title: H4 cells, VPS35 KO Clone 16 + VPS35-GFP sample 2

status: Public on Apr 17 2023

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

growth_protocol: Grown in DMEM media containing 4.5 g/L glucose (Sigma, D5796) supplemented with 10% fetal bovine serum (Sigma, F7524), 100U/mL penicillin and 0.1mg/mL streptomycin

extract_protocol:
RNA extracted from confluent 6-well plates using the Qiagen RNeasy kit (Qiagen, 74134)
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

value: Brain

value: Neuroglioma

value: VPS35 KO Clone 16 + VPS35-GFP


title: H4 cells, VPS35 KO Clone 15 + VPS35-GFP sample 2

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: Brain

tag: tissue

tag: cell line

tag: cell type

tag: Sex

value: Male

tag: genotype

value: VPS35 KO Clone 15 + VPS35-GFP


title: H4 cells, VPS35 KO Clone 16 + VPS35-GFP sample 1


title: H4 cells, VPS35 KO Clone 15 + VPS35-GFP sample 1


title: C9-7_LPS, iPSC-MG, C9orf72, day 28-30/40-42

status: Public on May 23 2023

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N. Fifth Street

country: USA

institute: TGen

description:
B8_LPS_stimulated_092_5_V8_Sattler_IPSC_microglia_S33
genecounts_Stim_Master.csv

data_processing:
base calling was performed using Illumina' bcl2fastq software
adapter trimming was performed using cutadapt to remove the first 3 bases from end of R2, as specifed by Takara Bio
reads were aligned to the human genome using STAR v.2.7.10a with default options
alignment (BAM) fies from STAR were converted into gene counts tables using featureCounts v. 1.6.4 with default options
Assembly: GRCh38
Supplementary files format and content: raw gene counts tables from featureCounts

molecule: total RNA

source_name: cell line

growth_protocol:
IPSCs were differentiated into microglia following an established protocol (McQuade et al., 2018). Briefly, iPSCs were maintained in mTeSR Plus Kit (Stemcell Technologies # 05825) in 10cm dishes. At DIV -1 of HPCs differentiation, five to seven day old iPSCs cultures were then used to generate cluster of differentiating 43 positive (CD43+) hematopoietic progenitor cells (HPCs) following a 12 day commercially available kit (STEMdiff Hematopoietic Kit; Stemcell Technologies # 05310). IPSCs were cleaned and 1/3 dish was gently dissociated with dispase (Stemcell Technologies # 07923) for 12-15 minutes at 37°C. IPSCs were then collected and spun down at 500rpm for 1-2 minutes and resuspended in 2mL of mTeSR Plus media with 20 µM ROCK inhibitor Y-27632 (Stemcell Technologies # 72304). Matrigel, hESC-Qualified Matrix (Corning # 354277) coated six well plates were used to start the HPC differentiation. Using a 5mL serological pipette, one drop or two drops of iPSCs were seeded per well into matrigel. Then, next day, on DIV 0 of HPCs differentiation, wells with 80 small colonies per well were selected to start HPCs differentiation. IPSCs were fed following the manufacturer’s instructions. On DIV 12 of HPCs differentiation, only the non-adherent HPCs were transferred to a new six well plate to start microglia differentiation (DIV 12/0).
Matrigel, GFR (growth factor reduced) Membrane Matrix (Corning # 356231) coated six well plates were prepared to start microglia differentiation (DIV12/0). HPCs were differentiated into microglia for 28 days using serum free media conditions. HPCs in suspension were collected and spun down at 300 xG for 6 minutes and resuspended into microglia basal media (MBM, 2mL/well) containing: DMEM/F12 no phenol (Gibco # 11-039-021), 2% Insulin Transferin Selenite (Gibco # 41400045), 2% B27 (Gibco # 17504-044), 0.5% N2 (Gibco # 17502-048), 1% Glutamax (Gibco # 35050-061), 1% NEAA (Gibco # 11140-050), 1% Pen/Strep (Gibco # 15140-122), 400μM 1-Thioglycerol (Sigma # M1753), 5μg/mL human insulin (Sigma # I2643) and supplemented with 3 growth factors (GFs): 100ng/mL human recombinant interleukin-34 (IL-34; Peprotech # 200-34), 25ng/mL macrophage colony-stimulating factor (M-CSF; Gibco # PHC9501) and 50ng/mL transforming growth factor β1 (TGFβ1; Miltenyi Biotec # 130-108-969) (MBM + 3GFs); cytokines and growth factors known to be essential for the development of microglia (Butovsky et al., 2014, Greter et al., 2012, Wang et al., 2012, Abud et al., 2017, Pandya et al., 2017, Abutbul et al., 2012, Chen et al., 2002, Elmore et al., 2014). Microglia differentiation starts (DIV 12/0) once the HPCs are transferred and plated at a density of 200 000 cells per well of a six well. Cells will predominantly grow in suspension. On DIV 2, 4, 6, 8 and 10 of microglia differentiation, 1mL of MBM + 3GFs media was added to each well. On DIV 12, a partial media change was done. IPSC-MGs from one six well plate were spun down at 300 xG for 6 minutes and resuspended into MBM + 3 GFs and split back into the same six well plate. On DIV 14, 16, 18, 20, 22, 24, 1mL media was added per well. On DIV 25, MBM + 3GFs was changed to maturation media composed of MBM supplemented with the 5 growth factors (MBM +5 GFs): 100ng/mL IL34, 25ng/mL M-CSF and 50ng/ml TGFβ1, 100ng/mL cluster of differentiation 200 (CD200; Novoprotein # C31150UG) and100ng/mL fracktaline chemokine C-X3-C motif ligand 1 (CX3CL1; Peprotech # 300-31) (MBM + 5 GFs). The presence of CD200 and CX3CL1 in the culture media, both glial and neuronal molecules are critical for microglia maturation and maintenance of an in vivo-like microglia resting state phenotype in an in vitro setting (Barclay et al., 2002, Kim et al., 2011, Kierdorf and Prinz, 2013) (Figure 1A). At DIV 28, IPSC-MG reached maturation. 1mL of MBM + 5GFs media was added to the cultures every other day. Mature cells were used for experimentation within 10 days (DIV 28-DIV38).
For cortical neuron differentiation, 70% confluent iPS cells maintained in mTeSR Plus media on 10 cm dishes were used for embryoid bodies (EBs) formation. The cells were cultured in low attachment six well plates (Greiner bio-one # 657970) using WiCell Medium containing: DMEM/F12 (Gibco #11330057), 25% knock out serum replacement (Gibco # 10828-028), 1.3% L-glutamine (Gibco # 35050-061), 1.3% NEAA (Gibco # 11140-050), 0.1mM 2-Mercaptoethanol (Sigma# M3148) and placed on a shaker in the incubator for 8 days to allow EBs formation. EBs were then resuspended in Forebrain Neural Induction Media (FB-NIM) containing: DMEM/F12, 1% N2 supplement (Gibco # 17502-048), 1% NEAA, 2ug/mL heparin (Sigma # H3149), 10 μg/mL bFGF (Stemcell Technologies # 78003) and plated on to T25 flasks coated with basement membrane matrigel (Corning # 356234) to allow formation of neuronal rosettes. Neuronal rosettes were maintained in FB-NIM for the next 10 days and then, collected and maintained in suspension on a shaker with half FB-NIM media changes every other day to allow for neurosphere growth. Neurospheres were maintained for 20 days in FB-NIM and then resuspended using forebrain neuronal differentiation media (FB-DM) containing:  Neurobasal Medium (Corning # 21103-049), 2% B27 (Gibco # 17504-044), 10 ug/mL BDNF (Stem cell technologies # 78005), 10 ug/mL GDNF (Stem cell technologies # 78058), 1μg/mL laminin (Life technologies # 23017-015), 3.3 μg/mL cAMP (Stem cell technologies # 73884), 3.52 μg/mL Ascorbic acid (Stem cell technologies # 72132 ), 0.5mM L-glutamine and 1% NEAA and then plated on to T25 flasks. iPSC cortical neurons were harvested on DIV 65-72 for RNA sequencing analysis.

extract_protocol:
RNA was isolated with RNeasy Mini Kit (QIAGEN-74104) following the manufacturer’s instructions. RNA samples were measured for quantity with Quant-iT Ribogreen RNA Assay (Thermo Fisher, Cat. No. R11490) and quality with Agilent High Sensitivity RNA ScreenTape and buffer (Agilent, Cat. No. 5067-5579 & 5067-5580).
For each RNA sample, an indexed, Illumina-compatible, double-stranded cDNA whole transcriptome library was synthesized from 1 μg of total whole transcriptome library was synthesized from 1 μg of total Prep Kit – HI Mammalian (Takara Bio, Cat. No. 634876) and SMARTer RNA Unique Dual Index Kit (Takara Bio, Cat. No. 634418). Library preparation included ribosomal RNA depletion, RNA fragmentation (94◦ C for 3 min), cDNA synthesis, and a 12-cycle unique dual indexing enrichment PCR.

treatment_protocol: On DIV 28-30 iPSC-MG from 4 C9orf72 ALS/FTD patient lines and 5 control lines were plated on to 4 chambers glass slides as described above. For LPS stimulation - One hour after plating, iPSC-MGs were treated for 6 h with LPS (100ng/mL). All iPSC-MG were then collected and sent for RNA sequencing analysis. For Aβ (1-40) stimulation - iPSC-MGs were treated for 2 h with vehicle (DMSO) or 1µM Aβ (1-40) TAMRA (human Aβ, AnaSpec # AS-60488; (Paolicelli et al., 2017)) prepared in microglia basal media with growth factors. All iPSC-MGs were collected at 2 hours and sent for RNA sequencing analysis.

