title: OP-1250 1 Ribociclib 25 R3

city: SAN FRANCISCO

first: Alison

last: Parisian

address: 780 Brannan St

institute: Olema Pharmaceuticals

data_processing:
Gene counts and differential gene expression analyses were carried out using CLC Genomics Workbench (Qiagen)
Reads were mapped to GRCh38 reference
Reads which mapped exclusively to the murine reference genome GRCm39 were filtered out prior to analysis
Thresholds of absolute fold change > 2 and FDR-adjusted p-value ≤ 0.05 were used to determine differentially expressed genes
Assembly: hg38
Supplementary files format and content: Counts files

source_name: MCF7 xenograft

growth_protocol: MCF7 cells were implanted into immuno-deficient mice supplemented with estradiol and mice were treated by oral gavage with OP-1250, palbociclib, ribociclib, OP-1250+palbociclib or OP-1250+ribociclib for 28 days prior to study termination and sample collection.

extract_protocol:
RNA extraction, polyA selection
NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: Mice were dosed by oral gavage with 1 mg/kg or 10 mg/kg OP-1250, 25 mg/kg or 75 mg/kg palbociclib or ribociclib or the combination of OP-1250 and CDK4/6 inhibitor for 28 days prior to study termination and sample collection.

value: MCF7 xenograft

value: breast cancer xenograft

value: OP-1250 1mg/kg Ribociclib 25mg/kg


title: PBMC_normal_nonfasting_SCR [60]

status: Public on Sep 01 2023

type: RNA

city: Oslo

first: Kirsten

middle: B

last: Holven

address: Sognsvannsveien 9

department: Department of Nutrition

country: Norway

institute: University of Oslo

description: Gene expression data from PBMCs isolated from non-fasting blood samples collected at a screening visit for a randomized trial

hyb_protocol: Gene expression measurements were performed by hybridizing the amplified RNA to Illumina HumanHT-12 v4 Expression BeadChip (Illumina Inc., California, USA) according to the manufacturer’s instructions.

scan_protocol: Samples were scanned using Illumina HiScan System (Illumina Inc., California, USA).

data_processing:
The Illumina HumanHT-12 v4 Expression BeadChip provides genome-wide measurements of the expression of over 48,000 probe sets. IlluminaGenome Studio was used to calculate and report a detection P value, which represents the confidence that a given transcript is expressed above the background. A gene was defined as expressed when relevant probes with a P value below 0.01 were found in more than five samples. After hybridization and scanning, a manual quality control was performed investigating density plots and hierarchical clustering of raw probe densities. One probe per gene (max IQR) was selected for further analysis.
After correcting for background noise, using normexp background correction (neqc filtration, Limma), quantile normalization of the data was performed using the Illumina GenomeStudio software, version 1.7.0. Data were log2-transformed and exported to R [R Core Team (2023). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/] for biostatistical analysis.
Analyses in Bålsrud et al. (submitted):
For the PBMC gene expression analyses, in an initial untargeted approach, we fitted standard linear regression models for each of the 11925 mRNA transcripts with frailty index (FI) score as the main exposure. The main model was adjusted for age and BMI; we visualized the regression coefficients and P values in a Volcano plot. Two other models were fitted: a crude, unadjusted model, and a model adjusted for age, BMI, and proportion of monocytes and lymphocytes in blood (not shown). In a more targeted approach, we sought to explore cell type-specific genes. To derive an estimate of cell type proportions in the PBMC pool, we performed gene expression decomposition (in silico flow cytometry) using CIBERSORT [Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nature Biotechnology. 2019;37(7):773-82]. We fitted regression models for each CIBERSORT-predicted cell type with FI score as the main exposure (both crude models and models adjusted for age and BMI). We then extracted the top 30 genes/mRNA transcripts associated with CIBERSORT-predicted monocytes and associated them with the six serum inflammatory biomarkers in linear regression models adjusting for age and BMI. The resulting β coefficient matrix was visualized as a heatmap (ComplexHeatmap R package).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC, non-fasting blood sample, screening visit

label_protocol: Total RNA preparation (incl. biotin labelling) and amplification were performed using the Illumina Total Prep RNA Amplification Kit (Illumina Inc., California, USA).

extract_protocol: Blood samples were collected in non-fasting state in BD Vacutainer® CPTTM cell preparation tubes with sodium heparin (Becton Deckenson, NJ, USA). Within two hours of blood collection PBMCs were collected by density gradient centrifugation of the blood samples (1636g) for 25 min at room temperature. The cells were washed twice (300g, 10 min at RT) in phosphate-buffered saline (PBS) without calcium chloride and magnesium chloride. After the last washing step, excess PBS was discarded. The pellet was dissolved in the remaining liquid and transferred to an Eppendorf tube, centrifuged (13,000g, 3 min at 4 °C) and frozen at −80 °C until total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA quantity was measured using NanoDrop-1000 (NanoDrop Technologies, Inc., Delaware, USA), while RNA quality was checked with Aglient 2100 Bioanalyzer (Agilent Technologies, Inc., California, USA).

tag: fi score (range 0-1)

tag: sex (female/male)

value: Female

tag: age (y)

tag: bmi (kg(m2)

tag: monocytes (absolute values x109/l)

tag: lymphocytes (absolute values x109/l)


title: PBMC_normal_nonfasting_SCR [59]


title: OP-1250 1 Ribociclib 25 R2

type: SRA

state: California

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: cell line

tag: cell type

tag: treatment


title: WJL2297_RLF_N023

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

library_source: genomic

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
Assembly: The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Supplementary files format and content: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS

molecule: genomic DNA

organism: Mus musculus

source_name: vAbl-ProB

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. DNA-PKcs inhitors, DPKi #1 (Nu7441, 0.5 µM) and DPKi #2 (Nu7026, 20 µM)were added to some of the samples the same day as STI-571.

value: vAbl-ProB

value: pro-B cells

tag: genotype


title: Single granulosa cell (LCM) GC066_S115

city: Kashihara

first: Hiroki

last: Ikeda

address: 840 Shijo-Cho, Kashihara, Nara

country: Japan

institute: Nara Medical University

data_processing:
After trimming polyA/T sequences, adapter sequences, and poor quality reads, using fastp (v. 0.20.0) and cutadapt (ver. 1.16), the sequenced reads were aligned to the GRCm38 mouse genome assemblywith ERCC spike-in RNA sequences using the HiSAT2 (v. 2.1.0).
Best-matched reads on annotated genes were counted using HTSeq 0.10.0 with a modified GRCm38 gtf file which is extended up to 10 Kb downstream from transcription termination sites of reference genes.
Mapped reads on exons and exon-exon junctions were counted by featureCounts (v2.0.1) with the GRCm38 gtf file and the option "-J" "-p" "-M" "-O" "-t　exon" "-g　transcript_id".
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene, exon and exon-exon junction counts for every sample.

source_name: Granulosa cell

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in a medium containing 2iLIF [GSK inhibitor (CHIR99021; 3 µM), MEK inhibitor (PD0325901; 0.4 µM), and LIF (1 U/µL) (2iLIF)]

extract_protocol:
Cells were isolated with LCM in 6.4 μL of cell lysis buffer (1× GeneAmp PCR Buffer II [Thermo Fisher], 1.5 mM MgCl2 [Thermo Fisher], 0.5% sodium deoxycholate [SDc] [Nacalai Tesque], and 5 mM dithiothreitol [DTT] [Thermo Fisher] dissolved in deionized distilled water [Gibco] containing 4 U RNaseOUT [Thermo Fisher], 0.4 U porcine liver RNase inhibitor [Takara Bio], 0.05 mM dNTPs [Takara Bio], ERCC RNA Spike-In Mix 1 [Thermo Fisher], and 1.6 ng V1[dT]24 primer ) in the caps of PCR tubes, and spun down into the tubes by brief centrifugation.  Cells were then lysed at 70°C for 6 min, followed by the addition of 2.8 µL quenching buffer (25% Triton X-100 [Nacalai Tesque] and 1% bovine serum albumin [BSA] [Takara Bio]) and incubation at 70°C for 90 sec to quench the denaturing activity of SDc.
The cDNA synthesis and amplification onward were performed as described previously with minor modifications [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. In brief, the first-strand cDNA was synthesized by SuperScript III [Thermo Fisher] and incubating at 50℃  for 5 min followed by heat inactivation at 70℃  for 10 min.  The excess RT primers were degraded by exonuclease I and incubating at 37℃ for 30 min followed by heat inactivation at 80℃ for 25 min. The first-strand cDNA product was poly dA-tailed by TdT and incubating at 37℃  for 1 min followed by heat inactivation at 70℃ for 10 min. Second-strand cDNA synthesis were performed by adding 9.5 μL reaction mixture of ExTaq, Hot Start version [Takara Bio] and V3[dT]24 primer in the ExTaq buffer with the following thermal cycling program (95℃  for 3 min, 50℃  for 2 min, and 72℃  for 3 min). cDNA amplification was performed by addingthe mixture of V1[dT]24 and ExTaq, Hot Start version [Takara Bio] in the ExTaq buffer with the following thermal cycling program (95℃  for 1 min; 20 cycles of 95℃  for 30 sec, 67℃  for 1 min and 72℃  for 3 min with a 6 sec elongation per cycle; and 72℃  for 10 min).  The amplified cDNA was purified with a 0.6× volume of AxyPrep MAG PCR clean-up reagent (Axygen) according to the manufacturer's instructions. Preparation of the libraries for SC3-seq was performed essentially as previously described (Nakamura et al., 2015)(Nakamura et al., 2017).  For Y-adapter sequencing, single-cell cDNAs were pre-amplified using the primers (V3[dT]24, V1[dT]24) and ExTaq HS with the thermal cycling program (95℃  for 3 min; 4 cycles of 95°C for 30 sec, 67℃  for 1 min and 72℃  for 5 min; 72℃  for 10 min). Pre-amplified cDNAs were then subjected to the primer-dimer removal, sonication, end polishing, and the size selection as in SC3-seq. Then, purified cDNA was dA-tailed in a 10 μL dA tailing mixture with incubation at 72℃  for 10 min. The dA-tailed product was subjected to the Y-shaped adaptor ligation by adding a mixture of Y-adaptor and NEB Next Quick Ligation Reaction Buffer and incubating at 20℃  for 15 min and at 72℃  for 20 min. The ligation product was purified with a 0.9×volume of AxyPrep reagent, and subjected to additional PCR amplification in 20 μL with the thermal cycling program (95℃  for 3 min, 55℃  for 1 min, and 72℃  for 1 min; 11 cycles of 95℃  for 30 sec, 60℃  for 1 min, and 72℃  for 1 min; and 72℃  for 3 min), followed by DNA purification with a 0.9×volume of AxyPrep reagent.

treatment_protocol: Mouse ovaries were excised from 8-week-old female mice and snap-frozen in liquid N2. Then, the frozen ovaries were sunk in 10% PVA in cryomolds, and again frozen in liquid N2. The embedded ovaries were sectioned using a CM1860UV cryostat at a thickness of 15 μm, dried at room temperature for more than 1 h, fixed and stained with 1% cresyl violet acetate dissolved in 50% isopropanol, washed with 100% isopropanol, and dried for more than 1 h. Cells in the frozen sections were isolated using a laser microdissection system PALM MB4 (Zeiss).

tag: collecting conditions

value: LCM

tag: class

value: Neighboring

tag: analysis target

value: gene expression (sc3-seq.)


