title: ectopic ossification

city: HONGO, BUNKYO-KU

first: Taku

last: Saito

institute: The University of Tokyo

data_processing:
Illumina NovaSeq 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
We performed the downstream analysis steps using the Seurat R package. Cells with less than 1,000 genes per cell and a mitochondrial read content greater than 5% were filtered out. Downstream analysis steps for each sample type included normalization, identification of genes with high variability among single cells, scaling based on UMI count and batch effects, dimensionality reduction (UMAP), unsupervised clustering, and discovery of cell type-specific markers with different expression levels.
Genome_build: mm10

source_name: Achilles tendons

extract_protocol:
The Achilles tendons were harvested and minced in ice-cold PBS . The harvested tissues were digested in RPMI 1640 medium (#30264-85, Nacalai Tesque Inc.) containing 0.3% Type 1 Collagenase (#CLS1, Worthington, NJ, USA) and 0.4% Dispase II (#04942078001, Roche, Basel, Switzerland) at 37 °C for 45 min with constant agitation. Cells were filtered through 100-µm, 70-µm, and 40-µm strainers, centrifuged, counted, and resuspended at a concentration of 1,000 cells/µL.
Single-cell libraries were prepared using the Chromium Controller (10x Genomics, CA, USA) according to the protocol of Chromium Next GEM Single Cell 3ʹ Reagent Kits (v3.1 10x Genomics). Libraries were prepared using Chromium Controller (10x Genomics). Alignment, quantification, and aggregation of sample count matrices was performed using the 10x Genomics Cell Ranger pipeline (v.5.0.0), retaining an average of 61,308 reads/cell mapped read depth normalization.

value: tendon


title: CGc_RAW_2

status: Public on Jun 24 2022

type: SRA

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus Muscularis (mm10) using HISAT
DEG assessed using DeSeq2
Assembly: mm10
Supplementary files format and content: excel file with count data for each sample.

molecule: total RNA

organism: Mus

source_name: Macrophage

growth_protocol: RAW264.7 cells were exposed to 1 ug/mL LPS, or LPS together withh 100 uM of caffeic acid, chlorgenic acid, or the corresponding cystiene adducts

extract_protocol:
Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard Illumina

treatment_protocol: 6 hours treatment prior to RNA extraction

tag: cell line

tag: cell type

value: Macrophage

tag: treatment

value: LPS + chlorogenic acid-Cys


title: LNCaP_vehicle_4h_1_AR

city: Belfast

first: Ian

middle: G

last: Mills

address: 97 Lisburn Road

department: Centre for Cancer Research and Cell Biology

country: United Kingdom

institute: Queens University

library_source: genomic

data_processing:
Fastq files were generated with Illumina pipeline software (bcl2fastq version 2.19 using the default thresholds).
Reads were mapped to the GRCh37/hg19 reference genome using bowtie2 (version 2.2.6) and subsequently filtered to remove PCR duplicates.
Prior to peak calling, Encode curated blacklisted regions were removed from bam files.
The MACS algorithm (version 2.1.2) was used to analyse the resulting alignments and identify both transcription factor and histone binding regions.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed files

molecule: genomic DNA

organism: Homo sapiens

source_name: LNCaPs

extract_protocol:
Following treatment, cells were fixed with 1% formaldehyde and chromatin prepared by sonication in Bioruptor plus. Fragmentation efficiency was analysed using fragment analyser and ChIP carried out using diagenode iDeal ChIP-seq kit for transcription factors (Cat# C01010170).
Libraries were prepared using Diagenode MicroPlex Library Preparation Kit v2 (Cat# C05010014) and purified and purified/size selected using Agencourt® AMPure® XP beads (Beckman Coulter, Cat. No. A63881).

treatment_protocol: Prostate cancer cells (LNCaPs) were cultured in RPMI media supplemented with 10% charcoal dextran stripped FBS for 72h before addition of 1nM R1881 or 0.01% ethanol for 4h and 24h.

value: LNCaP

value: Prostate cancer cell line

tag: passages

value: Vehicle

tag: time

tag: chip antibody

value: AR (Abcam, ab74272)


title: CGc_RAW_1


title: LNCaP_R1881_4h_1_O-GlcNAc

value: O-GlcNAc [RL2] (Abcam, ab2739)


title: Cac_RAW3

value: LPS + Caffeic acid-Cys


title: LNCaP_R1881_4h_2_AR


title: P45_SCC

city: Stanford

first: Carolyn

last: Lee

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University School of Medicine

data_processing:
Samples were pseudoaligned and quantified to the hg38 reference genome using Salmon (version 1.5.1)  to generate count matrices
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing transcript by sample count matrix

molecule: polyA RNA

source_name: Skin

extract_protocol:
Total RNA was then isolated from human tissues using QIAshredder (Qiagen) and Trizol (ThermoFisher) followed by DNA removal with the TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions.
RNA-Seq libraries were prepared with the mRNA Seq Sample Prep Kit (Illumina, Inc.) as recommended by the manufacturer.

tag: tissue

value: Skin

tag: condition

value: cutaneous squamous cell carcinomas (cSCC)


title: Filtrate treated T120 N1

city: Seattle

first: E. Virginia

last: Armbrust

state: WA

address: 616 NE Northlake Place

department: Oceanography

institute: University of Washington

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39,25 run in paired-end mode with cut adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1:true, Leading and Trailing thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Reads were mapped to the genome of T. pseudonana (Thaps3 FilteredModels2) using Hisat2-2.1.0.
We calculated the number of T. pseudonana reads that aligned to the gene models from resulting SAM alignment files with aligned sequences used in subsequent analyses.
Genome_build: Thaps3 FilteredModels2
Supplementary_files_format_and_content: csv files include TPM values for each sample,

organism: Thalassiosira pseudonana

source_name: Thalassiosira pseudonana

extract_protocol:
Total RNA was extracted from 0.2 µm membrane filters with the Zymo Direct-zol RNA MiniPrep Plus kit.
Poly-A-selection, library preparation and sequencing were performed at the Northwest Genomics Center (University of Washington) with standard Illumina NextSeq protocols

tag: strain

value: CCMP 1335

value: Bacteria filtrate treated

tag: time of sampling


title: Control T120 N3

value: Control


title: Ankle WT rep1

city: Wenzhou

first: Yi

last: Zhang

state: Zhejiang

address: Wenzhou Medical University

country: China

institute: Zhang Lab

data_processing:
Clean data were aligned to the mouse genome (mm39) using the hisat2 v(2.2.1).
Aligned reads were quantified using HTSeq(0.11.3) using GENCODE vM27 annotation.
Differential gene expression was estimated with DESeq2 version v1.28.1.
Genome_build: mm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Ankle joint

extract_protocol:
Total RNA was isolated and extracted using TRIzol Reagent (ThermoFisher). For mRNA sequencing, libraries were produced by a VAHTS Universal V6 RNA-seq Library Prep Kit for MGI based on the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSU and 1 x PBS was injected subcutaneously in a volume of 100ul into the right ankle joint separately. 8 hours post-MSU and post-PBS mice were sacrificed.

value: Ankle joint

tag: age

value: 10 weeks

value: untreated


title: Axenic_YEPSlight_2

city: Cologne

first: Jasper

middle: Robert Lisette

last: Depotter

address: Zülpicher Straße 47a

country: Germany

institute: University of Cologne

data_processing:
The reads were then mapped to the reference genome using Bowtie 2 (v2.3.5.1) with the first 15 nucleotides on the 5’-end of the reads being trimmed due to inferior quality
Reads were counted to the U. hordei loci using the R package Rsubread (v1.34.7). Here, multi-mapping reads were counted and the default minimum mapping quality score of 0 was used, to include reads that would have multiple best mapping locations. For the gene loci, reads were counted that were mapped to the predicted coding regions. For the LTR-RT loci, reads were only counted that mapped within LTR-RT loci, excluding the reads that mapped onto the 10% of either edge of the locus.
Assembly: GCA_022749175.1
Supplementary files format and content: tab-deliminated file including the read counts for every sample

organism: Ustilago hordei

source_name: fungal tissue

extract_protocol:
RNA was isolated by using the TRIzol® extraction method (Invitrogen; Karlsruhe, Germany) according to the manufacturer’s instructions. Subsequently, total RNA samples were treated with Turbo DNA-Free™ Kit (Ambion/Applied Biosystems; Darmstadt, Germany) to remove any DNA contamination according to the manufacturer’s instructions.
NEB Next® Ultra™ RNA Library Prep Kit (NEB, Ipswich, MA, USA)

value: fungal tissue

value: fungal cells


title: P45_Normal_Skin

value: Normal Skin


title: Cac_RAW2

value: Macrophage


title: P44_SCC


title: Hippocampus, Cre3_CamiCre

city: Kunigami-gun

first: Mohieldin

last: Youssef

state: Okinawa

address: 1919-1 Tancha

department: Cell Signal Unit

country: Japan

institute: Okinawa Institute of Science and Technology

description:
CamiCre_DE.txt
Ken_CamiCre_featurecounts.merged.counts.tsv

data_processing:
fastq files were analyzed by RNA-seq analysis pipeline nf-core 2.0, alignment by STAR 2.6.1d, counting by FeatureCounts
Differential expression using EdgeR 3.11 using OmicsBox 1.4.11, TMM normalization and cut-off of at least 0.2 CPM in two samples
Genome_build: GRCm38
Supplementary_files_format_and_content: Two Tab delimited .txt files containing TMM normalized reads for all genes for each Cre line after EdgeR differential expression analysis and contain gene symbol, FC, LogFC, CPM, Log CPM, p-value

source_name: Brain

extract_protocol:
Total RNA was purified from mouse hippocampi using Isogen II reagent (Nippon Gene).
500 ng of the total RNA samples were enriched for mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacture’s protocol. All libraries were normalized and pooled for paired-end 150bp sequencing with a single lane of SP flowcell of Illumina NovaSeq 6000.

