title: Mouse 4: single-cell RNA sequencing of the mouse main olfactory epithelium

city: Geneva

first: Ivan

last: Rodriguez

address: 30 quai Ernest Anrsermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: 3' end single-cell RNA sequencing of the mouse main olfactory epithelium using 10X Genomics Chromium technology

data_processing:
fastq files were pre-processed with Cell Ranger version 6.0.1. A modified version of the Ensembl release 102 of the Mus musculus GTF annotation was used. This GTF file was updated with the re-annotation of the 3'UTR of olfactory receptor genes.
For a detailed description of the analysis of the data, please refer to the methods section of Flores Horgue et al. (2021).
Genome_build: GRCm38
Supplementary_files_format_and_content: *_barcodes.tsv.gz files are Cell Ranger output files containing the list of cell barcodes for the corresponding samples.
Supplementary_files_format_and_content: *_features.tsv.gz files are Cell Ranger output files containing the list of gene names.
Supplementary_files_format_and_content: *_matrix.mtx.gz files are Cell Ranger output files corresponding to the UMI count matrix for the corresponding samples.
Supplementary_files_format_and_content: MOE_all_cells_10X_scRNAseq_filtered_UMI_counts.txt  is a tab-separated file corresponding to the digital gene expression matrix of the single-cell RNA sequencing dataset. Rows are genes, columns are cells, and the corresponding gene counts (UMIs) are matrix entries.
Supplementary_files_format_and_content: MOE_all_cells_10X_scRNAseq_filtered_metadata.txt is a space-separated file containing the meta data information for all the cells in MOE_all_cells_10X_scRNAseq_filtered_UMI_counts.txt.

source_name: main olfactory epithelium, nasal cavity

growth_protocol: 8-weeks-old males C57BL/6 were used (n=4). Mice were housed in group of 4 and maintained on a normal 12h light/dark cycle in a 24°C temperature room, with ad libitum access to food and water. All experiments were performed during daytime.

extract_protocol:
Mice were euthanized with intraperitoneal injection of pentobarbital (150mg/Kg) and their olfactory epithelia were immediately extracted and processed for tissue dissociation using the Papain Dissociation System (cat #LK003150, lot #35S16330; Worthington® Biochemical Corporation, New Jersey, USA) following the manufacturer’s protocol, with slight modifications; the EBSS solutions and the medium solution with serum were adapted from Saxena et al. (DOI: 10.2144/0000113878). To ensure the exclusive isolation of live nucleated cells, cell suspensions were incubated with 2 μg/ml of Hoechst 33342 (a UV fluorescent adenine-thymine binding dye; #H1399, Life Technologies) at 37°C for 15 min. In order to exclude dead cells, 1 μM of DRAQ7 (a far-red fluorescent DNA intercalating dye; #DR71000, BioStatus) was added to the cell suspensions before fluorescence activated cell sorting (FACS). Approximately 80000 Hoechst+/DRAQ7- cells were collected from each single-cell suspension pool, each in a final volume of 100μl. After FACS sorting, cell suspensions were concentrated at 800 cells/microliter before loading on the 10X Genomics Chromium controller. For a detailed description of the protocol, please refer to the methods section of Flores Horgue et al. (2021).
cDNA libraries were constructed following the 10X Genomics Chromium Next GEM Single Cell 3' v3.1 protocol (dual index libraries).

tag: gender

value: male

tag: age

value: main olfactory epithelium


title: P35 Het rep 4

status: Public on May 02 2022

type: SRA

city: Exeter

first: Nicholas

middle: E

last: Clifton

address: RILD Building

country: United Kingdom

institute: University of Exeter

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed of adapters using Trimmomatic and passed through FastQC quality control. Reads were aligned to the mouse genome (GRCm38) with STAR and mapped to genes using featureCounts.
Assembly: GRCm38
Supplementary files format and content: Featurecounts ouput. Tab telimited text file containing raw gene counts for each gene

molecule: total RNA

organism: Mus musculus

source_name: Frontal cortex

extract_protocol:
RNA was extracted using an AllPrep DNA/RNA micro kit (QIAGEN)
Library preparation and sequencing were performed by Novogene. cDNA libraries with 250-300 bp inserts were prepared using poly-A capture. A single batch of Illumina high-throughput sequencing was performed at 12Gb read depth per sample with 150bp paired-end reads

tag: strain

tag: genotype

value: Het

tag: developmental stage

tag: tissue

value: Frontal cortex


title: GIST-T1_H3K79me2

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

country: USA

institute: UMass Medical School

library_source: genomic

data_processing:
All Chip-Seq and CUT&Tag data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: KIT-dependent GIST cell line GIST-T1

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 or paired-end 37 bp sequencing on an Illumina NextSeq 550 were prepared with a ThruPLEX DNA-seq Kit (Takara).

tag: cell line

tag: cell type

value: Gastrointestinal stromal tumor (GIST)

tag: antibody

value: H3K79me2, Cell Signaling Technology Cat# 5427

tag: technique

value: ChIP-seq

tag: target

value: Endogenous H3K79me2


title: P35 Het rep 5


title: mRNA_2078_6.3_mkd_Liver

city: Indianapolis

first: Kamin

last: Johnson

state: IN

address: 9330 Zionsville Rd

institute: Corteva Agriscience

data_processing:
Basecalls performed using Illumina CASAVA software version 1.8
The raw mRNA sequencing reads for each sample were processed with the fastq-mcf tool from the ea-utils software package (v1.1.0) for adapter sequence removal and trimming low quality bases (parameters for minimum remaining sequence length option set to 50 and quality threshold set to 30).
Trimmed reads were subsequently mapped to the rat reference genome (version 6.0.80) using the hisat2 mapping software (v2.0.3) run using default parameter settings and in stranded mode
Using HTSeq (v0.7.2), the reads mapped to the antisense strand of each gene were counted and tabulated across samples that was used for downstream data normalization and gene expression analysis.
Similarly, the microRNA raw reads for each sample were processed for adapter sequence removal using the cutadapt bioinformatics tool (v1.16, with the minimum-length parameter (-m) set to 14 bases and minimum-overlap (-O) parameter set to 6 bases).
The trimmed microRNA reads were mapped to the rat reference genome (version 6.0.80) using the bowtie2 mapping software (v2.3.2) using default parameter settings.
the coverageBed function of the bedtools software (v2.17.0) was used to obtain counts of microRNA reads that overlapped microRNA and mRNA features in the rat reference genome annotation (using the -s strandedness option enabled). The resulting mapped read counts were tabulated across samples and used for downstream data normalization and microRNA expression analysis.
Assembly: Rattus norvegicus (version 6.0.80)
Supplementary files format and content: one tab-delimited text matrix file include raw mRNA count values for each Sample and one tab-delimited text matrix file include raw mRNA count values for each Sample

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was extracted from organs stored in RNAlater using a mirVana RNA isolation kit (catalog number AM1560; ThermoFisher Scientific) according to the manufacturer’s instructions.  RNA quantity was measured using a NanoDrop ND-1000 spectrophotometer.  Total RNA quality was examined using an Agilent Bioanalzyer (Agilent Technologies).  miRNA was purified from the same tissue homogenate as the Total RNA,  using mirvana (catalog number AM1560; ThermoFisher Scientific, Waltham, MA) and quanitified using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).
).  A sequencing library was prepared from 1ug total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit and protocol (Illumina, San Diego, CA).  Briefly, mRNAs were fragmented using ZnCl2 solution, reverse transcribed into cDNA using random primers, end repaired to create blunt end fragments, 3’ A-tailed, and ligated with Illumina paired-end library adaptors. Ligated cDNA fragments were PCR amplified using Illumina paired-end library primers and purified PCR products were checked for quality and quantity on the Agilent TapeStation (Agilent, Santa Clara, CA).  Average library insert size was 300bp, and final sequencing concentration was determined by quantitation on the Agilent TapeStation (Agilent, Santa Clara, CA). For the microRNA libraries, sequencing libraries from each small RNA sample were prepared using 1 µg input with the TruSeq small RNA kit according to manufacturer’s instructions (Illumina, Inc., San Diego, CA). Briefly, Illumina TruSeq adapters are ligated onto purified smRNA ends, reverse transcribed, and the cDNA are PCR-amplified using Illumina indexed TruSeq primers. PCR-amplified libraries were checked for quality and quantified using the Agilent Tapestation 4200 with D1000 screentape.  Equal amounts of library were pooled based on nano-molarity concentration and then size-selected using a PippinHT automated DNA size selector (Sage Science Inc., Beverly, MA).  The size-selected samples were ethanol precipitated to concentrate and then checked for quality and quantity using an Agilent TapeStation 4200 with D1000 screentape.

