title: GEX_p21165-s010_RTe17-RLf17-wk10-wk26

value: mixed sample(Week10 and Week26 for  RTe17, RLf17 - R66M gp120)


title: input_shFoxA1_EtOH

status: Public on Oct 11 2023

type: SRA

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

library_source: genomic

data_processing:
ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic v0.36. The resulting reads were mapped to the human reference genome (hg38) using BWA-MEM v0.7.12 in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1.
Peaks (summit +/- 150 bp) were called using MACS2 software suite v2.1.1.20160309at an FDR < 0.05 using sequenced libraries of respective input DNA as control. Peaks in mitochondrial chromosome and scaffold regions were removed.
Peak annotations, intersections, and bed files were performed using HOMER v4.11.1 and binding intensity heatmaps were generated using deepTools v3.5.0.
Assembly: hg38
Supplementary files format and content: Bedgraph and bigwig for ChIP samples and input as well as ChIP peak text files corrected using respective input controls

molecule: genomic DNA

organism: Homo sapiens

source_name: LNCaP

growth_protocol: LNCaP cells with either shFoxA1-mediated knockdown or shEV (empty vector) control were first androgen deprived by culturing them in RPMI medium containing 2% charcoal-stripped serum (CSS) for 48h. Then, cells were treated with vehicle (EtOH, 0.1% final) or 10nM R1881 (Steraloids, Cat#E3164-000) in freshly added CSS medium for another 24h.

extract_protocol:
Lysates were clarified from sonicated nuclei and cross-linked protein-DNA complexes were isolated with an mTOR-specific antibody, de-crosslinked and purified using a QIAquick PCR purification kit (Qiagen, Cat#28106).
Libraries were prepared at Novogene Bioinformatics Technology Co., Ltd using the NEBNext Ultra II DNA Library Prep kit according to manufacturer's recommendations and sequenced as paired-end 150bp reads on an Illumina NovaSeq 6000 sequencer.

tag: cell line

value: LNCaP

tag: cell type

value: Human prostate cancer

tag: treatment

value: shFoxA1 + 24h EtOH (0.1% final) treatment


title: GEX_p21165-s009_RTe17-RLf17-wk55-wk63

city: Atlanta

first: rohini

last: mopuri

state: GA

address: 954 Gatewood Rd NE

country: USA

institute: Emory National Primate Research Center

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene and HTO counting was done with Cellranger6.0.1 into a single set of files for each capture. VDJ was done using cellranger v3.1.0.
Assembly: Mmul10,ensembl100
Supplementary files format and content: Tab separated values and matrix files

molecule: polyA RNA

organism: Macaca mulatta

source_name: Blood

extract_protocol:
CD14-, CD3-, CD20+, IgG+, and gp120-His double positive antigen specific, IgG+ circulating B cells from PBMC cryopreserved at weeks 10, 26, 55, 63, and 90 (necropsy). A cell hashing antibody that was unique for each animal was included in the phenotyping panel, so that sorted cells could be pooled for 10X Genomics sequencing and later deconvoluted by hashtag barcode. The following hashtags were used at : TotalSeq-C anti-human Hashtag 1, TotalSeq-C anti-human Hashtag 2 , TotalSeq-C anti-human Hashtag 3, TotalSeq-C anti-human Hashtag 4 , TotalSeq-C anti-human Hashtag 5 , TotalSeq-C anti-human HLA-DR , TotalSeq-C anti-human CD20, TotalSeq-C anti-human CD22 , TotalSeq-C anti-human HLA A/B/C , TotalSeq-C anti-human CD40.
Following reverse transcription, the cDNA was prepared to create gene expression libraries, BCR VDJ libraries and feature barcode libraries.

tag: tissue

value: Blood

value: Antigen Specific B lymphocytes

tag: condition

value: mixed sample(Week55 and Week63 for RTe17, RLf17 - R66M gp120)

tag: library type

value: mRNA


title: input_shEV_EtOH

value: shEV (empty vector) control + 24h EtOH (0.1% final) treatment


title: transfection reagent only

type: RNA

city: Kagoshima

first: Yuya

last: Tomioka

country: Japan

institute: Kagoshima University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

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

molecule: total RNA

source_name: mock 1

label_protocol: For cRNA amplification and labeling, Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) were used following the manufacter’s instructions.

growth_protocol: Normal cell culture medium RPMI 1640

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA transfection using Lipofectamin RNAiMAX

value: lung adenocarcinoma


title: 62D P  [JR5]

city: East Lansing

first: G. Andres

last: Contreras

state: MI

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

library_source: transcriptomic

data_processing:
Data quality control was performed with FastQC v.0.11
After data filtering, clean reads were mapped to the rattus_norvegicus_rnor_6_0_gca_000001895_4 reference genome using HISAT 2.1.0
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: tab delimited .txt file

organism: Rattus norvegicus

source_name: Thoracic Aorta Perivascular Fat

growth_protocol: APVAT was separated from the aorta then minced and digested (using Liberase TL). Cells were expanded and used for adipogenesis experiments

extract_protocol:
RNA was extracted using the Maxwell®RSC simplyRNA cells kit (AS1390, Promega, Madison, WI)
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: Cells were induced with a standard adipogenic cocktail (insulin, IBMX, PPARg agonist, corticoid)

value: Thoracic Aorta Perivascular Fat

value: Stromal Vascular Fraction Derived Preadipocytes

value: Lateral Preadipocyte


title: 61V A  [JR4]

value: Ventral Adipocyte


title: GEX_p21165-s007_RVh17-RGi17-wk55-wk63

value: mixed sample(Week55 and Week63 for RVh17, RGi17 - R66M gp120)


title: mouse 1, replicate 1, scRNAseq, TCR

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

institute: University of Missouri

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v7.0.1
Assembly: mm10 and GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: spleen

extract_protocol:
5 x 10^6 magnetic column purified CD4 T cells harvested from spleens of two B6.H2g7 donor mice were adoptively transferred to two separate NOD.Rag1^null mice and recovered from host spleens 14 days later by flow cytometric sorting for single cell sequencing analysis. Splenocytes from NOD.Rag1^null mice were individually homogenized using glass homogenizers in ice cold HBSS. Cells were washed and resuspended in PBS after which cells were incubated with antibodies against CD4 and T cell receptor beta and a Viability dye. Cells were washed and resuspended in PBS supplemented with 0.04% w/v BSA and 0.4 U/ul RNase I. Alive CD4 T cells were sorted into the same buffer using a BDFACS Melody (BD Bioscience).
Gene expression library and TCR library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics)

value: splenocytes

value: spleen

tag: strain

tag: age

value: 6-8 weeks old


title: mouse 2, replicate 1, scRNAseq, GEX

description: 10x Genomics


title: GEX_p21165-s008_RVh17-RGi17-wk10-wk26

value: mixed sample(Week10 and Week26 for RVh17, RGi17 - R66M gp120)


title: 62V P   [JR6]

value: Ventral Preadipocyte


title: mouse 1, replicate 1, scRNAseq, GEX

description: 10x Genomics


title: mouse 2, replicate 1, scRNAseq, TCR

description: 10x Genomics


title: GEX_p21165-s005_RSb17-RYf17-MA277-wk55-wk63-capture2

value: mixed sample(Week55 and Week63 for RSb17,RYf17,MA277 - Z1800M trimer)


title: 61D A  [JR3]

value: Lateral Adipocyte


title: 61D P  [JR1]


title: GEX_p21165-s006_6S0-MA277-wk10-wk26

value: Blood

value: Antigen Specific B lymphocytes

value: mixed sample(Week10 and Week26 for 6S0,MA277 - Z1800M gp120 , Z1800M trimer)


title: GEX_p21165-s004_RSb17-RYf17-MA277-wk55-wk63-capture1

value: mRNA


title: Brain, CUG300-CWG-cPIP, rep2

city: Honjo, Chuo-ku, Kumamoto

first: Kazuya

last: Matsuo

department: IMEG

institute: Kumamoto University

data_processing:
Local Run Manager was used for demultiplexing and FASTQ file generation after base calling.
The adapter sequence and low-quality ends were trimmed using Trim Galore! version 0.6.6.
The remaining reads were aligned to the mouse genome (UCSC mm10) and gene expression was counted using RSEM version 1.3.3 with STAR version 2.7.9a.
Gene expression for each sample was analyzed with DESeq2 version 1.36.0 and expressed as normalized counts in regularized logarithm.
Clustering analysis was performed with DEGreport version 1.32.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized log2 values for each sample

source_name: Brain hippocampus

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: Brain hippocampus

tag: genotype

value: wild type

tag: developmental stage

value: AAV9-CUG300 + CWG-cPIP


title: GEX_p21165-s003_RSb17-RYf17-wk10-wk26

value: mixed sample(Week10 and Week26 for RSb17,RYf17 - Z1800M trimer)


title: GEX_p21165-s002_15C172-RFj17-wk10-wk26

value: mixed sample(Week10 and Week26 for 15C172,RFj17 - Z1800M trimer)


title: Brain, CUG300-vehicle, rep3

value: AAV9-CUG300 + vehicle


title: Brain, CUG300-vehicle, rep2


title: GEX_p21096-s004_RRb17-wk10-wk26-RPz16-wk10-wk26

value: mixed sample(Week10 and Week26 for RRb17,RPz17 - Z1800M gp120)


title: Brain, CUG300-vehicle, rep1


title: GEX_p21096-s003_ROa17-wk10-wk26-RLk17-wk10-wk26

value: mixed sample(Week10 and Week26 for RLk17,ROa17 - Z1800M gp120)


title: Man_NW_19_6hr fast_0months

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy3-labelled samples were hybridized against the Cy5-labelled reference pool according to the manufacturers' procedure using 2x Hybridization buffer (Agilent). Samples were applied to 8x60K v3 microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential with GE Wash buffer 2 for 1 minute at 37C, followed by acetonitrile for 1 minute at room temperature, and finally with a stabilization and drying solution for 30 seconds at room temperature according to Agilents' recommendations. Slides were covered by an ozone-barrier slide before scanning.

scan_protocol: Scanned with an Agilent Scanarray scanner (G2505C US22502548) with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (12.2.07) to obtain raw median signal and background values for both Cy3 and Cy5. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy5-reference pool, and values  were log2 transformed. For final data analysis, 2 duplicate RNA samples were taken along and confirmed for reproducibility but excluded for overall analyses thereafter: US22502548_257236338304_S01_GE2_1200_Dec17_2_2.txt and US22502548_257236338312_S01_GE2_1200_Dec17_1_2.txt.

source_name: PBMCs

label_protocol: 100 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). Two samples were taken along as duplicates. Half of the Cy5-labeled samples (40 individual samples, equally spread over all the groups) were used for the reference pool.

