title: J02_052


title: J02_042

status: Public on Jun 03 2023

type: RNA

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.

data_processing: Probe intensities were normalized with MAS5.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: fresh frozen tumor

label_protocol: RNA (1 μg; RIN value >6) was used for generation of second-strand cDNA, and cRNA was amplified with the Oligo dT primer, then biotinated and fragmented with One-Cycle Target Labeling or and control reagents (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from tumor tissues obtained at the surgery with the aid of the Qiagen RNeasy® mini kit (QIAGEN Sciences, Germantown, MD).

treatment_protocol: The patients agreed to have their research specimens cryopreserved for future use after undergoing radical breast cancer surgery, and also received endocrine therapy following the surgery.

tag: tissue

value: breast tumor

tag: menopause

tag: ct

tag: cn

tag: er

value: Positive

tag: pgr

tag: hg

value: No


title: J02_050

value: postmenopausal

value: Negative

value: Yes


title: J02_039


title: J02_053

value: premenopausal


title: MCT 1

type: SRA

city: Boston

first: Scott

middle: C

last: Fligor

state: MA

address: 300 Longwood Ave

department: Surgery

country: USA

institute: Boston Children's Hospital

library_source: transcriptomic

data_processing:
Data processing was performed by Novogene Inc: "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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). 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 <=0.05 found by DESeq2 were assigned as differentially expressed."
Assembly: GCF_000003025.6
Supplementary files format and content: Processed data are provided as a tab-delimited text file including read counts for all genes across all samples, including FPKM values

organism: Sus scrofa domesticus

source_name: Liver

extract_protocol:
Liver sections were flash frozen in liquid nitrogen and stored a -80C. RNA was harvested using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene, Inc.

tag: dose

value: Isovolumetric Vehicle Control (3ml/kg)

tag: breed

value: Yorkshire

value: Liver

tag: treatment

value: MCT


title: MCT 3


title: SEFA-6179 3

value: 48 mg/kg


title: J02_038


title: J02_037


title: D_IC β Hltf-KO

city: Lubbock

first: Beverly

middle: S

last: Chilton

state: TX

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

library_source: transcriptomic single cell

data_processing:
short-read sequencing (Illumina NovaSeq) of barcoded libraries by Genewiz  single index
data analysis of tissue images and sequencing files in FASTQ format with Space Ranger
space ranger aggr pipeline aggregated data from replicate samples and from replicate regions
read 2 sequences were mapped against the reference mouse genome C57BL/6J (GRCm38/mm10) and read 1 sequences were used for UMI filtering to obtain spatial information
Spaceranger count combined a brightfield microscope slide image and FASTQ files from spaceranger mkfastq and performed alignment, tissue detection, fiducial detection, barcode/UMI counting, and prepared a full resolution slide image for visualization in Loupe Browser.
Assembly: The pipeline used the Visium spatial barcodes to generate feature-spot matrices, determine clusters, and perform gene expression analyses. The pipeline used a probe aligner algorithm for FFPE tissues.
Supplementary files format and content: Scalefactors, JSON
Supplementary files format and content: Images, PNG

organism: Mus musculus

source_name: pancreas

extract_protocol:
Visium for FFPE uses RNA-templated ligation (RTL) probes targeting the whole transcriptome.
Spatially barcoded, ligated products were released from the slide, and harvested for qPCR with KAPA SYBR Fast qPCR master mix. Sample index sets were selected to distinguish each of the 4 samples in a multiplexed sequencing run. Samples were amplified using Ilumina-compatible indexing primers,
Visium Mouse Transcriptome Probe Set v1.0

treatment_protocol: Abdominal tissue sections (5 µm) from IC and ID β Hltf KO newborn mice were processed with the RNeasy FFPE kit for DV200 analysis. Replicate sections from IC and ID β Hltf KO newborn mice were placed within fiducial frames of capture areas A,B and C,D respectively, on Visium GEX slide V11D13-089-A1.

value: pancreas

tag: cell type

value: whole tissue

tag: genotype

value: Beta Hltf-KO


title: NK exo #7

city: Rome

first: Andrea

last: Pelosi

state: RM

address: Viale di San Paolo, 15

department: Laboratories

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: microRNA expression data of exosomes derived from interleukin-2 activated NK cells

hyb_protocol: The Biotin labelled RNA was subsequently hybridized to a GeneChip™ miRNA 4.1 array plate (Thermo Fisher Scientific). The hybridization, wash and staining procedures were done in according to the manufacturer’s protocol (Thermo Fisher Scientific).

scan_protocol: The scanning procedure was done in a GeneTitan™ Instrument (Thermo Fisher Scientific).

data_processing: The .cel file output were used as input in Partek Genomics Suite 7.0 (Partek) for generation of quantile normalized data with RMA alghoritm. Differential expression analysis between NK cells and NK exosomes groups was performed by ANOVA one-way method and p-values were calculated with FDR.

source_name: Exosomes purified from culture supernatant of activated and in vitro expanded NK cells from peripheral blood of healthy donors

label_protocol: Total RNA (140 ng per sample) was used as start material for the microarray. Biotin labelled RNA was generated using the FlashTag Biotin HSR Labelling Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.

growth_protocol: NK cells were isolated from peripheral blood of healthy volunteers and cultured in NK MACS medium (Miltenyi Biotec) in presence of interleukin-2 (600 u/mL).

extract_protocol: Total RNA extraction was performed with miRNeasy micro kit following the manufacturer’s protocol (Qiagen)

treatment_protocol: For exosome isolation, NK cells were seeded in RPMI supplemented with exosome-depleted Fetal Bovine Serum (FBS) and 600 U/ml IL-2 for 48 hours. Then, exosomes were isolated by supernatant ultracentrifugation.

value: peripheral blood

tag: disease

value: healthy donor

tag: source type

value: exosomes


title: NK exo #3


title: C_IC β Hltf-KO


title: NK cells #5

description: microRNA expression data of interleukin-2 activated NK cells

source_name: Activated and in vitro expanded NK cells from peripheral blood of healthy donors

value: cells


title: NK exo #4


title: NK cells #3


title: NK exo #5


title: Pooled mouse experiment

city: Cambridge

first: Bryan

last: Bryson

address: 400 Technology Square

department: Biological Engineering

institute: MIT

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Murine lungs were dissociated using a GentleMACS Dissociator (Miltenyi Biotec) in digestion buffer (RPMI with 10mM HEPES, DNAse I 50ug/ml, Liberase TM 100ug/ml, and 2% FBS). After running the m_lung_01 program, samples were incubated at 37C for 30 minutes before running the m_lung_02 program. Samples were filtered with a 70 uM filter, washed once, then RBCs were lysed for 5 minutes using RBC Lysis Buffer (Sigma-Aldrich). Samples were then quenched with FACS buffer (PBS with 2% FBS and 2 mM EDTA) and washed once.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Cells were then counted prior to proceeding with MULTI-seq barcoding. Samples were multiplexed as previously described. In brief, samples were barcoded with 2.5uM of the LMO anchor and barcode for 5 minutes on ice in PBS before adding 2.5 uM of the LMO co-anchor and incubating for an additional 5 minutes. Samples were quenched with 1% BSA in PBS and washed once. Barcoded cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lung cells

value: Lung

tag: strain

tag: age

value: 7-8 weeks old


title: B_ID β Hltf-KO


title: FAH seven days withdrawal condition, biological rep2

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology and Dermato-Cosmetology

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description: Gene expression data from liver tissue of FAH mice after seven days NTBC therapy discontinuation

hyb_protocol: 5.5 μg fragmented aRNA was hybridized to Affymetrix Mouse Gene 2.0 arrays along with a hybridization cocktail solution and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the quality control matrices were confirmed with the Affymetrix GCOS software following the manufacturer’s guidelines.

data_processing: Background correction, quantile normalization and summarization were done with Robust Multi-array Analysis algorithm using Transcriptome Analysis Console (TAC) 4.0.2 (Applied Biosystems)

source_name: FAH liver after seven days NTBC therapy withdrawal

label_protocol: Total RNA (100 ng) was used for amplification and in vitro transcription using the Genechip Whole Transcriptome PLUS Reagent Kit  following the manufacturer’s instructions (Affymetrix). The amplified RNA was purified with magnetic beads and 15 μg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: Unless specified otherwise, all mice received continuous NTBC treatment (8 mg/l) through their drinking water, supplemented with 3 % (w/v) dextrose for taste. Mice were fed with irradiated LabDiet® 5LJ5 chow ad libitum, which is a low-tyrosine and low-phenylalanine diet that acts as a surrogate for the protein-restricted diet of HT1 patients. All mouse caring, breeding and experimental procedures were performed in accordance with the ethical standards of the Vrije Universiteit Brussel and National Rules on Animal Experimentation. Mice were group-housed in individual ventilated cages (IVC) in a temperature (19 – 23 °C) and humidity (30 – 70% relative humidity) regulated environment with a 14/10-hour light/dark cycle under continuous NTBC treatment (8 mg/l) administered through their drinking water. Cage environment was enriched with cardboard shelters, nesting material and wooden sticks.

extract_protocol: Total RNA was extracted from all samples using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich) according to the manufacturer’s instructions. The isolated RNA was quantified at 260 nm using a Nanodrop spectrophotometer (Thermo Scientific). Total RNA was reverse transcribed into cDNA using iScriptTM cDNA Synthesis Kit (Bio-Rad) followed by cDNA purification with the Genelute PCR clean up kit (Sigma-Aldrich).

treatment_protocol: At the age of 11 weeks, NTBC therapy was discontinued for seven consecutive days for the FAH 7 days withdrawal group whereas it was administered continuously for the FAH control group.

tag: gender

value: male

value: liver

value: 12 weeks


title: J02_032

tag: tissue

value: breast tumor

value: Positive

value: No


title: J02_031

tag: menopause


title: J02_030

tag: ct


title: NK cells #6


title: J02_036

tag: cn


title: J02_035

tag: er


title: FAH seven days withdrawal condition, biological rep1


title: FAH seven days withdrawal condition, biological rep3


title: A_ID β Hltf-KO


title: NK exo #2


title: NK cells #7


title: NK cells #4


title: J02_034

tag: pgr


title: NK cells #2


title: Liver NASH Bisulfite-Seq rep3

city: shanghai

first: Fei

last: Mao

state: State...

address: Fudan university

country: China

institute: Fudan University

library_source: genomic

data_processing:
The raw reads were quality controled by FastQC.Raw sequencing reads were aligned to the mouse mm10 genome and analyzed through a streamlined analysis and annotation pipeline.
Assembly: mm10
Supplementary files format and content: Excel files include methylated regions  for each sample

molecule: genomic DNA

extract_protocol:
Livers were removed, flash frozen on dry ice, and genomic DNA was harvested using Qiagen kit.
Genomic DNA was subjected to sonication, bisulfite treatment and library preparation, following a standard WGBS protocol.