value: cell line

value: iPSC

value: iPSC- microglia

tag: treatment

value: 100ng/mL LPS treatment, 6 h


title: C9-7_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
B7_NonStimulated_092_5_V7_Sattler_IPSC_microglia_S32
genecounts_Stim_Master.csv

value: vehicle treatment, 6h


title: H4 cells, VPS35 KO Clone 16 sample 2

value: VPS35 KO Clone 16


title: H4 cells, VPS35 KO Clone 9 + VPS35-GFP sample 2

value: VPS35 KO Clone 9 + VPS35-GFP


title: H4 cells, VPS35 KO Clone 9 + VPS35-GFP sample 1


title: C9-4_LPS, iPSC-MG, C9orf72, day 28-30/40-42

description:
B6_LPS_stimulated_FTD27_1_V6_Sattler_IPSC_microglia_S31
genecounts_Stim_Master.csv


title: H4 cells, VPS35 KO Clone 15 sample 1

value: VPS35 KO Clone 15


title: H4 cells, VPS35 KO Clone 16 sample 1


title: H4 cells, VPS35 KO Clone 15 sample 2


title: H4 cells, VPS35 KO Clone 9 sample 2

value: VPS35 KO Clone 9


title: H4 cells, VPS35 KO Clone 9 sample 1


title: Control-6_LPS, iPSC-MG, control, day 28-30/40-42

description:
LPS_stimulated_JH082_Control_v5_Sattler_IPSC_microglia_S7
genecounts_Stim_Master.csv

value: Control


title: H4 cells, WT sample 5

value: WT


title: H4 cells, WT sample 6


title: H4 cells, WT sample 4


title: H4 cells, WT sample 1


title: H4 cells, WT sample 2


title: H4 cells, WT sample 3


title: tMCAO, day 7, scRNAseq

status: Public on Mar 21 2023

city: guangzhou

first: Fanning

last: Zeng

state: Guangdong

address: Nanshitou Street, Haizhu District

department: Department of Anesthesiology

country: China

institute: Zhujiang hospital, Southern Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Beads with unique molecular identifiers (UMI) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized into the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin.
Briefly, 10× beads were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD).
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2×150 chemistry.
The FASTQ files were generated by using the 10× Genomics Cell Ranger toolkit (v.3.0.1), which were extracted barcodes and UMI, filtered and mapped reads to the GRCh38 reference genome, and obtained a matrix containing normalized gene counts versus cells per sample. Then we further analyzed these outputs using Seurat (v.4.1.2) for quality control and downstream analysis with default parameters, unless otherwise indicated. We removed out low-quality cells according to the following quality control procedures: (1) cells with less than 200 genes or more than 3000 genes and genes expressed in less than 3 cells were removed. (2) over 10% of mitochondrial-derived UMI counts were filtered out. After quality control, the datasets were log-normalized. The top 2000 highly variable genes (HVGs) were chosen for canonical correlation analysis and the first 30 reduced dimensions were adopted for integration anchors. Finally, a total of 53484 single cells were applied in downstream analyses, including 16345, 11056, 16246 and 9837 single cells on postoperative days 1, 3 and 7 and sham surgery groups, respectively.
Then the data were scaled using the ScaleData function. Principal components analysis (PCA) was performed, and we selected the top 30 PCs for clustering cells with a resolution parameter of 1.0. The same PCs were used to generate the Uniform manifold approximation and projection (UMAP). Each cluster was annotated based on high expression of known marker genes and visualized by FeaturePlot function. Cldn5, Ly6c1, Ly6a, Itm2a (Endothelial Cells); Cldn11, Mag, Opalin, Ermn, Mog (Oligodendrocytes); Acta2, Des, Tpm2, Filip1l (Vascular Smoothmuscle Cells); Ttr, Clic6, Sostdc1, Car12, Prlr, Htr2c (Choroid plexus cells); VKcnj8, Atp13a5, Anpep, Abcc9, Cd248 (Pericytes); Hexb, C1qa, Tmem119, GRP34, OLFML3 (Microglia); Rtn1, Sox4 (Neuron); F3, Gja1, Slc1a3, Gjb6(Astrocyte); Calml4, Chchd10, Clu (Ependymal); Olig1, Olig2, Pdgfra, Tnr, C1ql1, Matn4 (Oligodendrocyte progenitor cells); Cd8a, Klrd1, Cd4 (T cells); Trem1, Mmp8 (Neutrophil); Cd14, Cd86 (Monocyte); Cd19, Cd79a (B cells).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

organism: Mus musculus

extract_protocol:
After 1, 3, and 7 days of ischemia-reperfusion, mice were anesthetized, fixed, and perfused with ice-cold PBS to remove blood. The ischemic hemisphere (tMCAO ipsilateral brain) and ipsilateral hemisphere (Sham ipsilateral brain) were immediately dissected, minced with a scalpel, and digested with papain (Worthington, Biochemical Corporation, USA) at 37°C for 30 minutes. During incubation, the minced brain tissue was gently shaken four times with a 10 ml pipette. After incubation, the tissue was centrifuged at 300g for 5 min at RT. The supernatant is then discarded and the cell pellet is resuspended in DNase diluted albumin inhibitor solution. Afterwards, the suspended single cells were passed through a pre-wetted (with HBSS) 40 μm cell strainer and centrifuged at 300 g for 5 min at 4°C. The cell pellet was then resuspended in 10 ml of 30% Percoll in PBS and centrifuged at 700 g for 10 min. After removing the fraction of myelin debris floating on the surface, the pelleted cells were immediately resuspended with FACS buffer (PBS, 1% BSA). Cells were loaded onto 10x Genomics Chromium chips according to the manufacturer's instructions.
Beads with unique molecular identifiers (UMI) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized into the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2×150 chemistry

value: male

value: tMCAO, day 7

tag: age

value: 8 weeks old

value: total RNA


title: sham,  scRNAseq

description: 10x Genomics

value: Brain

value: sham,  scRNAseq


title: Old adult CBA/CaJ mouse LW-2

status: Public on Feb 18 2023

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out using Partek Flow. Alignment was conducted with TopHat2 using mouse genome (mm10) and the default option set
Aligned reads were quantified to annotation model (Partek E/M) using mm10 and RefSeq transcripts 83 (2017-11-01) with the settings: a) strict paired-end compatibility, b) require junction reads to match introns, c) min read overlap with feature 100% of read length, d) min reads 10
Gene counts were analyzed using DESeq2 to determine normalized expression measures and adjusted p-value (FDR step up) for old versus young samples
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of normalized counts and comparison measures

source_name: Auditory nerve cells

extract_protocol:
Microdissections were performed to isolate the cochle lateral wall from mouse cochlear structures. Two cochleas from each mouse were pooled for individual samples. Total RNA was purified from each sample using the miRNeasy Mini Kit per the manufacturer’s instructions. Quality of each total RNA isolation was assessed using the Agilent 2100 Bioanalyzer and low-quality samples showing degradation or contamination were excluded.
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq RNA Library Prep Kit

value: Isolated lateral wall

tag: strain

value: CBA/CaJ


title: tMCAO, day 1, scRNAseq

description: 10x Genomics

value: tMCAO, day 1


title: Old adult CBA/CaJ mouse LW-3


title: tMCAO, day 3, scRNAseq

description: 10x Genomics

value: tMCAO, day 3


title: Old adult CBA/CaJ mouse LW-1


title: Young adult CBA/CaJ mouse LW-3

value: 2 mo


title: Young adult CBA/CaJ mouse LW-1


title: Control_S8

status: Public on Jan 25 2023

city: Freiburg

first: Julian

last: Wolf

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Sequencing data (fastq files) were uploaded to and analyzed on the Galaxy web platform (usegalaxy.eu) 38, as previously described 39-41. Quality control was performed with FastQC Galaxy Version 0.72 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ last access on 08/21/2021).
Reads were mapped to the human reference genome (Gencode, release 38, hg38) with RNA STAR Galaxy Version 2.7.8a 42 with default parameters using the Gencode annotation file (Gencode, release 38, https://www.gencodegenes.org/human/releases.html).
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 2.0.1 43 with default parameters using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (version 2022.02.0+443, R version 4.1.2). Gene symbols and gene types were determined based on ENSEMBL release 108 (Human genes, GRCh38.p12, download on 11/15/2022) 44.
T-distributed stochastic neighbor embedding (t-SNE) was applied to assess unsupervised clustering and to check for potential batch effects 45. Differential gene expression was analyzed using the R package DESeq2 Version 1.34.0 46 with default parameters (Benjamini-Hochberg adjusted p-values).
Assembly: human, Gencode, release 38, hg38
Supplementary files format and content: csv, normalized reads (DESeq2)

source_name: healthy conjunctiva

extract_protocol:
Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA).
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3’ RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers.

value: healthy conjunctiva


title: Control_S7


title: Young adult CBA/CaJ mouse LW-2


title: Control_S5


title: Control_S6


title: Control_S4


title: Control_S1


title: Treg (Repeat), HTO-derived cDNA

status: Public on Jan 23 2023

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

description: In the features.tsv file, disregard the human hashtags, namely the h_totalseq_XXXX.

library_source: other

data_processing:
Sequenced samples were demultiplexed, aligned and gene/barcode matrices were generated following the pre-processing pipeline with Cell Ranger software (10X Genomics version 6.0.0). The procedure included converting Illumina BCL files to FASTQs, which were aligned with mouse genome refdata-gex-mm10-2020-A as a reference for getting the gene/barcode matrices.
Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, etc..).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: spleen

extract_protocol:
Briefly, single-cell splenic suspensions were incubated with a cocktail of the following biotinylated antibodies at 4oC for 15 min: CD11b (M1/70), CD11c (N418), CD19 (6D5), CD45R/B220 (RA3-6B2), TCRgd (GL3), PanNK (DX5), CD105 (MJ7/18), CD16/32 (93) and Ter119 (TER-119). Non-T cells were removed by incubating the suspension with streptavidin-coated magnetic beads at 4oC for 15 min, followed by magnetic separation. The unbound pure T cells were incubated with pooled MHC class I tetramer (APC) (GP33, GP276, NP396) and then stained for viability using Live/Dead Fixable eFluor 780. T cells from individual mice were identified via labeling with uniquely barcoded TotalSeq-C antibodies towards pan-CD45 and MHC at 1:100 according to the manufacturer’s protocol during surface staining (Biolegend). Tregs and Tetramer+ CD8+ T cells were purified via fluorescently activated cell sorting using a BD Aria. Live cells were spun down, resuspended in 0.04% PBS-BSA (Fisher #MT20031CV and Sigma #A9418-100G), and counted to determine a cell stock concentration. A cell suspension volume was calculated to capture approximately 7,000 cells per sub-population.
Cells were added to a Master Mix containing Reagent mix, RT Primers, Additive A, and RT Enzyme Mix to create a reaction for Tregs and one for Tetramer+ CD8+ T cells. These reactions were then loaded into separate lanes on Chromium Chip A and run through the 10X Genomics Chromium Controller. All libraries were sequenced on a NovaSeq™ 6000 S2 kit for 150 cycles at the UPMC Genome Core. Each Gene Expression library was sequenced at a depth of at least 20,000 reads/cell. Each Feature Barcode and TCR library was sequenced at a minimum depth of 5,000 reads/cell.