value: Brain

tag: genotype

value: Cre


title: Hippocampus, Cre4_CamiCre


title: LNCaP_R1881_4h_1_AR

value: LNCaP

value: Prostate cancer cell line

value: AR (Abcam, ab74272)


title: Control T120 N2


title: P44_Normal_Skin

value: Skin


title: Hippocampus, Cre2_CamiCre


title: Cac_RAW1

value: LPS + Caffeic acid-Cys


title: CGA_RAW3

value: LPS + Chlorogenic acid


title: Hippocampus, Cre1_CamiCre


title: Hippocampus, WT4_CamiCre

value: WT


title: Control T120 N1

value: CCMP 1335

value: Control


title: Filtrate treated T72 N2

value: Bacteria filtrate treated


title: P34_Normal_Skin


title: P34_SCC

value: cutaneous squamous cell carcinomas (cSCC)


title: CGA_RAW2


title: Hippocampus, WT3_CamiCre


title: Filtrate treated T72 N1


title: CGA_RAW1


title: Hippocampus, WT2_CamiCre


title: P33_SCC


title: Control T72 N3


title: CA_RAW2

value: LPS + Caffeic acid


title: Hippocampus, Cre4_T29

description:
T29_DE.txt
Ken_Cre_T29_featurecounts.merged.counts.tsv


title: CA_RAW3


title: P33_Normal_Skin


title: Filtrate treated T72 N3


title: Control T72 N2


title: Control T72 N1


title: Hippocampus, Cre3_T29


title: P32_Normal_Skin


title: Filtrate treated T24 N3


title: Hippocampus, Cre2_T29


title: Filtrate treated T24 N2


title: LPS_RAW3

value: LPS


title: Control for H202 T2 N1

value: 2 h


title: LPS_RAW1

value: Macrophage


title: P29_Normal_Skin

value: Normal Skin


title: Hippocampus, WT1_CamiCre

value: Brain


title: CA_RAW1


title: Hippocampus, WT4_T29


title: P24_SCC


title: P32_SCC


title: Filtrate treated T24 N1


title: Control T24 N3


title: Control RAW3


title: Hippocampus, WT3_T29


title: Control T24 N1


title: P24_Normal_Skin


title: P16_SCC


title: Control RAW1


title: Control RAW2


title: P29_SCC


title: Hippocampus, WT1_T29


title: Control T24 N2


title: LPS_RAW2


title: Hippocampus, Cre1_T29

value: Cre


title: Hippocampus, WT2_T29


title: P16_Normal_Skin


title: Control_sgRbpj_ATAC_Rep_1_1

status: Public on Jun 23 2022

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

description: ATAC-Seq in mature T cells

data_processing:
Quality control of FASTQ files was done using the seeFastq command within systemPipeR.
The fastq files were aligned using TopHat v.2.1.1.
Count tables were generated from BAM files using the summarizeOverlaps function.
ChIP-seq and ATAC-seq aligment was performed using Bowite 2 v.2.3.5.1.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 and followed by MSPC to combine peak sets.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Count tables of raw read counts per gene in csv format.
Supplementary_files_format_and_content: ChIP-seq: Peaks and bigWig files.

source_name: Hybridoma mature T cell line

growth_protocol: Hybridoma mature T cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin.

extract_protocol:
ATAC-Seq was performed using a kit (Active Motif 53150)
Lybrary-prep kit: ATAC-Seq kit (Active Motif 53150)

treatment_protocol: Hybridoma mature T cells depleted of RBPJ were generated using the CRISPR/Ca9 technology as previously described (Yuan et al. Cell Rep 2019, doi: 10.1016/j.celrep.2018.12.097).

value: T cell


title: sgRbpj_2-12_ATAC_Rep_2_1

description: ATAC-Seq in mature T cells


title: Input_sgRbpj_2-12_histone_marks_Rep_2_1

description: ChIP-Seq in mature T cells

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907)
Lybrary-prep kit: Illumina TruSeq ChIP Library Sample Prep Kit SetA (#IP-202-1012); Diagenode MicropPlex Library Preparation kit v2 (C05010012); Diagenode MicroPlex Library Preparation kit v3 (C05010001)


title: Input_sgRbpj_2-12_histone_marks_Rep_1_1

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_ATAC_Rep_1_1

description: ATAC-Seq in mature T cells


title: Input_Control_sgRbpj_histone_marks_Rep_1_1

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_H3K4me3_Rep_1_1

description: ChIP-Seq in mature T cells

value: H3K4me3; Diagenode pAb-003-050


title: sgRbpj_2-12_H3K4me3_Rep_2_1

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_H3K4me1_Rep_2_1

description: ChIP-Seq in mature T cells

value: H3K4me1; abcam ab8895


title: Input_Control_sgRbpj_histone_marks_Rep_2_1

description: ChIP-Seq in mature T cells


title: SUM159 SHP2 sh2 3

type: RNA

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

hyb_protocol: Affymetrix Human Gene 1.0 st v1 GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: All gene arrays were processed in R (http://www.r-project.org/) using Bioconductor package oligo. Robust multi-array mean was performed using the following command: expr <- rma(read.celfiles(filenames)). Probes with the largest interquartile range were selected as representative for corresponding genes (using array annotation from Bioconductor package hugene10sttranscriptcluster.db).

label: biotin

source_name: SUM159 SHP2 sh2

label_protocol: 100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Cultures of SUM159 cells expressing inducible CTRL miR, SHP2 miR1 or SHP2 miR2 for 15 days. Cells were grown in Nutrient Mixture F-12 (Sigma #N6658-500mL), 5% FCS (Sigma #F7524), 1% Pen/Strep (Gibco #15140-122), Normocin (InvivoGen #ant-nr-1), Insulin 10µg/mL (Sigma #I5500-50mg), Hydrocortisone 500ng/mL (Sigma #H0888-1g).

extract_protocol: After 15 days cultures, RNA was extracted with Qiagen RNeasy Kits to obtain total RNA from SUM159 cells in the presence or absence of SHP2

treatment_protocol: Doxycycline, added the day after seeding the cells in cultures and refreshed every 2 days

tag: transfection

value: SHP2 miR2


title: SUM159 SHP2 sh2 2


title: SUM159 SHP2 sh1 2

source_name: SUM159 SHP2 sh1

value: SHP2 miR1


title: SUM159 Ctrl shRNA 1

source_name: SUM159 Ctrl shRNA

value: CTRL miR


title: SUM159 SHP2 sh2 1


title: sgRbpj_2-12_H3K4me1_Rep_1_1

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_ATAC_Rep_3_1

description: ATAC-Seq in mature T cells


title: Control_sgRbpj_H3K4me1_Rep_2_1

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_H3K27ac_Rep_2_1

description: ChIP-Seq in mature T cells

value: H3K27ac; Diagenode pAb-174-050


title: sgRbpj_2-12_H3K27ac_Rep_1_1

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_H3K27ac_Rep_1_1

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_H3K27ac_Rep_2_1

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_H3K4me1_Rep_1_1

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_ATAC_Rep_3_1

description: ATAC-Seq in mature T cells


title: Control_sgRbpj_ATAC_Rep_2_1

description: ATAC-Seq in mature T cells


title: SUM159 Ctrl shRNA 2


title: Control_sgRbpj_H3K4me3_Rep_2_1

description: ChIP-Seq in mature T cells


title: BioNICD1_DEP_RBPJ_Input

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_RBPJ_Input

description: ChIP-Seq in mature T cells


title: Biocontrol_RBPJ_Input

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_H3K4me3_Rep_1_1

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_RBPJ_Input

description: ChIP-Seq in mature T cells


title: BioNICD1_WT_RBPJ_Input

description: ChIP-Seq in mature T cells


title: BioNICD1_WT_RBPJ_Rep_2

description: ChIP-Seq in mature T cells

value: RBPJ; Cell Signaling #5313


title: BioNICD1_WT_RBPJ_Rep_1

description: ChIP-Seq in mature T cells


title: Biocontrol_RBPJ_Rep_2

description: ChIP-Seq in mature T cells


title: Biocontrol_RBPJ_Rep_1

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_RBPJ_Rep_2

description: ChIP-Seq in mature T cells


title: BioNICD1_DEP_RBPJ_Rep_2

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_RBPJ_Rep_3

description: ChIP-Seq in mature T cells


title: sgRbpj_2-12_RBPJ_Rep_1

description: ChIP-Seq in mature T cells


title: Control_sgRbpj_RBPJ_Rep_1

description: ChIP-Seq in mature T cells


title: sgRbpj+BioNICD1_WT_Rep_1_1

description: RNA-Seq in mature T cells

extract_protocol:
RNA-Seq samples were prepared essentially as as previously described (Giaimo et al. NAR 2018, doi:  10.1093/nar/gky551)
Lybrary-prep kit: TruSeq® Stranded Total RNA LT-Ribo-Zero Gold kit (Illumina RS-122–2301/2) or others.

treatment_protocol: Hybridoma mature T cells depleted of RBPJ were generated using the CRISPR/Ca9 technology as previously described (Yuan et al. Cell Rep 2019, doi: 10.1016/j.celrep.2018.12.097). Hybridoma mature T cells were infected with plasmids encoding for GFP-KYOT2 wildtype or an RBPJ-interacting defective GFP-KYOT2 mutant (WW/AA) or with GFP control; Alternatively infected with NICD1-ER and treated for 4, 8 or 24 hours with 1 uM of (Z)-4-hydroxytamoxifen (4-OHT) or ethanol (EtOH) as a control; Alternatively infected with BioNICD1 wildtype or an EP300-interacting defective BioNICD1 mutant (DEP) or with a Bio control; Alternatively the RBPJ-depleted background or its control were infected with BioNICD1 wildtype, or a BioNICD1 wiltype complete of the PEST domain or with a Biocontrol; Alternatively, hybridoma mature T cells were treated for 24 hours with 20 ug/ml of gamma-secreatse inhibitor (GSI; DAPT).


