title: HEALTHY CTRL sample 1


title: Foxo1 Mutation  RNA-seq rep2

status: Public on Jan 26 2022

type: SRA

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: Foxo1 Mutation Liver Rep2

library_source: transcriptomic

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.1.1
For each sample, reads counts of all genes were computed using HTSeq v0.6.0.Differentially-expressed genes between control and ENT were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: Reads count for each gene in two biological replicates of mouse wildtype and foxo1 mutation liver.

molecule: polyA RNA

organism: Mus musculus

source_name: mouse Liver Tissue

extract_protocol:
For RNA-seq, RNA was isolated from was isolated from Liver Tissue using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 100ng of mRNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 150 bp.

tag: strain

tag: age

value: 23 weeks

tag: tissue

value: Liver tissue


title: WT-Sham1

city: Guangzhou

first: Xiang

last: Li

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Original data were filtered to remove reads with joints, indeterminate base information and low quality, followed by sequencing error rate check and GC content distribution check to obtain clean reads used in subsequent analysis.
Clean reads were then mapped to mm10 genome with HISAT2 compares software.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Expression_Gene.txt: Tab-delimited text file includes FPKM values for each Sample.

molecule: total RNA

source_name: Heart

extract_protocol:
Total RNAs from the ventricular tissues of the sham group and the pressure overload group were isolated using TRIzol® Reagent (Thermo Fisher Scientific, USA). Each group contains two independent samples.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: group

value: WT-Sham

value: Ventricular tissue


title: Foxo1 Mutation  RNA-seq rep1

description: Foxo1 Mutation Liver Rep1


title: Fto Knockout  RNA-seq rep2

description: Fto knockout Mouse Liver Rep2

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.1.1
For each sample, reads counts of all genes were computed using HTSeq v0.6.0.Differentially-expressed genes between control and ENT were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: Reads count for each gene in two biological replicates of mouse wildtype and Fto knockout liver.

extract_protocol:
For RNA-seq, RNA was isolated from was isolated from Liver Tissue using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 100ng of mRNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: EC109

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to mm10 mouse transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include UMI values for each cell

source_name: mouse embryonic cells

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq 4000 platform in 150 bp pair-ended manner

tag: cell type

value: Endothelial Cells

tag: development stage

tag: genotype

value: Nr2f2-CrexER lineage-labeled ECs with Gja5-EGFP as an arterial indicator


title: EC110


title: Caco-2 cells, grown on Transwell inserts, TiO2-control, replicate 3

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

label: biotin

organism: Homo sapiens

source_name: Caco-2 cells, grown on a Transwell PET insert (0.4 µm pore size, 1.12 cm2 surface area) for 21 days, then exposed to TiO2-control medium for 6 hrs

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: A Caco-2 cell line (HTB-37), derived from a human colorectal adenocarcinoma, was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cells were grown (at passage number 29-45) in DMEM supplemented with 10 % FBS, 1 % penicillin-streptomycin, and 1 % MEM non-essential amino acid, further referred to as DMEM+. The cells were seeded at a density of ~75,000 cells per cm2 on 12-well Transwell PET inserts (0.4 µm pore size, 1.12 cm2 surface area, Corning Amsterdam, The Netherlands) and cultured in DMEM+ for 21 days. The medium was changed every two to three days. In the microfluidic device, the cells were seeded at a density of 75,000 cell per cm2 and were allowed to attach to the membrane for 24 h, without the fluid flow. The membrane was then inserted in the microfluidic chip and cells were exposed to a continuous flow of 100 µL/h DMEM+ until day 21 of culturing . By doing so, the shear stress in the AP compartment was ~0.002 dyne/cm2 at the cell membrane area, where the cells were grown. The DMEM+ medium contained sodium bicarbonate (10 mM) to optimize the pH buffering capacity.

extract_protocol: Cells were first washed with PBS. RNA was then isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: The metal-oxide nanomaterials were prepared and dispersed according to the Nanogenotox dispersion protocol (https://www.anses.fr/en/system/files/nanogenotox_deliverable_5.pdf). At day 21 post-seeding Caco-2 cells in either the gut-on-chip or Transwell were exposed to equal deposited doses based on the in vitro sedimentation, diffusion and dosimetry (ISDD) modelling. For the gut-on-chip, suspensions of 100 µg/mL TiO2 and 80 µg/mL ZnO were prepared in DMEM+. For each nanomaterial a dispersion solution in DMEM+ without metal served as control group. Solutions were perfused via the upper channel with a flow rate of 100 µL/h. DMEM+ without nanomaterials was pumped through the basolateral channel with an equal flow rate. After about 42 min the upper chamber was fully filled with the solution and the flow was stopped for 6 h in order to exclude the possible influence of laminar flow in gut-on-chip system resulting in the different exposure doses. This enabler the best comparison of the cellular response by cells grown in the two systems. In the Transwells, the cell culture medium of the AP side was replaced with 500 uL nanomaterial suspension of 50 µg/mL for TiO2 or 10 µg/mL ZnO and the medium of the basolateral side was refreshed with DMEM+ without nanomaterial culture medium followed by 6 h incubation.

tag: cell line

value: Caco-2 (HTB-37)

tag: passage number

value: between 29-45

tag: growing condition

value: static

tag: treatment

value: TiO2-control medium


title: Caco-2 cells, grown on Transwell inserts, TiO2-control, replicate 2


title: KO1

value: Cdh5-Cre;Notch1fl/fl embryos (KO)


title: ALS sample 12

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using GRCh38 (Gencode release 27) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19
Supplementary_files_format_and_content: counts, FPKMs, TPMs

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 500-ng total RNA (Illumina). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

value: Blood

tag: disease state

value: Amyotrophic Lateral Sclerosis


title: EC88

value: Dll4-tdTomato reporter mouse lines


title: ALS sample 10

value: Peripheral blood mononuclear cells (PBMCs)


title: EC87


title: EC112

value: Unc5b-tdTomato reporter mouse lines


title: ALS sample 9


title: ALS sample 15


title: ALS sample 8


title: ALS sample 14


title: control 231 healthy

first: Yudan

last: Liang

address: No.601, West Huangpu Avenue

department: Integrated Chinese and Western Medicine Postdoctoral research station

institute: Jinan University

description: Gene expression in human blood

hyb_protocol: 0.6 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 40 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. After hybridization, microarrays were washed.

scan_protocol: After washed and fixed, the hybridized arrays were scanned with using the Agilent Microarray Scanner(Agilent p/n G2565BA) for one-color scans.

data_processing: Open the Agilent Feature Extraction (FE) software. Add the images (.tif) to be extracted to the FE Project. Set FE Project Properties. Check the Extraction Set Configuration. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: peripheral blood_healthy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (RNeasy Mini Kit , QIAGEN, p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Peripheral blood were isolated using lymphocyte separation liquid within two hours and subjected for isolation of total cellular RNA, then stored at -80°C,Add 1ml Trizol per 5x10^6 cells.

value: whole blood

tag: gender

value: female

tag: subject status

value: healthy control


title: Foxo1 WT  RNA-seq rep2

description: Wildtype Liver Rep2

value: 23 weeks

value: Liver tissue


title: Foxo1 WT  RNA-seq rep1

description: Wildtype Liver Rep1


title: EC84

value: Mural Cells


title: control 28 healthy

description: Gene expression in human blood

value: male


title: control 26 healthy

description: Gene expression in human blood


title: Fto WT  RNA-seq rep1

description: Wildtype Mouse Liver Rep1


title: ALS sample 13


title: Fto Knockout  RNA-seq rep1

description: Fto knockout Mouse Liver Rep1


title: EC108

value: Endothelial Cells

value: Nr2f2-CrexER lineage-labeled ECs with Gja5-EGFP as an arterial indicator


title: patient 252 CSU

description: Gene expression in human blood

source_name: peripheral blood_CSU

value: chronic spontaneous urticaria (CSU) patient


title: ALS sample 6


title: EC114

value: Tie2-Dre;Nr2f2-CrexER X Unc5b-tdTomato


title: patient 221 CSU

description: Gene expression in human blood


title: ALS sample 5


title: Fto WT  RNA-seq rep2

description: Wildtype Mouse Liver Rep2


title: EC107


title: ALS sample 11


title: EC86


title: GMI3

city: Madison

first: Alicia

last: Truchon

state: WI

address: 1630 Linden Drive

department: Plant Pathology

country: USA

institute: University of Wisconsin - Madison

description: wildtype bacterial culture, 0.1% oxygen

data_processing:
Illumina CASAVA v1.8 used for basecalling
Reads were filtered for quality, removing reads with adaptor contamination, greater than 10% uncertain nucleotides, or more than 50% of nucleotides with a Qpred less than or equal to 5. Over 95% of reads were of good quality, and were mapped to the R. solanacearum GMI1000 genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000009125.1) using Bowtie2 -2.2.3
Gene expression was calculated using HTseq v0.6.1
Differential gene expression was calculated using DESeq 1.18.0. P-values calculated by DESeq were adjusted to control for the false discovery rate (FDR) using the Benjamini-Hochberg approach
Genome_build: Genome_build: GCA_000009125.1
Supplementary_files_format_and_content: .txt file including raw readcounts for each sample

organism: Ralstonia solanacearum

growth_protocol: Column: 50 mL of modified Van den Mooter medium (DOI: 10.1128/mBio.02471-14) with 30 mM potassium nitrate was inoculated with R. solanacearum to an initial concentration of 10^7 CFU/mL. (OD600=0.01). The cultures were then incubated without shaking at 28degC in 0.1% oxygen for 12 hours.