extract_protocol: Blood from participants was collected using Vacutainer® EDTA tubes. After blood collection, PBMC were isolated using Ficoll-Paque Plus density gradient media (GE Healthcare Bio Science, Madrid, Spain). In brief, the anticoagulant treated blood was diluted with an equal volume of a phosphate-buffered saline (PBS) solution. Next, the blood was layered carefully over Ficoll without intermixing (10 ml of Ficoll for 20 ml of blood mixed with PBS) in a centrifuge tube and centrifuged at 400 g for 30 min at 20°C. PBMC, together with platelets, were harvested from the interface between Ficoll and plasma layers. This layer was then centrifuged in PBS at 300 g for 10 min at 20°C to wash PBMC and to remove the platelets. PBMC pellet was finally suspended in Tripure Reagent (Roche Diagnostics, Barcelona, Spain) and stored at -80ºC. Total RNA from PBMC samples was extracted using Tripure Reagent (Roche Diagnostics, Barcelona, Spain) and then purified with E.Z.N.A. Total RNA Kit I (Omega Biotek, Vermont, USA), following the manufacturer’s instructions. Finally, RNA was precipitated with isopropanol. Isolated RNA was quantified using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). Its integrity was confirmed using agarose gel electrophoresis and the RIN tool using the Agilent 2100 Bioanalyzer System. All samples showed superieor quality and were taken along.

treatment_protocol: Apparently healthy subjects aged 18 to 45 years old, including men and women were recruited and classified into two groups depending on their body mass index (BMI). Normal-weight (NW) group (BMI <25 kg/m2) was composed of 20 subjects and overweight-obese (OW-OB) group (BMI ≥25 kg/m2) of 27 subjects. The inclusion criteria were: subjects with no chronic disease who did not take regular medication or drugs. To avoid potential bias, both groups include approx. 50% men/women and there was no difference in their average age. We recruited 6 additional NW individuals presenting 1 metabolic alteration related to MetS (high plasma total or LDL-cholesterol, plasma triglycerides, or plasma C-reactive protein (CRP) concentrations, or hypertension). They were classified as metabolically obese normal-weight (MONW) individuals. Subjects from the OW-OB group followed a 6-month weight loss program which included a low-calorie food plan (30% reduction in the individual energy requirements) with dietary sessions and exercise counselling. Dietary sessions were offered by a nutritionist every fifteen days who provided face-to-face counselling that was individually adjusted to each subject with the aim of reducing 5% to 10% of its body weight. Neither dietary supplements nor vitamins were provided and all participants consumed self-selected foods. 20 out of the 27 OW-OB subjects who started the study completed the 6-month weight loss program. All the volunteers underwent what we call the fasting test which consisted of collecting blood samples after 4h and after 6 hours after having had a standard breakfast. The blood extractions were performed by skilled health personnel once in the NW and MONW groups, and three times (at the baseline point, and after 3 and 6 months of nutritional intervention) in the OW-OB group. Basic anthropometric parameters were collected: height, weight and waist-hip ratio. Blood pressure was measured with a sphygmomanometer (OMRON HEM705CP, Hoofddorp, The Netherlands) after the volunteer remained seated for fifteen minutes and body composition (fat percentage) was recorded by bioelectrical impedance (OMRON BF306). Additionally, hours of sleep and exercise, as well as food habits (24-h dietary recall) were recorded. Blood extraction was performed after 6h of fast. The following circulating parameters were measured in the analytical service of the Son Espases University Hospital (HUSE): plasma glucose (mg/dL), triglycerides (TG, mg/dL), total cholesterol (mg/dL), high-density lipoprotein cholesterol (HDL-C, mg/dL), gamma-glutamyl transpeptidase (GGT, U/L), and C-reactive protein (CRP, mg/dL). Low-density lipoprotein cholesterol (LDL-C, mg/dL) was calculated using the Friedewald formula whenever TG levels were inferior to 400 mg/dL. Insulin levels (µU/mL) were measured with a commercial ELISA kit of Mercodia (AD bioinstruments, S.L., Terrassa, Spain). Body fat was measured using a DEXA scanner (GE Healthcare/DEXA Lunar Prodigy Primo and Lunar iDEXA; Madison, WI)) connected with an enCore™ software using automatic total body scan mode.

tag: gender

value: Man

tag: group

value: NW

tag: fasting time

tag: timepoint

tag: sample type

value: reference pool


title: Brain, CUG300-CWG-cPIP, rep3


title: Brain, CUG10-vehicle, rep3

value: AAV9-CUG10 + vehicle


title: 61V P   [JR2]

value: Thoracic Aorta Perivascular Fat

value: Stromal Vascular Fraction Derived Preadipocytes

value: Ventral Preadipocyte


title: GEX_p21096-s002_RLK17-wk63

value: Blood

value: Antigen Specific B lymphocytes

value: sample(Week63 RLk17 - Z1800M gp120)


title: Brain, CUG10-vehicle, rep2

value: Brain hippocampus

value: wild type


title: GEX_p21096-s001_ROa17-wk63-wk55-RLK17-wk55

value: mixed sample(Week63 for ROa17, Week55 for ROa17,RLk17 - Z1800M gp120)

value: mRNA


title: Man_OW/OB_4_4hr fast_0months

value: OW/OB


title: Brain, CUG10-vehicle, rep1


title: Brain, CUG300-CWG-cPIP

data_processing:
Local Run Manager was used for demultiplexing and FASTQ file generation after base calling.
The adapter sequence and low-quality ends were trimmed using Trim Galore! version 0.6.6.
The remaining reads were aligned to the mouse genome (UCSC mm10) and gene expression was counted using RSEM version 1.3.3 with STAR version 2.7.9a.
Gene expression for each sample was analyzed with DESeq2 version 1.36.0 and expressed as normalized counts in regularized logarithm.
Alternative splicing was quantified using JCEC files in rMATS (version 4.1.2).
Assembly: mm10

value: AAV9-CUG300 + CWG-cPIP


title: Woman_OW/OB_2_6hr fast_0months

value: Woman


title: DSP-1012550009801-A-D10

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

country: Germany

institute: Klinikum rechts der Isar

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4

source_name: DRGs  T8 to T12

extract_protocol:
Murine DRG T8 to T12 were extracted bilaterally from TPAC (Ela-TGFα; Ptf1a-Cre; Trp53fl/fl;RelAfl/fl , n=6, 47-54 weeks old), KPC (Ptf1a-Cre; LSL-Kras+/G12D; Trp53+/fl , n=3, 20-21 weeks old) and age-similar tumor-free control mice (Ela-TGFα; Trp53fl/fl;RelAfl/fl , n=3, 48-50 weeks old for TPAC and LSL-Kras+/G12D; Trp53+/fl , n=1, 20 weeks old; Trp53+/fl , n=1, 21 weeks old and LSL-Kras+/G12D; n=1, 22 weeks old for KPC). Following the extraction, DRGs were briefly washed in ice-cold, fresh PBS (D5262, Sigma-Aldrich) and fixated in freshly prepared 4% PFA (15710, Electron Microscopy Sciences; diluted with PBS) for 24 hours at room temperature. The samples were consecutively dehydrated, paraffine embedded and sectioned. For the human spatial transcriptome studies, two patient derived biopcies with pancreatic ductal adenocarcinoma analysed with HE staining for the neural invasion were fixed in freshly prepared 4% PFA (15710, Electron Microscopy Sciences; diluted with PBS) for 24 hours at room temperature. Three FFPE tissue sections of 5-μm from DRG biopsy tissue microarray (TMA) with VILI (n=6) and AIH (n=8) (TMA construction described below in the Immunoprofiling with CO-Detection by indEXing (CODEX)) were mounted on positively charged histology slides. Sections were incubated at 65 °C for 1 hour. Then, sections were deparaffinized in 3 xylol baths of 5 minutes and rehydrated in ethanol gradient from 100% EtOH 2 baths of 5 minutes, followed by 95% EtOH 5 minutes. Slides were then washed in 1X PBS. Antigen retrieval was carried out with Tris-EDTA pH 9.0 buffer at 100°C for 20 minutes at low pressure. Slides were first immersed into hot water for 10 seconds and then immersed into Tris-EDTA buffer. The cooker vent kept open during the procedure to ensure low pressure and it was allowed to reach 100°C. Slides were then washed with 1X PBS, and incubated in proteinase K containing PBS (1ug/ml) for 15 minutes at 37°C and washed again in 1X PBS. Tissue were post-fixed in 10% neutral-buffered formalin (NBF) for 5 minutes, washed two times 5 minutes in NBF stop buffer (0.1M Tris Base, 0.1M Glycine) and finally one time in 1X PBS. The mix of Whole Transcriptome Atlas probes (WTA, Nanostring) was dropped on each section and covered with HybriSlip Hybridization Covers. Slides were then incubated for hybridization overnight at 37°C in a Hyb EZ II hybridization oven (Advanced cell Diagnostics). The day after, HybriSlip covers were gently removed and 25 minutes stringent washes were performed twice in 50% formamide and 2X saline sodium citrate (SSC) at 37 °C. Tissues were washed for 5 min in 2× SSC, then blocked in Buffer W (Nanostring Technologies) for 30 min at room temperature in a humidity chamber. Next, 500 nM Syto83 and antibodies targeting NeuN (Channel-647, host-mouse, company -abCam, clone # EPR12763, dilution 1:100); GFAP (Channel-488, host-mouse, company -Novus, clone # GA-5, dilution 1:200); CD68 (Channel-594, host-mouse, company -Santa Cruz, clone # KP1, dilution 1:200) in Buffer W were applied to each section for 1 h at room temperature. Slides were washed twice in fresh 2× SSC then loaded on the GeoMx DSP. DSP Instrument (NanoString Technologies, Inc.), nCounter (NanoString Technologies, Inc.), Immunohistochemistry Pressure Cooker (BioSB), PCR instrument (Biorad) was used.
DNA oligonucleotide probes were designed to bind mRNA targets. From 5′ to 3′, each probe is comprised of a 35- to 50-nucleotide target complementary sequence, an ultraviolet (UV) photo cleavable linker and a 66-nucleotide indexing oligonucleotide sequence containing a unique molecular identifier (UMI), RNA ID sequence and primer binding sites. Oligomers from ROIs were disintegrated by UV irradiation, passed through capillaries, pooled into collection plates, and resealed with DAPI fluoromount G mounting medium.
Entire slides were imaged at ×20 magnification and morphologic markers were used to select Region Of Interest (ROI) either using circle or organic shapes. Automatic segmentation of ROI based on NeuN marker was used to defined Area of Illumination (AOIs). This allowed to separate Neurons (NeuN+) and cells around. A total of AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited in a 96-well plate for subsequent processing. The indexing oligonucleotides were dried down overnight and resuspended in 10 μl of DEPC-treated water. Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, and unique i5 and i7 sample indices were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer’s protocol. Pooled libraries were single-sequenced at 27 base pairs and with the single-index workflow on an Illumina NovaSeq S4 instrument. FastQ files were converted into DCC files according to manufacturer’s pipeline. Digital Count Conversion files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.4.2.2 (Nanostring).