title: ESM1-WT tumor 2

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Alignment was carried out using the Burrows-Wheeler Aligner mem
Aligned to mm10 reference genome
peak calling using MACS2 (with parameter setting-nomodel-shift 75)
GO enrichment analysis and peak annotation using HOMER
Genome_build: mm10

source_name: Tumor tissue

extract_protocol:
Sequencing was carried out by the UCLA ICNN at UCLA. Samples were multiplexed in 1 lanes.
PE 2x75 using Illumina HiSeq4000

treatment_protocol: All animal experiments were performed at the UAB under an Institutional Animal Care and Use Committee (IACUC)-approved protocol according to NIH guidelines (#20295).

tag: strain

tag: genotype/variation

value: WT

tag: rna sample type

value: WT group


title: OP-1250 1 Ribociclib 25 R1


title: Single granulosa cell (LCM) GC064_S114


title: WJL2296_RLF_N023


title: PBMC_normal_nonfasting_SCR [57]


title: Ribociclib 25 R3

value: Ribociclib 25mg/kg


title: Single granulosa cell (LCM) GC058_S113

value: Non-neighboring


title: WJL2295_RLF_N023


title: Ribociclib 25 R2


title: PBMC_normal_nonfasting_SCR [55]


title: WJL2299_RLF_N023


title: PBMC_normal_nonfasting_SCR [56]


title: PBMC_normal_nonfasting_SCR [58]


title: PBMC_normal_nonfasting_SCR [54]


title: WJL2294_RLF_N023


title: Single granulosa cell (LCM) GC051_S111


title: Ribociclib 25 R1


title: WJL2292_RLF_N023


title: WJL2293_RLF_N023


title: Single granulosa cell (LCM) GC050_S110


title: PBMC_normal_nonfasting_SCR [53]


title: OP-1250 1 R3


title: PBMC_normal_nonfasting_SCR [52]


title: Single granulosa cell (LCM) GC047_S109


title: OP-1250 1 R1


title: OP-1250 1 R2


title: Single granulosa cell (LCM) GC046_S108


title: PBMC_normal_nonfasting_SCR [50]


title: Single granulosa cell (LCM) GC057_S112


title: Single granulosa cell (LCM) GC045_S107


title: WJL2289_RLF_N023

value: WT + DPKi #2


title: PBMC_normal_nonfasting_SCR [49]


title: WJL2288_RLF_N023


title: Vehicle R2

value: Vehicle


title: Single granulosa cell (LCM) GC043_S106


title: PBMC_normal_nonfasting_SCR [47]


title: PBMC_normal_nonfasting_SCR [51]


title: Vehicle R1


title: WJL2287_RLF_N023


title: Vehicle R3


title: PBMC_normal_nonfasting_SCR [61]


title: WJL2286_RLF_N023


title: PBMC_normal_nonfasting_SCR [48]


title: OP-1250 1 Palbociclib 25 P4

value: OP-1250 1mg/kg Palbociclib 25mg/kg


title: WJL2290_RLF_N023

value: WT + DPKi #1


title: PBMC_normal_nonfasting_SCR [46]


title: Single granulosa cell (LCM) GC042_S105


title: OP-1250 1 Palbociclib 25 P3

value: MCF7 xenograft


title: WJL2291_RLF_N023


title: Single granulosa cell (LCM) GC041_S104


title: PBMC_normal_nonfasting_SCR [45]


title: Single granulosa cell (LCM) GC040_S103


title: WJL2285_RLF_N023


title: Single granulosa cell (LCM) GC038_S102


title: WJL2284_RLF_N023


title: OP-1250 1 Palbociclib 25 P2

value: breast cancer xenograft


title: PBMC_normal_nonfasting_SCR [44]


title: OP-1250 1 Palbociclib 25 P1


title: Palbociclib 25 P4

value: Palbociclib 25 mg/kg


title: WJL2283_RLF_N023


title: Single granulosa cell (LCM) GC037_S101


title: PBMC_normal_nonfasting_SCR [43]

value: Female


title: PBMC_normal_nonfasting_SCR [42]


title: Single granulosa cell (LCM) GC036_S100


title: Palbociclib 25 P3


title: WJL2281_RLF_N023

value: vAbl-ProB


title: WJL2280_RLF_N023

value: pro-B cells


title: Single granulosa cell (LCM) GC024_S95

value: LCM


title: Single granulosa cell (LCM) GC035_S99

value: Neighboring


title: PBMC_normal_nonfasting_SCR [41]


title: Palbociclib 25 P1


title: PBMC_normal_nonfasting_SCR [40]


title: OP-1250 10 P4


title: WJL2279_RLF_N023


title: Palbociclib 25 P2


title: Single granulosa cell (LCM) GC022_S93

value: gene expression (sc3-seq.)


title: Single granulosa cell (LCM) GC023_S94


title: OP-1250 10 P3


title: WJL2282_RLF_N023


title: WJL2278_RLF_N023


title: OP-1250 10 P2


title: Single granulosa cell (LCM) GC021_S92


title: WJL2277_RLF_N023


title: PBMC_normal_nonfasting_SCR [38]


title: Single granulosa cell (LCM) GC020_S91


title: PBMC_normal_nonfasting_SCR [39]


title: PBMC_normal_nonfasting_SCR [36]


title: PBMC_normal_nonfasting_SCR [37]


title: WJL2275_RLF_N023


title: PBMC_normal_nonfasting_SCR [35]


title: Single granulosa cell (LCM) GC019_S90


title: PBMC_normal_nonfasting_SCR [34]


title: Single granulosa cell (LCM) GC018_S89


title: OP-1250 1 P4


title: OP-1250 1 P3


title: WJL2274_RLF_N023


title: OP-1250 1 P1


title: WJL2271_RLF_N023


title: Single granulosa cell (LCM) GC015_S86


title: PBMC_normal_nonfasting_SCR [32]


title: WJL2276_RLF_N023

value: WT


title: Vehicle P4


title: PBMC_normal_nonfasting_SCR [33]


title: WJL2273_RLF_N023


title: Single granulosa cell (LCM) GC017_S88


title: OP-1250 1 P2


title: WJL2272_RLF_N023


title: OP-1250 10 P1


title: Single granulosa cell (LCM) GC016_S87


title: Single granulosa cell (LCM) GC013_S84


title: Single granulosa cell (LCM) GC014_S85


title: WJL2270_RLF_N023


title: Single granulosa cell (LCM) GC012_S83


title: PBMC_normal_nonfasting_SCR [31]


title: WJL2268_RLF_N023


title: Vehicle P3


title: Vehicle P2


title: PBMC_normal_nonfasting_SCR [30]


title: Single granulosa cell (LCM) GC011_S82


title: Vehicle P1


title: PBMC_normal_nonfasting_SCR [27]


title: PBMC_normal_nonfasting_SCR [29]


title: PBMC_normal_nonfasting_SCR [28]


title: Elacestrant 3

description: J_Differential_expression_analysis_table.csv

data_processing:
Trim reads (Trimmomatic v.0.36
Mapped to GRCh38 reference with STAR v.2.5.2b
Counts generated using featureCounts from Subread package v.1.5.2 (strand-specific)
Differential expression relative to vehicle calculated using DESeq2
Assembly: hg38
Supplementary files format and content: Counts files
Supplementary files format and content: Differential expression relative to vehicle

growth_protocol: Prior to experiment CAMA1 cells were cultured in Richter’s IMEM supplemented with nonessential amino acids and 10% fetal bovine serum

treatment_protocol: CAMA1 cells were plated in estradiol-depleted charcoal dextran stripped serum-containing media and dosed for 24 hours with 316 nM compound or 100 pM 17-beta estradiol.

value: breast cancer cell line

value: Elacestrant


title: WJL2267_RLF_N023


title: Elacestrant 2


title: WJL2269_RLF_N023


title: WJL2266_RLF_N023


title: Single granulosa cell (LCM) GC010_S81


title: Elacestrant 1


title: Single granulosa cell (LCM) GC009_S80


title: Lasofoxifene 3

description: G_Differential_expression_analysis_table.csv

value: Lasofoxifene


title: Single granulosa cell (LCM) GC008_S79

value: Non-neighboring


title: PBMC_normal_nonfasting_SCR [26]


title: WJL2265_RLF_N023

value: WT + DPKi #2


title: PBMC_normal_nonfasting_SCR [25]


title: Single granulosa cell (LCM) GC007_S78


title: WJL2263_RLF_N023


title: Lasofoxifene 2


title: WJL2262_RLF_N023


title: PBMC_normal_nonfasting_SCR [23]


title: Lasofoxifene 1


title: Single granulosa cell (LCM) GC006_S77


title: PBMC_normal_nonfasting_SCR [24]


title: PBMC_normal_nonfasting_SCR [21]


title: Single granulosa cell (LCM) GC004_S75


title: WJL2261_RLF_N023


title: 4OH-tamoxifen 2

description: F_Differential_expression_analysis_table.csv


title: WJL2264_RLF_N023


title: WJL2260_RLF_N023


title: PBMC_normal_nonfasting_SCR [20]


title: Single granulosa cell (LCM) GC003_S74


title: 4OH-tamoxifen 3


title: WJL2258_RLF_N023


title: 4OH-tamoxifen 1


title: PBMC_normal_nonfasting_SCR [19]


title: WJL2257_RLF_N023


title: PBMC_normal_nonfasting_SCR [22]


title: WJL2259_RLF_N023


title: OP-1250 2

description: D_Differential_expression_analysis_table.csv


title: Single granulosa cell (LCM) GC002_S73


title: Single granulosa cell (LCM) GC001_S72


title: PBMC_normal_nonfasting_SCR [18]


title: Single granulosa cell (LCM) GC005_S76


title: WJL2256_RLF_N023


title: WJL2255_RLF_N023


title: Single mESC (LCM) SL36_S84

source_name: Embryonic stem cell

treatment_protocol: For preparation of LCM samples, the mESCs were pelleted and washed with phosphate buffer saline (PBS).  The mESCs were then suspended in 1 × PBS containing 10% polyvinyl alcohol (PVA) (Sigma), embedded in a cryomold, and snap-frozen in liquid nitrogen. Subsequently, the frozen cell blocks were sectioned using a CM1860UV cryostat (Leica), and mounted on MembraneSlide 1.0 PEN slides (Carl Zeiss).  The sectioned cell blocks were dried overnight and fixed with 80% ethanol.  The fixed sections were then stained with 1% cresyl violet acetate (MP Biomedicals) dissolved in 80% ethanol, washed with 100% ethanol, and dried for more than 1 hour. Mouse ovaries were excised from the 8-week-old female mice and snap-frozen in liquid N2.  The frozen ovaries were sunk in 10% PVA in cryomolds, and again frozen in liquid N2.  The embedded ovaries were sectioned using a CM1860UV cryostat, dried overnight, fixed and stained with 1% cresyl violet acetate dissolved in 50% isopropanol, washed with 100% isopropanol, and dried for more than 1 hour.