extract_protocol:
After 16h total incubation, sub-samples were collected for dilution plating to determine CFU/ml and the tubes were capped and centrifuged at room temperature for 5 min at 8000 rpm. The supernatant was removed and pellets were frozen in liquid nitrogen. RNA extractions were carried out using a modified version of the Quick-RNATM MiniPrep kit (Zymo Research, Irvine, CA, USA), as follows. Pellets were resuspended in 400 uL of ice cold TE pH 8 with 1 mg/mL lysozyme, 0.25 uL Superase Inhibitor (Ambion, Austin, TX, USA), and 80 uL of 10% SDS, vortexed for 10s, transferred to a new 2 mL tube, and shaken at ~300 rpm for 2 min. 800 uL of RNA-Lysis lysis buffer was added, the tubes were vortexed again for 10s, cleaned according to the kit manufacturer's instructions, and eluted in 100 uL of water. Nucleic acid concentrations were estimated using a nanodrop, normalized to 200 ng/uL, and cleaned using the DNA-free DNAse kit (Invitrogen, Carlsbad, CA, USA). Samples were incubated at 37C for 1 hour, with 2 uL more of DNAse added at 30 min. After DNAse inactivation, samples were further cleaned by chloroform extraction, then precipitated overnight at -20C with 100 microM Sodium Acetate pH 5.5 and 66 % ethanol. Samples were checked for concentration on a Nanodrop, for DNA contamination by PCR using the qRT-PCR primers serC_F/R, and for RNA integrity (RIN) using an Agilent Bioanalyzer 21000 (Agilent, Santa Clara, CA, USA). All samples had RIN values above 7.3.
NEBNext uLtraTM Directional RNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA) following the manufacturer's recommendation and starting with 3 mg of RNA per sample

value: wildtype

value: 16 hpi

value: Untreated

tag: extraction

value: Column


title: ∆norA1

description: ∆norA bacterial culture, 0.1% oxygen

source_name: bacterial cells

value: deltanorA


title: ∆hmpX3

description: ∆hmpX bacterial culture, 0.1% oxygen

value: deltahmpX


title: ∆hmpX2

description: ∆hmpX bacterial culture, 0.1% oxygen


title: patient 182 CSU

description: Gene expression in human blood

value: whole blood


title: EC83


title: EC77


title: control 232 healthy

description: Gene expression in human blood

value: female


title: control 29 healthy

description: Gene expression in human blood

value: healthy control


title: EC76


title: ∆hmpX1

description: ∆hmpX bacterial culture, 0.1% oxygen


title: SCS-rep3

city: 北京

first: li

middle: gao

last: jie

state: beijing

address: Building 104, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

library_source: genomic

data_processing:
Library strategy: 6mA-Seq
Raw data from Illumina Hiseq sequencing were analyzed by FastQC (v 0.11.8)
The raw reads were trimmed to remove low-quality bases and adaptor sequences with Trim Galore (v0.6.7) and Cutadapt (v3.5 with Python 3.9.7).
Trimmed reads were mapped with the reference genome of E. coli, human and human mitochondrion by HIAST-3N.
STREME (v5.4.1) was used for motif enrichment analysis
Genome_build: ASM584v2 and GRCh38.p13
Supplementary_files_format_and_content: methylation-rate.tsv

molecule: genomic DNA

organism: Escherichia coli

source_name: E. coli SCS110

extract_protocol:
E. coli DNA was extracted using Ezup Column Bacteria Genomic DNA purification kit (Sangon Biotech, Shanghai, China) according to the manufacture’s recommended procedure.Mitochondrial DNA of HepG2 cells were harvested and washed once in PBS buffer. Mitochondrial DNA was extracted using the high purity plasmid DNA kit (Tsingke biotech, Beijing, China) according to the manufacture’s recommended procedure. The extracted DNA was eluted in 200 µL H2O and further enriched by 0.4× KAPA pure beads (Roche).
Genomic DNA was fragmented to obtain 200 to 500 bp fragments by using a JY92-II N Ultrasonic Homogenizer (Scientz) with the following settings: 130 W peak incident power for 48 cycles (1 cycle = 5 s on and 5 s off). The mixture (50 μL) of fragmented genomic DNA (10 ng) and spike-in DNA were end repaired and dA-tailed using Hieff NGS® Fast-Pace End Repair/dA-Tailing module (YEASEN Biotechnology Co., Ltd., Shanghai, China) according to the manufacture recommended protocol. As for the adapter ligation, 60 μL of end-repaired DNA, 5 μL of custom adapter (15 μM), 5 μL of Fast-Pace DNA ligase, and 30 μL of Fast-Pace DNA ligation Enhancer (YEASEN Biotechnology, Shanghai, China) were incubated at 20°C for 12 h in a 100-μL solution. The DNA was purified by 0.8× KAPA Pure beads (Roche) to remove the excess adaptor. The purified DNA was then denatured by heating at 95oC for 10 min in 10% DMSO (v/v) solution and chilling on ice for 5 min. The ABE8e deamination reaction was conducted in a 10-µL reaction mixture containing 10 ng DNA, 50 mM Tris-HCl (pH 7.5), 10 mM DTT, and 2.8 µM ABE8e. After incubation at 37oC for 4 h, the reaction was stopped by heating to 95oC for 10 min. The resulting DNA was purified by 0.8× KAPA Pure beads (Roche) to remove the DTT and ABE8e. The purified DNA was subjected to PCR amplification. The PCR solution (25 µL) included 10 µL of purified DNA, 12.5 µL of TSINGKE Master Mix (Tsingke Biotech), 1 μL of pre-P7 primer (10 μM), 1 μL of pre-P5 primer (10 μM), and 0.5 μL of H2O. The amplification program started at 98°C for 30 s, followed by 4 cycles at 98°C for 10 s, 60°C for 30 s, and 72°C for 1 min. PCR products were sequentially purified using 0.8× KAPA Pure beads (Roche) followed by the second round PCR amplification. The PCR solution (50 µL) included 20 µL of purified DNA, 0.5 µL of Phusion Plus DNA polymerase (Thermo Fisher Scientific), 10 µL of 5× Phusion Plus buffer, 10 µL of 5× Phusion GC Enhance, 1 μL of P7 primer (15 μM), 1 μL of P5 primer (15 μM), and 7.5 μL of H2O. The amplification program started at 98°C for 30 s, followed by 13 cycles at 98°C for 30 s, 72°C for 45 s, and ended with 1 cycle at 72°C for 5 min. The PCR products were purified using 0.8× KAPA Pure beads (Roche) and agarose gel using agarose gel extraction kit (Zymo Research).

tag: treament

value: untreated


title: ALS sample 3

value: Blood

value: Peripheral blood mononuclear cells (PBMCs)

value: Amyotrophic Lateral Sclerosis


title: tas3c1_Rep2

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing:
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences.
The reads were mapped to the Arabidopsis genome using SOAP2 v2.21 (M4v0r1)
Bioinformatics analyses to categorize miRNA reads
Genome_build: tair10
Supplementary_files_format_and_content: txt file, which has two columns: small RNA sequence, counts

organism: Oryza sativa

source_name: RNA from tas3c1 seedlings

growth_protocol: Sterilized seeds were grown on 1/2 MS medium (pH 5.7) with 3% sucrose and 0.7% agar in a growth chamber, which was set at 12 h/32 °C for the light period, 12 h/28 ℃ for the dark period, and a relative humidity of 70%.

extract_protocol:
To construct sRNA libraries, 30 ug of total RNAs was extracted from seeding shoots using TRIzol® Reagent (Invitrogen, USA). After RNAs were resolved on a 15% urea PAGE, gel slices containing 15-40 nt RNAs were recovered, smashed and placed in 500 μL 0.4 M NaCl solution. The resulting mixture was agitated at 30 rpm at 4 °C overnight followed by supernatant collection and sRNA recovery as described previously
SRNA libraries were constructed using the Next Multiplex Small RNA Library Prep kit (NEB, USA) following the manufacturer’s instructions and sequenced on an Illumina HiSeq2500 platform with the SE50 sequencing strategy at Berry Genomics Co., Ltd.

tag: cultivar

value: cv. Nipponbare

tag: genotype/variation

value: one-week-old shoots


title: SCS-rep1

tag: strain


title: EC80

value: Mural Cells


title: BM cells with 30% of supernatant from 4T1 cells, Bx471 and maraviroc, replicate 1

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description: Gene expression data of Balb/c BM cells cultured for 4h with RPMI supplemented with 30% of supernatant from 4T1 mammary carcinoma cells in the presence of Maraviroc (5 microM) and BX471 (10 microM)

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit - Following labeling, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST arrays. GeneChips were washed and stained (streptavidin,R-phycoerythrin conjugate and biotinylated anti-streptavidin) in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GeneChip® Scanner 3000 7G . Affymetrix GeneChip® Command Console® Software (AGCC)- used to view CEL file images.