value: Liver

tag: Sex

value: WT


title: NK cells #1


title: NK exo #1


title: J02_033

tag: hg


title: J02_029


title: Liver NASH Bisulfite-Seq rep2


title: Liver NASH Bisulfite-Seq rep4


title: Liver WT Bisulfite-Seq rep3

value: NASH


title: Liver NASH Bisulfite-Seq rep1


title: FAH control condition, biological rep3

description: Gene expression data from liver tissue of FAH mice under NTBC treatment

source_name: FAH liver under continuous NTBC therapy


title: Liver WT Bisulfite-Seq rep4


title: Liver WT Bisulfite-Seq rep2


title: FAH control condition, biological rep2


title: Liver WT Bisulfite-Seq rep1


title: Cell line_Twist_rep2

city: Baltimore

first: Venu

last: Raman

state: Maryland

address: 720 Rutland Ave, Traylor 338

department: Radiology

institute: Johns Hopkins University

description: miRNA expression in Twist over expressing cell line

hyb_protocol: CORE facility

scan_protocol: CORE facility

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: 016436_D_20070426) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cell line, Twist over expressing, replicate 2

label_protocol: CORE facility

growth_protocol: MCF-7/Twist and MCF-7 cell lines were grown at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: CORE facility

treatment_protocol: Untreated

tag: cell line


title: Liver WT RNA-seq rep4

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by thesoftware of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Hisat2.
HTSeq(0.9.1) statistics were used to compare the Read Count values on each gene as theoriginal expression of the gene.
Assembly: mm10
Supplementary files format and content: normalized counts values for each Sample

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: treatment


title: FAH control condition, biological rep1


title: Cell line_rep2

description: miRNA expression in wild type cell line

source_name: Cell line, wild type, replicate 2


title: Mouse Cerebellum P0

city: Copenhagen N

first: Sophia

middle: Julia

last: Häfner

address: Ole Maaløes Vej 5

department: Biotechnology Research and Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

description: Ion Proton platform using Ion PIChip Kit v.3

data_processing:
Data was analyzed as previously reported. Briefly, sequencing reads were mapped to a corrected mouse or human rRNA reference sequence. To facilitate comparison with other studies, we have used the human rRNA sequence numbering according to snoRNABase throughout this study. An alignment table of these rRNA sequences is provided in Krogh and Jansson et al, 2016.The RiboMethseq score (RMSscore) represents the fraction of molecules methylated at each nucleotide position, and is calculated by comparing the number of read-end counts at the queried position to six flanking positions on either side.
Supplementary files format and content: excel file with RMS scores per adapter, average, and standard deviations
Supplementary files format and content: See published protocol for details.

source_name: brain

growth_protocol: H9 and HUES4 cells were grown under feeder-free conditions on plates coated with hESC-qualified Matrigel (Corning Life Sciences, #354277) in mTeSR™1 medium (Stem Cell  Technologies, #85850). KOLF2 iPS cells were grown under feeder-free conditions on Matrigel-coated plates inTeSR™-E8™ (Stem Cell Technologies, #05990).

extract_protocol:
Total RNA preparation was performed usingQIAZOL (Qiagen) and chloroform according tothe protocol from the manufacturer
RiboMeth-seq library construction and sequencing were performed as previously described. Triplicate libraries were produced for each cell line or  condition analyzed, and grown to ∼70–80% confluence before collection. A portion of 5 μg of total RNA wasused for input. RNA was partially degraded in alkali at denaturing temperatures. The 20–40-nucleotide fragments were purified by PAGE and linkers addedusing a system relying on a modified Arabidopsis tRNA ligase joining 2′,3′-cyclic phosphateand 5′-phosphate ends. The libraries were sequenced on the Ion Proton platform using Ion PI Chip Kit v.3 (Life Technologies).
RiboMeth-seq

treatment_protocol: HUES4, H9, and KOLF2 iPS cells were differentiated into ecto-, endo-, and mesoderm using the STEMdiff Trilineage Differentiation Kit (Stem Cell Technologies, #05230) according to the manufacturer’s instructions.

value: brain


title: J02_024


title: J02_027


title: J02_026


title: Mouse embryonic stem cells

tag: cell type

value: mouse embryonic stem cells


title: Mouse Olfactory Bulb P0

tag: genotype


title: Liver WT RNA-seq rep2


title: Monocytes, MCD-fed, normal saline gavaged, rep1

status: Public on Jun 04 2023

city: Beijing

first: YangLu

last: Yang

state: Beijing

address: Beijing Xicheng District Yongan Road NO.95

institute: Beijing Friendship Hospital, Capital Medical University

description: 10x Genomics

data_processing:
We used Cell Ranger Single Cell Software Suite v.3.0.2 (http://support.10xgenomics.com/) developed by 10× Genomics to process the raw FASTQ files. We used the mm10 genome and transcriptome (refdata-cellranger-mm10-1.2.0.tar.gz) as the reference.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Eight-week-old weight-matched male wild-type (WT) C57BL/6 mice and Rag1-/- mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA). These mice were fed either a normal control diet (NCD), a methionine/choline-deficient diet (MCD, 10401, Beijing HFK Bioscience, Beijing, China), or an MCD diet with melatonin (100g/kg per day) treatment by oral gavage for six weeks. The immune cells were harvested, and then the expression levels of various cell surface and intracellular markers were detected. All samples were examined through a FACS Aria II flow cytometer (BD Biosciences, CA, USA), and the data were analyzed using FlowJo software (Treestar, Ashland, OR, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: 7AAD-CD45+Ly6G-CD11b int F4/80 hi monocytes

value: 12-14 weeks old

tag: diet

value: methionine/choline-deficient diet (MCD)


title: Cell line_rep1

description: miRNA expression in wild type cell line

source_name: Cell line, wild type, replicate 1


title: J02_028


title: J02_023

value: postmenopausal

value: Negative

value: Yes


title: Liver WT RNA-seq rep3

value: male


title: H9 SNORD52 OE1 ESCs

value: human embryonic stem cells

value: SNORD52 overexpression

value: constitutive transgene expression


title: Mouse Hippocampus P0


title: H9 SNORD52 KO2 ESCs

value: SNORD52 knock-out


title: H9 SNORD52 OE2 ESCs


title: Mouse Cerebellum Adult


title: J02_021

value: breast tumor

value: premenopausal

value: Positive

value: No


title: Mouse Olfactory Bulb Adult

value: brain

value: WT


title: J02_022


title: Liver NASH RNA-seq rep3

value: Liver

value: NASH


title: Mouse Hippocampus Adult


title: iPS mesoderm

value: induced pluripotent stem cells

value: Directed differentiation to mesoderm


title: J02_020


title: Liver WT RNA-seq rep1


title: Liver NASH RNA-seq rep2


title: Liver NASH RNA-seq rep4


title: Mouse Cortex P0


title: Liver NASH RNA-seq rep1


title: J02_018

value: postmenopausal


title: Mouse Cortex E17


title: HUES4 mesoderm


title: Heart, DOX_NMN, rep4

city: London

first: Tianqing

last: Peng

state: Ontario

address: 800 Commissioners Road

country: Canada

institute: Western University

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)
Clean Data was then aligned to GrCM38/mm10 using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample
Assembly: mm10
Supplementary files format and content: xlsx file include RPKM values for each sample
Supplementary files format and content: xlsx file include read counts for each sample

source_name: heart

growth_protocol: Animals were housed in a temperature and humidity-controlled facility with 12-h light and dark cycles, with free access to water and food.

extract_protocol:
Total RNA was isolated from the heart tissues with TRIzol™ reagent (Invitrogen) according to the manufacturer’s protocol. 2 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA   Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s   recommendations

treatment_protocol: Male C57BL/6 mice aged 8 weeks were treated with a single dose of DOX (15 mg/kg, i.p., Pfizer). Sham mice received the same volume of sterile saline. NMN (500 mg/kg, i.p., ApexBio) or saline was given 30 min prior to DOX injection. After 5 days of DOX administration, mice were sacrificed with hearts harvested and subjected to RNA-seq analysis

value: heart

value: wild type

value: DOX+NMN i.p.


title: Heart, DOX_NMN, rep3

value: male


title: HUES4 endoderm

value: human embryonic stem cells

value: Directed differentiation to endoderm


title: H9 SNORD52 KO1 ESCs

value: SNORD52 knock-out


title: Mouse Cortex E15.5


title: Mouse Cortex E14


title: Mouse Cortex Adult


title: J02_017

value: breast tumor

value: Negative


title: J02_016

value: Positive

value: No


title: J02_015

value: Yes


title: iPS endoderm

value: WT


title: Mouse Cortex E12.5

value: brain


title: Heart, DOX_NMN, rep1


title: J02_014

value: premenopausal


title: Mouse Cortex E11


title: H9 early neural precursors

value: Neural induction


title: H9 mesoderm

value: Directed differentiation to mesoderm


title: H9 late neural precursors

value: Neural differentiation


title: Heart, DOX_Vehicle, rep3

value: heart

value: wild type

value: DOX+Saline i.p.


title: Heart, DOX_NMN, rep2

value: male

value: DOX+NMN i.p.


title: SH-SY5Y, RBD, 48 hours biol rep2

city: Luzhou

first: Zheng

last: Bao

state: Sichuan

address: No. 25, Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters --dta -p 10
Counts were calculated using featurecounts with parameters -t exon -T 10 -p -g gene_id -f. Normalized counts were calculated using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: SH-SY5Y cells were maintained in DME/F-12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
The biotin labelled nascent RNA was purified by Dynabeads MyOne Streptavidin T1 magnetic beads. Beads with purified nascent RNA were resuspended in Click-iT reaction wash buffer for downstream RNA-seq library preparation.
RNA libraries for RNA-seq were prepared using  the Universal V6 RNA-seq Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol:
The cells were seeded into 12 well plate at a density of 6 x 10^4 cells/well and cultured for at least 24 h to allow them to adhere to the plates.
Then, the cells were treated with 1ug/ml wild type RBD  for 12 h, 24 h or 48 h, respectively.

value: human neuroblastoma cells

value: RBD

tag: time

value: Hour 48


title: H9 mature neurons

value: human embryonic stem cells

value: Neural Maturation


title: H9 endoderm

value: Directed differentiation to endoderm


title: SH-SY5Y, RBD, 48 hours biol rep3

value: WT


title: Heart, DOX_Vehicle, rep2

tag: strain


title: Heart, DOX_Vehicle, rep4


title: NK exo #6

value: peripheral blood

tag: disease

value: healthy donor

tag: source type

value: exosomes


title: J02_013

tag: tissue

value: breast tumor

value: premenopausal

value: Positive

value: No


title: SH-SY5Y, RBD, 48 hours biol rep1


title: iPS ESCS

value: induced pluripotent stem cells


title: SH-SY5Y, RBD, 12 hours biol rep3

value: Hour 12


title: Heart, DOX_Vehicle, rep1

value: heart

tag: gender

value: male

value: wild type

value: DOX+Saline i.p.


title: J02_012

tag: menopause

value: postmenopausal

tag: ct

value: Negative


title: J02_010

tag: cn

tag: er


title: J02_009

tag: pgr


title: SH-SY5Y, RBD, 12 hours biol rep2

value: human neuroblastoma cells

value: RBD


title: J02_011

tag: hg


title: HUES4 ESCs

tag: cell line

value: human embryonic stem cells

value: WT


title: Heart, Sham_NMN, rep4

tag: treatment

value: Saline+NMN i.p.


