title: S1P4 KO, vehicle control, replicate 4

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
FastQC software was used to verify signal quality, adaptor content and duplication rate. After adapter removal and data trimming by Trimmomatic version 0.38, reads of a length between 30-150bp were accepted for further analysis.
Trimmed reads were aligned to the murine mm10 genome (Ensembl) with Star 2.7.3a. The maximum ratio of mismatches to mapped length accepted was 10% and reads matching multiple genes or different genomic regions were excluded
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using pairwise comparisons with DESeq2 version 1.26.0.
Genome_build: mm10
Supplementary_files_format_and_content: library size normalized counts

source_name: mouse brain microvascular endothelial cells

growth_protocol: Mouse brain microvascular endothelial cells (MBMECs) were isolated as described previously (Gurnik et al., 2016). In short, after the removal of olfactory lobes, brain stem, cerebellum and meninges, brains were stored on ice in buffer A (buffer A: 15mM HEPES, 153mM NaCl, 5.6mM KCl, 1.7mM CaCl2, 1.2mM MgCl2 and 1% BSA, pH 7.4). Multiple mouse brains were pooled and subsequently homogenized at 2000rpm with the help of a dounce homogenizer as described above. The homogenate was digested with 0,75% Collagenase Type II (Worthington, Troisdorf, Germany) in buffer A (1:1:1 v/v/v, ca. 3000U Collagenase II per brain) on a thermo rocker for 1h at 37°C, 600rpm. Myelin was removed via density gradient centrifugation with 25% BSA for 35min at 2000xg and the remaining cell & vessel pellet was digested in buffer A with collagenase/dispase (Roche, Taufkirchen, Germany; 0.1U Collagenase and 0.8U dispase per mouse brain) and DNase I (Worthington, 2U DNase per brain) in buffer A on a thermo rocker for 20min at 37°C, 600rpm. The cell suspension was centifuged (400g, 4min, RT) and the pellet was resuspended in MCDBcomplete medium. MBMECs were seeded in in 6-well plates (2 wells per 5 mouse brains). EC extravasation from microvessels and attachment to plate or flask surfaces was allowed for 12h in MCDBcomplete before the medium was changed to MCDBpuromycin for 48h to remove non-endothelial cell types.

extract_protocol:
MBMECs were harvested directly from transwell inserts in 350μl RLTplus lysis buffer (3 inserts/condition/350μl RLTplus). RNA was isolated using an RNeasy Plus Microkit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Genomic DNA contaminants were digested on microkit columns during RNA isolation. RNA concentrations were measured via QuBit 4 fluorometer (ThermoFisher Scientific, Schwerte, Germany). For RNA sequencing, RNA was frozen immediately after isolation and stored at -80°C until its transfer to the sequencing facility.
mRNA library preparation with equal amounts of RNA from each sample (100ng) was achieved with VAHTS Stranded mRNA-seq Library preparation kit (Vazyme) following manufacture’s protocol.

treatment_protocol: MBMECs were seeded on 24well-transwell inserts immediately after puromycin treatment. Upon barrier completion (48h post-seeding), MBMECs were treated either from the apical compartment side or from the basolateral compartment side with Restimulation medium (MCDB131 glutamine-free (GIBCO) supplemented with 1% fatty-acid-free BSA, 1% glutamine solution 200mM and 1% penicillin/streptomycin) containing either 50nM Sphingosine-1-phosphate (Tocris, Bristol, UK) , 500nM S1P4 agonist CYM50260 (Tocris) or the respective vehicle control. 24h after pharmacological treatment, transwell inserts were placed on ice, medium was removed and RNA isolation was performed.

tag: mouse strain

value: S1P4 KO/KO

tag: vessel type

value: cortex/midbrain microvessel

value: vehicle control

tag: endothelial purity

value: pure primary MBMEC (48h puromycin)


title: S1P4 KO, vehicle control, replicate 3

status: Public on Oct 04 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: treatment


title: APC+/+;BMAL1-/- CT24 (S52)

city: Windsor

first: Phillip

last: Karpowicz

state: Ontario

address: 401 Sunset Ave

department: Biomedical Sciences

country: Canada

institute: University of Windsor

description:
Karpowicz_Windsor_82_052_S52
collected 24h post synchronization

data_processing:
Raw transcriptome sequencing reads were aligned against GRCm38 and Ensembl release 96 transcript annotations using STAR v2.5 (Dobin et al., 2013)
RSEM v1.3.0 (Li and Dewey, 2011, BMC Bioinformatics) was used for transcript quantification.
low quality samples were removed and Transrcipts Per Million (TPM) for remaining samples were merged into one file
Quantile normalization was performed for each expression table using preprocessCore package. Genes with null expression in at least one sample within an expression table were removed from that table
rhythmic analysis was performed using MetaCycle2d, base expression >0.5, relative amplitude >0.05, BH q-value <0.1
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-separated values tables, identified with 'star_rsem_allgenes', report the TPM values for all genes in each genotype, obtained after STAR alignment and RSEM quantification.
Supplementary_files_format_and_content: comma-separated values tables, identified with 'quant-norm_filtered_CT-header', contain the data after quantile normalization and removal of null-expressing genes in each genotype. Sample (column) names were replaced by the corresponding time post synchronization (CT)
Supplementary_files_format_and_content: STAR alignment stats

source_name: Primary Derived

growth_protocol: 2 organoids lines (biological replicates) per genotype  were grown in ENR or EN media (the second for APCmin genotypes).

extract_protocol:
RNA was extracted using the Qiagen Rneasy mini Purification Kit (Cat# 74105)
Libraries were prepared using 96 NEB - NEBNext Ultra II Directional RNA Library Prep Kit including quality control and DNase treatment (#E7765, New England Biolabs Inc). Sequencing was done on a 1 Flowcell, Illumina NovaSeq6000 (Illumina), S2, 100 Cycles, v1 chemistry Read 1: 101bp, Index Read 1: 8bp, Index Read 2: 8bp
Each library was sequenced in two separate lanes, which generated 2 fastq files for each sample

treatment_protocol: each organoid line (n=8) were treated with 0.1µm dexamethasone for 1h. Dexamethasone replaced with  fresh media. Samples were collected every 2h from 24-48h post synchroniztion

tag: cell type

value: Intestinal Organoids

tag: clock function

value: Circadian Clock Mutant

tag: strain

tag: genotype

tag: time

tag: synchronization

value: 1h 0.1µm Dexamethasone


title: APC+/+;BMAL1-/- CT28 (S59)

description:
Karpowicz_Windsor_89_059_S59
collected 28h post synchronization


title: APC+/+;BMAL1-/- CT24 (S51)

description:
Karpowicz_Windsor_81_051_S51
collected 24h post synchronization


title: KU cytoDNA rep2

city: Hong Kong

first: Danny

last: Leung

address: Clear Water Bay

country: Hong Kong

institute: Hong Kong University of Science and Technology

library_source: genomic

data_processing:
library strategy: CytoDNA-seq
Reads quality trimmed using Trim Galore
Bowtie alignment to mm10
CytoDNA regions were defined by 100bp bins with RPKM over 10x that of the genome average
Bins in blacklist regions or chromatin immunoprecipitation input peaks were removed
Bins that were within 100 base pairs were merged
Genome_build: mm10
Supplementary_files_format_and_content: bed

molecule: genomic DNA

source_name: KU cytoDNA

growth_protocol: A mixed glial cell population was obtained from P5 pups and was cultured for two weeks in T75 flasks with DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (10,000 U/mL; Thermo Fisher Scientific). An enriched microglial cell preparation was obtained by shaking the flasks at 37 °C for 2 hours. Microglia were plated on poly-L-lysine-coated glass coverslips at a final density of 50,000 cells per well in a 24-well plate or 200,000 cells per well in poly-L-lysine coated 6-well plates and grown for 24 hours. The purity of the microglial cultures was assessed using immunostaining for the microglia specific marker, Iba1. Cultures with over 90% Iba1 positive cells were used for further experiments. For all experiments, the medium was changed to serum free media 12 hours before any treatment.

extract_protocol:
Primary cultured microglia were lysed in a lysis buffer containing 10 mM HEPES (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% (v/v) glycerol, 0.1% (v/v) Triton X-100 plus protease inhibitors for 5 min on ice. Cell nuclei were removed by low-speed centrifugation (1500 g, 10 minutes). Cytoplasmic extracts were treated with 1 mg/ml Proteinase K at 56 °C for 2 hours. The aqueous supernatant was incubated with 500 mg/ml DNase-free RNase A (QIAGEN) for 30 minutes at 37 °C and followed by phenol/chloroform extraction. The DNA-containing aqueous phase was precipitated and resuspended in TE buffer. DNA concentrations were adjusted according to the protein concentration of cytoplasmic fractions and analyzed on a 2% agarose gel infused with ethidium bromide. The DNA concentrations were determined by Qubit Assays on a Qubit 4 Fluorometer.
CytoDNA sequencing was performed on two biological replicates. Library preparation for cytoplasmic DNA was performed according to the KAPA Hyper Prep Kit (KR0961 – v6.17, KAPA biosystems) protocol, omitting the library amplification step to avoid sequence enrichment bias. The cytoplasmic DNA library was then analyzed on the Advanced Analytical Technologies Fragment Analyzer Automated CE System using an Agilent HS NGS Fragment Kit (Part # DNF- 474-0500), and size selected using AMPure XP beads (Beckman Coulter) for fragment sizes between 200-700 base pairs.

treatment_protocol: Cultured microglia cells were incubate in DMEM containing 1 µM KU-60019  for 48 hours

value: Cultured microglia from postnatal day 5 mice

value: KU-60019 treatment for 48 hours

tag: molecule subtype

value: cytoplasmic DNA


title: KU cytoDNA rep1


title: APC+/+;BMAL1-/- CT26 (S56)

description:
Karpowicz_Windsor_86_056_S56
collected 26h post synchronization


title: S1P4 KO, vehicle control, replicate 1


title: wild-type spleen, day 5, Seq-Well plate 3

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

country: USA

institute: University of Massachusetts Medical School

description:
SpWT5-3
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz

data_processing:
Convert paired-end reads to single-ended, extracting the 12-base cell barcode and 8-base unique molecule identifier (UMI) from R1 read and appending them to the R2 read name as a colon-separated pair. Reads with Ns in either the cell barcode or UMI are discarded. (custom Python script)
Align reads to rat rn6 genome, with RefSeq gene annotations. (tophat2 v2.0.12)
Quantify transcript counts using RefSeq rn6 gene annotations. (ESAT v1.0, https://github.com/garber-lab/ESAT)
Build t-SNE map of all cells (custom R script, using the dim_reduce() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Density-based clustering (custom R script, using the cluster_sc() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Cell type identification (custom R script based on density-based cluster boundaries and known marker genes to identify major cell types)
Viral transcript counting - NCBI magic-blast (https://ncbi.github.io/magicblast/) of all transcript sequence reads against the KRV virus genome (U79033.1), followed by a custom Python script to quantify the number of unique viral transcripts in each cell, using UMIs to remove PCR duplicates.
Genome_build: rn6
Supplementary_files_format_and_content: Ifnar_KO_exp_rawCounts.txt.gz: raw transcript counts from ESAT, 12889 genes x 4765 cell transcript counts matrix
Supplementary_files_format_and_content: Ifnar_KO_exp_phenotype.txt.gz: per-cell phenotype information, 4765 cell x 6 column cell phenotype information. Columns: sample (sample ID), plate (Seq-Well plate ID, 5 for each sample), tSNE1, tSNE2 (t-SNE mapping coordinates), cellType (assigned cell type), KRV (KRV virus transcript count)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: spleen