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: Pregnant

tag: agent

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

value: Approximately 24 hours

tag: gestation day definition

value: The morning of observing a vaginal plug was considered gestation day 0

tag: corn oil vehicle dose level

value: 2 ml/kg body weight

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: Mouse 3: single-cell RNA sequencing of the mouse main olfactory epithelium

tag: strain

tag: gender

value: male

tag: age


title: mRNA_2084_20_mkd_Liver

tag: developmental stage


title: Mouse 2: single-cell RNA sequencing of the mouse main olfactory epithelium

tag: tissue

value: main olfactory epithelium


title: Mouse_M056-01-T03 (CD19+CD45+TER119+CD11b+)

city: Yangzhou

first: Zhe

last: Yang

state: Jiangsu province

address: No.88, South University Road, Yangzhou

department: medical college

country: China

institute: Yangzhou university

data_processing:
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify
Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM).
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Monoclonal cell line of ER1 and its differentiated cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: According to the difference of sorting markers of flow cytometry, the cells at different differentiation stages of ER1 cells were selected for monoclonal culture to establish cell lines

tag: cell line

tag: cell type

value: B lymphocytes

tag: genotype

tag: treatment

value: Sorted monoclonal culture


title: P35 WT rep 4

value: WT

value: Frontal cortex


title: mRNA_2077_6.3_mkd_Liver

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

tag: pregnancy status at gestation day 21


title: mRNA_2079_6.3_mkd_Liver

tag: agent

tag: exposure

tag: interval between last dosing and necropsy


title: P35 WT rep 3


title: mRNA_2074_6.3_mkd_Liver

tag: gestation day definition

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)


title: P35 Het rep 3

tag: strain

value: Het


title: Mouse_M056-01-T02 (CD19-CD45+TER119-CD11b+)


title: Spleen WT 3

city: Boston

first: Andrew

last: Wight

address: 450 Brookline Ave

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

data_processing:
BAM files were generated from provided fastq files using Rsubread version 2.6.4 using default settings
Read counts were generated using Rsubread version 2.6.4 using default settings, considering only those reads that were correctly paired
Genome_build: mm10
Supplementary_files_format_and_content: Read counts are presented as a .csv file, with each row corresponding to one gene and each column to one sample. Entrez gene IDs are given

molecule: polyA RNA

source_name: Spleen FoxP3+ Treg

growth_protocol: Cells isolated ex-vivo and sorted based on FoxP3-YFP expression

extract_protocol:
RNA was extracted using Qiagen RNEasy Plus micro kit, following manufacturer's instructions
Library was constructed by GeneWiz following their ultra-low input RNA pipeline

value: B6.IL23RWT FoxP3Cre-YFP

value: Endpoint MC38 flank tumor


title: Mouse 1: single-cell RNA sequencing of the mouse main olfactory epithelium

tag: gender

tag: age


title: mRNA_2072_2.0_mkd_Liver

tag: developmental stage

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rna integrity number (rin) of isolated total rna


title: Mouse_M056-01-T01 (CD19-CD45+TER119+CD11b+)

tag: cell line

tag: cell type


title: mRNA_2070_2.0_mkd_Liver

value: Female

value: Pregnant


title: Ace3: Olfr151-positive cells, exposed to acetophenone

description: FAC-sorted olfactory sensory neuron bulk RNA-seq

data_processing:
RNA-seq reads were mapped onto the GRCm38 mouse genome assembly including the IRES-tau-GFP sequence with STAR version 2.7.0a using the Ensembl v99 gene annotation file (GTF) with the 3'UTR of Olfr151 and Olfr16 reannotated (see methods of the paper). Mutlimapped reads were filtered out with the option --outFilterMultimapNmax set to 1.
Gene expression quantification was carried using featureCounts version 1.6.3 and a modified version of the aforementioned GTF file.
Differential gene expression analysis between non-exposed and exposed samples was performed using the DESeq2 Bioconductor package version 1.30.1 in R version 4.0.3. After fitting a negative binomial generalized linear model (GLM), the Wald test (two-tailed) was used to test for significance of gene expression differences as a function of biopsies at a log2 fold change threshold of 0. To control the false discovery rate, the Wald test p-values were adjusted for multiple comparisons using the Benjamini–Hochberg procedure
Genome_build: GRCm38
Supplementary_files_format_and_content: *featureCounts.txt files are featureCounts output files

source_name: olfactory sensory neuron, nasal cavity

growth_protocol: 7 week-old Olfr151(tm26Mom/tm26Mom) were used (n=24). Mice were housed in group of 4 and maintained on a normal 12h light/dark cycle in a 24°C temperature room, with ad libitum access to food and water. All experiments were performed during daytime.

extract_protocol:
Individuals were euthanized, their olfactory epithelium extracted and processed for tissue dissociaton (for a detailed description of the protocol, please refer to the methods section of Assens et al. (2021)).To ensure the exclusive isolation of live nucleated cells, cell suspensions were incubated with 2 μg/ml of Hoechst 33342 (a UV fluorescent adenine-thymine binding dye; #H1399, Life Technologies) at 37°C for 15 min. In order to exclude dead cells, 1 μM of DRAQ7 (a far-red fluorescent DNA intercalating dye; #DR71000, BioStatus) was added to the cell suspensions before fluorescence activated cell sorting (FACS). A hundred GFP+/Hoechst+/DRAQ7- cells were collected from each cell suspension, resulting in 400 cells per biological pool. Cells were collected directly in lysis buffer from the Qiagen RNeasy plus micro kit and total RNA was isolated following the manufacturer's protocol. After the initial cell lysis step, 10 µL of 1:1000000 ERCC spike-ins mix 1 from ThermoFisher was added to each sample. The quality and quantity of total RNA were evaluated with a Bioanalyzer (Agilent).
The SMARTer™ Ultra Low RNA kit from Clontech was used for reverse transcription and cDNA amplification (12 PCR cycles) according to the manufacturer’s specifications, starting with a total volume of 9.5 µL per sample as total RNA input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at equimolarity and loaded at 2 nM for clustering on an Illumina HiSeq 4000 sequencer. Reads of 50 bases were generated using the SBS HS v3 chemistry on an Illumina HiSeq 4000 sequencer.

treatment_protocol: Isolated individuals were exposed for 5 hours (starting at 8 a.m.) to 5% Acetophenone in DMSO (exposed condition) or to DMSO alone (non-exposed condition). Each experiment was conducted on three consecutive days. Each day, 4 mice from each condition were analyzed.

tag: genetic background

tag: treatment

tag: tissue

value: Main olfactory epithelium

tag: sorted cells

value: 200 Olfr151-positive cells


title: Ace1: Olfr151-positive cells, exposed to acetophenone

value: 5% Acetophenone in DMSO (exposed condition)


title: Ace2: Olfr151-positive cells, exposed to acetophenone


title: E18 WT rep 5

tag: genotype


title: P35 WT rep 1


title: mRNA_2068_2.0_mkd_Liver

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

tag: pregnancy status at gestation day 21

tag: agent

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0

value: 2 ml/kg body weight


title: mRNA_2065_2.0_mkd_Liver

tag: strain

tag: interval between last dosing and necropsy

tag: gestation day definition

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)


title: mRNA_2063_0.63_mkd_Liver

tag: developmental stage

tag: rna integrity number (rin) of isolated total rna


title: E18 Het rep 5


title: F3: Olfr151-positive cells, not exposed

tag: genetic background

value: DMSO alone (non-exposed condition)


title: F1: Olfr151-positive cells, not exposed

tag: treatment


title: mRNA_2061_0.63_mkd_Liver


title: E18 Het rep 4

tag: tissue

value: Frontal cortex


title: E18 WT rep 3

value: WT


title: P35 WT rep 2


title: mRNA_2053_0.2_mkd_Liver


title: mRNA_2069_2.0_mkd_Liver


title: P35 Het rep 2

value: Het


title: E18 Het rep 3


title: mRNA_2051_0.2_mkd_Liver


title: E18 WT rep 2


title: E18 Het rep 2


title: F2: Olfr151-positive cells, not exposed

tag: sorted cells


title: E18 WT rep 1

tag: genotype


title: E18 WT rep 4


title: mRNA_2060_0.63_mkd_Liver

tag: rat body weight at gestation day 0 (grams)


title: mRNA_2062_0.63_mkd_Liver

tag: sex/pregnancy status


title: P35 Het rep 1


title: mRNA_2044_0.2_mkd_Liver

tag: pregnancy status at gestation day 21


title: E18 Het rep 1


title: mRNA_2046_0.2_mkd_Liver

tag: agent


title: mRNA_2055_0.63_mkd_Liver

tag: exposure


title: mRNA_2043_0.063_mkd_Liver

tag: strain


title: Monocyte-derived M2a macrophages (D2) [AB-LIB]

city: Biberach an der Riss

first: Madhura

middle: Meghsham

last: Modak

address: Birkendorfer Strasse 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

description: M2a AB-LIB

library_source: other

data_processing:
Single cell data was processed using CellRanger v3.0.2. using standar parameters to process FeatureBarcode data. The feature barcode FASTQ files are labelled AB-LIB and the RNA FASTQ are labelled Gen-Lib. Reads were aligned to human reference transcriptome GRCh38.93 from Ensembl. Count matrices were processed for each sample individually.
Cells were filtered using Scanpy v.1.5 with the following parameters: minimum number of genes: 500, maximum number of genes: 3500, maximum fraction of mitochondrial genes 0.20. On average each sample contained ~3.500 cells after filtering for a total of 21.000 cells.
All 6 samples were concatenated and total UMI counts per cell were normalized using SCRAN, and then converted to log (normalize values +1).
Subsequently, highly variable genes (HVG) were identified and principal component analysis (PCA) was computed using the Seurat 2 method.
UMAP was computed using 50 PCAs. In the resulting UMAPs we could validate that all 2 replicates clustered together for the three conditions.
Assembly: GRCh38.93
Supplementary files format and content: .h5 raw feature barcode file from CellRanger v3.0.2

molecule: other

source_name: Monocyte-derived macrophages

extract_protocol:
Single-cell transcriptomics libraries were generated via the Chromium Controller and the Single Cell 3′ Reagent Kit v3 (10x Genomics) according to the manufacturer’s instructions. Briefly, ~8,700 cells per sample were loaded onto a B Chip, aiming to capture 5,000 cells, with an expected 4.6% doublet rate. The Chromium Controller ran for droplet generation and reverse transcription was performed in the droplets.
80 ng of cDNA were used for the gene expression library preparation. Samples were prepared according to the 10X Genomics’ protocol, except for an additional 1 x SPRISelect Beads (Beckman Coulter, Brea, CA) to ensure full removal of primer and adaptor dimers prior to the final elution for gene expression libraries. Libraries were quantitatively and qualitatively assessed using the Qubit 4 Fluorometer (ThermoFisher) and the Fragment Analyzer (Agilent) respectively. Gene expression libraries were 440bp in average length. Libraries were normalized, pooled and sequenced on an Illumina HiSeq 4000.