treatment_protocol: Splenol Tregs and Tetramer+ CD8+ T cell were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with lymphocytic choriomeningitis virus (LCMV) Clone 13 (Cl 13) for 16d

value: spleen

value: Treg

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

tag: infection

value: naïve or LCMV

tag: library type

value: HTO

tag: hashtags

value: m_totalseq_1-ACCCACCAGTAAGAC, uninfected-Foxp3Cre-YFP;  m_totalseq_2-GGTCGAGAGCATTCA, uninfected-Foxp3Cre-YFP;  m_totalseq_3-CTTGCCGCATGTCAT, infected-Foxp3Cre;  m_totalseq_4-AAAGCATTCTTCACG, infected-Foxp3Cre;  m_totalseq_5-CTTTGTCTTTGTGAG, uninfected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_6-TATGCTGCCACGGTA, uninfected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_7-GAGTCTGCCAGTATC, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_8-TATAGAACGCCAGGC, infected-Ifngr1L/L_Foxp3Cre-YFP


title: Treg (Repeat), mRNA-derived cDNA

value: mRNA


title: Control_S2


title: Treg, TCR-derived cDNA

value: TCR


title: Treg, mRNA-derived cDNA


title: Treg, HTO-derived cDNA

value: m_totalseq_1-ACCCACCAGTAAGAC, uninfected-Foxp3Cre-YFP;  m_totalseq_2-GGTCGAGAGCATTCA, infected-Foxp3Cre;  m_totalseq_3-CTTGCCGCATGTCAT, infected-Foxp3Cre;  m_totalseq_4-AAAGCATTCTTCACG, infected-Foxp3Cre;  m_totalseq_5-CTTTGTCTTTGTGAG, uninfected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_6-TATGCTGCCACGGTA, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_7-GAGTCTGCCAGTATC, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_8-TATAGAACGCCAGGC, infected-Ifngr1L/L_Foxp3Cre-YFP;


title: CD8, TCR-derived cDNA

value: CD8 T cells

value: LCMV


title: CD8, HTO-derived cDNA

value: m_totalseq_2-GGTCGAGAGCATTCA, infected-Foxp3Cre;  m_totalseq_3-CTTGCCGCATGTCAT, infected-Foxp3Cre;  m_totalseq_4-AAAGCATTCTTCACG, infected-Foxp3Cre;   m_totalseq_6-TATGCTGCCACGGTA, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_7-GAGTCTGCCAGTATC, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_8-TATAGAACGCCAGGC, infected-Ifngr1L/L_Foxp3Cre-YFP


title: Genomic DNA from 202232290047_R01C01

status: Public on Jan 12 2023

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridised to the Illumina Infinium  MethylationEPIC Beadchips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using an HiSCAN with standard recommended Illumina scanner settings.

data_processing:
See original publication
matrix processed value definition: Beta values with dasen + noob normalization, filtered for quality probes.
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from four villi sites per placenta using a standard salting-out procedure, combined in equimolar amounts. The combined samples were purified using the Qiagen DNeasy Kit according to standard instructions.

tag: group

tag: depression

value: Non-Depressed

value: Exposed

value: No

value: Vaginal

value: Male

value: Chorionic Villi

tag: trophoblasts

tag: stromal

tag: hofbauer

tag: endothelial

tag: nrbc

tag: syncytiotrophoblast


title: CD8, mRNA-derived cDNA

tag: tissue

value: spleen

tag: cell type


title: Genomic DNA from 202232290002_R05C01

value: Depressed

value: Cesarean


title: Control_S3

value: healthy conjunctiva


title: Genomic DNA from 202242400050_R07C01

value: Non-Exposed


title: Genomic DNA from 202242400049_R02C01

value: Female


title: Genomic DNA from 202232290038_R07C01


title: Genomic DNA from 202242400013_R06C01


title: Genomic DNA from 202232290038_R03C01


title: Genomic DNA from 202240580237_R07C01


title: Genomic DNA from 202232290037_R08C01


title: Genomic DNA from 202232290037_R02C01


title: Genomic DNA from 202242400013_R08C01


title: Genomic DNA from 202242400049_R05C01


title: Genomic DNA from 202232290037_R04C01


title: Genomic DNA from 202242400049_R01C01


title: Genomic DNA from 202232290037_R07C01


title: Genomic DNA from 202240580237_R06C01


title: Genomic DNA from 202242400050_R02C01


title: Genomic DNA from 202232290032_R08C01


title: Genomic DNA from 202242400013_R02C01


title: Genomic DNA from 202232290038_R05C01


title: Genomic DNA from 202242400013_R04C01


title: Genomic DNA from 202232290038_R04C01


title: Genomic DNA from 202242400050_R01C01


title: Genomic DNA from 202232290032_R04C01


title: Genomic DNA from 202232290032_R02C01


title: Genomic DNA from 202232290047_R02C01


title: Genomic DNA from 202232290038_R08C01


title: Genomic DNA from 202242400049_R08C01


title: Genomic DNA from 202232290002_R02C01


title: Genomic DNA from 202232290038_R02C01


title: Genomic DNA from 202242400013_R01C01


title: Genomic DNA from 202242400049_R07C01


title: Genomic DNA from 202240580237_R03C01


title: Genomic DNA from 202232290032_R01C01


title: Genomic DNA from 202242400049_R06C01


title: Genomic DNA from 202242400050_R05C01


title: Genomic DNA from 202240580237_R02C01


title: Genomic DNA from 202242400013_R05C01


title: Genomic DNA from 202232290038_R06C01


title: Genomic DNA from 202232290002_R04C01


title: Genomic DNA from 202240580237_R04C01


title: Genomic DNA from 202232290047_R08C01


title: Genomic DNA from 202232290037_R05C01


title: Genomic DNA from 202232290047_R04C01


title: Genomic DNA from 202232290037_R01C01


title: Genomic DNA from 202232290047_R03C01


title: Genomic DNA from 202242400050_R08C01


title: Genomic DNA from 202242400049_R03C01


title: Genomic DNA from 202232290002_R07C01


title: Genomic DNA from 202232290032_R06C01


title: Genomic DNA from 202242400013_R03C01


title: Genomic DNA from 202232290002_R08C01


title: Genomic DNA from 202242400050_R03C01


title: Genomic DNA from 202240580237_R05C01


title: Genomic DNA from 202232290047_R05C01


title: Genomic DNA from 202242400050_R06C01


title: Genomic DNA from 202232290047_R07C01


title: Genomic DNA from 202232290037_R06C01


title: Genomic DNA from 202232290032_R05C01


title: Genomic DNA from 202232290032_R07C01


title: Genomic DNA from 202232290032_R03C01


title: Genomic DNA from 202240580237_R01C01


title: Genomic DNA from 202242400049_R04C01


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep3 [15_2D_SUSD2+_3]

status: Public on Oct 01 2022

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including raw counts

source_name: human reprogrammed fibroblast (giulitti et al. 2019, Nature Cell Biology, DOI: 10.1038/s41556-018-0254-5)

growth_protocol: Naïve hiPSCs were cultured on a confluent layer of mitotically inactive MEFs (DR4, ATCC) in RSeT medium (Stemcell Technologies). Cells were passaged every 4-5 days with TrypLE™ Select Enzyme (Life Technologies) as previously described (Giulitti and Pellegrini, 2019). Naïve cells were switched from 2D to 3D culture by detaching naïve colonies from 2D MEF, dissociating the colonies as single cells with TrypLE and then embedding them in 100% Matrigel (Corning) drops as described below. Optimal cell density was defined as 2k cells/µl, and 25µl of this was spread on tissue culture treated multiwell plates (Falcon) for maintenance. Medium change was performed every 24 hours and cells were passaged every 4 - 5 days. After 2 passages in 3D, we confirmed the absence of MEF contamination.

extract_protocol:
Qiagen RNeasy Mini Kit.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

treatment_protocol: SUSD2+ cells were FACS sorted from respective bulk samples

value: Naive human induced pluripotent stem cells


title: Macrophage, ischemic brain of Foxp3Egfp mice, rep1, scRNAseq

status: Public on Dec 31 2022

city: Guangzhou

first: Mengyan

last: Hu

address: Tianhe Road

institute: Sun Yat-sen University

description: 10x Genomics

data_processing:
Demultiplexing, alignment to the GRCh38 reference with the Mus musculus genome (GRCm38) by the STAR aligner v2.5.1b with default settings, and quantification of sequencing reads for each sample were performed using Cell Ranger (Version 4.0.0) with the default parameter. The filtered gene-barcode matrices for single cells were analyzed using Seurat (V4) following the tutorial at https://satijalab.org/seurat/.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Foxp3Egfp mice were flushed with PBS and single cell suspensions were prepared after flow sorting of CD45+CD11b+CD3-F4/80+ cells using a BD FACSAria cell-sorting system (BD Biosciences, San Jose, CA).
Cells were droplet separated using Chromium™ Single Cell 3’ v3 Reagent Kit with the 10x Genomics microfluidic system creating cDNA library with individual barcodes for individual cells. Barcoded cDNA transcripts from stroke mice were pooled and sequenced using the novaseq 6000 Sequencing System.

value: Macrophage

value: ischemic brain

value: 6-8 weeks old


title: Macrophage, ischemic brain of Foxp3Egfp mice, rep2, scRNAseq

description: 10x Genomics


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep2 [14_2D_SUSD2+_2]


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep4 [16_2D_SUSD2+_4]


title: Genomic DNA from 202240580237_R08C01


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep1 [13_2D_SUSD2+_1]


title: Naive hiPSCs cultured on MEF, RSeT, rep1 [9_2D_bulk_1]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep4 [8_3D_SUSD2+_4]


title: Naive hiPSCs cultured on MEF, RSeT, rep2 [10_2D_bulk_2]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep3 [7_3D_SUSD2+_3]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep2 [6_3D_SUSD2+_2]


title: Naive hiPSCs cultured on MEF, RSeT, rep4 [12_2D_bulk_4]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep3 [3_3D_bulk_3]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep1 [5_3D_SUSD2+_1]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep2 [2_3D_bulk_2]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep3


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep1 [1_3D_bulk_1]


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep4


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep3


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep2


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep4


title: Naive hiPSCs cultured in 3D matrigel, RSeT, SUSD2+, rep2


title: Naive hiPSCs cultured in 3D matrigel, RSeT, rep1


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep4


title: Naive hiPSCs cultured on MEF, RSeT, rep4


title: genomic DNA from eutopic endometrium Sample_82

status: Public on Sep 12 2023

city: Herston

first: Sally

last: Mortlock

state: Queensland

address: AWaGHR Centre, School of Public Health, The University of Queensland

department: School of Public Health

country: Australia

institute: University of Queensland

description:
genomic DNA from eutopic endometrium
Endometriosis eutopic endometrium sample

hyb_protocol: All DNA samples were adjusted to the same volume and concentration for sodium bisulfite conversion followed by DNAm analysis on the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina scan protocol was performed at the University of Southern California Epigenome Center.