title: sgRbpj+BioNICD1_WT_Rep_3_1

description: RNA-Seq in mature T cells


title: sgRbpj+BioNICD1_WT_Rep_2_1

description: RNA-Seq in mature T cells


title: sgRbpj+Biocontrol_Rep_2_1

description: RNA-Seq in mature T cells


title: BioNICD1_DEP_RBPJ_Rep_1

description: ChIP-Seq in mature T cells


title: sgRbpj+Biocontrol_Rep_1_1

description: RNA-Seq in mature T cells


title: Control_sgRbpj_RBPJ_Rep_2

description: ChIP-Seq in mature T cells


title: Control_sgRbpj+BioNICD1_WT_Rep_1_1

description: RNA-Seq in mature T cells


title: sgRbpj+Biocontrol_Rep_3_1

description: RNA-Seq in mature T cells


title: Control_sgRbpj+BioNICD1_WT_Rep_3_1

description: RNA-Seq in mature T cells


title: Control_sgRbpj+Biocontrol_Rep_3_1

description: RNA-Seq in mature T cells


title: Control_sgRbpj+Biocontrol_Rep_2_1

description: RNA-Seq in mature T cells


title: Control_sgRbpj+BioNICD1_WT_Rep_2_1

description: RNA-Seq in mature T cells


title: Control_KYOT2_Rep_3

description: RNA-Seq in mature T cells


title: Control_sgRbpj+Biocontrol_Rep_1_1

description: RNA-Seq in mature T cells


title: GSI_Rep_1

description: RNA-Seq in mature T cells


title: GFP-KYOT2_WT_Rep_3

description: RNA-Seq in mature T cells


title: GFP-KYOT2_WWAA_Rep_3

description: RNA-Seq in mature T cells


title: GFP-KYOT2_WWAA_Rep_2

description: RNA-Seq in mature T cells


title: DMSO_Rep_1

description: RNA-Seq in mature T cells


title: GSI_Rep_2

description: RNA-Seq in mature T cells


title: DMSO_Rep_2

description: RNA-Seq in mature T cells


title: GFP-KYOT2_WWAA_Rep_1

description: RNA-Seq in mature T cells


title: SUM159 SHP2 sh1 1


title: GFP-KYOT2_WT_Rep_1

description: RNA-Seq in mature T cells


title: Control_KYOT2_Rep_2

description: RNA-Seq in mature T cells


title: Control_KYOT2_Rep_1

description: RNA-Seq in mature T cells


title: GFP-KYOT2_WT_Rep_2

description: RNA-Seq in mature T cells


title: NICD1-ER_8h_OHT_Rep_3

description: RNA-Seq in mature T cells


title: NICD1-ER_4h_OHT_Rep_2

description: RNA-Seq in mature T cells


title: NICD1-ER_24h_OHT_Rep_3

description: RNA-Seq in mature T cells


title: NICD1-ER_24h_OHT_Rep_2

description: RNA-Seq in mature T cells


title: NICD1-ER_24h_OHT_Rep_1

description: RNA-Seq in mature T cells


title: NICD1-ER_8h_OHT_Rep_1

description: RNA-Seq in mature T cells


title: NICD1-ER_24h_EtOH_Rep_2

description: RNA-Seq in mature T cells


title: NICD1-ER_24h_EtOH_Rep_3

description: RNA-Seq in mature T cells


title: NICD1-ER_4h_OHT_Rep_1

description: RNA-Seq in mature T cells


title: sgRbpj_2-14_Rep_1

description: RNA-Seq in mature T cells


title: NICD1-ER_24h_EtOH_Rep_1

description: RNA-Seq in mature T cells


title: sgRbpj_2-14_Rep_2

description: RNA-Seq in mature T cells


title: NICD1-ER_8h_OHT_Rep_2

description: RNA-Seq in mature T cells


title: NICD1-ER_4h_OHT_Rep_3

description: RNA-Seq in mature T cells


title: sgRbpj_2-12_Rep_2

description: RNA-Seq in mature T cells


title: PAT_2909_wk12

type: genomic

city: Barcelona

first: Antonio

last: Gomez

address: Pg Vall d'Hebron 119-129

department: Rheumatology research Group

country: Spain

institute: VHIR

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: DNA methylation was quantified using the Illumina Infinium MethylationEPIC BeadChip using an Illumina iScan System to quantify DNA methylation at > 850,000 CpG sites across the human genome. Samples were assigned a unique code for identification and randomized with regards to group and other variables to avoid batch effects. The Illumina GenomeStudio software was used to extract the raw signal intensities of each probe (without background correction or normalization).DNA methylation data was processed and analysed using the minfi package in R. Probes displaying a detection P value > 0.05 in more than 5% of samples were removed. Probes containing SNPs in close proximity to the CpG site (within 10 base pairs), probes located in sexual chromosomes as well as potentially cross-reactive probes were filtered using rmSNPandCH function from DMRcate Bioconductor packages. Data was normalized in the R package minfi using the preprocessNoob method

label: Cy3, Cy5

source_name: Whole Blood

label_protocol: Standard Illumina labelling protocol

growth_protocol: N/A. Primary patient samples.

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

treatment_protocol: Untreated.

tag: disease state

value: Rheumatoid Arthritis patient

tag: gender

value: F

tag: response

value: NR

tag: patient

tag: week


title: PAT_2912_wk12

value: R


title: Control_sgRbpj_Rep_1

description: RNA-Seq in mature T cells

tag: cell type


title: PAT_2117_wk12


title: PAT_2916_wk12

value: M


title: PAT_2913_wk0


title: PAT_2116_wk12


title: Control_sgRbpj_Rep_2

description: RNA-Seq in mature T cells


title: PAT_2115_wk0


title: PAT_2608_wk0


title: PAT_2116_wk0


title: PAT_2916_wk0


title: PAT_2912_wk0


title: PAT_2909_wk0


title: PAT_2913_wk12


title: sgRbpj_2-12_Rep_1

description: RNA-Seq in mature T cells


title: PAT_2608_wk12


title: PAT_2114_wk0


title: PAT_2113_wk0


title: PAT_2111_wk0


title: PAT_2113_wk12


title: PAT_2007_wk12


title: PAT_2006_wk12


title: PAT_2114_wk12


title: PAT_2007_wk0


title: PAT_2111_wk12


title: PAT_2108_wk0


title: PAT_2006_wk0


title: PAT_1919_wk0


title: PAT_1914_wk0


title: PAT_1913_wk0


title: PAT_2115_wk12


title: PAT_1911_wk0


title: PAT_1919_wk12


title: PAT_1907_wk0


title: PAT_1922_wk12


title: PAT_1911_wk12


title: PAT_1922_wk0


title: PAT_1906_wk0


title: PAT_1913_wk12


title: PAT_2117_wk0


title: PAT_1910_wk0


title: PAT_1908_wk0


title: PAT_1906_wk12


title: PAT_2108_wk12


title: PAT_1613_wk12


title: PAT_1613_wk0


title: PAT_1607_wk12


title: PAT_1607_wk0


title: PAT_1516_wk12


title: PAT_1512_wk0


title: PAT_1420_wk12


title: PAT_1420_wk0


title: PAT_1507_wk0


title: PAT_1507_wk12


title: PAT_1419_wk0


title: PAT_1512_wk12


title: PAT_1412_wk12


title: PAT_1313_wk0


title: PAT_1412_wk0


title: PAT_1417_wk0


title: PAT_1408_wk12


title: PAT_1419_wk12


title: PAT_1417_wk12


title: PAT_1408_wk0


title: PAT_1414_wk0


title: PAT_1516_wk0


title: PAT_1610_wk0


title: PAT_1414_wk12


title: PAT_1313_wk12


title: PAT_1308_wk0


title: PAT_1418_wk0


title: PAT_1308_wk12


title: PAT_1201_wk12


title: PAT_1202_wk0


title: PAT_1201_wk0


title: PAT_1213_wk0


title: PAT_1176_wk12


title: PAT_1176_wk0


title: PAT_1202_wk12


title: PAT_1171_wk12


title: PAT_1213_wk12


title: PAT_1169_wk12


title: TNFalpha_siICR_2

city: Beijing

first: shuangjin

last: ding

address: No.5 YiHeYuan Road, Haidian District Beijing 100871, China

department: College of Future Technology

institute: Peking University

data_processing:
Removed sequencing reads which containing low-quality, adaptor-polluted and high content  of unknown base (N) reads before downstream analyses.
Then map clean reads to GRCh38.p12 whloe genome using Bowtie2.
Calculate gene expression level for each sample with RSEM.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Matrix table with RPKM values for every gene and every sample

source_name: Human Umbilical Vein Endothelial Cells

extract_protocol:
RNA was harvested using Trizol reagent. Then use Fragment Analyzer to test the quality of RNA samples.
RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: Treated with 25ng/mL TNF-α for 12 hours.

value: Human Umbilical Vein Endothelial Cells

tag: genotype/variation

value: siRNA-ICR

tag: treatment

value: treated with TNF-α for 12 hours


title: PAT_1168_wk0


title: TNFalpha_NC_1

value: siRNA-scramble


title: TNFalpha_NC_2


title: PAT_1162_wk0


title: PAT_1178_wk0


title: PAT_1178_wk12


title: PAT_1162_wk12


title: PAT_1169_wk0


title: PAT_1179_wk0


title: PAT_1171_wk0


title: PAT_1199_wk0


title: PAT_1199_wk12


title: NC_2

value: untreated


title: NC_1


title: PAT_1156_wk0


title: PAT_1156_wk12


title: PAT_1195_wk12


title: PAT_1195_wk0


title: DKO1

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

description: HCT116 with DNMT3B knockout and DNMT1 hypomorph mutations

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Raw IDAT files for each sample were processed using the Bioconductor package “SeSAMe” (Version 1.8.2) for extraction of probe signal intensity values, normalization of probe signal intensity values, and calculation of β-values from the normalized probe signal intensity values. CpG probes with a detection p-value > 0.05 in any one sample were excluded from the analysis.

label: Cy5 and Cy3

source_name: HCT116 Colorectal Carcinoma epithelial cells

label_protocol: Standard Illumina protocol

growth_protocol: HCT116 and DKO1 cells were grown in McCoy's 5A with 10% FBS and Penicillin-Streptomycin (Life Technologies cat no.16600-082). RKO cells were grown in RPMI with L-glutamine supplemented with Non-essential Amino Acids, Sodium Pyruvate, 10% FBS, and Penicillin-Streptomycin (Life Technologies cat no.11875-093). Cell culturing utilized standard laboratory practices and cells were grown and incubated at 37°C containing 5% CO2.

extract_protocol: DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (cat no. 69504)

treatment_protocol: GSK5032-resistant HCT116 and RKO cells were generated by treating with increasing doses of the DNMT1-specific inhibitor GSK5032, beginning with the IC50 concentration and increasing to over 100-fold that concentration for greater than 100 days.

tag: agent

value: Untreated

tag: cell line

value: DNMT1 hypomorph, DNMT3B knockout


title: 0124 Macula Retina [0124mRet]

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

library_source: transcriptomic single cell

data_processing:
For each sample a cell by gene count matrix is provided
Assembly: HG38
Supplementary files format and content: 10X Genomics sparse data matrix

source_name: Retina

extract_protocol:
The human eyeball was immediately removed within 6 hours after death, and placed in cold phosphate buffered saline (PBS). The retina and RPE /choroid was carefully removed under a dissecting microscope and both tissue layers were dissociated straightaway using the Papain dissociaton system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer's recommendations.

tag: Sex

value: Female

tag: race

value: White

tag: medhx

value: Hypertension

tag: phenotype

value: Early AMD

tag: sequenced estimated number of cells


title: WT BMDMs, so/sp H37Rv ∆esxH Mtb-infected 4, at 72 hours

city: St. Louis

first: Jennifer

last: Philips

state: MO

address: 660 S. Euclid Avenue, Campus Box 8051

department: Department of Medicine, Division of Infectious Diseases

institute: Washington University School of Medicine

description:
sample.16d
Merged_differential_expression_results.tsv

data_processing:
The raw CPM values that were generated underwent filtering, with removal of mitochondrial RNA, autosomal rRNA, and low-expressed genes with less than 1 CPM in the smallest group size, followed by Voom transformation of counts. Differentially expressed genes were then determined using the “limma” package from bioconductor.org.
Assembly: mm10
Supplementary files format and content: Tab separated values with fold changes, confidence intervals, P values, and adjusted P values.