title: J02_008

value: breast tumor


title: Cell line_Twist_rep1

source_name: Cell line, Twist over expressing, replicate 1


title: H9 ESCs

tag: cell type


title: Heart, Sham_NMN, rep3

tag: genotype


title: SH-SY5Y, RBD, 12 hours biol rep1


title: Heart, Sham_NMN, rep2


title: SH-SY5Y, RBD control, 0 hour biol rep1

value: untreated

value: Hour 0


title: SH-SY5Y, RBD control, 0 hour biol rep2


title: Heart, Sham_NMN, rep1


title: Heart, Sham_Vehicle, rep4

value: Saline+Saline i.p.


title: NGS - MEL2

city: Chicago

first: Ruli

last: Gao

state: IL

address: Simpson Querrey, 7th Floor

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

description:
10xgenomics 3'scRNAseq
MEL3BM

data_processing:
For NGS, the reads are analyzed by cellranger-arc 4.0 to generate gene expression matrix.
For Nanopore, the reads are analyzed by scNanoGPS to generate gene expression, isoform, SNV matrices. The detailed process is described at: https://github.com/gaolabtools/scNanoGPS_v0.10/ .
deconvolution into single cells
make consensus sequencces of single molecules
calculate same cell multiomics
Assembly: GRCh38
Supplementary files format and content: NGS: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Nanopore: matrix.tsv.gz, matrix_isoform.tsv.gz, matrix_SNV.vcf.gz

source_name: Skin

extract_protocol:
Single nuclei of cell lines were prepared by following the 10X Genomics  protocol(CG000365 Rev C).   Single nucleus suspensions of frozen tumor tissues were prepared according to the method as previously described (dx.doi.org/10.17504/protocols.io.t3aeqie)
NGS libraries were prepared by following 10X genomics 3'scRNAseq protocol.   For Nanopore long-read sequencing, cDNA libraries were prepared with SQK-LSK110 ligation sequencing kit.

value: Skin

value: nuclei of tumor

value: unknown

tag: tumor stage

value: Melanoma brain metastatis


title: Heart, Sham_Vehicle, rep3

value: heart

value: male

value: wild type


title: Heart, Sham_Vehicle, rep2


title: J02_006

value: premenopausal

value: Positive

value: No


title: NGS - MEL1

description:
10xgenomics 3'scRNAseq
MEL3ECM

value: Primary melanoma


title: Heart, Sham_Vehicle, rep1


title: J02_004

value: postmenopausal


title: ZIKV3

city: Houston

first: Michael

last: Jochum

address: 1 Baylor Plaza

department: Obstetrics and Gynecology

institute: Baylor College of Medicine

description: AGO-HITS-CLIP

data_processing:
Ribonomics analyses. Reads were pre-processed and quality filtered using FastqQC (v0.11.9). Barcodes and adapters were trimmed using Trimmomatic79 (v0.33). Reads were aligned to custom human + ZIKV + hsa-miRbase transcriptome (see GRCh38.p13_and_NC_012532.1_and_hsamiRbase22.1.gtf) using STAR80 (v2.7.8). PCR duplicate reads were removed using Picard81 (v2.24.0). Unique reads were counted using HTseq82 (v0.11.1). Counts from the 5 mock and 4 infected biological replicates were used for differential expression (DE) analysis in R (v4.0.2) using DEseq283 (v3.12). AGO-HITS-CLIP peaks were called with Piranha84 (v1.2.1) or PureCLIP85 (v1.3.1). Positive or negative-sense reads-per-million-scaled (RPM) reads, and CLIP peaks were converted to bigwig files for visualization on the UCSC genome browser86 (hg38). Host miRNAs with different accumulation levels were analyzed by mirPath26 (v3, DIANA Tools) using the MicroT-CDS database25 (v5) and visualized using the Kanehisa Laboratories Pathway Viewer.
Assembly: GRCh38.p13_and_NC_012532.1_and_hsamiRbase22.1.gtf deposited to GitHub
Supplementary files format and content: htseq counts matrix

source_name: Placenta

extract_protocol:
Argonaut High-throughput Sequencing UV-crosslinking and Immunoprecipitation (AGO-HITS-CLIP). Cell pellets were then subject to UV-crosslinking (25 kilograys), spun down, washed, and flash-frozen in liquid nitrogen, and stored at -80C. We then performed AGO-HITS-CLIP as described previously77,78 except for the use of photoactivatable ribonucleoside (PAR) analog thiouridine, as done in PAR-CLIP, which we did not include. Cell pellets were lysed (recipe ), DNAse (cat.) and RNAse (cat.) treated, and subject to immunoprecipitation of argonaut 2 (cat . ). Several high-salt stringent washes purified RISC-associated RNAs, proteinase (cat. ) treated, then 32P-radiolabeled, and size-selected by gel purification. These RNAs were then eluted and prepared for NGS using the TruSeq small RNA library (cat.) by ligations of the 3’ and 5’ adapters, reverse transcribed (cat.), and barcodes were added during PCR amplification of cDNA by the minimum number of PCR cycles (10-15 cycles) using a high-fidelity polymerase (cat.). TapeStation confirmed the purity of NGS libraries, and the libraries were single-end sequenced using the Illumina HiSeq 2500 platform (50-51 bp reads).
Truseq small RNA

value: Placenta

value: Primary

value: Trophoblast

value: ZIKV


title: ZIKV4

description: AGO-HITS-CLIP


title: NGS - RCC1

description:
10xgenomics 3'scRNAseq
RCC12P

source_name: Kidney

value: Kidney

value: Primary RCC


title: J02_003

source_name: fresh frozen tumor

value: breast tumor


title: J02_005


title: ZIKV2

description: AGO-HITS-CLIP


title: J02_007


title: ZIKV1

description: AGO-HITS-CLIP

value: Mock


title: NGS - H2030

description:
10xgenomics 3'scRNAseq
MO-H2030

value: nuclei of cancer cell line

value: unknown


title: J02_001


title: J02_002

value: Yes


title: S34

data_processing:
Spatial transcriptomics analysis. Spatial transcriptomes were aligned to a custom human and ZIKV transcriptome and transcripts counts were quantified using Space Ranger (v1.3.0) and bash scripts. Downstream analyses were done in R using the Seurat scRNA-seq analysis package 34. H&E slides were annotated by a trained pathologist and transferred to spatial barcodes using the Loupe Browser (v5) and spatial transcriptomes were annotated based on PCA dimension reduction and clustering analysis to identify broad cell-types. The spatial transcriptomes were then integrated with published murine single-nuclei RNA-seq (snRNA-seq) dataset to assess cell-type annotations (GEO accession GSE152248). The Marsh & Blelloch, eLife. (2020) snRNA-seq dataset included murine placentas sampled at E9.5-E14.5: E9.5, E10.5, E12.5, E14.5 across 2,933 independently filtered (nFeature_RNA > 500 & nFeature_RNA < 4000 & nCount_RNA > 500 & nCount_RNA < 10000 & percent.mt < 10 & percent.ribo < 20) high-quality transcriptomes.
Assembly: mm10_and_NC_012532.1.v2 deposited to GitHub
Supplementary files format and content: h5 counts matrix
Library strategy: Spatial transcriptomics

extract_protocol:
Spatial transcriptomics in murine placentae. At E18.5 placentas were dissected and preserved in RNA-later at -25C for 18 hours. Tissues were dehydrated by incubation in 30% sucrose at 4oC for 6 hours. At the Baylor College of Medicine Pathology and Histology Core placentas were fresh-frozen in optimal cutting temperature compound (OCT) with a liquid nitrogen and isopentane bath. Tissue blocks were cryosectioned at 10 microns for quality control H&E staining and 10x Genomics Visium Tissue Optimization. The Tissue Optimization slide revealed optimal permeabilization was observed after 12 minutes. Finally, the tissue blocks were cryosectioned and placed on Visium Gene Expression slides (v2) for H&E staining and Visium spatial transcriptomics library preparation following the manufacturer’s instructions. Visium libraries were sequenced (Illumina, NovaSeq 6000) at the Baylor College of Medicine Genomic and RNA Profiling Core.
Visium (v2)

value: ZIKV-Vehicle


title: S32

value: Mock-Vehicle


title: S33


title: NGS - A375

description:
10xgenomics 3'scRNAseq
MO-A375


title: S31

value: ZIKV-Enoxacin


title: Mock4

description: AGO-HITS-CLIP


title: SH-SY5Y, RBD control, 0 hour biol rep3

value: human neuroblastoma cells

value: WT

value: untreated

tag: time

value: Hour 0


title: Mock5

description: AGO-HITS-CLIP

value: Placenta

value: Primary


title: Mock3

description: AGO-HITS-CLIP

value: Trophoblast


title: S13


title: S12


title: p53-V272M + ATO

city: Shanghai

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

description:
190312-C2_S67
Sample2_(V272M+ATO)

data_processing:
Raw sequence reads were initially processed using FastQC (Babraham Institute, Cambridge, UK) for quality control, then adapter sequences and poor-quality reads were removed using Cutadapt.
Quality-filtered reads were then mapped to the human genome using STAR software, and only uniquely mapped reads were kept.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes FPKM value of each sample

source_name: colon

growth_protocol: HCT116 (p53-/-) cells were cultured at 37 ℃ in medium suggested in the repository, supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
Total RNA was isolated using a Total RNA Purification Kit (B518651, Sangon Biotech)
Sequencing libraries was constructed from 1 μg of purified mRNA using an Illumina TruSeq RNA Sample Prep Kit (cat# FC-122-1001)
Libraries were pooled and 150-bp paired-end reads were sequenced on the Illumina HiSeq Xten platform.

treatment_protocol: HCT116 (p53-/-) cells infected with p53-V272M, or p53-R282W were treated with 1 μg ml−1 ATO for 24 h.

tag: tissue source

value: colon

tag: ato treatment

value: yes


title: p53-R282W + ATO

description:
190312-E2_S73
Sample4_(R282W+ATO)

value: HCT116 (p53-/-) cells  infected with p53-R282W


title: S09

value: Mock


title: Mock2

description: AGO-HITS-CLIP


title: p53-V272M

description:
190312-C1_S66
Sample1_(V272M)

value: HCT116 (p53-/-) cells  infected with p53-V272M

value: no


title: p53-R282W

description:
190312-E1_S72
Sample3_(R282W)


title: S07


title: Mock1

description: AGO-HITS-CLIP


title: J02_025

data_processing: Probe intensities were normalized with MAS5.

extract_protocol: RNA was extracted from tumor tissues obtained at the surgery with the aid of the Qiagen RNeasy® mini kit (QIAGEN Sciences, Germantown, MD).