data_processing:
Background correction with dye-bias, signal intensity normalization and Beta value generation performed using the SeSAME R package. Samples with a low overall intensity signal (median unmethylated or methylated signal <9), a detection p-value >0.05 in more than 1% of DNAm sites were removed. Probes with a detection p-value >0.05 in more than 10% of samples and probes not overlapping between batches were removed. Probes were masked based on the SeSAME package. 759,345 DNAm sites for 984 samples remained.
Normalized Beta and Normalized M-value

label: Cy3 and Cy5

source_name: endometrium sample 82

extract_protocol: Genomic DNA was extracted and purified from endometrial samples

tag: gender

tag: sample type

value: endometrium

tag: disease state

value: Endometriosis

tag: cycle phase

value: PE

tag: plate

tag: terminus

tag: batch

tag: euro

value: EUR

tag: recruiment


title: genomic DNA from eutopic endometrium Sample_92

source_name: endometrium sample 92

value: MSE

tag: age


title: genomic DNA from eutopic endometrium Sample_84

source_name: endometrium sample 84


title: genomic DNA from eutopic endometrium Sample_81

description:
genomic DNA from eutopic endometrium
Control eutopic endometrium sample

source_name: endometrium sample 81

value: Control


title: Naive hiPSCs cultured on MEF, RSeT, rep3


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep3


title: Naive hiPSCs cultured on MEF, RSeT, rep2


title: Naive hiPSCs cultured on MEF, RSeT, rep1


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep1


title: Silenz_I_Exp_R1

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk 37.31
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with RSEM 1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts

source_name: Ctrl- mouse endothelial cells

growth_protocol: Immortalised mouse endothelial cells (ECs) were cultured in D-MEM with Glutamax supplemented with 20% FBS and 1% penicillin (100 U/ml) and streptomycin (100 μg/ml) (Thermo Fisher Scientific, USA) and grown in a 5% CO2 incubator at 37° C

extract_protocol:
Total RNA was extracted using mini RNase kit reagent (Qiagen, Tübingen, Germany).
Poly-A enriched library were generated with the TruSeq RNA-Seq Library Preparation Kit v2 (#RS-122-2001, Illumina) according to the manufacturer’s instructions. Library quality control was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Indexed libraries were sequenced at CRS4 Next Generation Sequencing facility with the HiSeq 3000 instrument to generate ~40M 50bp single-end reads per sample.

treatment_protocol: Stealth RNAi duplexes designed against mouse Pdcd10 (Thermo Fisher Scientific, USA, PDCD10HSS174173; PDCD10HSS117454; PDCD10HSS117455) or stealth RNAi negative control (Thermo Fisher Scientific, USA, cat#12935115) were transfected in ECs cells (siPdcd10-ECs and Ctrl-ECs respectively) using Lipofectamine RNAiMAX (Thermo Fisher Scientific, USA) according to the manufacturer's protocol.

tag: condition

value: Ctrl-Silenced

value: Immortalised aortic endothelial cells


title: CTRL_II_Exp_R1

source_name: Pdcd10-silenced mouse endothelial cells


title: Silenz_II_Exp_R1


title: Silenz_III_Exp_R1


title: CTRL_I_Exp_R1


title: Input_Runx2-FLAG_Cho_2

status: Public on Sep 06 2022

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
DNA-sequence information was aligned to the unmasked mouse genome by bowtie
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the negative control
In the analysis with ATAC_Col2, ATAC_Col10 and ATAC_Sp7 data sets, to identify the cell-type specific and shared regions, we selected ATAC-seq peaks with the ATAC-seq normalized peak intensity based on the following criteria: raw fe > 30, fold change > 5, and p-value < 0.05, for cell-type specific regions. The differential accessible regions were called as below. C2: C2-Cho-distinct peaks; C10: C10-Cho-distinct peaks; S7: S7-Ob-distinct peaks; C2C10: peaks with high intensity in both C2-Cho and C10-Cho but not in S7-Ob; C10S7: peaks with high intensity in both C10-Cho and S7-Ob but not in C2-Cho; C2S7: peaks with high intensity in both C2-Cho and S7-Ob but not in C10-Cho. These peaks were listed in "ATAC_C2_C10_Sp7_peaks.xlsx”
In the analysis with ATAC_POB_Runx2_cHetKO and ATAC_POB_Runx2_cHomKO data sets, to identify the differential binding regions between the genotypes, DiffBind was applied with the following parameters "summits = 150" in the step of "dba.count" to resize peaks. To obtain statistically different chromatin-accessible regions, we selected the peaks based on FDR < 0.05. The differential accessible regions were listed in “ATAC_Runx2KO_peaks. xlsx”
In the analysis with ATAC_3T3cells data sets, to identify Runx2-responsive and osteoblast induction-responsive regions, DiffBind was applied with the following parameters "summits = 250" in the step of "dba.count" to resize peaks. Pairwise comparison was performed among ATAC-seq profiles of day 0 GFP expression samples, day 0 Runx2 expression samples, day 3 GFP expression samples, day 3 Runx2 expression samples, and no expression samples (None). The Runx2-responsive and the osteoblast induction-responsive regions were selected as ATAC-seq peaks whose intensity was statistically upregulated by both Runx2 expression and osteogenic induction on day 3, based on the following criteria: FDR < 0.05, fold change > 4. The Runx2-responsive regions were listed in “ATAC_3T3_Runx2_responsive_regions.xlsx”.
Genome_build: mm9
Supplementary_files_format_and_content: peak files

source_name: P1 rib chondrocytes

extract_protocol:
Rib chondrocytes were manually dissected from the neonatal mouse ribs. The ribs were initially digested in 2 mg/mL Pronase (53702, EMD Millipore Corporation) for 30 min at 37 °C, washed three times with phosphate buffered saline (PBS), and then digested in 0.2% collagenase D (1088858, Roche Applied Science) for 3 h at 37 °C. Calvarial osteoblasts were manually dissected from osteoblast-enriched partial calvarias consisting of the frontal bone and a rostral part of the parietal bone. The partial calvarias were digested in five changes of 0.1% collagenase D and 0.2% dispase for 10 min each at 37 °C.   Cultured 3T3 cells were digested in trypsin-EDTA solution 1X (Wako, 206-17291) for 5 to 15 min at  37 °C.
ChIP-seq libraries were constructed using a ThruPLEX®-FD Prep Kit (R40012, Rubicon Genomics) according to the manufacturer′s instructions. ATAC-seq libraries were constructed as previously described (Buenrostro et al., 2013).

treatment_protocol: For in vitro cell culture, osteogenic medium contains 10% FBS/DMEM supplemented with 50 μg/ml ascorbic acid phosphate, 10 mM β-glycerophosphate, and 100 ng/ml rhBMP‑2

value: Rib chondrocytes at P1

tag: strain

tag: genotype

value: Runx2-BioFL/+ knock-in


title: CTRL_III_Exp_R1


title: Naive hiPSCs cultured on MEF, RSeT, SUSD2+, rep2


title: ChIP-seq_Runx2-FLAG_Cho_rep2


title: Nsp6_rep1: Fly Heart Nsp6 Replicate 1

status: Public on Aug 24 2022

city: Baltimore

first: Hangnoh

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Fly Heart Nsp6 Replicate 1

data_processing:
RNA-Seq mapping and gene level quantification were performed by Novogene (Beijing, China).
HISAT2 2.0.5 (PMID: 31375807) was used for mapping the short reads with the --dta and --phred33 options.
The mapped reads were counted using featureCounts 1.5.0-p3 with its default parameters (PMID: 24227677).
For mapping and counting the reads, the Drosophila gene annotation from Ensembl (Release 100, corresponding to Flybase 6.28) was used.
Genome_build: Berkeley Drosophila Genome Project (BDGP) reference genome release 6
Supplementary_files_format_and_content: Tab-delimited text files include Flybase gene IDs and read counts for each sample.

organism: Drosophila melanogaster

source_name: Heart

growth_protocol: All flies were raised at 25°C on standard Drosophila medium (Meidi Laboratories).  We used the y[1] M{RFP[3xP3.PB] GFP[E.3xP3]=vas-int.Dm}ZH-2A w[*]; M{3xP3-RFP.attP}ZH-86Fb flies (Bloomington Drosophila Stock Center ID BL-24749) to generate the transgenic flies.

extract_protocol:
For each heart sample, one-week old adult fly hearts (total 50) were dissected and collected into ice-cold TRIzol LS reagent. For blood samples, hemocytes were collected into artificial hemolymph from ~15 third instar larvae and lysised by TRIzol LS reagent. Total RNAs were extracted according to the manufacturer's instructions (Direct-zol RNA Microprep, Zymo Research). RNA quality and concentration were checked by agarose gel electrophoresis, NanoDrop 8000 Spectrophotometer and Agilent 2100.
RNA libraries were prepared by Novogene (Beijing, China) using standard Illumina protocols.

tag: developmental stage

value: One week old adult fly

value: 4xHand-Gal4 > UAS-Nsp6


title: Orf7a01: Fly Hemocyte Orf7a Replicate1

description: Fly Hemocyte Orf7a Replicate1

source_name: Hemocyte

value: Third instar larvae

value: Tub-Gal4 > UAS-Orf7a


title: Nsp6_rep2: Fly Heart Nsp6 Replicate 2

description: Fly Heart Nsp6 Replicate 2


title: Hand_rep2: Fly Heart Control Replicate 2

description: Fly Heart Control Replicate 2

value: 4xHand-Gal4 > w1118


title: Orf7a02: Fly Hemocyte Orf7a Replicate2

description: Fly Hemocyte Orf7a Replicate2


title: Orf7a03: Fly Hemocyte Orf7a Replicate3

description: Fly Hemocyte Orf7a Replicate3


title: Tub02: Fly Hemocyte Control Replicate2

description: Fly Hemocyte Control Replicate2


title: Hand_rep1: Fly Heart Control Replicate 1

description: Fly Heart Control Replicate 1


title: Ctr 3

status: Public on Jul 06 2022

city: Halle

first: Robert

last: Eckenstaler

address: Kurt-Mothes-Str. 3

department: Institute of Pharmazie

institute: Martin-Luther-University

description: control replicate 3

data_processing:
Sequencing and data procession were performed by Novogene.
Alignment: to human genome (GRCh38) with HiSat2 (v2.0.5)
Annotations: Ensembl (GRCh38.p13)
Abundance measurements: HTSeq (v0.6.1)
Differential gene expression: DESeq2 software package (v1.20.0)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files including FPKM for abundance measurements

source_name: cultured endothelial cells

growth_protocol: HUVECs were cultured in ready-to-use basal endothelial cell medium (EBM-2, Promocell) supplemented with 2% fetal calf serum (FCS), basic fibroblast growth factor (bFGF), VEGF, insulin-like growth factor-1 (IGF-1), epidermal growth factor (EGF), hydrocortisone, ascorbic acid, gentamycin sulfate and amphotericin-B at 37°C in humidified air with 5% CO2.