extract_protocol: Seq-Well S^3 Master Protocol (June 2019) (http://shaleklab.com/wp-content/uploads/2019/07/SeqWell-S3-Protocol.pdf)

value: Wild-type

tag: days post infection


title: WT, S1P basal, replicate 3

value: S1P basal


title: wild-type spleen, day 5, Seq-Well plate 1

description:
SpWT5-1
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: APCmin/-;BMAL1+/+ CT46 (S48)

description:
Karpowicz_Windsor_72_048_S48
collected 46h post synchronization

value: Intestinal Adenoma Organoids

value: Circadian Clock Normal


title: WT, S1P basal, replicate 4


title: wild-type spleen, day 1, Seq-Well plate 5

description:
SpWT1-5
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: wild-type spleen, day 5, Seq-Well plate 2

description:
SpWT5-2
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: WT, S1P basal, replicate 2


title: wild-type spleen, day 5, Seq-Well plate 4

description:
SpWT5-4
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: wild-type spleen, day 5, Seq-Well plate 5

description:
SpWT5-5
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: WT, S1P basal, replicate 1


title: wild-type spleen, day 1, Seq-Well plate 3

description:
SpWT1-3
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: HDMB03_rep2

city: Shanghai

first: Yujie

last: Tang

address: 280 South Chongqing Road

department: Pathophysiology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-seq data sets were mapped to the reference genome of human (GRCh38) using STAR v2.7
Aligned reads were assigned to genes using GENCODE annotations from (gencode.vM20.primary_assembly.annotation.gtf; downloaded in January 2019) and featureCounts (subread version 1.5.2)
The value of fragments per kilobase of transcript per million read pairs (FPKM) was computed by StringTie
Differentially expressed genes (DEGs) were calculated using DESeq2
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every expressed gene and every sample

organism: Homo sapiens

source_name: Group 3 subtype Medulloblastoma cell

growth_protocol: MB002 and HDMB03 were cultured in Tumor Stem Media (TSM) comprising DMEM/F12 (11330-032, Gibco), Neurobasal(-A) (10888-022, Gibco), B27(-A) (12587-010, Gibco), human EGF (20 ng/ml, 100-15, PeproTech, NJ, USA), human FGF-basic (20 ng/ml, 100-18B, PeproTech), human LIF (10 ng/ml, 300-05, PeproTech), 0.2% Heparin Solution (10 ng/ml, 07980, Stem Cell Technology), and 1×Antibiotic-Antimycotic (15240-062, Gibco).D425 and UW228 were cultrued in DMEM (BI-01-052-1ACS, Biological Industries) supplemented with 10% fetal bovine serum (FBS, F2442, Sigma)

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher Scientific, 15596-026) according to the manufacturers’ protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: JQ1, THZ1 or lentivirus treatment as previous description

value: untreated

value: Group 3 subtype Medulloblastoma cell

tag: cell line


title: HDMB03_rep1


title: MB002_shARL4D-2_rep2

value: lentivirus infected for four days


title: MB002_shARL4D-2_rep1


title: S1P4 KO, vehicle control, replicate 2

value: S1P4 KO/KO


title: MB002_SCR_rep4


title: wild-type spleen, day 1, Seq-Well plate 2

description:
SpWT1-2
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: APCmin/-;BMAL1+/+ CT46 (S45)

description:
Karpowicz_Windsor_69_045_S45
collected 46h post synchronization


title: APCmin/-;BMAL1+/+ CT44 (S44)

description:
Karpowicz_Windsor_66_044_S44
collected 44h post synchronization


title: APCmin/-;BMAL1+/+ CT44 (S41)

description:
Karpowicz_Windsor_63_041_S41
collected 44h post synchronization


title: MB002_SCR_rep3


title: WT, S1P apical, replicate 4

value: cortex/midbrain microvessel

value: S1P apical


title: WT, S1P apical, replicate 3

value: pure primary MBMEC (48h puromycin)


title: wild-type spleen, day 1, Seq-Well plate 4

description:
SpWT1-4
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: wild-type spleen, day 1, Seq-Well plate 1

description:
SpWT1-1
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: MB002_shARL4D-1_rep1


title: APCmin/-;BMAL1+/+ CT42 (S37)

description:
Karpowicz_Windsor_57_037_S37
collected 42h post synchronization


title: WT, S1P apical, replicate 2


title: WT, S1P4 agonist basal, replicate 4

value: 500nM S1P4 agonist basal


title: MB002_SCR_rep2


title: Mock-Ifnar1 ko S3

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

description:
S3
Mock-infected

data_processing:
All raw sequencing reads were processed using an in-house pipeline (Dolphin) at the University of Massachusetts Medical School.
The clean read pairs were aligned to the rat reference genome and rRNA sequences were filtered from the mapped reads.
The RNA-Seq by Expectation Maximization (RSEM) method was used to determine the expression levels of genes by providing mapped transcript counts in the RNA-seq reads (Li and Dewey 2011).
The differentially expressed genes (DEGs) were identified using DESeq2 and significant differences in genes were identified as fold change >2 between uninfected and virus-infected samples and if the adjusted P value (Padj) was <0.05 (Love, Huber et al. 2014).

growth_protocol: LEW.1WR1 rats (RT1B/Du) were from Biomere (Worcester, MA). Animals were housed in viral antibody–free conditions, confirmed monthly to be serologically free of rat pathogens (Mordes, Leif et al. 2002), and maintained in accordance with institutional and national guidelines (Institute of Laboratory Animal Resources (U.S.) 1996). KRV-UMass strain was prepared and titered by plaque assay as previously described (Zipris, Hillebrands et al. 2003).

extract_protocol:
Spleens were homogenized in 1 mL TRIzol reagent using TissueRuptor (Qiagen) and total RNA was extracted following TRIzol method (Invitrogen). RNA concentrations were quantified using a NanoDrop spectrophotometer (NanoDrop).
Approximately 10 mg total RNA for each of the 12 rat samples was treated with TurboDNase (ThermoFisher Scientific) and ribosomal RNA (rRNA) depletion was performed using a Ribo-ZeroTM Gold rRNA removal kit (Illumina). For RNA-seq, we prepared strand-specific libraries by following the protocol from Zhang and colleagues (Zhang, Theurkauf et al. 2012). The quality of the prepared libraries was confirmed using the Advanced Analytical Technologies, Inc. Fragment Analyzer through the Molecular Biology Core Lab (UMass Medical School).
The 12 libraries were pooled and sequenced with paired end reads (75 bp each) using Illumina NextSeq 500 according to the manufacturer’s specifications.

treatment_protocol: Weanling WT and Ifnar1-/- rats of 21-25 days of age of either sex were infected with a single i.p. dose of KRV-UMass strain (1 X 107 PFU) on day 0. Spleens were harvested from mock-infected (i.e., injected with culture media) WT rats (n=2) and Ifnar1-/- rats (n=2) or KRV-infected WT rats (n=4) and Ifnar1-/- rats (n=4) at 5 dpi.

tag: condition

value: Ifnar1 ko


title: KRV-WT S11

description:
S11
Virus-infected

value: WT


title: MB002_shARL4D-1_rep2


title: APCmin/-;BMAL1+/+ CT38 (S32)

description:
Karpowicz_Windsor_48_032_S32
collected 38h post synchronization

value: 1h 0.1µm Dexamethasone


title: APCmin/-;BMAL1+/+ CT40 (S36)

description:
Karpowicz_Windsor_54_036_S36
collected 40h post synchronization


title: WT, S1P apical, replicate 1


title: KRV-WT S2

description:
S2
Virus-infected


title: Mock-WT S6

description:
S6
Mock-infected


title: MB002_SCR_rep1


title: APCmin/-;BMAL1+/+ CT36 (S28)

description:
Karpowicz_Windsor_42_028_S28
collected 36h post synchronization


title: UW228_rep2

source_name: SHH subtype Medulloblastoma cell

value: SHH subtype Medulloblastoma cell


title: WT, S1P4 agonist basal, replicate 1


title: UW228_rep1


title: KRV-Ifnar1 ko S7

description:
S7
Virus-infected


title: Mock-Ifnar1 ko S4

description:
S4
Mock-infected


title: D425_JQ1_rep1

value: 1 μM JQ1 treated for 24 hours


title: WT, S1P4 agonist basal, replicate 3


title: WT, S1P4 agonist apical, replicate 3

value: 500nM S1P4 agonist apical


title: APCmin/-;BMAL1+/+ CT42 (S40)

description:
Karpowicz_Windsor_60_040_S40
collected 42h post synchronization


title: APCmin/-;BMAL1+/+ CT38 (S29)

description:
Karpowicz_Windsor_45_029_S29
collected 38h post synchronization


title: D425_THZ1_rep2

value: 100 nM THZ1 treated for 6 hours


title: D425_THZ1_rep1


title: KRV-Ifnar1 ko S5

description:
S5
Virus-infected


title: WT, S1P4 agonist apical, replicate 4


title: APCmin/-;BMAL1+/+ CT36 (S25)

description:
Karpowicz_Windsor_39_025_S25
collected 36h post synchronization

value: Intestinal Adenoma Organoids


title: WT, vehicle control, replicate 4

value: vehicle control


title: KRV-WT S1

description:
S1
Virus-infected


title: APCmin/-;BMAL1+/+ CT30 (S16)

description:
Karpowicz_Windsor_24_016_S16
collected 30h post synchronization

value: Circadian Clock Normal


title: APCmin/-;BMAL1+/+ CT40 (S33)

description:
Karpowicz_Windsor_51_033_S33
collected 40h post synchronization


title: D425_JQ1_rep2

value: Group 3 subtype Medulloblastoma cell


title: D425_DMSO_rep1

value: 0.1% DMSO treated for 24 hours


title: APCmin/-;BMAL1+/+ CT34 (S24)

description:
Karpowicz_Windsor_36_024_S24
collected 34h post synchronization


title: WT, S1P4 agonist basal, replicate 2


title: Mock-WT S8

description:
S8
Mock-infected


title: WT, S1P4 agonist apical, replicate 2


title: WT, S1P4 agonist apical, replicate 1


title: APCmin/-;BMAL1+/+ CT32 (S20)

description:
Karpowicz_Windsor_30_020_S20
collected 32h post synchronization


title: APCmin/-;BMAL1+/+ CT32 (S17)

description:
Karpowicz_Windsor_27_017_S17
collected 32h post synchronization


title: D425_DMSO_rep2


title: KRV-Ifnar1 ko S12

description:
S12
Virus-infected


title: APCmin/-;BMAL1+/+ CT34 (S21)

description:
Karpowicz_Windsor_33_021_S21
collected 34h post synchronization


title: WT, vehicle control, replicate 3


title: KRV-WT S10

description:
S10
Virus-infected


title: KRV-Ifnar1 ko S9

description:
S9
Virus-infected


title: Patient 4 kidney single-cell RNA-seq

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V3.0.2
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat R package
Genome_build: GRCh38 for human data
Supplementary_files_format_and_content: the barcode, gene, expression matrix file of each sample

source_name: normal kidney

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v3 user guide to perform single cell suspension which were prepared before. Briefly, the single-cell samples were passed through a 40μm cells strainer and counted using a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated torecover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the oils onto the 10x Genomics single-cell-A chip and run this machine. After droplet generation, samples were transferred onto a PCR tube and reverse transcription was performed using T100 Thermal Cycler (BIO-RAD). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics followed by a Silane DynaBead clean-up as outlined in the user guide. Purified cDNA was amplified for 11-12 cycles before being cleaned up by using SPRIselect beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to determine cDNA concentration.
10X Genomics Single Cell 3' v3 Reagent Kit

tag: tissue

value: human kidney


title: Patient 4 RCC single-cell RNA-seq

source_name: chromophobe renal cell carcinoma

value: human chromophobe renal cell carcinoma


title: APCmin/-;BMAL1+/+ CT26 (S5)

description:
Karpowicz_Windsor_9_005_S5
collected 26h post synchronization


title: Microglia_Plcg2_KO_Rep3

city: La Jolla

first: Hui

last: Jing

state: CA

address: 10550 N Torrey Pines Rd

department: Department of Chemistry

institute: The Scripps Research Institute

data_processing:
Transcript abundance was quantified using Salmon (v1.3.0) with GENCODE vM25 annotation.
Gene level quantification was performed using tximeta (v1.8.4). Differential gene expression was analyzed by DESeq2 (v1.30.1).
Statistical analysis was performed in R (v4.0.4). Log2 fold expression changes were estimated using apeglm (v1.12.0) and P values were adjusted using the Benjamini-Hochberg procedure to control for multiple hypothesis testing.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Comma-separated values files include TPM values for each sample.

