinia infected


title: OP2 (miRNA-seq)

value: peripheral blood


title: Experiment 1 uninfected (scRNA-seq)

description: TNBC


title: CL1-5(TO-ERα)#18 [D+E-T+1]


title: Cell #196

source_name: in vitro hPSC-derived astrocyte

value: iPSC #4

value: in vitro hPSC-derived astrocyte

tag: action potential (ap) type

value: Type 0

tag: spontaneous synaptic activity

value: no

tag: condition

value: healthy

value: untreated


title: Cell #195


title: Cell #194


title: Cell #188

source_name: in vitro hPSC-derived neuron

value: in vitro hPSC-derived neuron

value: Type 4

value: yes


title: Cell #191

value: Type 5


title: Cell #189

value: Type 3


title: 921 + Mn rep1

city: Nashville

first: Lillian

last: Juttukonda

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
RNAseq data were trimmed to remove all bases below Q3 and had adapter sequence removed, using FaQCs (Lo and Chain, 2014).
Trimmed sequence were aligned to the Staphylococcus aureus subsp. aureus str. Newman reference genome (accession number GCF_000010465.1) using BWA (Li and Durbin, 2009) and default alignment options.
Read counts were generated using HT-Seq v0.6.1p1 (Anders et al., 2015) and default options.
Genome_build: Staphylococcus aureus subsp. aureus str. Newman reference genome (accession number GCF_000010465.1)

organism: Staphylococcus aureus

source_name: Bacterial cells

growth_protocol: S. aureus WT strains were streaked onto TSA and incubated at 37 °C for 24 h. Single colonies were selected in biological triplicate and used to inoculate 5 ml of TSB. Cultures were grown for 15 h at 37 °C.  Cultures were back-diluted 1:100 in 5 ml TSB and grown at 37 C until mid-log phase. Cultures were centrifuged, the supernatant removed, and the cell pellets resuspended in TSB.

extract_protocol:
.  RNA was isolated using Tri reagent and chloroform and precipitated with isopropanol. RNA was isolated using the Qiagen RNeasy Mini Kit. Precipitated RNAs were treated with DNase I (ThermoFisher) following the manufacturer’s instructions.
Total RNA quality was assessed using the 2100 Bioanalyzer (Agilent). At least 200ng of DNase-treated total RNA with a RNA integrity number greater than 6 was used for rRNA depletion and generation of cDNA libraries via the ScriptSeq Complete (Bacterial) kit (Illumina/Epicenter) following the manufacturer’s protocol. Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (KAPA Biosystems).
RNA sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core using the Illumina HiSeq 3000 platform (Illumina).

treatment_protocol: Equal volumes of the resuspended cultures were added to TSB, TSB supplemented with MnCl2 (final concentration of 1 mM MnCl2), TSB supplemented with small molecule VU0026921 (final concentration 100 micromoles), or TSB supplemented with MnCl2 and small molecule VU0026921 (final concentrations 1 mM and 100 micromolar, respectively). Cells were incubated for 30 min at 37 °C, centrifuged, and the remaining cell pellet subjected to RNA extraction.

tag: strain

value: Newman


title: Cell #192

tag: cell line


title: 921 + Mn rep2


title: 921 + Mn rep3


title: 921 rep3


title: Cell #176


title: Cell #179


title: Cell #175


title: 921 rep2


title: CL1-5(TO-ERα)#18 [D-C+T-1]

value: Lung

value: epithelial

tag: disease

value: adenocarcinoma


title: CL1-5(TO-ERα)#18 [D-E+T-2]

value: 17β-estradiol (1nM)


title: Cell #174


title: CL1-5(TO-ERα)#18 [D+E-T-1]

value: Doxycycline (1μg/ml)


title: CL1-5(TO-ERα)#18 [D+E-T-2]


title: CL1-5(TO-ERα)#18 [D-C+T-2]


title: 921 rep1


title: Mn rep3

value: TSB + 1 mM MnCl2


title: Cell #172

value: iPSC #4


title: CL1-5(TO-ERα)#18 [D-E-T+2]

value: TNFα (45U/ml)


title: CL1-5(TO-ERα)#18 [D-E+T-1]


title: CL1-5(TO-ERα)#18 [D-E-T+1]


title: CL1-5(TO-ERα)#18 [D-E-T-2]