title: PBMC_normal_nonfasting_SCR [16]


title: OP-1250 1


title: Single mESC (LCM) SL35_S83


title: Fulvestrant 3

description: C_Differential_expression_analysis_table.csv

value: Fulvestrant


title: Single mESC (LCM) SL34_S82


title: WJL2254_RLF_N023

value: WT + DPKi #1


title: PBMC_normal_nonfasting_SCR [14]


title: WJL2253_RLF_N023


title: PBMC_normal_nonfasting_SCR [17]


title: Single mESC (LCM) SL33_S81


title: Fulvestrant 1


title: Single mESC (LCM) SL32_S80


title: OP-1250 3


title: Fulvestrant 2


title: WJL2252_RLF_N023


title: Estradiol 3

description: B_Differential_expression_analysis_table.csv

value: Estradiol


title: PBMC_normal_nonfasting_SCR [13]


title: PBMC_normal_nonfasting_SCR [11]


title: Single mESC (LCM) SL31_S79


title: WJL2251_RLF_N023


title: PBMC_normal_nonfasting_SCR [10]


title: PBMC_normal_nonfasting_SCR [12]


title: Estradiol 2


title: Single mESC (LCM) SL30_S78


title: WJL2250_RLF_N023


title: PBMC_normal_nonfasting_SCR [15]


title: Estradiol 1


title: PBMC_normal_nonfasting_SCR [9]


title: Vehicle 3

value: Vehicle


title: WJL2248_RLF_N023


title: WJL2247_RLF_N023


title: PBMC_normal_nonfasting_SCR [7]


title: Vehicle 1


title: Single mESC (LCM) SL27_S75


title: PBMC_normal_nonfasting_SCR [8]


title: Vehicle 2


title: WJL2246_RLF_N023


title: Single mESC (LCM) SL26_S74


title: Sample B18

city: Suqian

first: Xiaoming

last: Ma

state: Jiangsu

address: No.138 Huanghe Road, Suqian

country: China

institute: The affiliated hospital of xuzhou medical university

description: adjacent normal tissues

data_processing:
Illumina RTA and bcl2fastq2 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were mapped using hisat2 software.
Read count extraction and normalization were performed using htseq-count .
Supplementary files format and content: excel  files include mRNA counts for each Sample
Supplementary files format and content: excel  files include circRNA counts for each Sample

source_name: colorectal

extract_protocol:
RNA was harvested using TRIzol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: colorectal


title: WJL2245_RLF_N023


title: Single mESC (LCM) SL25_S73


title: PBMC_normal_nonfasting_SCR [6]

value: Female


title: WJL2249_RLF_N023

value: vAbl-ProB


title: WJL2244_RLF_N023

value: pro-B cells


title: Single mESC (LCM) SL24_S72

value: LCM


title: Sample B12

description: adjacent normal tissues


title: PBMC_normal_nonfasting_SCR [4]


title: Sample B11

description: adjacent normal tissues


title: Single mESC (LCM) SL28_S76


title: Single mESC (LCM) SL23_S71


title: Sample B10

description: adjacent normal tissues


title: WJL2243_RLF_N023


title: PBMC_normal_nonfasting_SCR [3]


title: Single mESC (LCM) SL29_S77


title: WJL2242_RLF_N023


title: PBMC_normal_nonfasting_SCR [1]


title: CV55

type: genomic

city: BETHESDA

first: Rust

last: Turakulov

state: MD

address: 10 Central rd

department: NCI

institute: NIH

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R packages: meffil, minfi

label_protocol: Illumina beachip kit and standard protocol

extract_protocol: DNA was extracted from FFPE tissue with  Qiagen DNA extraction kit and followed with Illumina restotation kit.

tag: disease state

value: Medulloblastoma, grade 4

tag: Sex

tag: age

value: FFPE

value: Brain, left cerebellar pontine mass


title: Sample B9

description: adjacent normal tissues


title: PBMC_normal_nonfasting_SCR [5]

tag: sex (female/male)

tag: age (y)

tag: bmi (kg(m2)


title: Single mESC (LCM) SL22_S70

value: gene expression (sc3-seq.)


title: WJL2241_RLF_N023

tag: cell line


title: Single mESC (LCM) SL21_S69


title: WJL2240_RLF_N023

tag: cell type

value: WT


title: PBMC_normal_nonfasting_SCR [2]

tag: monocytes (absolute values x109/l)

tag: lymphocytes (absolute values x109/l)


title: CV53

value: Medulloblastoma, non-WNT/non-SHH

value: Male

value: Brain, posterior fossa, CP angle


title: Sample A13

description: colorectal cancer tissues


title: WJL2239_RLF_N023

tag: genotype

tag: treatment


title: Single mESC (LCM) SL20_S68

tag: collecting conditions

tag: class

tag: analysis target


title: CV52

value: Choroid Glioma

value: Brain, third ventricular


title: WJL2238_RLF_N023


title: CV51

value: High-grade glioma (astrocytoma), grade 3-4

value: Brain, right frontal lobe


title: Single mESC (LCM) SL19_S67


title: Sample A11

description: colorectal cancer tissues

value: colorectal


title: Sample A10

description: colorectal cancer tissues


title: Single mESC (LCM) SL17_S65


title: Sample A9

description: colorectal cancer tissues


title: WJL2236_RLF_N023


title: CV50

value: High-grade glioma

value: Brain, left temporal tumor


title: Single mESC (LCM) SL16_S64


title: CV49

value: Meningioma, WHO grade G3

value: Brain, left parasagittal


title: Sample A12

description: colorectal cancer tissues


title: MIA PaCa2 PHLac-high, repeat 4

city: Oxford

first: Pawel

last: Swietach

state: I have read and agree

address: Department of Physiology, Anatomy and Genetics, Parks Road

department: Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
Alignment by STAR
Remove duplicated by SAMTools
Run featuresCount (subread)
Analyse in DESeq2
Assembly: Homo_sapiens hg38
Supplementary files format and content: CVS file with expression level, fold-change and p.adj value

source_name: Pancreatic ductal adenocarcinoma

growth_protocol: Cells were cultured in RPMI (Sigma-Aldrich, R0883) supplemented with 10% FBS, 1% penicillin–streptomycin mixture, 1% GlutaMAX (35050-038, Gibco, Waltham, MA, USA), 1% sodium pyruvate (11360-039, Gibco, Waltham, MA, USA). Media were incubated in a 5% CO2-enriched atmosphere and contained 44 mM [HCO3-]

extract_protocol:
The RNA from sorted cells was extracted using column-based RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol. Once eluted, the RNA samples were stored at -80°C. The 500 μg of each sample was submitted to Oxford Genomic Centre for library preparation and RNA sequencing.
The mRNA fraction was selected from the total RNA and then converted to cDNA. Second strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples were digested with uridine. The prepared libraries were size selected, multiplexed and their quality was checked before paired end sequencing.

treatment_protocol: Protocol was implemented for sorting cells according to lactic acid permeability, which requires a brief treatment with lactate-containing medium followed by washout

value: Pancreatic ductal adenocarcinoma

value: MIA PaCa-2

value: Adenoma


title: Single mESC (LCM) SL15_S63

value: LCM

value: gene expression (sc3-seq.)


title: WJL2235_RLF_N023

value: vAbl-ProB

value: pro-B cells


title: MIA PaCa2 PHLac-low, repeat 4

value: WT


title: CV47

value: Pilocytic astrocytoma

value: Female

value: FFPE

value: Brain, suprasellar


title: Single mESC (LCM) SL14_S62


title: WJL2234_RLF_N023


title: MIA PaCa2 PHLac-high, repeat 3


title: Single mESC (LCM) SL13_S61


title: WJL2233_RLF_N023


title: MIA PaCa2 PHLac-low, repeat 3


title: WJL2232_RLF_N023


title: Single mESC (LCM) SL12_S60


title: WJL2237_RLF_N023


title: CV44

value: Dysembryoplastic neuroepithelial tumor

value: Male

value: Brain, left parietal lobe


title: CV45

value: Left craniotomy for tumor resection

value: Brain


title: MIA PaCa2 PHLac-high, repeat 2

value: Pancreatic ductal adenocarcinoma


title: MIA PaCa2 PHLac-low, repeat 2

value: MIA PaCa-2


title: CV43

value: Meningioma, meningothelial subtype

value: Brain, meninges, right sphenoid wing


title: Single mESC (LCM) SL11_S59

value: LCM

value: gene expression (sc3-seq.)


title: MIA PaCa2 PHLac-high, repeat 1

value: Adenoma


title: Single mESC (LCM) SL10_S58


title: Single mESC (LCM) SL09_S57


title: CV42

value: GBM


title: WJL2231_RLF_N023

value: vAbl-ProB

value: pro-B cells


title: WJL2229_RLF_N023

value: WT + DPKi #2


title: CV48

value: Glioma with mitoses

value: Female

value: FFPE


title: CV41

value: Atypical teratoid/rhabdoid tumor

value: Brain, posterior fossa


title: WJL2228_RLF_N023

value: WT


title: Single mESC (LCM) SL08_S56


title: MIA PaCa2 PHLac-low, repeat 1

value: Pancreatic ductal adenocarcinoma


title: CV46

value: DLGNT vs. PA

value: Male

value: Cervical spine


title: WJL2227_RLF_N023


title: CV40

value: Astrocytoma with foci with high-grade features, consider HGAP

value: Brain, fourth ventricle


title: Single mESC (LCM) SL07_S55

value: LCM

value: gene expression (sc3-seq.)


title: HD6 [scATAC-seq]

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

library_source: genomic single cell

data_processing:
Illumina bcl2fastq2 Conversion Software 2.20. Quality score is encoded in a +33 offset ASCII (Sanger like)
The raw sequencing reads were filtered, demultiplexed, aligned to the human genome (refdata-cellranger-atac-GRCh38-1.1.0, gencode.v28.basic annotation), and accessible chromatin regions were detected using the 10x Genomics Cell Ranger-atac pipeline (version1.1.0).
Assembly: hg38
Supplementary files format and content: Output of cellranger-atac count: For each sample, the bed file indicates the accessible chromatin regions, with chromosome, start and stop position of each peak; a tab-separated values fragment file (fragment.tsv) and its associated samtools tabix index, containing the list of fragments; a comma-separated values file (singlecell.csv) containing information about cells called and their associated QC metrics, with column "is__cell_barcode" indicating whether the barcode is a true cell (=1) or not (=0).

source_name: peripheral blood

extract_protocol:
PBMCs were freshly isolated from human venous blood by Lymphoprep centrifugation. Red blood cell lysis was performed using red blood lysis buffer and platelets were removed by centrifugation. Human ILCs were identified as lineage negative and interleukin-7 receptor α (CD127) positive lymphocytes. Total ILCs were sorted as CD45+Lin-CD127+CD7+ to at least 98% purity using FACSAria. Single nuclei were isolated, transposed and one scATAC-seq library per healthy donor was generated using the 10x Chromium Single Cell ATAC Reagent Kits.
Chromium Single Cell ATAC Reagent Kits

value: peripheral blood

value: total innate lymphoid cells

value: healthy


title: WJL2226_RLF_N023

value: vAbl-ProB

value: pro-B cells


title: HD5 [scATAC-seq]


title: Single mESC (LCM) SL06_S54


title: Brain_Nrl_04 [N.CNS.4_R]