treatment_protocol: Monocytes, isolated from peripheral blood, were stimulated with M-CSF (100ng/ml)  for 6 days. On day 6 the respective cytokine coktails were added for 24 hr and macrophages were differented to M1 (IFN-γ + LPS), M2a (IL4+IL-13) and M2c (IL-10) macrophages

tag: cell type

value: Macrophages

value: Peripheral blood

tag: stimulation

value: MCSF + IL-4 + IL-13


title: Monocyte-derived M2c macrophages (D2) [AB-LIB]

description: M2c AB-LIB

value: MCSF + IL-10


title: Monocyte-derived M2a macrophages (D2) [GEN-LIB]

description: M2a GEN-LIB

library_source: transcriptomic single cell


title: E14 Het rep 5


title: Monocyte-derived M2c macrophages (D2) [GEN-LIB]

description: M2c GEN-LIB


title: mRNA_2041_0.063_mkd_Liver

value: Adult

value: Crl:CD (SD); Sprague-Dawley

value: Female

value: Pregnant

tag: interval between last dosing and necropsy

tag: gestation day definition

tag: corn oil vehicle dose level


title: mRNA_2042_0.063_mkd_Liver

tag: developmental stage

value: Ketoconazole

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: mRNA_2047_0.2_mkd_Liver

value: Daily via oral gavage from gestation days 6 to 20


title: Monocyte-derived M1 macrophages (D2) [AB-LIB]

description: M1 AB-LIB

tag: tissue

value: MCSF + IFN-γ + LPS


title: E14 WT rep 5


title: E14 WT rep 4


title: mRNA_2040_0.063_mkd_Liver

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0


title: E14 WT rep 3


title: E14 Het rep 4


title: Monocyte-derived M2a macrophages (D1) [AB-LIB]

description: M2a AB-LIB


title: Monocyte-derived M2c macrophages (D1) [AB-LIB]

description: M2c AB-LIB


title: E14 WT rep 2


title: L3: Olfr16-positive cells, exposed to lyral

growth_protocol: 7 week-old Olfr16(tm2Mom/tm2Mom) were used (n=24). Mice were housed in group of 4 and maintained on a normal 12h light/dark cycle in a 24°C temperature room, with ad libitum access to food and water. All experiments were performed during daytime.

extract_protocol:
Individuals were euthanized, their olfactory epithelium extracted and processed for tissue dissociaton (for a detailed description of the protocol, please refer to the methods section of Assens et al. (2021)).To ensure the exclusive isolation of live nucleated cells, cell suspensions were incubated with 2 μg/ml of Hoechst 33342 (a UV fluorescent adenine-thymine binding dye; #H1399, Life Technologies) at 37°C for 15 min. In order to exclude dead cells, 1 μM of DRAQ7 (a far-red fluorescent DNA intercalating dye; #DR71000, BioStatus) was added to the cell suspensions before fluorescence activated cell sorting (FACS). A hundred GFP+/Hoechst+/DRAQ7- cells were collected from each cell suspension, resulting in 400 cells per biological pool. Cells were collected directly in lysis buffer from the Qiagen RNeasy plus micro kit and total RNA was isolated following the manufacturer's protocol. After the initial cell lysis step, 10 µL of 1:1000000 ERCC spike-ins mix 1 from ThermoFisher was added to each sample. The quality and quantity of total RNA were evaluated with a Bioanalyzer (Agilent).
The SMARTer™ Ultra Low RNA kit from Clontech was used for reverse transcription and cDNA amplification (12 PCR cycles) according to the manufacturer’s specifications, starting with a total volume of 9.5 µL per sample as total RNA input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at equimolarity and loaded at 11 pM for clustering on a Single-read Illumina Flow cell for the MOR23 experiment. Reads of 50 bases were generated using the SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer.

treatment_protocol: Isolated individuals were exposed for 5 hours (starting at 8 a.m.) to 5% Lyral in DMSO (exposed condition) or to DMSO alone (non-exposed condition). Each experiment was conducted on three consecutive days. Each day, 4 mice from each condition were analyzed.

tag: genetic background

tag: treatment

value: 5% Lyral in DMSO (exposed condition)

value: Main olfactory epithelium

tag: sorted cells

value: 400 Olfr16-positive cells


title: Monocyte-derived M2a macrophages (D1) [GEN-LIB]

description: M2a GEN-LIB


title: Monocyte-derived M1 macrophages (D2) [GEN-LIB]

description: M1 GEN-LIB


title: mRNA_2030_0_mkd_Liver

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Corn oil (vehicle)

value: 2 ml/kg body weight


title: E14 Het rep 2

tag: genotype

value: Het

value: Frontal cortex


title: D5: Olfr16-positive cells, not exposed

value: DMSO alone (non-exposed condition)


title: mRNA_2032_0_mkd_Liver

value: Adult

tag: pregnancy status at gestation day 21

tag: agent

tag: exposure


title: D3: Olfr16-positive cells, not exposed


title: E14 Het rep 1

tag: strain


title: D1: Olfr16-positive cells, not exposed


title: Monocyte-derived M1 macrophages (D1) [AB-LIB]

description: M1 AB-LIB

tag: cell type

value: Macrophages

value: Peripheral blood

tag: stimulation


title: E14 Het rep 3


title: mRNA_2027_0_mkd_Liver

value: Crl:CD (SD); Sprague-Dawley

value: Female

value: Pregnant

tag: interval between last dosing and necropsy

tag: gestation day definition

tag: corn oil vehicle dose level


title: mRNA_2034_0.063_mkd_Liver

tag: developmental stage

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: mRNA_2025_0_mkd_Liver

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0


title: L1: Olfr16-positive cells, exposed to lyral

tag: genetic background

tag: treatment

value: 5% Lyral in DMSO (exposed condition)

tag: tissue

value: Main olfactory epithelium


title: Monocyte-derived M1 macrophages (D1) [GEN-LIB]

description: M1 GEN-LIB

value: MCSF + IFN-γ + LPS


title: mRNA_2026_0_mkd_Liver

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Corn oil (vehicle)

value: 2 ml/kg body weight


title: mcervix_D18

city: Dallas

first: Anne

last: Cooley

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

description: scRNA-seq

data_processing:
scRNA-seq libraries were demultiplexed and mapped to the mouse reference genome (mm10) by using the Cellranger software (ver 3.0.2, 10X Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively. The contents include: filtered gene counts, genes, and cell-barcodes.

source_name: cervical tissue

extract_protocol:
Cervices were collected by dissection below the transition zone and all vaginal tissue was removed. Tissues were minced with a sterile razor. Minced cervices were dissociated with 10mg/ml cold protease (Sigma-Aldrich) with 1mg/ml DNase I (Roche) and 0.5 M EDTA (Fisher Scientific). After a 60 min incubation at 4ºC, cells were filters through a 40 µm cell strainer (BD Biosciences) and washed twice with fresh ice cold 1x PBS and then resuspended in 1x PBS +0.005% BSA.
Library prepared following 10x v3 gene expression protocol.

value: cervix

tag: timepoint

value: Gestation day 18


title: 0PAT_32℃_dup2

city: Shanghai

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

data_processing:
Raw data were processed to align to the TP53 reference sequence with ORFcall software developed by the Broad Institute (Giacomelli et al., 2018). Reads corresponding to each p53 mutant were then tallied. Reads of each p53 mutant were normalized so that the mean reads of 6 truncation mutations and 6 synonymous mutations in different libraries will be equal.
Genome_build: TP53 CDS
Supplementary_files_format_and_content: excel table includes normalized reads of each sample

source_name: Pleura/pleural effusion, lymphocyte, Myeloid

growth_protocol: U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 32 or 37℃ under 5% CO2.

extract_protocol:
Genomic DNA (gDNA) was purified using Blood Genomic DNA Mini Kit (CW2087M, CWbio). PCR reactions were carried out on gDNA to amplify mutant p53 DNA fragments. Each reaction contained a total volume of 50 μL with 1 μg gDNA, 25 μL of VAHTS HiFi Amplification Mix (N616-01, Vazyme) and 2.5 μL of each (5 μM) primer. The parameters for PCR were 95℃ for 3 min, 27 cycles of 98 ℃ for 20 s, 58 ℃ for 15 s, and 72 ℃ for 45 s, followed by one cycle of 72 ℃ for 5 min. The primers used for this reaction were TCCGCCTCCTCTTCCTCCAT (Forward) and ACACCGGCCTTATTCCAAGC (Reverse). Amplicons were separated from non-specific fragments by electrophoresis on a 1% agarose gel stained with GelSafe (EP106-01, DANAGEN), extracted from the gel, and purified using a Wizard® SV Gel and PCR Clean-Up System (A9282, Promega).
Sequencing libraries were constructed from 50 ng of purified amplicons using an TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme).

treatment_protocol: This cell library was treated with 0, 5, 10 μM PAT or sub-physiological temperature (32 ℃) for 7 days.