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: BM cells cultured for 4h with RPMI supplemented with 30% of supernatant from 4T1 mammary carcinoma cells, Bx471 and Maraviroc.

label_protocol: Affymetrix GeneChip WT Terminal Labeling Kit - sense-strand cDNA is fragmented with a combination of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 and its yield is further labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: BM cells were harvested from the femur and tibia of Balb/c mice, ACK red cell lysis, and then were cultured for 4 hours in the presence of RPMI (10%FCS), RPMI supplemented with 30% of filtered supernatant from confluent 4T1 cultured with complete media, or RPMI supplemented with 30% of filtered supernatant from confluent 4T1 cultured with complete media and BX471 and Maraviroc.

extract_protocol: RNA was purified using the miRNA easy kit from Qiagen and following the manufacture instruction.

treatment_protocol: cultured cells were lysed with TRIZOL and stored at -80◦C till RNA extraction was performed.

tag: strain background

value: Balb/c

value: BM cells

value: stimulated by tumor conditioned media with CCR1 and CCR5 antagonists


title: MDA-MB-231-WT rep2

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

data_processing:
In our project, we sequenced 4 samples on BGISEQ-500 Platform in total
After reads filtering, we map clean reads to reference genome (hg38) using HISAT
IGV(Integrative Genomics Viewer) tool can be used to review the mapping result.
we use StringTie to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks ) and predict the coding ability of those new transcripts using CPC
After genome mapping, we use GATK to call  SNP  and  INDEL  variant for each sample.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: breast cancer cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: triple-negative breast cancer cells

value: WT


title: ∆norA3

description: ∆norA bacterial culture, 0.1% oxygen

value: deltanorA

tag: age

value: 16 hpi

value: Untreated

value: Column


title: tas3c1_Rep3

tag: tissue


title: ∆norA2

description: ∆norA bacterial culture, 0.1% oxygen


title: EC79

tag: cell type

tag: development stage


title: BM cells with supernatant from 4T1 cells, replicate 3

description: Gene expression data of Balb/c BM cells cultured for 4h with RPMI supplemented with 30% of supernatant from 4T1 mammary carcinoma cells

value: stimulated by tumor conditioned media


title: patient 218 CSU

description: Gene expression in human blood

value: whole blood

value: female

value: chronic spontaneous urticaria (CSU) patient


title: BM cells with supernatant from 4T1 cells, replicate 2

source_name: BM cells cultured for 4h with RPMI supplemented with 30% of supernatant from 4T1 mammary carcinoma cells


title: BM cells with supernatant from 4T1 cells, replicate 1


title: ALS sample 4

value: Blood

value: Peripheral blood mononuclear cells (PBMCs)

value: Amyotrophic Lateral Sclerosis


title: EC78

value: Mural Cells

tag: genotype


title: ALS sample 7


title: MDA-MB-231-WT rep1

tag: cell line


title: SCS-rep2

value: untreated


title: K12-rep2

source_name: E. coli K12


title: GMI2

description: wildtype bacterial culture, 0.1% oxygen

value: wildtype


title: patient 32 CSU

description: Gene expression in human blood

value: male


title: K12-rep1


title: tas3b1_Rep2

source_name: RNA from tas3b1 seedlings

value: cv. Nipponbare

value: one-week-old shoots


title: C6aI rep 4

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

description: Tube 8 of 12

data_processing:
NovaSeq SPlanepaired-end150bp read length, v1sequencing chemistry
FASTQ were mapped Giardia WB genome using STAR v2.7.0f. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R using edgeR v3.26.8 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Genome_build: Giardia WB, AACB03000000; wb.fa includes DNA sequences of all the genes in fasta format
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts from STAR mapping for each sample

organism: Giardia duodenalis

source_name: trophozoites

growth_protocol: Trophozoites were grown in TYDK  with 10uM metronidazole for the resistance lines and without for revertant and wildtype. Upon reaching 70-80% confluence,  ten 10ml tubes containing TYDK without drug were seeded for WB and C6NR while 12 tubes of TYDK without drug were seeded for C60.5 and C6aI.

extract_protocol:
Performed according to the instructions provided with the Trizol reagent. RNA was then treated with DNaseI and extracted again by phenol chloroform extraction
Sequencing libraries were prepared from 250 ng total RNA using the TruSeq stranded mRNA library preparation kit (Cat# 20020594/5, Illumina Inc.) including polyA selection.The library preparation was performed according to the manufacturers’ protocol (#1000000040498).

treatment_protocol: Upon reaching 80% confluence, trophozoites were detached on ice (10m),  pelleted and lysed in 1ml of Trizol and collected in Eppendorf tubes. Samples were frozen immediatedly in liquid nitrogen and kept at -80 until RNA extraction

value: C6aI = WB-M2

tag: metrondiazole resistant

value: Yes

value: trophozoites


title: tas3b1_Rep1

source_name: RNA from tas3b1seedlings


title: BM cells with 30% of supernatant from 4T1 cells, Bx471 and maraviroc, replicate 3

value: Balb/c

value: BM cells

tag: treatment

value: stimulated by tumor conditioned media with CCR1 and CCR5 antagonists


title: ALS sample 1

tag: disease state


title: GMI1

description: wildtype bacterial culture, 0.1% oxygen

value: 16 hpi

value: Untreated

value: Column


title: BM cells with 30% of supernatant from 4T1 cells, Bx471 and maraviroc, replicate 2


title: BM cells with RPMI, replicate 3

description: Gene expression data of Balb/c BM cells cultured for 4h with RPMI

source_name: BM cells cultured for 4h with RPMI

value: control in RPMI media


title: mt-rep2

source_name: human HepG2 cell


title: MDA-MB-231-miR3662-KO rep2

value: triple-negative breast cancer cells


title: tas3a1_Rep2

source_name: RNA from tas3a1seedlings


title: MDA-MB-231-miR3662-KO rep1


title: mt-rep1


title: ALS sample 2

value: Blood

value: Peripheral blood mononuclear cells (PBMCs)

value: Amyotrophic Lateral Sclerosis


title: C60.5 rep5

description: Tube 8 of 12


title: tas3a1_Rep1


title: SAS_L1

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the (http://mascotton.njau.edu.cn/info/1054/1118.htm) TM-1 reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: TM-1
Supplementary_files_format_and_content: xls include RPKM values for each Sample

organism: Gossypium hirsutum

source_name: leaf

growth_protocol: The cotton seedlings  grew in normal soil , then transferred to a solution containing  different alkali

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following of the merchant's recommended protocol.
The paired-end libraries was 300 bp ( ± 50 bp)

treatment_protocol: 125mM NaHCO3 and same pH NaOH Treat the cotton seedings for 12h

value: SAS

value: leaf


title: tas3c1_Rep1

value: cv. Nipponbare

value: one-week-old shoots


title: C60.5 rep4

description: Tube 7 of 12

value: Yes


title: EC75

source_name: mouse embryonic cells

value: Endothelial Cells


title: K12-rep3

value: untreated


title: SAS_L3


title: SAS_R2

source_name: root

value: root


title: C6aI rep 5

description: Tube 9 of 12

value: C6aI = WB-M2

value: trophozoites


title: C60.5 rep3

description: Tube 5 of 12


title: C60.5 rep1

description: Tube 2 of 10


title: FT5

city: Jinan

first: Zhiyuan

last: Dou

address: No.44, Wenhua Xi Road

department: Obstetrics and Gynecology Department

institute: Qilu Hospital of Shandong University

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene.
Genome_build: hg38
Supplementary_files_format_and_content: normalized expression abundance FPKM

source_name: fallopian tube

extract_protocol:
6 high-grade serous ovarian cancer and 5 fallopian tube were used for RNA extraction and RNAseq. Total RNA was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Control


title: AS_L2

value: AS


title: BM cells with RPMI, replicate 2

value: Balb/c

value: BM cells

value: control in RPMI media


title: Culture growing on arabinogalactan 2

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of data was performed using FastQC package
Reads were aligned to Aspergillus nidulans (FGSC A4) genome using hisat2 (version 2.1.0)
Differential gene expression testing was performed using DESeq2 (version 1.20.0)
Genome_build: Genome: http://www.aspergillusgenome.org/download/sequence/A_nidulans_FGSC_A4/archive/A_nidulans_FGSC_A4_version_s10-m04-r12_chromosomes.fasta.gz; Genome features file (GFF): http://www.aspergillusgenome.org/download/gff/A_nidulans_FGSC_A4/ archive/A_nidulans_FGSC_A4_version_s10-m04-r12_features_with_chromosome_sequences.gff.gz
Supplementary_files_format_and_content: Excel file containing the following collumns for each sample: Gene ID, Count, Transcript length, RPKM

organism: Aspergillus nidulans

source_name: fungal mycelia

growth_protocol: Strains were maintained on Barratt’s minimal medium agar plates (Barratt et al. 1965) and conidia collected freshly from plates incubated at 37 °C for 6 d were used in all experiments. For submerged cultivation 100 ml aliquots of Barratt’s minimal broth supplemented with 5 g/l yeast extract (in 500 ml Erlenmeyer flasks) were inoculated with 50,000,000 conidia and were incubated for 16 h at 37 °C and at 3.7 Hz shaking frequency. Mycelia were separated by filtration, were washed and transferred into 100 ml fresh Barratt’s minimal broth containing 20 g/l glucose, lactose or arabinogalactan or containing no carbon source. Cultures were further incubated at 37 °C and at 3.7 Hz shaking frequency for 4 h (glucose containing cultures) or for 12 h.