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
MAP-RSeq version 3.0 and the STAR tool were used to align the raw RNA seq reads to the reference human genome build hg38
QC was performed by FastQC pre- and post-read trimming
The RNA paired end reads were aligned using the STAR aligner 2.6.1c
Gene counts were generated using subread featuerCounts
Assembly: hg38
Supplementary files format and content: tab-delimited files with RNA-Seq gene expression

source_name: brain

extract_protocol:
Formalin fixed paraffin embedded (FFPE) brain biopsy samples were cut (4 microns, 8 slides) for RNA extraction. Total RNA was extracted using the Qiagen miRNeasy Micro Kit and RNA quantification was evaluated with the Qubit RNA HS Assay kit. A minimum of 100 ng of RNA was submitted for RNA sequencing.
Library was prepared using the Illumina® TruSeq® Stranded Total RNA access kit

value: brain

tag: tissue type

value: normal brain tissue


title: WJL2230_RLF_N023

value: WT + DPKi #1


title: Single mESC (LCM) SL05_S53


title: Brain_Nrl_03 [N.CNS.3_R]

tag: tissue


title: Brain_Nrl_02 [N.CNS.2_R]


title: Single mESC (LCM) SL04_S52


title: WJL2223_RLF_N023


title: WJL2224_RLF_N023


title: WJL2222_RLF_N023


title: Brain_Nrl_01 [N.CNS.1_R]


title: Single mESC (LCM) SL03_S51


title: Brain_PCNSV_13 [LV.12]

value: primary CNS vasculitis


title: high salt [AN 013]

city: Baton Rouge

first: Krisztian

last: Stadler

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

description: AN 013

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: mouse- GRCm38.84
Supplementary files format and content: tab-delimited text containing DESeq2 normalized counts

organism: Rattus norvegicus

source_name: isolated cortical glomeruli

extract_protocol:
RNA was isolated by the TRIzol method.
Lexogen - QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina
RNA-Seq; Sequencing Platform – Illumina Next-Seq500

value: isolated cortical glomeruli

tag: strain

value: Dahl SS/JrHsdMcwiCrl

value: male

value: high salt


title: high salt [AN 021]

description: AN 021

tag: Sex


title: high salt [AN 015]

description: AN 015


title: Brain_PCNSV_12 [LV.10]


title: Single mESC (LCM) SL01_S49


title: WJL2221_RLF_N023


title: high salt [AN 023]

description: AN 023


title: high salt [AN 011]

description: AN 011


title: WJL2220_RLF_N023


title: high salt [AN 009]

description: AN 009


title: WJL2225_RLF_N023


title: WJL2219_RLF_N023


title: normal salt [AN 024]

description: AN 024

value: normal salt


title: Brain_PCNSV_11 [LV.09]


title: high salt [AN 017]

description: AN 017


title: Brain_PCNSV_10 [LV.08]


title: Single mESC (fresh) S44_S44

value: Fresh


title: WJL2218_RLF_N023


title: Single mESC (fresh) S43_S43


title: Single mESC (LCM) SL02_S50

value: LCM


title: normal salt [AN 022]

description: AN 022


title: Brain_PCNSV_09 [LV.07]


title: normal salt [AN 018]

description: AN 018


title: Brain_PCNSV_08 [GV.06]


title: WJL2216_RLF_N023

value: WT


title: Single mESC (fresh) S42_S42

value: gene expression (sc3-seq.)


title: Single mESC (fresh) S41_S41


title: Single mESC (fresh) S40_S40


title: Single mESC (fresh) S45_S45


title: normal salt [AN 014]

description: AN 014


title: Brain_PCNSV_06 [GV.02]


title: CV54

tag: disease state

value: Diffuse pediatric-type high-grade glioma

value: Female

tag: age

value: FFPE

value: Brain, right frontal


title: Single mESC (fresh) S39_S39


title: WJL2214_RLF_N023

value: vAbl-ProB

value: pro-B cells


title: normal salt [AN 012]

description: AN 012


title: WJL2215_RLF_N023


title: Single mESC (fresh) S38_S38


title: normal salt [AN 016]

description: AN 016


title: normal salt [AN 010]

description: AN 010


title: Brain_PCNSV_04 [AB.17]

value: brain


title: Brain_PCNSV_05 [GV.01]

value: primary CNS vasculitis


title: WJL2212_RLF_N023


title: Single mESC (LCM) SL18_S66


title: WJL2217_RLF_N023

value: WT + DPKi #2


title: Single mESC (fresh) S37_S37


title: WJL2211_RLF_N023


title: Brain_PCNSV_03 [AB.16]


title: Liver Ginkgetin, replicate2

city: Wuhan

first: Chaoyang

address: Jiefang Avenue #1277

institute: Wuhan Union Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mRatBN7.2 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver tissue

value: treated with ginkgetin


title: Single mESC (fresh) S36_S36


title: Brain_PCNSV_07 [GV.05]


title: Liver Ginkgetin, replicate3


title: Single mESC (fresh) S35_S35


title: Liver Ginkgetin, replicate1


title: Brain_PCNSV_01 [AB.14]


title: Brain_PCNSV_02 [AB.15]


title: WJL2209_RLF_N023


title: WJL2213_RLF_N023


title: WJL2208_RLF_N023


title: HCT116_CDT1_DOX_ON

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

institute: University of Geneva

data_processing:
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 using bwa v.0.7.17
The sam files were converted to bam files by removing duplicated reads and keeping only the uniquely mapped reads using samtools v.1.15.1
The bigwig file signal was extracted from the alignments of the bam file using deeptools v.3.5.1
Visualisation of the bigwig files was performed by pyGenomeTracks v.3.6
Assembly: Human GRCh37/hg19
Library strategy: EdU-seq

source_name: Human cell line

growth_protocol: HCT116 cells were cultured in RPMI supplemented with 10% FBS , 1% penicillin/streptomycin and 1% glutamine.

extract_protocol:
After fixation, the cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-it Kit. Purification of genomic DNA was then performed by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina Hi-Seq 4000 sequencer.

treatment_protocol: To induce CDT1-HA overexpression, cells were treated with 500 ng/ml doxycycline. HCT116-CDT1 DOX cells were cultured with or without doxycycline for three days before being exposed to 100 ng/ml nocodazole for 9 h to induce mitotic arrest. Cells in mitosis were isolated by shake-off, washed twice with PBS, released in warm medium containing 25 μM EdU and 2 mM hydroxyurea. The cells were then collected after 12 h and fixed with 90% methanol overnight.

value: Human cell line

value: Human colorectal cancer

value: with doxycycline - CDT1 overexpression (ON)


title: Single mESC (fresh) S34_S34

value: Fresh


title: Single mESC (fresh) S32_S32


title: HCT116_CDT1_DOX_OFF

value: no doxycycline - CDT1 (OFF)


title: WJL2207_RLF_N023


title: hypoxia_96hrs_iPSCline_0524-1

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

data_processing:
RNA-Seq reads were aligned to the Ensembl GRCh38 human genome reference using STAR v2.7.3 (Dobin et al., 2013) in gene annotation mode
Gene-level counts were filtered to remove lowly expressed genes which did not have at least 1 count per million in all four samples, resulting in 17,777 remaining genes
Gene counts were further normalized by GC content, gene length, and sequencing depth using the CQN R package v1.36.0 and DESeq2 v1.30.1
Genome_build: GRCh38
Supplementary_files_format_and_content: hypoxia_rawcounts.csv, hypoxia_filtered_normalized.csv

source_name: subpallial organoids

growth_protocol: standardized protocols for organoid differentiation based on Pasca AM et al, 2015 and Birey et al, 2017.

extract_protocol:
Qiagen RNeasy Mini kit
KAPA Hyper Prep Stranded RNA-Seq with RiboErase

treatment_protocol: Hypoxia exposure to < 1% oxygen for 12 or 24 hours

value: Induced pluripotent stem cells

value: subpallial organoids

value: hypoxic

tag: time

value: 96 hours

tag: line


title: Liver Control, replicate2

value: treated with vehicle


title: Exposed to filtered aerosol, Sample_MD_268_3F

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

data_processing:
Quality selection (Q>20) and adpater trimming with Trimgalor v0.6.9
Mapping single PASS with STAR v2.7.10b using the  human genome GRCh38 and Ensembl exon-exon junctions from Ensembl v 108
Assembly: GRCh38
Supplementary files format and content: Read counts from RNASTAR (GeneCounts)

source_name: lung

growth_protocol: Cell exposures were performed with the human alveolar epithelial cell line A549 and the human bronchial bronchial epithelial cell line BEAS-2B, both obtained from American Type Culture Collection (ATCC, Rockville, MD). A549 cells were maintained in RPMI 1640 supplemented with 10% (v/v) FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin and the BEAS-2B cells in complete KGM medium

extract_protocol:
Extraction of total RNA with Trizol reagent and purification following recommendation from Invitrogen (precipitation by isopropanol)
TruSeq mRNA kit v2 from Illumina

treatment_protocol: 24 h before exposure of 4 x 10^5 A549 cells or 5 x 10^5 BEAS-2B cells were seeded on 24 mm Transwell® inserts corresponding to a cell density of 8.6 x 10^4 or 1.1 x 10^5 cells/cm² growth area, respectively. Cells were exposed at the ALI in Vitrocell CF 6/3 modules for 4 h with a flow rate of 100 mL/min and a relative humidity of 85% using HEPES supplemented RPMI 1640 medium in the basolateral compartment

value: lung

tag: cell line

value: bronchial epithelial cell

value: wild type

value: Filtered smoke


title: hypoxia_96hrs_iPSCline_2242-1

tag: cell type


title: Single mESC (fresh) S31_S31

value: gene expression (sc3-seq.)


title: WJL2210_RLF_N023

value: vAbl-ProB

value: pro-B cells


title: Single mESC (fresh) S30_S30


title: Clean air control, Sample_MD_268_3C

value: Control


title: hypoxia_96hrs_iPSCline_1205-4


title: WJL2206_RLF_N023

value: WT + DPKi #1


title: WJL2205_RLF_N023

value: WT + DPKi #2


title: hypoxia_96hrs_iPSCline_0307-1


title: WJL1411_RLF_N019


title: WJL2204_RLF_N023

value: WT


title: Liver Control, replicate3

value: liver tissue


title: Single mESC (fresh) S28_S28

value: Fresh


title: Single mESC (fresh) S33_S33


title: Exposed to complete aerosol, Sample_MD_268_3A

value: Wood smoke


title: Single mESC (fresh) S29_S29


title: Exposed to filtered aerosol, Sample_MD_268_2F


title: Liver Control, replicate1


title: WJL1410_RLF_N019


title: Single mESC (fresh) S27_S27


title: control_96hrs_iPSCline_0524-1

value: Induced pluripotent stem cells

value: subpallial organoids

value: control


title: Clean air control, Sample_MD_268_2C

value: lung


title: control_96hrs_iPSCline_2242-1

value: 96 hours


title: WJL1409_RLF_N019


title: Single mESC (fresh) S26_S26


title: control_96hrs_iPSCline_1205-4


title: WJL1408_RLF_N019


title: Exposed to complete aerosol, Sample_MD_268_2A

value: bronchial epithelial cell

value: wild type


title: Single mESC (fresh) S25_S25

value: gene expression (sc3-seq.)


