title: CIART-/-_Mock [scRNA-seq]

value: CIART Knockout

value: Mock


title: CTC-11-A10

status: Public on Dec 07 2022

type: RNA

city: Bangkok-noi

first: Chandhanarat

last: Chandhanayingyong

state: Bangkok

address: 2 Wanglang road

department: Orthopaedic Surgery

country: Thailand

institute: Mahidol University

hyb_protocol: The hybridization reactions were prepared using the standard chemistry reagents provided in PanCancer progression panel kit (Nanostring) according to the manufacturers’ instructions.

scan_protocol: Scanning was performed using the NanoString nCounter Digital Analyzer.

data_processing: Following the manufacturer's guidelines and using the NanoString nSolver analysis software, counts were firstly corrected to background noise using the geometric mean of 8 negative and 6 positive control spike-ins in each lane. Housekeeping genes with raw count >50 and selected by the geNorm algorithm were retained for normalisation. The original raw data from Nanostring nCounter platform is recorded in a RCC file.

label: NanoString

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal adenocarcinoma

extract_protocol: Total RNA was extracted from FFPE tissue using a high-purity FFPE RNA isolation kit (Roche) according to the manufacturer’s instructions.

tag: age

tag: tussue

value: primary colorectal cancer


title: Cardiomyocyte CIART-/- MOI0.3_2 [bulk RNA-seq]

type: SRA

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

description:
counts.CM.downsample.txt
rld.CM.txt

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human GRCh37 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw reads counts were extracted using htseq-count v0.11.2.
Differential expression analysis was performed using DESeq2 v1.26.0
Assembly: hg19
Supplementary files format and content: txt file storing raw counts or normalized counts per gene per sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) or TRIzol.
RNAseq libraries were prepared using the TruSeq Stranded mRNA Library Preparation kit (Illumina) according to the manufacturer's instructions.

tag: cell line

tag: cell type

value: Cardiomyocytes

tag: genotype

tag: treatment

value: SARS-CoV-2 Infection


title: WT_Mock [scRNA-seq]

library_source: transcriptomic single cell

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v5.0.0)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus SARS-CoV-2 viral genome (NC_045512.2) and to extract gene expression UMI counts matrix.
Assembly: hg19
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

extract_protocol:
At 24 hpi, hPSC-AWOs were dissociated into a single cell suspension using Accutase cell detachment solution (Innovative Cell Technologies) and incubated at 37 oC for ~5 min followed by gentle pipetting to break apart groups of cells. Cells were then washed twice in 1x PBS and filtered using a 40 μm Flowmi cell strainer (Bel-Art Scienceware). Cell count and cell viability were then determined using trypan blue staining and a Countess II automated cell counter (ThermoFisher Scientific).
Target cell inputs of 10,000 cells for each condition were then loaded into a Chromium Controller using Chromium Next GEM (Gel Bead-In Emulsion) single Cell 5’ Library & Gel Bead Kit v1.1 (10× Genomics) according to manufacturer’s instructions. After generation of GEMs, cDNA synthesis and library preparation of all samples was completed using the Chromium Single Cell 5’ Library Kit v1.1 (10× Genomics) according to manufacturer’s instructions.

value: Airway Organoids

value: WT


title: CIART-/-_SARS-CoV-2 [scRNA-seq]


title: CTC-02-A7


title: LUGI [32940]

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

label: cy3, cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood was purified using Proteinase K and phenol/chloroform with standard protocols. Genomic DNA extracted from saliva was extracted using the PerformaGene ND-100 Kit protocol.

tag: breed

value: Cane Lupino del Gigante


title: SWFD [32898]

value: Saarlos Wolfdog


title: CWFD [32875]

value: Czechoslovakian Wolfdog


title: CMS17


title: CMS20


title: CWFD [32887]


title: CWFD [32874]


title: CMS19


title: CWFD [32886]


title: Cardiomyocyte CIART-/- MOI0.3_1 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: CWFD [32921]


title: Cardiomyocyte WT MOI0.3_3 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: CMS18


title: Cardiomyocyte WT MOI0.3_2 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: Cardiomyocyte WT MOI0.3_1 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: CMS16


title: Cardiomyocyte CIART-/- MOI0.3_3 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: MUTT [33364]

source_name: Saliva

value: Mixed Breed


title: CMS14


title: Alveolar CIART-/- MOI0.1_3 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt

value: Alveolar Organoids


title: MUTT [24886]


title: MUTT [33356]


title: Alveolar CIART-/- MOI0.1_2 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: Alveolar CIART-/- MOI0.1_1 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: CMS13


title: MUTT [25294]


title: CMS12


title: CMS15


title: CMS11


title: Alveolar WT MOI0.1_3 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: MUTT [33355]


title: Alveolar WT MOI0.1_2 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: CMS10


title: Alveolar WT MOI0.1_1 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: Airway CIART-/- MOI0.1_3 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: CMS9


title: Airway CIART-/- MOI0.1_2 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: CMS37


title: CMS36


title: MUTT [33353]


title: CMS35


title: MUTT [33365]


title: CMS34


title: Airway CIART-/- MOI0.1_1 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: CMS33


title: Airway WT MOI0.1_2 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: MUTT [33352]


title: MUTT [33339]


title: MUTT [33367]


title: Airway WT MOI0.1_1 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: MUTT [33332]


title: Cardiomyocyte CIART-/- Mock_3 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: MUTT [33343]


title: Cardiomyocyte CIART-/- Mock_1 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: Cardiomyocyte CIART-/- Mock_2 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: MUTT [33354]


title: MUTT [33366]


title: CMS29


title: CMS31


title: MUTT [33342]


title: Cardiomyocyte WT Mock_2 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: Airway WT MOI0.1_3 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: Cardiomyocyte WT Mock_1 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: MUTT [33324]


title: CMS28


title: CMS25


title: MUTT [33347]


title: CMS27


title: Alveolar CIART-/- Mock_3 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: CMS32


title: CMS26


title: MUTT [33323]


title: MUTT [33341]


title: CMS30


title: Alveolar CIART-/- Mock_2 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: CMS23


title: MUTT [33340]


title: Alveolar CIART-/- Mock_1 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: MUTT [33331]


title: MUTT [27460]


title: Cardiomyocyte WT Mock_3 [bulk RNA-seq]

description:
counts.CM.downsample.txt
rld.CM.txt


title: Alveolar WT Mock_2 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: Alveolar WT Mock_3 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: CWFD [32873]


title: Alveolar WT Mock_1 [bulk RNA-seq]

description:
counts.ALO.downsample.txt
rld.ALO.txt


title: CMS22


title: CMS21


title: CWFD [32884]


title: CMS8


title: CMS7


title: CMS6


title: Airway CIART-/- Mock_3 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: GSD- [31031]

value: German Shepherd Dog


title: CWFD [32872]


title: Airway CIART-/- Mock_1 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: Airway WT Mock_3 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: CMS5


title: Airway CIART-/- Mock_2 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: LUGI [32962]


title: FONN [31398]

value: Fonni's dog


title: FONN [31399]


title: CMS3


title: FONN [31397]


title: Airway WT Mock_1 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt


title: CMS1


title: 12mid34conETOH

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

description: Gene Expression

data_processing:
rna-seq processing with the nf-core rnaseq version 1.0 pipeline
pathway analysis with the advaitabio ipathwayguide platform
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with raw rnaseq gene counts for every gene for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: animal id 28 rnaseq control replicate 5

growth_protocol: The mPFC from CRF1:GFP mice (adult) was microdissected, tissue was dissociated and sorted, and RNA was isolated from sorted cells.

extract_protocol:
Total RNA was isolated from FACS-sorted cells using Direct-zol RNA MiniPrep Kit (Zymo Research) then 160pg of RNA from each sample taken into the SMARTseq HT library prep kit (Takara).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ethanol

tag: tissue

value: mPFC

value: mPFCCRF1+ neurons


title: CMS4


title: FONN [31396]


title: Cardiomyocyte 48h MOI=1_3 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: CNCS [31334]

value: Cane Corso


title: Cardiomyocyte 48h MOI=1_2 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: CNCS [31335]


title: 09mid28conCTRL

description: Gene Expression

source_name: animal id 28 rnaseq control replicate 6

value: control


title: Cardiomyocyte 48h MOI=1_1 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: 08mid27conCTRL

description: Gene Expression

source_name: animal id 27 rnaseq control replicate 5


title: CIRN [31388]

value: Cirneco dell'Etna


title: 07mid26conCTRL

description: Gene Expression

source_name: animal id 26 rnaseq control replicate 4


title: LAGO [31423]

value: Lagotto Romagnolo


title: 06mid25conCTRL

description: Gene Expression

source_name: animal id 25 rnaseq control replicate 3


title: LUPO [31345]

value: Cane Lupo Italiano


title: CMS2

value: primary colorectal cancer


title: Cardiomyocyte 48h MOI=0.1_2 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt

value: Cardiomyocytes

value: WT

value: SARS-CoV-2 Infection


title: Airway WT Mock_2 [bulk RNA-seq]

description:
counts.AWO.downsample.txt
rld.AWO.txt

value: Airway Organoids

value: Mock


title: Cardiomyocyte 48h MOI=0.1_1 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: SPIN [31565]

value: Spinone Italiano


title: 11mid31conETOH

description: Gene Expression

source_name: animal id 27 rnaseq control replicate 4


title: 05mid24conCTRL

description: Gene Expression

source_name: animal id 24 rnaseq control replicate 2


title: Cardiomyocyte 48h MOI=0.01_3 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: 04mid23conCTRL

description: Gene Expression

source_name: animal id 23 rnaseq control replicate 1


title: 03mid22conETOH

description: Gene Expression

source_name: animal id 22 rnaseq ETOH replicate 2


title: 10mid30conETOH

description: Gene Expression

source_name: animal id 26 rnaseq control replicate 3


title: ITGY [31417]

value: Italian Greyhound


title: Cardiomyocyte 48h MOI=0.01_2 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: Cardiomyocyte 48h MOI=0.01_1 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: BERG [31490]