tag: cell lines

tag: p53 mutations

value: 827 p53 mutations

tag: culture temperature

tag: pat treatment

value: no treatment


title: mcervix_IL

description: scRNA-seq

value: In-labor


title: Monocyte-derived M2c macrophages (D1) [GEN-LIB]

description: M2c GEN-LIB

tag: cell type

value: Macrophages

value: Peripheral blood

tag: stimulation

value: MCSF + IL-10


title: 5PAT_37℃_dup1

value: 5 μM PAT


title: 5PAT_37℃_dup2


title: mcervix_D15

description: scRNA-seq

value: Gestation day 15


title: AA1

city: Jinan

first: Liwen

last: Yu

state: Shandong province

address: No.107, Wen Hua Xi Road

institute: Shandong University

description: barcode appendix: -4

data_processing:
Cellranger standard processing
**Cell filter**  Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells:  1.gene counts 500-Inf per cell.  2.UMI counts  3. the percentage of mitochondrial genes < 25% %(customized).  4.DoubletFinder for detecting doublets.
**Cell clustering**  Cell clustering contains the following steps:  1)Normalizing the data  After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
PCA(Principal component analysis): To overcome the extensive technical noise in any single gene for scRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
t-SNE (t-distributed Stochastic Neighbor Embedding) visualization: Seurat continues to use t-SNE as a powerful tool to visualize and explore these datasets. The tSNE aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Genome_build: Mus_musculus.GRCm38.96

source_name: aorta

extract_protocol:
The whole aorta was dissected into five segments and the single cell suspension was obtained by enzymatic digestion. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp)

treatment_protocol: No treatment.

tag: strain

value: aorta

tag: age

tag: Sex

value: male


title: 0PAT_37℃_dup2


title: TA2

description: barcode appendix: -3


title: 10PAT_37℃_dup2

value: 10 μM PAT


title: E14 WT rep 1

tag: genotype

value: WT

tag: developmental stage

value: Frontal cortex


title: L5: Olfr16-positive cells, exposed to lyral

tag: genetic background

value: 5% Lyral in DMSO (exposed condition)

value: Main olfactory epithelium

tag: sorted cells

value: 400 Olfr16-positive cells


title: CM cells, post-MI, rep 3

city: Saint Petersburg

first: Pavel

last: Docshin

state: Saint Petersburg

address: 2 Akkuratova st.

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

data_processing:
STAR 2.7
Raw RNASeq reads were aligned with STAR 2.7 against Rnor_6.0 (GCA_000001895.4) and transcript annotations (ensemble 97)
Assembly: rn6
Supplementary files format and content: The matrix table includes normalized abundance measurements (DESeq output) for all samples. Differential expression analysis was performed using the DESeq2 Bioconductor package.

source_name: primary cell culture

growth_protocol: Cardiac mesenchymal cells were maintained in DMEM/F12 supplemented with 20% endothelial cell media (ECM), 10% fetal bovine serum (HyClone), 100 μM MEM NEAA amino acid solution, 2 mm L-Glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using ExtractRNA kit (Evrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA sample preparation kit (Illumina)  following manufacturer's protocols.

treatment_protocol:
Myocardial infarction was induced by permanent ligation of the left coronary artery.
24 hours after the operation, post-infarction tissues were sampled to obtain primary cell cultures of cardiac mesenchymal cells.

tag: cell line

value: primary cell culture

value: mesenchymal stem cells

tag: disease state

value: myocardial infarction

tag: time

value: Day 1


title: mcervix_NP

description: scRNA-seq

tag: tissue

value: cervix

tag: timepoint

value: Non-pregnant


title: D_A

extract_protocol:
The aorta tissue was dissected into five segments and the single cell suspension was obtained by enzymatic digestion. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp)

value: Apoe-/-

tag: condition

value: Ang II-induced AAA abdominal aortic aneurysm

value: abdominal aortic aneurysm


title: AA2

description: barcode appendix: -5

value: aorta


title: IN_A


title: AOAR

description: barcode appendix: -1

value: male


title: 10PAT_37℃_dup1

tag: cell lines

tag: p53 mutations

value: 827 p53 mutations

tag: culture temperature

value: 10 μM PAT


title: 0PAT_37℃_dup1

tag: pat treatment

value: no treatment


title: CM cells, control, rep 1

tag: cell type

value: WT

value: healthy


title: TA1

description: barcode appendix: -2

tag: strain

tag: age


title: scATAC-Seq library of preMegE cells

city: Lund

first: Göran

last: Karlsson

state: Scania

address: Kilinkgatan 26 BMC B12

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

data_processing:
ScATAC-Seq:Cell identification: The sequencing data were processed using cellranger-atac pipeline (v 1.1.0) from 10x Genomics to obtain the aligned reads. The pipeline annotates each aligned read with a cell barcodes (corrected or uncorrected). Mouse mm10 genomic assembly was used as the reference. The number of fragments associated with each barcode was used as a filter to remove the background barcodes. Barcode multiplets were removed using 10x Genomics recommended scripts for v1.1.0. Additionally, the cells with percentage mitochondrial contamination > 3 or less than -1 (both values in log2 scale) were removed.
ScATAC-Seq: Peak calling: Fragments associated with valid cell barcodes was obtained from cellranger-atac generated BAM files. Only properly aligned read-pairs, each with MAPQ > 20 were retained. Based on the read pairs, both ends of the fragments (accounting for soft clipping of reads during alignment) were identified and these were considered as cut sites and used in downstream analysis. A cell-barcode was allowed only one cut site for a particular genomic location. The cut sites were aggregated from all the cell barcodes, de-duplicated and saved in BED format where each line is 1 nucleotide-long range with start position indicating the cut site. MACS2 was called on the aggregated BED files separately for each chromosome to speed up the peak calling process. Default MACS2 parameters were overridden with  -s=150 --nomodel --shift=-75 --extsize=150 and the genome size parameter was set as the respective chromosome size. The narrow peaks from each chromosome were merged to create a reference peak set for use in the downstream analyses. For each cell, the number of cut sites within the peak set was counted, and the resulting cell-peak matrix was saved in the MTX format.
ScRNA-Seq: The data were processed using Cellranger 3.0.2 to generate counts matrices against the mm10 transcriptome. Seurat v2 R package was used to filter and normalize the data.
Genome_build: mm10
Supplementary_files_format_and_content: ScATAC-Seq: MTX format sparse matrix contain insertion site counts in peak and cells. ScRNA-Seq: MTX format sparse matrix containing UMI counts in genes and ells.

source_name: Bone marrow from all bones

extract_protocol:
ScRNA-Seq: LSKCD34+Flt3intCD9high, LSKCD34+Flt3intCD9low, and LSKCD34+Flt3int cells were sorted from the bone marrow of age-matched C57BL/6J mice, and loaded into 10X Chromium lanes, and the libraries were prepared as per the instruction manual of 10X Chromium. The final libraries were paired-end sequenced using 26 cycles for Read 1, 8 cycles for i7 index, and 98 cycles for read 2.  SCATAC-Seq: LSKCD34-Flt3- (LT-HSC), LSKCD34+Flt3- (ST-HSC), LSKCD34+Flt3int (LSKFlt3int), LSKCD34+Flt3high (LMPP), LSKFlt3-CD150+CD48+ (MPP2), Lin-Sca1-Kit+FcgRII/IIIlowCD150+EndoglinlowCD41-/low (Pre-MegE), LSKCD34+Flt3intCD9high (LSKCD9high), and LSKCD34+Flt3intCD9low (LSKCD9low) cells were sorted, and nuclei isolated following 3 minutes of cell lysis as per low input protocol from 10X Genomics, CA, USA. Single-cell chromatin accessibility profiles were generated by tagmentation followed by library preparation according to the Chromium Single Cell ATAC Reagent Kits User Guide (Satpathy A, 2019). The libraries were run on TapeStation (Agilent, CA, USA) and sequenced on Nova-Seq (Illumina Inc, CA, USA) using SP100 flow cell with the following specification: 48 (49 for MPP2 and preMegE) cycles for read 1N, 8 cycles for i7 index, 16 cycles for i5 index and 48 (50 for MPP2 and preMegE)  cycles for read 2N.
ScRNA-Seq: As per 10x genomics instructions for Chromium (v2). ScATAC-Seq. As per 10x genomics instructions for v1 and v1.1 of single cell ATAC protocol

tag: genotype/variation

value: 8-12 weeks

value: Bone marrow from all bones

value: preMegE cells


title: CM cells, post-MI, rep 1

value: primary cell culture

value: mesenchymal stem cells

tag: genotype

value: myocardial infarction


title: scATAC-Seq library of FLT3int cells

value: FLT3int cells


title: 0PAT_32℃_dup1


title: CM cells, post-MI, rep 2

value: Day 1


title: scATAC-Seq library of FLT3intCD9hi cells

value: FLT3intCD9hi cells


title: CM cells, control, rep 3


title: myocardium, control, rep 3

source_name: tissue

value: tissue


title: scATAC-Seq library of LMPP cells

value: LMPP cells


title: myocardium, post-MI, rep 3


title: myocardium, post-MI, rep 1


title: LI

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Reads were processed using 10X’s Cell Ranger version 3.0.2 using the mm10 reference genome, resulting in a filtered HDF5 file
Further processing and analysis of scRNA-Seq data were performed in R version 3.6.3 using the Seurat package version 3.2.1
Cell Ranger output was imported using the Read10X_h5. Seurat objects were created using only genes appearing in at least 3 cells. Cells were further filtered to exclude those with fewer than 1000 genes detected, more than 5000 genes detected, or more than 10 percent mitochondrial reads.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 (.h5) files generated by CellRanger 3.0.2
Supplementary_files_format_and_content: TSV file contains cell (barcode) metadata from final processed Seurat object. Includes cluster identities and UMAP embedding coordinates

source_name: Large intestinal sorted GFP+ TCRb+ cells and GFP+ TCRb- cells

extract_protocol:
Standard Illumina/10X protocols
single cell RNAseq


title: myocardium, post-MI, rep 2


title: myocardium, control, rep 1


title: scATAC-Seq library of MPP2 cells

value: MPP2 cells


title: OKC-4 Human odontogenic keratocyst tissue

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

description: Odontogenic keratocyst tissue collected from human patient #4

data_processing:
FastQC was used for trimming adapter sequences and discarding low quality reads.
The reads were mapped on the human reference genome (GRCh37/hg19) and gene expression matrix was generated using TopHat and Cufflinks.
Differentially expressed genes (DEGs) were identified using DEGseq, an R package for DEG analysis, with adjusted p-value < 0.05 and |fold change| > 4 threshold.
Gene ontology analysis was performed using clusterProfilter, a R package for interpretation of omics data.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Human odontogenic keratocyst

extract_protocol:
Total RNA for RNA-seq was isolated using RNeasy Mini Kit, and mRNA libraries were prepared using the TruSeq Stranded mRNA Preparation kit
mRNA libraries were prepared using the TruSeq Stranded mRNA Preparation kit (Illumina) according to the manufacturer’s instructions.