source_name: Neonatal microglia

growth_protocol: Mixed glial cultures were prepared from postnatal day 2-3 mouse forebrains from Plcg2+/+ and Plcg2-/- littermates and used to derive microglia as described before41 with some modification. Briefly, each forebrain was dissected, stripped of meninges, and digested in 5 mL 0.25% trypsin in dissection buffer (Ca2+, Mg2+-free HBSS with 10 mM HEPES, 3g glucose and 50 U/mL penicillin-streptomycin) for 15 min at 37 ̊C and triturated. Dissociated cells were collected into 10 mL DMEM medium supplemented with 10% FBS, 1× GlutaMax and 50 U/mL penicillin-streptomycin. The digestion, trituration and collection were repeated one more time with the residual undigested cell clumps. Digested cells were passed through 70-micron strainer, pelleted by centrifugation at 500 g for 5 min, resuspended and plated into 2 poly-D-lysine (#A3890401, Gibco) coated T75 tissue culture flasks in 15 mL microglia medium, which consisted of DMEM supplemented with 10% FBS, 1× GlutaMax, 50 U/mL penicillin-streptomycin and 5 ng/mL of mouse granulocyte macrophage-colony stimulating factor (GM-CSF, #315-03, Peprotech). Medium was replaced on day 3, and another 10 mL of fresh medium was added on day 7. On day 12~13, after establishment of the astrocyte monolayer, the flasks were shaken for 30 min at 180 rpm to obtain the loosely attached microglia. Microglia were subsequently plated at a density of 4 × 105/mL in 6-cm dish (3 mL/dish) or half-area 96-well plate (50 μL/well) in Macrophage-SFM media (#12065074, Gibco) supplemented with 1% FBS and 0.5 ng/mL of GM-CSF. Cells were allowed to sit for at least 72 h prior to subsequent analysis.

extract_protocol:
Total RNA was extracted from cell pellets using RNeasy Mini Kit (QIAGEN, #71104) with RNase-free DNase set (QIAGEN, #79254) for on column DNA digestion according to manufacturer’s instruction.
RNA samples were sent to Genewiz (https://www.genewiz.com/) for library preparation via polyA selection.
Genewiz (https://www.genewiz.com/) performed 150-bp paired-end sequencing on Illumina HiSeq to obtain ~20 million reads per sample.

value: microglia

tag: age

value: postnatal day 2-3


title: APCmin/-;BMAL1+/+ CT30 (S13)

description:
Karpowicz_Windsor_21_013_S13
collected 30h post synchronization


title: WT, vehicle control, replicate 1

value: cortex/midbrain microvessel

value: pure primary MBMEC (48h puromycin)


title: APCmin/-;BMAL1+/+ CT28 (S12)

description:
Karpowicz_Windsor_18_012_S12
collected 28h post synchronization


title: APCmin/-;BMAL1+/+ CT28 (S9)

description:
Karpowicz_Windsor_15_009_S9
collected 28h post synchronization


title: Microglia_Plcg2_KO_Rep2


title: WT, vehicle control, replicate 2


title: APCmin/-;BMAL1+/+ CT26 (S8)

description:
Karpowicz_Windsor_12_008_S8
collected 26h post synchronization


title: Microglia_Plcg2_WT_Rep3


title: Patient 3 RCC single-cell RNA-seq

source_name: clear cell renal cell carcinoma

value: human clear cell renal cell carcinoma


title: Patient 2 RCC single-cell RNA-seq


title: JIA Th1 culture, 2

city: Nashville

first: Anna

last: Patrick

state: TN

address: 2141 Blakemore Avenue

institute: Vanderbilt University Medical Center

data_processing:
Sequencing performed at Paired-End 150 bp on the Illumina NovaSeq 6000
Data processing by Illumina’s Dragen RNASeq pipeline
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: peripheral blood mononuclear cells

growth_protocol: PBMCs from patients were grown on anti-CD3 coated plates in the presence of anti-CD28 and IL-12 for 5 days.

extract_protocol:
RNA was harvested using TRIreagent. DNAase treatment applied.  Illumina Tru-Seq Stranded RNA Sample Prep Kit  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Th1 polarization with anti-CD3, anti-CD28, and IL-12

tag: disease state

value: juvenile idiopathic arthritis


title: JIA Th1 culture, 3


title: APCmin/-;BMAL1+/+ CT24 (S4)

description:
Karpowicz_Windsor_6_004_S4
collected 24h post synchronization

value: 1h 0.1µm Dexamethasone


title: Patient 1 RCC single-cell RNA-seq

source_name: papillary renal cell carcinoma

value: human papillary renal cell carcinoma


title: JIA Th1 culture, 1


title: APC+/+;BMAL1+/+ CT46 (S94)

description:
Karpowicz_Windsor_124_094_S94
collected 46h post synchronization

value: Intestinal Organoids


title: control Th1 culture, 3

value: healthy control


title: APC+/+;BMAL1+/+ CT46 (S93)

description:
Karpowicz_Windsor_123_093_S93
collected 46h post synchronization


title: Microglia_Plcg2_WT_Rep1


title: Microglia_Plcg2_WT_Rep2


title: Liver_YAP-KO_Male_24hour_APAP_rep1

type: RNA

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

description: Liver gene expression data from male YAP knockout 24 hours after 300 mg/kg APAP overdose.

hyb_protocol: 45C, 17hr plus or minus 1hr, 60rpm using GeneChip Hybridization oven 645

scan_protocol: Single Scan using Affymetrix GeneChip Scanner 3000 7G with autoloader

data_processing: The data were analyzed withAffymetrix Standard GeneChip using Affymetrix default analysis settings and global scaling as normalization method. The scaling parameter was set to 500.

label: biotin

source_name: YAP-KO Male

label_protocol: TdT terminal labeling with the GeneChip WT Plus Labeling Kit

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

treatment_protocol: 100 mg of liver was cut and homogenzied in Trizol.

value: Liver Lysate

value: YAP-KO


title: control Th1 culture, 2


title: APC+/+;BMAL1+/+ CT44 (S90)

description:
Karpowicz_Windsor_120_090_S90
collected 44h post synchronization

value: Circadian Clock Normal


title: Microglia_Plcg2_KO_Rep1


title: Tat stimulated-rep1

city: Huddinge

first: Peter

last: Svensson

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Fastq files were aligned to the hg38 genome together with reference HIV-1 sequence HXB2 (K03455) using bowtie2-2.4.2 and converted to BAM files using SAMtools-1.12
ChIP-seq reads were loaded into Galaxy unfiltered (for FLAG) or with MAPQ score >20 (for Tat) (separate processed files for input)
Bigwig files were generated with Bamcoverage in Galaxy.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: T cell line with HIV-1 and ZFP3-FLAG

growth_protocol: Cell were cultured in cytokine-free media (RPMI 1640 medium (Hyclone, Cat# SH30096_01), 10% FBS (Life Technologies, Cat# 10270-106), 1% Glutamax (Life Technologies, Cat# 35050), 1% Penicillin-streptomycin (Life Technologies, Cat# 15140-122)).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min in room temperature. ChIP was performed using the iDeal ChIP protocol (Diagenode, Cat# C01010180).
Libraries were prepared using NEBNext Ultra II DNA library kit

treatment_protocol: Cells were treated with DMSO (unstimulated) or PMA/i (stimulated) for 24h.

value: T cell line with HIV-1 and ZFP3-FLAG

value: J-lat 1C10

tag: chip antibody

value: Tat (Abcam, ab43014)

value: PMA/i


title: Tat unstimulated-rep2

value: DMSO


title: Tat unstimulated-rep1


title: control Th1 culture, 1


title: Liver_YAP-KO_Male_0hour_APAP_rep1

description: Liver gene expression data from male YAP knockout fasted mice.


title: APCmin/-;BMAL1+/+ CT24 (S1)

description:
Karpowicz_Windsor_3_001_S1
collected 24h post synchronization

value: Intestinal Adenoma Organoids


title: APC+/+;BMAL1+/+ CT44 (S89)

description:
Karpowicz_Windsor_119_089_S89
collected 44h post synchronization


title: AS3MT_WT_D4_5

city: Oxford

first: Sam

last: Washer

state: Oxfordshire

address: NDMRB, Roosevelt Drive

department: Centre for Medicines Discovery

country: United Kingdom

institute: University of Oxford

description:
2907_AS3MT_WT_D4_5
RNAseq_Jan19_AS3MT_gene_counts_-O_29.01.19

data_processing:
fastq sequence quality checked with MultiQC
Alignment to human genome using STAR
Mapped reads counted using FeatureCounts of Subread Package
Differential expression caluclated using DESeq2
GO Analysis undertaken using Goseq
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: txt file of counts from FeatureCounts per sequencing run

source_name: AS3MT Wild Type

growth_protocol: Standard SH-SY5Y tissue culture in 10% FBS supplemented DMEM/F12 GlutaMAX media, passaging when reaching 80% confluency using Accutase into T75 tissue culture treated plasticware.

extract_protocol:
Cells were lifted with Accutase and split into two 1.5ml tubes, one for DNA and other for RNA. Tubes were spun at max speed for 1m to pellet cells before removing media. Pellets for RNA were resuspended in TRIZol reagent before extraction using TRIzol and Direct-zol miniprep kit (Invitrogen, Carlsbad, CA, USA).
cDNA libraries were generated using the TruSeq DNA HT Library Preparation Kit (Illumina Inc., San Diego, CA, USA)

value: Age Matched SH-SY5Y Cell Line

tag: genotype/variation

value: AS3MT Wild Type

tag: sequencing run

tag: technical repeat


title: AS3MT_WT_D4_6

description:
2907_AS3MT_WT_D4_6
RNAseq_Jan19_AS3MT_gene_counts_-O_29.01.19

tag: cell type


title: Liver_WT_Male_24hour_APAP_rep1

description: Liver gene expression data from male floxed YAP 24 hours after 300 mg/kg APAP overdose.

source_name: WT Male

value: Wildtype


title: Liver_WT_Male_0hour_APAP_rep1

description: Liver gene expression data from male floxed YAP fasted mice.