title: Exposed to filtered aerosol, Sample_MD_268_1F

value: Filtered smoke


title: WJL1407_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: hypoxia_24hrs_iPSCline_0524-1

value: hypoxic

value: 24 hours


title: Single mESC (fresh) S24_S24


title: Single mESC (fresh) S23_S23


title: Exposed to complete aerosol, Sample_MD_268_1A


title: hypoxia_24hrs_iPSCline_2242-1


title: Single mESC (fresh) S22_S22


title: hypoxia_24hrs_iPSCline_1205-4


title: Exposed to filtered aerosol, Sample_3F

value: alveolar epithelial cell


title: Clean air control, Sample_3C

value: Control


title: Clean air control, Sample_MD_268_1C


title: Exposed to complete aerosol, Sample_3A


title: control_24hrs_iPSCline_0524-1


title: hypoxia_24hrs_iPSCline_0307-1


title: Single mESC (fresh) S21_S21

value: Fresh


title: Single mESC (fresh) S20_S20


title: Exposed to filtered aerosol, Sample_2F


title: WJL1403_RLF_N019


title: control_96hrs_iPSCline_0307-1


title: WJL1402_RLF_N019

value: WT + DPKi #1


title: WJL1406_RLF_N019


title: WJL1401_RLF_N019

value: WT + DPKi #2


title: WJL1404_RLF_N019


title: control_24hrs_iPSCline_2242-1

value: Induced pluripotent stem cells

value: subpallial organoids


title: Single mESC (fresh) S19_S19


title: Single mESC (fresh) S18_S18


title: Clean air control, Sample_2C

value: lung


title: Single mESC (fresh) S17_S17


title: control_24hrs_iPSCline_0307-1

value: control


title: Exposed to complete aerosol, Sample_2A

value: Wood smoke


title: Single mESC (fresh) S16_S16


title: Single mESC (fresh) S15_S15


title: WJL1398_RLF_N019


title: Exposed to filtered aerosol, Sample_1F

value: wild type


title: hypoxia_12hrs_iPSCline_2242-1

value: 12 hours


title: hypoxia_12hrs_iPSCline_0524-1


title: Clean air control, Sample_1C


title: Exposed to complete aerosol, Sample_1A


title: Single mESC (fresh) S13_S13

value: gene expression (sc3-seq.)


title: WJL1399_RLF_N019

value: vAbl-ProB


title: hypoxia_12hrs_iPSCline_1205-4


title: WJL1397_RLF_N019

value: pro-B cells


title: WJL1396_RLF_N019


title: WJL1395_RLF_N019


title: hypoxia_12hrs_iPSCline_0307-1

value: hypoxic


title: control_12hrs_iPSCline_0524-1


title: WJL1400_RLF_N019

value: WT


title: Single mESC (fresh) S12_S12


title: WJL1394_RLF_N019


title: WJL1405_RLF_N019


title: Single mESC (fresh) S11_S11


title: control_24hrs_iPSCline_1205-4

value: 24 hours


title: WJL1393_RLF_N019


title: Single mESC (fresh) S10_S10


title: U937 monocytes, LysoPPC /FSL-1_2

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix  human Gene 2.1 ST array plates were washed, stained and scanned according to the protocol described in GeneTitan®Instrument User Guide for Expression Arrays Plates (P/N 702933)

scan_protocol: Scanning was done on an Affymetrix GeneTitan (Single Channel ), software AGCC 3.2.4.1515W

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187

source_name: U937, 1h pretreated with LysoPPC before supplementing FSL-1 for 2h

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: myeloid leukemia cell line U937 were grown in RPMI 1640 supplemented with 10% FCS and GlutaMax

extract_protocol: RNA was extracted with TriFast Reagent (VWR International, Radnor, PA) and subsequent RNA cleanup and concentration was performed using the Rneasy MinElure Cleanup Kit (Qiagen, Venlo, Netherlands)

treatment_protocol: myeloid leukemia cell line U937 were pretreated with 10µM LysoPPC before supplementing 1µg/ml FSL-1 or sham treated. RNA was isolated 3h post treatment.

value: myeloid leukemia cell line U937


title: U937 monocytes, LysoPPC /FSL-1_3

value: 1h pretreated with LysoPPC before supplementing FSL-1 for 2h


title: U937 monocytes, LysoPPC /FSL-1_4


title: Single mESC (fresh) S14_S14

value: Fresh


title: control_12hrs_iPSCline_0307-1


title: WJL1390_RLF_N019

value: WT + DPKi #1


title: Single mESC (fresh) S08_S8


title: Single mESC (fresh) S06_S6


title: control_12hrs_iPSCline_1205-4

value: Induced pluripotent stem cells


title: WJL1392_RLF_N019


title: Single mESC (fresh) S07_S7


title: U937 monocytes, LysoPPC /FSL-1_1


title: Single mESC (fresh) S05_S5


title: WJL1389_RLF_N019

value: WT + DPKi #2


title: WJL1391_RLF_N019


title: VSMCs,PDGF-BB+PTUPB,rep2

city: 长沙市

first: 辉

last: 吴

state: 湖南省

address: 中南大学湘雅医学院新校区

department: 检验系

institute: 中南大学湘雅三医院

description: PDGF-BB+PTUPB

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or  fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by  Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N:  0.1) to be high quality clean data.
Alignment:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded  from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2  (v2.0.1).
Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed  properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: rat primary aortic smooth muscle Cells

growth_protocol: VSMCs was maintained in in DMEM supplemented with 20% fetal bovine serum, and 100 U/mL penicillin/streptomycin . The culture medium was changed every 3 days. The cells were cultured in a CO2 incubator at 37°C with 95% air and 5% CO2.

extract_protocol:
Total RNA was extracted from homogenized tissues or VSMCs using TRIzol (Invitrogen) reagent. 1 μg total RNA was used for following library preparation.
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed  using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand  cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and  add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of  Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina  Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to  manufacturer’s instructions.

treatment_protocol: VSMCs pretreated with PTUPB (0.5 μM,MCE) for 2 h and then stimulated with or without PDGF-BB (10ng/mL,MCE) for 24 h. The control group was treated with an equal volume of DMSO. To avoid the effects of cytokines in serum, the cells were serum-starved with 0% FBS for 12 h before any drug treatments, and then stimulated with low serum concentration (2%) during drug treatment. All of the experiments were performed using 4-8 passages of VSMCs.

value: rat primary aortic smooth muscle Cells

value: PTUPB  pretreatment (0.5 uM,2h) followed by PDGF-BB (10ng/mL) stimulation for 24 h


title: Single mESC (fresh) S09_S9


title: VSMCs,PDGF-BB+PTUPB,rep3

address: 中南大学湘雅医学院新校区

description: PDGF-BB+PTUPB


title: Single mESC (fresh) S04_S4


title: VSMCs,PDGF-BB+PTUPB,rep1

address: 中南大学湘雅医学院新校区

description: PDGF-BB+PTUPB


title: VSMCs,PDGF-BB,rep3

address: 中南大学湘雅医学院新校区

description: PDGF-BB


title: control_12hrs_iPSCline_2242-1

value: subpallial organoids

value: control


title: WJL1387_RLF_N019


title: WJL1388_RLF_N019


title: WJL1385_RLF_N019


title: Single mESC (fresh) S02_S2


title: U937 monocytes, LysoPPC_4

source_name: U937 , 1h treatment with LysoPPC

value: 1h treatment with LysoPPC


title: U937 monocytes, FSL-1_4

source_name: U937, 1h sham treatment, before supplementing FSL-1 for 2h


title: U937 monocytes, FSL-1_2

value: 1h sham treatment, before supplementing FSL-1 for 2h


title: Single mESC (fresh) S03_S3

value: gene expression (sc3-seq.)


title: U937 monocytes, FSL-1_3


title: VSMCs,PDGF-BB,rep1

address: 中南大学湘雅医学院新校区

description: PDGF-BB


title: U937 monocytes, LysoPPC_3


title: VSMCs,Control,rep3

address: 中南大学湘雅医学院新校区

description: Control

value: Equal volume of DMSO


title: U937 monocytes, FSL-1_1


title: WJL1384_RLF_N019

source_name: vAbl-ProB

value: vAbl-ProB

value: pro-B cells


title: VSMCs,Control,rep2

address: 中南大学湘雅医学院新校区

description: Control

value: WT


title: WJL1383_RLF_N019


title: BLM EVs, rep3 [B3]

city: Chang Sha

first: shan

middle: shan

last: Liu

state: Hunan

address: 139 Renmin Zhong Lu

institute: THE SECOND XIANGYA HOSPITAL OF CENTRAL SOUTH UNIVERSITY

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
Agilent 2100 Bioanalyzer used to evaluate the quality and concentration of the libraries
Quantification of miRNA expression determined by mirdeep2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: alveolar macrophage

extract_protocol:
Primary alveolar macrophages were isolated from PBS or BLM mice. After incubation at 37°C for 72 h, the supernatants were harvested and AMs-derived EVs were separated by unltracentrifugation. EVs were flash frozen on dry ice, and totla RNA was harvested using Trizol reagent. TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina) (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: BLM-induced


title: Single mESC (fresh) S01_S1

value: Fresh


title: VSMCs,Control,rep1

address: 中南大学湘雅医学院新校区

description: Control


title: WJL1382_RLF_N019

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
Assembly: The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Supplementary files format and content: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS


title: VSMCs,PDGF-BB,rep2

address: 中南大学湘雅医学院新校区

description: PDGF-BB


title: U937 monocytes, ctrl_4

source_name: U937 , sham treated

value: myeloid leukemia cell line U937

value: sham treated


title: BLM EVs, rep1 [B1]


title: BLM EVs, rep2 [B2]


title: U937 monocytes, LysoPPC_1


title: U937 monocytes, ctrl_3


title: U937 monocytes, LysoPPC_2


title: WJL1381_RLF_N019


title: U937 monocytes, ctrl_2


title: WJL1386_RLF_N019


title: HSC-3-S5, rep4

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

institute: Fujita Health University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA was hybridized to the Agilent expression microarray according to the manufacturer's instruction.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Data processig was performed using Agilent Feature Extraction v11.0.1.1.

label_protocol: Labeled cRNA was prepared from total RNA using the Agilent’s Quick Amp Labeling Kit.

growth_protocol: HSC-3 and HSC-3-S5 cells were cultured at standard plate in Dulbecco's modified Eagle's medium containing 10% fetal calf serum.

extract_protocol: Total RNA was isolated using TRIzol reagent according to the manufacturer's instruction.

value: tongue cancer cell

value: HSC-3-S5 cells


title: Z_37_3

city: Beijing

first: Jialong

last: Zhang

address: Malianwa Street

institute: China Agricultural University

data_processing:
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2/ HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM Fragmen(ts Per Kilobases per Millionreads) values were used to show gene expression level.
Assembly: SL 3.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome
Supplementary files format and content: text files include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: seeds

value: seeds

value: SlWRKY37 knockout

value: imbibition

value: 6 hours


title: PBS EVs, rep3 [S3]

value: control


title: WJL1378_RLF_N019

city: Stanford

first: Jinglong

last: Wang

address: 1291 Welch Rd, CCSR Room 1240

institute: Stanford University

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

value: WT + DPKi #1


title: WJL1379_RLF_N019


title: Z_37_1


title: PBS EVs, rep1 [S1]


title: Z_37_2


title: WJL1377_RLF_N019

value: WT + DPKi #2


title: CRD  rep 3

city: Jerusalem

first: Morris

last: Nechama

state: Israel

address: Hadassah Medical Center, Ein Karem

department: Pediatric

country: Israel

institute: Hadassah Hebrew University Medical Center

data_processing:
Raw fastq files per sample were generated with bcl2fastq, v2.18.0.12.
Reads were quality-trimmed at both ends, then poly-G sequences and adapter sequences were removed from the 3' end, and poly-T stretches were removed from the 5' end, with cutadapt version 1.18, using parameters -O 1, --match-read-wildcards and -m 18.
The last 3 bases were removed with fastx_trimmer and low quality reads were discarded with fastq_quality_filter, parameter -q 20 and -p 90, using the FASTX package, version 0.0.14.
Processed reads were aligned with Tophat, version 2.1.1, using parameters -G genes.gtf, -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 22, --read-realign-edit-dist 3, --no-coverage-search, --library-type fr-firststrand, and the GRCm38 mouse genome.
Raw counts were calculated with htseq-count, version 0.6.0, and differential expression was done with DESeq2, v1.22.1, after discarding genes with less than 10 raw counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel table with a header row followed by a row for each gene. Columns A-I include general gene details, columns J-O show the raw counts in each sample, columns P-U are for the DESeq2 normalized counts per sample, column V has the baseMean, columns W-AA include the comparison results (log2FoldChange, padj, etc.). A '?' denotes missing values.