value: epithelial neoplasm in jaw

tag: disease name

value: Odontogenic keratocyst


title: CM cells, control, rep 2


title: myocardium, control, rep 2


title: AM-5 Human ameloblastoma tissue

description: Ameloblastoma tissue collected from human patient #5

source_name: Human ameloblastoma

value: Ameloblastoma


title: OKC-1 Human odontogenic keratocyst tissue

description: Odontogenic keratocyst tissue collected from human patient #1


title: wt E9.5 ATAC-seq, G1, replicate 1

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way, RMB, Pod B, 912E, UCSF

institute: UCSF

description: gDNA

data_processing:
Quant-seq and Hyperprep RNA-seq libraries were all processed as follows. Adapters were trimmed with Cutadapt v1.18 using input parameters of "-m 20 -a "A{18}" -a "T{18}" -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC". Trimmed reads were aligned using STAR v2.7.1a to mm10/Gencode M14 using input commands of "--outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.05 --seedSearchStartLmax 25 --winAnchorMultimapNmax 100". Aligned reads were counted using FeatureCounts v1.6.4.
miRNA-seq libraries were processed as follows. Reads were trimmed and demultiplexed using Cutadapt v1.18 using input parameters of "-a adapters.fa -u 4 --max-n 0 -e 0 -m 17 -M 30 --discard-untrimmed --overlap 10". mIRNA sequences were aligned to mature mouse miRNAs in miRBase v21 using the default settings in STAR v2.7.1a. Only uniquely aligned reads were retained and those between 20-24 bp were counted.
Drop-seq single-cell RNA-seq libraries were processed using Drop-seq tools v1.12. This workflow was set to call STAR v2.7.1a and align to mm10.
10X single-cell RNA-seq libraries were processed using the default parameters of CellRanger v3.0.2. Reads were aligned to mm10.
ATAC-seq libraries were processed as follows. Adapters were trimmed with Cutadapt v1.18 using input parameters of "-b adapters -B adapters -m 17 -e 0 -O 7 -p". Trimmed reads were aligned with Bowtie2 v2.3.5 to mm10 using input commands of "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 2000". Mitochondrial reads were removed with Samtools v1.9 and duplicate reads were removed with Picard Markduplicates v2.20.2.
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts

source_name: E9.5 mouse embryos

growth_protocol: All mice were fed standard lab chow and maintained on a 12hr light/dark cycle.

extract_protocol:
For each ATAC-seq sample, 50 000 fresh FAC-sorted cells were resuspended in 10mM Tris-HCl (pH7.5), 10 mM NaCl and 3mM MgCl2. Cells were then lysed in 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 3 min on ice.
Transposition and library construction were performed as detailed by Corces et al., 2017 (PMID:28846090).

treatment_protocol: For all mRNA-seq experiments, live cells were dissociated at 37°C in HBSS containing 1% trypsin and 10uM EDTA, and then stained for DNA content by incubation with 10ng/ml Hoechst 33342 (ThermoFisher) in HBSS +2% FBS for 45 minutes at 37°C prior to sorting.

value: wt

value: embryo

tag: embryonic stage

tag: cell cycle phase

tag: library

value: ATAC-seq


title: scATAC-Seq library of FLT3intCD9lo cells

value: WT

value: 8-12 weeks

value: Bone marrow from all bones

value: FLT3intCD9lo cells


title: p27-/- E9.5 single-cell mRNA, G1, replicate 1

description:
mRNA
10X barcodes & UMI are available in Read 1: Cell Barcode (16bp), UMI (10bp), polyA tail

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions (Invitrogen)
10X libraries were prepared according to the manufacturer's instructions for Chromium (10X Genomics).

value: Single-cell RNA-seq (10X Chromium)


title: wt E9.5 ATAC-seq, G2/M, replicate 1

description: gDNA


title: scATAC-Seq library of LTHSC cells

value: LTHSC cells


title: wt E9.5 ATAC-seq, G2/M, replicate 2

description: gDNA


title: wt E9.5 ATAC-seq, G2/M, replicate 3

description: gDNA


title: scATAC-Seq library of STHSC cells

value: STHSC cells


title: OKC-3 Human odontogenic keratocyst tissue

description: Odontogenic keratocyst tissue collected from human patient #3


title: wt E9.5 ATAC-seq, G1, replicate 2

description: gDNA


title: minimal change disease_sample89

first: Sehoon

last: Park

address: Daehak-ro 101

institute: Seoul National University Hospital

data_processing:
Bowtie2 (version 2.1.0.0) for mapping
featureCounts was used to quantify gene expression (uniquely mapped reads)
Genome_build: GRCh73.p13
Supplementary_files_format_and_content: tab-delimited text files include raw read counts

source_name: Kidney tubulointerstitium

extract_protocol:
Biopsy cores from kidney disease patients were obtained from punch biopsies performed between 2010 and 2017 and stored in RNAlater (Qiagen, Hamburg, Germany) at -80°C. We collected samples from 46 patients with IgA nephropathy, 3 with diabetes mellitus nephropathy, 3 with focal segmental glomerulosclerosis, 3 with lupus nephritis, 4 with membranous nephropathy, and 9 with minimal change disease, according to sample availability. Patients with profound kidney dysfunction and those with an estimated glomerular filtration rate (eGFR) < 30 mL/min/1.73 m2 were not considered for this study. To establish the control group, normal cortical tissues were collected from the non-cancer-affected cortex of 22 renal carcinoma patients who exhibited no evidence of CKD (eGFR < 60 mL/min/1.73 m2 or detected dipstick albuminuria). These nephrectomy control group samples were also stored in RNAlater immediately after surgical excision via the same protocol used for the biopsy core tissues. The frozen cortical tissues from the nephrectomy controls were initially cut into the size of a biopsy core, and all collected kidney tissues were manually microdissected under a stereomicroscope (Olympus, Japan) to remove glomeruli. After thorough removal of glomeruli, total RNA was extracted from the remaining tubulointerstitial tissues using an RNeasy Micro Kit (Qiagen, Hamburg, Germany).
A TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) was used to construct cDNA libraries. Paired-end RNA-seq was performed on the HiSeq 2500 platform (Illumina, CA, USA), and 100-base-pair sequences were obtained as in FASTQ format.

value: Kidney tubulointerstitium

tag: diagnosis

value: minimal change disease

tag: estimated gfr (ckd-epi)

tag: technical outlier

value: No


title: AM-4 Human ameloblastoma tissue

description: Ameloblastoma tissue collected from human patient #4

tag: tissue


title: AM-2 Human ameloblastoma tissue

description: Ameloblastoma tissue collected from human patient #2


title: miR-302-/- E7.5 single-cell mRNA, G1, replicate 1

source_name: E7.5 mouse embryos


title: p27-/- E9.5 single-cell mRNA, G2/M, replicate 1


title: miR-302-/- E7.5 single-cell mRNA, G2/M, replicate 1


title: minimal change disease_sample90


title: minimal change disease_sample88


title: wt E9.5 ATAC-seq, G1, replicate 3

description: gDNA


title: minimal change disease_sample87


title: minimal change disease_sample86


title: wt E9.5 single-cell mRNA, G2/M, replicate 2

description:
mRNA
Drop-seq barcodes & UMI are available in Read 1: Cell Barcode (12bp), UMI (8bp), polyA tail

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions (Invitrogen)
The published Drop-seq protocol (Macosko et al., 2015), with a few revisions to the published protocol: we added 0.5M NaCl to the lysis buffer to enhance RNA binding, 2) used beads manufactured by Biosearch (non-catalog), 3) used a flow-rate of 3ml/hr for both the cell suspension and beads as well as a flow-rate of 11ml/hr for the oil, 4) a custom fabricated PDMS device that generates droplets 120um in diameter and 5) used 6000 beads per PCR reaction. 100,000 cells were inputted from each phase of each of the two E9.5 samples. Viability of all input populations exceeded 90%. Cells were resuspended at 100,000 cells per ml, with beads at 120,000 beads per ml to target 5% cell capture.

value: Single-cell RNA-seq (Drop-seq)


title: minimal change disease_sample84


title: minimal change disease_sample85


title: Cisplatin+ICB tumor 1 [NP60]

city: Nedlands

first: Nicola

last: Principe

state: WA

address: 6 Verdun St

country: Australia

institute: University of Western Australia

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0 and Real Time Analysis (RTA) v3.4.4
Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data
Sequences mapped to the GRCm38/mm10 genome using Kallisto (v0.46.0)
Transcripts with low counts were removed and count matrices were complied using Tximport (v1.18)
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrices

source_name: AB1HA mesothelioma tumor

growth_protocol: BALB/c.AusBP mice were inoculated subcutaneously with 5x105 AB1HA tumor cells on the right hand flank. Mice were monitored and tumors were measured (mm^2) 3 times a week.