treatment_protocol: no treatment

value: Ela-TGF{alpha}; Trp53fl/fl;RelAfl/fl

value: DRGs  T8 to T12

tag: slide id

tag: roi number

tag: segment type

value: Full ROI

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: GEX_p21065_s001_RRb17-RPz16-15C172-RFj17

tag: tissue

tag: cell type

tag: condition

value: mixed sample(Week63 for RRb17,RPz16 - Z1800M gp120 ; 15C172,RFj17- Z1800M trimer)

tag: library type


title: GEX_p21165-s001_RRb17-RPz16-15C172-RFj15-wk55

value: mixed sample(Week55 for RRb17,RPz16 - Z1800M gp120 ; 15c172,RFj17 - Z1800M trimer)


title: MoS2_NIR_1

city: chongqing

first: ke

last: li

address: shazheng street 174

country: China

institute: chongqing university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Mouse breast cancer cells

growth_protocol: 10% FBS, 1% penicillin/streptomycin, high glucose DMEM

extract_protocol:
About 10e6 4T1 cells were isolated from different group and the mRNA library constructed using QIAseq FX Single Cell RNA Library Kit (QIAGEN) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cell cultured with medium, MoS2 and MoS2+NIR

tag: cell line

tag: cell states

value: photothermal therapy

tag: intervention


title: Brain, CUG300-CWG-cPIP, rep1

tag: strain

tag: genotype

tag: developmental stage

tag: treatment


title: DSP-1012550009801-A-D09

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: Brain, CUG10-vehicle

tag: tissue

value: AAV9-CUG10 + vehicle


title: Man_OW/OB_30_4hr fast_6months

tag: gender

value: Man

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type

value: reference pool


title: Man_NW_17_6hr fast_0months

value: NW


title: YCCEL1 Olaparib rep2

city: Philadelphia

first: Italo

last: Tempera

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
Illumina HiSeq 2500 paired-end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605.1) using HiC-Pro v2.10.0 pipeline
DESeq2 was used to estimate significance of differential contact based on raw count matrix files.
Only significantly changed associations (FDR<5%) were kept
Interactions were plotted as circos graph using the circlize package (version 0.4.12) of R (version 4.0.5)
Assembly: NC_007605.1
Supplementary files format and content: Raw counts for each interactions
Supplementary files format and content: p- and q-value of interactions are provided in the matrix file

organism: human gammaherpesvirus 4

growth_protocol: YCCEL1 and SNU719 cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 10% and supplemented with 1% penicillin-streptomycin in a humidified incubator containing 5% CO2 at 37 ̊C

extract_protocol:
Libraries of total ligation products were produced using Ultralow Library Systems V2 as per manufacturer’s protocol.
Purified libraries were then enriched for only EBV genome ligation products using myBaits enrichment kit as per manufacturer’s protocol.

treatment_protocol: Treatment with PARP inhibitor Olaparib was given 72 h before collection at a concentration of 5 µM. 5 million cells per condition were collected for in-situ Hi-C as per Rao et al. Cell 2014.

value: Olaparib (5uM)

tag: cell line

tag: cell type

value: Gastric adenocarcinoma


title: Man_OW/OB_30_6hr fast_6months


title: Man_NW_19_4hr fast_0months


title: YCCEL1 DMSO rep2

tag: treatment

value: DMSO


title: YCCEL1 Olaparib rep1


title: DSP-1012550009801-A-D07

tag: genotype

tag: slide id

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: DSP-1012550009801-A-D06

tag: tissue

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: Man_OW/OB_30_4hr fast_0months

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: YCCEL1 DMSO rep1

tag: treatment

tag: cell line

tag: cell type


title: SNU719 Olaparib rep2

value: Gastric tubular adenocarcinoma


title: DSP-1012550009801-A-D05

tag: genotype

tag: slide id

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Woman_OW/OB_2_4hr fast_0months

value: OW/OB


title: Brain, CUG300-vehicle

tag: tissue

value: Brain hippocampus

tag: strain

value: wild type

tag: developmental stage

value: AAV9-CUG300 + vehicle


title: SNU719 Olaparib rep1


title: DSP-1012550009801-A-D04

value: DRGs  T8 to T12

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: DSP-1012550009801-A-D03

value: Full ROI


title: Man_OW/OB_8_6hr fast_0months

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: Woman_OW/OB_10_4hr fast_6months

value: Woman


title: Woman_OW/OB_2_6hr fast_6months


title: Man_NW_7_4hr fast_0months


title: Man_OW/OB_21_4hr fast_6months


title: DSP-1012550009801-A-D08

tag: genotype

value: Ela-TGF{alpha}; Trp53fl/fl;RelAfl/fl

tag: slide id

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Man_NW_17_4hr fast_0months


title: SNU719 DMSO rep2

tag: treatment

tag: cell line

tag: cell type


title: SNU719 DMSO rep1


title: DSP-1012550009801-A-D01

tag: tissue

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: sequencingsaturation


title: Mutu1 HiC

value: EBV-related Burkitt lymphoma


title: Man_OW/OB_30_6hr fast_0months

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: DSP-1012550009801-A-C12

tag: genotype

tag: slide id

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: U2OS, typeIII, erythropoietin, 8h, rep3

city: Princeton

first: Aaron

middle: E

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Reads were demultiplexed using Picard v2.21.1, from within viral-ngs v.1.25.0 with the read structure ‘5S8B15M8B101T’ and Q10M2 mismatch tolerance.
Demultiplexed reads were mapped to the human genome hg38 using STAR v2.7.10a.
Uniquely mapped reads were counted based on the GENCODE comprehensive gene annotation on the primary assembly using htseq-count v1.99.2.
Assembly: hg38, GENCODE release 39
Supplementary files format and content: gene-level counts

growth_protocol: U2OS osteosarcoma cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using an RNeasy mini kit (Qiagen). 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using bulk RNA barcoding and sequencing (BRB-Seq) with some modifications. Reverse transcription (RT) was performed with 50 ng total RNA per sample using SuperScript IV (Invitrogen) and a distinctly barcoded oligo(dT)30 primer for each sample (modified with the Illumina TruSeq Read 1 priming site instead of Nextera Read 1) with the following thermocycling program: 50 °C, 15 min; 55 °C, 15 min; 60 °C, 15 min; 80 °C, 15 min. After RT, up to 24 barcoded first-strand cDNA samples were pooled into a single tube. For each cDNA pool, second-strand cDNA was synthesized by the Gubler-Hoffman nick translation approach per the BRB-Seq protocol. Then, instead of Tn5 tagmentation, each cDNA pool was fragmented and end-repaired with the NEBNext Ultra II FS DNA Module (NEB) at 37 °C for 6 min, followed by 65 °C for 30 min. 37.5 pmol DNA adaptor containing Illumina Read 2 was duplexed and ligated using optimized ligation conditions at 20 °C for 2 h before purifying ligation products with sequential 1.0X AMPure XP SPRI cleanups (Beckman Coulter). Each cDNA pool was amplified with 12 cycles of PCR using a P5 containing primer and a distinct multiplexed i7 indexing primer (Chromium i7 Multiplex Kit, 10X Genomics, Pleasanton, CA), size-selected with 0.55/0.75X double-sided size-selection with SPRIselect (Beckman Coulter), then amplified for another 6 cycles of PCR using P5 and P7 primers, before a final 0.7X SPRIselect cleanup.

treatment_protocol: U2OS osteosarcoma cells were plated at 200,000 cells/well in 12-well plates and the following day treated with either 1000 IU/ml IFN-beta or 100 ng/ml IFN-lambda3 (in the case of naïve cells) or 100 ng/ml EPO (in the case of chimera-expressing cells) for 0, 1, 3, or 8 h.

tag: cell line

tag: cell type

value: osteosarcoma

value: typeIII

tag: treatment

value: erythropoietin

tag: time

tag: replicate


title: U2OS, typeIII, erythropoietin, 8h, rep1


title: Man_NW_8_6hr fast_0months

tag: gender

value: Man

tag: group

value: NW

value: reference pool


title: U2OS, typeIII, erythropoietin, 8h, rep2


title: U2OS, typeIII, erythropoietin, 3h, rep3


title: YCCEL1 Input rep2

data_processing:
Illumina HiSeq 2500 paired-end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605.1) using BWA
Peak calling was performed using MACS2 with input DNA used as a reference set
deepTools 3.5.2 was used to generate bigWig files
UCSC Genome Browser was used for data visualization
Assembly: NC_007605.1
Supplementary files format and content: Coverage file in bigWig format
Supplementary files format and content: MACS2 narrowPeak output (except for Input samples)

extract_protocol:
DNA was purified using Promega Wizard SV Gel and PCR Clean-up Kit
Libraries for sequencing were made using NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: 25 milion cells per immunoprecipitation were collected and fixed with 1% formaldehyde for 15 min and then quenched with 0.25 M glycine for 5 min on ice. After 3 washes with 1X PBS, pellets were resuspended in 10 mL each of a series of two lysis buffers and resuspended in 1mL of the third lysis buffer before fragmentation in Covaris ME220 Ultrasonicator to generate chromatin fragments roughly 200–500 bp in size. Chromatin was centrifuged to clear debris and a 1:20 of this cleared chromatin was kept as standard input for comparison against immunoprecipitations. Chromatin was incubated rotating at 4° 1h with 25 µg H3K4me1 and 25 µg H3K27ac, then chromatin–antibody complexes were precipitated using 50 µL of Dynabeads Protein A incubated rotating at 4° overnight.