title: APC+/+;BMAL1+/+ CT42 (S85)

description:
Karpowicz_Windsor_115_085_S85
collected 42h post synchronization

tag: clock function


title: APC+/+;BMAL1+/+ CT40 (S82)

description:
Karpowicz_Windsor_112_082_S82
collected 40h post synchronization

tag: strain


title: FLAG-rep2

value: FLAG (Sigma-Aldrich, F1804, lot SLCF4933)

tag: treatment


title: AS3MT_KO_C6_1

description:
2907_AS3MT_KO_C6_1
RNAseq_Jan19_AS3MT_gene_counts_-O_29.01.19

source_name: AS3MT Knockout

value: CRISPR Edited SH-SY5Y Cell Line

value: AS3MT Knockout


title: AS3MT_WT_D4_2

description:
2907_AS3MT_WT_D4_2
RNAseq_Jan19_AS3MT_gene_counts_-O_29.01.19


title: APC+/+;BMAL1+/+ CT42 (S86)

description:
Karpowicz_Windsor_116_086_S86
collected 42h post synchronization

value: Intestinal Organoids

tag: genotype

tag: time

value: 1h 0.1µm Dexamethasone


title: AS3MT_KO_C6_4

description:
2907_AS3MT_KO_C6_4
RNAseq_Jan19_AS3MT_gene_counts_-O_29.01.19


title: APC+/+;BMAL1+/+ CT40 (S81)

description:
Karpowicz_Windsor_111_081_S81
collected 40h post synchronization

tag: synchronization


title: AS3MT_KO_C6_3

description:
2907_AS3MT_KO_C6_3
RNAseq_Jan19_AS3MT_gene_counts_-O_29.01.19


title: DHA 20μM-3

first: Yi

middle: You

last: Cai

state: Shanghai

address: No. 600 Yishan Road

department: Gastroenterology

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with  gene counts and fpkm for every gene and every sample

growth_protocol: HCT116 cells were cultured in RPMI 1640 medium that contained 1% Penicillin-Streptomycin Solution and 10% fetal bovine serum. The cell culture environment was sterile, humidified and thermostatic at 37℃ with 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The control groups were treated with DMSO and the DHA 20μM groups were treated with 20μM DHA.

value: Colorectal cancer cell line

value: 20μM DHA


title: input DNA PMAi-rep1


title: DHA 20μM-2


title: DHA 20μM-1


title: Tat stimulated-rep2


title: APC+/+;BMAL1+/+ CT38 (S78)

description:
Karpowicz_Windsor_108_078_S78
collected 38h post synchronization

value: Circadian Clock Normal


title: APC+/+;BMAL1+/+ CT38 (S77)

description:
Karpowicz_Windsor_107_077_S77
collected 38h post synchronization


title: Control-3

value: control DMSO


title: input DNA DMSO-rep1

value: T cell line with HIV-1 and ZFP3-FLAG

value: J-lat 1C10


title: APC+/+;BMAL1+/+ CT36 (S74)

description:
Karpowicz_Windsor_104_074_S74
collected 36h post synchronization


title: AS3MT_WT_6

description:
2683_AS3MT_WT_6
AS3MT_gene_counts_26.07.18


title: input DNA PMAi-rep2

value: PMA/i


title: AS3MT_WT_5

description:
2683_AS3MT_WT_5
AS3MT_gene_counts_26.07.18


title: Control-1


title: Control-2


title: NDCS-1

city: Fukuoka

first: Eijiro

last: Shimada

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Orthopaedic Surgery

country: Japan

institute: Kyushu University

data_processing:
Paired-end sequencing reads (151 bp) generated from WGBS were verified its sequence quality with FastQC.
Before starting analysis, TrimGalore was used to remove adapter sequences.
The cleaned reads were aligned to the homo sapiens genome (hg38) using bismark.
Mapped data (BAM file format) were performed sorting and indexing using SAMtools.
Genome_build: hg38
Supplementary_files_format_and_content: Each file consists of chromosomal location, the number of methylated reads and number of unmethylated reads in each location.

extract_protocol:
Genomic DNA was extracted using a QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. The integrity of the genomic DNA was checked by running an agarose gel electrophoresis and gDNA was were quantified using Quant-IT PicoGreen (Invitrogen).
The WGBS libraries were prepared using Accel-NGS Methyl-Seq DNA library kit (Swift BioSciences). Briefly, Fragmentation of 200ng of genomic DNA was performed using the Covaris LE220 focused-ultrasonicator (Covaris, Woburn, MA) to a target peak size of 400-700bp. The fragmented DNA were then subject to bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA, USA), according to manufacturer’s instructions. The bisulfite-treated ssDNA fragments were repaired and the truncated adapter 1 and 2 ligated to the 3′ end and 5’ end of fragments, respectively. The truncated adapter-ligated DNA was amplified with an indexed primer to complete the WGBS libraries with full-length adapter. The final libraries were then quantified using qPCR according to the qPCR Quantification Protocol Guide Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using the TapeStation DNA screentape D1000 (Agilent). And then we sequenced using the NovaSeq6000 platform (Illumina,San Diego, USA).

value: human chondrosarcoma cell line


title: FLAG-rep1

value: DMSO


title: input DNA DMSO-rep2


title: OUMS-27


title: AS3MT_WT_4

description:
2683_AS3MT_WT_4
AS3MT_gene_counts_26.07.18

value: Age Matched SH-SY5Y Cell Line


title: CFSCsakATCC29544LSP2_RNAseq

city: Dublin

first: Yu

last: Cao

address: University College Dublin, Belfield, Dublin 4

country: Ireland

institute: University College Dublin

data_processing:
Raw sequence reads were mapped against the C. sakazakii ATCCTM29544 complete genome (NCBI GenBank accession number CP011047) using Segemehl with mapping accuracy set at 100%
Expression values of each gene were calculated using the transcript per million (TPM) method
Annotation of the transcriptomic data was carried out based on PATRICK database (version 3.4.5) and BLAST
Gene expression level alterations larger than 4-fold, between 2- and 4-fold, between 2- and 0.5-fold-, between 0.25- and 0.5-fold and smaller than 0.25-fold respectively defined as highly-up regulated, up regulated, no change, down regulate and highly-down regulated
Genome_build: CP011047
Supplementary_files_format_and_content: text file with TPM

organism: Cronobacter sakazakii

source_name: Cronobacter sakazakii ATCCTM29544

extract_protocol:
RNeasy Mini Kit (Qiagen, USA)
Commercial Illumina RNA-seq library preparation protocol

value: Bacterial cell

tag: growth stage

value: LSP

value: Static growth at 25 degrees C until LSP


title: CFSCsakATCC29544LSP1_RNAseq


title: AS3MT_WT_2

description:
2683_AS3MT_WT_2
AS3MT_gene_counts_26.07.18

tag: cell line

value: AS3MT Wild Type


title: APC+/+;BMAL1+/+ CT36 (S73)

description:
Karpowicz_Windsor_103_073_S73
collected 36h post synchronization

source_name: Primary Derived


title: APC+/+;BMAL1+/+ CT34 (S70)

description:
Karpowicz_Windsor_100_070_S70
collected 34h post synchronization


title: CFSCsakATCC29544DP2_RNAseq

value: DP

value: Desiccation on stainless steel coupon for 4 h at 25 degrees C from ESP


title: HDMB03-H3K27ac

data_processing:
All ChIP-seq data sets were aligned using Bowtie 2 (version 2.3.0) to build version GRCh38/HG38 of the human genome.
The SAM file generated by Bowtie 2 is  converted to BAM file with samtools (version 1.9)
Multi-mappers and duplicates were filtered out by sambamba (version 0.7.1)
ChIP-seq peaks over input sample were identified using a peak-finding algorithm, MACS2 version 2.2.6
A q value threshold of enrichment of 0.05 was used for all data sets. Active enhancers were defined as regions of ChIP-seq enrichment for H3K27ac outside of promoters(±12.5kb)
Genome_build: GRCh38/HG38

growth_protocol: MB002 and HDMB03 was cultured in Tumor Stem Media (TSM) comprising DMEM/F12 (11330-032, Gibco), Neurobasal(-A) (10888-022, Gibco), B27(-A) (12587-010, Gibco), human EGF (20 ng/ml, 100-15, PeproTech, NJ, USA), human FGF-basic (20 ng/ml, 100-18B, PeproTech), human LIF (10 ng/ml, 300-05, PeproTech), 0.2% Heparin Solution (10 ng/ml, 07980, Stem Cell Technology), and 1×Antibiotic-Antimycotic (15240-062, Gibco).D425 was cultrued in DMEM (BI-01-052-1ACS, Biological Industries) supplemented with 10% fetal bovine serum (FBS, F2442, Sigma)

extract_protocol:
ChIP assays were performed by Shanghai Jiayin Biotechnology Co., Ltd, according to the standard crosslinking. ChIP protocol with modifications. Briefly, cells were harvested and crosslinker with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with anti-Histone H3K27ac (AM, 39133). The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (#DP214)
The ChIP-Seq library was prepared using ChIP-Seq DNA sample preparation kit (NEBNext® Ultra™II DNA) according to the manufacturer’s instructions.

value: Group 3 subtype Medulloblastoma cell

tag: antibody


title: UW228-H3K27ac

source_name: SHH subtype Medulloblastoma

value: SHH subtype Medulloblastoma


title: APC+/+;BMAL1+/+ CT32 (S65)

description:
Karpowicz_Windsor_95_065_S65
collected 32h post synchronization

value: Intestinal Organoids

value: 1h 0.1µm Dexamethasone


title: UW228 input


title: HDMB03 input


title: CFSCsakATCC29544RP1_RNAseq

tag: tissue

value: RP

value: Rehydration in water for 30 min at 25 degrees C from DP


title: CFSCsakATCC29544RP2_RNAseq


title: AS3MT_KO_4

description:
2683_AS3MT_KO_4
AS3MT_gene_counts_26.07.18

value: CRISPR Edited SH-SY5Y Cell Line

value: AS3MT Knockout


title: APC+/+;BMAL1+/+ CT32 (S66)

description:
Karpowicz_Windsor_96_066_S66
collected 32h post synchronization

value: Circadian Clock Normal


title: D425 input


title: CFSCsakATCC29544DP1_RNAseq


title: AS3MT_KO_2

description:
2683_AS3MT_KO_2
AS3MT_gene_counts_26.07.18


title: APC+/+;BMAL1+/+ CT30 (S62)

description:
Karpowicz_Windsor_92_062_S62
collected 30h post synchronization


title: D425-H3K27ac


title: AS3MT_KO_6

description:
2683_AS3MT_KO_6
AS3MT_gene_counts_26.07.18


title: AS3MT_KO_5

description:
2683_AS3MT_KO_5
AS3MT_gene_counts_26.07.18


title: CFSCsakATCC29544ESP2_RNAseq

value: ESP

value: Static growth at 25 degrees C until ESP


title: AS3MT_WT_1

description:
2683_AS3MT_WT_1
AS3MT_gene_counts_26.07.18

value: Age Matched SH-SY5Y Cell Line


title: APC+/+;BMAL1+/+ CT30 (S61)

description:
Karpowicz_Windsor_91_061_S61
collected 30h post synchronization


title: D. simulans HA 3

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Ave.