extract_protocol:
Whole tumors were harvested and stored in RNAlater (Life Technologies) at -80C. RNA was extracted from frozen tumors using the RNeasy Plus Mini Kit & Tissue Ruptor (QIAGEN). 1ug of RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols at the Australian Genome Research Facility (Melbourne, VIC, Australia)
RNA-Seq (100-base pair single-end on Illumina HiSeq platform)

treatment_protocol: When tumors were 20-25mm^2 (approx 10-11 days post inoculation), mice were treated with either PBS, anti-CTLA-4 (100ug) & anti-PD-L1 (100ug) ICB, 5-FU (75mg/kg), Cisplatin (6mg/kg) according to the appropriate treatment group. All treatments were administered intraperitoneally except 5-FU which was administered intravenously via tail vein injection. Mice receiving ICB were administered with 2 additional doses of anti-PDL-1 (100ug) 2 days apart. Tumors from all groups were harvested 2 days after the last anti-PD-L1 dose or 7 days after treatment initation for analysis

value: tumor

tag: cell line

value: AB1-HA mesothelioma

tag: treatment

value: Cisplatin+ICB

tag: timepoint

value: 7 days post treatment


title: miR-302+/- E7.5 single-cell mRNA, G1, replicate 1

value: embryo


title: wt E9.5 single-cell mRNA, G2/M, replicate 1

value: wt


title: wt E9.5 single-cell mRNA, S, replicate 2

value: S


title: Cisplatin+ICB tumor 3 [NP62]


title: wt E9.5 single-cell mRNA, G1, replicate 2


title: wt E9.5 single-cell mRNA, G1, replicate 1


title: Cisplatin+ICB tumor 4 [NP63]


title: minimal change disease_sample82


title: miR-302+/- E7.5 single-cell mRNA, G2/M, replicate 1


title: p27-/- E9.5 3' end count mRNA, G2/M, replicate 3

description: mRNA

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions (Invitrogen)
Quant-seq libraries were prepared according to the manufacturer's instructions (Lexogen)

value: Quant-seq 3' end counting


title: Cisplatin+ICB tumor 2 [NP61]


title: wt E9.5 single-cell mRNA, S, replicate 1


title: Cisplatin+ICB tumor 5 [NP64]


title: Membranous nephropathy_sample81

value: Membranous nephropathy


title: 5-FU+ICB tumor 5 [NP54]


title: 5-FU+ICB tumor 3 [NP52]


title: Membranous nephropathy_sample79


title: Membranous nephropathy_sample80


title: minimal change disease_sample83


title: 5-FU+ICB tumor 4 [NP53]


title: p27-/- E9.5 3' end count mRNA, G1, replicate 3

description: mRNA


title: Membranous nephropathy_sample78


title: 5-FU+ICB tumor 2 [NP51]


title: 5-FU+ICB tumor 1 [NP50]


title: p27-/- E9.5 3' end count mRNA, G2/M, replicate 2

description: mRNA


title: Lupus nephritis_sample75

value: Lupus nephritis


title: Lupus nephritis_sample76


title: Lupus nephritis_sample77


title: Cisplatin tumor 4 [NP44]

value: Cisplatin


title: p27-/- E9.5 3' end count mRNA, G2/M, replicate 1

description: mRNA


title: Cisplatin tumor 3 [NP43]


title: p27-/- E9.5 3' end count mRNA, G1, replicate 2

description: mRNA


title: p27+/+ E9.5 3' end count mRNA, G2/M, replicate 3

description: mRNA


title: Cisplatin tumor 1 [NP40]


title: Cisplatin tumor 2 [NP42]


title: FSGS_sample73

value: FSGS


title: FSGS_sample74


title: Diabetic nephropathy_sample71

value: Diabetic nephropathy


title: FSGS_sample72

value: Kidney tubulointerstitium


title: 5-FU tumor 4 [NP33]

value: 5-Florouracil (5-FU)


title: 5-FU tumor 3 [NP32]


title: Diabetic nephropathy_sample70

value: No


title: Diabetic nephropathy_sample69


title: 5-FU tumor 2 [NP31]


title: p27+/+ E9.5 3' end count mRNA, G2/M, replicate 2

description: mRNA


title: p27+/+ E9.5 3' end count mRNA, G2/M, replicate 1

description: mRNA


title: p27+/+ E9.5 3' end count mRNA, G1, replicate 2

description: mRNA


title: Control_sample68

value: Control


title: p27-/- E9.5 3' end count mRNA, G1, replicate 1

description: mRNA


title: p27+/+ E9.5 3' end count mRNA, G1, replicate 1

description: mRNA


title: ICB tumor 4 [NP23]

value: tumor

value: ICB (anti-CTLA-4/anti-PD-L1)


title: 5-FU tumor 1 [NP30]

value: AB1-HA mesothelioma


title: p27+/+ E9.5 3' end count mRNA, G1, replicate 3

description: mRNA


title: Control_sample66


title: ICB tumor 5 [NP24]

value: 7 days post treatment


title: miR-302-/- E8.5 3' end count mRNA, G2/M, replicate 3

description: mRNA

source_name: E8.5 mouse embryos

value: embryo


title: miR-302-/- E8.5 3' end count mRNA, G2/M, replicate 2

description: mRNA


title: miR-302-/- E8.5 3' end count mRNA, G1, replicate 3

description: mRNA


title: ICB tumor 3 [NP22]


title: 5-FU tumor 5 [NP34]


title: Control_sample65


title: miR-302-/- E8.5 3' end count mRNA, G2/M, replicate 1

description: mRNA


title: miR-302-/- E8.5 3' end count mRNA, G1, replicate 2

description: mRNA


title: Control_sample63


title: miR-302-/- E8.5 3' end count mRNA, G1, replicate 1

description: mRNA


title: Control_sample62


title: miR-302+/- E8.5 3' end count mRNA, G1, replicate 3

description: mRNA


title: Control_sample61


title: Control_sample67


title: miR-302+/- E8.5 3' end count mRNA, G2/M, replicate 3

description: mRNA


title: Control_sample59


title: PBS tumor 3 [NP13]

value: PBS


title: Control_sample58


title: PBS tumor 1 [NP11]


title: miR-302+/- E8.5 3' end count mRNA, G2/M, replicate 2

description: mRNA


title: PBS tumor 2 [NP12]


title: Control_sample56


title: Control_sample57


title: Control_sample55


title: miR-302+/- E8.5 3' end count mRNA, G1, replicate 1

description: mRNA


title: leukemia stem cells with conditional deletion of Plcg1 in AML1-ETO9a mouse model_Sample 4

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

description:
4_A
mRNA single end RNAseq of leukemia stem cells with conditional deletion of Plcg1 in AML1-ETO9a mouse model

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads  (Illumina) were aligned to reference genome mm10 and gtf.-transcriptome annotation release M7 (GENCODE) using STAR two-pass mode ( star 2.4.2a).
GENCODE M7 gtf.-file was used for quantification, performed by STAR (star 2.4.2a) , followed by normalization, transformation and differential gene expression analysis in DEseq2 -1.12.4.
Genome_build: mm10
Supplementary_files_format_and_content:
[tab.counts]  counts for each sample
[tab_pclg1_in_amleto.tsv_DESeq2results_countsNormalized.txt]  counts, data matrix
[tab_pclg1_in_amleto.tsv_DESeq2results_countsNormalizedTransformed.txt]  counts, data matrix, transformed by regularized logarithm (base 2), see manual of DEseq2

source_name: Plcg1 -/- in AML1-ETO9a stem cells (LCSs)

extract_protocol:
RNA extraction was performed using Trizol reagent (Invitrogen) according manufacturer instructions.
Library was generated using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) followed by Nextera XT Kit (Illumina).

value: Kit+ AML1-ETO9a leukemia stem cells (LSCs)

value: Plcg1 -/-


title: Control_sample64


title: leukemia stem cells with conditional deletion of Plcg1 in AML1-ETO9a mouse model_Sample 2

description:
2_A
mRNA single end RNAseq of leukemia stem cells with conditional deletion of Plcg1 in AML1-ETO9a mouse model


title: wt E9.5 embryo miRNA, replicate 9

description: miRNA

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions (Invitrogen)
miRNA libraries were prepared as described in Belair et al. 2019. In brief, miRNAs were purified from total RNA using the miRNeasy kit (Qiagen). miRNAs were then ligated to 3’ adaptors with NNNN at each 5’ end to reduce ligation bias and a unique barcode for each sample. Each 3’ ligated sample was then size-selected for miRNAs and pooled. The pool was ligated to a common 5’ adapter, reverse-transcribed, amplified for 14 cycles and single-end sequenced on a Hi-seq4000.

value: wt

value: miRNA


title: wt E9.5 embryo miRNA, replicate 8

description: miRNA


title: leukemia stem cells with wild-type Plcg1 in AML1-ETO9a mouse model_Sample 1

description:
1_A
mRNA single end RNAseq of leukemia stem cells with wild-type Plcg1 in AML1-ETO9a mouse model

source_name: Plcg1 +/+ in AML1-ETO9a stem cells (LCSs)

value: Plcg1 +/+


title: leukemia stem cells with conditional deletion of Plcg1 in AML1-ETO9a mouse model_Sample 6

description:
6_A
mRNA single end RNAseq of leukemia stem cells with conditional deletion of Plcg1 in AML1-ETO9a mouse model


title: leukemia stem cells with wild-type Plcg1 in AML1-ETO9a mouse model_Sample 3

description:
3_A
mRNA single end RNAseq of leukemia stem cells with wild-type Plcg1 in AML1-ETO9a mouse model


title: ICB tumor 2 [NP21]


title: Control_sample54


title: miR-302+/- E8.5 3' end count mRNA, G1, replicate 2

description: mRNA

value: Quant-seq 3' end counting


title: ICB tumor 1 [NP20]


title: wt E9.5 embryo miRNA, replicate 6

description: miRNA


title: Control_sample52


title: wt E9.5 embryo miRNA, replicate 7

description: miRNA


title: Control_sample51


title: Control_sample50


title: S2

first: Giyong

last: Jang

address: Daehakro

institute: Seoul national university, college of medicine

data_processing:
Sequencing of the QC-passed libraries was performed on the NovaSeq 6000 sequencing system (Illumina) in paired-end with 101-nt read length.
The pre-processed trimmed reads were mapped to the genomic DNA reference UCSC hg 19 (original GRCH3 7 from NCBI, Feb. 2009) using the HISAT2 program, which is capable of splice junction processing.
After reading the mapping, transcript assembly was performed using the StringTie  program.
As a result, the expression profile values for each sample were obtained for the known transcripts, and the read count and FPKM (Fragment per Kilobase of transcript per Million mapped reads) were acquired based on the transcript/gene.
Assembly: hg19

source_name: pancreas

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10 units/ml human recombinant insulin (Merck, 91077C), 15% fetal bovine serum (FBS), and 1% penicillin-streptomycin (PS) solution.