tag: chip antibody

value: Gastric adenocarcinoma


title: DSP-1012550009801-A-C11

tag: tissue

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: sequencingsaturation


title: U2OS, typeIII, erythropoietin, 3h, rep2

tag: genotype


title: DSP-1012550009801-A-C10

tag: slide id

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: DSP-1012550009801-A-D02


title: YCCEL1 Input rep1

tag: cell line

tag: cell type


title: U2OS, typeIII, erythropoietin, 3h, rep1

tag: treatment

tag: time

tag: replicate


title: DSP-1012550009801-A-C09

tag: tissue

tag: roi number

tag: segment type


title: Woman_NW_15_4hr fast_0months

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: YCCEL1 H3K4me1 ChIP-seq rep2

tag: chip antibody

value: H3K4me1 (Active Motif 39299)


title: U2OS, typeIII, erythropoietin, 1h, rep3

tag: genotype


title: Woman_OW/OB_26_4hr fast_6months

value: OW/OB


title: DSP-1012550009801-A-C08

tag: slide id

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Woman_OW/OB_10_6hr fast_6months

tag: gender

tag: group


title: Woman_OW/OB_11_6hr fast_0months

tag: age

tag: fasting time


title: DSP-1012550009801-A-C07

tag: tissue

tag: roi number

tag: segment type


title: Woman_NW_2_4hr fast_0months

tag: timepoint

tag: sample type


title: YCCEL1 H3K4me1 ChIP-seq rep1

tag: chip antibody

tag: cell line

tag: cell type


title: LCL HiC

source_name: LCL

tag: treatment

value: LCL

value: B lymphocyte


title: DSP-1012550009801-A-C06

tag: genotype

tag: slide id

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Woman_OW/OB_18_6hr fast_6months

tag: gender

tag: group

tag: age

tag: fasting time


title: YCCEL1 H3K27ac ChIP-seq rep2

value: H3K27ac (Active Motif 39133)


title: U2OS, typeIII, erythropoietin, 1h, rep2

tag: time

tag: replicate


title: U2OS, typeIII, erythropoietin, 1h, rep1

tag: cell line


title: U2OS, typeIII, untreated, n/a, rep3

tag: cell type

value: untreated


title: YCCEL1 H3K27ac ChIP-seq rep1

tag: chip antibody


title: DSP-1012550009801-A-C05

tag: genotype

tag: tissue

value: DRGs  T8 to T12

tag: roi number

tag: segment type

value: Full ROI

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: SNU719 Input rep2

value: Gastric tubular adenocarcinoma


title: SNU719 Input rep1


title: DSP-1012550009801-A-C03

value: Ptf1a-Cre; LSL-Kras+/G12D

tag: slide id

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Woman_OW/OB_18_4hr fast_0months

tag: gender

value: Woman

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: U2OS, typeIII, untreated, n/a, rep1

tag: cell line

tag: cell type

value: osteosarcoma

tag: genotype

value: typeIII

tag: treatment

tag: time

tag: replicate


title: DSP-1012550009801-A-C02

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: U2OS, typeI, erythropoietin, 8h, rep3

value: typeI

value: erythropoietin


title: DSP-1012550009801-A-C01

value: Ptf1a-Cre; LSL-Kras+/G12D; Trp53+/f

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: DSP-1012550009801-A-B12

tag: genotype


title: SNU719 H3K4me1 ChIP-seq rep1

tag: chip antibody

tag: cell line

tag: cell type


title: Man_NW_10_4hr fast_0months

tag: gender

value: Man

tag: group

value: NW

tag: age

tag: fasting time

tag: timepoint

tag: sample type

value: reference pool


title: U2OS, typeI, erythropoietin, 8h, rep2

tag: treatment

tag: time

tag: replicate


title: Woman_OW/OB_17_4hr fast_6months

value: OW/OB


title: SNU719 H3K27ac ChIP-seq rep1


title: U2OS, typeI, erythropoietin, 3h, rep3


title: Untargeted-miniSOG_U-2 OS, arsenite-stress, label, post-enrichment, rep2

city: Beijing

first: Ziqi

last: Ren

address: Chengfu Road No.292

department: College of Chemistry and Molecular Engineering

institute: Peking University

description: Column Name: Untargeted-mS_U2OS_AS_label_enrich2

data_processing:
The adaptors sequence in reads were removed by Cutadapt (v.1.18) and quality controlled by FastQC (v0.11.8) to ensure the adaptors were completely removed. Then reads were mapped by hisat2 (v2.1.0) to the human genome assembly GRCh38 (hg38) with Homo_sapiens.GRCh38.87.gtf annotations using the command: hisat2 -x $refGenome -1 $clean_file1 -2 $clean_file2 -p 8 2>$AligDir/$output.log|samtools view -hb >$AligDir/$output.bam
The mapped reads were then sorted by command: samtools sort -n $output.bam -O BAM -o $outputSort -T $outputSort.temp -@ 4 -m 2G 2>$outputSort.log
The sorted reads were counted by htseq-count (v0.7.2) using the command: htseq-count -s no -f bam $outputSort $refGTF >$output 2>$output.log. Same library was re-detected with deeper sequencing depth on Illumina platform to get enough reads for analysis. The final counts used for further analysis were counted by the sum of counts from the two sequencing testment.
Assembly: GRCh38 (hg38)
Supplementary files format and content: HEK293T_allcounts.xlsx, contains counts of all genes (sum of two rounds of sequencing) from HEK293T stable cells stably expressing G3BP1-miniSOG or untargeted-miniSOG under all condition
Supplementary files format and content: U2OS_allcounts.xlsx, contains counts of all genes from U-2OS stable cells stably expressing G3BP1-miniSOG or untargeted-miniSOG under arsenite-stress

source_name: U-2 OS

growth_protocol: HEK293T cells were cultured in complete medium consisting of Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum at 37°C with 5% CO2. U-2 OS cells were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
RNAs were extract following the TRIzol Reagent manufacturer’s instructions, digested with 1-2 μL DNaseI at 37°C for 30 min, and then incubated with click reagents consisting of 0.1 mM biotin-azide, 2 mM THPTA, 0.5 mM CuSO4 and 5 mM sodium ascorbate. After 10 min of CuAAC reaction at room temperature, RNAs were purified with RNA Clean&Concentrator kit  and eluted with pre-warmed nuclease-free water. The RNA integrity was detected by Fragment Analyzer. Approximately 1 μg RNA was kept as pre-enrichment samples, while the remaining was purified with streptavidin beads and the post-enrichment samples were purified by TRIzol Reagent.
Total RNAs were used for library construction and libraries were constructed by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) following the manuyfacturer's instructions.

treatment_protocol:
HEK293T and U-2 OS cells stably expressing G3BP1-miniSOG and untargeted miniSOG were cultured to 90% confluency. To induce stress, cells were incubated in complete media supplemented with either 0.5 mM sodium arsenite for 40 min or 0.4 M D-sorbitol for 130 min in 37°C. Cells were then washed once with 1× HBSS and the medium was replaced by HBSS containing 10 mM propargylamine (PA)  and 0.5 mM sodium arsenite or 0.4 M sorbitol. For unstressed samples, cells were rinsed with HBSS once and then incubated in HBSS containing 10 mM PA. After 5 min of incubation under 37°C, cells were illuminated with blue LED (emission peak 465-475 nm, 24 mW/cm2) for 15 min at room temperature, samples without PA probe were set as control.
For detection of SG transcriptome during disassembly, HEK293T cells stably expressing G3BP1-miniSOG or untargeted miniSOG were cultured to 90% confluency and incubated with complete medium containing 0.5 mM sodium arsenite for 1 hr. Thereafter, stressed cells were washed 3 times with pre-warmed complete medium at 37°C. After recoverying in complete medium for 40 min or 160 min, cells were washed once with HBSS, incubated with HBSS in the presence of 10 mM PA for 5 min at 37°C, and illuminated with blue LED for 15 min at room temperature.

value: U-2 OS

value: Untargeted miniSOG-NES stably expression

value: 0.5 mM arsenite, 1 hr


title: mir163-biol rep 2

city: Taichung City

first: Jeng-Shane

state: Taiwan (R.O.C.)

address: Room 516, Life Science Building,145 Xingda Rd., South Dist.

country: Taiwan

institute: National Chung Hsing University

data_processing:
Raw sequences were obtained from the Illumina bcl2fastq v2.17.1.14 and expected to generate 6 G per sample.
Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation.
For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
The reference genome and gene annotations were retrieved from Ensembl database.
Assembly: TAIR10
Supplementary files format and content: WT-163 file includes FPKM values

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana (Col-0) was grown in a controlled environment at 22°C under 16 h light/8 h dark with cool fluorescent light at 100 μmolm-2 s-1.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
Library construction of all samples were used by NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: The 7-day-old seedlings were used.

tag: tissue

value: seedlings

tag: ecotype

value: mir163 mutant

value: 7-day-old seedlings without treatment


title: U2OS, typeI, erythropoietin, 3h, rep2


title: DSP-1012550009801-A-B10

value: Ptf1a-Cre; LSL-Kras+/+

value: DRGs  T8 to T12

tag: slide id

tag: roi number

tag: segment type

value: Full ROI

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: SNU719 H3K4me1 ChIP-seq rep2

tag: chip antibody

value: H3K4me1 (Active Motif 39299)

tag: cell line

tag: cell type

value: Gastric tubular adenocarcinoma


title: Woman_NW_13_6hr fast_0months

tag: gender

value: Woman

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: Man_OW/OB_21_6hr fast_6months


title: DSP-1012550009801-A-B09

tag: genotype

value: Ptf1a-Cre; LSL-Kras+/G12D

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: deduplicatedreads


title: SNU719 H3K27ac ChIP-seq rep2

value: H3K27ac (Active Motif 39133)


title: Woman_MONW_2_6hr fast_0months

value: MONW


title: Man_OW/OB_21_4hr fast_0months

value: Man

value: reference pool


title: DSP-1012550009801-A-B08

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: U2OS, typeI, erythropoietin, 1h, rep3

tag: cell line

tag: cell type

value: osteosarcoma

value: typeI

tag: treatment

value: erythropoietin

tag: time

tag: replicate


title: Untargeted-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, post-enrichment, rep4

description: Column Name: Untargeted-mS_T3_label_enrich4

tag: genotype

value: Untargeted miniSOG-NES stably expression

value: 3 hr recovery post arsenite stress


title: DSP-1012550009801-A-B07

value: Ptf1a-Cre; LSL-Kras+/G12D; Trp53+/f

tag: tissue

tag: slide id

tag: roi number


title: U2OS, typeI, erythropoietin, 8h, rep1


title: Untargeted-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, post-enrichment, rep3

description: Column Name: Untargeted-mS_T3_label_enrich3


title: Woman_NW_15_6hr fast_0months

tag: gender

tag: group

value: NW

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: DSP-1012550009801-A-B11

value: DRGs  T8 to T12

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: U2OS, typeI, erythropoietin, 1h, rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: time

tag: replicate


title: Man_OW/OB_1_6hr fast_0months

tag: gender

tag: group

value: OW/OB

tag: age

tag: fasting time

tag: timepoint


title: DSP-1012550009801-A-C04

value: Ptf1a-Cre; LSL-Kras+/+

tag: tissue

tag: slide id

tag: roi number

tag: segment type

value: Full ROI

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: sequencingsaturation


title: Untargeted-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, post-enrichment, rep2

description: Column Name: Untargeted-mS_T3_label_enrich2

tag: cell line

tag: genotype


title: Untargeted-miniSOG_U-2 OS, arsenite-stress, label, post-enrichment, rep1

description: Column Name: Untargeted-mS_U2OS_AS_label_enrich1

value: U-2 OS

tag: treatment

value: 0.5 mM arsenite, 1 hr


title: U2OS, typeI, erythropoietin, 3h, rep1

tag: cell type

tag: time

tag: replicate


title: U2OS, typeI, erythropoietin, 1h, rep1


title: DSP-1012550009801-A-B06

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Man_OW/OB_4_6hr fast_6months