value: Bergamasco shepherd


title: 02mid21conETOH

description: Gene Expression

source_name: animal id 21 rnaseq ETOH replicate 1

value: ethanol


title: Cardiomyocyte 48h Mock_2 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: Cardiomyocyte 48h Mock_1 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: ITGY [31416]


title: Cardiomyocyte 48h MOI=0.1_3 [bulk RNA-seq]

description:
counts.CM.48h.txt
rld.CM.48h.txt


title: FONN [31402]

value: Fonni's dog


title: Nfkbizfl/flVil1-Cre_read1 [ATAC-Seq]

city: Ota-ku

first: Soh

last: Yamazaki

state: Tokyo

address: 5-21-16 Omorinishi

department: Biohemistry

country: Japan

institute: Toho University School of Medicine

description: Open chromatin regions in jejuna of IEC-specific Nfkbiz-deficient mouse

library_source: genomic

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings)
Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome.
The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: mm10
Supplementary_files_format_and_content: 01BBToho_ATAC_mergedregs.xlsx

extract_protocol:
The tissue was manually disassociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017) using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina).
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems)

value: jejunum

tag: gender

value: male

tag: strain

value: IEC-specific Nfkbiz-deficient


title: Alveolar 48h MOI=1_3 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt

value: Alveolar Organoids


title: Control_read1 [ATAC-Seq]

description: Open chromatin regions in jejuna of control mouse

value: control


title: FONN [31401]


title: M0980 (L30) scRNA-seq

city: Columbus

first: Janek

middle: S

last: Walker

state: Ohio

address: 410 W 12th Ave

department: Division of Hematology, Department of Internal Medicine

institute: The Ohio State University

description: Eµ-PRMT5/TCL1 Sp 4

data_processing:
Sequencing was carried out on an Illumina Nextseq 500 to achieve 75 bp reads.
Read counts were normalized to library size, scaled by 10,000, log-transformed, and based on the following criteria: cells with less than 250 genes detected or with a proportion of unique molecular identifiers mapped to mitochondrial genes over 0.15 were excluded from analysis; genes detected in less than 5 cells were also excluded.
Cell-to-cell variation in gene expression driven by the number of detected molecules and mitochondrial gene expression was regressed out using linear regression.
Following the Single Cell 3′ Reagent Kits (v2) user guide (manual part no. CG00052 Rev A.), data was processed by the Cell Ranger pipeline (v2.0.1; 10x Genomics). Count matrices were analyzed using the Seurat package (v2.2.1) in R.
Read counts were normalized to library size, scaled by 10,000, log-transformed, and filtered. Dimensionality reduction was performed with principal component analysis followed by UMAP projection and graph-based clustering using the first 10 principal components.
Genome_build: GRCm38
Supplementary_files_format_and_content: 10X barcode TSV tables, 10X feature TSV tables, expression matrices, and Loupe visualization files generated by 10X software

source_name: Spleen

extract_protocol:
Cells were washed and partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics Barcode but uses a pool of ~750,000 barcodes to separately index each cell’s transcriptome. The silane magnetic beads and Solid Phase Reversible Immobilization beads were used to clean up the GEM reaction mixture and the barcoded cDNA was then amplified in a PCR step.
Libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v2): Single Cell 3′ Library & Gel Bead Kit v2 (PN-120237), Single Cell 3′ Chip Kit v2 (PN-120236) and i7 Multiplex Kit (PN-120262) (10x Genomics). Optimal cDNA amplicon size was achieved using Covaris machine prior to library construction. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adapter ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.
scRNA-seq

tag: transgene

value: Spleen

tag: barcode


title: Alveolar 48h MOI=1_2 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: MANN [31453]

value: Mannara


title: MANN [31452]


title: Alveolar 48h MOI=1_1 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: M1040 (L27) scRNA-seq

description: Eµ-PRMT5/TCL1 Sp 3


title: SPIN [31560]


title: FONN [31400]


title: M0942 (L26) scRNA-seq

description: Eµ-PRMT5/TCL1 Sp 2


title: Alveolar 48h MOI=0.1_3 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: Alveolar 48h MOI=0.1_1 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: Alveolar 48h MOI=0.1_2 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: CHOW [29849]

value: Chow Chow


title: SALU [27781]

value: Saluki


title: M0299 (L23) scRNA-seq

description: Eµ-TCL1 Sp 3


title: M0228 (L20) scRNA-seq

description: Eµ-TCL1 Sp 2


title: M0244 (L18) scRNA-seq

description: Eµ-TCL1 Sp 1


title: Alveolar 48h MOI=0.01_2 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt

value: WT

value: SARS-CoV-2 Infection


title: M0317 (L31) scRNA-seq

description: Eµ-PRMT5 Sp 4


title: Alveolar 48h MOI=0.01_1 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: Alveolar 48h Mock_3 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt

value: Mock


title: Alveolar 48h Mock_2 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: CHOW [29714]


title: E4474 (L25) scRNA-seq

description: Eµ-PRMT5 Sp 3


title: CHOW [29743]


title: Alveoar 48h Mock_1 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt


title: CHOW [29713]


title: Airway 48h MOI=1_3 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt

value: Airway Organoids


title: CHIH [26585]

value: Chihuahua


title: CHOW [29844]


title: M0799 (L22) scRNA-seq

description: Eµ-PRMT5 Sp 2


title: M0942 (L17) scRNA-seq

description: Eµ-PRMT5/TCL1 LN 4

source_name: Lymph Node

value: Lymph Node


title: M0995 (L21) scRNA-seq

description: Eµ-PRMT5 Sp 1


title: PHAR [30612]

value: Pharaoh Hound


title: Airway 48h MOI=1_1 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: Airway 48h MOI=1_2 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: PHAR [30616]


title: Airway 48h MOI=0.1_3 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: M0955-RT (L14) scRNA-seq

description: Eµ-PRMT5/TCL1 LN 2


title: CHOW [29749]


title: M1040 (L15) scRNA-seq

description: Eµ-PRMT5/TCL1 LN 3


title: Airway 48h MOI=0.1_2 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: PHAR [30625]


title: Airway 48h MOI=0.1_1 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: M0322 (L16) scRNA-seq

description: Eµ-TCL1 LN 3


title: Airway 48h MOI=0.01_3 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: PHAR [31087]


title: Airway 48h MOI=0.01_2 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: M0244 (L10) scRNA-seq

description: Eµ-TCL1 LN 1


title: PHAR [30631]


title: PHAR [30621]


title: Airway 48h MOI=0.01_1 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: PHAR [31085]


title: Airway 48h Mock_3 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: PHAR [31083]


title: PHAR [30627]


title: Airway 48h Mock_2 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: M0955-RT (L19) scRNA-seq

description: Eµ-PRMT5/TCL1 Sp 1


title: 5b

city: Guangzhou

first: Gang

last: Zhang

state: Guangdong

address: NO.63, Duobao road,Liwan district,Guangzhou city,Guangdong prov.

department: pediatric surgery

country: China

institute: Third Affiliated Hospital of Guangzhou Medical University

data_processing:
TMM (trimmed mean of M-values) was used to normalize the gene expression
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt files include TMM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with gene reads count for every gene and every sample

source_name: CPAM tissue

extract_protocol:
total RNA  was extracted with Takara RNAiso Plus (Takara, Dalian, China)
RNA-seq library was prepared with approximately 1μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA). Briefly, ribosomal RNA was removed from the total RNA. Next, the ribominus RNAs were fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. The library quality and concentration was assessed by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer.

value: lung

tag: disease

value: CPAM tissue


title: PHAR [30632]


title: Airway 48h Mock_1 [bulk RNA-seq]

description:
counts.AWO.48h.txt
rld.AWO.48h.txt


title: M0322 (L24) scRNA-seq

description: Eµ-TCL1 Sp 4


title: M0980 (L9) scRNA-seq

description: Eµ-PRMT5/TCL1 LN 1


title: PHAR [30630]


title: gl2_E375G R392M_3

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
Basecalls performed using Illumina bcl2fastq2 Conversion Software
ChIP-seq reads were aligned to the Arabidopsis thaliana genome (TAIR10.24) using Bowtie 2 version 2.2.3 : parameters: -q --phred33 --end-to-end --sensitive -p 16 -t
peaks were called using MACS2 ver 1.4.2 after merging replicate samples : parameters: -f BAM -g 0.135e9
Genome_build: TAIR10.24
Supplementary_files_format_and_content: Peak calls in .txt file format generated by MACS2

organism: Arabidopsis thaliana

source_name: Seedlings, Columbia (Col) ecotype

growth_protocol: Seeds from EYFP-tagged GL2, gl2_dSTART, gl2_dZip, gl2_Amo and gl2_R392M;E375G lines and the gl2-5 null mutant control were surface sterilized and grown on 0.8% agar containing 1X Murashige and Skoog media and 1% sucrose. (Note that the EYFP:GL2 and mutant EYFP:gl2 transgenic lines were constructed by floral dip mediated transformation of gl2-5 null mutants. Whereas the wild-type EYFP:GL2 transgene rescued the gl2 mutant phenotype, none of the mutant EYFP:gl2 transgenes exhibited a wild-type phenotype.) Seeds from each of the genotypes were stratified for 3 to 5 days at 4°C and then transferred to 23°C and continuous light for 10 days.