extract_protocol:
Total RNA was isolated from lyophilized mycelia using TRISOL reagent (Chomczynski 1993). RNA concentration and purity were determined using NanoDrop and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Exponentially phase mycelia were transferred in to fresh media containing 20 g/l glucose, 20 g/l lactose, 20 g/l arabinogalactan or containing no carbon source.

tag: culturing condition

value: arabinogalactan


title: C6aI rep 3

description: Tube 4 of 12


title: BM cells with RPMI, replicate 1


title: mt-rep3


title: tas3a1_Rep3


title: C6aI rep 2

description: Tube 11 of 12


title: Culture growing on lactose 3

value: lactose


title: SAS_L2

value: SAS


title: C6aI rep 1

description: Tube 1 of 12


title: AS_R2


title: tas3b1_Rep3


title: SAS_R3


title: AS_R1


title: WT_Rep3

source_name: RNA from WT seedlings

value: WT


title: FT4


title: WT_Rep2

value: cv. Nipponbare


title: C6NR rep 1

description: Tube 10 of 10

value: C6NR = WB-M1NR

value: No-revertant of WB-M1


title: WT_Rep1

source_name: RNA from WT  seedlings

value: one-week-old shoots


title: SAS_R1


title: AS_L3

value: leaf


title: HGSOC2

source_name: ovarian cancer

value: Tumor


title: FT3


title: C60.5 rep2

description: Tube 3 of 12

value: Yes


title: FT1


title: Culture growing on arabinogalactan 3


title: FT2


title: HGSOC6


title: AS_L1


title: C6NR rep 5

description: Tube 7 of 10

value: trophozoites


title: Culture growing on arabinogalactan 1


title: C6NR rep 4

description: Tube 6 of 10


title: WB rep 5

description: Tube 8 of 10

value: WB

value: No


title: HGSOC5


title: AS_R3

value: AS

value: root


title: HGSOC4


title: C6NR rep 3

description: Tube 4 of 10


title: HGSOC3


title: C6NR rep 2

description: Tube 3 of 10


title: Culture growing on lactose 1


title: Carbon starved culture 2

value: no carbon source


title: Culture growing on lactose 2


title: Carbon starved culture 3


title: CK_L3


title: SKOV3 cells, siHJURP rep3

source_name: SKOV3 cells, siHJURP

extract_protocol:
SKOV3 cells were treated with siHJURP or siNC. 24 hours later, total RNA was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovarian cancer cells (adherent cells)

value: siHJURP

value: HJURP silencing


title: WB rep 3

description: Tube 4 of 10


title: Carbon starved culture 1


title: WB rep 2

description: Tube 3 of 10


title: Culture growing on glucose 3

value: glucose


title: WB rep4

description: Tube 6 of 10


title: CK_R2


title: CK_R3


title: CK_L1


title: HGSOC1


title: SKOV3 cells, siHJURP rep1


title: Culture growing on glucose 2


title: WB rep 1

description: Tube 1 of 10


title: SKOV3 cells, NC rep3

source_name: SKOV3 cells, NC

value: negative control

value: control


title: CK_R1


title: Culture growing on glucose 1


title: PDAML5-EOC4-VDJ

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

description: PDAML5_EOC4_filtered_contig_annotations.csv

data_processing:
Library strategy: VDJ-seq
The standard pipeline for Cell Ranger version 3.1.0 (10x Genomics) was used to obtain unique molecular identifier (UMI) counts for GEX, cell surface antibodies, and VDJ information. The number of barcode mismatches was set to be 0 to minimize the demultiplexing error. Seurat v3 was used across the study for sample basic quality control, normalization, data integration, visualization, and differential expression. Default methods were used unless otherwise specified for specific tasks. Data from all samples were integrated for visualization using the standard workflow on Seurat v3 by identifying the anchors between individual samples using the top 2000 variable genes within each and reducing dimensions by principal component analyses then uniform manifold approximation and projection.
Genome_build: Software cellranger used the pre-built GRCh38 in the pipeline.
Supplementary_files_format_and_content: The processed data contain the gene and protein expression matrices, VDJ annotations with cell barcodes.

source_name: Bone marrow mononuclear cells

growth_protocol: Bone marrow aspirate was collected from enrolled patients at different time points.

extract_protocol:
BM mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
CD3+ T cells were purified from cryopreserved BMMCs from AML patients. The 10x Genomics 5’ Single Cell Immune profiling platform was used for scRNA-seq of enriched T cells. Reverse transcription of mRNA into barcoded first strand cDNA, as well as construction of gene expression (GEX), VDJ, and antibody-derived tag (ADT) sequencing libraries was performed according to the experimental protocol and reagents provided by 10x Genomics without modifications. The 10x Genomics 3’v3 Single Cell Immune profiling platform was used for scRNA-seq of BMMCs. cDNA amplification was performed according to manufacturer’s instructions with the addition of 1 ul 0.2 uM ADT additive primer per sample to amply ADT tags.

treatment_protocol: No treatment

tag: individual

value: Sorted T cells

tag: age range

tag: Sex

value: M

value: refractory or relapsed AML (R-AML)

tag: disease category

value: Responder

value: pembrolizumab and decitabine

tag: time

value: End of cycle 4

tag: library type

value: 10x 5' VDJ


title: MRL/lpr-renal pelvis

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

description:
Gene expression in 6 months of age
4-MRL/lpr-renal pelvis

hyb_protocol: Gene Expression Hybridization Kit (Agilent) was used, and 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 25x fragmentation buffer and 10x GE blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μL of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE (G4852A) for 17 hours at 65°C.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Ver.12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Renal pelvis from MRL/lpr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).

growth_protocol: All mice were maintained under specific pathogen-free conditions.

extract_protocol: Total RNA from cells was purified using RNeasy Mini Kit (Qiagen)  following the manufacturer's recommendations. RNA samples were checked for RNA integrity on a Bioanalyzer 2100 II (Agilent Technologies).

treatment_protocol: Kidney and renal pelvis of mice were collected after euthanasia.

value: MRL/MpJ-Faslpr/lpr

tag: gender

value: Male

tag: age

value: 6 months

value: renal pelvis


title: SKOV3 cells, NC rep1

tag: cell type

value: ovarian cancer cells (adherent cells)


title: PDAML5-EOC4-ADT

description:
PDAML5_EOC4_barcodes.tsv.gz
PDAML5_EOC4_features.tsv.gz
PDAML5_EOC4_matrix.mtx.gz

data_processing:
Library strategy: ADT-seq
The standard pipeline for Cell Ranger version 3.1.0 (10x Genomics) was used to obtain unique molecular identifier (UMI) counts for GEX, cell surface antibodies, and VDJ information. The number of barcode mismatches was set to be 0 to minimize the demultiplexing error. Seurat v3 was used across the study for sample basic quality control, normalization, data integration, visualization, and differential expression. Default methods were used unless otherwise specified for specific tasks. Data from all samples were integrated for visualization using the standard workflow on Seurat v3 by identifying the anchors between individual samples using the top 2000 variable genes within each and reducing dimensions by principal component analyses then uniform manifold approximation and projection.
Genome_build: Software cellranger used the pre-built GRCh38 in the pipeline.
Supplementary_files_format_and_content: The processed data contain the gene and protein expression matrices, VDJ annotations with cell barcodes.

molecule: protein

value: 10x 5' cell surface antibody


title: MRL/MpJ-renal pelvis

description:
Gene expression in 6 months of age
3-MRL/MpJ-renal pelvis

source_name: Renal pelvis from MRL/MpJ

value: MRL/MpJ

tag: tissue


title: PDAML5-EOC4-GEX

data_processing:
The standard pipeline for Cell Ranger version 3.1.0 (10x Genomics) was used to obtain unique molecular identifier (UMI) counts for GEX, cell surface antibodies, and VDJ information. The number of barcode mismatches was set to be 0 to minimize the demultiplexing error. Seurat v3 was used across the study for sample basic quality control, normalization, data integration, visualization, and differential expression. Default methods were used unless otherwise specified for specific tasks. Data from all samples were integrated for visualization using the standard workflow on Seurat v3 by identifying the anchors between individual samples using the top 2000 variable genes within each and reducing dimensions by principal component analyses then uniform manifold approximation and projection.
Genome_build: Software cellranger used the pre-built GRCh38 in the pipeline.
Supplementary_files_format_and_content: The processed data contain the gene and protein expression matrices, VDJ annotations with cell barcodes.