extract_protocol:
A TruSeq Stranded mRNA LT Sample Prep Kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreas

value: Derivative cells

value: Pancreatic epithelial cell

value: hypoxia and gemcitabine


title: Control_sample53

value: Kidney tubulointerstitium

value: Control

value: No


title: Control_sample49


title: wt E9.5 embryo miRNA, replicate 4

description: miRNA


title: wt E9.5 embryo miRNA, replicate 5

description: miRNA


title: S1


title: wt E9.5 embryo miRNA, replicate 1

description: miRNA


title: wt E9.5 embryo miRNA, replicate 2

description: miRNA


title: Control_sample47


title: A

value: Monocyte


title: wt E9.5 embryo miRNA, replicate 3

description: miRNA


title: 5637 cells, siMYBL2-2

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

growth_protocol: 5637 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
The RNA was isolated from 5637 cells using RNeasy Mini Kit (cat. #74101; Qiagen, Duesseldorf, Germany) followed the manufacturer’s protocol. In each RNA sample, contamination of genomic DNA is removed through DNase I digestion (cat. #79254; Qiagen). The NanoPhotometer (cat. #N60; Implen, Munich, Germany) was used to measure the quantity of each RNA sample.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: Transfection of siRNA follows Lipofectamine 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: bladder cancer cells

value: WT

value: siRNA transfection


title: wt E8.5 embryo miRNA, replicate 3

description: miRNA

value: embryo


title: 5637 cells, siMYBL2-1


title: IgAN_sample45

value: IgAN


title: 68_MC38shC

type: RNA

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

description: Normalization and summarizzation performed with RMA algorith

hyb_protocol: Arrays were prepared according to Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit

scan_protocol: Scanner 3000 7G

data_processing: Expression console software and Transcriptome console software 3.0 from Affymetrix

label_protocol: Arrays were prepared according to Affymetrix specifications with GeneChip™ WT Pico Reagent Kit

growth_protocol: cells were cultured in minimum supplemented medium (DMEM+10% FBS + 1% PEN/STREP)

extract_protocol: Total RNA from the cells was extracted with the Trizol protocol followed by Qiagen RNeasy Mini Kit

treatment_protocol: Subculturing of plasmid or shRNA expressing cell lines is done in DMEM + 10% FBS + 4-6 µM puromycin

tag: sample type

value: colon carcinoma cell line; lentiviral transduction of shControl


title: 69_MC38shKras

value: colon carcinoma cell line; lentiviral transduction of shKras


title: wt E8.5 embryo miRNA, replicate 2

description: miRNA

value: wt

value: miRNA


title: wt E8.5 embryo miRNA, replicate 1

description: miRNA


title: IgAN_sample44


title: IgAN_sample43


title: Control_sample48


title: B

value: pancreas

tag: cell type


title: IgAN_sample42


title: wt E7.5 embryo miRNA, replicate 3

description: miRNA


title: wt E7.5 embryo miRNA, replicate 2

description: miRNA


title: IgAN_sample46


title: IgAN_sample41


title: wt E7.5 embryo miRNA, replicate 1

description: miRNA


title: IgAN_sample40


title: IgAN_sample39


title: wt E9.5 full-length transcripts, G2/M, replicate 3

description: mRNA

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions (Invitrogen)
Hyperprep libraries were prepared according to the manufacturer's instructions.  (Kapa RNA Hyperprep full-length transcripts (Roche))

value: Hyper prep RNA-seq


title: wt E9.5 full-length transcripts, G2/M, replicate 2

description: mRNA


title: 5637 cells, siNC


title: wt E9.5 full-length transcripts, G2/M, replicate 1

description: mRNA


title: IgAN_sample38


title: sample96

first: Kuang-Chen

last: Tsai

state: State...

address: No.1095 Jie Fang Avenue, Hankou, Wuhan 430030, P.R. China.

institute: Huazhong university of science and technology

data_processing:
Image to base conversion via CASAVA
Trim_galore performs quality control and data cleaning on sequence data
Sequence mapping via HISAT2 v 2.2.1
Transcript count matrix generated by Subreads v 2.0.3
DEseq2 normalize matrix
Assembly: Homo_sapiens.GRCh37.75.gtf

source_name: tumor

extract_protocol:
RNA was harvested using TRIzol (Takara). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq PE Cluster Kit v3-cBot-HS（Illumia） following manufacturer's protocols.

tag: disease state

value: hepatocellular carcinoma

value: tumor

value: without treatment


title: IgAN_sample37

value: Kidney tubulointerstitium


title: sample82


title: sample98


title: sample90


title: sample93


title: sample91


title: sample83


title: wt E9.5 full-length transcripts, G1, replicate 3

description: mRNA


title: IgAN_sample36

value: No


title: IgAN_sample35


title: wt E9.5 full-length transcripts, G1, replicate 2

description: mRNA


title: sample81


title: sample79


title: wt E9.5 full-length transcripts, G1, replicate 1

description: mRNA


title: IgAN_sample34


title: wt E8.5 full-length transcripts, G2/M

description: mRNA


title: sample76


title: IgAN_sample33


title: sample74


title: IgAN_sample32


title: wt E9.5 3' end count mRNA, G2/M, replicate 1

description: mRNA

value: Quant-seq 3' end counting


title: sample73


title: IgAN_sample31


title: IgAN_sample30


title: IgAN_sample29


title: sample72


title: wt E8.5 3' end count mRNA, G2/M, replicate 2

description: mRNA


title: sample69


title: wt E9.5 3' end count mRNA, G2/M, replicate 2

description: mRNA


title: sample70


title: wt E9.5 3' end count mRNA, G1, replicate 1

description: mRNA


title: sample68


title: sample78


title: wt E9.5 3' end count mRNA, G1, replicate 2

description: mRNA


title: IgAN_sample26


title: sample49


title: wt E8.5 3' end count mRNA, G2/M, replicate 1

description: mRNA


title: wt E8.5 3' end count mRNA, G1, replicate 2

description: mRNA


title: wt E8.5 full-length transcripts, G1

description: mRNA


title: sample67


title: IgAN_sample25


title: wt E8.5 3' end count mRNA, G1, replicate 1

description: mRNA


title: wt E7.5 3' end count mRNA, G2/M, replicate 2

description: mRNA


title: IgAN_sample24


title: IgAN_sample27


title: IgAN_sample28


title: wt E7.5 3' end count mRNA, G2/M, replicate 1

description: mRNA


title: IgAN_sample22


title: sample123


title: sample119


title: sample114


title: IgAN_sample19


title: wt E7.5 3' end count mRNA, G1, replicate 1

description: mRNA


title: miR-302+/- E8.5 3' end count mRNA, G2/M, replicate 1

description: mRNA


title: IgAN_sample21


title: sample110


title: wt E7.5 3' end count mRNA, G1, replicate 2

description: mRNA


title: TEAD1 ChIPseq

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

description: TEAD1 immunoprecipitated DNA

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
Reads were aligned to the human genome (hg38) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: hg38
Supplementary files format and content: bigiwg

source_name: Primary HUVECs from pooled donors at 48h

growth_protocol: Pooled human umbilical vein endothelial cells (HUVECs) were purchased from Lonza (#CC-2519) and cultured in endothelial basal medium (EBM, Lonza) supplemented with hydrocortisone (1 µg/mL), bovine brain extract (12 µg/mL), gentamicin (50 µg/mL), amphotericin B (50 ng/mL), human recombinant epidermal growth factor (10 ng/mL), and 10% fetal bovine serum (FBS, Life Technologies).

extract_protocol:
HUVECs were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 μg of antibody. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: HUVECs were cultured for 48 hours before endogous chromatin immunoprecipitation was performed.

value: HUVECs

value: Wild type

tag: chip antibody


title: IgAN_sample18

value: Outlier_excluded from main analysis


title: PANC1_KD2

city: Tainan City

first: Po-Hsien

last: Huang

address: No.1, University Road

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Cheng Kung University

description: Bisulfite-treated mRNA

data_processing:
Base-calling conducted by Illlumina bcl2fastq2
Sequence reads were first filtered to remove low-quality reads (Q < 20) and adapter contaminations by Galaxy Trim Galore! with read1 parameters “-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC” and read2 parameters “-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT”. A number of libraries were sequence twice to make each sample with approximately 30M expected mapped reads, therefore the reads of two runs were pooled after filtered and trimmed. The filtered reads then mapped to in silico converted human genome GRCh38 using the splice-aware alignment tool meRanGh from meRanTK with parameters “-mmr 0.1”.
5-methylcytosine calling was conducted by meRanCall with parameters “-md 5 –ei 0.1 –cr 0.99 -mcov 10 –gref -mr 0.05 -fdr 0.05”
The Multi-Join tool in Galaxy (usegalazy.org) was utilized to combine multiple 5-methylcytosine sites called from libraries in each cell line, and only sites present in at least 2 control (CT) libraries in each cell line were kept.
By comparing the average methRate of CT and KD samples, the sites with at least 0.05 decreased methR in each cell lines were identified. Finally, the differential mehtylated  sites that are common in at least 2 cell lines were classified into NSUN2-m5C sites.
Assembly: hg38
Supplementary files format and content: NSUN2-dependent 5-methylcytosine sites text file

growth_protocol: BxPC-3 cells were maintained in the RPMI medium supplemented with 10% FBS, 100 units/ml penicillin and 100 ug/ml streptomycin. MiaPaCa-2 cells were maintained in the DMEM medium supplemented with 10% FBS, 100 units/ml penicillin and 100 ug/ml streptomycin. PANC1 cells were maintained in the DMEM medium supplemented with 10% FBS, 100 units/ml penicillin and 100 ug/ml streptomycin. All three cells were incubated at 37℃ and maintained with 5% CO2.