extract_protocol:
The 10-day old Arabidopsis seedlings of each genotype were harvested and crosslinked with 1% formaldehyde for 10 min in a vacuum chamber. Glycine was added to a final concentration of 0.125 M, and the reaction was terminated by incubation for 5 min under vacuum. Chromatin was fragmented using a Covaris 220 focused ultrasonicator (Duty Cycle: 10%; Intensity: 5; Cycles per Burst: 200) to produce <500 bp fragments. ChIP experiment was performed with a ChIP-grade anti-GFP antibody as previously described (Khosla et al., Plant Cell 2014; doi: 10.1105/tpc.113.120360). Immunoprecipitated DNA was prepared for sequencing.
The ChIP-Seq was performed using the Illumina HiSeq 2500 Sequencing System at the University of Kansas Medical Center – Genomics Core (Kansas City, KS). Fragmented input and immunoprecipitated chromatin (20ng) was used to initiate the TruSeq ChIP Sample Prep Kit library preparation protocol (Illumina cat#IP-202-1012). The fragmented chromatin underwent end repair and 3’ adenylation prior to illumina indexed adapter ligation. Library sizing (target size – 320bp) was performed using the Sage Pippin Prep automated size selection system. PCR amplification of the sized library fraction was performed using Illumina adaptor specific priming with final library purification using KAPA Pure magnetic bead purification (KAPA cat#KK8002).  Following Agilent TapeStation 4200 QC for sizing of the library preparation and library quantification using the Roche Lightcycler96 with Roche FastStart Essential Green Master qPCR kit (Roche cat#06402712001 ) and KAPA Library Quant (Illumina) DNA Standards (KAPA cat#KK4903), the CHiP-Seq libraries were adjusted to a 2.125nM concentration and pooled for multiplexed sequencing.

treatment_protocol: Three replicates of each genotype were processed.

tag: ecotype

value: Columbia (Col)

value: 10 day-old seedlings

value: EYFP:gl2_E375G R392M mutant

tag: chip antibody

value: anti-GFP (ab290, Abcam)

tag: background

value: gl2-5 homozygous background


title: M0228 (L13) scRNA-seq

description: Eµ-TCL1 LN 2


title: gl2_E375G R392M_2


title: PHAR [30609]


title: 4b


title: 4a

source_name: normal lung tissue

value: normal lung tissue


title: 5a


title: Nfkbizfl/fl_rep1

hyb_protocol: 0.60 μg of Cy3 dye labeled cRNA were fragmented and hybridized at 65 ℃ for 17 hours onto Agilent SurePrint G3 Mouse GE v3 8x60K Microarray

scan_protocol: Agilent SureScan Microarray Scanner (G4900DA)

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 12.1.1.1, which performs background subtractions. We only used features which were flagged as no errors (Detected flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated, and population outliers (Not Detected and Compromised flags). Quantile Normalization was performed using Agilent GeneSpring software version 14.9.1.

source_name: ilea of control mouse

label_protocol: Agilent Low Input Quick Amp Labeling Kit  (Agilent Technologies).

extract_protocol: The ileal fragment was ground with a Zirconia bead (TOMY, ZB-50) in Sepasol-RNA Super G (nacalai tesque) using Micro Smash MS-100R (TOMY Digital Biology), and total RNA was extracted according to the manufacturer's recommendations of Sepasol-RNA Super G.

value: ileum

tag: genotype/variation

value: control

value: male

tag: strain background


title: Nfkbizfl/fl_rep2

value: female

tag: age


title: Nfkbizfl/flVil1-Cre_rep2

source_name: ilea of IEC-specific Nfkbiz-deficient mouse

value: knockout


title: PHAR [31093]

source_name: Saliva


title: PHAR [31094]


title: 2b


title: Nfkbizfl/flVil1-Cre_rep1


title: G2R4TA

city: Kannapolis

first: Dragan

last: Milenkovic

state: NC

address: 600 Laureate Way

department: Department of Food Bioprocessing & Nutrition Sciences

institute: North Carolina State University

description: processed Diabetic+Bean extract group.txt

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: Excel files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: adipose tissue of diabetic+ bean extract male Wistar rats

extract_protocol:
RNA extraction from adipose tissue samples was carried out according to the protocol proposed  in the RNeasy Lipid Tissue Mini Kit
The sequencing library was prepared by  random fragmentation of the cDNA, followed by the 5 'and 3' ligation adapters. Adapter-ligated
fragments were amplified by PCR and visualized on agarose gels. Double stranded next generation  sequencing was commercially performed by MAcrogen (Seoul, Korea)

treatment_protocol:
260 mg/kg/day of black beans extract
Intraperitoneal injection of a single low dose of Streptozotocin, N-(Methylnitrosocarbamoyl)-α-D-glucosamine (STZ) (Sigma-Aldrich) solution (25mg/kg) dissolved in sodium citrate buffer (0.1 mol/L, pH 4.5)

value: Wistar

tag: cell line

value: adipose tissue

value: organ

value: WT

value: diabetic+bean extract

tag: time

value: Day 31


title: CHOW [31244]

value: Chow Chow


title: gl2_E375G R392M_1

value: Columbia (Col)

value: 10 day-old seedlings

tag: genotype


title: PHAR [31088]

value: Pharaoh Hound


title: G2R8TA

tag: cell type

tag: treatment


title: PHAR [30640]

tag: breed


title: GL2_2

value: EYFP:GL2 wild type

value: anti-GFP (ab290, Abcam)

value: gl2-5 homozygous background


title: gl2-5_2

value: gl2-5 null mutant


title: PHAR [30638]


title: 3a

tag: tissue

value: lung

value: normal lung tissue


title: GL2_1


title: 2a


title: 1b

value: CPAM tissue


title: PHAR [31084]


title: G4R1TA

description: processed Diabetic group.txt

source_name: adipose tissue of diabetic male Wistar rats

tag: strain

value: Wistar

value: diabetic


title: G4R2TA

description: processed Diabetic group.txt

value: adipose tissue

value: organ


title: gl2-5_1


title: G2R1TA

value: WT

value: diabetic+bean extract


title: GL2_3


title: gl2_dZip_2

value: EYFP:gl2_dZip mutant


title: 1a


title: G6R4TA

description: processed Healthy group.txt

source_name: adipose tissue of healthy male Wistar rats

value: no treatement

value: Day 31


title: PHAR [30626]

value: Pharaoh Hound


title: PHAR [31090]


title: gl2_dZip_1

value: Columbia (Col)

value: 10 day-old seedlings


title: G6R2TA

description: processed Healthy group.txt


title: gl2_dSTART_2

value: EYFP:gl2_dSTART mutant

value: anti-GFP (ab290, Abcam)

value: gl2-5 homozygous background


title: G6R3TA

description: processed Healthy group.txt


title: PHAR [30639]


title: Serum-ISO-24hrs-rep3

type: protein

city: Beijing

first: Xianda

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

institute: Peking University Third Hospital

hyb_protocol: Cytokine arrays were used according to the manufacturer’s instructions. All sample measurements were performed in duplicate. The array plate were washed, incubated with a biotin-conjugated beads for half an hour, washed again, and developed for half an hour with PE-conjugated streptavidin.

scan_protocol: Driven by the flowing sheath fluid, the microspheres pass through the red and green laser successively in a single row. The red laser is used to determine the fluorescence code of the microspheres, and the green laser is used to measure the fluorescence intensity of the molecules reported by the Luminex X-200.

data_processing: By comparing the signal intensities, relative expression levels of cytokines can be made. The intensities of signals can be quantified by densitometry.

label: PE-Streptavidin

molecule: protein

source_name: serum, ISO, 24hrs

label_protocol: Samples were labeled according to the manufacturer’s instructions

extract_protocol: Weigh out tissue and cut into cubes. Prepare protein extraction reagent containing inhibitors. Add ice-cold Protein Extraction Reagent containing protease inhibitors. Grind in a blender on low power using 30-second bursts until fully homogenized. Allow material to cool for 1 minute between bursts. Centrifuge the lysate at 14,000xg for 15 minutes and transfer the supernatant to a new tube for further analysis.

treatment_protocol: Mice were subcutaneous injected with a single dose of isoproterenol (ISO, 5 mg/kg body weight) or vehicle saline (10 ml/kg body weight). Hearts and vessels were harvested and immediately frozen in liquid nitrogen.

value: 22 weeks

tag: gender

value: male

value: serum


title: PHAR [30628]


title: gl2_dSTART_1


title: Serum-ISO-24hrs-rep2


title: Serum-ISO-24hrs-rep1


title: gl2_Amo_3

value: EYFP:gl2_Amo mutant


title: G4R6TA

description: processed Diabetic group.txt

value: Wistar

value: adipose tissue

value: diabetic


title: PHAR [30622]


title: Serum-ISO-3hrs-rep3

source_name: serum, ISO, 3hrs


title: PHAR [31086]


title: gl2_Amo_1


title: PHAR [31092]


title: penile corpus cavernosum-old_s10

first: qi

middle: wei

last: Liu

address: No.600 Tianhe Road

department: Urology

institute: Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
The Cell Ranger suite version 3.1.0 was used to perform barcode processing and single-cell gene UMI counting
For basic processing and visualization, the scRNA-seq data were merged and analyzed using Seurat suite version 3.2.2 in R (v.4.0.2)
The FindVariableGenes() function were utilized to identify variable genes, keeping default parameters.
After performing principal component analysis (PCA), the top 20 principal components (PCs) were selected. For clustering, we applied the FindClusters() function, which implements the shared nearest neighbor modularity optimization.
The remaining individual cells were filtered using the following parameters: the minimum percentage of mitochondria was 0, maximum percentage of mitochondria was 30%, minimum number of UMI was changed to 200, maximum number of UMIs was changed to 50,000, minimum number of nGene was set to 250, and maximum number of nGene was set to 6,000.  Finally, genes expressed in less than 3 cells were deleted. We identified markers genes for each cluster using the FindMarkers() function.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: penile corpus cavernosum

extract_protocol:
For tissue dissociation, we continuously anesthetized all the rats with pentobarbital at one time and rapidly harvested their penile corpus cavernousm tissues (without tunica) with sterile instruments. Tissues were immediately minced to small fragments ~1 mm2, followed by enzymatic digestion with collagenase (~2h), elastase (~30min), and DNase (~1h) at 37 °C. Digestion was terminated by DMEM complete medium. The dissociated cells were centrifuged at 4 °C, filtered through a 70 μm filter, underwent red blood cell lysis and removal of dead cells using Dead Cell Removal Kit (Miltenyl Biotec).
ScRNA-seq libraries were prepared  using standard Illumina protocols

value: Sprague-Dawley rats

value: 23 months

value: penile corpus cavernosum


title: penile corpus cavernosum-old_s11


title: Serum-ISO-3hrs-rep2


title: penile corpus cavernosum-old_s9


title: Serum-ISO-3hrs-rep1


title: CHOW [29738]