source_name: Kidney- Nephron Progenitor Cells

extract_protocol:
NPCs were extracted by FACS based cell sorting based on  GFP+.  RNA was extracted from these cells by TRIzol reagent according to manufactorer instructions
Libraries were prepared with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit, according to the manufacturer's instructions.

treatment_protocol: CD-1 females were mated with Six2 Cre tg/+ males. After plaq identification the mice were randomely assigned to either control diet or 30% daily caloric intake throughout pregnany. At E18.5, embryo kidneys were extracted and digested in HBSS solution containing collagenase/dispase . the NPC's were FACS based cell sorted based on  GFP+. RNA was extracted and analysed for gene expression

value: Nephron Progenitor Cells

tag: strain/ genotype

value: CD-1/ Six2 Cre tg/+

value: Kidney

tag: diet

value: 30% daily caloric intake


title: WJL1376_RLF_N019

value: vAbl-ProB

value: pro-B cells

tag: genotype

value: WT


title: CRD  rep 2


title: Z_Y3_2

value: SlLBD40 knockout

tag: treatment


title: Z_Y3_3


title: CRD  rep 1


title: Z_Y3_1


title: WJL1375_RLF_N019


title: WJL1380_RLF_N019


title: HSC-3-S5, rep3

value: tongue cancer cell


title: Control  rep 3


title: WJL1374_RLF_N019


title: HSC-3, rep4

value: HSC-3 cells


title: HSC-3, rep3


title: HSC-3-S5, rep2

value: HSC-3-S5 cells


title: HSC-3, rep2


title: Z_WT_3

value: seeds


title: U937 monocytes, ctrl_1

value: myeloid leukemia cell line U937

value: sham treated


title: HSC-3, rep1


title: HSC-3-S5, rep1


title: Met3_174

city: Irvine

first: Devon

last: Lawson

address: 839 Health Science Road, Sprague Hall 140

institute: University of California, Irvine

description:
Single-cell RNA-Seq [10X Genomics]
PolyA RNA

data_processing:
Sequencing reads were aligned utilizing 10x Genomics Cell Ranger Count 3.0.2 to the dual indexed mm10/GRCh38 genome provided by Cell Ranger.
Cells in dataset were subsequently trimmed and analyzed in Seurat v3, with assigned cell type labels and quality control metrics for each cell passing initial quality filtering included in the metadata sheets.
Genome_build: mm10/GRCh38
Supplementary_files_format_and_content: Space-delimited text files contain a matrix of counts; rows are genes and columns are samples.
Supplementary_files_format_and_content: TSV/MTX sets are output from the Cell Ranger pipeline and can be used to generate a matrix using Seurat's Read10X function.
Supplementary_files_format_and_content: Metadata sheets include quality control and cell type label information for the cells analyzed in the associated study.

organism:
Homo sapiens
Mus musculus

source_name: Metastatic brain with MDA-MB-231BR2

extract_protocol:
Single cell suspension from mouse brain was prepared using the Adult Brain Dissociation Kit, Mouse and Rat (Miltenyi Biotec) with some modifications. Briefly, whole dissected brains were chopped into 8 pieces of equal size and placed into C tube (Miltenyi Biotec) containing enzyme P and A. Brain tissue was digested using gentleMACS Octo Dissociator with heaters operating the Adult brain dissociation protocol (Miltenyi Biotec). After digestion, the cell suspension was strained over a sterile 70μm strainer (Fisher Scientific) and washed with 5mL FACS buffer containing ice cold DMEM/F12, 50mM HEPES, and 2% BSA. After removal of myelin by density centrifugation, the cell pellet was washed and remaining red blood cells were lysed with red blood cell lysis buffer. Cells were then re-suspended in FACS buffer and blocked with anti-CD16/32 for 15 minutes on ice. Next, cells were stained with fluorescent antibodies on ice for 15 minutes shielded from light. The labeled cells were washed with 500μL of FACS buffer and resuspended in 500μL of FACS buffer, strained through 40μm strainer prior to sorting on BD FACSAria Fusion sorter. For sorting of microglia, astrocytes, and cancer cells, cells were gated for size based on forward and side scatter, single cells, and Sytox Blue viability (Thermofisher, S34857). All myeloid cells (CD45+ CD11b+) and astrocytes (CD45-, ACSA2+) were sorted from control and metastatic mouse brains into 500μL of chilled FACS buffer. GFP+ 231BR cells were sorted from metastatic brains into 500μL of FACS buffer.
FACS isolated mouse microglia cells were centrifuged for 10 minutes at 300g and washed with 0.04% BSA in PBS. Cells were resuspended to achieve approximately 1,000 cells/µL. Final cell suspensions were counted on the Countess II automated cell counter to determine actual concentration for droplet generation. Cells were loaded onto the 10x Genomics Chromium Single Cell Gene Expression 3’ v2 Chemistry kits for GEMs generation. Following the Chromium Single Cell 3′ Reagents Kits version 2 user guide (CG00052 Rev B), cells were loaded to achieve approximately 10,000 cells for capture. Libraries were sequenced on the Illumina HiSeq 4000 platform to achieve an average of read depth of 50,000 mean reads per cell.

tag: mouse host genotype

value: Foxn1 nu/nu

tag: mouse diagnosis

value: Breast cancer brain metastasis

value: Brain

value: Astrocytes (CD45-, ACSA2+), myeloid cells (CD45+ CD11b+), and 231BR cells

tag: batch

value: Group 3


title: Control  rep 1

value: Nephron Progenitor Cells

value: CD-1/ Six2 Cre tg/+

value: Kidney

value: control


title: Z_WT_1

value: WT

value: imbibition

value: 6 hours


title: Met2_173


title: Z_WT_2


title: Control  rep 2


title: WJL1372_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: Caenorhabditis elegans: N2, replication 3 of water

city: Nanchang

first: Fang

last: Xu

state: Jiangxi

address: NO.999 XUEFU ROAD, HONGGUTAN DISTRICT

department: School of life science

institute: Nanchang University

data_processing:
cutadapt（V 2.7)
fastqc（v 0.11.8）
Use HISAT2 (v 2.1.0) to construct the index of the reference genome, and use Hisat2 (v 2.1.0) to align clean reads to the reference sequence to calculate the gene alignment rate.
RSeQC (V 3.0.1) is used to evaluate the quality of the comparison results of this transcriptome sequencing
Genome_build: GCF_000002985.6 WBcel235
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Caenorhabditis elegans N2 strain growth on E.coli OP50 strain bacteria at NGM plates, and harvested at day 6.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NR604-VAHTS® Fast RNA-seq Library Prep Kit for Illumina

treatment_protocol: 2 groups of sample treated with or without D-mannose, and divided as 3 replications pregroup

value: 6 days

value: water


title: WJL1370_RLF_N019


title: Caenorhabditis elegans: N2, replication 2 of water


title: Quiescent R2 Cells (R2SC_4)

city: Birmingham

first: James

last: George

state: Alabama

address: 725 ZRB, 1720 2nd Ave South

department: Surgery

institute: Univ. Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.20.0 was used for basecalling using 10X Genomics CellRanger mkfastq version 3.0.0
Aligned FASTQ files using 10X Genomics CellRanger count version 3.0.0 with paramters --id; --transcriptom; --fastqs; --sample
Genome_build: 10X Genomics mm10 version 3.0.0
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing only cellular barcodes in MEX format

source_name: Kidney Mononuclear Phagocytes

extract_protocol:
Qiagen
10X Genomics ver 3

treatment_protocol: 20 minutes ischemia by clamping the renal hilum under ketamine/xylazine anesthesia at 37 plus-or-minus 0.3 degrees C.

value: Resident Kidney Macrophages

value: No treatment


title: Met1_132

value: Foxn1 nu/nu

value: Breast cancer brain metastasis

value: Group 1


title: Quiescent R2 Cells (R2SC_3)


title: WJL1369_RLF_N019


title: Quiescent R2 Cells (R2SC_2)


title: Caenorhabditis elegans: N2, replication 1 of water


title: WJL1373_RLF_N019


title: WJL1368_RLF_N019


title: Day 6 Post IRI R2 Cells (JG14)

value: Post ischemia Day 6


title: WJL1371_RLF_N019


title: Caenorhabditis elegans: N2, replication 3 of mannose

value: D-mannose


title: WJL1367_RLF_N019


title: Day 6 Post IRI R2 Cells (JG13)


title: Caenorhabditis elegans: N2, replication 2 of mannose


title: WJL1365_RLF_N019

value: WT + DPKi #2


title: Day 6 Post IRI R2 Cells (JG11)


title: myocardial infarction-5

city: ChangZhou

first: Lichan

last: Tao

address: Juqian Road 185, Changzhou, Jiangsu province, China

institute: The Third affiliated Hospital of Soochow Uniersity

description: coding and non-coding RNAs expression in mouse hearts 3 weeks following myocardial infarction

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48°C on Aligent mRNA and noncoding RNA Array. GeneChips were washed and stained in the Aligent Fluidics Station.

scan_protocol: The arrays were scanned by the Aligent.

data_processing: Agilent Feature Extraction Software  was used to analyze array images to get raw data and then offered RMA normalization. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 75 percent of samples in any 1 condition out of 2 conditions have flags in P were chosen for further data analysis.

source_name: heart

label_protocol: Trizol extraction of total RNA was performed using mirVanaTM RNA Isolation Kit according to the manufacturer's instructions.

growth_protocol: Tissues for detection was collected from border areas of ventricular tissues 21 days post-myocardial infarction (MI) or a sham control

extract_protocol: Total RNA was extracted from border areas of ventricular tissues 21 days post-myocardial infarction (MI) or a sham control

tag: gender

value: male

value: myocardial infarction

value: heart


title: myocardial infarction-4

tag: tissue


title: WJL1366_RLF_N019

value: WT + DPKi #1


title: myocardial infarction-3

tag: strain


title: WJL1364_RLF_N019

value: WT


title: Fa H2O2-2

city: Loma Linda

first: Yuetan

last: Dou

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

data_processing:
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RNA-seq fastq files were trimmed with trimmomatic, aligned to P. gingivalis W83 genome, and reads were qunatified with cutfflinks. Gene differential expression was analyzed using cuffdiff with FPKM threshold of 1.
Assembly: Porphyromonas gingivalis W83, Filifactor alocis ATCC 35896
Supplementary files format and content: original process to.csv file, with all genes reads in two files, P. gingivalis and F. alocis respectively.

organism: Filifactor alocis ATCC 35896

source_name: culture

growth_protocol: Anaerobic condotions (80% N2, 10% H2, 10%CO2)

extract_protocol:
Briefly, RNA were harvested by Qiagen RNA kit. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The first- and the second- strand cDNA synthesis, the RNA-seq barcode ligation, and other steps of libraries construction were performed by using Nextflex RNA-Seq kit according to the protocol of manufacturer (Bioo Scientific, Austin, TX).
cDNA in library were taged by specific barcode sequence and exposed to sequencing.