title: Mn rep2


title: Cell #169


title: Cell #165


title: Untreated rep3

value: TSB


title: Cell #168

value: healthy


title: Mn rep1


title: Cells treated with BI6727 and MK-0752, replicate 3

city: Madison

first: Nihal

last: Ahmad

state: WI

address: 1300 University Avenue

institute: University of Wisconsin-Madison

data_processing:
From the RNA-seq data, gene abundances were estimated using RSEM (v1.3.0), with read mapping performed using the STAR aligner (v2.5.3a).
Reads were mapped to the GRCh38 assembly of the human genome with the GENCODE v31 comprehensive transcript annotation.
The “--forward-prob 0” option was used for RSEM to reflect the fact that the RNA-seq libraries were strand-specific.
Genome_build: hg38
Supplementary_files_format_and_content: Each processed file contains gene_id, transcript_id(s), length of gene, effective_length, expected_count, TPM, and FPKM of the whole transcriptome.

source_name: SK-MEL-2 Human Melanoma Cell

growth_protocol: SK-MEL-2 cells were cultured in EMEM (Corning) supplemented with 10% FBS at standard cell culture conditions (37°C, 5% CO2 in a humidified incubator). All cell lines were routinely authenticated (upon thawing or cultured for >3 months) using STR testing.

extract_protocol:
Total RNA was isolated from cells using QIAGEN RNeasy Mini Kits.
A total of 16 samples were submitted to the University of Wisconsin Biotechnology Center Gene Expression Center for quality control, library construction and further analysis. The purity and integrity of total RNA were assessed on the NanoDrop One Spectrophotometer and Agilent 2100 BioAnalyzer, respectively. Samples that met the TruSeq Stranded mRNA Sample Preparation Guide (Rev. E) input guidelines were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation kit. The quality and quantity of prepared libraries were assessed by analysis on the Agilent 2100 Bioanalyzer and Qubit fluorimeter. An equimolar pool of all libraries with 30 million targeted reads per sample was sequenced on the Illumina NovaSeq S4 flowcell with 2x150bp sequencing. Images were analyzed using the standard Illumina Pipeline (v1.8.2).

treatment_protocol: SK-MEL-2 cells were seed to 10 mm flasks 24 hours before treatment. On the day of treatment, the cell culture medium was replaced with DMSO, BI6727, MK-0752, and BI+MK. The cells were collected 48 hours after treatment.

value: treated with 20nM BI6727+ 100uM MK0752 for 48h


title: Cells treated with BI6727 and MK-0752, replicate 4


title: Cells treated with BI6727 and MK-0752, replicate 1


title: Cell #155

value: in vitro hPSC-derived neuron

value: untreated


title: Untreated rep2


title: Cell #167

value: yes


title: Cell #166

value: Type 5


title: Cell #158

value: Type 4


title: CL1-5(TO-ERα)#18 [D-E-T-1]


title: Cell #156

value: Type 2


title: Cells treated with BI6727 and MK-0752, replicate 2


title: Cells treated with MK-0752, replicate 4

value: treated with 100uM MK-0752 for 48h


title: Cell #124

value: ESC (H9)


title: Cell #133

value: Type 3


title: Cell #132

value: in vitro hPSC-derived astrocyte

value: Type 0

value: no


title: Cells treated with MK-0752, replicate 3


title: Cell #129


title: Cells treated with BI6727, replicate 2

value: treated with 20nM BI6727 for 48h


title: Cells treated with MK-0752, replicate 2


title: Cell #115


title: Cells treated with BI6727, replicate 4


title: Cell #125


title: Cells treated with BI6727, replicate 3


title: Cells treated with MK-0752, replicate 1


title: Cell #119


title: 190731_DM1_wound

city: Ann Arbor

first: Lam

last: Tsoi

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
data processing including quality control, read alignment and gene quantification were conducted using the 10X Cell Ranger software
Seurat was then used for normalization, data integration, and clustering analysis
Genome_build: GRCh37
Supplementary_files_format_and_content: 10X read count files

source_name: skin biopsy

extract_protocol:
Skin was harvested via punch biopsy from diabetic and non-diabetic control patient wounds.
Samples were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C, and strained through a 70μM mesh. Epidermal and dermal cells were combined in a 1:1 ratio for scRNA-seq by the University of Michigan Advanced Genomics Core on the 10 Chromium system. Libraries were sequencing on the Illumina NovaSeq 6000 sequencer.