value: Chow Chow


title: Serum-ISO-1hrs-rep3

source_name: serum, ISO, 1hrs


title: penile corpus cavernosum-old_s7


title: gl2-5 input

value: gl2-5 null mutant


title: PHAR [31091]

value: Pharaoh Hound


title: penile corpus cavernosum-old_s8


title: penile corpus cavernosum-old_s6


title: PHAR [31089]


title: gl2_dSTART input

value: Columbia (Col)

value: 10 day-old seedlings


title: Serum-ISO-1hrs-rep2


title: penile corpus cavernosum-old_s12


title: PHAR [31098]


title: gl2_Amo input

value: anti-GFP (ab290, Abcam)


title: Serum-ISO-0.5hrs-rep3

source_name: serum, ISO, 0.5hrs


title: penile corpus cavernosum-old_s5


title: Serum-ISO-1hrs-rep1


title: PHAR [30853]


title: Alveolar 48h MOI=0.01_3 [bulk RNA-seq]

description:
counts.ALO.48h.txt
rld.ALO.48h.txt

value: Alveolar Organoids

value: WT

value: SARS-CoV-2 Infection


title: gl2_E375G R392M input

value: EYFP:gl2_E375G R392M mutant

value: gl2-5 homozygous background


title: Serum-ISO-0.5hrs-rep2

value: 22 weeks

value: male

value: serum


title: gl2_dZip input

value: EYFP:gl2_dZip mutant


title: GL2 input

value: EYFP:GL2 wild type


title: PHAR [30634]


title: penile corpus cavernosum-old_s4

value: Sprague-Dawley rats

value: 23 months

value: penile corpus cavernosum


title: penile corpus cavernosum-old_s3


title: gl2_Amo_2

value: EYFP:gl2_Amo mutant


title: PHAR [31081]

value: Pharaoh Hound


title: Serum-ISO-0.5hrs-rep1


title: M0701 (L32) scRNA-seq

description: Eµ-PRMT5 Sp 5

tag: transgene

value: Spleen

tag: barcode


title: Hippocampus, 7-month-old 5×FAD mice, rep1 [5H_3]

first: Zhongdi

last: Cai

state: Beijing

address: Institute of Medicinal Biotechnology, No.2 Tiantan Xili, Dongcheng District, Beijing

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: gene expression

data_processing:
The Illumina HiSeq 2500 at the LC-BIO (Hangzhou, China) was employed for the paired-end sequencing according to the manufacturer’s recommendations.
The clean reads were obtained using Trimmomatic (version 0.36).
Raw data were analyzed using the Empirical Analysis of Digital Gene Expression Data (edgeR) in R.
The frequency of the lncRNA counts was normalized as reads per million to analyze the expression pattern of lncRNAs between 5×FAD mice and WT mice.
Assembly: the mouse reference genome (http://asia.ensembl.org/ index.html)

source_name: Hippocampus

growth_protocol: All the mice were given food and water ad libitum and kept in a constant temperature and humidity environment according to the Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Total RNA was isolated from the cerebral cortex and hippocampus using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
To construct the lncRNA library, sequencing of paired ends mode was used. rRNA was removed from the total RNA of all tissue samples using the Ribo-off rRNA Depletion kit (Vazyme Biotech Co., Ltd) based on the enzymatic reaction between the DNA probe and RNaseH. The VAHTSTM Stranded mRNA-seq Library Prep Kit by Illumina® (Vazyme Biotech Co., Ltd) was employed for fragmentation, cDNA synthesis, cDNA fragment modification, magnetic bead purification and fragmentation sorting, and library amplification according to the manufacturer’s recommendations. After quality control and purification, the lncRNA library was obtained to meet the requirements of Illumina platform sequencing.

treatment_protocol: The mice were then sacrificed by cervical dislocation and their brains were quickly removed and preserved via flash freezing in liquid nitrogen.

value: Hippocampus


title: penile corpus cavernosum-old_s2


title: PHAR [30635]


title: Hippocampus, 7-month-old 5×FAD mice, rep1 [5H_2]

description: gene expression


title: penile corpus cavernosum-old_s1


title: Serum-Vehicle-rep3

source_name: serum, vehicle


title: Serum-Vehicle-rep2


title: penile corpus cavernosum-young_s12

value: 3 months


title: penile corpus cavernosum-young_s11


title: PHAR [31082]


title: PHAR [31095]


title: Hippocampus, 7-month-old WT mice, rep1 [TH_3]

description: gene expression

value: WT


title: Serum-Vehicle-rep1


title: Plaque-ISO-24hrs-rep3

source_name: plaque, ISO, 24hrs

value: vessel


title: Plaque-ISO-24hrs-rep2


title: penile corpus cavernosum-young_s10


title: Hippocampus, 7-month-old WT mice, rep1 [TH_2]

description: gene expression


title: Hippocampus, 7-month-old WT mice, rep1 [TH_1]

description: gene expression


title: PHAR [30637]


title: penile corpus cavernosum-young_s9


title: Cerebral cortex, 7-month-old 5×FAD mice, rep1 [5C_3]

description: gene expression

source_name: Cerebral cortex

value: Cerebral cortex


title: penile corpus cavernosum-young_s8


title: Plaque-ISO-24hrs-rep1


title: pericytes, KO,  p14, rep 3

city: Harbin

first: zifeng

last: dai

state: Heilongjiang province

address: 23 Youzheng Street, Nangang District

department: Neurosurgery

institute: First Affiliated Hospital of Harbin Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default  parameters. Then clean reads were separately aligned to reference genome with orientation mode  using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software. The mapped reads of  each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?  t=example) in a reference-based approach[2].
To identify DEGs (differential expression genes) between two different samples, the expression  level of each transcript was calculated according to the transcripts per million reads (TPM)  method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  [3] was used to quantify gene abundances.  Essentially, differential expression analysis was performed using the  DESeq2[4]/DEGseq[5]/EdgeR[6]with Q value ≤ 0.05, DEGs with |log2FC|>1 and Q value <=  0.05(DESeq2 or EdgeR) /Q value <= 0.001(DEGseq) were considered to be significantly different  expressed genes). In addition, functional-enrichment analysis including GO and KEGG were  performed to identify which DEGs were significantly enriched in GO terms and metabolic  pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome  background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools  (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do)  [7].
All the alternative splice events that occurred in our sample were identified by using recently  releases program rMATS(http：//rnaseq-mats.sourceforge.net/index.html)  [8]. Only the isoforms that  were similar to the reference or comprised novel splice junctions were considered, and the splicing  differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention  events.
Assembly: GRCm39 (http://www.ensembl.org/Mus_musculus/Info/Index)
Supplementary files format and content: Counts, TPMs

source_name: cerebellum

extract_protocol:
P14 mouse cerebella were homogenized in cold sucrose buffer (0.3 M sucrose, 5 mM HEPES, pH 7.4). The supernatant and the layer of myelin on the top of the pellet were collected by centrifugation of the cerebellar homogenate and discarded. The pellet was resuspended in sucrose buffer, and the large vasculature was separated from microvessels by centrifugation. Next, the supernatant was clarified by centrifugation. Finally, the micro-vasculatures were enriched in the pellets. The microvascular pellets were digested into single-cell suspension by 1 mg/mL collagenase/dispase (Roche, 10269638001) and 0.5 μL/mL benzonase (Merck Millipore, E1014) in Dulbecco’s modified eagle medium (DMEM) (Corning, 10-017-CV) at 37 °C for 5–10 min. After erythrocytes were lysed on ice for 5 min, the single cell suspension was incubated with complex of anti-biotin microbeads (Miltenyi Biotec, 130-090-485) and conjugated with rat anti-PDGFRβ-biotin antibody (Thermo Fisher Scientific, 14-1402-82) at 4 °C for 45 min. Then, the supernatant containing pericyte-PDGFRβ antibody -magnetic microbead complexes were passed through MS column (Miltenyi Biotec, 130-042-201) to collect the pericytes.
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).

value: cerebellum

value: postnatal day 14 (p14)

value: pericyte


title: pericytes, KO,  p14, rep 2


title: penile corpus cavernosum-young_s7


title: Cerebral cortex, 7-month-old 5×FAD mice, rep1 [5C_2]

description: gene expression


title: Plaque-ISO-3hrs-rep3

source_name: plaque, ISO, 3hrs

value: 22 weeks

value: male


title: pericytes, KO,  p14, rep 1


title: pericytes, Control, p14, rep 3


title: penile corpus cavernosum-young_s6


title: Cerebral cortex, 7-month-old 5×FAD mice, rep1 [5C_1]

description: gene expression


title: Cerebral cortex, 7-month-old WT mice, rep1 [TC_3]

description: gene expression


title: Plaque-ISO-3hrs-rep1


title: Plaque-ISO-1hrs-rep3

source_name: plaque, ISO, 1hrs


title: Plaque-ISO-3hrs-rep2


title: penile corpus cavernosum-young_s5


title: Cerebral cortex, 7-month-old WT mice, rep1 [TC_2]

description: gene expression


title: pericytes, Control, p14, rep 1


title: PHAR [30606]


title: Plaque-ISO-1hrs-rep2


title: penile corpus cavernosum-young_s4


title: pericytes, Control, p14, rep 2


title: Cerebral cortex, 7-month-old WT mice, rep1 [TC_1]

description: gene expression


title: Nfkbizfl/flVil1-Cre_rep3 [jejunum]

description: Gene expression in jejuna of IEC-specific Nfkbiz-deficient mouse

data_processing:
adaptor trimmed
quality filtering
cell barcode mapping
mapping with Bowtie2
Genome_build: GRCm39 RefSeq RNA
Supplementary_files_format_and_content: TT2_mouse_5Seq_table2.xlsx

extract_protocol:
The jejunal fragment was ground with a Zirconia bead (TOMY, ZB-50) in Sepasol-RNA Super G (nacalai tesque) using Micro Smash MS-100R (TOMY Digital Biology), and total RNA was extracted according to the manufacturer's recommendations of Sepasol-RNA Super G.
After reverse transcription and template switching, the cDNA was amplified and subjected to fragmentation/end-repair/polyA-tailing/ligation using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs).  Barcoded libraries (~300 bp) were obtained by PCR using NEBNext Ultra IIQ5 Master Mix (New England Biolabs).