treatment_protocol: Treated by 0.25 mM of hydrogen peroxide

value: culture

value: 0.25 mM H2O2 stress


title: WJL1363_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: Fa H2O2-3


title: myocardial infarction-2


title: Quiescent R1 Cells (JG23)

value: Infiltrating Macrophages


title: Fa H2O2-1


title: myocardial infarction-1


title: WJL1362_RLF_N019


title: Day 1 Post IRI R1 + R2 Cells (JG21)

value: Resident and Infiltrating Mononuclear phagocytes

value: Post-ischemia Day 1


title: WJL1361_RLF_N019


title: Quiescent R1 Cells (JG25)

value: No treatment


title: Caenorhabditis elegans: N2, replication 1 of mannose

value: 6 days


title: Quiescent R1 Cells (JG24)


title: Susceptible callus line AN-9, non exposed to fungal filtrate SCL2

city: Malaga

first: Clara

last: Pliego

state: Malaga

address: Cortijo de la Cruz

department: Department of Genomics and Biotechnology

country: Spain

institute: IFAPA

data_processing:
Raw data in a FASTQ format were processed using fastp.
Raw reads were processed to remove reads containing adapter and poly-N sequences and reads with low quality and were calculated the Q20, Q30 and GC content of the clean data (clean reads).
High quality paired-end clean reads were mapped to the reference genome downloaded from genome website browser (NCBI) using HISAT2 software.
Differential expression analysis of three biological replicates per condition was performed using DESeq2 R package. Benjamin and Hochberg’s approach were used to adjust P values for controlling the False Discovery Rate (FDR) and select genes with an adjusted Pvalue < 0.05 as differentially expressed genes.
The main purpose of this study is to compare and analyse differential expressed genes (DEGs) and differential pathways after growing two different avocado lines (S, Susceptible and T, Tolerant) on media supplemented with Rosellinia necatrix filtrates.
A differential expression analysis is made. The input data for differential gene expression analysis is read counts from gene expression level analysis. The differential gene expression analysis contains three steps: read counts normalization; model dependent p-value estimation; FDR value estimation based on multiple hypothesis testing.
Assembly: not provided
Supplementary files format and content: Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.

organism: Persea americana

source_name: Callus

growth_protocol: The embryogenic cultures were maintained on Murashige and Skoog (MS) medium (Murashige & Skoog, 1962) supplemented with 0.1 mg l-1 picloram (MSP medium) and solidified with 6 g l-1 agar in darkness at 25 ± 1 °C and were subculture at 4-week intervals in MSP medium. The pH medium was adjusted to 5.74 before to autoclaving at 0.1 MPa and 121 °C for 15 min.

extract_protocol:
For RNA extraction, the embryogenic callus from L3 and AN9 exposed and no exposed to fungal exudates were macerated with liquid nitrogen. And, afterwards, RNA was extracted using ´Spectrum plant RNA kit´ (Sigma Aldrich) following manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer.

treatment_protocol: The virulent CH53 fungal strain of Rosellinia necatrix was cultured on potato dextrose agar (PDA) in darkness at 25 °C. To obtain the fungal filtrate, six 1cm-fragments of PDA with fungal mycelium were incubated on 500ml of PDA liquid medium during 9 days at 25 °C in darkness. This medium was filtrated through 2 layers paper to eliminate hyphae and remains of the fungus; the medium obtained was sterilized through 0.2 µm filtration and frozen until its use.

tag: cultivar

value: Anaheim

value: Callus

tag: phenotype

value: Susceptible

value: Embryogenic

value: Non exposed to fungal filtrate


title: Day 1 Post IRI R1 + R2 Cells (JG22)


title: Susceptible callus line AN-9, non exposed to fungal filtrate SCL3


title: CAPE+Chito_1/50 3

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, version 20101214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Plants grew in growth chamber for 6 days on vertical 1/2 MS plates, 23°C, light/dark 16 h/8 h, light intensity of ca 120 μmol photons m-2 s-1. On the 6th day, seedlings were transferred into the 6-well plates with liquid 1/2 MS, and chitosan or mock treated for 24 h under the same cultivation conditions.

extract_protocol:
protocol from Plant Total RNA Mini Kit, QIAGEN
performed by sequencing service company (Eurofins Genomics)

value: whole seedlings

value: all cell types

tag: treatment time


title: Susceptible callus line AN-9, non exposed to fungal filtrate SCL1


title: Day 1 Post IRI R1 + R2 Cells (JG20)


title: CAPE+Chito_1/50 2


title: sham-4

value: male

value: sham

value: heart


title: Day 6 post IRI R1 Cells (JG18)

value: Post ischemia Day 6


title: Susceptible callus line AN-9, exposed to fungal filtrate SCLF3

value: Exposed to fungal filtrate


title: WJL1359_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: WJL1360_RLF_N019


title: sham-5


title: sham-2


title: CAPE+Chito_1/50 1


title: sham-1


title: Day 6 post IRI R1 Cells (JG16)

value: Infiltrating Macrophages


title: sham-3


title: Susceptible callus line AN-9, exposed to fungal filtrate SCLF2


title: Tolerant callus line L3, non exposed to fungal filtrate TCL3

value: Tolerant


title: WJL1357_RLF_N019


title: 48 CAMA1 OP-1250 24hr

city: SAN FRANCISCO

first: Alison

last: Parisian

address: 780 Brannan St

institute: Olema Pharmaceuticals

data_processing:
Data was analyzed and visualized using the Arpeggio Biosciences Insights portal
Assembly: hg38
Supplementary files format and content: Counts files
Library strategy: Pro-Seq

molecule: nuclear RNA

growth_protocol: Prior to experiment MCF7 cells were cultured in Eagle’s MEM supplemented with 0.01 mg/mL human recombinant insulin and CAMA1 cells were cultured in Richter’s IMEM supplemented with nonessential amino acids

extract_protocol:
Run-on and subsequent PRO-seq library preparation experiments were performed on permeabilized cell pellets in a freeze buffer as described, but with modifications, from the Mahat 2016 Protol. Briefly, permeabilized cells were mixed with run-on buffer and incubated at 30°C for 5 minutes. Run-on reaction was stopped and RNA was extracted. RNA was fragmented. RNA was cleaned up using columns and reconstituted to a final volume. Biotinylated RNAs were enriched using the streptavidin beads. Binding and incubation occured. Bound beads were washed with a high salt buffer, twice with binding buffer, and once with low salt buffer. RNA was removed from the streptavidin beads. Extracted RNA was dissolved and subjected to a second round of biotinylated RNA enrichment. After the second round, the isolated RNA was dissolved and immediately proceeded to cDNA synthesis.
The RNA libraries were prepared and sequenced using the Illumina NextSeq500, single read, 1x75 bps

treatment_protocol: MCF7 or CAMA1 cells were plated in estradiol-depleted charcoal dextran stripped serum-containing media for 24 hours prior to dosing with 316 nM compound or 100 pM 17-beta estradiol and harvested after 15 min, 1 hr, 6 hr or 24 hr treatment. For estradiol pretreated conditions, cells were treated for 24 hours with 17-beta estradiol prior to compound treatment and harvested after 15 min, 1 hr, 6 hr or 24 hr treatment. Harvested samples were processed for precision run-on sequencing.

value: breast cancer cell line

tag: time point

value: 24 hr


title: WJL1358_RLF_N019

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. DNA-PKcs inhitors, DPKi #1 (Nu7441, 0.5 µM) and DPKi #2 (Nu7026, 20 µM)were added to some of the samples the same day as STI-571.


title: WJL1356_RLF_N019


title: Day 6 post IRI R1 Cells (JG15)


title: Chito_1/50 3


title: Susceptible callus line AN-9, exposed to fungal filtrate SCLF1

value: Anaheim

value: Callus


title: Chito_1/1000 3


title: 47 CAMA1 OP-1250 24hr


title: Chito_1/50 1


title: WJL1354_RLF_N019

value: WT + DPKi #1


title: WJL1355_RLF_N019


title: Chito_1/50 2


title: Tolerant callus line L3, non exposed to fungal filtrate TCL2

value: Embryogenic

value: Non exposed to fungal filtrate


title: 46 CAMA1 24 HOUR ESTRADIOL + OP-1250 24hr

value: Estradiol + OP-1250 24 hr


title: WJL1353_RLF_N019

value: WT + DPKi #2


title: Chito_1/1000 2

value: whole seedlings

value: all cell types


title: 45 CAMA1 24 HOUR ESTRADIOL + OP-1250 24hr


title: Chito_1/1000 1


title: WJL1352_RLF_N019

value: WT


title: CAPE 3

value: CAPE


title: 44 CAMA1 Tamoxifen 24hr

value: Tamoxifen 24 hr


title: WJL1351_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: Tolerant callus line L3, exposed to fungal filtrate TCLF1

value: Tolerant

value: Exposed to fungal filtrate


title: 43 CAMA1 Tamoxifen 24hr

value: breast cancer cell line

value: 24 hr


title: CAPE 1


title: WJL1349_RLF_N019


title: 42 CAMA1 Fulvestrant 24hr

value: Fulvestrant 24 hr


title: mock 3

value: mock


title: CAPE 2


title: 41 CAMA1 Fulvestrant 24hr


title: Tolerant callus line L3, non exposed to fungal filtrate TCL1

value: Anaheim

value: Callus

value: Embryogenic


title: 40 CAMA1 Estradiol 24hr

value: Estradiol 24 hr


title: WJL1348_RLF_N019


title: 39 CAMA1 Estradiol 24hr


title: mock 2

value: whole seedlings


title: WJL1347_RLF_N019


title: Tolerant callus line L3, exposed to fungal filtrate TCLF3


title: mock 1

value: all cell types


title: Tolerant callus line L3, exposed to fungal filtrate TCLF2


title: WJL1346_RLF_N019


title: Steer #6 infected metacarpal skin

city: Orient Point

middle: Jiangtao

last: Zhu

state: NY

department: Plum Island Animal Disease Center

institute: USDA-ARS

description: Design Format: IS-45220-4-V1

hyb_protocol: One Cy3 labled sample was cohybrided with the Cy5 labled control in one hybridization chamber (Agilent) containing an Agilent microarray (Array design #:Agilent-019963; 4 X 44k per slide). The chambers were incubated in a incubator at 65 C in a rotating cartridge overnight. After incubation, the arrays were washed with Agilent washing buffers according to amnufacturer's protocol.

scan_protocol: After hybridization and washing, the arrays were scanned at 5 micrometer per pixel with a Cy3 to Cy5 ratio of approximately 1 using a GenPix 4000B scanner (Molecular Devices) and the images were saved as tiff files.

data_processing:
The expression data were extracted from the tiff files using Agilent Genpix 7.0 software and the raw data were saved as gpr files for statisitcal analysis using R with librarys(limma, MASS, statmod, splines). LOESS method was applied to normalize interarray variation with a background subtraction of 15.
The gpr files were named based on the Agilent array serial number, the array number of the slide, such as 251996310039_1, the date of the experiment, and the tissues.  The normalized Cy3 results of each sample were used as gene expression levels (photon per pixel) (provided in the Matrix). Averaged Expression is the mean expression of the probe. Fold Change is the difference in expression level (fold) between compared tissues.  adj.P.Val is false discover rate.

organism: Bos taurus

source_name: tissue total RNA

label_protocol: Low input RNA two color labeling kit (Agilent Technologies) was used to lable cRNA according to the manufacturer's protocol. Pooled total RNA isolated from all infected or non-infected metacarpal skin was labeled with Cy5 as universal control. All Individual RNA samples were individually labeled with Cy3.