value: breast tumor

value: Positive

value: No


title: MRP8_DG_20: Rat, perforant pathway stimulation (PPS), Control, DG

status: Public on Jun 02 2023

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

institute: Omiics ApS

description: Ago2 IP RNA, small RNA seq

data_processing:
FASTX-Toolkit (0.0.13) was used to quality filter reads and cutadapt (1.2.1) was used to remove adaptor sequences
Using Bowtie (0.12.8), reads were mapped to miRNAs from miRBase v22 allowing zero mismatches, but allowing for non-templated 3’ A and T bases
Assembly: Reference: mature miRNAs from miRBase v22
Supplementary files format and content: Text files with raw read counts for miRNAs in each sample

organism: Rattus norvegicus

extract_protocol:
Frozen hippocampal tissue is homogonized and immunoprecipitation is done using Ago2 antibody
Immunoprecitated RNA was prepared using TruSeq small RNA library prep

tag: strain

value: Sprague-Dawley

tag: model

value: perforant pathway stimulation (PPS)

tag: period

value: Control

value: Dentate Gyrus


title: MRP8_DG_31: Rat, perforant pathway stimulation (PPS), Control, DG

description: Ago2 IP RNA, small RNA seq

tag: tissue


title: MRP7_DG_37: Rat, perforant pathway stimulation (PPS), Chronic, DG

description: Ago2 IP RNA, small RNA seq

value: Chronic


title: MRP8_DG_17: Rat, perforant pathway stimulation (PPS), Control, DG

description: Ago2 IP RNA, small RNA seq


title: MRP6_DG_74: Rat, perforant pathway stimulation (PPS), Day of first seizure, DG

description: Ago2 IP RNA, small RNA seq

value: Day of first seizure


title: MRP5_DG_6: Rat, perforant pathway stimulation (PPS), 16 days, DG

description: Ago2 IP RNA, small RNA seq

value: 16 days


title: MRP6_DG_69: Rat, perforant pathway stimulation (PPS), Day of first seizure, DG

description: Ago2 IP RNA, small RNA seq


title: MRP7_DG_43: Rat, perforant pathway stimulation (PPS), Chronic, DG

description: Ago2 IP RNA, small RNA seq


title: MRP6_DG_64: Rat, perforant pathway stimulation (PPS), Day of first seizure, DG

description: Ago2 IP RNA, small RNA seq


title: MRP5_DG_28: Rat, perforant pathway stimulation (PPS), 16 days, DG

description: Ago2 IP RNA, small RNA seq


title: MRP7_DG_75: Rat, perforant pathway stimulation (PPS), Chronic, DG

description: Ago2 IP RNA, small RNA seq


title: MRP4_DG_9: Rat, perforant pathway stimulation (PPS), 10 days, DG

description: Ago2 IP RNA, small RNA seq

value: 10 days


title: MRP4_DG_5: Rat, perforant pathway stimulation (PPS), 10 days, DG

description: Ago2 IP RNA, small RNA seq


title: MRP5_DG_19: Rat, perforant pathway stimulation (PPS), 16 days, DG

description: Ago2 IP RNA, small RNA seq


title: MRP3_DG_3: Rat, perforant pathway stimulation (PPS), 72 hours, DG

description: Ago2 IP RNA, small RNA seq

value: 72 hours


title: MRP3_DG_1: Rat, perforant pathway stimulation (PPS), 72 hours, DG

description: Ago2 IP RNA, small RNA seq


title: MRP2_DG_16: Rat, perforant pathway stimulation (PPS), 24 hours, DG

description: Ago2 IP RNA, small RNA seq

value: 24 hours


title: MRP4_DG_4: Rat, perforant pathway stimulation (PPS), 10 days, DG

description: Ago2 IP RNA, small RNA seq


title: MRP3_DG_2: Rat, perforant pathway stimulation (PPS), 72 hours, DG

description: Ago2 IP RNA, small RNA seq


title: MRP2_DG_15: Rat, perforant pathway stimulation (PPS), 24 hours, DG

description: Ago2 IP RNA, small RNA seq


title: MRP2_DG_11: Rat, perforant pathway stimulation (PPS), 24 hours, DG

description: Ago2 IP RNA, small RNA seq


title: MRP1_DG_36: Rat, perforant pathway stimulation (PPS), 1 hour, DG

description: Ago2 IP RNA, small RNA seq

value: 1 hour


title: MRP1_DG_26: Rat, perforant pathway stimulation (PPS), 1 hour, DG

description: Ago2 IP RNA, small RNA seq


title: MRP8_CA3_31: Rat, perforant pathway stimulation (PPS), Control, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP8_CA3_20: Rat, perforant pathway stimulation (PPS), Control, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP1_DG_24: Rat, perforant pathway stimulation (PPS), 1 hour, DG

description: Ago2 IP RNA, small RNA seq


title: NGS - RCC2

description:
10xgenomics 3'scRNAseq
RCC12BM

value: Kidney

value: nuclei of tumor

value: unknown

value: RCC brain metastatis


title: MRP7_CA3_75: Rat, perforant pathway stimulation (PPS), Chronic, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP8_CA3_17: Rat, perforant pathway stimulation (PPS), Control, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP6_CA3_74: Rat, perforant pathway stimulation (PPS), Day of first seizure, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP7_CA3_37: Rat, perforant pathway stimulation (PPS), Chronic, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP6_CA3_64: Rat, perforant pathway stimulation (PPS), Day of first seizure, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP4_CA3_4: Rat, perforant pathway stimulation (PPS), 10 days, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP4_CA3_9: Rat, perforant pathway stimulation (PPS), 10 days, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP6_CA3_69: Rat, perforant pathway stimulation (PPS), Day of first seizure, CA3

description: Ago2 IP RNA, small RNA seq


title: J02_019

value: breast tumor

tag: menopause

value: postmenopausal

tag: ct

value: Positive

value: Negative


title: MRP7_CA3_43: Rat, perforant pathway stimulation (PPS), Chronic, CA3

description: Ago2 IP RNA, small RNA seq

value: Sprague-Dawley

value: perforant pathway stimulation (PPS)


title: MRP5_CA3_6: Rat, perforant pathway stimulation (PPS), 16 days, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP3_CA3_3: Rat, perforant pathway stimulation (PPS), 72 hours, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP5_CA3_19: Rat, perforant pathway stimulation (PPS), 16 days, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP3_CA3_2: Rat, perforant pathway stimulation (PPS), 72 hours, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP1_CA3_36: Rat, perforant pathway stimulation (PPS), 1 hour, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP2_CA3_16: Rat, perforant pathway stimulation (PPS), 24 hours, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP2_CA3_15: Rat, perforant pathway stimulation (PPS), 24 hours, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP3_CA3_1: Rat, perforant pathway stimulation (PPS), 72 hours, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP2_CA3_11: Rat, perforant pathway stimulation (PPS), 24 hours, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP8_CA1_31: Rat, perforant pathway stimulation (PPS), Control, CA1

description: Ago2 IP RNA, small RNA seq

value: Control


title: MRP1_CA3_24: Rat, perforant pathway stimulation (PPS), 1 hour, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP8_CA1_20: Rat, perforant pathway stimulation (PPS), Control, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP4_CA3_5: Rat, perforant pathway stimulation (PPS), 10 days, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP7_CA1_75: Rat, perforant pathway stimulation (PPS), Chronic, CA1

description: Ago2 IP RNA, small RNA seq

value: Chronic


title: MRP1_CA3_26: Rat, perforant pathway stimulation (PPS), 1 hour, CA3

description: Ago2 IP RNA, small RNA seq


title: MRP5_CA3_28: Rat, perforant pathway stimulation (PPS), 16 days, CA3

description: Ago2 IP RNA, small RNA seq

value: 16 days


title: MRP6_CA1_74: Rat, perforant pathway stimulation (PPS), Day of first seizure, CA1

description: Ago2 IP RNA, small RNA seq

value: Day of first seizure


title: MRP7_CA1_37: Rat, perforant pathway stimulation (PPS), Chronic, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP6_CA1_69: Rat, perforant pathway stimulation (PPS), Day of first seizure, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP6_CA1_64: Rat, perforant pathway stimulation (PPS), Day of first seizure, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP7_CA1_43: Rat, perforant pathway stimulation (PPS), Chronic, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP5_CA1_28: Rat, perforant pathway stimulation (PPS), 16 days, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP4_CA1_4: Rat, perforant pathway stimulation (PPS), 10 days, CA1

description: Ago2 IP RNA, small RNA seq

value: 10 days


title: MRP5_CA1_19: Rat, perforant pathway stimulation (PPS), 16 days, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP4_CA1_5: Rat, perforant pathway stimulation (PPS), 10 days, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP4_CA1_9: Rat, perforant pathway stimulation (PPS), 10 days, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP3_CA1_2: Rat, perforant pathway stimulation (PPS), 72 hours, CA1

description: Ago2 IP RNA, small RNA seq

value: 72 hours


title: MRP3_CA1_3: Rat, perforant pathway stimulation (PPS), 72 hours, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP3_CA1_1: Rat, perforant pathway stimulation (PPS), 72 hours, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP2_CA1_11: Rat, perforant pathway stimulation (PPS), 24 hours, CA1

description: Ago2 IP RNA, small RNA seq

value: 24 hours


title: MRP2_CA1_15: Rat, perforant pathway stimulation (PPS), 24 hours, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP2_CA1_16: Rat, perforant pathway stimulation (PPS), 24 hours, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP8_CA1_17: Rat, perforant pathway stimulation (PPS), Control, CA1

description: Ago2 IP RNA, small RNA seq


title: MRP1_CA1_36: Rat, perforant pathway stimulation (PPS), 1 hour, CA1

description: Ago2 IP RNA, small RNA seq

value: 1 hour


title: MRP1_CA1_26: Rat, perforant pathway stimulation (PPS), 1 hour, CA1

description: Ago2 IP RNA, small RNA seq


title: M_RS_30_BR2

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

description: QuantSeq 3’mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen Inc, #015) were supplied by the Investigator. Single read sequencing was performed using using the NextSeq 500/550 High-Output v2.5   (75 cycles) Kit (#20024906)

data_processing:
Basic assessments of sequence data quality were performed using FastQC and multi QC
Raw sequencing reads were trimmed and filtered using cutAdapt
Sequenced reads were aligned to the C. neoformans H99 reference sequence CNA3  using Hisat2.
Mapped reads were assigned per gene using featureCounts and the longest transcript per gene annotation from https://github.com/ewallace/CryptoTranscriptome2018/.
All analysis code is available at https://github.com/ewallace/CryptoGat201RNASeq_draft
Assembly: CNA3
Supplementary files format and content: tab-separated text file

organism: Cryptococcus neoformans H99

source_name: Yeast cells

growth_protocol: Grow a culture of C. neoformans in YPD for 5 days.  In duplicate, pre-warm 4 x 100mL each of RPMI and RPMI + serum at 37C, in incubators shaking at 60rpm.  Fix and freeze 3mL of stationary-phase culture:  Place 4 x 3.5ml of one stationary-phase culture in separate falcon tubes.  Resuspend each cell pellet in a different pre-warmed medium condition (RPMI and RPMI + serum at 37C), and start stopwatch. Transfer to 100mL total in shaking flasks in appropriate incubator as soon as possible.  At 30, 120 and 240 minutes after inoculation, fix and freeze 10mL from each condition, as above.

extract_protocol:
Fix and freeze yeast culture:  Pre-chill a 50mL tube with 7.5mL 100% Methanol  on dry ice (tightly capped so CO2 does not dissolve in MetOH).   Add 15mL of culture to the chilled MetOH, cap tube, shake to mix, place on dry ice for up to 5 min.  Spin 2 min at ~2500g, pour off supernatant.  Resuspend cell pellet in 1mL ice-cold H2O and transfer to 2mL screw-cap tube.   Spin 1min at 5000g, remove supernatant carefully, and freeze pellet in sealed tube at -80C.  Freeze-dry the pellet in a lyophilizer until dry.   Extract RNA using the RNAeasy plant and fungi kit (Qiagen)
500 ng of RNA from each sample was used as input for cDNA library preparation using the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina platforms according to the manufacturer’s instructions.