value: jejunum

value: female

value: IEC-specific Nfkbiz-deficient


title: penile corpus cavernosum-young_s2

value: Sprague-Dawley rats

value: penile corpus cavernosum


title: Control_rep3 [jejunum]

description: Gene expression in jejuna of control mouse

value: control


title: Plaque-ISO-0.5hrs-rep3

source_name: plaque, ISO, 0.5hrs


title: D12 M2

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
Raw data was quality filtered and trimmed by fastx_toolkit, and adaptor sequences were removed using Cutadapt
The reads were collapsed to remove identical UMI containing reads
Using Bowtie reads were mapped to tRNA sequences from Genomic tRNA Database (GtRNAdb) allowing one mismatch. Unmapped reads were then mapped to miRNAs from miRBase v22 allowing zero mismatches, but allowing for non-templated 3’ A and T bases
Unmapped reads were then sequentially mapped against other relevant RNA datasets allowing one mismatch: snRNA from RNAcentral, snoRNA from snoDB, Y RNA from refSeq and Gencode, rRNA from refSeq, piRNA from RNAcentral, RNA families in Rfam, mRNA from refSeq, followed by the human genome (hg19)
Assembly: hg19
Supplementary files format and content: Tab delimited txt files with raw read count matrix showing expression of each molecule in each sample

source_name: donor 12 primary monocytes

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from blood of healthy female donors and monocytes were allowed to adhere for 1h. Monocyte-derived macrophages were polarised into M1 (GM-CSF+LPS+IFNγ) or M2 (M-CSF+IL-4+IL-13) types over a 10 day  protocol.

extract_protocol:
Extracellular vesicles (EVs) were isolated from the conditioned media of M1 and M2 macrophages using size exclusion chromatography. Total RNA was extracted from EVs using a Total RNA Purification Kit (Cat No. P4-0058 – 17200, Norgen), following the supplementary protocol for exosomal RNA.
RNA samples were prepared for small RNA sequencing using Qiagen’s QIAseq small RNA Library Prep kit.

value: monocyte EV

tag: rna population

value: RNA from extracellular vesicles


title: D12 M1

value: GM-CSF+LPS+IFNgamma


title: Plaque-ISO-1hrs-rep1


title: Nfkbizfl/flVil1-Cre_rep2 [jejunum]


title: D10 M2

source_name: donor 10 primary monocytes


title: Plaque-ISO-0.5hrs-rep2


title: Control_rep2 [jejunum]


title: D10 M1


title: Plaque-ISO-0.5hrs-rep1


title: Sleep-deprivation

city: Tsukuba

first: Kanako

last: Iwasaki

state: Ibaraki

address: Tennodai 1-1-1

institute: WPI-IIIS, University of Tsukuba

description: MGI

data_processing:
The WPRE-polyA sequence was added to pre-built reference (refdata-gex-mm10-2020-A, 10X Genomics). Reads were mapped to the reference by Cell Ranger 6.1.2 with include-introns option.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files compressed by the standard GNU zip

extract_protocol:
Whole brains were quickly dissected after cervical dislocation, submerged in ice-cold PBS, embedded in OCT compound (Tissue-Tek, SAKURA Finetek), and frozen in a bath of isopentane chilled with dry ice. Coronal sections with 100-µm thickness were prepared and then the primary motor areas were further dissected. Frozen samples were homogenized using SingulatorTM 100 System (singulator 100, genomics) with Standard Nuclei Isolation according to the manufacturer’s specifications. The nuclei were isolated with sucrose density gradient cenrifugation. After removing cell debris with 40 μm Flowmi™ Cell Strainer (H13680-0040, Bel-Art), the cell concentration was calculated with cell counter (CellDrop FL, DeNovix).
snRNA-seq library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual index). Approximately 11,000-17,000 nuclei were added to reverse transcription mix targeting recovery of 10,000 nuclei.

value: Sleep deprivation with gentle handling


title: Plaque-Vehicle-rep3

source_name: plaque, vehicle

value: vessel


title: Nfkbizfl/flVil1-Cre_rep1 [jejunum]


title: D9 M2

source_name: donor 9 primary monocytes


title: Control_rep1 [jejunum]


title: Ad-lib-sleep

description: MGI

value: Cerebral cortex

value: No sleep deprivation


title: AAV-SIK3-WT

description: MGI

value: Local administration of AAV8-hSyn-FLAG-SIK3(WT)


title: Plaque-Vehicle-rep1


title: D9 M1


title: AAV-SIK3-Ex13del

description: MGI

value: Local administration of AAV8-hSyn-FLAG-SIK3(Ex13del)


title: penile corpus cavernosum-young_s3

value: 3 months


title: D7 M2

source_name: donor 7 primary monocytes


title: Heart-ISO-24hrs-rep3

source_name: heart, ISO, 24hrs

value: 22 weeks

value: male

value: heart


title: penile corpus cavernosum-young_s1

source_name: penile corpus cavernosum


title: D7 M1


title: C6, infected by S. sclerotiorum, 24hl, rep2

city: Shenyang

first: Mingzhu

last: Zhao

state: Liaoning

address: Dongling Roat

department: Institute of Crop Research

institute: Liaoning Academy of Agricultural Sciences

description: Helianthus annuus Linn.

data_processing:
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.  Differential expression analysis of two conditions/groups was performed using the DESeq2. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 found by DESeq2 were assigned as differentially expressed.
Assembly: Helianthus_annuus.HanXRQr1.0.genome.fa (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/127/325/GCF_002127325.1_HanXRQr1.0/GCF_002127325.1_HanXRQr1.0_genomic.fna.gz)
Supplementary files format and content: text files include FPKM and count values for each Sample

organism: Helianthus annuus

source_name: leaf

extract_protocol:
Total RNA was extracted from sunflower leaves using RNAprep Pure Plant Kit (TIANGEN Biotech, BeiJing, China) according to manufacturer’s instructions. RNA concentration and purity was measured using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: leaf

tag: phenotype

value: DR

tag: inbred line

tag: infection

value: infected by S. sclerotiorum, 24h


title: C6, infected by S. sclerotiorum, 24hl, rep3

description: Helianthus annuus Linn.


title: D6 M2

source_name: donor 6 primary monocytes


title: C6, mock-inoculated controll, rep3

description: Helianthus annuus Linn.

value: mock-inoculated control


title: C6, infected by S. sclerotiorum, 24hl, rep1

description: Helianthus annuus Linn.


title: Heart-ISO-24hrs-rep2


title: Heart-ISO-24hrs-rep1


title: C6, mock-inoculated controll, rep2

description: Helianthus annuus Linn.


title: Heart-ISO-3hrs-rep3

source_name: heart, ISO, 3hrs


title: Plaque-Vehicle-rep2


title: D5 M2

source_name: donor 5 primary monocytes

value: monocyte EV


title: C6, mock-inoculated controll, rep1

description: Helianthus annuus Linn.


title: B728, infected by S. sclerotiorum, 24hl, rep3

description: Helianthus annuus Linn.

value: DS


title: Heart-ISO-3hrs-rep1


title: Mut Rep 3

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: Bldg 76 Cooper Rd

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University Of Queensland

data_processing:
Data was trimmed to remove PCR primers, adapters and short reads using TRIMMOMATIC v.0.36.6 with the following settings: ILLUMINACLIP: TruSeq2-SE:2:30:10 LEADING:32 TRAILING:32 SLIDINGWINDOW:4:20 MINLEN:25.
Trimmed reads were mapped to the human genome assembly hg38 using HISAT2 v.2.1.0 allowing 1 mismatch.
Feature counting was performed using featureCounts v1.6.4 with counting mode set to “Union”, strand to “Unstranded”, feature type was “exone” and ID attribute was Gene_ID.
Genome_build: hg38
Supplementary_files_format_and_content: Text file containing raw  counts for each gene and each sample.

source_name: placental cell line

growth_protocol: Male human placental trophoblast cells BeWo (ATCC – CCL-98) were maintained in Ham's F-12K (Kaighn's) medium supplemented with 10% (v/v) FBS at 37C with 5% CO2.

extract_protocol:
Total RNA was isolated from cells  using TRIreagent (Sigma, USA) according to the manufacturer’s instructions.
Libraries were constructed using TruSeq 2 Library Preparation Kit (Illumina, USA).

treatment_protocol: All infections were performed at MOI=1 by incubation of cells with 50 μl of inoculum per cm2 of growth area for 1h at 37 ºC. Inoculated cells were then maintained in the growth medium containing a reduced amount of FBS (2%) for 72h.

value: BeWo (ATCC CCL-98)

tag: virus strain

value: ZIKV MR769 xrRNA2' mutant

value: infected at MOI=1 for 72h


title: Mut Rep2


title: Mut Rep 1


title: Heart-ISO-1hrs-rep3

source_name: heart, ISO, 1hrs

tag: age


title: D6 M1

value: GM-CSF+LPS+IFNgamma

value: RNA from extracellular vesicles


title: Heart-ISO-1hrs-rep2


title: Heart-ISO-3hrs-rep2


title: Heart-ISO-1hrs-rep1


title: WT Rep 3

tag: cell line

value: ZIKV MR768


title: D5 M1


title: Heart-ISO-0.5hrs-rep3

source_name: heart, ISO, 0.5hrs


title: B728, mock-inoculated control, rep2

description: Helianthus annuus Linn.


title: CD8T_mock_donor07

city: Greifswald

first: Maren

last: Depke

department: Klinik fuer Innere Medizin C

country: Germany

institute: Universitaetsmedizin Greifswald KoeR

description:
gene expression data of mock electroporated CD8+ T cells after 21 d
mock_07

hyb_protocol: Arrays were hybridized according to Affymetrix standard workflows by Atlas Biolabs GmbH, Berlin, Germany.