source_name: Differentiated murine hematopoietic cells

growth_protocol: Murine hematopoietic stem cells were isolated from 8-12 week-old C57BL6J mice. Hematopoietic cells were differentiated by culturing for 7 days in Dulbecco’s Modified Eagle Medium (DMEM) with 10% FBS, 2 mM L-glutamine, and 1 mM pyruvate (DMEM complete). DMEM complete media was supplemented with 20% L929 cell supernatant (as a source of macrophage colony stimulating factor (M-CSF), 100 U/mL final concentration), 10 units/ml penicillin, and 10 units/ml streptomycin. Following differentiation, BMDMs were washed with PBS, resuspended in DMEM complete with 10% L929 cell supernatant, and plated for infection the following day.Cells were maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
At 72 hpi, macrophages were lysed in TRI Reagent and total RNA was extracted. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 500ng to 1ug total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94°C for 8 min. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Differentiated BMDMs were washed with PBS, resuspended in DMEM complete with 10% L929 cell supernatant, and 1.6 x 10^6 BMDMs were plated in 6-well plates for infection the following day. BMDMs were uninfected, infected with so/sp treated Mtb at an MOI of 5 for 72 hours, or infected with 5µmF Mtb at an MOI of 5 for 72 hours. Cells were maintained in a humidified atmosphere with 5% CO2 at 37°C.

value: BMDMs differentiated from hematopoietic cells

tag: genotype

value: WT

tag: strain

value: BMDM differentiation

tag: time

value: 72 hours post infection


title: WT BMDMs, so/sp H37Rv ∆esxH Mtb-infected 3, at 72 hours

value: Differentiated murine hematopoietic cells


title: 0106 Peripheral Choroid [0106tCho]

source_name: Choroid

tag: age

value: Male

value: cerebral infarct

value: Neo AMD


title: 0122 Peripheral Choroid [1022tCho]

value: cataract surgery

value: Normal


title: 0122 Macula Retina [1022mRet]


title: WT BMDMs, so/sp H37Rv ∆esxH Mtb-infected 1, at 72 hours

description:
sample.16a
Merged_differential_expression_results.tsv


title: 0122 Macula Choroid [1022mCho]


title: PAT_1157_wk0

tag: disease state

value: Rheumatoid Arthritis patient

tag: gender

value: F

tag: response

value: R


title: siICR_2

tag: cell type

value: Human Umbilical Vein Endothelial Cells

value: siRNA-ICR

value: untreated


title: HCT116_parental

value: Vehicle

value: Wild type


title: RKO_GSK5032

source_name: RKO Colorectal Carcinoma epithelial cells

value: RKO


title: PAT_1157_wk12

tag: patient

tag: week


title: siICR_1

tag: genotype/variation

tag: treatment


title: 0124 Peripheral Choroid [0124tCho]

tag: Sex

value: Female

value: White

value: Hypertension

value: Early AMD


title: PAT_1151_wk0


title: PAT_1130_wk0


title: PAT_1152_wk0

value: NR


title: TNFalpha_siICR_1

value: treated with TNF-α for 12 hours


title: PAT_1152_wk12


title: 0925 gex [0925gex]

source_name: Retina, Choroid

tag: race

value: Cataract Surgery


title: RKO_parental

tag: agent

tag: cell line


title: WT BMDMs, so/sp H37Rv ∆esxH Mtb-infected 5, at 72 hours

description:
sample.16e
Merged_differential_expression_results.tsv

value: Differentiated murine hematopoietic cells

value: BMDMs differentiated from hematopoietic cells

value: WT

value: BMDM differentiation

value: 72 hours post infection


title: 0124 Peripheral Retina [0124tRet]

tag: medhx

tag: phenotype

tag: sequenced estimated number of cells


title: 0124 Macula Choroid [0124mCho]


title: HCT116_GSK5032

tag: genotype


title: 0122 Peripheral Retina [1022tRet]

tag: age

value: cataract surgery

value: Normal


title: WT BMDMs, so/sp H37Rv ∆esxH Mtb-infected 2, at 72 hours

description:
sample.16b
Merged_differential_expression_results.tsv

tag: strain

tag: time


title: 0106 Macula Retina [0106mRet]

value: Male

value: cerebral infarct

value: Neo AMD


title: PAT_1151_wk12

tag: disease state

value: Rheumatoid Arthritis patient

tag: gender

value: F

tag: response

value: R


title: PAT_1137_wk0

tag: patient

tag: week


title: PAT_1130_wk12


title: WT BMDMs, so/sp H37Rv ∆cpsA Mtb-infected 3, at 72 hours

description:
sample.15c
Merged_differential_expression_results.tsv

tag: cell type

tag: treatment


title: 0826 Peripheral Retina [0826tRet]

tag: Sex

value: Female

tag: race

value: Black

value: Hypertension


title: WT BMDMs, so/sp H37Rv ∆cpsA Mtb-infected 2, at 72 hours

description:
sample.15b
Merged_differential_expression_results.tsv

tag: cell line


title: 0106 Peripheral Retina [0106tRet]

value: White

tag: medhx


title: WT BMDMs, so/sp H37Rv ∆cpsA Mtb-infected 5, at 72 hours

description:
sample.15e
Merged_differential_expression_results.tsv

value: Differentiated murine hematopoietic cells


title: 0826 Macula Choroid [0826mCho]

tag: phenotype


title: WT BMDMs, so/sp H37Rv ∆cpsA Mtb-infected 4, at 72 hours

description:
sample.15d
Merged_differential_expression_results.tsv

value: BMDMs differentiated from hematopoietic cells


title: PAT_1126_wk12


title: PAT_1127_wk12


title: WT BMDMs, so/sp H37Rv ∆ppsD::ppsD Mtb-infected 4, at 72 hours

description:
sample.14d
Merged_differential_expression_results.tsv

value: WT


title: 0925 hash [0925hash]

value: Cataract Surgery

tag: sequenced estimated number of cells


title: PAT_1126_wk0


title: 0716 Peripheral Retina [0716tRet]

value: Atrophic AMD


title: 0824 Peripheral Choroid [0824tCho]

value: Heart Disease


title: WT BMDMs, so/sp H37Rv ∆cpsA Mtb-infected 1, at 72 hours

description:
sample.15a
Merged_differential_expression_results.tsv

tag: genotype

value: BMDM differentiation

value: 72 hours post infection


title: 0826 Macula Retina [0826mRet]

tag: age

value: Normal


title: WT BMDMs, so/sp H37Rv ∆ppsD::ppsD Mtb-infected 3, at 72 hours

description:
sample.14c
Merged_differential_expression_results.tsv

tag: strain


title: WT BMDMs, so/sp H37Rv ∆ppsD::ppsD Mtb-infected 5, at 72 hours

description:
sample.14e
Merged_differential_expression_results.tsv

tag: time


title: 0826 Peripheral Choroid [0826tCho]


title: PAT_1124_wk0

tag: disease state


title: 0824 Macula Choroid [0824mCho]

value: Male


title: 0716 Macula Retina [0716mRet]


title: PAT_1127_wk0

value: Rheumatoid Arthritis patient

tag: gender


title: 0727 Macula Retina [0727mRet]

value: Early AMD


title: 0824 Macula Retina [0824mRet]


title: 0727 Peripheral Choroid [0727tCho]


title: 0727 Macula Choroid [0727mCho]


title: 0716 Macula Choroid [0716mCho]


title: 0716 Peripheral Choroid [0716tCho]


title: WT BMDMs, so/sp H37Rv ∆ppsD::ppsD Mtb-infected 1, at 72 hours

description:
sample.14a
Merged_differential_expression_results.tsv


title: 0524 Peripheral Choroid [0524tCho]

value: Glaucoma


title: PAT_1124_wk12

value: F

tag: response

value: R


title: 0824 Peripheral Retina [0824tRet]


title: PAT_1114_wk0

value: NR

tag: patient


title: 0524 Peripheral Retina [0524tRet]

value: White


title: 0727 Peripheral Retina [0727tRet]

value: Female


title: PAT_1111_wk12

tag: week


title: PAT_1111_wk0


title: WT BMDMs, so/sp H37Rv ∆ppsD::ppsD Mtb-infected 2, at 72 hours

description:
sample.14b
Merged_differential_expression_results.tsv

value: Differentiated murine hematopoietic cells

tag: cell type

value: BMDMs differentiated from hematopoietic cells


title: WT BMDMs, so/sp H37Rv ∆ppsD Mtb-infected 4, at 72 hours

description:
sample.13d
Merged_differential_expression_results.tsv

value: WT

tag: treatment


title: 0524 Macula Choroid [0524mCho]

tag: Sex


title: 0715 Peripheral Retina [0715tRet]

tag: race


title: 0511 Macula Retina [0511mRet]

value: Cataract Surgery


title: 0511 Peripheral Retina [0511tRet]


title: WT BMDMs, so/sp H37Rv ∆ppsD Mtb-infected 5, at 72 hours

description:
sample.13e
Merged_differential_expression_results.tsv

tag: cell line


title: 0715 Macula Retina [0715mRet]

tag: medhx


title: 0511 Macula Choroid [0511mCho]

tag: phenotype


title: maternal serum-VSD6

city: Quanzhou

first: Yiru

last: Yang

address: Zhongshan North Road

institute: the Second Affiliated Hospital of Fujian Medical University

data_processing:
Bcl2fastq (v2.19 for myocardium and maternal serum; v2.20 for amniotic fluid) was used to perform recognition on the original image and convert it into the original sequence.
The Fastx-toolkit (v0.0.14) was used to evaluate and filter the quality.
The expression was normalized using the transcripts read number per million (TPM) method of myocardium and maternal serum and counts per million (CPM) method of amniotic fluid.
Genome_build: miRBase V22
Supplementary_files_format_and_content: The expression of txt file was normalized using the counts per million (CPM) method. DESeq was used to calculate the expression of each sample, intragroup mean and perform differential expression analysis.
Supplementary_files_format_and_content: transcripts read number per million (TPM) method of myocardium and maternal serum

organism: Rattus norvegicus

source_name: maternal serum

extract_protocol:
Corresponding kits were used to extract total RNA/miRNA from wax blocks of the myocardium (RecoverAll™ Total Nucleic Acid Isolation Kit, Ambion, Thermo Fisher Scientific), amniotic fluid (HiPure Universal RNA Mini Kit, Magen) and maternal serum (miRNeasy Mini Kit, QIAGEN).
A cDNA library of amniotic fluid-derived miRNAs (QIAseq miRNA Library Kit, QIAGEN) and myocardium-derived and serum-derived miRNAs (TruSeq Small RNA Library Preparation kit, Illumina) was constructed.