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: Untargeted-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, post-enrichment, rep1

description: Column Name: Untargeted-mS_T3_label_enrich1

tag: cell line


title: Untargeted-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, post-enrichment, rep4

description: Column Name: Untargeted-mS_T1_label_enrich4

tag: genotype

value: 1 hr recovery post arsenite stress


title: Man_MONW_9_6hr fast_0months

value: MONW


title: U2OS, typeI, untreated, n/a, rep2

tag: treatment

value: untreated


title: Woman_OW/OB_18_6hr fast_0months

value: Woman

value: reference pool


title: Woman_OW/OB_17_6hr fast_6months


title: DSP-1012550009801-A-B05

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: sequencingsaturation


title: DSP-1012550009801-A-B03

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Untargeted-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, post-enrichment, rep3

description: Column Name: Untargeted-mS_T1_label_enrich3


title: DSP-1012550009801-A-B04


title: U2OS, typeI, untreated, n/a, rep1

tag: cell type

value: osteosarcoma

value: typeI

tag: time

tag: replicate


title: U2OS, naive, IFN-lambda3, 8h, rep3

tag: cell line

tag: genotype

value: naive

tag: treatment


title: DSP-1012550009801-A-B02

tag: tissue

tag: slide id

tag: roi number


title: DSP-1012550009801-A-B01

tag: segment type

tag: area

tag: roi x coordinate


title: U2OS, typeI, untreated, n/a, rep3


title: DSP-1012550009801-A-A12

value: Ptf1a-Cre; LSL-Kras+/G12D

tag: roi y coordinate

tag: rawreads

tag: sequencingsaturation


title: Untargeted-miniSOG_HEK293T, sorbitol-stress, label, post-enrichment, rep4

description: Column Name: Untargeted-mS_Sorbitol_label_enrich4

value: Untargeted miniSOG-NES stably expression

value: 0.4 M sorbitol, 150 min


title: Untargeted-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, post-enrichment, rep1

description: Column Name: Untargeted-mS_T1_label_enrich1


title: Woman_NW_13_4hr fast_0months

tag: gender

tag: group

value: NW

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: Man_OW/OB_4_4hr fast_6months

value: Man

value: OW/OB


title: Woman_OW/OB_11_4hr fast_0months


title: U2OS, naive, IFN-lambda3, 8h, rep1

tag: cell line

tag: cell type

tag: genotype

tag: time

tag: replicate


title: U2OS, naive, IFN-lambda3, 8h, rep2

tag: treatment


title: Man_NW_7_6hr fast_0months


title: Man_OW/OB_1_4hr fast_0months


title: Untargeted-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, post-enrichment, rep2

description: Column Name: Untargeted-mS_T1_label_enrich2


title: Untargeted-miniSOG_HEK293T, sorbitol-stress, label, post-enrichment, rep2

description: Column Name: Untargeted-mS_Sorbitol_label_enrich2


title: Woman_NW_11_6hr fast_0months


title: DSP-1012550009801-A-A09

tag: tissue

value: DRGs  T8 to T12

tag: slide id

tag: roi number

tag: segment type

value: Full ROI

tag: area

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Woman_NW_2_6hr fast_0months

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint


title: Man_OW/OB_23_6hr fast_6months

tag: sample type


title: U2OS, naive, IFN-lambda3, 3h, rep2

tag: cell line

tag: cell type

tag: genotype

tag: time

tag: replicate


title: U2OS, naive, IFN-lambda3, 3h, rep1

tag: treatment


title: Untargeted-miniSOG_HEK293T, sorbitol-stress, label, post-enrichment, rep1

description: Column Name: Untargeted-mS_Sorbitol_label_enrich1


title: DSP-1012550009801-A-A08

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: sequencingsaturation


title: DSP-1012550009801-A-A11

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Man_MONW_3_6hr fast_0months

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type


title: Untargeted-miniSOG_HEK293T, unstressed, label, post-enrichment, rep4

description: Column Name: Untargeted-mS_basal_label_enrich4

tag: cell line

tag: genotype

tag: treatment

value: unstressed


title: U2OS, naive, IFN-lambda3, 1h, rep3

tag: cell type

tag: time

tag: replicate


title: Woman_OW/OB_2_4hr fast_6months


title: U2OS, naive, IFN-lambda3, 3h, rep3


title: Untargeted-miniSOG_HEK293T, sorbitol-stress, label, post-enrichment, rep3

description: Column Name: Untargeted-mS_Sorbitol_label_enrich3


title: DSP-1012550009801-A-A10

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: sequencingsaturation


title: U2OS, naive, IFN-lambda3, 1h, rep2


title: Untargeted-miniSOG_HEK293T, unstressed, label, post-enrichment, rep2

description: Column Name: Untargeted-mS_basal_label_enrich2


title: Untargeted-miniSOG_HEK293T, unstressed, label, post-enrichment, rep3

description: Column Name: Untargeted-mS_basal_label_enrich3


title: U2OS, naive, IFN-lambda3, 1h, rep1


title: Woman_OW/OB_26_4hr fast_0months

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.

tag: gender

tag: group

tag: age

tag: fasting time

tag: timepoint


title: Man_NW_10_6hr fast_0months

tag: sample type


title: Man_NW_8_4hr fast_0months


title: Man_OW/OB_4_6hr fast_0months


title: U2OS, naive, IFN-beta, 8h, rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: IFN-beta

tag: time


title: U2OS, naive, IFN-beta, 8h, rep1

tag: replicate


title: Untargeted-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep4

description: Column Name: Untargeted-mS_AS_label_enrich4

value: 0.5 mM arsenite, 1 hr


title: DSP-1012550009801-A-A05

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Untargeted-miniSOG_HEK293T, unstressed, label, post-enrichment, rep1

description: Column Name: Untargeted-mS_basal_label_enrich1


title: DSP-1012550009801-A-A04

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: sequencingsaturation


title: Untargeted-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep2

description: Column Name: Untargeted-mS_AS_label_enrich2

tag: cell line

tag: genotype


title: U2OS, naive, IFN-beta, 3h, rep3

tag: cell type

tag: treatment

tag: time


title: DSP-1012550009801-A-A07

tag: tissue

tag: slide id


title: Untargeted-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep3

description: Column Name: Untargeted-mS_AS_label_enrich3


title: DSP-1012550009801-A-A03

tag: roi number

tag: segment type


title: Untargeted-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep1

description: Column Name: Untargeted-mS_AS_label_enrich1


title: DMSO_Noc_Rep3

city: St Louis

first: Laura

last: DeVault

address: 4523 Clayton Avenue

department: developmental biology

institute: Washington University

data_processing:
nf-core/rnaseq version 3.6 using STAR/salmon and default parameters
Salmon transcript quantifications imported with tximport v1.22 and summarized to the gene level
Assembly: Genome GRCm39 with gencode M28 annotations
Supplementary files format and content: tab separated file with a header. The first column is the gene, subsequence columns are the library names (eg sample_1). Rows are genes. Values are raw counts from Salmon

source_name: embryonic DRG

growth_protocol: Neurons were cultured in growth media (Neurobasal, 2% B27, 50 ng/ml nerve growth factor, 1 µM 5-fluoro-2’-deoxyuridine , 1 µM uridine , and penicillin/ streptomycin) and spotted onto PDL poly-D-lysine, laminin coated plates.

extract_protocol:
RNA was extracted using ReliaPrep RNA extraction kit (Promega). At least 1.4 ug was used for construction of sequencing library
Ribosomal depletion, Kapa RiboErase HMR (Roche) was used to prepare libraries. Libraries were prepared by GTAC@MGI.

treatment_protocol: At 6 DIV, neurons were pretreated with DMSO or 500nM DLK inhibitor (GNE3511). After 15 minutes, neurons were then treated with DMSO, or 200nM nocodazole for 16 hours

value: embryonic DRG


title: DMSO_Noc_Rep4


title: U2OS, naive, IFN-beta, 8h, rep3

tag: replicate


title: U2OS, naive, IFN-beta, 3h, rep2


title: G3BP1-miniSOG_U-2 OS, arsenite-stress, omit probe, post-enrichment, rep2

description: Column Name: G3BP1-mS_U2OS_AS_noprobe_enrich2

value: U-2 OS

value: G3BP1-miniSOG stably  expression


title: U2OS, naive, IFN-beta, 3h, rep1

value: osteosarcoma


title: DSP-1012550009801-A-A06

tag: area

tag: alignedreads

tag: deduplicatedreads


title: G3BP1-miniSOG_U-2 OS, arsenite-stress, omit probe, post-enrichment, rep1

description: Column Name: G3BP1-mS_U2OS_AS_noprobe_enrich1


title: G3BP1-miniSOG_U-2 OS, arsenite-stress, label, pre-enrichment, rep2

description: Column Name: G3BP1-mS_U2OS_AS_label_input2


title: DMSO_DMSO_Rep4


title: U2OS, naive, IFN-beta, 1h, rep2


title: Woman_OW/OB_10_4hr fast_0months

tag: gender

value: Woman

tag: group

tag: age

tag: fasting time

tag: timepoint

tag: sample type

value: reference pool


title: Man_OW/OB_8_6hr fast_6months


title: DMSO_Noc_Rep1

tag: cell type

tag: genotype


title: Woman_OW/OB_26_6hr fast_0months


title: Woman_NW_14_6hr fast_0months


title: U2OS, naive, IFN-beta, 1h, rep1

tag: cell line

value: naive

tag: treatment

tag: time


title: Man_OW/OB_1_4hr fast_6months


title: DMSO_Noc_Rep2


title: G3BP1-miniSOG_U-2 OS, arsenite-stress, label, post-enrichment, rep2

description: Column Name: G3BP1-mS_U2OS_AS_label_enrich2


title: G3BP1-miniSOG_U-2 OS, arsenite-stress, label, pre-enrichment, rep1

description: Column Name: G3BP1-mS_U2OS_AS_label_input1


title: U2OS, naive, untreated, n/a, rep6

value: untreated


title: U2OS, typeIII, untreated, n/a, rep2

value: typeIII


title: DMSO_DMSO_Rep2


title: U2OS, naive, untreated, n/a, rep5


title: G3BP1-miniSOG_U-2 OS, arsenite-stress, label, post-enrichment, rep1

description: Column Name: G3BP1-mS_U2OS_AS_label_enrich1


title: DMSO_DMSO_Rep1


title: Man_OW/OB_8_4hr fast_6months


title: Woman_OW/OB_26_6hr fast_6months


title: U2OS, naive, IFN-beta, 1h, rep3


title: G3BP1-miniSOG_HEK293T, 3 hr recovery post arsenite stress, omit probe, post-enrichment, rep2

description: Column Name: G3BP1-mS_T3_noprobe_enrich2

value: 3 hr recovery post arsenite stress


title: Man_OW/OB_8_4hr fast_0months

value: Man


title: DSP-1012550009801-A-A02

value: Ptf1a-Cre; LSL-Kras+/G12D

tag: tissue

tag: slide id

tag: roi number

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Man_OW/OB_21_6hr fast_0months

tag: gender

tag: group

value: OW/OB

tag: age

tag: fasting time


title: Man_NW_21_4hr fast_0months

value: NW

tag: timepoint

tag: sample type


title: U2OS, naive, untreated, n/a, rep4

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: replicate


title: DLKi_Noc_Rep4


title: DMSO_DMSO_Rep3


title: G3BP1-miniSOG_HEK293T, 3 hr recovery post arsenite stress, omit probe, post-enrichment, rep1