value: 10x 5' gene expression


title: NK-M3

city: jinan

first: jing

address: 44 Wenhua Xi Road

department: Department of Pathogenic Biology

institute: Shandong University

hyb_protocol: Not Applicable

scan_protocol: DAT files from image signals to digital signals (i.e., .CEL files) using AGCC software (Affymetrix® GeneChip® Command Console® Software)

data_processing: The official Expression Console software provided by affymetrix was used for data processing: including RMA normalization, discrimination of whether the probe signal is significantly higher than the background signal, and integration of the probe signal into a probe set signal.

source_name: LUNG

label_protocol: Not Applicable

growth_protocol: Male BALB/c mice were purchased from Vital River Laboratories (Beijing) and maintained in a specific pathogen-free animal care facility of Shandong University.

extract_protocol: Total miRNA was extracted from mouse lung macrophages by using Trizol reagent (Invitrogen), and complementary DNA was synthesized by using the Mir-X™ miRNA qRT-PCR SYBR® Kit (Takara). Real-time quantitative PCR involved use of the SYB green qPCR Mix (Takara) in a CFX96 real-time PCR instrument (Bio-Rad, USA).

treatment_protocol: mice received an intravenous tail-vein injection of 20 l anti-asialo GM1 or control normal rabbit IgG antibody (isotype) in 80 l PBS 1 day before and 1 day after C. muridarum infection, then every 3 days injected 10 l anti–asialo GM1 or isotype in 90 l PBS until the end of the test

tag: infection

value: chlamydia lung infection


title: NK-M2


title: NK-M1


title: MRL/lpr-kidney

description:
Gene expression in 6 months of age
2-MRL/lpr-kidney

source_name: Kidney from MRL/lpr

tag: genotype

value: kidney


title: CK_L2

value: leaf


title: MRL/MpJ-kidney

description:
Gene expression in 6 months of age
1-MRL/MpJ-kidney

source_name: Kidney from MRL/MpJ


title: PDAML5-EOC2-ADT

description:
PDAML5_EOC2_barcodes.tsv.gz
PDAML5_EOC2_features.tsv.gz
PDAML5_EOC2_matrix.mtx.gz

value: Sorted T cells

value: M

value: End of cycle 2


title: SKOV3 cells, siHJURP rep2

tag: cell line

value: siHJURP

value: HJURP silencing


title: C57BL/6-COL17A1-spleen3

description:
4 hour contact time
6-COL17A1-3

source_name: Cultured spleen cells with COL17A1 stimulation

growth_protocol: A spleen of a 6-month old mouse was collected and minced on the culture dish. Then, 10 mL of 1 x phosphate buffered saline (-) (PBS) was added, filtered using 100 μm cell strainers, and centrifuged at 1,000 rpm for 5 minutes (min). After supernatant aspiration, the cells were resuspended and incubated with 10 mL of 0.017M tris buffer containing 0.75 % ammonium chloride (pH 7.65) for 5 min, and 10 mL of PBS was added. This solution was filtered using 40 μm cell strainers, and centrifuged at 1,000 rpm for 5 min. After washing with PBS twice, the collected cells were resuspended in RPMI1640 with L-glutamine without antibiotics and harvested in 24-well-culture plates.

treatment_protocol: These cultured cells were stimulated with recombinat human COL17A1 (0.4μg/mL, #MBS1265558, MyBioSource; San Diego, CA, USA) or PBS. The endotoxin level in rhCOL17A1 was less than 1.0 endotoxin unit per 1.0 μg the protein, as determined by a limulus amebocyte lysate test. All MLT experiments were performed using 2.5 x 107 cells/mL and 500 μL medium/well.

tag: treatment

value: with COL17A1 stimulation

tag: strain

value: spleen


title: SUM159 FMD HI rep2

city: Milan

first: Valter

last: Longo

address: via Adamello 16

institute: IFOM - the FIRC Institute of Molecular Oncology

data_processing:
Reads were aligned to the hg38 reference genome with STAR with default parameters and the --quantMode GeneCounts to generate gene counts.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: 1,5x10^6 SUM159 cells resuspended in 100 μl of PBS and injected in 8-weeks old female NOD scid gamma mice

extract_protocol:
Cells extracted from tumor masses were washed in PBS 1% BSA and pellets were resuspended in blocking buffer (PBS 10% BSA) and incubated for 30 min at 4C light protected. After a wash in PBS 1% BSA, cells were incubated  for 45min at 4C, with FITC-conjugated anti-human CD24 antibody (Miltenyi Cat. #: 130-112-844) and vioblue-conjugated anti-human CD44 antibody (Miltenyi Cat. #: 130-113-899) staining. Finally, cells were washed with PBS 1% BSA and sorted with MoFlo Astrios Cell Sorter (Beckman Coulter).  Total RNA was isolated from cells, previously sorted, using the miRNeasy Mini Kit (QIAGEN, #217004), according to the manufacturer’s instructions
mRNA-seq indexed library preparation was performed starting from 500 ng of total RNA with the TruSeq stranded mRNA (Illumina).

treatment_protocol: Mice were fed with standard diet or underwent FMD cycles (4 consecutive days per week)

value: Breast cancer cell line

value: Fasting-mimicking diet

tag: cell population

value: CD44+CD24-High sorted cells


title: SUM159 FMD LO rep3

value: CD44+CD24-Low sorted cells


title: PDAML5-EOC2-VDJ

description: PDAML5_EOC2_filtered_contig_annotations.csv

tag: disease state

value: refractory or relapsed AML (R-AML)

value: Responder

value: pembrolizumab and decitabine

value: 10x 5' VDJ


title: SUM159 FMD HI rep3


title: SUM159 FMD LO rep2


title: PDAML5-EOC2-GEX

tag: individual

value: 10x 5' gene expression


title: NK+M2

last: Li

value: chlamydia lung infection


title: NK+M3


title: SUM159 FMD HI rep1


title: C57BL/6-COL17A1-spleen2

description:
4 hour contact time
5-COL17A1-2

value: Male

value: 6 months


title: PDAML5-Day0-VDJ

description: PDAML5_Day0_filtered_contig_annotations.csv

value: Sorted T cells

tag: age range

value: M

value: Day 0


title: C57BL/6-COL17A1-spleen1

description:
4 hour contact time
4-COL17A1-1

value: with COL17A1 stimulation


title: Zfp57 ChIP-seq of TSa2i-c57-p63

city: Shanghai

first: Qing

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

data_processing:
ChIP-seq reads were aligned to mm9 with Bowtie2 (version 2.2.2) with parameters -t -q -N 1 -L 25. All unmapped reads, multiplely mapped reads and PCR duplicates were removed. To generate the ChIP-Seq signals for each histone modification shown in the UCSC genome browser, we normalized the read counts by computing the number of reads per kilobase of bin per million reads sequenced (RPKM). To minimize the batch and cell type variation, the RPKM values were further normalized through Z-score transformation, by subtracting the mean of RPKM across the genome and divided by the standard deviation of RPKM across the genome.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). The expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
MethylC-seq reads were aligned to mm9 using BSMAP with parameters –r 0 –w 100 –v 0.1 –A AGATCGGAAGAGC. Multiple-mapped reads and PCR duplicates were removed. After mapping, those reads with total CG coverage less than 5 within 200 bp were removed. Methylation level was calculated using methylated CpG versus total CpG in each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited wig files including number of reads in 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited wig files for methylC-seq including the average mCG level in 200bp bins.
Supplementary_files_format_and_content: Tab-delimited txt files for RNA-seq including FPKM values for each gene

source_name: haploid mESCs

growth_protocol: 2i-14, 2i-O48 and 2i-O48-TKO cells were cultured in 2i/L medium,which include DMEM, 100×NEAA, 100×Nucleosides, 100×L-Glutamine, 100×P/S, 100×β-mercaptoethanol, 15% FBS and 1,000 U/ml LIF,1 μM PD0325901 and 3 μM CHIR99021. a2i-8 haploid ESCs were cultured in a2i/L medium which was same as 2i/L medium except 1 μM PD0325901 was replaced by 1.5 μM CGP77675.Ma2i-C57, Ma2i-14 and switched 2i/L haploid ESCs were cultured in Ma2i/L medium which include DMEM/F12  and Neurobasal  supplemented with B27 (GIBCO) and N2 cell-supplements (GIBCO), 100×P/S, 2 mM Glutamax (GIBCO), and 1,000 U/mL LIF, 1.5 μ M CGP77675 and 3 μ M CHIR99021.

extract_protocol:
The cells(>5×10^6) were treated with formaldehyde to 1% final concentration followed by incubation for 10 min at 37ºC.Cells  were resuspended in 100 µl lysis buffer (containing 0.3% SDS) plus protease inhibitors.The lysate is sonicated to shear the crosslinked DNA to lengths between 200 and 500 bp. The lysate was incubated with corresponding antibody overnight. Histone-DNA complex were isolated and reverse crosslinked overnight.DNA was extracted to build a library.
DNA was end-repaired, adenylated and ligated to TruSeq sequencing adapters. After purification with DNA clean beads (Vazyme), DNA was amplified by Phusion High-Fidelity DNA Polymerase (catalog no. M0530L; New England Biolabs) or Pfu Turbo Cx Hotstart DNA polymerase (for bisulfite-treated DNA libraries). The amplified DNA was size-selected using  DNA clean beads for 200 to 500-bp DNA fragments. All libraries were sequenced using an Illumina HiSeq 2500 system according to the manufacturer’s instructions.