department: Biology

institute: Wesleyan University

data_processing:
FASTQC on each of the 6 raw fastq files
Bowtie2 alignment using the D. sechellia, D. simulans, and D. melanogaster reference genomes available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa, Drosophila_simulans.ASM75419v3.dna.toplevel.fa, Drosophila_melanogaster.BDGP6.dna.toplevel.fa)
Cuffdiff for quantification and differential expression analysis using the D. sechellia, D. simulans, and D. melanogaster reference genomes available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa, Drosophila_simulans.ASM75419v3.dna.toplevel.fa, Drosophila_melanogaster.BDGP6.dna.toplevel.fa) and gene files available at the time of analysis (Drosophila_sechellia.dsec_caf1.42.gff3, Drosophila_simulans.ASM75419v3.42.gff3, Drosophila_melanogaster.BDGP6.95.gff3) with geometric library normalization
Genome_build: Drosophila_sechellia.dsec_caf1.dna.toplevel.fa
Genome_build: Drosophila_simulans.ASM75419v3.dna.toplevel.fa
Genome_build: Drosophila_melanogaster.BDGP6.dna.toplevel.fa
Supplementary_files_format_and_content: Tab-delimited Cuffdiff output in text format

organism: Drosophila simulans

source_name: Whole adults

growth_protocol: Flies were reared on cornmeal medium using a 16:8 light:dark cycle at 20 degrees Celsius

extract_protocol:
Total RNA was extracted from whole female adults using Promega SV Total RNA Isolation System
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were exposed to 0.23% HA mixed into instant Drosophila food or control food for a period of 24 hours


title: AS3MT_KO_1

description:
2683_AS3MT_KO_1
AS3MT_gene_counts_26.07.18


title: MB002-H3K27ac

source_name: Group 3 subtype Medulloblastoma cell


title: APC+/+;BMAL1+/+ CT34 (S69)

description:
Karpowicz_Windsor_99_069_S69
collected 34h post synchronization


title: CFSCsakATCC29544LEP2_RNAseq

value: Bacterial cell

value: LEP

value: Static growth at 25 degrees C until LEP


title: D. simulans HA 2


title: CFSCsakATCC29544ESP1_RNAseq


title: MB002 input


title: D. simulans HA 1


title: APC+/+;BMAL1+/+ CT28 (S57)

description:
Karpowicz_Windsor_87_057_S57
collected 28h post synchronization


title: CFSCsakATCC29544LEP1_RNAseq


title: APC+/+;BMAL1+/+ CT28 (S58)

description:
Karpowicz_Windsor_88_058_S58
collected 28h post synchronization


title: RNaseL KO lipofectamine 2

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 216 Shultz Laboratory

department: Molecular Biology

institute: Princeton University

data_processing:
Reads were split by barcodes and assigned to the respective samples
Reads were mapped to HG19 using TopHat 2 set to map first stranded reads with default parameters
Intron and exon reads were counted using HTseq-count in Intersection (strict) mode
Genome_build: HG19
Supplementary_files_format_and_content: ChitrakarSolorio_IntronExonCounts_Korennykh2021.xlsx  (Excel sheet with intron and exon counts)

molecule: cytoplasmic RNA

source_name: Lung carcinoma epithelium

growth_protocol: Grown in RMPI supplemented with 10% FBS

extract_protocol:
At the endpoint, media was aspirated and cells were lysed with hypotonic buffer and dounce homogenization. Nuclei and organelles were pelleted, then RNA from cytoplasmic fraction was isolated using RNeasy (Qiagen; as per manufacturers instructions). RNA integrity was verified by an RNA 6000 Nano Chip, using BioAnalyzer and 2100 Expert software (Agilent Technologies).
rRNA was depleted, followed by fragmentation, adapter ligation, PCR amplification, and finally sequencing on Illumina NovaSeq 6000 platform.
RNA-Seq directional, paired-end

treatment_protocol: A549 cells in a 12-well plate were mock transfected with Lipofectamine 2000 as per manufracturer's instructions, treatment time 12h

value: RNaseL KO

tag: type

value: Adherent


title: RNaseL KO lipofectamine 1


title: APC+/+;BMAL1+/+ CT26 (S53)

description:
Karpowicz_Windsor_83_053_S53
collected 26h post synchronization

data_processing:
Raw transcriptome sequencing reads were aligned against GRCm38 and Ensembl release 96 transcript annotations using STAR v2.5 (Dobin et al., 2013)
RSEM v1.3.0 (Li and Dewey, 2011, BMC Bioinformatics) was used for transcript quantification.
low quality samples were removed and Transrcipts Per Million (TPM) for remaining samples were merged into one file
Quantile normalization was performed for each expression table using preprocessCore package. Genes with null expression in at least one sample within an expression table were removed from that table
rhythmic analysis was performed using MetaCycle2d, base expression >0.5, relative amplitude >0.05, BH q-value <0.1
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-separated values tables, identified with 'star_rsem_allgenes', report the TPM values for all genes in each genotype, obtained after STAR alignment and RSEM quantification.
Supplementary_files_format_and_content: comma-separated values tables, identified with 'quant-norm_filtered_CT-header', contain the data after quantile normalization and removal of null-expressing genes in each genotype. Sample (column) names were replaced by the corresponding time post synchronization (CT)
Supplementary_files_format_and_content: STAR alignment stats

extract_protocol:
RNA was extracted using the Qiagen Rneasy mini Purification Kit (Cat# 74105)
Libraries were prepared using 96 NEB - NEBNext Ultra II Directional RNA Library Prep Kit including quality control and DNase treatment (#E7765, New England Biolabs Inc). Sequencing was done on a 1 Flowcell, Illumina NovaSeq6000 (Illumina), S2, 100 Cycles, v1 chemistry Read 1: 101bp, Index Read 1: 8bp, Index Read 2: 8bp
Each library was sequenced in two separate lanes, which generated 2 fastq files for each sample


title: D. simulans Control 3


title: APC+/+;BMAL1+/+ CT26 (S54)

description:
Karpowicz_Windsor_84_054_S54
collected 26h post synchronization


title: WT lipofectamine 2

value: WT


title: D. simulans Control 2


title: APC+/+;BMAL1+/+ CT24 (S50)

description:
Karpowicz_Windsor_80_050_S50
collected 24h post synchronization


title: WT lipofectamine 1


title: APC+/+;BMAL1+/+ CT24 (S49)

description:
Karpowicz_Windsor_79_049_S49
collected 24h post synchronization


title: CFSCsakATCC29544EEP2_RNAseq

value: EEP

value: Static growth at 25 degrees C until EEP


title: D. simulans Control 1


title: Day 6 MB-3 replicate 8

status: Public on Oct 03 2021

city: Tsurumi-ku, Yokohama

first: Yuki

last: Sakamoto

state: Kanagawa

address: 1-7-22, Suehiro-cho

department: CSRS

institute: RIKEN

data_processing:
Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Reads were mapped to the Arabidopsis reference using Bowtie 0.12.9.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited data with transcript tag counts and the number of total mapped reads for each sample

organism: Arabidopsis thaliana

source_name: Cultured mesophyll protoplasts

growth_protocol: Plants were grown at 22℃ constant temperature under continuous light (30 to 40 μmol/m2/sec) on half-strength MS medium containing MS vitamins, 1 % sucrose, 0.05 % MES and 0.8 % Gelzan CM-Gelrite

extract_protocol:
Total RNA was extracted using Rneasy Plant Mini Kit (QIUAGEN) according to manufacturer's instructions, including on-column Dnase digeston
Isolated RNA was subjected to library preparation using the Kapa stranded mRNA sequencing kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) as adapters and Agencourt AMPure XP (Beckman Coulter) beads instead of KAPA Pure Beads.

treatment_protocol: Protoplasts were isolated from 1st to 5th rosette leaves of 23-DAS  plants, embedded into 0.75 % sodium alginate/ D(-)-mannitol gels and incubated in liquid Gamborg B5 medium containing B5 vitamins, 2 % D(+)-glucose, 0.05 % MES, 0.4 M D(-)-mannitol, 1 mg/L 2,4-D and 176 μg/L thidiazuron funder dark condition.

tag: accession

value: protoplasts

tag: age

value: 6 days after incubation


title: Day 14 MB-3 replicate 1

value: 14 days after incubation


title: CFSCsakATCC29544EEP1_RNAseq


title: Day 14 control replicate 2

value: control


title: Day 6 MB-3 replicate 7


title: Day 14 MB-3 replicate 2


title: Day 6 MB-3 replicate 6


title: Day 6 yucasin replicate 8

value: yucasin


title: Day 6 yucasin replicate 7


title: Day 14 control replicate 1


title: Day 6 yucasin replicate 6


title: CFSCsakATCC29544MEP2_RNAseq

value: MEP

value: Static growth at 25 degrees C until MEP


title: Day 6 control replicate 8


title: Day 6 control replicate 7


title: Day 6 control replicate 6


title: Day 4 -2,4-D replicate 11

value: 4 days after incubation

value: without 2,4-D


title: CFSCsakATCC29544MEP1_RNAseq

value: Bacterial cell


title: Day 4 -2,4-D replicate 10


title: Day 4 MB-3 replicate 6


title: Day 4 -2,4-D replicate 9


title: Day 4 MB-3 replicate 5


title: Day 14 control replicate 3


title: Day 14 MB-3 replicate 3


title: Day 4 MB-3 replicate 4


title: J3

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

data_processing:
CellRanger (v3.1.0) was used for raw data preprocessing. Each library was aligned to an indexed mm10 genome using Cell Ranger Count
Output from cellRanger was loaded into R and further analyzed using Seurat pipeline (version 3.1.2).
Genome_build: mm10
Supplementary_files_format_and_content: Count data objects generated by CellRanger, ie cellular barcodes present in dataset, IDs of quantified genes and a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes

source_name: tumors collected 3 days after treatment

growth_protocol: WT mice were subcutaneously injected with 300 000 TC-1 cells. Tumor growth was observed about 5 days latter

extract_protocol:
Tumors were digested with enzymes to obtain a cell suspension. ILC were cell sorted using a Aria3 cell sorter and defined as CD45+, lin- CD90+ and CD127+ cells.Fifteen thousand cells were captured thanks to Single cell 3’ Gel Bead kit v3 and Single cell 3’GEM kit v3 on each well of a Chip B (10X Genomics).
Library preparation, from reverse transcription to final amplification, was performed thanks to Single cell 3’ library kit v3 (10X Genomics) by following manufacturer’s instructions. Each library was 2*75bp paired-end sequenced on a NextSeq550 device (Illumina) at a depth of 200 million of reads, resulting in a read depth of 20000 reads per cell.

treatment_protocol: TC-1 tumors were treated IP with PBS or with Cisplatin (6mg/kg) once, when the tumor reached 40mm². Tumors were collected 1, 3 or 7 days after treatment,

value: Innate lymphoid cells

value: Cisplatin

tag: days


title: J1

source_name: tumors collected 1 day after treatment


title: Day 4 yucasin replicate 5


title: J7

source_name: tumors collected 7 days after treatment


title: Day 4 yucasin replicate 4


title: Day 4 yucasin replicate 6


title: NT

source_name: no treatment

value: PBS


title: Day 4 control replicate 10


title: D35 Met (b)

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Single-end FASTQ reads were aligned to human genome build GRCh38 using hisat2 with defaut parameters
SAM files were processed and sorted to BAM format using sambamba v 0.63
Transcript counts were generated with htseq-count (v0.5.4p3)
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data are raw counts of transcripts as determined by htseq-count

source_name: hPSCs

growth_protocol: hESC-derived pancreatic β-like cells are generated by dissociating hESC colonies into single cells and growing them in a suspension culture for 35 days. There is a set of 4 media, with specific growth factor treatment for each point of differentiation.

extract_protocol:
Organoids were removed and RNA was extracted using the Nucleo Spin RNA kit from Macherey-Nagel
Libraries were prepared using the TruSEQ Stranded Total RNA Prep with  Ribo-Zero Human Cat. No. RS-122-2201 as per manufacturer's protocol. Libraries sequenced using 150bp paired-end on HiSeq 2500 Platform.