value: Sprague-Dawley

tag: tissue

value: maternal serum

tag: embryonic day


title: WT BMDMs, so/sp H37Rv ∆ppsD Mtb-infected 2, at 72 hours

description:
sample.13b
Merged_differential_expression_results.tsv

tag: genotype

value: BMDM differentiation

value: 72 hours post infection


title: PAT_1109_wk0

value: M

tag: age


title: maternal serum-VSD7

tag: strain


title: WT BMDMs, so/sp H37Rv ∆ppsD Mtb-infected 1, at 72 hours

description:
sample.13a
Merged_differential_expression_results.tsv

tag: time


title: 0511 Peripheral Choroid [0511tCho]

value: Normal

tag: sequenced estimated number of cells


title: WT BMDMs, 5µmF H37Rv Mtb-infected 5, at 72 hours

description:
sample.12e
Merged_differential_expression_results.tsv


title: maternal serum-VSD5


title: maternal serum-VSD4


title: WT BMDMs, 5µmF H37Rv Mtb-infected 4, at 72 hours

description:
sample.12d
Merged_differential_expression_results.tsv


title: WT BMDMs, so/sp H37Rv ∆ppsD Mtb-infected 3, at 72 hours

description:
sample.13c
Merged_differential_expression_results.tsv


title: maternal serum-VSD3


title: 0524 Choroid Retina [0524mRet]

value: Male

value: Early AMD


title: N11_44

city: Boston

first: Julia

last: TCW

state: Massachusetts

address: 700 Albany St.

institute: Boston University

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.3a).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1) and DESeq2 (v.3.14)
Genome_build: hg38
Supplementary_files_format_and_content: populationAPOE_featureCounts.txt (Tab-delimited text file of raw read counts)

source_name: APOE44 Mixed cortical cultures (Neuron+astrocytes)

growth_protocol: Directed differentiation of astrocytes, microglia, BMECs and mixed cortical cultures containing neurons and astoryctes

extract_protocol:
Total RNA was extracted from differentiated CNS cells in a single batch using the Total RNA isolation kit (Rneasy kit from Qiagen).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina, and sequenced as paired-end 100bp reads on the Illumina HiSeq 2500.

treatment_protocol: No treatment

tag: apoe genotype

tag: batch

tag: rin

tag: grsnoapoe

tag: cell type proportion


title: N12_44

tag: cell type

value: Mixed cortical cultures (Neuron+astrocytes)

tag: Sex

value: F


title: N13_44


title: 0715 Macula Choroid [0715mCho]

tag: race

value: Glaucoma


title: maternal serum-VSD2


title: N9_44


title: N10_44


title: 0715 Peripheral Choroid [0715tCho]

value: White

tag: medhx


title: WT BMDMs, 5µmF H37Rv Mtb-infected 2, at 72 hours

description:
sample.12b
Merged_differential_expression_results.tsv

tag: cell line

tag: treatment


title: N7_33

source_name: APOE33 Mixed cortical cultures (Neuron+astrocytes)


title: WT BMDMs, 5µmF H37Rv Mtb-infected 3, at 72 hours

description:
sample.12c
Merged_differential_expression_results.tsv


title: maternal serum-VSD1

tag: tissue

tag: embryonic day


title: N8_44


title: WT BMDMs, so/sp H37Rv Mtb-infected 5, at 72 hours

description:
sample.11e
Merged_differential_expression_results.tsv

tag: genotype


title: N3_33


title: N5_33


title: N2_33


title: M12_44

source_name: APOE44 Microglia

value: Microglia


title: M10_44


title: M13_44


title: maternal serum-NC6

tag: strain


title: WT BMDMs, so/sp H37Rv Mtb-infected 3, at 72 hours

description:
sample.11c
Merged_differential_expression_results.tsv

value: Differentiated murine hematopoietic cells

tag: time


title: maternal serum-NC4


title: M9_44


title: N6_33


title: N4_33


title: N1_33


title: WT BMDMs, so/sp H37Rv Mtb-infected 4, at 72 hours

description:
sample.11d
Merged_differential_expression_results.tsv

value: BMDMs differentiated from hematopoietic cells


title: M11_44


title: maternal serum-NC7


title: maternal serum-NC2


title: WT BMDMs, 5µmF H37Rv Mtb-infected 1, at 72 hours

description:
sample.12a
Merged_differential_expression_results.tsv

value: WT


title: M6_33

source_name: APOE33 Microglia


title: WT BMDMs, so/sp H37Rv Mtb-infected 1, at 72 hours

description:
sample.11a
Merged_differential_expression_results.tsv


title: maternal serum-NC3


title: M5_33


title: maternal serum-NC5


title: maternal serum-NC1


title: WT BMDMs, Uninfected 4, at 72 hours

description:
sample.9d
Merged_differential_expression_results.tsv


title: M7_33


title: M8_44


title: myocardium-non-VSD7

source_name: myocardium

value: myocardium


title: WT BMDMs, so/sp H37Rv Mtb-infected 2, at 72 hours

description:
sample.11b
Merged_differential_expression_results.tsv


title: M4_33


title: WT BMDMs, Uninfected 5, at 72 hours

description:
sample.9e
Merged_differential_expression_results.tsv


title: myocardium-non-VSD6

value: Sprague-Dawley


title: M3_33


title: WT BMDMs, Uninfected 2, at 72 hours

description:
sample.9b
Merged_differential_expression_results.tsv


title: M2_33


title: M1_33


title: myocardium-non-VSD4


title: B13_44

source_name: APOE44 BMECs

value: BMECs


title: B12_44


title: B11_44


title: WT BMDMs, Uninfected 1, at 72 hours

description:
sample.9a
Merged_differential_expression_results.tsv

value: BMDM differentiation


title: myocardium-non-VSD3


title: B9_44


title: B8_44


title: myocardium-non-VSD2


title: B6_33

source_name: APOE33 BMECs


title: B7_33


title: WT BMDMs, Uninfected 3, at 72 hours

description:
sample.9c
Merged_differential_expression_results.tsv

value: 72 hours post infection


title: RNA-Seq MI_72h_rep3

city: Shanghai

first: Han

last: Yuru

state: Shanghai

address: 279 Zhouzhu Rd. Pudong New District, Shanghai

institute: Shanghai University of Medicine and Health Sciences

description:
MI_72h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (63 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.

data_processing:
The cutadapt (V1.18)was used to remove adapter sequences, low quality bases, and read parameters of less than 50 bases "-a AGATCGGAAGAGC-a AGATCGGAAGC-trim-n-m 50-q 20,20". The clean data were mapped to the mm10 reference genome using Hisat2 (v2.1.0)to obtain BAM files. The featureCounts software was used to obtain the number of reads of genes from the BAM files in each sample and the fragments per kilobase million (FPKM) values in genes was calculated by R software.
Assembly: mm10
Supplementary files format and content: The csv file includes the FPKM values and count values for each sample

source_name: myocardial tissue

extract_protocol:
Total RNA was extracted from the samples and the quality of the RNA was tested. Then, mRNA was purified from the total RNA using oligo dT magnetic beads.
Fragmentation of mRNA was performed under high temperature conditions using divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5X). Synthesis of first-strand cDNA using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H) as the template for mRNA. Second strand cDNA synthesis was carried out with DNA polymerase I and RNase H. The remaining overhangs were transformed to blunt-ended by exonuclease/polymerase activity. The 3ʹ end of the DNA fragment was adenylated and then the NEBNext adapters with a hairpin loop structure were attached in preparation for hybridisation. Library fragments were purified using the Ampoule XP system (Beverly Beckman Coulter, USA) to prioritize cDNA fragments of 250-300 bp in length. The cDNA was ligated using 3 μl of USER Enzyme (NEB, USA) for 15 minutes at 37°C using an adapter of the selected size, then used for 5 minutes at 95°C, followed by PCR. PCR was then conducted using Phusion High Fidelity DNA polymerase, universal PCR primers and index (X) Primer. Next, the PCR products were purified (Ampoule XP system) and the library quality was evaluated on the Agilent Bioanalyzer 2100 system.

value: myocardial tissue

value: Cardiomyocytes


title: RNA-Seq MI_72h_rep1

description:
MI_72h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (61 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: B4_33


title: B5_33


title: RNA-Seq MI_72h_rep2

description:
MI_72h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (62 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: B10_44

value: M


title: B2_33


title: myocardium-non-VSD5


title: B1_33


title: myocardium-VSD7


title: RNA-Seq MI_24h_rep3

description:
MI_24h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (60 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: A13_44

source_name: APOE44 astrocytes

value: Astrocytes


title: RNA-Seq MI_24h_rep2

description:
MI_24h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (59 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: myocardium-VSD5


title: myocardium-non-VSD1


title: myocardium-VSD4


title: RNA-Seq MI_6h_rep3

description:
MI_6h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (57 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: RNA-Seq MI_24h_rep1

description:
MI_24h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (58 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: RNA-Seq MI_6h_rep2

description:
MI_6h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (56 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: A12_44


title: A11_44


title: A8_44


title: myocardium-VSD2


title: myocardium-VSD6


title: B3_33


title: A7_33

source_name: APOE33 astrocytes


title: A9_44


title: myocardium-VSD1


title: RNA-Seq MI_6h_rep1

description:
MI_6h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (55 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: A6_33


title: A10_44


title: A4_33


title: A5_33


title: RNA-Seq MI_1h_rep2

description:
MI_1h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (53 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: A3_33


title: RNA-Seq MI_1h_rep3

description:
MI_1h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (54 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: myocardium-NC7


title: RNA-Seq MI_1h_rep1

description:
MI_1h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (52 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: myocardium-VSD3


title: A2_33


title: myocardium-NC5


title: N_RC2C_44

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.3a).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1) and DESeq2 (v.3.14)
Genome_build: hg38
Supplementary_files_format_and_content: isogenicAPOE_featureCounts.txt (Tab-delimited text file of raw read counts)

source_name: Mixed cortical cultures (Neuron+astrocytes) from Indiv4

growth_protocol: Directed differentiation of astrocytes, microglia, BMECs and mixed cortical cultures containing neurons and astroyctes

tag: indivdual


title: RNA-Seq MI_10m_rep3

description:
MI_10m_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (51 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: A1_33

tag: apoe genotype


title: RNA-Seq control_rep3

description:
control_rep3
The mice in the control group received the same operation, sutured through the inferior artery, but not ligated

value: control


title: RNA-Seq MI_10m_rep2

description:
MI_10m_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (50 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: N_MC2E_33

value: Mixed cortical cultures (Neuron+astrocytes)

tag: batch

value: F


title: N_RC2I_44

tag: rin


title: N_RC1I_33

source_name: Mixed cortical cultures (Neuron+astrocytes) from Indiv3

tag: grsnoapoe


title: myocardium-NC6


title: N_MC2C_33

tag: cell type proportion


title: myocardium-NC1


title: N_RC1H_33

tag: cell type


title: N_CD1F_44

tag: Sex


title: N_RC1B_33


title: RNA-Seq control_rep1

description:
control_rep1
The mice in the control group received the same operation, sutured through the inferior artery, but not ligated


title: N_TCW2KO3

source_name: Mixed cortical cultures (Neuron+astrocytes) from Indiv2


title: N_TCW2KO2


title: RNA-Seq MI_10m_rep1

description:
MI_10m_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (50 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: S_RNA_lncRNA

city: Harbin

first: Yao

last: Wang

address: 59 Mucai Street, Xiangfang District

department: Department of Veterinary Medicine

institute: Northeast Agricultural university

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: Sciatic Nerve

growth_protocol: The rats were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: The sciatic nerves of the rats were exposed surgically and squeezed with vascular forceps at the same force and duration to prepare a sciatic nerve injury model[20]. Each nerve was marked with sutures near the distal end of the clamp, and the wound was sutured layer by layer for closing. In the sham operation group, only nerve exposure was performed without inflicting nerve damage.