value: Yeast cells

value: GAT201 deletion (Madhani Collection)

tag: i7 index


title: M_RS_240_BR2


title: M_RS_240_BR1


title: MRP5_CA1_6: Rat, perforant pathway stimulation (PPS), 16 days, CA1

description: Ago2 IP RNA, small RNA seq


title: M_RS_120_BR2


title: C8

city: Saskatoon

first: Sateesh

last: Kagale

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

institute: National Research Council Canada

data_processing:
Basecalls performed using CASAVA
Short Illumina reads were filtered using Trimmomatic by trimming adapter and low quality sequences and removing reads shorter than 75 bp
Filtered reads were aligned to the wheat reference genome (IWGSC v1.1) using STAR
Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and the expected read counts and transcripts per million (TPM) values were generated
Genome_build: IWGSCv1.1
Supplementary_files_format_and_content: Matrix table with TPM values for each sample

organism: Triticum aestivum

growth_protocol: Seedlings were grown in a green house at Agriculture and Agri-Food Canada under 20 °C/16 °C and 16 h/8 h day/night temperature and photoperiod. After two weeks, temperatures were raised to 24 °C/18 °C, while photoperiod remained constant. All pots were fertilized weekly with N: P: K (15-20-15) and an additional micronutrient solution.

extract_protocol:
Total RNA was extracted from the ground flag leaf samples using the Qiagen RNeasy plant RNA extraction kit (Qiagen, Hilden, DE) by following the manufacture’s recommendations.
TruSeq RNA sequencing libraries were constructed following the manufacturer’s instructions (Illumina, http://www.illumina.com/)

treatment_protocol: Five weeks after sowing, at spike initiation (Feekes scale stage 8), eight pots were assigned to each of the seven abiotic stresses or stress combinations and the control for a total of 64. Single treatments included: control (C), heat (H), drought (D) and salinity (S). Combined treatments were: heat and drought (HD), salinity and heat (SH), salinity and drought (SD) and, lastly, a salinity, heat and drought (SHD) treatment. Control plants were maintained at 100 % field capacity using tap water. To apply heat stress, plants were placed in two greenhouses. The first maintained day/night temperatures of 24 °C/18 °C and housed C, D, S, DS treatments. The second housed the treatments requiring heat stress (H, HD, SH, SHD) and the day-time temperature was set to 30 °C from 9 am to 3 pm before returning to the standard 24 °C/18 °C temperatures. Drought treatments (D, HD, SD, SHD) were imposed by maintaining pots at 40 % field capacity. Salinity treatments were given increasing NaCl concentrations starting at 20 mM, then to 40 mM for the first two weeks and lastly 80 mM which was maintained for the remainder of the experiment. All treatments involving salinity (S, SH, SD, SHD) were watered with 250 ml salt water to either 100 % or 40 % field capacity. Treatments continued until physiological maturity.

value: Flag leaf

value: Stettler

tag: process


title: MRP1_CA1_24: Rat, perforant pathway stimulation (PPS), 1 hour, CA1

description: Ago2 IP RNA, small RNA seq


title: M_RS_30_BR1


title: M_RS_120_BR1


title: C4


title: C2


title: M_R_240_BR2


title: M_R_120_BR2


title: C1


title: M_R_30_BR2


title: SHD7

value: Salt and Heat and Drought


title: SHD6


title: SHD5


title: M_Y_0_BR2


title: M_R_240_BR1


title: M_R_120_BR1


title: M_R_30_BR1


title: SHD4


title: SH8

value: Salt and Heat


title: SH4


title: B_RS_240_BR2

value: GAT201 disruption (Bahn Collection)


title: B_RS_120_BR2


title: SH3


title: SD8

value: Salt and Drought


title: SD6


title: SD5


title: SH2


title: SD1


title: B_RS_240_BR1


title: B_RS_30_BR2


title: B_RS_30_BR1


title: B_RS_120_BR1


title: S5

value: Salt


title: B_R_120_BR2


title: S8


title: S3


title: B_R_30_BR2


title: S1


title: B_Y_0_BR2


title: HD7

value: Heat and Drought


title: B_R_240_BR1


title: HD4


title: M_Y_0_BR1


title: B_R_30_BR1


title: B_Y_0_BR1


title: a_RS_240_BR2

value: wild type


title: H3

value: Heat


title: B_R_240_BR2


title: a_RS_120_BR2


title: a_RS_30_BR2


title: a_RS_120_BR1


title: D6

value: Drought


title: D8


title: H1


title: D4


title: a_RS_240_BR1


title: a_R_240_BR2


title: HD8


title: a_R_120_BR2


title: a_R_30_BR2


title: B_R_120_BR1


title: cardiomyocyte cells, WT [WT02_S2]

first: Shengyu

last: Li

address: 6670 Bertner Ave, R10-109, floor 10

institute: Houston Methodist Research Insitute

data_processing:
Kallisto was used to map RNA-seq reads to the rat (Rattus norvegicus) reference genome mRatBN7.2 and quantify transcript abundance. The bootstrapping technique of Kallisto was used to repeat the analysis 100 times
DESeq2 was used to estimate the significance of differential expression and calculate p value from transcript abundance data
Benjamini-Hochberg method was used to calculate the adjusted p value. DEGs were defined using the adjusted p value no more than 0.05.
Assembly: mRatBN7.2
Supplementary files format and content: comma-delimited csv files include TPM values for each Sample, the p and adjusted-p between WT and KO.

extract_protocol:
RNAs of NRVMs were extracted by using Qiagen Kit.
Total RNAs isolated from NRVMs were processed to generate cDNA libraries that were sequenced on the Illumina HiSeq 2500 platform.

value: heart

value: NRVMs

value: cardiomyocyte

value: WT


title: a_Y_0_BR2

value: Yeast cells


title: cardiomyocyte cells, KO [KO01_S3]

value: KO


title: cardiomyocyte cells, WT [WT01_S1]


title: a_R_240_BR1


title: HD3

value: Flag leaf


title: H4

value: Stettler


title: 01-039_C3D1

city: LYON

first: Nicolas

last: Rama

address: 28 rue Laennec

country: France

institute: CRCL

description: 10x Genomics

data_processing:
library strategy: Spatial Transcriptomics Visum (10x genomics)
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1.
For each FFPE section, FASTQ files and histology images were processed using 10X Space Ranger v2.0 to obtain gene expression matrix associated to each spot.
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 files and matrix files

source_name: metastasis biopsies

extract_protocol:
FFPE tissue sections were placed on Visium slides and prepared according to 10X Genomics protocols. After H&E staining, imaging and decrosslinking steps, tissue sections were incubated with human specific probes targeting 17,943 genes (10Xgenomics, Visium Human Transcriptome Probe Set v1.0). Probes hybridized on mRNA were captured onto Visium slides.
Gene Expression library were prepared following the provided protocol and sequenced on an Illumina NovaSeq 6000 with 50,000 reads per spot targeted sequencing depth.

tag: time point

value: After one month of treatment

value: metastasis biopsies


title: a_R_120_BR1


title: a_R_30_BR1


title: 01-039_C1D1

description: 10x Genomics

value: At inclusion


title: H2


title: 01-034_C3D1

description: 10x Genomics


title: A_RS_240_BR2


title: 01-034_C1D1

description: 10x Genomics


title: A_RS_30_BR2


title: D1


title: A_RS_120_BR1


title: cardiomyocyte cells, KO [KO02_S4]

tag: cell line


title: a_RS_30_BR1

tag: treatment


title: A_RS_30_BR1

tag: cell type


title: NP137_sample (C3D1) [scRNA-seq]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Endometrial metastasis biopsies

extract_protocol:
Endometrial metastasis biopsies were dissociated for single cell RNA sequencing using the Tumor Dissociation kit by Miltenyi Biotec (cat. no. 130–095-929). Then, the cells were spun down at 300 x g for 7 min at 4°C, resuspended in RPMI, passed through a 70μm strainer . After centrifugation, the cells were resuspended in 100 μl of RPMI. The number of live cells was determined with a Luna-FL Dual fluorescence cell counter (Logos Biosystems).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Endometrial metastasis biopsies

value: after one month


title: A_RS_120_BR2


title: A_R_240_BR2


title: Control_sample (C1D1) [scRNA-seq]

description: 10x Genomics

value: at inclusion


title: A_R_120_BR2

value: wild type


title: A_Y_0_BR2


title: 01-040_C1D1 [R220324]

description:
Patient_Raw_Count.csv
Patient_DeSEQ2Normalized_Count.csv

data_processing:
Fastq files were processed with Star, v2.5.2b (mapped on the reference genome:gencode.v27)  and read count  were analysed with R (ver 4.2.0) package DeSEQ2 (ver 1.36.0).
Assembly: gencode.v27
Supplementary files format and content: tab delimited file containing raw count
Supplementary files format and content: tab delimited file containing DeSEQ2 normalized count

source_name: tumor tissue

extract_protocol:
Patient microbiopsies RNA were extracted with RNA easy FFPE kit  (Qiagen)
RNA-Seq library was produced  with Illumina TruSeq® Exome kit (RNA Library Prep for Enrichment & TruSeq® RNA Enrichment) according to the manufacturer (0.1µg of RNA for the library prep).

value: tumor tissue

tag: sample type

value: FFPE


title: A_R_30_BR2


title: a_Y_0_BR1


title: Fibroblasts rep 1

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina, USA) following the manufacturer’s instructions

scan_protocol: After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: Fibroblasts

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)

value: mouse fibroblast

value: Mixture C57BL/6, CD1 and C3H


title: 02-020_C3D1 [R210539]

value: After 1 month of NP137  treatment


title: Fibroblasts rep 2

description: replicate 2


title: A_R_240_BR1


title: A_R_120_BR1


title: Control-NSC rep 2

description: replicate 2

source_name: Control-NSC

value: mouse control Neural Stem Cell (NSC)


title: 02-020_C1D1 [R210538]


title: A_RS_240_BR1

value: Yeast cells


title: A_R_30_BR1


title: 02-015_C3D1 [R190247]

value: frozen sample


title: Control-NSC rep 1

description: replicate 1


title: 02-015_C1D1 [R190245]


title: HIS_DIS_D_LS_Epi [scRNA-Seq]

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

data_processing:
CellRanger version 3.1 (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v4.0).
Seurat R package (version 4.0, https://satijalab.org/seurat/) was used for the single-cell data integration. We first merged single-cell data of samples with the common sequencer and the identical reagent kit version. To harmonize merged groups into a single dataset without batch effects, correspondences between cells in three merged datasets were identified by the FIndIntegrationAnchors function, and used for data integration with the IntegratedData function in Seurat R package.
Principal component analysis and graph-based clustering analysis were performed with Seurat R package (version 4.0, https://satijalab.org/seurat/). Sixty principal components (PCs) were selected for Uniform Manifold Approximation and Projection (UMAP) for Dimension Reduction. With a resolution of 0.8, cells were clustered by the FindClusters function. Then, differentially expressed genes of each cluster compared to all other cells were found by the FindAllMarkers function. Differentially expressed genes between psoriasis and control within each cluster were found by the FindMarkers function. The average gene expression of psoriasis vs. control cells within a cluster was calculated by the AverageExpression function.
Assembly: GRCh38
Supplementary files format and content: barcode table, gene table and gene expression matrix files generated by Cell Ranger version 3.1.