treatment_protocol: 100μM metformin (in water) is added to  the suspension culture at every media change

tag: developmental stage

value: Pancreatic Beta-like cells

value: 100 microM metformin

value: hPSCs-derived organoid


title: D35 (c)

value: Untreated


title: D35 Met (a)


title: Day 4 control replicate 6

value: protoplasts


title: Day 4 control replicate 9


title: D35 Met (c)


title: Day 4 control replicate 4


title: Day 4 control replicate 5


title: RNA_INTSF52_EXP_Day 2

city: Bloomington

first: Kimberly

middle: A

last: Rosvall

state: IN

address: Dept of Biology, Indiana Univ., 1001 E. 3rd St, Jordan Hall

institute: Indiana University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using fastp version 0.20.1 with parameters "-l 17 --detect_adapter_for_pe -g -p"
RNA-Seq reads were mapped to the reference tree swallow transcriptome obtained previously by our laboratory (Bentz et al. 2019) using Bowtie2 version 2.4.2 with parameters “--mm -k 20 --very-sensitive” and filtered for primary mapped reads using samtools view version 1.10 with parameter “-F 256”.
Transcripts were quantified using samtools idxstats version 1.10 and custom shell scripts.
Genome_build: tree swallow transcriptome obtained previously by our laboratory (Bentz et al. 2019)
Supplementary_files_format_and_content: transcript_counts.tsv is a tab-delimited text file of raw RNA-seq read count values for each Sample

organism: Tachycineta bicolor

source_name: Experimental_Day 2_Ovary

extract_protocol:
Ovaries were frozen on dry ice in the field. Total RNA was extracted from each sample using Trizol (Invitrogen, Carlsbad, CA).
Total RNA was used for cDNA library construction using a TruSeq Stranded mRNA kit (Illumina) following the kit protocol.

treatment_protocol: Experimental: temporarily removed nest boxes to increase competition among free-living birds; Control: date-matched unmanipulated birds

value: ovary

value: adult

tag: Sex

value: female

value: Experimental

tag: period

value: Day 2


title: D20 Met (c)

value: Endocrine Progenitor


title: D35 (a)


title: RNA_INTSF50_EXP_Day 2


title: Day 2 control replicate 5

value: 2 days after incubation

value: control


title: Day 2 control replicate 6


title: Day 2 control replicate 4


title: D20 Met (b)


title: Day 0 replicate 11

source_name: Freshly isolated mesophyll protoplasts

value: 0 day after incubation

value: fresh


title: Day 4 control replicate 11

value: 4 days after incubation


title: RNA_INTSF12_EXP_Day 2


title: Day 0 replicate 10


title: D20 Met (a)


title: Day 0 replicate 9


title: Day 0 replicate 8


title: D35 (b)


title: Day 0 replicate 6


title: RNA_INTSF4_EXP_Day 0

source_name: Experimental_Day 0_Ovary

value: Day 0


title: Day 0 replicate 7


title: D20 (c)


title: RNA_INTSF3_EXP_Day 0


title: D20 (b)


title: Day 0 replicate 4


title: Day 0 replicate 5


title: Day 0 replicate 3


title: RNA_INTSF37_EXP_Day 2


title: Day 0 replicate 2


title: D20 (a)


title: RNA_INTSF18_EXP_Day 0


title: Day 0 replicate 1


title: D13 Met (c)

value: Pancreatic Progenitor


title: RNA_INTSF16_EXP_Day 0


title: D13 Met (b)

value: 100 microM metformin


title: RNA_INTSF15_EXP_Day 0


title: 23 DAS leaf replicate 2

source_name: Rosette leaves

value: 1st to 5th rosette leaves

value: 23 days after sowing

value: intact


title: D13 Met (a)

value: hPSCs-derived organoid


title: 23 DAS leaf replicate 1


title: RNA_INTSF38_CON_Day 2

source_name: Control_Day 2_Ovary

value: ovary

value: adult

value: Control


title: RNA_INTSF5_EXP_Day 0

value: female

value: Experimental


title: D13 (b)

value: Untreated


title: D0 (c)

value: hPSCs


title: D13 (a)


title: D0 (b)


title: D0 (a)


title: RNA_INTSF22_CON_Day 2

value: Day 2


title: J20/apoE4-KI_Vehicle_03 10x snRNA-seq

city: San Francisco

first: Alice

last: Taubes

address: 1650 Owens Street

department: Neurological Disease

institute: Gladstone Institute of Neurological Disease

data_processing:
The mouse reference (mm10 reference sequence build version “2020-A”) pre-mRNA genome was created via 10X Genomics Cellranger mkref function
Reads from each sample were aligned to their respective genomes and aggregated using the 10X Cellranger pipeline with no modifications.
Genome_build: mm10 reference sequence build version “2020-A”
Supplementary_files_format_and_content: filtered gene matrices
Supplementary_files_format_and_content: raw gene matrices

source_name: J20/apoE4-KI Mouse Hippocampus

growth_protocol: All protocols and procedures followed the guidelines of the Laboratory Animal Resource Center at the University of California, San Francisco (UCSF). Experimental and control mice had identical housing conditions from birth through sacrifice (12 h light/dark cycle, housed 5 animals/cage, PicoLab Rodent Diet 20). ApoE3-KI and apoE4-KI homozygous mouse lines (Taconic)51 were born and aged under normal conditions at the Gladstone Institute/UCSF animal facility. ApoE4-KI/Syn-Cre and apoE3-KI/Syn-Cre mice were generated by cross-breeding apoE-floxed-KI mice, which was generated in our lab52, with Syn-Cre mice11.

extract_protocol:
The snRNA-seq protocol was modified based on 10x Genomics Sample Preparation Demonstrated protocols, Isolation of Nuclei for Single Cell RNA Sequencing. All procedures and samples were harvested and run in randomized order at the same time to minimize any batch effects. Mouse hippocampi were acutely dissected on ice. Dissected hippocampi were placed in 2mL Hibernate A®/B27®/GlutaMAX™ (HEB) medium in a 5mL tube. The HEB medium was removed to a 15mL conical and kept on ice. 2mL of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Nonidet™ P40 Substitute in Nuclease-Free Water) were added to the tissue, and the hippocampi were homogenized by suctioning10x through a 21G needle. After homogenization, the tissue was lysed on ice for 15 min, swirling 2-3x during this incubation period. The reserved chilled HEB media was then returned to the lysed tissue solution, and the tissue was further triturated with 5–7 passes through a 1mL pipette. A 30m cell strainer (MACS Smart Strainer; Miltenyi Biotech 130-110-915) was washed with 1mL of PBS, and the lysed tissue solution was filtered through the strainer to remove debris and clumps. Filtered nuclei were centrifuged at 500 rcf for 5min at 4°C. The supernatant was removed, and nuclei were resuspended in 1mL of Nuclei Wash and Resuspension Buffer (1X PBS with 1.0% BSA and 0.2U/µl RNase Inhibitor), then centrifuged a second time at 500 rcf for 5 min at 4°C, and resuspended in 400 µl of Nuclei Wash and Resuspension Buffer. DAPI was added to a final concentration of 0.1µg/mL, and the nuclei solution was filtered through 35µm cell strainer before loaded onto the BD FACSAria-II at the Gladstone Institutes’ Flow Cytometry Core. The DAPI-positive nuclei were selected by gating on DAPI-positive events, excluding debris and doublets. RNA was extracted in accordance with the 10X Genomics isolation of nuclei for single cell RNA sequencing protocol.
Sequencing libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, 1000269) for J20/E4-KI mouse hippocampal samples according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer (PE100) at the UCSF Center for Advanced Technology Core. We sequenced the library to a target read depth of  26,924 post-normalization mean reads per cell, a median of 723 genes per nucleus for samples from J20/E4-KI mice.

treatment_protocol: 10-month-old J20/E4-KI mice (n = 3 per condition) received daily i.p. injections of vehicle or bumetanide (0.2 mg/kg body weight) for 12 weeks

value: J20/apoE4-KI Mouse Hippocampus

value: Vehicle treated


title: RNA_INTSF19_CON_Day 2


title: 23 DAS leaf replicate 3


title: J20/apoE4-KI_Vehicle_02 10x snRNA-seq


title: J20/apoE4-KI_Vehicle_01 10x snRNA-seq


title: Cell

city: GuangZhou

first: Yiliang

last: Wang

address: Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, Guangdong, PR China. Tel/fax.: +86 20 85223426.

institute: Jinan University

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data.At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream 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 bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were setas default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela  Pertea.et al. 2016) 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
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in  each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the  FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of  exon per million fragments mapped, calculated based on the length of the fragments  and reads count mapped to this fragment.
The Ballgown suite includes functions for interactive exploration of the transcriptome  assembly, visualization of transcript structures and feature-specific abundances for  each locus, and post-hoc annotation of assembled features to annotated features(Alyssa  C. Frazee et al.2014). Transcripts with an P-adjust <0.05 were assigned as differentially  expressed.  Cuffdiff provides statistical routines for determining differential expression in digital  transcript or gene expression data using a model based on the negative binomial  distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned  as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Microglia

growth_protocol: In short, mice brain was dissected from neonatal mice (1–3 days). After washing three times with 5 mL ice-cold wash media (low glucose DMEM supplemented with 1% penicillin-streptomycin) to remove blood. Next, both olfactory bulb and cerebellum were removed. The meningeal layer was carefully stripped to avoid the contaminations of monocytes in blood vessels and not to damage the cortices. The cortices were digested with 3 mL 0.25% trypsin-EDTA (Life Technologies, #25200072) for 20 min, and dispersed to single-cell level by passing through a cell strainer (70 µm). The cell suspension was centrifuged at 500 × g for 5 min at 4 °C and resuspended with growth medium then cultured at 37 °C in humidified 5% CO2, 95% air on poly-D-lysine (10 µg/mL) (Beyotime, #C0312) precoated 75 cm2 cell culture flasks. Medium was replaced every 4-5 days. After cells reached confluence (8–10 days) and microglia were isolated by mild trypsinization with 0.06% Trypsin-EDTA (Life Technologies, #25300054). In detail, treatment of the confluent mixed glial cultures with 0.06% Trypsin-EDTA resulted in detachment of an intact layer of cells containing almost all the astrocytes and leaving behind a highly enriched population of microglia. Microglia cultures stained CD11b+CD45lo >95%. After the isolation procedure, the attached microglia were allowed to recover for 48 h and cells were further plated as required for the specific experiments.

extract_protocol:
Total RNA were extracted by using TRIZol regaent following standard protocol
RNA degradation and contamination were monitored on 1% agarose gels. The RNA purity and RNA integrity were checking using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). A total amount of 3 μg RNA per sample was used as input material and ribosomal RNA (rRNA) was removed using Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), then rRNA free residue were further cleaned up using ethanol precipitation. Subsequently, sequence libraries were established using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, MA, USA) according to manufacturer’s instruction, which were purified using AMPure XP system. The seuquence libraries quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) following manufacturer’s recommendations. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform (Novogene, Beijing, China) and 150bp paired-end reads. Cuffdiff (v2.1.1) was used to calculate fragments per kilo-base of exon per million fragments (FPKMs) of both lncRNAs and coding genes in each sample(48). Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (48). Genes those exhibited a fold change > 4 and P-adjust <0.05 were filtered as differentially expressed genes.