description: Column Name: G3BP1-mS_T3_noprobe_enrich1


title: U2OS, naive, untreated, n/a, rep3

tag: time


title: U2OS, naive, untreated, n/a, rep2


title: G3BP1-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, pre-enrichment, rep2

description: Column Name: G3BP1-mS_T3_label_input2


title: U2OS, naive, untreated, n/a, rep1


title: DLKi_Noc_Rep2


title: G3BP1-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, pre-enrichment, rep1

description: Column Name: G3BP1-mS_T3_label_input1


title: DLKi_Noc_Rep3


title: Woman_NW_12_6hr fast_0months


title: rnaseq_ZR-75-1_S7

city: New York

first: Ekta

last: Khurana

address: 1305 York Ave

institute: Weill Cornell Medicine

data_processing:
The ATAC-seq raw data were processed with the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
RNA-seq data were aligned to hg38 using STAR (PMID: 23104886), counts was calculated using HTSeq (PMID: 25260700) and TPM was calculated as described by Wagner et al. (PMID: 22872506).
Assembly: GRCh38 [atac] GRCh38.79 [rna]
Supplementary files format and content: tab delimited text file containing counts of genes
Supplementary files format and content: bigwig

source_name: breast cancer cell line

growth_protocol: BT-474, HEK 293T, MCF-7, MDA-MB-231, and MDA-MB-361 were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, 11965-092); T-47D and AU-565 were cultured in RPMI Medium 1640 (Gibco, 00875-093); SK-BR-3 was cultured in McCoy’s 5A Medium (Gibco, 16600-082). All media were supplemented with 10% Fetal Bovine Serum (Omega Scientific, FB-12), 1% Sodium Pyruvate (Gibco, 11360-070), 1% Pen Strep (Gibco,15140-122), 1% HEPES Buffer (Gibco, 15630-080). T-47D media was additionally supplemented with 0.2 units/mL Bovine Insulin (Sigma Aldrich, I0516).

extract_protocol: Illumina TruSeq stranded mRNA Library prep

tag: tissue

value: breast


title: DLKi_DMSO_Rep4


title: rnaseq_T-47D_S6


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, omit probe, post-enrichment, rep3

description: Column Name: G3BP1-mS_T1_noprobe_enrich3

value: 1 hr recovery post arsenite stress


title: rnaseq_SK-BR-3_S3


title: DLKi_Noc_Rep1


title: Woman_MONW_1_6hr fast_0months

value: MONW


title: Woman_OW/OB_11_4hr fast_6months


title: Woman_NW_14_4hr fast_0months


title: G3BP1-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, post-enrichment, rep1

description: Column Name: G3BP1-mS_T3_label_enrich1


title: DLKi_DMSO_Rep2

value: embryonic DRG


title: rnaseq_MDA-MB-361_S2


title: rnaseq_MDA-MB-231_S8


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, omit probe, post-enrichment, rep2

description: Column Name: G3BP1-mS_T1_noprobe_enrich2


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, omit probe, post-enrichment, rep1

description: Column Name: G3BP1-mS_T1_noprobe_enrich1


title: DLKi_DMSO_Rep1


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, pre-enrichment, rep3

description: Column Name: G3BP1-mS_T1_label_input3


title: rnaseq_MCF7_S1


title: PthrpCE909_Ptch1-cHet

city: Houston

first: Shion

last: Orikasa

state: TX

address: 7500 Cambridge St

institute: University of Texas Health Science Center at Houston School of Dentistry

description: Postnatal day 36

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: mm10_trans_nono
Supplementary files format and content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Femur growth plate

extract_protocol:
Femurs were dissected and growth plate is extracted, growth plate cells were enzymatically dissociated and tdTomato+ cells were FACS-isolated. ~10,000 cells were loaded onto 10X Genomic Chromium platform
10X Genomics Chromium Single Cell 3' v3 Libraries

value: Femur growth plate

value: PTHrP-creER; Ptch1(fl/+); R26R-tdTomato


title: Woman_OW/OB_17_6hr fast_0months

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, pre-enrichment, rep2

description: Column Name: G3BP1-mS_T1_label_input2

value: G3BP1-miniSOG stably  expression


title: Woman_OW/OB_11_6hr fast_6months

value: Woman


title: Man_MONW_8_6hr fast_0months

value: reference pool


title: DLKi_DMSO_Rep3


title: rnaseq_BT-474_S5


title: PthrpCE909_Ptch1-cKO

description: Postnatal day 36

extract_protocol:
Femurs were dissected and growth plate is extracted, growth plate cells were enzymatically dissociated and tdTomato+ cells were FACS-isolated. ~26,000 cells were loaded onto 10X Genomic Chromium platform
10X Genomics Chromium Single Cell 3' v3 Libraries

value: Col1-GFP; PTHrP-creER; Ptch1(fl/fl); R26R-tdTomato


title: Man_OW/OB_23_4hr fast_0months


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, pre-enrichment, rep1

description: Column Name: G3BP1-mS_T1_label_input1


title: PTH hypoxia No.5

city: Tokyo

first: Yusuke

last: Joki

address: 2-1-1 Hongo

department: Cardiovascular Biology and Medicine

institute: Juntendo University, Graduate School of Medicine

data_processing:
The integrity and quantity of total RNA were measured using an Agilent 5400 fragment analyzer.
Alignment to the whole transcriptome, quantification of gene expression levels, and detection of differentially expressed genes, sequencing adaptors, low-quality reads, and bases were trimmed using the Trimmomatic-0.39 tool.
Sequence reads were aligned to the mouse reference genome (mm10) using STAR 2.7.9a software.
Aligned reads were subjected to downstream analyses using the StrandNGS 4.0 software.
Read counts allocated for each gene and transcript were quantified using a transcripts-per-million method.
Assembly: mm10
Supplementary files format and content: PTH PH hypoxia RNA-Seq_Quantified

source_name: lung

extract_protocol:
Total RNA was extracted using the RNeasy-Mini Kit. Extracted RNA was reverse-transcribed using a High-Capacity cDNA Reverse Transcription Kit. The integrity and quantity of total RNA were measured using an Agilent 5400 fragment analyzer.
Total RNA obtained from each sample was subjected to a sequencing library construction using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) and a NEBNext Poly(A) mRNA Magnetic Isolation Module, according to the manufacturer’s protocols.

treatment_protocol: C57BL/6J mice were housed in a hypoxia (10 % O2 + 90 % N2) chamber with a 12-h/light/dark cycle for 3 weeks. The PTH group was injected with PTH 1–34 at 40 ug/kg/day and the sham group was injected with saline.

value: lung

tag: strain

value: hypoxia (10 % O2) and injected with PTH


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, post-enrichment, rep3

description: Column Name: G3BP1-mS_T1_label_enrich3


title: Woman_NW_12_4hr fast_0months


title: rnaseq_AU-565_S4


title: PTH hypoxia No.4


title: atacseq_ZR-75-1_1

extract_protocol: The libraries were generated using the OMNI-ATAC protocol (PMID: 28846090), and the final library was purified with AMPure beads (Beckman Coulter, A63880).


title: Man_OW/OB_23_6hr fast_0months


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, post-enrichment, rep2

description: Column Name: G3BP1-mS_T1_label_enrich2


title: Woman_OW/OB_10_6hr fast_0months


title: atacseq_T-47D_1


title: PTH hypoxia No.3


title: WT hypoxia No.5

value: hypoxia (10 % O2)


title: G3BP1-miniSOG_HEK293T, 1 hr recovery post arsenite stress, label, post-enrichment, rep1

description: Column Name: G3BP1-mS_T1_label_enrich1


title: WT hypoxia No.2


title: G3BP1-miniSOG_HEK293T, sorbitol-stress, omit probe, post-enrichment, rep2

description: Column Name: G3BP1-mS_Sorbitol_noprobe_enrich2

value: 0.4 M sorbitol, 150 min


title: atacseq_MDA-MB-361_1


title: G3BP1-miniSOG_HEK293T, sorbitol-stress, omit probe, post-enrichment, rep1

description: Column Name: G3BP1-mS_Sorbitol_noprobe_enrich1


title: WT hypoxia No.1


title: atacseq_MDA-MB-231_1


title: WT normoxia No.5

value: normoxia


title: Man_OW/OB_1_6hr fast_6months

value: Man

value: OW/OB


title: G3BP1-miniSOG_HEK293T, sorbitol-stress, label, pre-enrichment, rep2

description: Column Name: G3BP1-mS_Sorbitol_label_input2


title: atacseq_MCF7_1

value: breast


title: Woman_OW/OB_18_4hr fast_6months


title: WT normoxia No.3


title: atacseq_BT-474_1


title: atacseq_SK-BR-3_1


title: Woman_NW_11_4hr fast_0months

value: NW


title: WT normoxia No.2


title: HoxB, RUNX1-ETO_ONLY, rep3

city: Portland

first: Julia

last: Maxson

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

data_processing:
read trimming (Trimmomatic)
read alignment (STAR)
differential analysis - pairwise (DESeq2)
differential analysis - group (DESeq2)
cellular composition (CIBERSORTx)
Assembly: mm10
Supplementary files format and content: The processed data file is a non-normalized counts matrix of genes by samples.

source_name: HoxB

extract_protocol:
RNeasy Plus Mini Kit (Qiagen) with on-column DNase digestion
BGI DNBSEQ Eukaryotic Strand-specific mRNA library

value: HoxB

value: Blood


title: HoxB, RUNX1-ETO_ONLY, rep1


title: Woman_OW/OB_17_4hr fast_0months


title: G3BP1-miniSOG_HEK293T, sorbitol-stress, label, post-enrichment, rep2

description: Column Name: G3BP1-mS_Sorbitol_label_enrich2


title: G3BP1-miniSOG_HEK293T, sorbitol-stress, label, post-enrichment, rep1

description: Column Name: G3BP1-mS_Sorbitol_label_enrich1


title: G3BP1-miniSOG_HEK293T, sorbitol-stress, label, pre-enrichment, rep1

description: Column Name: G3BP1-mS_Sorbitol_label_input1


title: G3BP1-miniSOG_HEK293T, 3 hr recovery post arsenite stress, label, post-enrichment, rep2

description: Column Name: G3BP1-mS_T3_label_enrich2

value: 3 hr recovery post arsenite stress


title: atacseq_AU-565_1


title: G3BP1-miniSOG_HEK293T, unstressed, omit probe, post-enrichment, rep2

description: Column Name: G3BP1-mS_basal_noprobe_enrich2

value: unstressed


title: Woman_MONW_10_6hr fast_0months

value: MONW


title: HoxB, RUNX1-ETO_FIRST, rep3


title: Man_NW_21_6hr fast_0months


title: IL-3+IL-33_Difamilast_2

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

institute: Institute of Science Tokyo

description:
TM15-8
Miyake15_RNASeq_expression_table.txt

data_processing:
Adapter trimming of sequencing data was performed by using cutadapt 4.1, and trimmed reads were mapped to reference RNA (build GRCm38 release-101) by using bowtie2-2.4.5 by the following parameters: -p 8 -N 1 -L 16 –very-sensitive-local –seed 656565 –nofw. Then, read counts of each gene in each samples were counted by using awk, sort, and uniq -c commands. Resulted gene-expression count data was summarized by same Gene Symbol and all of the expression table was full-outer joined by Gene Symbol by using dplyr-1.0.7 package.
Gene expression count table was provided as Miyake15_RNASeq_expression_table.txt.
Supplementary files format and content: GRCm38 release-101
Supplementary files format and content: Tab-separated values files

source_name: bone marrow-derived basophils

extract_protocol:
10,000 cells of BMBAs were stimulated with recombinant mouse IL-3(10ng/mL) plus IL-33 (10ng/mL) or control PBS in the presence difamilast (3μM) or vehicle DMSO for 4 hours. Stimulated BMBAs were then lysed by using lithium dodecyl sulfate-based lysis/storage buffer.
mRNA was isolated from total RNA by Dynabeads M-270 streptavidin (Thermo Fisher Scientific) immobilized with biotin-EcoP-(dT)25 (Integrated DNA Technologies). On-beads reverse transcription was performed by Superscript IV reverse transcriptase (Thermo Fisher Scientific), and free primers were digested by Exonuclease I treatment. Then, polyC-tailing, second strand synthesis, 1st round of WTA, and second round of WTA was performed by TAS-Seq workflow (Shichino et al. Commun Biol 2022). Whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Ligated products were purified and performed the barcoding PCR. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer (Illumina) and NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles) (Illumina).