extract_protocol:
About 1 X 10^7 cells were lysed with 900µl TRI reagent, and the total RNA was extracted with Direct-zol RNA miniPrep Plus (Zymo, Irvine, CA)  according to manufacturer's instruction. Average 30-40 µg total RNA was proceed to mRNA enrichment, which were done by oligo (dT)25 magnetic beads from Dynabeads mRNA DIRECT purification kit (Thermo Fisher Scientific, Waltham, MA). Then, the enriched mRNA samples were subjected to bisulfite conversion using EZ RNA methylation kit (Zymo, Irvine, CA) according to manufacturer's instruction. With one adjustment that the incubation step was modified into three cycles of 70℃ 10 minutes and 64℃ for 45 minutes followed by Amort et al. method.
About 20ng of bisulfite-treated mRNA was used to generate sequencing library. Libraries were built with NEBNext Ultra Ⅱ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) arrording to manufacturer's instruction. The fragmentation step was omitted due to previous bisulfite treatment had already resulted in fragmentation of RNA sequences to 200-500nt.

treatment_protocol: Cells were infected with lentivirus at the indicated multiplicity of infection (MOI) value of 2 to 3 in the presence of polybrene (BxPC-3: 2µg/ml, PANC1: 4µg/ml, and MiaPaCa-2: 2µg/ml). After 24 hours of incubation, the medium was changed to puromycin supplemented medium (BxPC-3: 1µg/ml, PANC1: 4µg/ml, and MiaPaCa-2: 1µg/ml) to select stable target gene knockdown clones.

value: pancreatic cancer cell

value: shNSUN2 Lentivirus


title: sample128


title: sample109


title: IgAN_sample20

value: IgAN


title: IgAN_sample23


title: PANC1_KD1

description: Bisulfite-treated mRNA


title: IgAN_sample17


title: IgAN_sample16


title: sample115


title: sample106


title: sample104


title: IgAN_sample15


title: Bulk RNA sequencing [BMPE]

city: Utrecht

first: Jens

last: Puschhof

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Organoids were lysed in RLT buffer, RNA was extracted and libraries prepared for bulk RNAseq
BULKBMP_data_ileum.csv

data_processing:
Sequencing data were demultiplexed, paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19. For MUC2-Neon reporter organoids, the sequence of mNeon green was added to the human reference genome and neon and MUC2 read counts were merged. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts (for scSeq data poisson corrected).

source_name: Human intestinal organoids

growth_protocol: Organoids were differentiated in enterocyte or goblet cell differentiation medium for 5 days in the absence or presence of BMP2 and 4, respectivelys

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: For scSeq, live cells  were sorted in 384-  well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a  24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA  kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

value: Intestine


title: sample102


title: IgAN_sample14


title: sample100


title: Bulk RNA sequencing [BMPB]

value: wt


title: Bulk RNA sequencing [BMPA]


title: IgAN_sample13


title: IgAN_sample12


title: IgAN_sample11


title: PANC1_CT3

description: Bisulfite-treated mRNA

value: control Lentivirus


title: Xeno_combination5d-3 [XCom5d3]

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

description: RNA-seq in a human GIST cell line xenograft treated with the indicated drug

data_processing:
RNA-seq data were aligned to hg19 using STAR with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Assembly: hg19
Supplementary files format and content: Gene expresion in FPKM are in text format

source_name: GIST-T1 cell line xenograft

growth_protocol: Cell lines were grown in Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs Cat# E7645S). Paired-end 150 bp sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: Cells were treated with the indicated drugs for either 24 hours or 5 days. Xenografts were treated with the indicated drugs for either 5 or 10 days.

value: KIT-dependent GIST cell line GIST-T62

value: Gastrointestinal stromal tumor (GIST)

value: Combination VTP50469 and imatinib 5 day treatment


title: Xeno_combination5d-4 [XCom5d4]

value: KIT-dependent GIST cell line GIST-T63


title: Xeno_combination5d-2 [XCom5d2]

value: KIT-dependent GIST cell line GIST-T61


title: Xeno_combination5d-1 [XCom5d1]

value: KIT-dependent GIST cell line GIST-T60


title: Control_sample60

value: Kidney tubulointerstitium

value: Control

value: No


title: MiaPaCa-2_KD2

description: Bisulfite-treated mRNA


title: Xeno_combination10d-4 [XCom10d4]

value: KIT-dependent GIST cell line GIST-T59

value: Combination VTP50469 and imatinib 10 day treatment


title: Single cell sequencing plate [HUB-JB-035]

description:
goblet_scSeq_counts.csv
HUB-JB-s035_H7L3VBGXG_S1
Cells were sorted into a 384 well plate and processed for singel cell sequencing

data_processing:
Single cell data were demultiplexed, paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19. For MUC2-Neon reporter organoids, the sequence of mNeon green was added to the human reference genome and neon and MUC2 read counts were merged. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg19
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated, poisson corrected counts from differentiated organoids samples

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq 500 using 60bp and 26bp paired end sequencing.

treatment_protocol: Live cells  were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to -80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

value: MUC-2 Neon reporter

value: Human intestinal organoids


title: Single cell sequencing plate [HUB-JB-036]

description:
goblet_scSeq_counts.csv
HUB-JB-s036_H7L3VBGXG_S2
Cells were sorted into a 384 well plate and processed for singel cell sequencing


title: IgAN_sample10

value: IgAN

value: Outlier_excluded from main analysis


title: IgAN_sample9


title: Xeno_combination10d-3 [XCom10d3]

value: KIT-dependent GIST cell line GIST-T58


title: IgAN_sample7


title: Xeno_combination10d-2 [XCom10d2]

value: KIT-dependent GIST cell line GIST-T57


title: Single cell sequencing plate [HUB-JP-018]

description:
enterocyte_scSeq_counts.csv
HUB-JP-018_HG22JBGXB_S2
Cells were sorted into a 384 well plate and processed for singel cell sequencing

value: wt

value: Intestine


title: Single cell sequencing plate [HUB-JB-034]

description:
goblet_scSeq_counts.csv
HUB-JB-034_HCYCWBGXC_S8
Cells were sorted into a 384 well plate and processed for singel cell sequencing


title: IgAN_sample8


title: Single cell sequencing plate [HUB-JB-037]

description:
goblet_scSeq_counts.csv
HUB-JB-s037_H7L3VBGXG_S3
Cells were sorted into a 384 well plate and processed for singel cell sequencing


title: Xeno_combination10d-1 [XCom10d1]

value: KIT-dependent GIST cell line GIST-T56

value: Gastrointestinal stromal tumor (GIST)


title: IgAN_sample6


title: Single cell sequencing plate [HUB-JP-016]

description:
enterocyte_scSeq_counts.csv
HUB-JP-016_HG3HMBGXB_S4
Cells were sorted into a 384 well plate and processed for singel cell sequencing


title: Single cell sequencing plate [HUB-JP-017]

description:
enterocyte_scSeq_counts.csv
HUB-JP-017_HG22JBGXB_S1
Cells were sorted into a 384 well plate and processed for singel cell sequencing


title: Xeno_VTP50469_5d-4 [XeVTP5d4]

value: KIT-dependent GIST cell line GIST-T55

value: VTP50469 5 day treatment


title: Single cell sequencing plate [HUB-JP-004]

description:
enterocyte_scSeq_counts.csv
HUB-JP-004_HLVN3BGX9_S1
Cells were sorted into a 384 well plate and processed for singel cell sequencing


title: PBS tumor 4 [NP14]

tag: strain

value: tumor

value: AB1-HA mesothelioma

value: PBS

value: 7 days post treatment


title: IgAN_sample2

value: Kidney tubulointerstitium

value: No


title: PANC1_CT2

description: Bisulfite-treated mRNA

value: pancreatic cancer cell

value: control Lentivirus


title: Xeno_VTP50469_5d-2 [XeVTP5d2]

value: KIT-dependent GIST cell line GIST-T53


title: IgAN_sample4

value: IgAN


title: PANC1_CT1

description: Bisulfite-treated mRNA

value: no treatment


title: IgAN_sample3


title: Xeno_VTP50469_5d-1 [XeVTP5d1]

value: KIT-dependent GIST cell line GIST-T52


title: Xeno_VTP50469_10d-4 [T1XeVTP4]

value: KIT-dependent GIST cell line GIST-T51

value: VTP50469 10 day treatment


title: Xeno_VTP50469_10d-3 [T1XeVTP3]

value: KIT-dependent GIST cell line GIST-T50

value: Gastrointestinal stromal tumor (GIST)


title: MiaPaCa-2_KD1

description: Bisulfite-treated mRNA

value: shNSUN2 Lentivirus


title: MiaPaCa-2_CT2

description: Bisulfite-treated mRNA


title: MiaPaCa-2_CT3

description: Bisulfite-treated mRNA


title: IgAN_sample1


title: Xeno_VTP50469_10d-2 [T1XeVTP2]

value: KIT-dependent GIST cell line GIST-T49