value: SD

value: male

value: Sciatic Nerve

tag: age

value: 30d after injury

value: sham operation group


title: myocardium-NC2

value: myocardium


title: myocardium-NC4

value: Sprague-Dawley


title: N_TCW2_44b


title: S21-Control

city: Kansas City

first: Daniel

middle: Paul

last: Heruth

address: 4th Floor PRC, 2401 Gillham Road

department: Pediatrics

institute: Children's Mercy

description: Healthy Control

data_processing:
The  base calling (.bcl) files were converted to FASTQ files using Illumina’s bcl2fastq v2.17.1.14 software.
The Tuxedo Suite pipeline (TopHat v1.3.0/Bowtie v0.12.7/Cufflinks v1.0.3) was used to map RNA-seq reads  (FPKM)
Transcript assembly and abundance estimation and comparing expression were conducted and  reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: GRCh38.83
Supplementary_files_format_and_content: tab-delimited text file of a matrix table generated and reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).

source_name: Peripheral blood T cells

extract_protocol:
Total RNA isolation from peripheral T cells
TruSeq Library, Whole transcriptome paired end sequencing ( 2 X 101 cycles)

value: Peripheral blood T cells

tag: condition

value: Healthy Control

tag: case, control

value: Control

tag: t cell number


title: N_TCW2_33C


title: S20-Case-L

description: 22q11.2 Deletion Syndrome with low T cell number

tag: tissue

value: 22q11.2 Deletion Syndrome

value: Case

value: Low


title: N_TCW1KO4

source_name: Mixed cortical cultures (Neuron+astrocytes) from Indiv1


title: S19-Case-L


title: N_TCW1KO3


title: N_MC2F_33


title: RNA-Seq control_rep2

description:
control_rep2
The mice in the control group received the same operation, sutured through the inferior artery, but not ligated

value: myocardial tissue

value: Cardiomyocytes

tag: treatment


title: myocardium-NC3

tag: embryonic day


title: N_TCW1KO1

value: Mixed cortical cultures (Neuron+astrocytes)


title: S16-Case-L


title: N_CD1D_44

value: M


title: N_RC2G_44

value: F


title: N_TCW1_33C


title: N_TCW2_33A


title: N_CD1D_2_44


title: M_RC2G_44

source_name: Microglia from Indiv4

value: Microglia


title: M_RC2I_44


title: A_RNA_lncRNA

tag: strain

value: SD

value: male

value: Sciatic Nerve

value: treated with AKBA


title: M_RC2C_44


title: S13-Case-N

description: 22q11.2 Deletion Syndrome with normal T cell number

value: Normal


title: N_TCW2_33B


title: N_TCW1KO2


title: N_TCW1_44b


title: N_TCW2KO1


title: M_RNA_lncRNA

value: 30d after injury

value: control


title: M_MC2E_33


title: M_MC2C_33


title: N_TCW1_44a


title: N_TCW1_44c


title: S11-Case-N

value: Peripheral blood T cells


title: N_TCW2_44c


title: N_TCW1_33B


title: N_TCW2_44a


title: S17-Case-L

value: 22q11.2 Deletion Syndrome


title: S14-Case-L

value: Case


title: N_TCW1_44x


title: M_CD1D_2_44

source_name: Microglia from Indiv3


title: S12-Control

description: Healthy Control

value: Healthy Control

value: Control


title: S15-Case-L

value: Low


title: M_MC2F_33


title: M_CD1D_44


title: M_RC1I_33


title: M_CD1F_44


title: S10-Control

description: Healthy Control


title: S9-Control

description: Healthy Control


title: S8-Control

description: Healthy Control


title: M_RC1H_33


title: M_RC1C_33_1


title: M_TCW2KO3

source_name: Microglia from Indiv2


title: S6-Case-N


title: M_TCW2_44d


title: M_TCW2_44c


title: M_TCW2KO1


title: S5-Control

description: Healthy Control


title: S7-Case-N


title: M_RC1C_33


title: M_TCW2KO2


title: S2-Case-N


title: M_TCW2_44b


title: S4-Case-L


title: M_TCW2_33A


title: M_TCW2_33B


title: M_TCW1KO2

source_name: Microglia from Indiv1


title: M_TCW1KO1


title: Mouse-SC-scRNAseq-Middle-aged-d10

city: Columbus

first: Cankun

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

description:
10x Genomics
counts.csv.gz
metadata.csv.gz

data_processing:
Basecalling with Illumina bcl2fastq
Read alignment, cell barcode demultiplexing, and UMI demultiplexing using cellranger 3.1.0
Assembly: mm10
Supplementary files format and content: CSV format, gene-cell raw count matrix and metadata for cells

source_name: Spinal cord

extract_protocol:
Mice were anesthetized with isoflurane and perfused with 1x PBS. The spinal cord was flushed through the spinal canal with PBS. Spinal cord tissues were homogenized with an 18-gauge needle in a protease inhibitor solution created using protease inhibitor cocktail tablets (Roche) per the manufacturer’s protocol, centrifuged at 800 g for 5 minutes, and the supernatant was collected and stored at -80°C. Tissue pellet was resuspended in a solution of HBSS with 1 mg/ml collagenase A (Roche) and 1 mg/ml DNase I (Sigma-Aldrich) and incubated at 37°C for 20 minutes. Mononuclear cells were separated from myelin via centrifugation in a 27% Percoll solution (GE Healthcare). Cells were stained for CD45 and sorted via flow cytometry. Mononuclear cells were isolated from 4 spinal cords per sample.
Libraries were sequenced on an Illumina Novaseq instrument and counted with CellRanger v3.1.0 using mm10 reference genome GENCODE vM23/Ensembl 98.

value: Spinal cord

value: Middle-aged

tag: timepoint

value: Adoptive transfer EAE


title: Mouse-SC-RNAseq-Young-naïve

description: Illumina

data_processing:
Basecalling with Illumina bcl2fastq
Read alignment, cell barcode demultiplexing, and UMI demultiplexing using cellranger 3.1.0
Assembly: mm10
Supplementary files format and content: CSV format, gene-cell raw count matrix and metadata for cells/samples

value: microglia

value: Young

tag: sample type

value: naive


title: Mouse-SC-scRNAseq-Middle-aged-d6


title: Mouse-SC-RNAseq-Middle-aged-naïve

description: Illumina


title: M_TCW2_33C

tag: indivdual

value: Microglia

tag: apoe genotype

value: M


title: M_TCW1KO3

tag: batch

value: F

tag: rin


title: S1-Case-N

value: Normal


title: Mouse-SC-scRNAseq-Young-d10


title: C43(DE3) [C43_DE3_LB_73]

city: Clayton

first: Kirill

last: Tsyganov

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

description:
V300012960_L01_7-3
MGIseq-2000

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with BWA mem aligner option (Li H et al. 2013 ) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GFF and FASTA files were downloaded from RefSeq database bl21_de3 (https://www.ncbi.nlm.nih.gov/nuccore/CP001509)
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical conts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: CP001509_bl21_de3
Supplementary_files_format_and_content: raw gene counts, summar QC metrices

organism: Escherichia coli

growth_protocol: Triplicate samples were grown overnight at 37 °C and used to inoculate 25mL Luria broth (LB) cultures and grown to mid-log phase (0.4-0.6).

extract_protocol:
Cells were pelleted and total RNA was purified using RNeasy Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard MiGen protocols

value: C43(DE3) purchased from Lucigen

tag: genotype background

value: F– ompT gal dcm hsdSB(rB- mB-)(DE3)

value: strain grown at 37C in luria broth


title: M_TCW1_44b

tag: cell type

tag: grsnoapoe

tag: cell type proportion


title: Mouse-SC-scRNAseq-Young-d6

tag: age


title: C43(DE3) [C43_DE3_LB_72]

description:
V300012960_L01_7-2
MGIseq-2000


title: M_TCW1_44a

tag: Sex


title: C43(DE3) [C43_DE3_LB_71]

description:
V300012960_L01_7-1
MGIseq-2000


title: M_TCW1_33C


title: M_TCW1_33B


title: LA_RC2I_44

source_name: Astrocytes from Indiv4

value: Astrocytes


title: M_TCW1_33A


title: C41(DE3) [C41_DE3_LB_63]

description:
V300012960_L01_6-3
MGIseq-2000

value: C41(DE3) purchased from Lucigen


title: LA_RC2G_44


title: Phf20-/-, GlcStarv, RNA-seq, rep2

city: Seoul

first: Se Won

last: Park

state: Gwanak-Gu

address: Gwanak-ro 1, Gwanak-gu, Seoul, Seoul Nat'l Univ Bldg504 Rm607

country: South Korea

institute: Seoul national university

data_processing:
RNA-seq reads were trimmed using Trimmomatic (v0.36)
After trimming, the reads were aligned to the mm10 genome assembly and the transcriptome using STAR (v2.5.3a) with GENCODE M16 annotation
RSEM (v1.3.0) was used to calculate the expected read counts, FPKM and TPM for each sample from the corresponding bam files
The TPM values were extracted and used for following downstream analyses such as hierarchical clustering, K-mean clustering, and GSEA
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements of genes

source_name: Mouse Embryonic Fibroblast (MEF)

growth_protocol: WT and Phf20-/- MEF cells were cultured at 37 ℃ in Dulbecco’s modified Eagle medium (DMEM)supplemented with 10 % fetal bovine serum (FBS) and ZellShield in a humidified incubator with 5 % CO2.