extract_protocol:
RNA was extracted using TRIZOLTM reagent (Thermo Fisher Scientific) according to manifacturer's instructions.
NEBNext® Ultra ™ RNA Library Prep Kit for Illumina® (New England BioLabs)

treatment_protocol: HUVECs were infected with VSV-G-pseudotyped lentiviral particles derived from pHIV-SFiG-1335 (EGFP) transfer plasmids with a multiplicity of infection (MOI) of 500. For control cells (Ctr.), empty pHIV-SFiG-1335 was transduced. For overexpression of constitutively active (Q63L) and dominant negative (T19N) RhoA, a sequence expressing the respective RhoA mutants was inserted into the pHIV-SFiG-1335 backbone.

value: human umbilical vein endothelial cells (HUVECs)

tag: passages

value: 2 to 7

tag: genotype/variation

value: wildtype levels of RhoA


title: Tub01: Fly Hemocyte Control Replicate1

description: Fly Hemocyte Control Replicate1


title: Ctr 2

description: control replicate 2

tag: cell type


title: Ctr 1

description: control replicate 1


title: Wild-type, exponential phase, biol rep 1

status: Public on Jun 26 2022

city: Busan

first: Soo Jae

last: Kwon

address: KIOST, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City, KOREA

country: South Korea

institute: KIOST

data_processing:
The raw reads were assembled and aligned with the reference AWRP genome by using TopHat2 v2.0.13
The differential expression was analyzed by using the Cuffdiff v2.2.0
Assembly: ASM400639v2
Supplementary files format and content: mean values of FPKM obtained from two biological replicates

organism: Clostridium sp. AWRP

source_name: Prokaryotic cell

growth_protocol: The wild-type AWRP and acetated adapted strain were cultivated in a bioreactor containing basal medium with the gas substrate (20% CO2 and 80% H2)

extract_protocol:
RNA was extracted manually using RiboEX solution (GeneAll, Republic of Korea).
RNA libraries for RNA-seq were prepared using Truseq RNA sample prep (Illumina) according to manufacturer's protocols.

treatment_protocol:
The harvested culture was stabilized by mixing with 2 volumes of RNAProtect Bacteria reagent (Qiagen) and incubating at room temperature for 20 min
The stabilized cells were harvested and resuspended in 100 μL of the lysozyme solution (15 mg/mL in 30 mM Tris Cl and 1 mM EDTA) and 10 μL of the proteinase K solution (Qiagen)

value: Prokaryotic cell

value: AWRP

value: WT

tag: growth phase

value: exponential phase


title: Wild-type, exponential phase, biol rep 2


title: WL8 (D9R2 wo Q 12-23-17)

status: Public on Jun 01 2022

city: New York

first: Manoj

last: Kandpal

state: NY

address: 1230 York Ave

department: Hospital Bioinformatics

institute: Rockefeller University

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 9_2

data_processing:
We trimmed and filterd the reads using cutadapt and Trimgalore_v0.4.0with default parameters.
Quality was further checked using fastqc.
We used STAR (version 2.5.2b) to map the filtered reads to genome build GRCh38. We used default parameters and --quantMode GeneCounts
Counts files obtained from STAR were used to provide raw counts to DESSeq2. Differential genes and normalizec counts were obtained using DESeq2.
The cutoff for the differential gene list was set as q-val less than 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Files containing raw and normalized count using DESeq2

source_name: day 9 of directed differentiation to nephron progenitor cells grown in the absence of glutamine

growth_protocol: H9 cells underwent directed differentiation to nephron progenitor cells over 10 days according to the protocol published by Morizane and Bonventre, 2017.

extract_protocol:
RNAeasy MiniKit (Qiagen) and DNA-free™ DNA Removal Kit (Life Technologies, AM1906)
RNA-Seq libraries were generated using Illumina stranded mRNA kits (Illumina). Library QC (quality and quantity) was performed using an Agilent 2100 Bioanalyzer (Agilent).
Sequencing was performed on an Illumina HiSeq4000 (single end 50bp) (Illumina).

treatment_protocol: Cell were grown either in the presence of absence of glutamine from D0 through D9 of the differentiation protocol. Cells were collected at the end of D9 and RNA was extracted.

tag: cell line

value: H9 human embryonic stem cells

tag: time

value: nephron progenitor cells

tag: treatment

value: glutamine deprivation


title: WL9 (D9R3 wo Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 9_3


title: WL7 (D9R1 wo Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 9_1


title: WL6 (D9R3+Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 0_3

source_name: day 9 of directed differentiation to nephron progenitor cells grown in the presence of glutamine

value: complete media


title: WL5 (D9R2+Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 0_2


title: WL20 (D9R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 20

source_name: day 9 of directed differentiation to nephron progenitor cells

treatment_protocol: Cells were collecte at each of the specified time points and RNA was extracted.


title: WL16 (D7R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 16

source_name: day 7 of directed differentiation to nephron progenitor cells


title: WL17 (D7R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 17


title: WL13 (D6R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 13

source_name: day 6 of directed differentiation to nephron progenitor cells


title: WL21 (D9R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 21


title: WL14 (D6R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 14


title: WL12 (D4R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 12

source_name: day 4 of directed differentiation to nephron progenitor cells


title: genomic DNA from eutopic endometrium Sample_70

source_name: endometrium sample 70

tag: gender

value: Female

tag: sample type

value: endometrium

tag: disease state

value: Control

tag: cycle phase

value: PE

tag: plate

value: EUR


title: WL4 (D9R1+Q 12-23-17)

description:
Processed data files: Allsamples_B2_DESeq2_raw_counts.txt, Allsamples_B2_DESeq2_normalized_counts.txt
Processed file column headers: D 0_1


title: WL10 (D4R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 10


title: WL9 (D3R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 09

source_name: day 3 of directed differentiation to nephron progenitor cells


title: WL6 (D1R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 06

source_name: day 1 of directed differentiation to nephron progenitor cells


title: WL8 (D3R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 08


title: WL15 (D6R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 15


title: WL2 (D0R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 02

source_name: day 0 of directed differentiation to nephron progenitor cells


title: WL4 (D1R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 04


title: WL3 (D0R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 03


title: WL5 (D1R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 05


title: 48h_WT_Cont

status: Public on May 25 2022

city: Ulju-gun

first: Wonhyo

state: Ulsan

address: Unist-gil 50

department: Biological Sciences

institute: UNIST

description: Prdx1 +/+ tMCAO 48h contralateral hemisphere

data_processing:
The single cell RNA libraries constructed by 10x Single Cell chip A kit are sequenced by llumina HiSeq2500 Instrument
Illumina fastq files are aligned on mm10 reference genome by Cell ranger
barcode, feature, and matrix file which are output file of Cell ranger are imported to R with Read10x function of Seurat  package
10x data are converted to seurat object CreateSeuratObject function of seurat package
Multiplet data are eliminated by doubletFinder package
Genome_build: mm10
Supplementary_files_format_and_content: Matrix file of barcodes and genes which shows gene expression of each single cells.

source_name: brain hemisphere

extract_protocol:
The brain hemisphere was removed after cold PBS transcardial perfusion, and tissues were cut into pieces and transferred to the gentleMACSTM C tubes (Miltenyi Biotec) containing the Adult Brain Dissociation kit mouse and rat (Miltenyi Biotec, 130-107-677) enzyme mixture. The brain tissue dissociated with gentleMACSTM program 37°C _ABDK_1 with run 30 min incubations on the MACSmix tube rotator. The supernatant was aspirated, the pellet was resuspended in 8ml of 40% Percoll (GE Healthcare) and overlaid on the top of 4ml of 80% Percoll. The myelin debris was removed using Percoll separation. The gradient is centrifuged at 2200rpm for 20 min without brake at 22°C. Cells were collected 40% to 80% interface and washed with PBS and stained with Zombie NIRTM Fixable viability kit (Biolegend, 423106). The cells were washed by PBS for two times.
BD FACS Aria III (BD Biosciences) was used for sorting brain single live cells. Each cell suspension was subjected to 3′ single-cell RNA sequencing using Single Cell A Chip Kit, Single Cell 3′ Library and Gel Bead Kit V2, and i7 Multiplex Kit (10x Genomics) with a cell recovery target of 9000, following the manufacturer’s instructions

treatment_protocol: C57B6L/J male mice, aged 8-9 weeks Prdx1+/+, Prdx1-/- mice36, and weighing 20−24g, were used for focal brain ischemia experiments. There was no significant difference in weight and age between Prdx1+/+ mice and any Prdx1-/- mice groups. We used a transient (60 min) middle cerebral artery occlusion (tMCAO) model induced through an intraluminal suture (Doccol, 701956PK5Re) under anesthesia with 1.5% isoflurane (SomnosuiteR, Kent Scientific). The method of inducing this tMCAO model 10-20% reduction in cerebral blood flow was confirmed by Laser Doppler Flowmetry (LDF, Primed 3000 system). The rectal temperature was maintained at 37±0.5°C during surgery using a heating pad system. 60 min after MCAO, the brain blood flow was reperfused by the withdrawal of the intraluminal suture.

tag: tissue

value: contralateral hemisphere


title: 48h_WT_Ipsil

description: Prdx1 +/+ tMCAO 48h ipsillateral hemisphere

value: ipsillateral hemisphere


title: oxsR untreated batch 2 rep3

city: Seoul

first: Sungmin

last: Hwang

address: Hwarangno 14-gil 5, Seongbuk-gu

institute: Korea Institute of Science and Technology

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
The sequencing artifacts and contamination of raw sequencing reads were assessed by FastQC v.0.11.9 and further adapter, poor-quality or short reads (< 10 bp) were trimmed by Cutadapt v.1.18.
The number of reads mapped to each transcript was counted by HTSeq v.0.11.0
Assembly: The preprocessed reads were aligned to the reference genome of GCF_000025685.1_ASM2568v1_genomic.gff by Bowtie2 v.2.3.4.3, followed by sorting and indexing by Samtools v.1.9.
Supplementary files format and content: DESeq2 v.1.32.0 was used to normalize the read counts and the resulting count matrix contains the raw gene counts for every gene except rRNAs and every sample.