tag: disease state

value: Diabetic

tag: tag

value: Wound skin tissue


title: 190731_DM1_distant

value: Distant skin tissue from wound


title: Cell #116

value: healthy


title: Untreated rep1

value: Newman

value: TSB


title: 277-FD-7

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the human reference genome (b37) using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: GRCh37
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

extract_protocol:
Skin was harvested via punch biopsy from diabetic and non-diabetic control patient wounds.
Libraries were sequencing on the Illumina NovaSeq 6000 sequencer.

value: Normal

value: skin biopsy


title: Cell #100

value: in vitro hPSC-derived neuron

value: Type 5

value: yes

value: untreated


title: Cell #98

value: ESC (H9)


title: 277-FD-5


title: Cells treated with DMSO, replicate 4

value: treated with DMSO for 48h


title: Cell #99


title: Cells treated with DMSO, replicate 2


title: Cells treated with BI6727, replicate 1


title: Cell #130

value: in vitro hPSC-derived astrocyte

value: Type 0


title: Cells treated with DMSO, replicate 3


title: Cell #111


title: Cell #63

value: Type 2

value: no


title: Cell #110


title: Cells treated with DMSO, replicate 1


title: 277-FD-3

value: Diabetic


title: Cell #105


title: 277-FD-2


title: Cell #107

value: Type 3


title: Cell #60

value: healthy


title: Cell #61


title: Cell #101

value: Type 1


title: IPEC-J2 input #1

city: Pullman

first: Michael

middle: E

last: Konkel

state: WA

institute: Washington State University

data_processing:
MiSeq Instrument Software was used to generate fastq files.
Reads were aligned to the genome using bowtie2 version 2.3.2 using default options.
Reads mapping to each CDS were counted using featureCounts from the subread package, version 1.5.3 using the --largestOverlap option.
Genome_build: Genbank file associated with accession CP006851.1 was used for mapping reads to the C. jejuni genome.
Supplementary_files_format_and_content: Comma delimited text file containing counts of mapped transcripts CDS.

organism: Campylobacter jejuni

source_name: IPEC-J2 input #1

growth_protocol: C. jejuni were grown in 250 mL MH broth cultures in a microaerobic environment shaking at 220 rpm on an orbital shaker, adjusted to an OD540 of 0.3 in phosphate buffered saline before injection into the intestinal lumen.

extract_protocol:
Bacterial pellets were collected by centrifugation and snap frozen. RNA Extraction was done using the Ambion Ribopure Bacteria kit. rRNA was depleted with 3’ biotinylated oligonucleotides that were designed to hybridize with C. jejuni 16S and 23S rRNAs.
Illumina MiSeq libraries were prepared using the KAPA stranded RNAseq kit

tag: strain/genotype

tag: culture time (hours)

tag: culture condition

value: Mueller-Hinton Broth


title: Cell #57

value: iPSC #2

tag: treatment


title: Cell #53


title: 277-FD-4

value: skin biopsy


title: Cell #86

value: iPSC #3

value: in vitro hPSC-derived neuron


title: IPEC-J2 4 hour #1

source_name: IPEC-J2 4 hour #1

value: Co-culture with IPEC-J2 cells


title: 277-FD-1


title: Cell #55

value: yes

value: untreated


title: 277-FD-6

value: Normal


title: IPEC-J2 4 hour #2

source_name: IPEC-J2 4 hour #2


title: IPEC-J2 2.5 hour #1

source_name: IPEC-J2 2.5 hour #1


title: IPEC-J2 2.5 hour #2

source_name: IPEC-J2 2.5 hour #2


title: Cell #44

value: ESC (H9)


title: Pig CiaD input #7

source_name: Pig CiaD input #7

value: F38011 ∆ciaD


title: Pig CiaD input #8

source_name: Pig CiaD input #8


title: IPEC-J2 input #2

source_name: IPEC-J2 input #2


title: Pig CiaD input #3

source_name: Pig CiaD input #3


title: Pig CiaD input #9

source_name: Pig CiaD input #9


title: Cell #46

value: Type 2


title: Cell #28

value: no


title: Cell #42


title: Cell #24

value: Type 4


title: Cell #22

value: Type 5


title: Pig CiaD input #2

source_name: Pig CiaD input #2


title: Cell #16

value: Type 3

value: healthy


title: Pig CiaD input #12

source_name: Pig CiaD input #12

value: Mueller-Hinton Broth


title: Cell #45