source_name: Hidreadenitis suppurativa lesional skin-Epidermis

extract_protocol:
6 mm punch skin biopsy tissues from human skin were bisected, and one of the two bisected skin tissues was incubated in culture medium for harvesting emigrating cells. Harvested skin tissue was immediately placed in 0.2% Dispase II (Sigma-Aldrich) and incubated in a humidified incubator at 37 Celsius and 5% CO2 for 3 hours. Then, epidermis and dermis were separated with forceps and sliced into small pieces with #10 blade scalpels. Epidermis and dermis were separately cultured in RPMI-1640 medium with L-glutamine (Cytiva) supplemented with 10% human albumin serum (Sigma-Aldrich) and without any enzyme or antibiotic agent in a humidified incubator at 37 Celsius and 5% CO2. Nonplastic adherent cells that had emigrated out of epidermis and dermis were harvested after 48 hours. The harvested cells from epidermis and dermis were filtered through a 40-µm cell strainer (Corning) and stored on ice.
The 10x Genomics Chromium Single Cell 3′ Reagents Kit user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep) was used to prepare the single cell suspension. The appropriate volume of each sample was diluted to recover 10,000 cells. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell chip. After droplet generation, samples were transferred into PCR tubes and we performed reverse transcription using a ProFlex PCR Thermocycler System (Applied Biosystems). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide.

tag: disease

value: Hidradenitis suppurativa

tag: group

value: Lesional

tag: skin anatomy

value: Epidermis

value: Unknown


title: HIS_DIS_D_LS_Der [scRNA-Seq]

source_name: Hidreadenitis suppurativa lesional skin-Dermis

value: Dermis


title: 02-014_C3D1 [R190244]


title: 01-040_C3D1 [R220325]


title: HIS_DIS_02M_LS_Epi [scRNA-Seq]


title: HIS_DIS_B_LS_Total [scRNA-Seq]

source_name: Hidreadenitis suppurativa lesional skin-Epidermis&Dermis

value: Epidermis and Dermis


title: alpNSCs-late rep 2

description: replicate 2

source_name: alpNSCs-late

value: mouse late adult lung (al) peripheral Neural Stem Cell (pNSC)


title: HIS_DIS_A_LS_Total [scRNA-Seq]


title: alpNSCs-late rep 1

description: replicate 1


title: 02-014_C1D1 [R190243]

value: at inclusion


title: HIS_DIS_01M_LS_Der [scRNA-Seq]


title: A_Y_0_BR1

value: wild type


title: 02-013_C3D1 [R190046]

value: tumor tissue


title: Control06 [scRNA-Seq]

source_name: Control skin from a healthy volunteer

value: Control

value: before treatment


title: 02-013_C1D1 [R190044]


title: Control03 [scRNA-Seq]


title: elpNSCs-late rep 2

description: replicate 2

source_name: elpNSCs-late

value: mouse late embryonic limb (el) peripheral Neural Stem Cell (pNSC)

value: Mixture C57BL/6, CD1 and C3H


title: elpNSCs-late rep 1

description: replicate 1


title: alpNSCs-early rep 1

description: replicate 1

source_name: alpNSCs-early

value: mouse early adult lung (al) peripheral Neural Stem Cell (pNSC)


title: alpNSCs-early rep 2

description: replicate 2


title: elpNSCs-early rep 2

description: replicate 2

source_name: elpNSCs-early

value: mouse early embryonic limb (el) peripheral Neural Stem Cell (pNSC)


title: 02-012_C3D1 [R190043]

value: After 1 month of NP137  treatment

value: frozen sample


title: Control02 [scRNA-Seq]


title: HIS_DIS_02M_LS_Der [scRNA-Seq]

value: Hidradenitis suppurativa

value: Lesional


title: elpNSCs-early rep 1

description: replicate 1


title: Psoriasis09_preTx_LS [scRNA-Seq]

source_name: Psoriasis lesional skin before treatment

value: Psoriasis


title: 01-039_C3D1 [R210537]

value: FFPE


title: 02-012_C1D1 [R190042]


title: Psoriasis10_preTx_LS [scRNA-Seq]

value: Epidermis and Dermis


title: 4T1, ARIH1-C355S-5-OE

city: hangzhou

first: liu

last: xiaolan

address: 1369 West Wenyi Road, Hangzhou 311121, China

institute: Zhejiang University Medical Center

data_processing:
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool.
The clean reads obtained were then aligned to the mm10/mouse genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie.
Differentially expressed genes (DEGs) were identified by DEseq2(for sample with replications) with a cut-off value of log2|fold-change|>1 and p-adjust <0.05.
The clusterProfiler was used to perform functional enrichment analysis for the annotated significant DEGs, the potential genes in identified modules ontology (GO) and KEGG pathway based on gene categories. Terms with pvalue<0.05 were considered significant.
Gene set enrichment analysis (GSEA) was performed by the function in package clusterProfiler with a gene list sorted by log2 fold-change.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: 4T1 breast cancer cells were maintained in 1640 (Hyclone, with L-glutamine) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424),which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry.High-quality RNA with a 260/280 absorbance ratio  of 1.8-2.2 was used for library construction and sequencing.
Illumina library construction was performed according to the manufacturer's instructions (Illumina,USA).

treatment_protocol: No special treatment

value: breast cancer cells

tag: genotype

value: ARIH1 C355S overexpression

value: no treatment


title: Psoriasis08_preTx_LS [scRNA-Seq]


title: Control01 [scRNA-Seq]


title: 4T1, ARIH1-WT-6-OE

value: ARIH1 WT overexpression


title: HIS_DIS_01M_LS_Epi [scRNA-Seq]

value: Epidermis

value: Unknown


title: Psoriasis08_postTx_week12_LS [scRNA-Seq]

source_name: Psoriasis lesional skin after treatment

value: after treatment


title: 01-039_C1D1 [R210536]

value: tumor tissue

value: at inclusion


title: Psoriasis07_preTx_NL_02 [scRNA-Seq]

source_name: Psoriasis nonlesional skin before treatment

value: Nonlesional

value: before treatment


title: 4T1, ARIH1-WT-5-OE


title: Masopust_038_B [HTO]

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Department of Microbiology and Immunology

institute: University of Minnesota

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
matrix-B.mtx.gz
features-B.tsv.gz
barcodes-B.tsv.gz

library_source: other

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Demultiplexing, barcode processing, alignment against the mm10–2.1.0 mouse transcriptome, and gene counting were performed using the 10X Genomics Cell Ranger v.7.0.0 software. Antibody reads were mapped to known barcodes.
Cell barcodes and unique molecular identifiers (UMIs) associated with the aligned reads were corrected and filtered. Filtered gene-barcode matrices containing only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.0. Cells with a high percentage of UMIs from mitochondrial genes (> 5% of a cell’s total UMI count) and expressing < 1000 genes were removed. Cells with an RNA library size between 1,000 and 20,000 UMI counts and a protein library size between 100 and 2,500 UMI counts were retained. Contaminating B cells (uniquely expressing high levels of Cd79a and Cd19) and macrophages (uniquely expressing high levels of Csf2ra) were removed. After contaminating cells (non-CD8+ T cells) were removed, T-cell receptor (TCR) genes were removed so they would not influence subsequent analyses. A list of murine TCR genes were downloaded from IMGT (The International ImMunoGeneTics Information website, http://www.imgt.org) and converted to gene symbols with SynGo. The filtered and integrated Seurat object was converted to an AnnData object for analyses with totalVI (Total Variational Inference) and scVI-tools (single- cell Variational Inference tools).
Assembly: mm10-2.1.0
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: EO771-ova tumor, mammary fat pad, spleen

growth_protocol: P14 immune chimeras were generated by transferring 5 x 10^4 naïve CD45.2+/Thy1.1+ P14 CD8+ T cells from female mice into 6–8-week-old B6 female mice. One day after cell transfer, mice were infected intraperitoneally with 2 x 10^5 PFU of the Armstrong strain of lymphocytic choriomeningitis virus (LCMV-Arm). >30 days after LCMV infection, 5 x 10^4 naïve CD45.1+/Thy1.2+ OT-I CD8+ T cells from female mice were transferred 1 day prior to tumor implantation. For tumor implantation, 1 x 10^6 EO771.ova cells were resuspended in 1:1 FBS:Matrigel and injected orthotopically into the 4th mammary fat pad of 12-15 week-old nulliparous female B6 mice. Tissues were harvested at 29 days post-implantation.

extract_protocol:
Spleens were prepared through physical dissociation. Red blood cells in spleen samples were lysed using Ammonium-Potassium-Chloride lysis buffer (155mM ammonium, 1mM K+, 155mM Cl-, 0.1mM EDTA) lysis buffer, 2 minutes at room temperature. Mammary fat pad and EO771 tumors were digested in 1mg/mL collagenase IV (C6885, Sigma-Aldrich), 10% FBS, 0.5mM MgCl2, 0.5mM CaCl2, 1mM HEPES, 2μM L-glutamine, RPMI solution for 30 minutes in a shaking 37oC incubator prior to processing in gentleMACS C tubes and dissociator. MFP and tumor suspensions were subsequently separated on a 44:67 Percoll® (17-081-09, Cytiva) gradient. Suspensions were stained with Live/Dead dye (Ghost-Dye 780, Tonbo), fluorescent-conjugated antibodies (CD8a (53-6.7), CD44 (IM7), Thy1.1 (HIS51), CD45.1 (A20), Thy1.2 (30-H12)), and oligonucleotide-conjugated Biolegend TotalSeqTM A antibodies (1 hour, room temperature). P14 (Live, CD8a+, Thy1.1+), OT-I (Live, CD8a+, CD45.1+), and endogenous polyclonal CD8+ (Live, CD8a+, CD44+, Thy1.1-, CD45.1-) T cells were sorted using a FACS Aria II (BD Biosciences).
The CITE-seq experiment was performed following “BioLegend’s TotalSeqTM-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 or v3.1 (Single Index) Protocol”. Briefly, the cell suspension was loaded onto a 10X Genomics Chromium Controller at a concentration of 1,400 cells per microliter to target ~60,000 cells per two technical replicates. The single cells, reagents, and 10X Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs) and then reverse transcription of poly-adenylated mRNA was performed inside each droplet. The 10X Genomics Chromium Single Cell 3′ v3.1 dual index protocol was used to prepare RNA. The Biolegend Protocol was used to prepare the hashtag-derived-tag (HDT) and antibody-derived-tag (ADT) libraries.
50,000 or 10,000 sequencing reads per cell for scRNA-seq or ADT&HDT libraries, respectively, were generated on the Illumina NovaSeq S4 flow cell.