organism: Haloferax volcanii

source_name: Haloferax volcanii

growth_protocol: Strains H26 wild-type and mutant (ΔoxsR) were streaked on fresh ATCC974 medium plates from -80°C stock and grown for five days. Colonies were transferred to fresh ATCC974 liquid media in 13 ×100 mm culture tube and incubated at 42°C for 17 h (aeration by rotary shaking, 200 rpm) to log-phase (OD600nm of 0.3 to 0.7). Cells were transferred to fresh ATCC974 liquid medium in 13 ×100 mm culture tube and similarly incubated for 15 h until early log phase (OD600 nm of 0.3 to 0.5). The culture was transferred to a 125 mL Erlenmeyer flask in 50 mL of ATCC974 liquid medium and similarly incubated for 10 h to reach an early log phase. An aliquot (10 mL) of cell culture was transferred to 15 mL conical tubes for each strain and centrifuged for 5 min at 5,000 x g at room temperature to remove the complex medium. Cells were washed twice with GMM to remove any remaining ATCC974 medium. The cells were resuspended 50 mL of GMM and divided into two 125 mL Erlenmeyer flasks (25 mL per flask). Cells were exposed to 1.5 mM of HOCl or the mock only water for 1 h at 42°C with aeration at 200 rpm. After treatment, 10 mL cultures were transferred to 15 mL conical tubes and harvested by centrifugation (5 min at 5,000 x g, 22°C). The supernatant was removed, and the cell pellets were flash frozen on an ice bath with 100 % ethanol and NaCl. Cell pellets were stored at -80°C.

extract_protocol:
The RNA was extracted using TRI Reagent® (#T9424, Sigma-Aldrich). To verify RNA integrity, the samples were separated by 0.8 % (w/v) agarose gel electrophoresis (at 90 V for 20 min) in 1X TAE buffer using 2X RNA Loading Dye (#R0641, Thermo Fisher Scientific). The samples were then treated with TURBO DNase-free kit (AM1907, Invitrogen) to remove traces of DNA.
Only RNA samples with DNA below the limit of PCR detection were further processed. From each sample preparation, total RNA ≥ 6 μg in 50 μL with RIN value ≥ 6 was used to prepare a cDNA library and analyzed by high throughput sequencing (Novogene). The abundance of rRNA was reduced using the Ribo-ZeroTM Magnetic kit, and the cDNA was prepared using a 250 to 300 bp insert strand-specific library. The library was sequenced using the Illumina Platform PE150, Q30≥ 80% yielding 2G raw data / sample.

value: oxsR deletion

value: untreated


title: oxsR untreated batch 2 rep2


title: 24h_WT_Cont

description: Prdx1 +/+ tMCAO 24h contralateral hemisphere


title: oxsR untreated batch 1 rep3


title: 24h_WT_Ipsil

description: Prdx1 +/+ tMCAO 24h ipsillateral hemisphere


title: oxsR untreated batch 2 rep1


title: WL1 (D0R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 01


title: oxsR NaOCl batch 2 rep4

value: NaOCl treated


title: oxsR NaOCl batch 2 rep2


title: oxsR NaOCl batch 2 rep3


title: oxsR untreated batch 1 rep1


title: oxsR NaOCl batch 1 rep2


title: oxsR NaOCl batch 1 rep3


title: WL19 (D9R1)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 19


title: wt untreated batch 2 rep4

value: wt


title: wt untreated batch 2 rep3


title: wt untreated batch 2 rep2


title: WL18 (D7R3)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 18


title: wt untreated batch 1 rep3


title: genomic DNA from eutopic endometrium Sample_43

description:
genomic DNA from eutopic endometrium
Control eutopic endometrium sample

source_name: endometrium sample 43

value: Menstrual

tag: terminus

tag: batch

tag: euro

tag: recruiment

tag: age


title: genomic DNA from eutopic endometrium Sample_57

description:
genomic DNA from eutopic endometrium
Endometriosis eutopic endometrium sample

source_name: endometrium sample 57

value: Endometriosis

value: ESE


title: wt untreated batch 1 rep2

tag: strain


title: wt NaOCl batch 2 rep4


title: wt NaOCl batch 2 rep3


title: wt NaOCl batch 1 rep4


title: wt NaOCl batch 2 rep1


title: wt NaOCl batch 1 rep2


title: Hfx vol: NEBHvo_120 - rep4

status: Public on Apr 14 2022

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_4
ΔpyrE

data_processing:
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Hbt sal genome (GCF_000006805.1), Hfx vol (GCF_000025685.1_ASM2568v1), Hca his (GCF_000223905.1_ASM22390v1), or Hfx med (GCF_000306765.2_ASM30676v2) genomes (as appropriate) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset). Note that these BAM files are sorted by name, not by read.
Counts mapping to rRNA genes as a percentage of counts mapping to all genes were obtained and reported.
Supplementary files format and content: *.count: Tab-delimited text files include raw counts.

source_name: Archaeal cells

growth_protocol: Cells (3-4 biological replicates) were precultured to stationary phase, and then diluted back to a starting OD. These cultures were then grown to mid-log phase in appropriate rich media.

extract_protocol:
~3-5mL of cells in mid-log phase were flash-frozen in Liq N2 and stored at -80C. Total RNA was extracted from cell pellets using the Agilent Absolutely RNA Miniprep kit. RNA was measured using Nanodrop and quality-checked using Bioanalyzer.
1-10ng of total RNA was used as input for rRNA removal by the various kits tested here. The kit protocol included creation of a dsDNA library from the depleted RNA as template. This library was quality-checked using DNA High Sensitivity chip on the Bioanalyzer.

tag: genotype

value: <delta>pyrE


title: Hfx vol: NEBHvo_120 - rep3

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_3
ΔpyrE


title: Hfx vol: NEBHvo_120 - rep1

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_1
ΔpyrE


title: Ke01

status: Public on Jan 21 2022

first: Jong Hee

address: 81, Irwon-ro, Gangnam-gu

department: Department of Dermatology

institute: Samsung Medical Center

description: scRNA-seq

data_processing:
Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.
The 10x sequencing data was mapped to human reference genome (GRCh38; official Cell Ranger reference) for generating raw gene expression matrix.
Genome_build: hg38

source_name: Skin

extract_protocol:
the keloid tissue was washed in phosphate-buffered saline (PBS). Excised keloids were immersed in physiological saline and immediately transferred to the lab. After sample was minced into small pieces with scalpel in a petri-dish, prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) was used to digest at 37ºC for 60 min. The debris were filtered out with a 70-μm cell strainer (#352340, Corning). The remaining tissue were transferred into dissociation solution containing 0.25% Trypsin for a second round of dissociation. Subsequently, the live cells were resuspended in PBS-0.04% bovine serum albumin. Cells were pelleted by centrifuging at 500 x g for 5min.
To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 9,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.

value: Skin

tag: pathology

value: Keloid

tag: location

value: Ear

value: Male


title: Brain CD45+ cells, Cd300a-fl/fl, 3 hr after MCAO

status: Public on Dec 22 2021

city: Tsukuba

first: Akira

last: Shibuya

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

institute: University of Tsukuba

data_processing:
Read alignment and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: Brain CD45+ cells

extract_protocol:
To isolate the brain cells, mice were sedated under deep anesthesia and perfused with PBS transcardially. Collected brain tissues were transferred to dounce homogenizer with 3.5ml of RPMI-1640 and grinded using loose and tight plunger. Homogenates were filtered through 70 micrometre cell strainer and then subjected to Percoll (GE Healthcare) gradient centrifugation. Cells were collected from the interlayer between 40% and 70% Percoll layers. Collected cells were filtered through 70 micrometre nylon mesh to obtain single-cell suspensions and PI-CD45+ hematopoietic cells were sorted by flow cytometry.
10X Genomics, Chromium Single Cell 3’ Library and Gel Bead Kit v3.

treatment_protocol: Transient cerebral ischemia (MCAO) was induced using the intraluminal filament technique. A silicon-coated nylon monofilament (Doccol Corporation) was inserted into the right internal carotid artery and left in situ for 60 min. Operation time per animal did not exceed 15 min. During the MCAO procedure, mice were kept on the 40°C heater and after 60 min, the inserted monofilament was withdrawn to allow reperfusion. We only included mice that showed reduction of blood flow of right middle cerebral artery which confirmed by doppler ultrasound.

tag: cell type

value: Brain CD45+ cells


title: Brain CD45+ cells, Cd300a-fl/fl, 1 hr after MCAO


title: FLM_G_3

status: Public on Dec 11 2021

city: Brookings

first: Natalie

last: Thiex

state: SD

address: 1066 Campanile Ave, Box 2022A ookings

department: Biology and Microbiology

institute: South Dakota State University

data_processing:
Fastq files were generated and multiplexed with bcl2fastq
Raw sequence reads were checked for their quality using FastQC
Sequence reads were trimmed for adapters, length of at least 20 nucleotides, Phred score quality of >= 20 using cutadapt and prinseq respectively
Cleaned sequence reads were aligned to the Mus musculus genome using Hisat2 and Gene expression levels in FPKM were quantified using Stringtie
Differential gene expression analysis was performed using DESeq2
Genome_build: Ensembl build v.mm10/GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and read count values for each Sample

source_name: fetal liver (gestational day 15-19)

growth_protocol: Fetal livers and bone marrow were isolated from C57BL/6J mice (The Jackson Laboratory, Bar Harbor, ME). FLM cell cultures were generated by isolating livers from gestational day 15-19 mouse fetuses in accordance with South Dakota State University Institutional Animal Use and Care Committee. Liver tissue was mechanically dissociated using sterile fine-pointed forceps and a single-cell suspension was created by passing the tissue through a 1 ml pipette tip (Fejer et al., 2013).  Cells were plated at 8x106 cells per 10 cm2 non-tissue culture treated dishes. Growth and differentiation medium for FLM-M consisted of 20% fetal bovine serum (FBS) and 30% L-cell supernatant, a source of M-CSF (Stanley et al., 1976; Waheed and Shadduck, 1979) and 50% Dulbecco’s modified growth medium containing 4.5 g/L glucose, 110 mg/L sodium pyruvate, 584 mg/L L-glutamine, 1 IU/ml penicillin and 100 μg/ml streptomycin. Growth medium for FLM-G consisted of high glucose Dulbecco’s modified growth medium containing 30 ng/ml recombinant mouse GM-CSF, 10% FBS, and 4.5 g/L glucose, 110 mg/L sodium pyruvate, 584 mg/L L-glutamine, 1 IU/ml penicillin and 100 μg/ml streptomycin. All cells were cultured for at least 8 weeks before experiments were conducted.