extract_protocol:
For RNA-seq, RNA were harvested using Trizol and purified using Qiagen RNeasy Kit. For ATAC-seq, DNA was fragmented with Mnase. For ChIP-seq, crosslinked DNA was fragmented with sonication and IP with H3K4me1 or H3K4me2 antibody.
All of the libraries (RNA-seq, ATAC-seq and ChIP-seq) were constructed following standard Illumina library preparation protocol

treatment_protocol: For glucose starvation samples, cells were treated with Glucose-free DMEM supplemented with dialyzed FBS for 24hrs

tag: genotype

value: Glucose starvation 24hr

tag: assay

value: RNA-seq


title: C41(DE3) [C41_DE3_LB_62]

description:
V300012960_L01_6-2
MGIseq-2000

tag: treatment


title: Phf20-/-, GlcStarv, RNA-seq, rep1


title: LA_RC2C_44


title: Phf20-/-, control, RNA-seq, rep2

value: control


title: M_TCW1_44c


title: C41(DE3) [C41_DE3_LB_61]

description:
V300012960_L01_6-1
MGIseq-2000


title: WT, GlcStarv, RNA-seq, rep2

value: WT


title: BL21(DE3) [BL21_DE3_LB_53]

description:
V300012960_L01_5-3
MGIseq-2000

value: BL21(DE3) purchased from Novagen #70235-3


title: LA_MC2C_33


title: BL21(DE3) [BL21_DE3_LB_52]

description:
V300012960_L01_5-2
MGIseq-2000


title: Phf20-/-, control, RNA-seq, rep1


title: WT, GlcStarv, RNA-seq, rep1


title: LA_RC1B_33

source_name: Astrocytes from Indiv3


title: LA_RC1I_33


title: LA_CD1D_44


title: WT, control, RNA-seq, rep2


title: LA_CD1F_44


title: LA_RC1H_33


title: LA_CD1D_2_44


title: LA_TCW2KO3

source_name: Astrocytes from Indiv2


title: LA_TCW2KO2_1


title: WT, control, RNA-seq, rep1


title: BL21(DE3) [BL21_DE3_LB_51]

description:
V300012960_L01_5-1
MGIseq-2000


title: LA_TCW2KO2


title: LA_MC2F_33


title: LA_TCW2KO1


title: LA_TCW2_44c


title: M_TCW2_44a


title: LA_TCW2_44b


title: Healthy control, patient 12

city: Edinburgh

first: John

middle: P

last: Thomson

state: Lothian

address: 27, Strathalmond Road

institute: Thomson Bioinformatics

scan_protocol: Human Myeloid Innate Immunity Panel panels were run as per manufacturer’s instructions

data_processing: Normalized Log2 NanoString gene expression data was prodiced using the nCounter software and downstream data analysis of differnetially expressedgenes carried out through custom R scripts

source_name: human monocytes

extract_protocol:
Up to 20-40mls of whole blood was collected from patients into citrate tubes and up to 10 million cells were stained for flow cytometry assessment and sorting.Monocytes were identified as Singles Dapi-CD45+non-granulocyte Lin(CD3/CD56/CD19+/-CD66b)- HLADR+ CD14+ and/or CD16+ cells.
For human monocytes 5000 cells were sorted using a human monocyte gating strategy directly into 2ul RLT buffer using a BD Fusion Sorter. Cell pellets were vortexed and centrifuged prior to immediate freezing until ready for processing.

tag: condition

tag: tissue

value: blood

value: monocytes


title: Healthy control, patient 09


title: LA_MC2E_33


title: LA_TCW2_33A


title: Phf20-/-, GlcStarv, ChIP-seq, H3K4me1

data_processing:
ChIP-seq reads were mapped to mm10 reference using Burrows-Wheeler Aligner (BWA) MEM algorithm (version 0.7.12).
Peak-calling was performed using MACS2 (version 2.1.2) callpeak command with --extensive 200 shift -100 parameters and control as corresponding input data.
The peaks were filtered by q-value < 0.01 and signal value > 5 and merged using bedtools (v2.25.0)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format for genome coverage

value: Mouse Embryonic Fibroblast (MEF)

value: ChIP-seq

tag: chip antibody


title: ARDS, patient 008

value: ARDS


title: Phf20-/-, control, ChIP-seq, Input


title: ARDS, patient 006


title: ARDS, patient 007


title: Phf20-/-, control, ChIP-seq, H3K4me2


title: LA_TCW2_33A_1

value: M


title: LA_TCW2_33C


title: ARDS, patient 005


title: LA_TCW1KO1

source_name: Astrocytes from Indiv1

value: F


title: LA_TCW1_44c


title: LA_TCW1_44a


title: LA_TCW1_44b


title: Healthy control, patient 10


title: LA_TCW1KO3


title: LA_TCW2_44a


title: LA_TCW1KO2


title: WT, GlcStarv, ChIP-seq, H3K4me2


title: ARDS, patient 004


title: Phf20-/-, GlcStarv, ChIP-seq, Input


title: LA_TCW1_33C


title: WT, GlcStarv, ChIP-seq, H3K4me1


title: Phf20-/-, control, ChIP-seq, H3K4me1


title: LA_TCW1_33B


title: WT, GlcStarv, ChIP-seq, Input


title: Phf20-/-, GlcStarv, ChIP-seq, H3K4me2


title: WT, control, ChIP-seq, H3K4me1


title: 390_min

city: Sydney

first: Walter

last: Muskovic

state: New South Wales

address: Level 1, C25 Lowy Cancer Research Centre, Gate 9 High St, UNSW

institute: Children's Cancer Institute Australia

data_processing:
Sequencing reads were trimmed to remove Illumina adapter sequences, with cutadapt, version 1.11.
Trimmed reads were aligned to the GRCh38 primary genome assembly + RNA Sequin standards using STAR, version 2.5.2a.
Read counts were quantified using featureCounts from Rsubread, version 1.34.6, with Ensembl GRCh38 v.29 gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: For each time point, two tab-delimited text files are provided. The  XXX_min_counts.tsv files contain the number of reads quantified for each Ensembl gene using featureCounts. The file XXX_min_normalised_counts.tsv files contain the same counts normalised across all time points using the median of ratios method implemented in the DESeq2 R package, version 1.24.0.

source_name: T98G glioblastoma cells

growth_protocol: T98G human glioblastoma cells were cultured in Gibco Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS) at 37°C in humidified atmosphere with 5% CO2. For each time point two million cells were seeded and allowed to equilibrate for 24 hours.

extract_protocol:
At the specified time points, T98G cells were lysed with TRIzol reagent (Ambion), homogenized and frozen for subsequent RNA isolation. Total RNA extraction and purification was performed using a miRNeasy Mini Kit and RNase-free DNase (Qiagen).
RNA samples were depleted of ribosomal RNA (rRNA) using Ribo-Zero biotinylated, target-specific oligos (Illumina) combined with RNAClean XP beads (Beckman Coulter). Following purification, rRNA-depleted samples were prepared for sequencing using an Illumina TruSeq Stranded Total RNA library prep kit. After individual library QC, the sample pool size and concentration were determined using a LabChip GX DNA High Sensitivity assay and qPCR using a KAPA Library Quantification Kit (Roche). Uniquely indexed samples were pooled in equimolar concentration, diluted and denatured as one and clustered across eight flow cell lanes.

treatment_protocol: Following 24 hours of equilibration, all time point samples were serum-starved by a 72 hour incubation in serum-free DMEM. Cells were stimulated with 20%FCS/DMEM at specified time points.

value: T98G human glioblastoma cells

tag: cell line

tag: time point (min)


title: MHCII-ve_Hypoxia_LPS_LYVE1+ve_2

description: gene expression over myeloid inflammation gene panel

scan_protocol: NanoString gene expression plates were run as per manufacturer’s instructions

source_name: Mouse macrophages

treatment_protocol: C57BL/6J mice were challenged with LPS and housed in 10% hypoxia for 5 days. Mice received i.p PBS or CSF1-Fc daily (4 days) until sacrificed on day 5. Lung digest CD64hiSiglecF-Ly6C-MHC- macrophages from PBS-treated mice and CD64hiSiglecF-Ly6C-MHC-Lyve1+ macrophages were sorted by flow cytometry and analysed by nanostring platform.

value: Hypoxic LYVE1+ve


title: 360_min


title: 400_min


title: 350_min


title: 370_min


title: MHCII-ve_Hypoxia_LPS_LYVE1+ve_1


title: 380_min


title: 340_min


title: WT, control, ChIP-seq, Input


title: MHCII-ve_Hypoxia_LPS_3

value: Hypoxic


title: 330_min


title: Vehicle treated BMDM

city: Indianapolis

first: Kaice

last: LaFavers

state: IN

address: 950 W Walnut

institute: Indiana University School of Medicine

description: BMDM treated with 5% dextrose vehicle

data_processing:
Cellranger (10X Genomic v.3.0.2) was used to process raw sequencing data including demultiplexing (bcl2fastq) and generate fastq files (as provided).
STAR was used to align the output fastq filesto the mm10 reference genome.
Expression levels for genes were tallied for each cell by UMIs from the aligned reads.
Expression matrices, gene and cell UMI files generated (as provided in processed data .zip files).
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tar archives files contain barcode.tsv.gz, features.tsv.gz and matrix.mtx.gx for loading into analysis tool of choice

source_name: macrophages

growth_protocol: Bone marrow derived macrophages were generated by plating bone marrow cells at a density of 1.5e6 cells/100 mm dish in RPMI-1640 with L-glutamine, 10% FBS and 1X pen/strep subbplemented with 50 ng/ml M-CSF. Additional media was added on day 3 and half the media replaced on day 6. Treatments were performed on day 7.

extract_protocol:
Macrophages were harvested with Tryple (10 min, RT) before removing dead cells with the Easy Sep Dead Cell Removal Kit. Cells were washed twice with PBS/2% FBS and filtered over a 40 um filter.
Libraries were prepared according to Chromium's instructions.Briefly, samples and reagents were partitioned into droplets. Within each droplet, the cell is lysed and incubated with reagents (oligos and master mix) and a reverse transcriptase reaction performed to generate full length barcoded cDNA from polyA-tailed mRNA transcripts. The droplets are then broekn and the cDNA molecules allowed to pool. This step is followed by bulk PCR-amplificaiton and enzymatic fragmention follow. Size selection is then used to optimize the insert size of the double-stranded cDNA prior to library construction. During library construction, Read 2 is added by Adapter ligation. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. In addition to these sequences required for Illlumina bridge amplification and sequencing, each fragment contains the 10x barcode, a unique molecular identifier added during the reverse transcriptase step and the cDNA insert seuqence used in the data analysis.

treatment_protocol: Cells were treated on Day 7 post harvest with either 1 ug/ml or vehicle (5% dextrose) for 18 hours.