value: wild-type

tag: chip-antibody

value: ZFP57 antibody (Abcam, Cat.No.ab45341, Lot.No.GR3270465-1)


title: Zfp57 ChIP-seq of 2i-14-p61


title: SUM159 FMD LO rep1

value: Breast cancer cell line

value: Fasting-mimicking diet


title: SKOV3 cells, NC rep2

value: ovarian cancer cells (adherent cells)

value: negative control

value: control


title: PDAML5-Day0-ADT

description:
PDAML5_Day0_barcodes.tsv.gz
PDAML5_Day0_features.tsv.gz
PDAML5_Day0_matrix.mtx.gz

tag: Sex

value: refractory or relapsed AML (R-AML)

tag: disease category

value: Responder

value: pembrolizumab and decitabine

value: 10x 5' cell surface antibody


title: C57BL/6-Cont-spleen3

description:
4 hour contact time
3-Cont-3

source_name: Cultured spleen cells without stimulation

value: without stimulation

value: Male

value: spleen


title: H3K27me3 ChIP-seq of TSa2i-14-p58

value: Histone H3K27me3 antibody ( Diagenode, Cat.No.C15410069, Lot.No. A1818P)


title: C57BL/6-Cont-spleen2

description:
4 hour contact time
2-Cont-2

value: 6 months


title: SUM159 CTR HI rep3

value: Untreated

value: CD44+CD24-High sorted cells


title: H3K27me3 ChIP-seq of  2i-14-p48

value: wild-type


title: PDAML5-Day0-GEX

value: Sorted T cells

value: M

tag: time

value: Day 0

tag: library type

value: 10x 5' gene expression


title: SUM159 CTR LO rep3

value: Breast cancer cell line

value: CD44+CD24-Low sorted cells


title: PDAML3-EOC4-VDJ

description: PDAML3_EOC4_filtered_contig_annotations.csv

value: F

value: refractory or relapsed AML (R-AML)

value: immune- related adverse events

value: End of cycle 4

value: 10x 5' VDJ


title: H3K4me3 ChIP-seq of 2i-14 transferred to SF/a2i for 10 passages

value: Histone H3K4me3 antibody (MERCK, Cat.No.04-745, Lot.No.3068440)


title: SUM159 CTR HI rep2


title: PDAML3-EOC4-ADT

description:
PDAML3_EOC4_barcodes.tsv.gz
PDAML3_EOC4_features.tsv.gz
PDAML3_EOC4_matrix.mtx.gz

value: pembrolizumab and decitabine

value: 10x 5' cell surface antibody


title: SUM159 CTR LO rep2

value: Untreated


title: PDAML3-EOC4-GEX


title: LH3

city: Frederiksberg C.

first: Josephine

last: Skat-Rørdam

address: Ridebanevej 9

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: Københavns Universitet

description: Initially animals were given a High Fat Low Vitamin C diet, for 16 weeks. For the remaining part of the study (16 weeks) animals were given a Low Fat High Vitamin C diet.

data_processing:
Base calling was performed on Novaseq 6000 (illumina) using RTA 2.0, and the resulting BCL files were converted to fastq files using the bcl2fastq software 2.19 (illumina)
Fastq files were trimmed for adaptor sequences and any reads below 50 nt. were discarded using the Trimmomatic 0.38.0 software with the input SLIDING WINDOW: number of bases to average across: 4, average quality required 20, HEADCROP: 9, MINLEN: 50
The trimmed reads were mapped using the HISAT2 2.1.0 mapper. The Cavia Porcellus genome and annotation  (CavPor.3.0.98) was acquired from ensemble, and used as reference genome
Initial transcript assembly was performed by StringTie 2.1.1 using the guinea pig annotation file (CavPor.3.0.98) as a guide. StringTie merge 2.1.1 was run on Stringtie output from all  samples with the guinea pig annotation file as a guide, and default parameters. For quantification StringTie was run on the StringTie merge file seperately for each sample by using the guinea pig annotation file as a guide, setting the -e parameter was set to "yes" and the output type to deseq2
Raw counts for each StringTie file was assembled into a collected file and to obtain translatability and more annotation, BioMart was used to find human orthologs for each transcript. To diminish background noise genes with raw counts below 200 across all samples were discarded. Finally Deseq2 was used for differential expression
Genome_build: CavPor3
Supplementary_files_format_and_content: raw_counts.txt: Matrix file with raw counts for each gene and each sample. Vst_norm_counts.txt: Normalized and transformed values for each sample, and each gene (normalized according to DESeqs' size factor, and vst tranformed).

organism: Cavia porcellus

source_name: Liver

extract_protocol:
Liver sections from the left lateral lobe were snap frozen in liquid nitrogen. 10 mg. liver tissue was purified using the RNeasy Lipid Tissue Mini Kit in accordance with manufacturers instructions. 25 ul of the purified RNA (200-500 ng/ml) was sent to Novogene for sequencing.
Total RNA was enriched for mRNA by using oligodT bead system. The mRNA was then fragmented by adding fragmentation buffer, after which the cDNA was synthesized by using mRNA template and random hexamer primers and a custom second strand synthesis buffer (illumina) together with dNATPs, RNase H and DNA polymerase I to initiante second strand synthesis. Secondly after a series of terminal repair, and ligation and sequencing adaptor ligation the double-stranded cDNA library was completed through size selection and PCR enrichment (Novogene).

treatment_protocol: Animals were given either a low fat (n=16), a high fat (n=16) or a high fat low vitamin C diet (n=48). After 16 weeks 8 animals from each group were euthanized, and the remaining animals in the high fat low vitamin C group were randomized and divided into 4 groups given one of the following diets: High fat low vitamin C (continuing on the same diet), high fat high vitamin C, low fat low vitamin C, low fat high vitamin C. After another 16 weeks all animals were euthanized an samples were collected for transcriptome analysis

value: Hartley

value: liver

tag: diet

value: Low Fat High Vitamin C

value: NAFLD

tag: time on diet

value: 32 weeks


title: H3K4me3 ChIP-seq of TSa2i-14-p58

value: wild-type


title: SUM159 CTR HI rep1

tag: cell type

value: Breast cancer cell line

value: CD44+CD24-High sorted cells


title: LH43

tag: tissue


title: PDAML3-EOC2-VDJ

description: PDAML3_EOC2_filtered_contig_annotations.csv

value: Sorted T cells

value: F

value: End of cycle 2


title: SUM159 CTR LO rep1

value: CD44+CD24-Low sorted cells


title: H3K9me3 ChIP-seq of 2i-O48-TKO transferred to SF/a2i/L for 5 passages

tag: genotype

value: Deletions of H19-DMR, IG-DMR and gene H19

value: Histone H3K9me3 antibody (Active Motif, Cat.No.39161, Lot.No.09919003)


title: PDAML3-EOC2-ADT

description:
PDAML3_EOC2_barcodes.tsv.gz
PDAML3_EOC2_features.tsv.gz
PDAML3_EOC2_matrix.mtx.gz

value: refractory or relapsed AML (R-AML)

value: immune- related adverse events

value: pembrolizumab and decitabine


title: LH4

value: Hartley


title: LH58

value: liver


title: NK+M1

tag: infection

value: chlamydia lung infection


title: H3K9me3 ChIP-seq of  2i-O48-TKO


title: H3K9me3 ChIP-seq of  ZFP57 KO

value: Deletion of  Zfp57


title: LH33

value: Low Fat High Vitamin C

value: NAFLD

value: 32 weeks


title: PDAML3-Day0-VDJ

description: PDAML3_Day0_filtered_contig_annotations.csv

tag: treatment

value: Day 0

value: 10x 5' VDJ


title: H3K9me3 ChIP-seq of 2i-14 transferred to SF/a2i/L for 5 passages

tag: strain

value: wild-type


title: hEC_hNo4_strt

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

data_processing:
10X Genomics CellRanger version 2.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 2.1.0) with default mapping arguments. For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 human transcriptome (UCSC) using Hisat2 (version 2.10). Uniquely mapped reads were counted by HTSeq package83 and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: human embryonic cells

extract_protocol: A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner

value: Body, Head

tag: development stage

value: CS 12


title: PDAML3-Day0-ADT

description:
PDAML3_Day0_barcodes.tsv.gz
PDAML3_Day0_features.tsv.gz
PDAML3_Day0_matrix.mtx.gz

value: Sorted T cells

value: F

tag: disease state

value: 10x 5' cell surface antibody


title: LL13

description: Initially animals were given a High Fat Low Vitamin C diet, for 16 weeks. For the remaining part of the study (16 weeks) animals were given a Low Fat Low Vitamin C diet.