treatment_protocol: BMBAs were generated by culturing bone marrow cells in the presence of 0.3 ng/mL of recombinant mouse IL-3 (BioLegend) for 7 days, followed by magnetic sorting of CD49b+ cells by using biotinylated anti-CD49b antibody (clone: DX5; BioLegend) and Mojosort streptavidin nanoparticles (BioLegend).

value: bone marrow-derived basophils

value: basophil

value: C57BL/6J WT

value: stimulated with IL-3(10ng/mL)+IL-33(10ng/mL), treated with difamilast (3μM)


title: IL-3+IL-33_Difamilast_1

description:
TM15-7
Miyake15_RNASeq_expression_table.txt


title: HoxB, RUNX1-ETO_FIRST, rep2


title: SUB235953, SUB235991, SUB235947, SUB235945, SUB235980 [s5b-hto]

city: Oklahoma City

first: Joel

last: Guthridge

state: OK

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
RNA-seq reads were aligned and counted using CellRanger version 5.0.0 with default settings
CellRanger output was demultiplexed, concatenated, and analyzed using Seurat version 4.0.3
Genome_build: GRCh38 and mm9
Supplementary_files_format_and_content: FASTQs, MarketMatrix (.tsv and .mtx), and Seurat object (.Rdata)

source_name: CD2-depleted PBMC

extract_protocol:
Cells were stained as per the CITE-seq_and_Hashing_protocol_190213 protocol (found here: https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf).  Cells were pooled 4 or 5 samples to a pool and captured using the Chromium Single Cell 3' Reagent Kit v2 Revision F (found at https://support.10xgenomics.com/single-cell-gene-expression/index/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v2-chemistry)
Libraries were constructed as per the manufacturer's protocol in the Chromium Single Cell 3' Kit v2, Revision F.  In brief, captured mRNAs were reverse transcribed prior to the breaking of cell/gel bead droplets.  cDNAs were recovered and underwent amplification.  SPRI beads were used to clean the libraries and split them into gene expression and antibody-dependent libraries.  The GEX libraries underwent end repair, polyA tailing, and fragmentation prior to further size selection to extract 300-500 bp fragments and the ligation of sequencing adaptors; the ADT libraries were likewise purified and had sequencing adaptors added.

value: CD2-depleted PBMC

tag: subject status

value: healthy controls and SLE patients


title: SUB235953, SUB235991, SUB235947, SUB235945, SUB235980 [s5b-gex]


title: Man_OW/OB_23_4hr fast_6months

extract_protocol: Blood from participants was collected using Vacutainer® EDTA tubes. After blood collection, PBMC were isolated using Ficoll-Paque Plus density gradient media (GE Healthcare Bio Science, Madrid, Spain). In brief, the anticoagulant treated blood was diluted with an equal volume of a phosphate-buffered saline (PBS) solution. Next, the blood was layered carefully over Ficoll without intermixing (10 ml of Ficoll for 20 ml of blood mixed with PBS) in a centrifuge tube and centrifuged at 400 g for 30 min at 20°C. PBMC, together with platelets, were harvested from the interface between Ficoll and plasma layers. This layer was then centrifuged in PBS at 300 g for 10 min at 20°C to wash PBMC and to remove the platelets. PBMC pellet was finally suspended in Tripure Reagent (Roche Diagnostics, Barcelona, Spain) and stored at -80ºC. Total RNA from PBMC samples was extracted using Tripure Reagent (Roche Diagnostics, Barcelona, Spain) and then purified with E.Z.N.A. Total RNA Kit I (Omega Biotek, Vermont, USA), following the manufacturer’s instructions. Finally, RNA was precipitated with isopropanol. Isolated RNA was quantified using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). Its integrity was confirmed using agarose gel electrophoresis and the RIN tool using the Agilent 2100 Bioanalyzer System. All samples showed superieor quality and were taken along.

value: reference pool


title: SUB235953, SUB235991, SUB235947, SUB235945, SUB235980 [s5b-cite]


title: G3BP1-miniSOG_HEK293T, unstressed, omit probe, post-enrichment, rep1

description: Column Name: G3BP1-mS_basal_noprobe_enrich1

value: G3BP1-miniSOG stably  expression


title: HoxB, RUNX1-ETO_FIRST, rep1


title: HoxB, RUNX1-ETO_ONLY, rep2


title: IL-3+IL-33_Difamilast_3

description:
TM15-9
Miyake15_RNASeq_expression_table.txt


title: G3BP1-miniSOG_HEK293T, unstressed, label, pre-enrichment, rep1

description: Column Name: G3BP1-mS_basal_label_input1


title: HoxB, EMPTY, rep2

value: Control vectors


title: IL-3+IL-33_DMSO_3

description:
TM15-6
Miyake15_RNASeq_expression_table.txt

value: stimulated with IL-3(10ng/mL)+IL-33(10ng/mL), treated with DMSO


title: SUB235985, SUB235955, SUB235966, SUB235964, SUB235998 [s5a-gex]


title: HoxB, EMPTY, rep3


title: G3BP1-miniSOG_HEK293T, unstressed, label, pre-enrichment, rep2

description: Column Name: G3BP1-mS_basal_label_input2


title: HoxB, EMPTY, rep1


title: IL-3+IL-33_DMSO_2

description:
TM15-5
Miyake15_RNASeq_expression_table.txt


title: IL-3+IL-33_DMSO_1

description:
TM15-4
Miyake15_RNASeq_expression_table.txt


title: SUB235985, SUB235955, SUB235966, SUB235964, SUB235998 [s5a-cite]


title: HoxB, CSF3R_ONLY, rep3


title: G3BP1-miniSOG_HEK293T, unstressed, label, post-enrichment, rep1

description: Column Name: G3BP1-mS_basal_label_enrich1


title: SUB235952, SUB235981, SUB235983, SUB235984, SUB235965 [s4b-hto]


title: G3BP1-miniSOG_HEK293T, unstressed, label, post-enrichment, rep2

description: Column Name: G3BP1-mS_basal_label_enrich2


title: PBS_DMSO_2

description:
TM15-2
Miyake15_RNASeq_expression_table.txt

value: stimulated with PBS, treated with DMSO


title: HoxB, CSF3R_ONLY, rep2


title: HoxB, CSF3R_ONLY, rep1


title: SUB235952, SUB235981, SUB235983, SUB235984, SUB235965 [s4b-cite]


title: PBS_DMSO_1

description:
TM15-1
Miyake15_RNASeq_expression_table.txt


title: G3BP1-miniSOG_HEK293T, arsenite-stress, omit probe, post-enrichment, rep1

description: Column Name: G3BP1-mS_AS_noprobe_enrich1

value: 0.5 mM arsenite, 1 hr


title: SUB235985, SUB235955, SUB235966, SUB235964, SUB235998 [s5a-hto]


title: 3SA_SKM_ERRa_ChIP

city: Montréal

first: Vincent

last: Giguère

address: 1160 Pine Ave West, McIntyre Bldg Room 710

institute: McGill University

data_processing:
ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic v0.36.
Paired-end (100bp) cleaned reads were mapped to the mouse reference genome (mm10) using BWA-MEM v0.7.12 with default parameters.
Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1.
Peaks were called using MACS2 software suite v2.1.1.20160309 at an FDR < 0.001 using sequenced libraries of input DNA as control. Peaks in mitochondrial chromosome and scaffold regions were removed.
Peak annotations were performed using the annotatePeaks from HOMER software suite v4.9.1.
Assembly: mm10
Supplementary files format and content: bigwig (.bw) files for each sample
Supplementary files format and content: tab-delimited text files of annotated liver and skeletal muscle ERRα peaks for both WT and ERRα 3SA phospho-mutant mice using respective inputs as controls

source_name: Skeletal muscle

growth_protocol: Livers or skeletal muscle (gastrocnemius & soleus) were isolated from 2-3 month-old WT and ERRα 3SA phospho-mutant mice on a C57BL/6N background.

extract_protocol:
Livers or skeletal muscle were crosslinked with 1% formaldehyde for 12 minutes followed by sonication (200-500 bp enrichment). Each ChIP-seq sample was prepared by pooling three ChIP samples prepared from a pool of crosslinked livers from two mice or a pool of crosslinked skeletal muscle from five mice.
ChIP DNA libraries were prepared using the NEB Ultra II DNA library preparation kit according to Illumina recommendations.