growth_protocol: The animal study including the approved Institutional Animal Care and Use Committee protocol was reported in Zhu JJ, Arzt J, Puckette MC, Smoliga GR, Pacheco JM, Rodriguez LL. Mechanisms of foot-and-mouth disease virus tropism inferred from differential tissue gene expression. PLoS One. 2013 May 28;8(5):e64119.

extract_protocol: Total RNA was extracted from each cell culture well using the RNeasy mini kit (Qiagen) following the manufacturer instructions. RNA quality was assessed using the Agilent 2100 bioanalyzer (Santa Clara, CA, USA) using an RNA nanochip. Quantification of RNA was conducted on a Nanodrop 1000 (Thermo Scientific).

treatment_protocol: The FMDV infection was described in Pacheco JM, Arzt J, Rodriguez LL (2010) Early events in the pathogenesis of foot-and-mouth disease in cattle after controlled aerosol exposure. Vet J 183:46–53.

tag: steer number

value: metacarpal skin

tag: infection status

value: FMDV infected tissue

source_name: Pooled total RNA of metacarpal skin


title: Steer #6 infected coronary band

description: Design Format: IS-45220-4-V1

value: coronary band


title: WJL1350_RLF_N019

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

tag: cell line

value: vAbl-ProB

tag: cell type


title: WJL1345_RLF_N019

value: pro-B cells


title: 37 CAMA1 DMSO 24hr

value: DMSO 24 hr


title: sos2-2_100N_rep3

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

data_processing:
For mRNA-seq, Kallisto_0.46.2 was used for quantification. TPM values were calculated for each transcript of genes.
For mRNA-seq, Differential expression analysis of genes was performed by Sleuth_0.30.0
For small RNA-seq, the adapter sequence was removed by cutadapt.
For small RNA-seq, the clean reads were mapped to Arabidopsis genome by using Bowtie2.2.5
For small RNA-seq, the annotation of Arabidopsis miRNAs was downloaded from https://www.mirbase.org/. FeatureCount_1.6.4 was used for the quantification of each miRNA
Assembly: Tair10
Supplementary files format and content: For mRNA-seq, tab-delimited text files include TPM values for each Sample
Supplementary files format and content: For small RNA-seq, tab-delimited text files include RPM for each Sample

source_name: whole-seedling

growth_protocol: The sterilized seeds of wild-type and sos2-2 were sown on MS medium containing 3% sucrose and 0.6% phytagel. Seeds were kept at 4 ℃ for 2 days and then transferred into a growth chamber under constant illumination at 22 ℃ for 10 days.

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen). The small RNA was extracted by using TRIzol reagent with MgCl2.
Standard mRNA-seq libraries were constructed by using Illumina RNA-seq kit (RS-122-2201). The small RNA-seq libraries were constructed by using Illumina sRNA-seq kit (RS-200-0012).

treatment_protocol: Ten-day-old seedlings of the wild type and sos2-2 mutant were treated in liquid MS medium containing 100 mM NaCl for 12 hours.

value: whole-seedling

value: sos2-2 mutant

value: 100 mM NaCl treatment


title: WJL1344_RLF_N019


title: 36 CAMA1 OP-1250 6hr

value: breast cancer cell line


title: sos2-2_100N_rep2


title: sos2-2_MS_rep2

value: MS medium


title: PBS EVs, rep2 [S2]

value: lung

value: control


title: sos2-2_100N_rep1


title: WJL1343_RLF_N019


title: 35 CAMA1 OP-1250 6hr


title: WJL1342_RLF_N019

value: WT + DPKi #1


title: 34 CAMA1 24 HOUR ESTRADIOL + OP-1250 6hr

value: Estradiol + OP-1250 6 hr


title: Steer #6 infected mid anterior lung

description: Design Format: IS-45220-4-V1

value: mid anterior lung


title: sos2-2_MS_rep1


title: WJL1341_RLF_N019

value: WT + DPKi #2


title: 38 CAMA1 DMSO 24hr

value: 24 hr


title: Steer #6 infected interdigital cleft skin

description: Design Format: IS-45220-4-V1

value: interdigital cleft skin

value: FMDV infected tissue

value: metacarpal skin


title: 33 CAMA1 24 HOUR ESTRADIOL + OP-1250 6hr


title: Steer #6 infected nasal turbinate epithelium

description: Design Format: IS-45220-4-V1

value: nasal turbinate epithelium


title: WT_100N_rep3

value: WT


title: Steer #6 infected tongue epithelium

description: Design Format: IS-45220-4-V1

value: tongue epithelium


title: Steer #6 infected dorsal soft palate

description: Design Format: IS-45220-4-V1

value: dorsal soft palate


title: 32 CAMA1 Tamoxifen 6hr

value: Tamoxifen 6 hr


title: WJL1340_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: WJL1507_RLF_N019


title: WT_100N_rep2

value: whole-seedling

value: 100 mM NaCl treatment


title: 31 CAMA1 Tamoxifen 6hr

value: breast cancer cell line


title: Steer #5 infected metacarpal skin

description: Design Format: IS-45220-4-V1


title: Steer #6 infected dorsal nasal pharynx

description: Design Format: IS-45220-4-V1

value: dorsal nasal pharynx


title: WJL1505_RLF_N019


title: WT_100N_rep1


title: WT_MS_rep3

value: MS medium


title: 30 CAMA1 Fulvestrant 6hr

value: Fulvestrant 6 hr


title: Steer #5 infected interdigital cleft skin

description: Design Format: IS-45220-4-V1


title: 29 CAMA1 Fulvestrant 6hr


title: Steer #5 infected coronary band

description: Design Format: IS-45220-4-V1

value: coronary band


title: WJL1504_RLF_N019


title: 28 CAMA1 Estradiol 6hr

value: Estradiol 6 hr


title: WT_MS_rep2


title: Steer #5 infected mid anterior lung

description: Design Format: IS-45220-4-V1

value: mid anterior lung

value: FMDV infected tissue


title: WJL1503_RLF_N019


title: 27 CAMA1 Estradiol 6hr


title: WJL1502_RLF_N019


title: WJL1506_RLF_N019


title: WJL1501_RLF_N019


title: WT_MS_rep1


title: 25 CAMA1 DMSO 6hr

value: DMSO 6 hr


title: 26 CAMA1 DMSO 6hr


title: 24 CAMA1 OP-1250 1hr


title: WJL1500_RLF_N019


title: WJL1499_RLF_N019


title: Steer #5 infected dorsal nasal pharynx

description: Design Format: IS-45220-4-V1

value: metacarpal skin


title: 23 CAMA1 OP-1250 1hr


title: Steer #5 infected nasal turbinate epithelium

description: Design Format: IS-45220-4-V1

value: nasal turbinate epithelium


title: Steer #5 infected dorsal soft palate

description: Design Format: IS-45220-4-V1

value: dorsal soft palate


title: Steer #5 infected tongue epithelium

description: Design Format: IS-45220-4-V1

value: tongue epithelium


title: WJL1498_RLF_N019

value: vAbl-ProB

value: WT + DPKi #1


title: Steer #4 infected metacarpal skin

description: Design Format: IS-45220-4-V1


title: WJL1497_RLF_N019

value: pro-B cells

value: WT + DPKi #2


title: 22 CAMA1 24 HOUR ESTRADIOL + OP-1250 1hr

value: breast cancer cell line

value: Estradiol + OP-1250 1 hr


title: 21 CAMA1 24 HOUR ESTRADIOL + OP-1250 1hr


title: WJL1496_RLF_N019

value: WT


title: zebrafish larva, neurons and glia, scRNAseq

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
using Cell Ranger (version 3.1.0; 10X Genomics, Pleasanton, CA. USA)
Assembly: ZebraFishGRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: zebrafish larva

extract_protocol:
About 150 7-day old larva were euthanized in 0.02% tricaine, and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase (Life Sciences) in a buffer containing 134 mM NaCl, 2.9 mM KCl, 1.2 mM MgCl2, 2.1 mM CaCl2, and 10 mM Na-HEPES (pH 7.8) at 28 °C for 2 hr, with intermittent trituration using a p200 pipette aid at 0, 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue, the final triturations were done using fire-polished Pasteur pipettes with decreased opening sizes (300, 200, 100 μm respectively). Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution (in 1xPBS containing 1 mM EDTA) at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution (L15 with 1% fetal bovine serum). The tissue was collected by spinning at 400 g for 3 min at 4°C, washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire-polished Pasteur pipettes with 80-100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count, Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: neurons and glia

value: zebrafish larva

value: mixed

tag: age

value: 7 day post-fertilization


title: WJL1495_RLF_N019

tag: genotype


title: 20 CAMA1 Tamoxifen 1hr

tag: treatment

value: Tamoxifen 1 hr


title: Steer #4 infected interdigital cleft skin

description: Design Format: IS-45220-4-V1

value: interdigital cleft skin

value: FMDV infected tissue


title: 19 CAMA1 Tamoxifen 1hr


title: Steer #4 infected coronary band

description: Design Format: IS-45220-4-V1

value: coronary band

value: metacarpal skin


title: M1B26 CD10P biological rep2

city: Lyon

first: Véronique

last: Maguer-Satta

address: 28 Rue Laennec, Bat Cheney D, 4ème étage

institute: Centre de Recherche en Cancérologie de Lyon

description: Gene expression data from CD10+ sorted M1B26 cells

hyb_protocol: 10 µg of labeled cRNA was fragmented and denaturated in hybridization buffer, then hybridized on chip during 16 hours at 45°C with constant mixing by rotation at 60 rpm in an Genechip hybridization oven 640 (Affymetrix). After hybridization, arrays were washed and stained with streptavidin-phycoerythrin (GeneChip® Hybridization Wash and Stain Kit) in a fluidic 450 (Affymetrix) according to the manufacturer’s instruction.

scan_protocol: The arrays were read with a confocal laser (Genechip scanner 3000, Affymetrix).

data_processing: CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0. The obtained data were normalized with Affymetrix Expression Console software using MAS5 statistical algorithm.

label: biotin

source_name: CD10+ sorted M1B26 cells

label_protocol: Total RNA (50 ng) was amplified and biotin-labeled using GeneChip® 3’ IVT PLUS kit. Before amplification, spikes of synthetic mRNA at different concentrations were added to all samples; these positive controls were used to ascertain the quality of the process. Biotinylated antisense cRNA for microarray hybridization was prepared. After final purification using magnetic beads, cRNA quantification was performed with a nanodrop and quality checked with Agilent 2100 Bioanalyzer (Agilent technologies, Inc, Palto Alto, CA, USA).

growth_protocol: All cell lines were grown in phenol red-free Dulbecco’s modified Eagle’s medium (DMEM)/F-12 nutrient mix supplemented with 2% horse serum, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 20 ng/ml EGF and 1% penicillin/streptomycin ). MC26 and M1B26 cells culture media wazs supplemented by BMP2 and IL6 (both at 10 ng/ml).

extract_protocol: Total RNA were extracted using RNeasy-Plus mini columns from Qiagen following manufacturer's recommendations.

treatment_protocol: Cells were trypsinized, washed in PBS and either frozen at -80°C or stained for CD10 membrane expression before flow cytometry sorting (see samples section).

value: M1B26 cells

tag: cell culture medium

value: Standard medium supplemented with 5ng/ml recombinant human BMP2 and 10 ng/ml recombinant human IL-6

tag: cell population

value: CD10+ sorted cells