value: Low Fat Low Vitamin C


title: hEC_hNo3_strt

value: Body, Head, Limb


title: H3K9me3 ChIP-seq of TSa2i-C57-p11

value: Histone H3K9me3 antibody (Active Motif, Cat.No.39161, Lot.No.09919003)


title: LL68

value: Hartley

value: liver


title: PDAML2-EOC4-VDJ

description: PDAML2_EOC4_filtered_contig_annotations.csv

tag: individual

value: refractory or relapsed AML (R-AML)

value: immune- related adverse events

value: pembrolizumab and decitabine

value: End of cycle 4


title: C57BL/6-Cont-spleen1

description:
4 hour contact time
1-Cont-1

value: without stimulation

tag: gender

value: Male

tag: age

value: 6 months

value: spleen


title: H3K9me3 ChIP-seq of TSa2i-C57-p63

value: wild-type

tag: chip-antibody


title: hEC_hNo1_strt

value: Body, Head

value: CS 10


title: LL44

value: NAFLD

value: 32 weeks


title: hEC_hNo5_strt

value: Body, Head, Limb

value: CS 13


title: H3K9me3 ChIP-seq of TSa2i-14-p18

value: Histone H3K9me3 antibody (Active Motif, Cat.No.39161, Lot.No.09919003)


title: H3K4me3 ChIP-seq of  2i-14-p48

value: Histone H3K4me3 antibody (MERCK, Cat.No.04-745, Lot.No.3068440)


title: XEN_XX_H3K27me3_r2

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Read sequences were trimmed using Trim Galore (0.6.4) with options [--paired --nextera] (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
The trimmed FASTQ files were aligned to the mm10 genome using bowtie2 (2.3.5) with the options [--local --very-sensitive-local -X 2000] (Langmead and Salzberg 2012)
SAM files were translated into BAM files, filtered for paired and mapped reads and sorted using samtools (1.10) with options [view -b -h -f 2 -q 20] and [sort] (Li et al., 2009).
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
BigWig tracks were created using deepTools (2.0) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] (Ramírez et al. 2016) and visualized using the UCSC Genome Browser (Kent et al. 2002).
Peaks were called using MACS2 (2.1.2) with options [callpeak -f BAMPE -g mm -q 0.05] (Zhang et al. 2008).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks
Supplementary_files_format_and_content: narrowPeak: Peak files

source_name: Extraembryonic endoderm stem cells

growth_protocol: Female XEN cell line was grown on 0.2% gelatin-coated flasks following the Rossant lab XEN stem cell protocol (https://lab.research.sickkids.ca/rossant/wp-content/uploads/sites/12/2015/08/XEN-Stem-Cell-protocol1.pdf) in serum-containing XEN medium (RPMI 1640 (Sigma, M3817)), 15% ESC-grade FBS (Gibco), 0.1 mM β-mercaptoethanol (Sigma), 1 mM sodium pyruvate (Gibco) and 2 mM L-glutamine (Life technologies). Female TSCs were cultured following the grown on MEFs in serum containing TSC medium (RPMI, 20 % fetal bovine serum, 1 mM sodium pyruvate, 100 mM 2-mercaptoethanol, 50 µg/ml penicillin/streptomycin and 2 mM L-Glutamine; FGF4 (25 ng/ml, R&D System) and Heparin (1 µg/ml, Sigma) were added to the medium fresh prior to each use) (Tanaka et al. 1998). Before sample collection, TSCs were passaged at least twice without MEFs to dilute out feeder cells. During this time cells were cultured in MEF-conditioned medium (70% MEF-conditioned medium, 30% TSC medium, FGF4 (37.5 ng/ml, R&D System), Heparin (1.5 µg/ml, Sigma)).

extract_protocol:
For each CUT&Tag reaction 100.000 cells were collected and washed once with Wash buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 10 mM Sodium butyrate, 1 mM PMSF). 10ul Concanavalin A (Bangs Laboratories) beads were equilibrated with 100ul Binding buffer (20 mM HEPES-KOH, pH 7.5, 10 mM KCl, 1 mM CaCl2, 1mM MnCl2) and afterwards concentrated in 10ul binding buffer. The cells were bound to the Concanavalin A beads  by incubating for 10 minutes at room temperature with rotation. Following this, the beads were separated on a magnet and resuspended in 100ul chilled Antibody buffer (Wash buffer with 0.05% Digitonin and 2mM EDTA) with subsequently 1ul of primary antibody and incubated on a rotator for 3h at 4°C. Primary antibodies were used 1:100 (H3K27ac, H3K27me3) or 1:200 (GATA2/3/4/6).  After magnetic separation the beads were resuspended in 100ul chilled Dig-wash buffer (Wash buffer with 0.05% Digitonin) containing 1ul of matching secondary antibodies and were incubated for 1h at 4°C with rotation. The beads were washed three times with ice cold Dig-wash buffer and resuspended in chilled Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with 1:250 diluted 3xFLAG-pA-Tn5 preloaded with Mosaic-end adapters. After incubation for 1h at 4°C with rotation, the beads were washed four times with chilled Dig-300 buffer and resuspended in 50ul Tagmentation buffer (Dig-300 buffer 10 Mm MgCl2). Tagmentation was performed for 1h at 37°C and subsequently stopped by adding 2.25 µL 0.5M EDTA, 2.75 µL 10% SDS and 0.5 µL 20 mg/mL Proteinase K and vortexing for 5 seconds. DNA fragments were solubilized overnight at 55°C followed by 30 minutes at 70°C to inactivate residual Proteinase K. DNA fragments were purified with the ChIP DNA Clean & Concentrator kit (Zymo Research) and eluted with 25 ul elution buffer according to the manufacturer's guidelines.
NGS libraries were generated by amplifying the CUT&Tag DNA fragments with i5 and i7 Nextera barcoded HPLC grade primers using NEBNext® HiFi 2x PCR Master Mix (New England BioLabs) on a thermocycler with the following program: 72 °C for 5 min, 98 °C for 30 sec, 98 °C for 10 sec, 63 °C for 10 sec (14-15 Cycles for step 3-4)  and 72°C for 1 min. Post PCR cleanup was performed with Ampure XP beads (Beckman Coulter). For this 0.95x volume of Ampure XP beads were mixed with the NGS libraries and incubated at room temperature for 10 minutes. After magnetic separation, the beads were washed three times on the magnet with 80% ethanol and the libraries eluted with Tris-HCl, pH 8.0. The quality of the purified NGS libraries was assessed with the BioAnalyzer High Sensitivity DNA system (Agilent Technologies). Sequencing libraries were pooled in equimolar ratios cleaned for another round with  1.2x volume of Ampure XP beads as before and eluted in 20ul Tris-HCl, pH 8.0. The sequencing library pool quality was assessed with the BioAnalyzer High Sensitivity DNA system (Agilent Technologies) and subjected to Illumina PE75 next generation sequencing on the NextSeq500 platform to approximately 5 million fragments per library.
CUT&Tag

tag: cell line

value: XX XEN cells

tag: target

tag: condition

value: XEN Medium

tag: replicate

tag: strain background

value: 129S2/SvHsd / CAST/Eij

tag: assay

value: CUT&Tag


title: XEN_XX_H3K27me3_r3


title: PDAML3-Day0-GEX

tag: cell type

value: Sorted T cells

tag: age range

tag: Sex

value: F

value: refractory or relapsed AML (R-AML)

tag: disease category

value: immune- related adverse events

value: pembrolizumab and decitabine

tag: time

value: Day 0

tag: library type

value: 10x 5' gene expression


title: PDAML2-EOC2-VDJ

description: PDAML2_EOC2_filtered_contig_annotations.csv

tag: disease state

tag: treatment

value: End of cycle 2

value: 10x 5' VDJ


title: H3K9me3 ChIP-seq of TSa2i-14-p58

tag: strain

tag: genotype

value: wild-type


title: LL53

value: Hartley

tag: tissue

value: liver

tag: diet

value: Low Fat Low Vitamin C

value: NAFLD

tag: time on diet

value: 32 weeks


title: LL17


title: PDAML2-EOC2-ADT

description:
PDAML2_EOC2_barcodes.tsv.gz
PDAML2_EOC2_features.tsv.gz
PDAML2_EOC2_matrix.mtx.gz

tag: individual

value: 10x 5' cell surface antibody


title: PDAML2-EOC2-GEX


title: PDAML3-EOC2-GEX


title: LH32

value: Low Fat High Vitamin C


title: HH84

description: Initially animals were given a High Fat Low Vitamin C diet, for 16 weeks. For the remaining part of the study (16 weeks) animals were given a High Fat High Vitamin C diet.