extract_protocol:
One day prior to harvesting RNA, FLM-M, FLM-G and BMM cells were plated in triplicate at 2.5 x 10^5 cells per well in a non-tissue culture treated six-well plate. Cells were harvested using trypsin and total RNA was purified using Genejet RNA purification kit per manufacturer's instructions (ThermoFisher Scientific Waltham, MA). Genomic DNA remaining in the RNA was removed using TURBO DNA-free kit (ThermoFisher Scientific Waltham, MA).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq2500 using a HiSeq SBS sequencing kit version 4.

value: fetal liver macrophages (FLM_G)


title: FLM_G_2


title: FLM_G_1


title: FLM_M_2

value: fetal liver macrophages (FLM_M)


title: FLM_M_3


title: FLM_M_1


title: BMM_2

source_name: bone marrow

value: bone marrow macrophages (BMM)


title: genomic DNA from eutopic endometrium Sample_40

source_name: endometrium sample 40

value: Female

value: endometrium

value: PE

value: EUR


title: BMM_3


title: BMM_1


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion, rep2

status: Public on Nov 26 2021

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

description:
stroke_cns_24h_2
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v6.0)
Read alignments and transcript counting were done individually for each sample using the cellranger count pipeline with standard parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CD45iv-CD45+ leukocytes from brain parenchyma

extract_protocol:
Mice were injected (intravenously; iv) with fluorochrome coupled anti-mouse CD45 antibody (clone 30-11F, Biolegend, 3 µg/mouse). Five minutes later, animals were intracardially perfused with cold PBS with 10 U/ml heparin under deep ketamine/xylazine anesthesia. During perfusion, blood was collected and transferred into a tube. To separate different CNS compartments, the forebrain and cerebellum were dissected from mice. Under binoculars, the dura was dissected from the calvaria and the pia was dissected from the brain parenchyma. All choroid plexuses were removed from the ventricles of the brain. Brain tissue was cut into pieces and digested with collagenase D (2.5 mg/ml, Roche Diagnostics) and DNase I (0.05 mg/ml, Sigma) at 37 °C for 20 min. Pia, dura, and CP were digested in medium containing 1 mg/ml Collagenase D (Roche) for 45 min at 37°C. Afterwards, digested tissue was passed through a 70 μm cell strainer. The parenchyma was centrifuged on a 70%/37% percoll gradient. The interphase was removed, washed and re-suspended in PBS with 2% FCS. Cells extracted from the CNS, pia and dura were sorted for CD45+CD45iv- cells.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit with v2 and 3 chemistry (both from 10X Genomics, #1000128, #1000157). Sample processing and library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter, A63881). Sequencing was carried out on a Illumina Novaseq using NovaSeq 6000 S4 Reagent Kit (300 Cycles, #20028312) the a 150-8-8-150 read setup.
scRNA-seq

value: brain parenchyma

value: CD45iv-CD45+ tissue-resident leukocytes (TRL)

tag: condition

value: transient middle cerebral artery occlusion 24h


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion, rep1

description:
stroke_cns_24h_1
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice

description:
ctrl_cns
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice

value: control


title: 49os

status: Public on Nov 11 2021

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

institute: IBBTEC

description: Pool of PCR products

data_processing:
Library strategy: Amplicon sequencing
CRISPResso Analysis of genome editing outcomes.
Either wild-type or integrated donor sequences are used as reference.
Genome_build: NM_145383.2 ; NM_214221.1
Supplementary_files_format_and_content: *_CRISPResso_quantification_of_editing_frequency.txt: CRISPResso quantification of editing frequency.
Supplementary_files_format_and_content: HITI_INDEL.fasta: CRISPRESSO Amplicons Reference.
Supplementary_files_format_and_content: HITI_INDEL_guides.txt: CRISPRESSO sgRNA Reference.

source_name: retina

extract_protocol:
Genomic DNA was extracted from frozen mouse and pig retina. 150 bp regions flanking the on-target sits of mRho/pRHO gRNAs were amplified by PCR. PCR products were pooled and used for library construction.
10 ng of PCR products were used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: gRNA-treated mouse and pig retina.

value: retina

value: wild type


title: pool_2191

description: Pool of PCR products

data_processing:
CRISPResso Analysis of genome editing outcames
Genome_build: GRCm39/mm39
Supplementary_files_format_and_content: Quantification of editing frequency as determined by the percentage and number of unmodified and modified reads; fasta of amplicons used as reference; txt file of amplicone guides

source_name: liver

extract_protocol:
Genomic DNA was extracted from frozen retina and liver samples. 150 bp regions flanking the on target and off-target sites of mRho and mAlb gRNA were amplified by PCR, pooled and used for library construction.
10 ng of PCR products were used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina
OTHER: Amplicon sequencing

treatment_protocol: gRNA- and scramble-treated retina and liver.

tag: tissue.

value: liver


title: pool_2086

description: Pool of PCR products


title: pool_2073

description: Pool of PCR products


title: pool_4_48od

description: Pool of PCR products


title: pool_3_49os

description: Pool of PCR products


title: pool_2_48os

description: Pool of PCR products


title: pool_1_47os

description: Pool of PCR products


title: Primed hiPSC well day 7 rep. 3

description: 3'DGE mRNA-seq

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a.
The expression levels of genes were determined with HTseq-counts 0.9.1.
Differential expression analysis was performed using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: HPD06 induced primed (isogenic, naïve hiPSCs-derived)

extract_protocol:
RNA was extracted with RNeasy Plus Micro Kit (Qiagen) following manufacturer instructions.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

value: Human primed induced pluripotent stem cells

tag: culture system

value: Glass coverslip in standard plate

tag: culture conditions

value: On 2.5percent Matrigel growth factor reduced (MRF, Corning), cultured in Essential 8 medium (E8, Stemcell Technologies)

tag: time point

value: Day 7 after seeding


title: Primed hiPSC well day 7 rep. 2

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 7 rep. 1

description: 3'DGE mRNA-seq


title: genomic DNA from eutopic endometrium Sample_731

data_processing:
Background correction with dye-bias, signal intensity normalization and Beta value generation performed using the SeSAME R package. Samples with a low overall intensity signal (median unmethylated or methylated signal <9), a detection p-value >0.05 in more than 1% of DNAm sites were removed. Probes with a detection p-value >0.05 in more than 10% of samples and probes not overlapping between batches were removed. Probes were masked based on the SeSAME package. 759,345 DNAm sites for 984 samples remained.
Normalized Beta and Normalized M-value

source_name: endometrium sample 731

extract_protocol: Genomic DNA was extracted and purified from endometrial samples

tag: gender

tag: sample type

tag: disease state

value: Endometriosis

tag: cycle phase

value: LSE

tag: plate


title: genomic DNA from eutopic endometrium Sample_699

source_name: endometrium sample 699

value: Female

value: ESE

tag: terminus

tag: batch

tag: euro

tag: recruiment


title: Primed hiPSC microfluidics day 7 rep. 2

description: 3'DGE mRNA-seq

value: Microfluidics


title: genomic DNA from eutopic endometrium Sample_725

source_name: endometrium sample 725

value: endometrium

value: Control

tag: age


title: Primed hiPSC well day 4 rep. 2

description: 3'DGE mRNA-seq

value: Day 4 after seeding


title: Primed hiPSC microfluidics day 7 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 4 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 4 rep. 2

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 4 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 1 rep. 3

description: 3'DGE mRNA-seq

value: Day 1 after seeding


title: Primed hiPSC well day 1 rep. 2

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 1 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 1 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 7 rep. 3

description: 3'DGE mRNA-seq

source_name: Human naïve induced pluripotent stem cells (naïve hiPSCs, HPD06, from Nat Cell Biol. 2019 Feb;21(2):275-286)

value: Human naive induced pluripotent stem cells

value: On a confluent layer of mitotically inactive MEFs (DR4, ATCC) in RSeT medium (Stemcell Technologies)


title: genomic DNA from eutopic endometrium Sample_693

source_name: endometrium sample 693


title: Naive hiPSC well day 7 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 7 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 7 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 7 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 7 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 4 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 4 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 4 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 4 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 4 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 1 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 1 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 1 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 1 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 1 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 1 rep. 1

description: 3'DGE mRNA-seq


title: HFF well day 7 rep. 3

description: 3'DGE mRNA-seq

source_name: fibroblasts (HFF-1, ATCC)

value: Fibroblast

value: On Vitronectin (25 microg/ml) in High Glucose Dulbecco’s modified Eagle Medium (DMEM, ThermoFisher Scientific) supplemented with 10percent Fetal Bovine Serum (FBS, ThermoFisher Scientific)


title: HFF well day 7 rep. 2

description: 3'DGE mRNA-seq


title: HFF well day 7 rep. 1

description: 3'DGE mRNA-seq


title: HFF microfluidics day 7 rep. 3

description: 3'DGE mRNA-seq


title: HFF microfluidics day 7 rep. 2

description: 3'DGE mRNA-seq


title: HFF microfluidics day 7 rep. 1

description: 3'DGE mRNA-seq


title: HFF well day 4 rep. 3

description: 3'DGE mRNA-seq


title: HFF well day 4 rep. 2

description: 3'DGE mRNA-seq


title: HFF well day 4 rep. 1

description: 3'DGE mRNA-seq


title: HFF microfluidics day 4 rep. 3

description: 3'DGE mRNA-seq


title: HFF microfluidics day 4 rep. 1

description: 3'DGE mRNA-seq


title: HFF well day 1 rep. 3

description: 3'DGE mRNA-seq


title: HFF well day 1 rep. 2

description: 3'DGE mRNA-seq


title: HFF well day 1 rep. 1

description: 3'DGE mRNA-seq


title: HFF microfluidics day 1 rep. 3

description: 3'DGE mRNA-seq


title: HFF microfluidics day 1 rep. 2

description: 3'DGE mRNA-seq


title: Naïve hiPSCs on Vitronectin coating, rep. 3

description: 3'DGE mRNA-seq

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a.
The expression levels of genes were determined with HTseq-counts 0.9.1.
Differential expression analysis was performed using edgeR
Genome_build: hg38_mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

growth_protocol: Seeded in microfluidics at 400 cells/mm2, on MEF feeder layer or Vitronectin coating. Both in RSET mediun under hypoxic conditions. Medium change was performed every 12 hours.