scan_protocol: Arrays were scanned according to Affymetrix standard workflows by Atlas Biolabs GmbH, Berlin, Germany.

data_processing: Raw data .CEL files were processed using the Transcriptome Analysis Console 4.0.2.15 (Affymetrix / Applied Biosystems by Thermo Fisher Scientific).  Expression data on gene level were generated using " Gene Level - SST-RMA" as summarization method. The parameter "Pos vs Neg AUC Threshold" was set to 0.7. During analysis, the genome version hg38 (Homo sapiens) and the annotation file Clariom_S_Human.r1.na36.hg38.a1.transcript.csv were applied.

label: biotin

label_protocol: RNA was processed for labeling according to Affymetrix standard workflows by Atlas Biolabs GmbH, Berlin, Germany.

growth_protocol: Cells were cultivated in TexMACS medium (Miltenyi) which was supplemented with antibiotics as well as with 155 U/ml IL-7 and 290 U/ml IL-15. Both cytokines were re-plenished every second day. On d 0, two days after mock or BCL11B KO electroporation, cells were activated with 10 µl/ml TransAct (Miltenyi). Furthermore, cells were re-stimulated with 2 µl/ml TransAct on d 14.

extract_protocol: TotalRNA was extracted from cells using TRIzol (Invitrogen).

treatment_protocol: After isolation of CD8+ T cells from Buffy Coat PBMCs, the cells were either directly cultivated in supplemented medium (non-treated condition, nt) or electroporated with either unspecific control gRNA-Cas9 (mock electroporated condition, mock) or with BCL11B-targeting gRNA-Cas9 (BCL11B knock-out condition, BCL11B KO). Further cultivation did not differ between the experimental conditions.

value: CD8+ T cells

tag: experimental group

value: mock


title: WT Rep 2

value: ZIKV MR767


title: tscko3

city: Nanjing

first: Xiaoli

last: Sun

address: 262 North Zhongshan Road, Nanjing, Jiangsu

institute: 2nd Affiliated Hospital, Nanjing Medical University

description: Gene expression after 7 days with tamoxifer treatment to get gene deletion

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BMMs tscsko 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bone marrow cells were flushed out of the tibias and femur bones with a syringe filled with DMEM media. The bone marrow cells were cultured with DMEM containing 10% FBS and 10 ng/ml of mouse M-CSF  for 7 days to obtain bone marrow derived-macrophages (BMMs)

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen, Carlsbad, CA, USA). 2 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: BMMs from floxed mice were treated with 1 μM 4-Hydroxytamoxifen for 7 days from the beginning of the culture to get gene deletion.

value: primary BMMs

value: male

tag: genotype


title: tscko1

source_name: BMMs tscsko 1

tag: cell type


title: tscko2

source_name: BMMs tscsko 2


title: tscwt3

source_name: BMMs tscswt 3


title: B728, infected by S. sclerotiorum, 24hl, rep2

description: Helianthus annuus Linn.

value: leaf


title: tscwt2

source_name: BMMs tscswt 2


title: CD8T_nt_donor07

description:
gene expression data of non-treated CD8+ T cells after 21 d
nt_07

value: nt


title: CD8T_BCL11BKO_donor07

description:
gene expression data of BCL11B KO CD8+ T cells after 21 d
KO_07


title: Heart-ISO-0.5hrs-rep2

last: Chen

value: 22 weeks

value: heart


title: B728, infected by S. sclerotiorum, 24hl, rep1

description: Helianthus annuus Linn.

value: infected by S. sclerotiorum, 24h


title: CD8T_BCL11BKO_donor06

description:
gene expression data of BCL11B KO CD8+ T cells after 21 d
KO_06


title: WT Rep 1

value: ZIKV MR766

tag: treatment


title: tscwt1

source_name: BMMs tscswt 1


title: B728, mock-inoculated control, rep3

description: Helianthus annuus Linn.

value: DS

value: mock-inoculated control


title: Heart-ISO-0.5hrs-rep1


title: Mock Rep 3

value: BeWo (ATCC CCL-98)

value: uninfected


title: Heart-Vehicle-rep3

source_name: heart, vehicle


title: Mock Rep 2


title: 8cell_Nr5a2_CUT_RUN_rep1

first: Bofeng

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
The paired-end reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no- mixed --no-discordant by Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012). All unmapped reads, non-uniquely mapped reads, and PCR duplicates were removed. For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across the whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values on a 100bp-window base. Peaks were called using MACS v1.4.2 (Zhang et al., 2008) with the parameters nolambda –nomodel. Promoters were defined as ±2.5 kb around the transcription starting sites (TSS). Peaks at least 2.5 kb away from TSSs were defined as distal peaks by BEDTools v2.29.0 (Quinlan and Hall, 2010) .
library strategy: CUT&RUN
data processing step
Assembly: mm9

source_name: Preimplantation embryo

extract_protocol:
To obtain mouse preimplantation embryos, 5-6-week-old C57BL/6N female mice were intraperitoneally injected pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU) 44-48 hours after PMSG injection. After mated with PWK/PhJ males (Jackson Laboratory), preimplantation embryos were collected in M2 medium at following time points after hCG injection: 43 h (late 2-cell) and 68-70 h (8-cell).
CUT&RUN was conducted following the published protocol (Skene et al., 2018). ESCs or embryos with zona pellucida removed were transferred into 0.2mL conventional, non-low-binding PCR tube (Axygen). The samples were resuspended by 60μL washing buffer (HEPES-KOH, pH = 7.5, 20mM; NaCl, 150mM; Spermidine, 0.5mM and with Roche complete protease inhibitor. Concanavalin-coated magnetic beads (Polyscience, 86057) 10-20μL for each sample were gently washed, resuspended by binding buffer (HEPES-KOH, pH = 7.9, 20mM; KCl, 10mM; CaCl2, 1mM; MnCl2, 1mM) and carefully added to the samples. The samples were then incubated at 23°C for 10 mins on Thermomixer (Eppendorf) at 400 rpm. The samples were then held at the magnetic stand to carefully aspirate buffer and were resuspended by 75μL antibody buffer (washing buffer plus 0.01% digitonin; EDTA, pH = 8.0, 2mM) with NR5A2 antibody (R&D, P-H2325-00) diluted at ratio of 1:100. The samples were then incubated at 4°C on Thermomixer for 3 hours at 400 rpm. After that, the samples were held at the magnetic stand and transfer to antibody buffer with rabbit anti-mouse IgG (Abcam, ab46540) diluted at ratio of 1:100. After that he samples were washed by 200μL dig washing buffer (washing buffer plus 0.01% digitonin) for once and 100μL for a second time. The samples were then resuspended by 75 μL dig washing buffer with pA-MNase (to a final concentration of 700ng/mL), and incubated at 4°C on Thermomixer for 1 hour at 400 rpm. The samples were washed by 200μL dig washing buffer twice at the magnetic stand. The samples were resuspended by 100μL dig washing buffer and balanced on ice for 2 mins. Targeted digestion was performed on ice by adding 2μL 100mM CaCl2 for 30 mins, and reaction was stopped by adding 100μL 2 × stop buffer (NaCl, 340mM; EDTA, pH = 8.0, 20mM; EGTA, pH = 8.0, 4mM; RNase A, 50μg/mL; glycogen, 100μg/mL) and fully vortexed. The samples were then incubated at 37°C of 30 mins for fragment releasing. The supernatants were purified by phenol-chloroform followed by ethanol purification.

value: wild-type

tag: developmental stage

tag: antibody


title: CD8T_mock_donor06

description:
gene expression data of mock electroporated CD8+ T cells after 21 d
mock_06


title: B728, mock-inoculated control, rep1

description: Helianthus annuus Linn.

tag: tissue


title: Heart-Vehicle-rep2

tag: gender

tag: strain


title: 8cell_Nr5a2_CUT_RUN_rep2


title: 2cell_Nr5a2_CUT_RUN_rep2

value: late 2-cell


title: CD8T_nt_donor06

description:
gene expression data of non-treated CD8+ T cells after 21 d
nt_06

value: CD8+ T cells


title: WT_castrate_rep3

status: Public on Dec 06 2022

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: WT castrate mice (rep3)

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and used a standard Illumina dual-index, paired-end constructs with the single Cell 14 bp barcode  in the i7 index read (14 nt), sample  index sequences in the i5 index read (8 nt), and Read 1 (98 nt) and Read 2 (10 nt) with standard Illumina sequencing primers in paired-end sequencing.
raw bcl files were processed using cellranger mkfastq and kallisto-bustools was used to align the fastq files to hg19. The gene matrix (.mtx) , genes file (.genes.txt) and barcodes file (.barcodes.txt) are submitted as processed data for each sample.
fastq files from output of  cell ranger mkfastq are submitted as raw files
Assembly: hg19
Supplementary files format and content: barcodes.txt, genes.txt  and matrix.mtx ( 3 files per sample, output from cellranger count) are submitted as processed files.

source_name: WT castrate

extract_protocol:
Mice were euthanized at ~6 months, and ventral prostate lobe was extracted via dissection.
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.

treatment_protocol: PTEN castrate mice were castrated at ~4 months, and PTEN castrate 4EBP1 mice were castrated and put on doxycycline at ~4 months. WT intact and PTEN intact mice were reared normally.

value: castrate

tag: crispr status

value: WT


title: Heart-Vehicle-rep1


title: Mock Rep 1


title: PTEN_castrate_rep1

description: PTEN  castrate mice (rep1)

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and used a standard Illumina dual-index, paired-end constructs with the single Cell 14 bp barcode  in the i7 index read (14 nt), sample  index sequences in the i5 index read (8 nt), and Read 1 (98 nt) and Read 2 (10 nt) with standard Illumina sequencing primers in paired-end sequencing.
raw bcl files were processed using cellranger mkfastq and kallisto-bustools was used to align the fastq files to hg19. The gene matrix (.mtx) , genes file (.genes.txt) and barcodes file (.barcodes.txt) are submitted as processed data for each sample.
fastq files from output of  cell ranger mkfastq are submitted as raw files
Genome_build: hg19
Supplementary_files_format_and_content: barcodes.txt, genes.txt  and matrix.mtx ( 3 files per sample, output from cellranger count) are submitted as processed files.