value: CD8+ T cell

tag: library type

value: HTO

tag: antibodies/tags

value: MHC H-2 + CD45 -- Spleen:TotalSeq-A0311, MFP:TotalSeq-A0312, Tumor:TotalSeq-A0313


title: Control04 [scRNA-Seq]

value: Control


title: Control05 [scRNA-Seq]


title: 4T1, ARIH1-C355S-4-OE


title: Psoriasis07_preTx_LS_02 [scRNA-Seq]

value: Psoriasis

value: Lesional


title: 01-034_C3D1 [R210532]

value: After 1 month of NP137  treatment

value: FFPE


title: Psoriasis07_preTx_LS [scRNA-Seq]

value: Epidermis and Dermis


title: 01-034_C1D1 [R210531]


title: Psoriasis08_postTx_week24_LS [scRNA-Seq]


title: Psoriasis07_postTx_week48_LS [scRNA-Seq]


title: Psoriasis07_postTx_week12_LS [scRNA-Seq]


title: 01-032_C3D1 [R190379]

value: frozen sample


title: 01-032_C1D1 [R190377]


title: Psoriasis05_preTx_LS [scRNA-Seq]


title: Masopust_038_A [ADT]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
matrix-A.mtx.gz
features-A.tsv.gz
barcodes-A.tsv.gz

value: EO771-ova tumor, mammary fat pad, spleen

value: ADT

value: CD103/TotalSeq-A0201, CD127/TotalSeq-A0198, CD279/TotalSeq-A0004, CD38/TotalSeq-A0557, CD39/TotalSeq-A0834, CD45.1/TotalSeq-A0178, CD49a/TotalSeq-A0850, CD62L/TotalSeq-A0112, CD69/TotalSeq-A0197, CX3CR1/TotalSeq-A0563, CXCR6/TotalSeq-A0926, KLRG1/TotalSeq-A0250, Ly108/TotalSeq-A0930, Ly6C/TotalSeq-A0013


title: Psoriasis04_preTx_LS [scRNA-Seq]


title: Psoriasis05_postTx_week12_LS [scRNA-Seq]

value: after treatment


title: Masopust_038_A [HTO]

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
matrix-A.mtx.gz
features-A.tsv.gz
barcodes-A.tsv.gz


title: Psoriasis03_preTx_LS [scRNA-Seq]


title: Masopust_038_A [mRNA]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
matrix-A.mtx.gz
features-A.tsv.gz
barcodes-A.tsv.gz

value: mRNA


title: Psoriasis02_preTx_LS [scRNA-Seq]


title: Psoriasis04_postTx_week12_LS [scRNA-Seq]


title: 01-030_C3D1 [R190240]

value: tumor tissue


title: Psoriasis01_preTx_LS [scRNA-Seq]

value: before treatment


title: 01-028_C3D1 [R190047]


title: TLE_HS_5 (Ago iCLIP)

description: Temporal lobe epilepsy with hippocampal sclerosis 5

data_processing:
Preprocessing: The iCLIP data was adapter trimmed, demultiplexed and quality filtered. Then identical reads were collapsed to remove PCR bias. UMI was then removed
Reads were mapped to the human genome using Bowtie2 with soft-clipping enabled. Uniquely mapping reads were used for further steps. Crosslinking sites in the human genome were found, with the assumption that sequencing reads start exactly one position downstream of the crosslinked nucleotide.
According to the genomic sequence 10 bp was added to each side of crosslinking sites and CLIPper was used to detect significant iCLIP peaks
miRNAs sequenced in the iCLIP data were quantified by mapping with Bowtie2 with soft-clipping enabled to mature human miRNAs from miRBase v22.
7mer and 8mer seeds from miRNAs detected in the iCLIP data were matched to significant iCLIP peaks in decending order of miRNA expression. Only one miRNA seed match was permitted in each iCLIP peak
Assembly: GRCh38 (hg38)
Supplementary files format and content: Table in excel format showing: chromosomal location of miRNA target site, the exact type of miRNA seed that binds the region, the miRNA found to bind, FDR of the iCLIP peak, overlap with gene 3'UTR, 5'UTR, CDS, antisense overlap with any gene, overlap with lncRNA or circRNA, overlap with TargetScan predicted miRNA target sites, total number of iCLIP reads used to form iCLIP peak, the number of iCLIP reads used to form iCLIP peak from each individuel sample.
Library strategy: Ago iCLIP

source_name: Hippocampus

extract_protocol:
Hippocampal tissue is triturated and crosslinked by 254 nm UV. Then cells are lysed and partially digested with RNase I. Ago immuno-precipitation is performed on the cell lysate with antibody coupled to Protein A dynabeads. RNA, still attached to antibody, is 3’ linker ligated and 5’ end labeled with 32P-γ-ATP. RNA is eluted from the beads, run on SDS-PAGE and transferred to a nitro-cellulose membrane where the Ago-RNA bands are cut out and treated with Proteinase K to remove Ago protein.
After RNA purification, RT-PCR and gel purification, the RNA is circularized by use of the CircLigase II enzyme. BamHI digestion lineralizes the RNA and after PCR amplification, the finished Ago iCLIP library is formed.

tag: disease state

value: temporal lobe epilepsy (TLE)

value: Hippocampus

tag: tissue type

value: sclerotic


title: TLE_HS_4 (Ago iCLIP)

description: Temporal lobe epilepsy with hippocampal sclerosis 4

tag: tissue


title: 01-028_C1D1 [R190045]

value: at inclusion


title: Microglia_iC3b_scRNAseq_rep2

city: San Francisco, CA

first: Katerina

last: akassoglou

address: 1650 Owens st

institute: Gladstone Institutes

description: 10X Genomics

data_processing:
Samples were demultiplexed and fastq files were used to align reads to the mm10 reference assembly (downloaded 2019) and aggregated using Cellranger count and Aggr packages (10x Genomics).
The R toolkit Seurat was used for QC, clustering analysis, and differential gene expression analysis of scRNA-seq data and performed in R v.4.0.2 unless otherwise stated. For scRNA-seq data visualizations, dittoseq package v1 was used to produce UMAPs, dot plots, and violin plots.
For BMDM scRNA-seq analysis, two independent experiments were integrated together and corrected for batch effect. Batch-corrected dataset QC parameters were: nFeature_RNA > 200; nFeature_RNA < 5000; < 5% and 25% mitochondrial and ribosomal genes, respectively. 17,625 QC-passed BMDMs were used with seurat integration workflow using default parameters. Jackstraw was performed with num.replicate of 100. RunUMAP, FindNeighbors and FindClusters functions were used with the first 20 significant PCs and a resolution of 0.5. DEGs were determined by FindAllMarkers with default parameters. Genes that met log2fc.threshold,0.25 with adjusted P value < 0.05 (Benjamini-Hochberg correction) were used for downstream analysis
For microglia scRNA-seq analysis, QC parameters were: nFeature_RNA > 1000; nFeature_RNA < 5500; < 5% and 20% mitochondrial and ribosomal genes, respectively. nCount_RNA in the 93rd percentile (nCount_RNA < 26,206) were used for downstream analysis. Data were normalized, scaled, and percent of mitochondrial and cell cycle genes regressed out following Seurat SCTransform. Jackstraw was performed with num.replicate of 100. FindNeighbors and FindClusters functions in seurat were used with the first 8 significant PCs and a resolution of 0.4 resolution, respectively. 16,186 microglial cells passed QC with an average of 3,469 genes per cell with 20,228 genes. Cluster DEGs were determined by FindAllMarkers with default parameters. Genes that met log2fc.threshold > 0.25 with adjusted P value < 0.05 (Benjamini-Hochberg correction) were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: tsv files containing barcodes, features, matrix

source_name: neonatal brain

extract_protocol:
Following stimulation, adherent cells were lifted with accutase (StemCell Technologies), viable cells were counted by trypan blue method, then resuspended in RPMI with 5% FBS and used for scRNA-seq.
For scRNA-seq library preparation, BMDMs or primary microglia were processed with Chromium Single Cell 3’ v2 kit according to manufactures guidelines (10x Genomics).
Libraries were balanced to achieve a minimum of 75,000 reads per cell and run on a NovaSeq 6000 (Illumnia) at 150 paired-end reads.

treatment_protocol: Fibrin-coated 24-well culture plates (Corning) were prepared Mendiola et al Nat Immunol 2020. 10 mg mL-1 iC3b (CompTech; A115) in HEPES pH 7.2 buffer was immobilized on culture plates by 1 hr incubation at 37°C followed by overnight incubation in a 37°C humified chamber to dry. For fibrin or iC3b stimulation, BMDMs or primary microglia were seeded into fibrin- or iC3b-coated wells at 5.0 x 105 cells mL-1. Control wells were treated with the same buffer void of fibrin or iC3b. For LPS stimulation, BMDMs or microglia were seeded into 24-well tissue culture treated plates at 5.0 x 10^5 cells mL-1, allowed to adhere overnight, then treated with 100 ng mL-1 LPS (Sigma-Aldrich, O55:B5)

value: neonatal brain

tag: batch number

value: microglia

value: C57Bl/6 wild type

value: 6h iC3b


title: Masopust_038_B [ADT]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
matrix-B.mtx.gz
features-B.tsv.gz
barcodes-B.tsv.gz

value: CD8+ T cell


title: Microglia_iC3b_scRNAseq_rep1

description: 10X Genomics


title: TLE_HS_3 (Ago iCLIP)

description: Temporal lobe epilepsy with hippocampal sclerosis 3


title: Masopust_038_B [mRNA]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
matrix-B.mtx.gz
features-B.tsv.gz
barcodes-B.tsv.gz


title: 01-024_C3D1 [R180368]

source_name: tumor tissue

value: After 1 month of NP137  treatment

value: frozen sample


title: TLE_HS_2 (Ago iCLIP)

description: Temporal lobe epilepsy with hippocampal sclerosis 2


title: Microglia_Fibrin_scRNAseq_rep2

description: 10X Genomics

value: 6h Fibrin


title: Psoriasis06_preTx_LS [scRNA-Seq]

value: Psoriasis

value: Lesional

value: Epidermis and Dermis


title: TLE_HS_1 (Ago iCLIP)

description: Temporal lobe epilepsy with hippocampal sclerosis 1


title: Microglia_Fibrin_scRNAseq_rep1

description: 10X Genomics


title: 01-024_C1D1 [R180367]

value: tumor tissue


title: TLE_nonHS_3 (Ago iCLIP)

description: Temporal lobe epilepsy without hippocampal sclerosis 3

value: nonsclerotic


title: TLE_nonHS_2 (Ago iCLIP)

description: Temporal lobe epilepsy without hippocampal sclerosis 2

value: temporal lobe epilepsy (TLE)


title: 01-030_C1D1 [R190239]


title: TLE_nonHS_1 (Ago iCLIP)

description: Temporal lobe epilepsy without hippocampal sclerosis 1

value: Hippocampus


title: TLE_HS_6 (Ago iCLIP)

description: Temporal lobe epilepsy with hippocampal sclerosis 6

value: sclerotic


title: Control10 [scRNA-Seq]

value: Control

value: before treatment


title: Control09 [scRNA-Seq]


title: Microglia_LPS_scRNAseq_rep2

description: 10X Genomics

value: neonatal brain

value: microglia

value: 2h LPS


title: Microglia_LPS_scRNAseq_rep1

description: 10X Genomics

value: C57Bl/6 wild type


title: in vitro 3M (D6)

city: Seattle

first: Charles

middle: E

last: Murry

state: WA

address: 850 Republican Street

department: Pathology

institute: University of Washington

description:
3m_invitro_rep_2
hPSC-CMs analyzed at day 140 of differentiation

data_processing:
a hybrid of human (hg38) and rat genome (Rnor_6.0) was constructed
reads were mapped to either human (for the hPSC-CMs) only or to the human-rat hybrid genome using STAR program (2.5.3a)
the STAR output were name-sorted using samtools sort
A customized python scripts were used to separate human from the rat reads and only the reads uniquely mapped to human genome were used for downstream analysis
Cufflinks was used to quantify reads and FPKM were calculated for genes
Genome_build: a hybrid of human  (hg38) and rat (Rnor_6.0) genome
Supplementary_files_format_and_content: FPKM table