tag: strain

tag: cell-type

value: bone marrow derived macrophages

value: 5percent dextrose


title: MHCII-ve_Hypoxia_LPS_2


title: MHCII-ve_Hypoxia_LPS_LYVE1+ve_3


title: LA_TCW1_33A

tag: indivdual

value: Astrocytes

tag: apoe genotype

tag: batch

tag: rin


title: 310_min

tag: cell type


title: 320_min


title: THP treated BMDM

description: BMDM treated with 1 ug/ml THP

value: 1 ug/ml truncated Tamm-Horsfall Protein


title: zQ175:CK2a'(+/-) rep 5

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Read quality was assessed using FastQC.
Raw reads were then trimmed to remove low quality 3’ ends and adaptor contamination using Trimmomatic with the following parameter: ILLUMINACLIP:all_illumina_adapters.fa:4:15:7:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18 112.
Processed reads were aligned to mouse reference genome GRCm38 via HiSat2 (v 2.1.0) using default parameters. Post-alignment cleaning removed duplicated mapping, unmapped reads and reads with MAPQ<60.
Gene-level expressions were quantified using Subread (v1.6.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Striatum

extract_protocol:
striatum samples were disected, flash frozen on N2 liquid, and RNA was harvested and extracyed using RNeasy Plus Universal Service with STD QC Standard Scale.
RNA libraries were prepared for sequencing using standard Illumina protocols. Libraries were prepared using Takara/Clontech Stranded Total RNA-Seq Kit. (Takara Picomammalian V2 method). All libraries pooled and sequenced on a lane of a NovaSeq S1 2x50-bp flow cell.

value: Huntington's disease-CK2a'(+/-)

tag: age

value: 12-14 months of age


title: MHCII-ve_Hypoxia_LPS_1


title: 290_min


title: 280_min


title: 270_min


title: Hyp_3

source_name: Mouse monocytes

treatment_protocol: Mice were treated with nebulized LPS (3mg), and were then housed in normoxia or hypoxia (10% O2) immediately thereafter for up to 5 days. Mice were treated with Colony Stimulating Factor (CSF)-1-Fc by subcutaneous injection (0.75microg/g/mouse) from day 1 to 4 post-LPS, prior to cull on day 5

value: Hypoxic + CSF1


title: zQ175:CK2a'(+/-) rep 4


title: WT, control, ChIP-seq, H3K4me2

value: WT

value: control


title: Hyp_2


title: 240_min


title: 230_min


title: 250_min


title: zQ175:CK2a'(+/-) rep 2


title: zQ175:CK2a'(+/-) rep 3


title: Hyp_4


title: 260_min


title: 220_min


title: 300_min


title: 190_min


title: zQ175:CK2a'(+/-) rep 1


title: Norm_4


title: Hyp_1


title: 170_min


title: 200_min


title: CK2a'(+/-) rep 1


title: Norm_3


title: CK2a'(+/-) rep 3


title: CK2a'(+/-) rep 2


title: S-f

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: Mmul10
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Macaca mulatta

source_name: brain

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rhesus macaque  were exposed to about 2.5%-3% sevoflurane inhalation anesthesia on approximately postnatal day 7 and then on P21 and P35, for four hour each time. We harvested the amygdala immediately after third times of sevoflurane treatment.

value: brain; amygdala

value: wild type

tag: Sex

value: female


title: zQ175 HD rep 5

value: Huntington's disease


title: 210_min


title: zQ175 HD rep 4


title: Norm_2


title: CSF1_2

value: Normoxic


title: 160_min

value: T98G human glioblastoma cells


title: Norm_1


title: CSF1_4


title: C-m

tag: genotype

value: male


title: CSF1_3


title: zQ175 HD rep 1


title: 110_min


title: 150_min


title: S-m

value: 2.5%-3% sevoflurane inhalation anesthesia


title: 120_min


title: zQ175 HD rep 3


title: WT rep 5

value: Control, wild type


title: zQ175 HD rep 2


title: 180_min


title: 090_min


title: WT rep 3


title: 130_min


title: C-f


title: CSF1_1


title: 100_min


title: 080_min


title: 140_min


title: WT rep 2


title: 070_min


title: WT rep 1


title: WT rep 4


title: 060_min


title: 050_min


title: Jurkat WT cells, treated, t=4, bio rep 7

city: Dunedin

first: Elizabeth

middle: C.

last: Ledgerwood

address: 710 Cumberland St

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Sequence reads were mapped to Hg19 using STAR (v2.7.1a)
Read counts were generated using htseq (v0.6.1)  with recommended parameters -m union and -s no
Assembly: Hg19
Supplementary files format and content: tab-delimited text files of read counts for each sample

source_name: Jurkat E6-1

growth_protocol: Jurkat cells were maintained in RMPI supplemented with 10% fetal bovine serum (FBS), 2 g/L sodium bicarbonate, 60 mg/L penicillin G and 100 mg/L streptomycin sulfate in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol according to the manufacturer's instructions
250 ng of RNA was used with the Illumina Tru-Seq library prep kit using half of the recommended reagents

treatment_protocol: Jurkat cells were resuspended in PBS at a density of 1 x 10^6 cells/mL, treated with 10 µM hydrogen peroxide, and harvested after 4 hours

value: Jurkat E6-1

value: Lymphoma

value: 10 µM hydrogen peroxide per 1 x 10^6 cells


title: Diabetes_1

first: Zheng

last: Li

address: 85th Wujin Road, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters. The reference genome was GRh38-1.2.0.
Assembly: GRh38-1.2.0
Supplementary files format and content: matrix files

source_name: Corpus Cavernosum

extract_protocol:
Fresh CC tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before 10× Genomics library preparation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000094, 10× Genomics) according to the manufacturer’s instructions. Final libraries were sequenced on an Illumina NovaSeq 6000.

value: Corpus Cavernosum

tag: disease

value: organic erectile dysfunction


title: Diabetes_2

description: 10x Genomics


title: 040_min


title: non-DM_3

description: 10x Genomics


title: Jurkat WT cells, treated, t=4, bio rep 8

tag: treatment


title: Jurkat WT cells, treated, t=4, bio rep 5


title: 030_min


title: Jurkat WT cells, treated, t=4, bio rep 6


title: 020_min


title: CB-20_cko_edl4

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 Bd Laurier

country: France

institute: Université Laval

description: GeneChip® WT Plus Reagent Kit protocol

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Command Console Software (AGCC) (Affymetrix, Thermofisher

data_processing: The imaged data were then analyzed using the Affymetrix Expression Console Software to perform the quality control, background subtraction and normalization of probe set intensities using Signal Space Transformation- Robust Multiarray Analysis (SST-RMA).  The microarray CEL files were imported and analyzed with Partek Genomics Suite 7.0 software (Partek Incorporated) and normalized by RMA.

source_name: Proximal adult epididymis

label_protocol: 100 ng total RNA samples were labeled using the GeneChip® WT Plus Reagent Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Thermofisher).

growth_protocol: 48h after surgery, tissues were collected

extract_protocol: QUIAGEN kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Epdididymis were dissected just after mouse death. Proximal epididymidis were snap frozed in liquid nitrogen until RNA extraction.

value: Proximal epididymis

value: cko

value: edl


title: CB-15_ctl_sham5

description: GeneChip® WT Plus Reagent Kit protocol

value: ctl

value: sham


title: CB-19_cko_sham4

description: GeneChip® WT Plus Reagent Kit protocol


title: non-DM_1

description: 10x Genomics


title: Jurkat WT cells, treated, t=4, bio rep 4

value: WT


title: CB-16_ctl_edl5

description: GeneChip® WT Plus Reagent Kit protocol


title: Jurkat WT cells, treated, t=4, bio rep 3


title: CB-14_ctl_edl4

description: GeneChip® WT Plus Reagent Kit protocol


title: CB-10_cko_edl3

description: GeneChip® WT Plus Reagent Kit protocol


title: CB-12_ctl_edl3

description: GeneChip® WT Plus Reagent Kit protocol


title: CB-13_ctl_sham4

description: GeneChip® WT Plus Reagent Kit protocol


title: CB-11_ctl_sham3

description: GeneChip® WT Plus Reagent Kit protocol


title: CB-9_cko_sham3

description: GeneChip® WT Plus Reagent Kit protocol


title: Normal_3

description: 10x Genomics

value: Normal


title: CB-8_ctl_edl2

description: GeneChip® WT Plus Reagent Kit protocol


title: 010_min


title: CB-6_cko_edl2

description: GeneChip® WT Plus Reagent Kit protocol


title: CB-5_cko_sham2

description: GeneChip® WT Plus Reagent Kit protocol


title: Jurkat WT cells, treated, t=4, bio rep 2


title: 000_min


title: CB-7_ctl_sham2

description: GeneChip® WT Plus Reagent Kit protocol


title: CCMP332_Control_rep3

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

data_processing:
Adapter trimming performed with kTrim v 1.1.0 [parameters: -t 15 -p 33 -q 20 -s 36 -m 0.5 using Illumina adapters]
Mapping to genome performed with STAR v 2.7.3a [parameters: --alignIntronMin 1 --alignIntronMax 22618]; initial index development parameters: --sjdbOverhang 99 --genomeSAindexNbases 12
Counts estimated from genes with HTSeq v 0.11.3 on python platform [parameters: --format=bam --order=pos --stranded=reverse --minaqual=10 --type=gene --idattr=ID --mode=union --nonunique=none]
Differential expression was performed in EdgeR using expected counts and the quasi-liklihood (QL) framework with Benjamini-Hochberg FDR correction. Genes with less than 1 count per million (CPM) in at least 3 samples were excluded from the analysis.
Assembly: ASM1318728v1
Supplementary files format and content: All files are tab delimited text files. One file is the HTSeq gene count output (cryptica_hyposalinity_HTSeq.txt) and one file is the edgeR logFC and FDR-corrected p-values output (cryptica_hyposalinity_edgeR.txt)

organism: Cyclotella cryptica

source_name: microalgae, diatom

growth_protocol: C. cryptica strain CCMP332 was grown until reaching exponential phase in artificial sea water at 24 parts per thousand salinity (ASW 24) at 15°C and 22 μmol photons m-2 s-1 irradiance under a 16:8 h light:dark cycle.

extract_protocol:
Qiagen Rneasy Plant RNA extraction
KAPA mRNA HyperPrep Kit with KAPA/Roche dual adapters

treatment_protocol: Cells were immediately exposed to freshwater (ASW 0) by centrifugation at 800 rcf for 3 min followed by resuspension and transer into ASW ). Cells were incubated at 15 ℃ and 20 μmol photons m-2 s-1 irradiance with gentle agitation

value: microalgae, diatom

tag: cell strain

value: 0 min in artificial seawater (ASW 24 ppt) at 15 C


title: Normal_2

description: 10x Genomics

tag: tissue


title: non-DM_2

description: 10x Genomics