treatment_protocol: Primary microglia was infected with HSV-1(MOI 0.5) for 12 hours.Corresponding microglia without HSV-1 infection were selected as control.

value: neonatal mice (1–3 days)

tag: cell type

value: Primary Microglia

value: Wild-type

tag: infection

value: without HSV-1 infection


title: HSV-1

tag: strain

value: Primary microglia

value: HSV-1 infection


title: RNA_INTSF8_CON_Day 0

source_name: Control_Day 0_Ovary

tag: treatment

value: Day 0


title: J20/apoE4-KI_Bumetanide_03 10x snRNA-seq

value: Bumetanide treated


title: RNA_INTSF9_CON_Day 0

value: ovary

value: adult


title: RNA_INTSF6_CON_Day 0

value: female

value: Control


title: RNA_INTSF7_CON_Day 0


title: RNA_INTSF24_CON_Day 2


title: apoE4-KI_Vehicle_03 10x snRNA-seq

data_processing:
The mouse reference (mm10-3.0.0, Ensembl 97) pre-mRNA genome was created via 10X Genomics Cellranger (v. 2.2.0) mkref function
Reads from each sample were aligned to their respective genomes and aggregated using the 10X Cellranger pipeline (v. 2.2.0) with no modifications.
Genome_build: mm10-3.0.0, Ensembl 97
Supplementary_files_format_and_content: filtered gene matrices
Supplementary_files_format_and_content: raw gene matrices

source_name: apoE4-KI Mouse Hippocampus

extract_protocol:
The snRNA-seq protocol was modified based on 10x Genomics Sample Preparation Demonstrated protocols, Isolation of Nuclei for Single Cell RNA Sequencing. All procedures and samples were harvested and run in randomized order at the same time to minimize any batch effects. Mouse hippocampi were acutely dissected on ice. Dissected hippocampi were placed in 2mL Hibernate A®/B27®/GlutaMAX™ (HEB) medium in a 5mL tube. The HEB medium was removed to a 15mL conical and kept on ice. 2mL of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Nonidet™ P40 Substitute in Nuclease-Free Water) were added to the tissue, and the hippocampi were homogenized by suctioning10x through a 21G needle. After homogenization, the tissue was lysed on ice for 15 min, swirling 2-3x during this incubation period. The reserved chilled HEB media was then returned to the lysed tissue solution, and the tissue was further triturated with 5–7 passes through a 1mL pipette. A 30m cell strainer (MACS Smart Strainer; Miltenyi Biotech 130-110-915) was washed with 1mL of PBS, and the lysed tissue solution was filtered through the strainer to remove debris and clumps. Filtered nuclei were centrifuged at 500 rcf for 5min at 4°C. The supernatant was removed, and nuclei were resuspended in 1mL of Nuclei Wash and Resuspension Buffer (1X PBS with 1.0% BSA and 0.2U/µl RNase Inhibitor), then centrifuged a second time at 500 rcf for 5 min at 4°C, and resuspended in 400 µl of Nuclei Wash and Resuspension Buffer. DAPI was added to a final concentration of 0.1µg/mL, and the nuclei solution was filtered through 35µm cell strainer before loaded onto the BD FACSAria-II at the Gladstone Institutes’ Flow Cytometry Core. The DAPI-positive nuclei were selected by gating on DAPI-positive events, excluding debris and doublets. RNA was extracted in accordance with the 10X Genomics isolation of nuclei for single cell RNA sequencing protocol.
Sequencing libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10x Genomics, 120267) for apoE4-KI mouse hippocampal samples according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer  (PE100) at the UCSF Center for Advanced Technology Core. We sequenced the library to a target read depth of over 25,000 reads per nucleus, resulting in 52,180 post-normalization mean reads per cell, a median of 979 genes per nucleus for samples from apoE4-KI mice.

treatment_protocol: Twelve-month-old apoE4-KI mice (n = 3 per condition) received daily i.p. injections of vehicle or bumetanide (0.2 mg/kg body weight) for 60 days

value: 12 mo old

value: apoE4-KI Mouse Hippocampus


title: iPSC DMSO Treated 2 RNA-seq

data_processing:
Sequence data were aligned with the STAR short read aligner and counts per feature were obtained with the featureCounts function from the Subread package.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data is a raw count file output from the Subread pipeline

source_name: Human iPSC-derived neurons

growth_protocol: Human iPSC lines were generated as described37 from skin fibroblasts of a subject with an apoE4/4 genotype and were maintained under feeder-free conditions in mTeSR1 medium (STEMCELL Technologies). Human iPSCs were routinely passaged at 1:2-1:4 by brief treatment with Accutase (Millipore) and scraping. The hiPSC protocol was approved by the Committee on Human Research at the University of California. hiPSCs were differentiated into neurons as described37. Human iPSCs were treated with collagenase IV (Stem Cell Technologies) and grown in suspension as embryoid bodies in hES medium without bFGF. The medium was replaced every day for 5 days. On day 5, embryoid bodies were grown in Neural Induction Medium containing Dulbecco’s modified Eagle’s medium/F12 and Neurobasal Medium (1:1, Thermo Fisher), 1% N2 Supplement (Life Technologies), 1% B27 Supplement (Life Technologies), nonessential amino acids, and 0.5% penicillin/streptomycin (Life Technologies) supplemented with inhibitors of the TGF-β receptor (SB431542, Stemgent; 5 μM) and the bone morphogenetic protein receptor (LDN-193189, Stemgent; 0.25 μM). On day 7, spheres were transferred to wells coated with Matrigel (BD Biosciences) and grown in Neural Progenitor Medium, which consisted of Neural Induction Medium without SB and LDN, but containing 10 ng/ml bFGF (PeproTech), 10 ng/mL epidermal growth factor (EGF) (PeproTech), and 2 μg/ml heparin (Sigma). Attached neuroepithelial cells were fed every other day for 7 days. Neural rosette structures appeared by around day 15, were lifted off the plate, and grown in suspension in Neural Progenitor Medium to form neurospheres. For neuronal differentiation, neurospheres were dissociated with Accutase and plated on culture plates coated with 100 μg/ml poly-l-ornithine (Sigma) and 10 μg/ml laminin (Sigma). Neuronal cultures were maintained in Neural Differentiation Medium consisting of Neural Progenitor Medium, brain-derived neurotrophic factor (10 ng/ml; PeproTech), and glial cell–derived growth factor (10 ng/ml; PeproTech) without bFGF, EGF, or heparin. Neurons were observed after several days and were further differentiated for 6 weeks.

extract_protocol:
Total RNA was extracted and purified with the Qiagen RNeasy Micro kit, which included a DNase treatment. cDNA was generated from full-length RNA (50 ng per sample) with the NuGEN RNA-Seq V2 kit, which uses the single primer isothermal amplification method to deplete ribosomal RNA, and sheared by Covaris to yield fragments of uniform size. The NuGen Ultralow system V2 was used for adding adapters and for barcoding and amplification. The resulting RNA libraries were purified with Agencourt XP magnetic beads, and quantified by qPCR after quality control with an Agilent Bioanalyzer. The libraries were pooled and sequenced with a HiSeq 4000 instrument (Illumina) for single-end (SE50) sequencing.
Sequence data were aligned with the STAR short read aligner67 and counts per feature were obtained with the featureCounts function from the Subread package68.

treatment_protocol: At xxx weeks, neurons were treated for 6 hours with 10 mM bumetanide (YH do you have the number of which bumetanide we used) or vehicle (DMSO) (n = 3 for each group)

value: Human iPSC-derived neurons

value: Treated with DMSO


title: RNA_INTSF23_CON_Day 2

value: Day 2


title: J20/apoE4-KI_Bumetanide_02 10x snRNA-seq

value: J20/apoE4-KI Mouse Hippocampus


title: S_10X010Wt

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.1, using the cellranger count function  was used to perform single cell 3' gene counting using default parameters
The cellranger aggr function was used to merge the WT and HET datasets with reads normalization by mapped reads enabled.
Genome_build: refdata-cellranger-GRCh38-1.2.0
Supplementary_files_format_and_content: h5 aggregated matrix data of filtered barcode matrices is provided

source_name: hiPSC-derived β-like cells

growth_protocol: iPSCs were trypsinized into single cells using TrypLETM Express (Gibco, 12605-010), and seeded in at a density of 1 million cells/ml into low-attachment plates in mTeSR™1 (STEMCELL Technologies, #85850) with 10 μM Y-27632 (STEMCELL Technologies, #72302). Media was changed the next day into mTeSR™1 without Y-27632, and cells were differentiated into definitive endoderm, primitive gut tube, pancreatic progenitor, endocrine progenitors, and finally β-like cells following a published protocol (Pagliuca et al., 2014)

extract_protocol:
1. 3D beta-like cell organoids were washed with PBS once.  2. Incubated with TrypLE for 1 min to dissociate the cells.  3. Diluted 5x with PBS.  4. Centrifuged at 250 rcf for 5 mins.  5. Supernatant discarded.   6. Cells resuspended in 0.04% BSA in PBS, and centrifuged at 150 rcf for 3 mins. Removed supernatant. This was repeated two more times.  7. Resuspended cells in 0.04% BSA in PBS and passed cells through a 40 μm strainer.  8. Counted cells. Ensured at least 50,000 live cells available, with at least 70% cell viability.  9. Resuspended cells at a density of 700 cells/ul. No dead cell removal was carried out.
Single cells were lysed in droplets using the 10X Chromium instrument  Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide

value: hiPSC-derived beta-like cells

tag: genotype/variation

value: wild type


title: RNA_INTSF11_CON_Day 0


title: iPSC Untreated 3 RNA-seq

value: Untreated


title: apoE4-KI_Vehicle_02 10x snRNA-seq

value: Vehicle treated


title: S_10X01_1_het

value: INS+/C109Y mutation


title: iPSC Untreated 2 RNA-seq


title: apoE4-KI_Vehicle_01 10x snRNA-seq


title: apoE4-KI_Bumetanide_03 10x snRNA-seq


title: iPSC Untreated 1 RNA-seq


title: iPSC Bumetanide Treated 3 RNA-seq

value: Treated with 10 uM Bumetanide


title: apoE4-KI_Bumetanide_02 10x snRNA-seq

value: Bumetanide treated


title: iPSC DMSO Treated 3 RNA-seq


title: 3D cholangiocytes

city: Toronto

first: Shinichiro

last: Ogawa

address: 101 College Street

institute: McEwen Stem Cell Institute

data_processing:
Raw data consisted of CellRanger-processed, filtered feature matrices
Dataseta were read in and concatenated using scanpy.read 10xmtx
Genome-build:hg38
Supplementary files format and content: .mtx, .txt (X2). Standard for 10x
Prepreprocessing pipeline (Cell Ranger 3.0)
Genome_build: GRCH38

source_name: Day 55 3D choalngiocytes

growth_protocol: We used s newly developed protocol for  hPSC-derived cholangiocyte differentiation

extract_protocol:
10x Genomics Microfluidic Platform RNA libraries were prepared for sequencing using standard Illumina protocols
10x Chromium single cell workflow

value: ES-derived cholangiocytes


title: human neural stem cells exposed to 1 μM bisphenol A

city: Jinan

first: Qinglu

state: Shandong

address: 10600 Century Avenue

institute: Shandong Sport University

data_processing:
FASTQ files were uploaded to the BaseSpace Suite (Illumina) and aligned using the RNA-Seq Alignment application (version 1.0.0), in which STAR was selected to align the sequences and the maximum number of mismatches was set to 14 following the recommendation by Lexogen. Output files were analyzed using Cufflinks Assembly and DE application (version 2.1.0) in the BaseSpace Suite to determine the differentially expressed genes (DEGs), used to generate an expression heatmap and an FPKM scatter plot.
these genes were analyzed using ClueGO (version 2.3.3) and CluePedia (version 1.3.3), which are Cytoscape software applications (version 3.5.1).
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: cortical region of human fetal brain tissue

growth_protocol: Cells reached to 80% confluency

extract_protocol:
Total RNA was harvested from human neural stem cells using Trizol reagent. Following the assessment of the quality of the RNA using a Qubit™ 3 Fluorometer (Invitrogen), samples were prepared using a QuantSeq 3' mRNA-Seq library prep kit FWD for Illumina (Lexogen) following the manufacturer’s protocol and then analyzed on a NextSeq 500 sequencing system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells exposed to 1 μM BPA for 24h

value: neural stem cell

value: 1 μM bisphenol A for 24h


title: iPSC Bumetanide Treated 2 RNA-seq


title: 2D cholangiocytes

source_name: Day 55 2D cholangiocytes


title: J20/apoE4-KI_Bumetanide_01 10x snRNA-seq


title: Wild type human neural stem cells


title: iPSC Bumetanide Treated 1 RNA-seq


title: apoE4-KI_Bumetanide_01 10x snRNA-seq


title: iPSC DMSO Treated 1 RNA-seq


title: G24_1

status: Public on Oct 02 2021

city: Yangling

first: Bo

last: Zhang

state: Shanxi

address: College of Horticulture, Northwest A﹠F University

description: Malus × domestica Borkh.