source_name: 253G1-GCaMP3 human PSC-cardiomyocytes

growth_protocol: 253G1-GCaMP3 hPSC-CMs were differentiated as previously described  (Kadota et al, Stem Cell Reports, 2017, PMID:28065644), and cultured in RPMI-1640 supplemented with B-27 until different time points after differentiation

extract_protocol:
Laser capture technique was used to localize the grafts in the rat heart slices
SMART-Seq v4 Ultra Low Input RNA kit for sequencing was used to establish library from the heart slices and Nextera XT DNA library preparation kit was used for library construction for the hPSC-CMs

treatment_protocol: 253G1-GCaMP3 hPSC-CMs were cultured in vitro for different period and some were transplanted into infarct rat hearts and harvested at different time points after transplantation

value: hPSC-derived cardiomyocytes

tag: time

value: day 140 of differentiation


title: BMDM_unstim_batch2_scRNAseq_rep4

description: 10X Genomics

source_name: bone marrow

value: bone marrow

value: BMDM

value: unstimulated


title: Control08 [scRNA-Seq]

value: Epidermis and Dermis


title: Control07 [scRNA-Seq]


title: in vitro 3M (A5)

description:
3m_invitro_rep_1
hPSC-CMs analyzed at day 140 of differentiation


title: Microglia_unstim_scRNAseq_rep1

description: 10X Genomics


title: in vitro 2W (D5)

description:
2w_invitro_rep_2
hPSC-CMs analyzed at day 34 of differentiation

value: day 34 of differentiation


title: in vitro D0 (A3)

description:
D0_in vitro_rep_1
hPSC-CMs analyzed at day 20 of differentiation

value: day 20 of differentiation


title: in vitro 1Y (A6)

description:
1y_invitro_rep_1
hPSC-CMs analyzed at one year after differentiation

value: one year after differentiation


title: BMDM_unstim_batch2_scRNAseq_rep3

description: 10X Genomics


title: Microglia from anti-CTLA4 treated sample 1

city: La Jolla

first: Kathryn

last: Lande

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

data_processing:
RNA sequencing was performed using the Illumina HiSeq 2500 platform on 51-bp single-end libraries prepared using the IlluminaTruSeq RNA sample preparation kit.
Reads were mapped and aligned using STAR to the Mus musculus genome mm10. Reads were quantified and normalized using HOMER to generate raw counts and fragments per kilobase of exon per million mapped fragments (FPKM).
Resulting FPKM values were processed by DESeq2 package to perform statistical analysis (Log2Fold change and p value). To identify enriched pathways, Gene Set Enrichment Analysis (GSEA) was performed using fgsea package on differentially expressed genes with L2FC>1.5 and p value<0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Glioma brain

extract_protocol:
Microglia (CD45intCX3CR1+) were sorted from the glioma bearing mice in different treatment  groups (IgG vs. αCTLA-4 vs. αCTLA-4+αCD4). Total RNA was isolated using Trizol–Qiagen  RNAeasy Micro kit and sent to Salk next generation sequencing core for ultra-low input RNA-Seq  cDNA library preparation and sequencing run on Illumina Hiseq2500.
cDNA library preparation

tag: strain

value: Glioma brain


title: BMDM_fibrin_batch2_scRNAseq_rep2

description: 10X Genomics

value: 6h Fibrin


title: in vitro 2W (A4)

description:
2w_invitro_rep_1
hPSC-CMs analyzed at day 34 of differentiation


title: BMDM_fibrin_batch2_scRNAseq_rep3

description: 10X Genomics


title: CSF, sample 48

city: Providence

first: Zachary

last: Levin

state: RI

address: 185 Meeting Street

institute: Brown University

data_processing:
Illumina adapter sequences removed by Trim Galore! (version 0.5.0) and QC performed using FastQC (version 0.11.5).
Reads were aligned with HiSat2 (version 2.1.0).
Samtools (version 1.9) view and sort commands were used to convert sam files to bam files.
Alignments were assembled into transcripts using StringTie (version 1.3.4) according to the differential expression workflow in StringTie manual.
Coverage tables were converted to read counts using tximport (version 1.22.0) for analysis using DESeq2 (version 1.34.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing matrix of raw read counts of genes (rows) for each sample (columns).

source_name: CSF

extract_protocol:
CSF was centrifuged at 2000 g for 20 minutes at room temperature and stored at -80°C. 10 mL frozen aliquots were thawed on ice and diluted 1:1 in PBS. Extracellular vesicles were isolated by ultracentrifugation at 100,000 g for 70 minutes at 4°C, resuspended in 100 µL of PBS supplemented with 1% DMSO, and stored at -80°C. RNA was extracted using the miRNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, ID: 217084).
cDNA was prepared according to a standard protocol for Illumina RNA sequencing.

treatment_protocol: CSF was centrifuged at 1500 relative centrifugal force (RCF) for 10 minutes at 4°C to remove debris. Supernatant was collected, flash frozen in liquid nitrogen, and stored at -80°C.

value: CSF


title: Microglia from anti-CTLA4 treated sample 2


title: Microglia from IgG treated sample 2

value: IgG


title: CSF, sample 47


title: in vitro 1Y (D7)

description:
1y_invitro_rep_2
hPSC-CMs analyzed at one year after differentiation


title: Microglia from IgG treated sample 1


title: CSF, sample 45


title: Microglia from CD4 depletion + anti-CTLA4 treated sample 3

value: CD4 depletion + anti-CTLA4


title: BMDM_fibrin_batch1_scRNAseq_rep1

description: 10X Genomics


title: Microglia from CD4 depletion + anti-CTLA4 treated sample 2


title: CSF, sample 44


title: BMDM_iC3b_batch1_scRNAseq_rep1

description: 10X Genomics

value: 6h iC3b


title: C2C12 wt cells, Dplate, biol rep 2

city: Pasadena

first: Rachael

last: Kuintzle

address: 391 S Holliston Ave, Bio 73, MC 140-18

department: Chemistry and Chemical Engineering

institute: California Institute Of Technology

data_processing:
TrimGalore was used to run Cutadapt to trim low-quality ends (with -q 28), to remove adapters, and to clip 3 bp from the 3' ends of reads after adapter/quality trimming, as well as to run FastQC for quality assessment.
Reads were aligned to the Mouse Dec. 2011 (GRCm38/mm10) genome using HISAT2 with default parameters.
Transcript abundances were computed with StringTie using the GENCODE annotation of the mouse genome (GRCm38), version M22 (Ensembl 97), downloaded 2019-06-27.
Assembly: mm10
Supplementary files format and content: tab-delimited text files (.gtf) include FPKM values for each Sample

growth_protocol: C2C12 cells were cultured at ≤ 90% confluency in DMEM with high glucose, no glutamine (Thermo Fisher Scientific) supplemented with 20% FBS, 1X Pen/Strep/L-glutamine, and 1X Sodium Pyruvate at 37 degrees C and 5% CO2.

extract_protocol:
For RT-PCR analysis, total RNA from cell lines was extracted using the RNeasy Mini Kit (Qiagen) following cell-lysate homogenization via QIAshredder column.
mRNA was isolated using polyA selection and converted into sequencing libraries using the NEBNext Ultra II RNA Library Prep Kit following the manufacturer's protocols.

treatment_protocol:
Notch gene-depleted C2C12 cells (C2C12-Nkd clone) were plated at 80k cells/well in a 12-well plated treated with recombinant ligand (2µg/mL Dll1-ext-Fc in PBS) or PBS only (negative control) in 10 µM DAPT (Notch signaling inhibitor).
Cells were allowed to plate down overnight, and DAPT was washed out the next morning. Cells were harvested for RNA extraction 6 hours after DAPT washout.
Wild type C2C12 cells were also plated on Dll1-ext-Fc as described above to compare the response of Notch target genes in the Notch-depleted C2C12-Nkd cell line vs. wild type.

value: myoblasts

value: WT

value: Dplate (cells culture on recombinant Dll1-ext-Fc)

value: Day 0


title: Microglia from CD4 depletion + anti-CTLA4 treated sample 1


title: C2C12-Nkd cells, no Dplate, biol rep 1

value: Nkd

value: No Dplate treatment


title: CSF, sample 43


title: C2C12 wt cells, Dplate, biol rep 1


title: CSF, sample 41


title: CSF, sample 42


title: in vitro D0 (D4)

description:
D0_in vitro_rep_2
hPSC-CMs analyzed at day 20 of differentiation

value: hPSC-derived cardiomyocytes


title: C2C12-Nkd cells, Dplate, biol rep 2


title: Sus-T_wT_4_PFC

city: Rome

first: Daniela

last: Laricchiuta

state: Rome

address: Via del fosso di fiorano, 64

department: Preclinical neuroscience

institute: IRCCS Fondazione Santa Lucia

data_processing:
For the processing of raw data (format conversion and de-multiplexing), Bcl2Fastq 2.20 version of the Illumina pipeline was used.
GRCm38.p6 genome was used to map the reads, and transcript abundances were estimated using Salmon v1.2
To obtain gene-level count matrices the quantification data were imported using tximport.
From here on, we separated the samples in four tables (one for each comparison, namely Res-T vs Sus-T woT; Res-T vs Sus-T wT; woT vs wT Sus-T; woT vs wT Res-T)  due to the following preprocessing strategies being dependent on the design matrix in use.
Differences in RNA composition between samples were corrected by the Trimmed mean of M-values (TMM) normalization (Robinson and Oshlack, 2010), and filtered for low counts based on a count per million reads (CPM) criteria.
Subsequently, ARSyNseq was used to remove the technical batch effect and NOISeqBIO was used to assess differential gene expression (q>0.95, equivalent to FDR-corrected P<0.05)
Assembly: GRCm38.p6
Supplementary files format and content: Matrix table with preprocessed gene counts for every gene and every sample

source_name: Medial Prefrontal Cortex

extract_protocol:
Amygdalae were punched and manual and enzymatic dissociations were performed using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, Bergisch Gladbach, Germany). Pyramidal neurons were then sorted by using the MoFlo Astrios EQ (Beckman Coulter, California, USA) into ice-cold lysis buffer (Reliaprep RNA Cell Miniprep System, Promega, Wisconsin, USA) and then stored at -80°C until RNA extraction.
RNA were prepared using the Ovation SoLo RNA-seq kit for Ultra-low input, with Ribosomal RNA removal, for Illumina PE sequencing

value: Pyramidal neurons

value: B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP)

value: Sus-T

tag: condition

value: with trauma


title: Sus-T_wT_3_PFC


title: BMDM_LPS_batch1_scRNAseq_rep1

description: 10X Genomics

value: bone marrow

value: BMDM

value: C57Bl/6 wild type

value: 6h LPS


title: CSF, sample 40

value: CSF


title: BMDM_LPS_batch1_scRNAseq_rep2

description: 10X Genomics


title: CSF, sample 39


title: C2C12-Nkd cells, Dplate, biol rep 1

tag: cell line


title: Sus-T_wT_1_PFC


title: Sus-T_wT_2_PFC


title: BMDM_unstim_batch1_scRNAseq_rep2

description: 10X Genomics

tag: treatment

value: unstimulated