extract_protocol:
RNA was collected with RLT lysis buffer 72 h after seeding in microfluidics. RNA extraction from microfluidic channels was performed in triplicates from each condition, each replicate made by pulling together the lysates obtained from 3 channels.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

tag: culture substrate

value: cultured on Vitronectin coating (50 µg/ml)


title: HFF microfluidics day 1 rep. 1

description: 3'DGE mRNA-seq

tag: cell type


title: Naïve hiPSCs on Vitronectin coating, rep. 2

description: 3'DGE mRNA-seq


title: Naïve hiPSCs on Vitronectin coating, rep. 1

description: 3'DGE mRNA-seq


title: HFF microfluidics day 4 rep. 2

description: 3'DGE mRNA-seq


title: Naïve hiPSCs on MEF feeder layer, rep. 3

description: 3'DGE mRNA-seq

value: cultured on a confluent layer of mitotically inactive MEFs (DR4, ATCC) in RSeT medium (Stemcell Technologies)


title: Naïve hiPSCs on MEF feeder layer, rep. 1

description: 3'DGE mRNA-seq


title: Naïve hiPSCs on MEF feeder layer, rep. 2

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 1 rep. 1

description: 3'DGE mRNA-seq

value: Human primed induced pluripotent stem cells

value: On 2.5percent Matrigel growth factor reduced (MRF, Corning), cultured in Essential 8 medium (E8, Stemcell Technologies)


title: 170od

description: Pool of PCR products

organism: Sus scrofa

tag: tissue

value: retina

tag: breed

value: Large White

tag: genotype

value: wild type


title: 166os

description: Pool of PCR products


title: Ischemic Stroke (IS)

status: Public on Oct 31 2021

city: Shanghai

first: Xiaojing

last: Shi

state: Please Select

address: 1954 Huashan Rd.

institute: Shanghai Jiao Tong University

description:
one sample from murine brain tissue
IS_R20023098-OES20309100-OES20309100

data_processing:
The Cell Ranger software pipeline (Version 3.1.0) provided by 10 × Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (Version 3.1.1).
To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we applied a criterion to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2-fold of standard deviations assuming a Gaussian distribution of each cells’ UMI/gene numbers. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where 30% of counts belonged to mitochondrial genes. Library size normalization was performed in Seurat on the filtered matrix to obtain the normalized count.
Top variable genes across single cells were identified using the method described in Macosko et al. Briefly, the average expression and dispersion were calculated for each gene, genes were subsequently placed into several bins based on the expression.
To remove the batch effects in scRNA-seq data, the mutual nearest neighbors (MNN) presented by Haghverdi et al was performed with the R package batchelor. Cells were clustered based on a graph-based clustering approach, and were visualized in 2-dimension using tSNE. Likelihood ratio test that simultaneously test for changes in mean expression and in the percentage of expressed cells was used to identify significantly differentially expressed genes (DEGs) between clusters.
We use the R package SingleR for unbiased cell type recognition of scRNA-seq to infer the cell of origin of each of the single cells independently and identify cell types. DEGs were identified using the Seurat package. p value < 0.05 and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode counts, gene files, cell barcode files

source_name: Murine brain tissue

extract_protocol:
Single-cell gel beads in emulsions (GEMs) were generated by loading single-cell suspensions onto a Chromium Single-Cell Controller Instrument (10 × Genomics). Approximately 12,000 cells were added to each channel. After that, reverse transcription reactions were engaged to generate barcoded full-length cDNA, and cDNA clean-up was performed with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Next, cDNA was amplified by PCR and the amplified cDNA was fragmented, end-repaired, A-tailed, and ligated to an index adaptor, and then the library was amplified. Every library was sequenced on a HiSeq X Ten platform (Illumina), and 150 bp paired-end reads were generated.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

tag: strain

value: 10 weeks

tag: condition

value: Ischemic Stroke (IS)

value: brain


title: control

description:
one sample from murine brain tissue
control_R20016596-OES20215100-OES20215100

value: control


title: Brain MCAO rep2

status: Public on Sep 24 2021

city: Tianjin

first: Kai

last: Zheng

address: No.154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

data_processing:
The single-cell RNA sequencing data was further analyzed by using the 10x Cell Ranger.Briefly, FASTQ files were generated by demultiplexing the Illumina sequencer's base call files (BCLs), and  then alignment, filtering, barcode and UMI counting were processed. STAR（Spliced Transcripts Alignment to  a Reference）was utilized to perform the read alignments to mouse reference transcriptome (mm10). Cell  Ranger was employed to conduct primary quality control (QC) on the FASTQ files to generate high quality  scRNA-seq data.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Brain

extract_protocol:
The brain was dissected and minced using a scalpel for digestion with papain for 30 minutes at 37°C. After incubation, the mixture was centrifuged at 300g for 5 minutes at room temperature. The cell suspension was then passed through a 40 μm cell strainer and centrifuged at 300 g for 5 minutes. Cell pellets were resuspended in 10 ml of 30% Percoll in PBS and then centrifuged at 700 g for 10 min to remove myelin debris. After the myelin debris fraction floating on the surface was removed, the pelleted cells were immediately resuspended with FACS buffer. Live/dead discrimination reagents for flow cytometry were prepared using Zombie NIR Fixable Viability Kit.
Single Cell 3’ Library was constructed mainly following Chromium Single Cell 3' Reagent Kits User Guide

value: Brain

value: 6-8 weeks

tag: treatment


title: Brain MCAO rep3


title: Brain MCAO rep1


title: Brain Sham rep3

value: sham


title: Brain Sham rep2


title: Brain Sham rep1


title: Naive hiPSC microfluidics day 4 rep. 1

description: 3'DGE mRNA-seq

value: Human naive induced pluripotent stem cells

tag: culture system

value: Microfluidics

tag: culture conditions

value: On a confluent layer of mitotically inactive MEFs (DR4, ATCC) in RSeT medium (Stemcell Technologies)

tag: time point

value: Day 4 after seeding


title: 45-yo Gastric ORGs MOCK [CoV_122020_11_S11]

status: Public on Sep 20 2021

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with RSEM 1.3.0 by using gencode pre-build genes annotations (hg38 primary assembly)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include expected counts for each sample as output from RSEM

source_name: 45-yo Gastric ORGs MOCK

growth_protocol: Fully grown gastric organoids at day 7 after single cell disaggregation were removed from surrounding extracellular matrix using a modified published protocol. Matrigel was dissolved with 60 min treatment of the droplets with Cell Recovery Solution (Corning) at 4°C. Organoids were retrieved from the plates using 1% BSA-coated cut-end tips and transferred to 1% BSA-coated 15 mL tubes. Cells were extensively washed with ice-cold PBS and centrifuged at 200 g for 5 min at 4°C. Supernatant was discarded, the pellet was resuspended in complete medium and transferred to non-tissue culture treated low-adhesive multiwell plates (pre-coated in 1% BSA). Organoids were cultured in suspension for 3 days to allow reversion of polarity, before use in infection experiments.

extract_protocol:
Pelletted organoids were extracted in RLT buffer
cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following manufacturer suggested protocol. cDNA generated with SMART-Seq v4 Kit were used for preparation of library with NEXTERA XT DNA Library Preparation kit, following the suggested protocol().

treatment_protocol: Reversed-polarity organoids were infected at a MOI of 1 by incubation with 250 µl of an expansion medium viral suspension for 2 hours. After infection, organoids were washed twice in DMEM to remove unbound virus. RP-GOs were dispersed in a 400 µl expansion medium at 37 °C with 5% CO2. For all organoid cultures 50 µl of supernatant were harvested at 0, 24, 48, and 72 hours post infection. An equal volume of expansion medium replaced the sampled supernatant at each collection time. An extra sample at 96 hours post infection was collected for the RP-GOs. Samples were stored at -80°C before titration through the FFA.

value: Cultured organoid (RP-Gos) from adult stomach tissue (age 45 year)

tag: passage

tag: sars-cov-2 infection

value: negative paired control


title: 45-yo Gastric ORGs MOCK [CoV_122020_12_S12]


title: 45-yo Gastric ORGs MOCK [CoV_122020_10_S10]


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_8_S8]

source_name: 45-yo Gastric ORGs HIGH dose

value: infected at MOI 10


title: 45-yo Gastric ORGs MOCK [CoV_122020_9_S9]


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_7_S7]


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_6_S6]


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_5_S5]


title: 45-yo Gastric ORGs LOW dose [CoV_122020_3_S3]

source_name: 45-yo Gastric ORGs LOW dose

value: infected at MOI 1


title: 45-yo Gastric ORGs LOW dose [CoV_122020_2_S2]


title: 45-yo Gastric ORGs LOW dose [CoV_122020_4_S4]


title: 45-yo Gastric ORGs LOW dose [CoV_122020_1_S1]


title: AK3 a

status: Public on Aug 18 2021

city: Phoenix

first: Eric

last: Alsop

address: 445 N. Fifth Street

institute: TGen

description:
Cell lysate
AK3_a_17_S37

data_processing:
cutadapt for quality filtering
sRNABench for small RNA
normalization in DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: miRNA_ALL_norm_counts.txt

source_name: Peritoneal macrophages isolated from Akita mice

extract_protocol:
Qiagen miRNeasy Mini Kit
NextFlex v3

value: Peritoneal macrophages

value: Akita


title: AK2 a

description:
Cell lysate
AK2_a_16_S36


title: AK1 a

description:
Cell lysate
AK1_a_15_S35


title: AK6 b

description:
Cell lysate
AK6_b_14_S34


title: AK5b

description:
Cell lysate
AK5b_13_S33


title: AK4 b

description:
Cell lysate
AK4_b_12_S32


title: AK3 b

description:
Cell lysate
AK3_b_11_S31


title: AK2 b

description:
Cell lysate
AK2_b_10_S30


title: AK1 b

description:
Cell lysate
AK1_b_9_S29


title: wt3a

description:
Cell lysate
wt3a_8_S28

source_name: Peritoneal macrophages isolated from WT mice

value: WT


title: wt2a

description:
Cell lysate
wt2a_7_S27


title: oxsR NaOCl batch 1 rep4

source_name: Haloferax volcanii

value: oxsR deletion

value: NaOCl treated


title: wt1a

description:
Cell lysate
wt1a_6_S26


title: wt5b

description:
Cell lysate
wt5b_5_S25


title: wt4b

description:
Cell lysate
wt4b_4_S24


title: wt3b

description:
Cell lysate
wt3b_3_S23


title: wt1b

description:
Cell lysate
wt1b_1_S22


title: wt untreated batch 1 rep1

value: wt

value: untreated


title: stz3 mono hi

description:
Cell lysate
stz3_mono_hi_S96

source_name: Monocytes Ly-6Chi sorted from WT mice treated with STZ

value: Monocytes Ly-6Chi

tag: agent

value: STZ


title: wt untreated batch 2 rep1


title: stz 2 mono hi

description:
Cell lysate
stz_2_mono_hi_S82


title: wt NaOCl batch 2 rep2


title: ctl 4 mono hi

description:
Cell lysate
ctl_4_mono_hi_S89

source_name: Monocytes Ly-6Chi sorted from WT mice treated with citrate buffer

value: citrate buffer