data_processing:
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
After eliminating the reads with sequencing adapters and the low-quality reads from the raw data, the remaining clean reads were aligned to the Malus Genome GDDH13 reference sequence (version 1.1) using the HISAT2 software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with Cufflinks.
Genome_build: ftp://ftp.bioinfo.wsu.edu/species/Malus_x_domestica/Malus_x_domestica-genome_GDDH13_v1.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Malus domestica

source_name: Apple peel samples with 24h light after unbagging

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the mRNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: apple fruit peel

tag: time


title: G24_3

department: College of Horticulture, Northwest A﹠F University

description: Malus × domestica Borkh.


title: G6_3

institute: College of Horticulture, Northwest A﹠F University

description: Malus × domestica Borkh.

source_name: Apple peel samples with 6h light after unbagging


title: G0_2

description: Malus × domestica Borkh.

source_name: Apple peel samples with 0h light after unbagging


title: G6_1

description: Malus × domestica Borkh.


title: G0_1

description: Malus × domestica Borkh.


title: G0_3

description: Malus × domestica Borkh.


title: 170721_9_(MoGene-2_0-st)

city: Seoul

first: Yongsik

last: Cho

address: 1 Gwanak-ro, Gwanak-gu, Seoul 08826. School of Biological Sciences, SNU

country: South Korea

institute: Seoul National Universiy

description:
Tendons transfected with Ctrp3-overexpression vectors_rep1
SAMPLE 9

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: The Achilles tendon was separated from soleus muscle and were homogenized using a tissue homogenizer, and total RNA was extracted using TRI reagent and the manufacturer's protocol.

treatment_protocol: For in vivo transfections, mice were anesthetized and the right hindlimb was shaved. Forty micrograms of plasmid DNA (in 30 µl sterile saline) was introduced using intratendinous injection of the musculotendinous junction between the Achilles tendon and the gastrocnemius muscle using a 31-gauge insulin syringe. Conductivity gel was applied to the shaved skin, with the Achilles tendon and gastrocnemius muscle located between the caliper electrodes with a 5-mm gap. Electroporation was done with a BTX Gemini X2 (Harvard Bioscience, Inc.) using 225 V/cm, 25 ms, 5 times.   For treatment with the neutralizing antibody for mice, a peritendinous injection was given around the Achilles tendon with 0.063 mg/kg of anti-CTRP3 antibody

value: Achilles tendon


title: 170721_8_(MoGene-2_0-st)

description:
Tendons transfected with control vectors_rep2
SAMPLE 8

label: biotin-labeled with TdT (terminal deoxynucleotidyl transferase)


title: 170721_10_(MoGene-2_0-st)

description:
Tendons transfected with Ctrp3-overexpression vectors_rep2
SAMPLE 10


title: G24_2

description: Malus × domestica Borkh.


title: 170721_5_(MoGene-2_0-st)

description:
Overuse-induced tendinopathy tendons with anti-CTRP3 antibody_rep1
SAMPLE 5


title: 170721_6_(MoGene-2_0-st)

description:
Overuse-induced tendinopathy tendons with anti-CTRP3 antibody_rep2
SAMPLE 6


title: 170721_7_(MoGene-2_0-st)

description:
Tendons transfected with control vectors_rep1
SAMPLE 7


title: 170721_4_(MoGene-2_0-st)

description:
Overuse-induced tendinopathy tendons with control IgG antibody_rep2
SAMPLE 4


title: 170721_1_(MoGene-2_0-st)

description:
Naïve tendons_rep1
SAMPLE 1

source_name: Naïve tendons_rep1


title: 170721_2_(MoGene-2_0-st)

description:
Naïve tendons_rep2
SAMPLE 2

source_name: Naïve tendons_rep2


title: D10-CAF2

city: Chiba city

first: Shunichi

last: Asai

address: 1-8-1 inohana,chuo-ku

institute: Chiba University Graduate School of Medicine

description: CAF samples not derived from same individuals who provided the normal and head and neck squamous cell cancer tissues.

data_processing:
NextSeq500 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FastQC version 0.11
Sequenced reads were aligned to UCSC Human hg38 using GeneGlobe: Data Analysis Center(Qiagen)
Annotation depended on miRBase21 Release 21.
Seq-data were analyzed using StrandNGS v4.0 and R v3.6.1.
Sequenced reads were normalized by trimmed mean of M-value normalization (TMM) .
Genome_build: UCSC Human hg 38
Supplementary_files_format_and_content: Processed datafiles include raw data and  normalized data for each sample.
Supplementary_files_format_and_content: Comparison was tested by moderated t-test. Multiple corrections were perfomed by Benjamini-Hochberg (FDR).

source_name: cancer associated fibroblast

growth_protocol: Cancer associated fibroblasts were cultured  in Dulbecco's Modified Eagle Medium with  penicillin/streptomycin and fetal bovine serum

extract_protocol:
Total RNA was harvested using Trizol reagent and  PureLink™ RNA Mini Kit (Invitrogen)
RNA libraries were prepared for sequencing using QIAseq miRNA Library Kit (Qiagen)

value: tongue

value: cancer associated fibroblast

tag: patient diagnosis

value: head and neck squamous cell cancer

tag: tumor stage


title: D06-A14T

source_name: head and neck squamous cell cancer tissue


title: D05-A19T

value: head and neck squamous cell cancer tissue


title: D04-A21T


title: D09-CAF1

value: oral floor


title: D03-A14N

source_name: normal oral epithelial tissue

value: normal oral epithelial tissue


title: D01-A21N


title: D02-A19N


title: 170721_3_(MoGene-2_0-st)

description:
Overuse-induced tendinopathy tendons with control IgG antibody_rep1
SAMPLE 3


title: T6

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
processed data file:
gene_counts.tsv
normalized_gene_counts.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalized_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

source_name: DG

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

value: Dentate gyrus granule cell

value: DG

tag: quality control

value: Passed


title: UN-SCC679_rep1

city: Pamplona

first: Luis

middle: M

last: Montuenga

state: Navarra

address: Edificio CIMA. Avda Pio XII 55

department: Solid Tumors Program

country: Spain

institute: Cener for Applied Medical Research (CIMA). University of Navarra

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 genome using align function of Rsubread
Calculate raw counts with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts from featureCounts

source_name: Lung Squamous carcinoma (LUSC)

extract_protocol: Samples were prepared with the Illumina TruSeq Stranded mRNA kit following manufacturer’s indications and sequenced as reverse paired-end (50 bp) runs on the Nextseq sequencer

value: A/J

tag: cell line

value: Lung Squamous carcinoma (LUSC)


title: UN-SCC680_rep2


title: UN-SCC680_rep3


title: UN-SCC679_rep3


title: UN-SCC680_rep1


title: UN-SCC679_rep2


title: T2

description:
processed data file:
gene_counts.tsv

value: Failed


title: K128


title: T1


title: K127


title: Female6-Control

city: Shenzhen

first: Xiaomin

last: Wu

state: Guangdong

address: Baocheng Longjing 2nd Road No.118, Bao’an District

department: Department of Orthopaedics and Traumatology

institute: People’s Hospital of Shenzhen Baoan District

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) and a spacer segment of polyethylene glycol toextend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device)

data_processing: Images were digitized using Array-Pro image analysis software (Media Cybernetics). Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression

source_name: human osteoarthritis synovial fluid

label_protocol: The assay started from 4 to 8μg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

growth_protocol: Synovial fluid samples were separated by centrifugation at 5,000 × g for 10 min at 4℃. Supernatants were collected and stored at -80 °C for exosome isolation

extract_protocol: Total RNA was extracted by Total RNA Purification Kit（LC Sciences, Cat. TRK-1001）following the manufacturer's instructions.

tag: tissue

value: osteoarthritis synovial fluid

tag: disease

value: Control

value: Female


title: Male5-Control

treatment_protocol: Synovial fluid samples were separated by centrifugation at 5,000 × g for 10 min at 4℃. Supernatants were collected and stored at -80 °C for exosome isolation

value: Male


title: Female2-OA

value: Osteoarthritis


title: Female3-OA


title: Male4-Control


title: Male1-OA


title: K125

description:
processed data file:
gene_counts.tsv


title: K124

description:
processed data file:
gene_counts.tsv


title: K118


title: K121


title: K119


title: K120


title: K115


title: K116


title: K123


title: G6_2

description: Malus × domestica Borkh.

value: apple fruit peel


title: K113


title: K114


title: K112


title: K122


title: K109


title: K108


title: K106


title: K117


title: K105


title: K104


title: K126

description:
processed data file:
gene_counts.tsv


title: K107


title: K101


title: K103


title: K102


title: K100

description:
processed data file:
gene_counts.tsv


title: K99


title: K98


title: K97


title: K96


title: K94


title: K93


title: K95


title: K111


title: K110


title: K92


title: K91


title: K90


title: K86


title: K87


title: K89


title: K84


title: K88


title: K83


title: K85


title: K81


title: K82


title: K78


title: K75


title: K77


title: K76


title: K79


title: K73


title: K74


title: K71


title: K62


title: K67


title: K66


title: K70


title: K72


title: K61


title: K53


title: K63

description:
processed data file:
gene_counts.tsv


title: K52


title: K60


title: K51


title: K50


title: K80


title: K45


title: K47


title: K48


title: K41


title: K40


title: K42


title: K38


title: K32


title: K39


title: K34


title: K29


title: K24


title: K18


title: K14


title: K28


title: K8


title: K4


title: K22


title: K2


title: K49


title: K46


title: K12


title: J90L


title: J90


title: J86L


title: J93


title: K36


title: J86


title: J84

description:
processed data file:
gene_counts.tsv


title: J80


title: J76


title: J77

description:
processed data file:
gene_counts.tsv


title: J51


title: J5


title: K10


title: J49


title: J50

description:
processed data file:
gene_counts.tsv


title: K6


title: J47


title: J4


title: T5

description:
processed data file:
gene_counts.tsv


title: J37


title: J19


title: J31


title: J35


title: J13


title: J20


title: J18


title: J36