source_name: PTEN castrate

growth_protocol: Mice were reared according to standard protocols

extract_protocol:
Mice were euthanized at ~6 months, and ventral prostate lobe was extracted via dissection.
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.
single cell RNA-Seq

value: PTEN


title: PTEN_intact_rep2

description: PTEN  intact mice (rep2)

source_name: PTEN intact

value: intact


title: 2cell_Nr5a2_CUT_RUN_rep1


title: CD8T_BCL11BKO_donor05

description:
gene expression data of BCL11B KO CD8+ T cells after 21 d
KO_05


title: CD8T_mock_donor05

description:
gene expression data of mock electroporated CD8+ T cells after 21 d
mock_05

value: mock


title: WT_intact_rep1

description: WT intact mice (rep1)

source_name: WT intact


title: WT_castrate_rep1

description: WT castrate mice (rep1)


title: PTEN_castrate_4ebp1_rep2

description: PTEN castrate 4EBP1 (rep2)

source_name: PTEN castrate 4EBP1

value: castrate 4EBP1


title: WT_castrate_rep2

description: WT castrate mice (rep2)


title: CD8T_nt_donor05

description:
gene expression data of non-treated CD8+ T cells after 21 d
nt_05

value: nt


title: PTEN_castrate_4ebp1_rep1

description: PTEN castrate 4EBP1 (rep1)


title: PTEN_castrate_rep3

description: PTEN  castrate mice (rep3)


title: PTEN_castrate_rep2

description: PTEN  castrate mice (rep2)


title: PTEN_intact_rep1

description: PTEN  intact mice (rep1)


title: WT_A

city: Nanning

first: Yan-Hua

last: Qi

state: China

address: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of L

institute: Guangxi university

data_processing:
Raw data of fastq format were firstly prosessed in-house perl scripts. In this step, clean data were obtained by software  SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle(https://github.com/najoshi/sickle)
Compare with the reference genome by software Bowtie2（http://www.bowtie-bio.sourceforge.net/bowtie2/manual）
Expression analysis was built using RSEM（http://deweylab.github.io/RSEM/）
FPKM of gene was calculated based on the length of the gene and reads count mapped to this gene.
The different expressed genes between mutant and wild type were calculated using edgeR（http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html）
Genome_build: Xanthomonas campestris pv. campestris 8004（CP000050.1）
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

organism: Xanthomonas campestris pv. campestris str. 8004

source_name: bacterial culture

growth_protocol: RNA isolated from cultures of Xcc strains grown to an OD600 of 1.0 in NYGB medium.

extract_protocol:
RNA was isolated from Xcc strains grown to OD600 of 1.0 in NYGB medium using Omega’s RNA kit
RNA sample were prepared for sequencing using IlluminaTruseqTM RNAsampleprepKit

value: Xcc 8004 wild type strain


title: WT_intact_rep3

description: WT intact mice (rep3)


title: WT_intact_rep2

description: WT intact mice (rep2)


title: WT_B


title: MH_B

value: Xcc 8004 pilH (XC_1184) deletion mutant


title: MH_A


title: MG_B

value: Xcc 8004 pilG (XC_1183) deletion mutant


title: PGM-117: DE442_TEXplus_3prime_dRNA-seq

city: St John's

first: Marc

middle: Patrick

last: Grüll

state: Newfoundland

address: 230 Elizabeth Ave

department: Biology

country: Canada

institute: Memorial University of Newfoundand

data_processing:
In house software used for data processing
TSSAR software used for detection of transcription start sites and transcription termination sites
In house pipeline used for operon detection
Supplementary_files_format_and_content: allData_transcripts: combined file for each strain containing dRNA-seq 5' and 3' data
Supplementary_files_format_and_content: dRNA_seq_TSSs: correspond to the dRNA-seq 5' data
Supplementary_files_format_and_content: dRNASeq_TTSs: correspond to the dRNA-seq 3' data

organism: Rhodobacter capsulatus DE442

growth_protocol: R. capsulatus cells were grown aerobically in RCV minimal medium for one day. Cells were then transferred to an anaerobic photosynthetic tube containing YPS medium. The anaerobic cultures were prepared to have an initial optical density of 20 Klett Units (KU). Cultures were grown for 15-16 hours.

extract_protocol:
500μ of culture were transferred into 100μl 95% Ethanol and 5% Phenol. Samples were spun down for 2 minutes and the pellets were stored at -80°C. Small RNA was extracted following the Macherey-Nagel protocol for DNA, RNA, and protein purification kit for small RNA fraction.
Libraries for 5' and 3' targeted sequencing were prepared following a newly developed protocol based on dRNA-seq. Libraries for total RNA seq were prepared following the Ion Torrent Ion Total RNA-Seq Kit V2 for whole RNA Libraries protocol.

tag: growth phase

value: Early Stationary

value: whole organism


title: PGM-135: DE442_totalRNA-seq

source_name: DE442 total RNA


title: PGM-121: DE442_TEXminus_3prime_dRNA-seq


title: MG_A


title: PGM-112: DE442_TEXminus_5prime_dRNA-seq


title: PGM-111: DE442_TEXplus_5prime_dRNA-seq


title: PGM-101: DE442_TEXplus_5prime_dRNA-seq


title: PGM-120: DE442_TEXplus_3prime_dRNA-seq


title: PGM-102: DE442_TEXminus_5prime_dRNA-seq


title: PGM-118: DE442_TEXminus_3prime_dRNA-seq


title: Hippocampus, 7-month-old 5×FAD mice, rep1 [5H_1]

description: gene expression

source_name: Hippocampus

value: Hippocampus


title: D14 PNX 3

city: Austin

first: Qi

last: Tan

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: Univesity of Minnesota

data_processing:
Mayo Clinic’s MAPR-Seq# software was used to process the raw paired end reads from the RNA sequencing experiments.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using MAPR-Seq# software
Trimmed sequence reads were mapped to GrCM38/mm10 using MAPR-Seq# software
Read count extraction and normalization were performed using MAPR-Seq# software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using Rneasy mirco kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Standard TruSeq v2 for mRNA (TMRNA) Library Prep Kit following manufacturer's protocols.

value: Lung

value: Primary sorted

value: Fibroblast

value: pneumonectomy


title: Bs168 with 10mM MgCl2 supplement, biol rep 2

city: College Station

first: Jennifer

last: Herman

state: Texas

address: 300 Olsen blvd

department: Biochemistry & Biophysics

institute: Texas A&M University

data_processing:
Trimmomatic/0.36-Java-1.8.0_92 to trim reads
use FastQC/0.11.6-Java-1.8.0 to a quality control
use  SAMtools/1.6-GCCcore-6.3.0 and HISAT2/2.1.0-intel-2017A-Python-2.7.12 to do mapping and count reads
use Deseq2 R package to do differential expression analysis
Assembly: NC_000964.fasta
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: bacterial cell

growth_protocol: 168 cells are treaked on LB plate at 37C degree overnight, inoculate single colony in 5mL CH medium with or without 10mM MgCl2 supplement to grow to OD600 ~0.2, and subcultutre into 25mL coresponding CH medium with or without 10mM MgCl2 supplement.

extract_protocol:
RNA was harvested using RNAprotect Bacteria reagent and RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
Total RNA were prepared for sequencing using TruSeq™ Stranded Total RNA and Ribo-Zero Gold (Illumina).

treatment_protocol: Collect cells at exponential stage around OD600 ~0.2

tag: bacillus genetic stock center

value: bacterial cell

tag: Stage


title: Bs168 with 10mM MgCl2 supplement, biol rep 1


title: D14 PNX 2


title: Bs168 without Mg supplement, biol rep 3

value: control


title: D14 PNX 1


title: Bs168 with 10mM MgCl2 supplement, biol rep 3


title: Bs168 without Mg supplement, biol rep 1


title: Bs168 without Mg supplement, biol rep 2


title: S3_14_3

city: shanghai

first: shi

last: yao

address: jinqi road

department: Horticultural Research Institute

institute: Shanghai Academy of Agricultural Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to CM3.6.1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: CM3.6.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Cucumis melo

source_name: 3_14,30 days after pollination

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following   the manufacturer’s protocol.
The libraries   were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,   CA, USA) according to the manufacturer’s instructions. Then these libraries were   sequenced on the Illumina sequencing platform paired-end reads were generated.

value: blade

tag: time

value: 30 days after pollination


title: S4_14_3

source_name: 4_14,45 days after pollination

value: 45 days after pollination


title: S4_14_2


title: S4_14_1


title: S3_14_2


title: S1_14_3

source_name: 1_14,10 days after pollination

value: 10 days after pollination


title: S3_14_1


title: S1_14_2


title: S4_6_2

source_name: 4_6,45 days after pollination


title: S4_6_3


title: S1_14_1


title: S4_6_1


title: S3_6_2

source_name: 3_6,30 days after pollination


title: S3_6_1


title: S3_6_3


title: S1_6_3

source_name: 1_6,10 days after pollination


title: S1_6_2


title: S1_6_1


title: T14_plus_P2

city: Rostock-Warnemünde

first: Christiane

last: Hassenrück

address: Seestraße 15

department: Biological Oceanography

institute: Leibniz Institute for Baltic Sea Research Warnemünde (IOW)

description: culture sample of Nodularia spumigena CCY9414 cultivated as control (in presence of phosphate) and collected after 14 days (biol rep 2)

data_processing:
Removal of adapters performed by the sequencing company. Those files are provided as raw data. Quality trimming was performed with BBduk.
Mapping against reference genome with bwa-mem. Removal of rRNA reads. Mapped reads were further filtered to remove secondary and supplementary alignments, as well as alignments shorter than 50 bp and those with less than 95% sequence identity across the whole read to the reference.
Mapped reads per gene were counted with featureCounts.
Differential gene expression was assessed with DESeq2 based on the count table.
Further details on data processing are available on: https://git.io-warnemuende.de/bio_inf/IOWseq000008_Cyanobloom_RNAseq_Nodularia
Assembly: GCF_000340565.2_ASM34056v3
Supplementary files format and content: tab-delimited read count matrix; column names correspond to the sample title specified in the SAMPLES section; row names refer to the locus tag as in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/340/565/GCF_000340565.2_ASM34056v3/GCF_000340565.2_ASM34056v3_genomic.gff.gz