value: Skeletal muscle

value: ERRalpha 3SA phospho-mutant

tag: Sex

value: male

tag: chip antibody

value: ERRa (Abcam, Cat# ab76228)


title: G3BP1-miniSOG_HEK293T, arsenite-stress, label, pre-enrichment, rep2

description: Column Name: G3BP1-mS_AS_label_input2


title: HoxB, CSF3R_FIRST, rep3

value: HoxB

value: Blood


title: 3SA_SKM_input


title: G3BP1-miniSOG_HEK293T, arsenite-stress, label, pre-enrichment, rep1

description: Column Name: G3BP1-mS_AS_label_input1


title: HoxB, CSF3R_FIRST, rep2


title: SUB235944, SUB235959, SUB235974, SUB236001, SUB235988 [s4a-gex]


title: WT_SKM_ERRa_ChIP

value: WT


title: SUB235944, SUB235959, SUB235974, SUB236001, SUB235988 [s4a-hto]


title: PBS_DMSO_3

description:
TM15-3
Miyake15_RNASeq_expression_table.txt

value: bone marrow-derived basophils

value: basophil

value: C57BL/6J WT


title: HoxB, CSF3R_FIRST, rep1


title: SUB235944, SUB235959, SUB235974, SUB236001, SUB235988 [s4a-cite]

value: CD2-depleted PBMC

value: healthy controls and SLE patients


title: WT_SKM_input


title: G3BP1-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep1

description: Column Name: G3BP1-mS_AS_label_enrich1

value: G3BP1-miniSOG stably  expression


title: SUB235986, SUB235958, SUB235967, SUB235987, SUB235975 [s3b-hto]


title: G3BP1-miniSOG_HEK293T, arsenite-stress, omit probe, post-enrichment, rep2

description: Column Name: G3BP1-mS_AS_noprobe_enrich2


title: 3SA_Liver_ERRa_ChIP

source_name: Liver

value: Liver


title: Control_Rep3

city: Tianjin

first: Fumihiko

last: Nakamura

address: 92 Weijin Road, Nankai District

institute: Tianjin University

data_processing:
HISAT2 was used for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genome
counts per genes were analyzed using HTSeq and normalized with Reads Per Kilobase of exon per Megabase of library size (RPKM)
Assembly: hg38
Supplementary files format and content: excel file contain all information of each gene including reading count and FPKM value of each samples

source_name: kidney; Embryo

growth_protocol: HEK293 cells were cultured in DMEM with 10%FBS and 1 % Pen/Strep, seeded at 1*10^4 cells/cm^2 in 60 mm dishes, cultured for 18-24 hours.

extract_protocol:
The cells were washed with PBS, harvested with 1 ml RNAisoPlus (Takara), incubated at room temperture for 5 mins, frozen in liquid N2.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were transfected with or without 50uM siRNA in 18.6 ul RNAiMate (GenePharm), incubated for 48 hours

value: treated with vehicle, 48 hours


title: SUB235952, SUB235981, SUB235983, SUB235984, SUB235965 [s4b-gex]


title: SUB235986, SUB235958, SUB235967, SUB235987, SUB235975 [s3b-gex]


title: Δckb2, MMS, rep2

city: shanghai

first: Xianwei

last: Wu

address: No.725 South Wanping Road

department: Institute of Respiratory Diseases

institute: Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

data_processing:
Quality-filtered RNA-seq reads were aligned to the C.glabrata genome (http://www.candidagenome.org) by STAR software (version 2.7.4).
Gene expressions were obtained and normalized by StringTie (V2.1.2) and DESeq2 (V1.20).
Significantly expressed genes were screened based on a 2-fold cut-off and p-value < 0.05.
Assembly: Candida glabrata CBS138 genome
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

organism: Nakaseomyces glabratus

growth_protocol: The WT , Δckb1 and Δckb2 strains were inoculated in YPD media and grown to saturation overnight. Cells were diluted to an OD600 of 0.1 and recovered to log phase for 4 hours shaking at 30°.

extract_protocol:
Total RNA was extracted by the acid phenol method. Three biological replicates were performed per condition. RNA was frozen at -80℃ and sent to Shanghai Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China) for further sequencing by Illumina novaseq6000 PE150.
RNA libraries for RNA-seq were prepared using Illumina NovaSeq Reagent Kit following manufacturer's protocols.

treatment_protocol: Log-phase cultures of WT , Δckb1 and Δckb2 strains were either treated with 0.01% MMS for 1 h, or left untreated.

value: Yeast cells

value: CgCKB2 knockdown

value: 0.01% MMS for 1 hour


title: Δckb2, MMS, rep3


title: Control_Rep2


title: Δckb2, MMS, rep1


title: 3SA_Liver_input

value: ERRalpha 3SA phospho-mutant


title: SUB235986, SUB235958, SUB235967, SUB235987, SUB235975 [s3b-cite]


title: WT_Liver_ERRa_ChIP

value: male


title: SUB235946, SUB235951, SUB235990, SUB235970, SUB235992 [s3a-hto]


title: Control_Rep1


title: WT_Liver_input


title: Δckb1, MMS, rep3

value: CgCKB1 knockdown


title: UBE2AB_KD_Rep3

value: treated with siUBE2A+siUBE2B siRNA 25 uM each, 48 hours


title: UBE2AB_KD_Rep2


title: TCDD - Statin Replicate 3

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

data_processing:
Following sequencing quality control, CellRanger v3.0.2 (10X Genomics) was used to align reads to a custom reference genome which included introns and exons to consider pre-mRNA and mature mRNA present in the nuclei.
Raw counts were further analysed using Seurat v4.0.0. Each sample was filtered for (i) genes expressed in at least 3 nuclei, (ii) nuclei which express at least 100 genes, and (iii) ≤1% mitochondrial genes.
Assembly: mm10
Supplementary files format and content: Processed data files for individual sample are CellRanger filtered_feature_bc_matrix outputs which includes barcodes (barcodes.tsv.gz),  features (features.tsv.gz), and the matrix (matrix.mtx.gz).
Supplementary files format and content: RData file represents the full processed Seurat R data object generated using Seurat v4.0.0.

source_name: liver

extract_protocol:
Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle.
Libraries were prepared using the 10X Genomics Chromium Single Cell 3’ v3.1 kit (10X Genomics)

treatment_protocol: Male C57BL/6 mice either gavaged with sesame oil vehicle or 30 ug/kg TCDD every 4 days for 28 days and fed with either normal chow or chow laced with 500 mg/kg simvastatin beginning 3 days prior to first TCDD treatment.

value: liver

tag: species

tag: species ontology_label

value: Mus musculus

tag: organ

tag: organ ontology_label

tag: mouse strain

tag: mouse strain_ontology_label

tag: age unit

tag: age unit_label

value: day

tag: preservation method

value: Snap Frozen

value: Illumina NovaSeq 6000

tag: metadata template_url

tag: biomaterial supplier

value: Charles Rivers Laboratories

tag: acclimation period

tag: acclimation period_unit

tag: acclimation period_unit_label

tag: average vivarium_temperature

tag: average vivarium_temperature_unit

tag: average vivarium_temperature_unit_label

value: degree celsius

tag: average vivarium_humidity

tag: average vivarium_humidity_unit

tag: average vivarium_humidity_unit_label

value: percent

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALPHA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8640

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog_no

tag: ad lib_feeding

value: Yes

tag: toxic substance

tag: toxic substance_ontology_label

tag: cas number

tag: smile string

tag: formula

tag: toxic substance_molecular_weight

tag: toxic substance_vendor

value: Accustandard;Sigma-aldrich

tag: toxic substance_catalog_number

tag: toxic substance_purity

tag: toxic substance_lot

tag: toxic substance_storage

value: Room temperature;4C

tag: vehicle substance

value: NCIT_C66537;animal feed

tag: vehicle substance_ontology_label

value: sesame oil;animal feed

tag: administration volume

value: 0.1;Not Applicable

tag: administration volume_unit

tag: administration volume_unit_label

value: milliliter;Not Applicable

tag: administration interval

value: 4;Not Applicable

tag: administration interval_unit

tag: administration interval_unit_label

value: day;Not Applicable

tag: administration number

value: 7;Not Applicable

tag: administration route

tag: administration route_ontology_label

value: oral gavage;animal feed

tag: dose unit

tag: dose unit_label

value: microgram per kilogram;milligram per kilogram per day

tag: time point

tag: time point_unit

tag: time point_unit_label

tag: euthanasia method


title: UBE2AB_KD_Rep1

tag: cell line

tag: treatment

value: treated with siUBE2A+siUBE2B siRNA 25 uM each, 48 hours


title: TCDD - Statin Replicate 2

tag: tissue

value: liver

tag: species

tag: species ontology_label

value: Mus musculus

tag: organ

tag: organ ontology_label

tag: mouse strain

tag: mouse strain_ontology_label

tag: age

tag: age unit

tag: age unit_label

value: day

tag: preservation method

value: Snap Frozen

value: Illumina NovaSeq 6000

tag: metadata template_url

tag: biomaterial supplier

value: Charles Rivers Laboratories

tag: acclimation period

tag: acclimation period_unit

tag: acclimation period_unit_label

tag: average vivarium_temperature

tag: average vivarium_temperature_unit

tag: average vivarium_temperature_unit_label

value: degree celsius

tag: average vivarium_humidity

tag: average vivarium_humidity_unit

tag: average vivarium_humidity_unit_label

value: percent

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALPHA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog_no

tag: ad lib_feeding

tag: toxic substance

tag: toxic substance_ontology_label

tag: cas number

tag: smile string

tag: formula

tag: toxic substance_molecular_weight

tag: toxic substance_vendor

tag: toxic substance_catalog_number

tag: toxic substance_purity

tag: toxic substance_lot

tag: toxic substance_storage

tag: vehicle substance

tag: vehicle substance_ontology_label

tag: administration volume


title: G3BP1-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep2

description: Column Name: G3BP1-mS_AS_label_enrich2

tag: cell line

tag: genotype

value: G3BP1-miniSOG stably  expression

tag: treatment

value: 0.5 mM arsenite, 1 hr


title: TCDD - Statin Replicate 1

tag: tissue

tag: species

tag: species ontology_label

tag: organ

tag: organ ontology_label

tag: mouse strain

tag: mouse strain_ontology_label

tag: age

tag: age unit

tag: age unit_label

tag: preservation method

tag: metadata template_url

tag: biomaterial supplier

tag: acclimation period

tag: acclimation period_unit

tag: acclimation period_unit_label

tag: average vivarium_temperature

tag: average vivarium_temperature_unit

tag: average vivarium_temperature_unit_label

tag: average vivarium_humidity

tag: average vivarium_humidity_unit

tag: average vivarium_humidity_unit_label

tag: light cycle

tag: cage type

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8640

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog_no

tag: ad lib_feeding

value: Yes

tag: toxic substance

value: Accustandard;Sigma-aldrich

value: Room temperature;4C

value: NCIT_C66537;animal feed

value: sesame oil;animal feed

value: 0.1;Not Applicable

tag: administration volume_unit

tag: administration volume_unit_label

value: milliliter;Not Applicable

tag: administration interval

value: 4;Not Applicable

tag: administration interval_unit

tag: administration interval_unit_label

value: day;Not Applicable

tag: administration number

tag: administration route

tag: administration route_ontology_label

tag: dose unit

tag: dose unit_label

tag: time point

tag: time point_unit

tag: time point_unit_label

tag: euthanasia method


title: SUB235946, SUB235951, SUB235990, SUB235970, SUB235992 [s3a-gex]

tag: tissue

value: CD2-depleted PBMC

tag: subject status

value: healthy controls and SLE patients


title: Δckb1, MMS, rep2

tag: cell line

tag: cell type

value: Yeast cells

tag: genotype

value: CgCKB1 knockdown

tag: treatment

value: 0.01% MMS for 1 hour

tag: time


title: WT, MMS, rep2

value: WT


title: SUB235957, SUB236000, SUB235978, SUB235995 [s2b-cite]


title: SUB235946, SUB235951, SUB235990, SUB235970, SUB235992 [s3a-cite]


title: Δckb1, MMS, rep1