organism: Nodularia spumigena CCY9414

source_name: bacterial cells

extract_protocol:
Cell cultures were preserved with a 5% phenol(v/v in ethanol) stop solution for 20 min prior to cell harvesting via centrifugation. Cell pellets were suspended in 1 ml TRIzol reagent, followed by bead-beating, incubation at 65°C for 10 min, and RNA extraction according to Steunou et al. (2006). RNA extracts were DNase I digested for 30 min and purified with phenol/chloroform followed by sodium acetate precipitation.
mRNA non-stranded library preparation with rRNA depletion performed by LGC, Biosearch Technologies, Berlin, Germany

value: bacterial cells

value: phosphate replete conditions


title: T14_plus_P3

description: culture sample of Nodularia spumigena CCY9414 cultivated as control (in presence of phosphate) and collected after 14 days (biol rep 3)


title: T14_minus_P2

description: culture sample of Nodularia spumigena CCY9414 cultivated in limiting conditions of phosphate and collected after 14 days (biol rep 2)

value: phosphate starvation (P-deplete)


title: T14_minus_P1

description: culture sample of Nodularia spumigena CCY9414 cultivated in limiting conditions of phosphate and collected after 14 days (biol rep 1)


title: T7_plus_P3

description: culture sample of Nodularia spumigena CCY9414 cultivated as control (in presence of phosphate) and collected after 7 days (bio rep 3)


title: T14_minus_P3

description: culture sample of Nodularia spumigena CCY9414 cultivated in limiting conditions of phosphate and collected after 14 days (biol rep 3)


title: T7_minus_P1

description: culture sample of Nodularia spumigena CCY9414 cultivated in limiting conditions of phosphate and collected after 7 days (biol rep 1)


title: T7_minus_P3

description: culture sample of Nodularia spumigena CCY9414 cultivated in limiting conditions of phosphate and collected after 7 days (biol rep 3)


title: T14_plus_P1

description: culture sample of Nodularia spumigena CCY9414 cultivated as control (in presence of phosphate) and collected after 14 days (biol rep 1)


title: T7_plus_P2

description: culture sample of Nodularia spumigena CCY9414 cultivated as control (in presence of phosphate) and collected after 7 days (bio rep 2)


title: T7_minus_P2

description: culture sample of Nodularia spumigena CCY9414 cultivated in limiting conditions of phosphate and collected after 7 days (biol rep 2)


title: iPSC 106 ECTO

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Bisulfite conversion and hybridization to the array was carried out by Life&Brain (Bonn, Germany). Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium EPIC Beadchip using the standard protocol from Illumina.

scan_protocol: Standard protocol from Illumina.

data_processing: Analysis was performed on RAW idat files using the R package minfi and the ssNoob normalization. Detection p values were calculated using the minfi package.

label: Cy5 and Cy3

source_name: iPSC

label_protocol: Standard protocol from Illumina.

growth_protocol: The iPSC lines were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew XF (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). EBs were generated following the protocol described in Ng ES, Davis RP, Azzola L, Stanley EG, Elefanty AG. Forced aggregation of defined numbers of human embryonic stem cells into embryoid bodies fosters robust, reproducible hematopoietic differentiation. Blood. 2005 Sep 1;106(5):1601-3. doi: 10.1182/blood-2005-03-0987. Epub 2005 May 24. PMID: 15914555.

extract_protocol: Genomic DNA was isolated with the NucleoSpin Tissue Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: Directed differentiation toward endodermal, mesodermal, and ectodermal lineage was induced with the STEMdiff Trilineage Differentiation Kit (Stemcell Technologies, Vancouver, Canada).

value: male

tag: differentiation timepoint

tag: sample group

value: ectoderm


title: iPSC 102 ECTO

value: female


title: TNFA_LO_1

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

data_processing:
Raw sequencing reads were aligned to a reference transcriptome generated from the Ensembl v104 human transcriptome with salmon v1.4.0 using options “--seqBias --useVBOpt --gcBias --posBias --numBootstraps 30 --validateMappings”.
Assembly: hg38
Supplementary files format and content: .sf files from salmon v1.4.0. The columns represent the following:  Name: the name of the target transcript provided in the input transcript database (FASTA file).  Length: the length of the target transcript in nucleotides.  EffectiveLength: the computed effective length of the target transcript.  TPM: the estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM).  NumReads: the estimate of the number of reads mapping to each transcript that was quantified.

source_name: Primary neuron

extract_protocol:
Frozen tissue was processed using Biosafety Level 2+ (BL2+) procedures approved by the Beth Israel Deaconess Medical Center (BIDMC) Institutional Biosafety Committee (IBC). Brain tissues and primary neurons were homogenized using Trizol (Thermo Fisher) reagent and RNA extracted by phase separation. Total RNA was quantified by nanodrop (DeNovix DS-11) and TapeStation 4200 (RNA Screen Tape; Agilent Technologies, Inc).
450 ng of total RNA was used for library preparation via the KAPA RNA HyperPrep kit with RiboErase (HMR; Roche) according to the manufacturer’s recommendations. Briefly, hybridization with hybridization oligos (HMR) was performed at 95oC for 2min followed by rRNA depletion using RNAse H which was performed at 45 oC for 30min. Following rRNA cleanup via KAPA pure beads, DNase digestion was performed at 37 oC for 30min followed by cleanup, RNA elution, fragmentation (6 min at 94oC for samples with RIN ≥ 7 or 5min at 85 oC for samples with RIN ≤ 7) and priming. First and second strand synthesis and A-tailing were performed according to manufacturer’s recommendations. 1.5 uM KAPA Unique Dual-Indexed (UDI; Roche) adapters were ligated to the second strand synthesis product in the presence of a ligation master mix in a reaction that was performed at 20 oC for 15min. Following cleanup, all libraries underwent 10 cycles of amplification. Successful library production, quality control, and quantification was assessed using Tapestation (High sensitivity D1000 Screen Tape; Agilent Technologies, Inc). Libraries were pooled and sequenced via NovaSeq 6000.

tag: group

value: TNF-low


title: T7_plus_P1

description: culture sample of Nodularia spumigena CCY9414 cultivated as control (in presence of phosphate) and collected after 7 days (bio rep 1)


title: TNFA_LO_3


title: iPSC 106 EB D7

value: EB


title: iPSC 102 EB D0


title: TNFA_HI_3

value: TNF-high


title: TNFA_HI_1


title: iPSC 102 EB D4


title: TNFA_HI_2


title: IFNG_LO_2

value: IFNG-low


title: IFNG_HI_3

value: IFNG-high


title: IFNG_LO_1


title: IFNG_HI_2


title: TNFA_LO_2


title: IFNG_HI_1


title: iPSC 104 ECTO


title: iPSC 104 ENDO

value: endoderm


title: iPSC C2.3 EB D7


title: iPSC C2.3 EB D0


title: iPSC 102 undifferentiated

value: undifferentiated


title: IFNB_LO_2

value: IFNB-low


title: iPSC 102 EB D7


title: iPSC 106 EB D0


title: IFNB_HI_3

value: IFNB-high


title: iPSC 106 undifferentiated


title: IFNG_LO_3


title: IFNB_HI_2


title: CTRL_3

value: Control


title: iPSC 102 ENDO


title: CTRL_1


title: IFNB_HI_1


title: Y10

source_name: Frontal cortex of brain

tag: age

tag: Sex

value: F

tag: matching group

value: Young


title: CTRL_2


title: iPSC 104 undifferentiated


title: IFNB_LO_1


title: Y9

value: M


title: iPSC 104 MESO

value: mesoderm


title: Y8


title: IFNB_LO_3


title: Y7


title: Y5


title: iPSC 106 EB D4

value: male


title: Y3


title: Y4


title: iPSC 106 ENDO


title: iPSC 106 MESO


title: Y2


title: Y1


title: O10

value: Old


title: iPSC C2.3 EB D4


title: O9

description: This case is the same with CONTROL12


title: O5


title: O7


title: O6


title: O4

description: This case is the same with CONTROL9


title: O3


title: O2


title: ICUVENT9

value: ICU/VENT


title: ICUVENT8


title: ICUVENT5


title: ICUVENT6


title: ICUVENT7


title: ICUVENT3


title: ICUVENT1


title: ICUVENT2


title: CONTROL23

description: Alzheimer Disease Braak IV/VI


title: CONTROL21

value: R


title: CONTROL20

value: Q


title: CONTROL19

value: P


title: CONTROL22

value: S


title: CONTROL17

value: N


title: CONTROL15

value: L


title: CONTROL18

value: O


title: CONTROL16


title: O1


title: ICUVENT4


title: CONTROL14

value: K


title: COVID21


title: COVID16


title: CONTROL13

value: J


title: COVID20


title: COVID18


title: COVID17


title: COVID15


title: HNEpC, PM2.5_treated_1

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

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

data_processing:
Raw reads were filtered with Seqtk to remove adaptor sequence and low-quality sequence.
Genome mapping was performed by "splices mapping" algorithm in Hista2 (version:2.0.4).
Annotation genome used was GRCh38.p4 (hg38).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count and FPKM values for each Sample

source_name: HNEpC

growth_protocol: Cells were cultured in an airway epithelial cell basal medium (PromoCell, C-21060) with growth medium kit (PromoCell, C- 21160) in a 5% CO2 incubator at 37℃.

extract_protocol:
RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Cells were treated with 2mL 100 μg/ml PM2.5 or same amount of normal culture medium for 24h.

tag: cell line

value: HNEpC

tag: cell type

value: nasal epithelial cell

tag: treatment


title: COVID14


title: COVID13


title: HNEpC, PM2.5_treated_3


title: HNEpC, Control_2

value: Control


title: HNEpC, Control_3


title: HNEpC, PM2.5_treated_2