value: High Fat High Vitamin C

value: NASH


title: PDAML2-EOC4-GEX

description:
PDAML2_EOC4_barcodes.tsv.gz
PDAML2_EOC4_features.tsv.gz
PDAML2_EOC4_matrix.mtx.gz

value: Sorted T cells

value: F

value: refractory or relapsed AML (R-AML)

value: End of cycle 4


title: PDAML2-EOC4-ADT

value: immune- related adverse events

value: pembrolizumab and decitabine


title: LL49


title: H3K9me3 ChIP-seq of  2i-14-p48

tag: chip-antibody

value: Histone H3K9me3 antibody (Active Motif, Cat.No.39161, Lot.No.09919003)


title: hEC_hNo2_strt

value: Body, Head

tag: development stage

value: CS 11


title: RNAseq of 2i-O48-TKO transferred to SF/a2i/L for 5 passages

value: Deletions of H19-DMR, IG-DMR and gene H19


title: H3K9me3 ChIP-seq of  2i-14-p13

value: wild-type


title: HH22

value: Hartley

value: liver


title: RNAseq of 2i-O48 transferred to SF/a2i/L for 5 passages

value: Deletions of H19-DMR and IG-DMR


title: XEN_XX_H3K27ac_r2

tag: cell line

value: XX XEN cells

tag: target

tag: condition

value: XEN Medium

tag: replicate

tag: strain background

value: 129S2/SvHsd / CAST/Eij

tag: assay

value: CUT&Tag


title: XEN_XX_GATA6_r2


title: RNAseq of  2i-O48


title: RNAseq of  2i-O48-TKO


title: PDAML2-Day0-VDJ

description: PDAML2_Day0_filtered_contig_annotations.csv

tag: cell type

value: Sorted T cells

tag: age range

tag: Sex

value: F

tag: disease category

tag: time

value: Day 0

tag: library type

value: 10x 5' VDJ


title: HH19

tag: strain

tag: tissue

tag: diet

value: High Fat High Vitamin C

tag: disease state

value: NASH

value: 32 weeks


title: XEN_XX_H3K27ac_r1


title: PDAML2-Day0-GEX

description:
PDAML2_Day0_barcodes.tsv.gz
PDAML2_Day0_features.tsv.gz
PDAML2_Day0_matrix.mtx.gz

tag: individual

value: refractory or relapsed AML (R-AML)

value: immune- related adverse events

tag: treatment

value: pembrolizumab and decitabine

value: 10x 5' gene expression


title: PDAML2-Day0-ADT

value: 10x 5' cell surface antibody


title: HH20

value: Hartley

value: liver

tag: time on diet


title: XEN_XX_H3K27me3_r1

tag: cell line

value: XX XEN cells

tag: target

tag: condition

value: XEN Medium


title: XEN_XX_GATA6_r1

tag: replicate

tag: strain background

value: 129S2/SvHsd / CAST/Eij

tag: assay

value: CUT&Tag


title: HH15


title: RNAseq of  2i-14-p50

tag: genotype

value: wild-type


title: PDAML1-EOC4-VDJ

description: PDAML1_EOC4_filtered_contig_annotations.csv

tag: cell type

value: Sorted T cells

tag: age range

tag: Sex

value: M

tag: disease category

value: Responder

value: End of cycle 4


title: HH30

tag: strain

tag: tissue

value: High Fat High Vitamin C

value: NASH

value: 32 weeks


title: RNAseq of TSa2i-C57-p58


title: HL75

description: Animals were maintained on the same diet for 32 weeks

tag: diet

value: High Fat Low Vitamin C

tag: disease state


title: XEN_XX_GATA4_r1


title: TS_XX_H3K27me3_r2

source_name: Trophoectoderm stem cells

value: XX TS cells

value: TSC Medium


title: PSCSR-seq analysis for whole cells and nuclei

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute Of Biological Sciences, Beijing (NIBS)

description: PSCSR-seq results for 293T whole cells, 293T nuclei, 3T3 whole cells and 3T3 nuclei

data_processing:
The PSCSR-seq analysis procedures are adapted from the method in the publication(S. Mi and T. Cai et al., Cell 133, 116, 2008). Briefly, the small RNA sequences, cell barcodes and molecules UMI are extracted from the raw reads using the customized scripts. The small RNA sequence with the length of 16nt~39nt were kept and mapped to the reference genome with no mismatch (bowtie v1.2.2). The small RNAs are annotated to according to the databases including miRbase (release v22.1), EBI RNAcenter database (release v11), EBML CDS database (ENSEMBL release v96). For certain small RNA gene, different UMIs (at least 2-base difference) were counted as the measurement of small RNA expression. The computational pipeline can be found at github (https://github.com/biocaitao/PSCSR-seq).
The single cells in PSCSR-seq were selected using TaKaRa ICell8 system protocol (“StandardCellSettings-V5” or “PBMCv4”). The cell barcodes of selected cells were exported. The valid cells were filtered from the background according to the exported barcodes (allowing 2 mismatches). (refer to https://github.com/biocaitao/PSCSR-seq ).
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: PSCSR-seq processed files contain: plain text files for cell barcodes and estimated expression of miRNAs and all small RNAs;

organism:
Homo sapiens
Mus musculus

source_name: cultured cell line

growth_protocol: A549 cells were cultured in DMEM/F-12 (11320082, Gibco), Hela, 3T3, and HEK293T cells were cultured in DMEM-basic (C11965500BT, Gibco) and K562 cells were cultured in RPMI Medium 1640 basic(1X) (C22400500BT,Gibco). All the cultured media were supplemented with 10% (v/v) foetal bovine serum (26140079, Gibco) and 1% penicillin-streptomycin (15140122, Gibco). Cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Cultured cancer cells, PBMCs, and tumor tissue were harvested and dissociated. Cells were dispensed into a ICELL8 nanowell chip for PSCSR-seq analysis.
single cell small RNA analysis used PSCSR-seq protocol, briefly, small RNAs were ligated with 3' adapters using T4 RNA Ligase 2, truncated KQ (NEB), the remained 3' adapter were removed by 5' Deadenylase (NEB) and Lambda Exonuclease (Thermo Fisher). 5'adapters were ligated to the small RNA using T4 RNA Ligase 1(NEB). The adapters carrying 8 random nucleotides (UMI) for the small RNA counting. The ligated small RNAs were reverse-transcribed using Superscript III (Thermo Fisher), and two rounds of PCRs were performed to introduce the barcodes for labeling cells and multiplexing samples. PSCSR library was size selected with Pippin Prep, and the size distribution was assessed using an Agilent 2100 BioAnalyzer; Single cell RNA-seq followed Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) from the 10X Genomics company.

value: HEK293T and 3T3

tag: passages


title: PDAML1-EOC4-GEX

description:
PDAML1_EOC4_barcodes.tsv.gz
PDAML1_EOC4_features.tsv.gz
PDAML1_EOC4_matrix.mtx.gz

tag: individual

value: refractory or relapsed AML (R-AML)

tag: treatment

value: pembrolizumab and decitabine

tag: time

tag: library type

value: 10x 5' gene expression


title: HL81

value: Hartley

value: liver

tag: time on diet


title: RNAseq of TSa2i-C57-p9

value: wild-type


title: HL52


title: TS_XX_H3K27me3_r1

tag: cell line

tag: target

tag: condition

tag: replicate

tag: strain background

value: CUT&Tag


title: PDAML1-EOC2-VDJ

description: PDAML1_EOC2_filtered_contig_annotations.csv

tag: cell type

value: Sorted T cells

tag: age range

tag: Sex

value: M

value: End of cycle 2

value: 10x 5' VDJ


title: RNAseq of TSa2i-14-p54

tag: strain

tag: genotype


title: PDAML1-EOC2-ADT

description:
PDAML1_EOC2_barcodes.tsv.gz
PDAML1_EOC2_features.tsv.gz
PDAML1_EOC2_matrix.mtx.gz

tag: disease state

tag: disease category

value: Responder

value: 10x 5' cell surface antibody


title: HL34

tag: tissue

tag: diet

value: High Fat Low Vitamin C

value: NASH

value: 32 weeks


title: TS_XX_H3K27ac_r2

value: XX TS cells

value: TSC Medium

tag: assay


title: TS_XX_H3K27ac_r1


title: HL29


title: RNAseq of 2i-14 transferred to SF/a2i/L for 5 passages


title: PDAML1-EOC2-GEX

tag: individual

value: refractory or relapsed AML (R-AML)

tag: treatment

value: pembrolizumab and decitabine

tag: time

tag: library type


title: PDAML1-Day0-VDJ

description: PDAML1_Day0_filtered_contig_annotations.csv

value: Day 0


title: RNAseq of TSa2i-14-p22


title: HL12

value: Hartley

value: liver

tag: time on diet


title: TS_XX_GATA3_r2

tag: cell line

tag: target

tag: condition

tag: replicate

value: CUT&Tag


title: XEN_XX_GATA4_r2

value: XX XEN cells

value: XEN Medium

tag: strain background

value: 129S2/SvHsd / CAST/Eij


title: RNAseq of  2i-14-p39

tag: strain

value: wild-type


title: TS_XX_GATA3_r1


title: PDAML1-EOC4-ADT

tag: cell type

value: Sorted T cells

tag: age range

tag: Sex

value: M

value: Responder

value: End of cycle 4


title: RNAseq of  2i-14-p18

tag: genotype


title: HL31

tag: tissue

tag: diet

value: High Fat Low Vitamin C

tag: disease state

value: NASH

value: 32 weeks


title: HL55


title: TS_XX_GATA2_r2

value: XX TS cells

value: TSC Medium

tag: assay


title: PDAML1-Day0-GEX

description:
PDAML1_Day0_barcodes.tsv.gz
PDAML1_Day0_features.tsv.gz
PDAML1_Day0_matrix.mtx.gz

tag: individual

value: refractory or relapsed AML (R-AML)

tag: disease category

tag: treatment

value: pembrolizumab and decitabine

tag: time

value: Day 0

value: 10x 5' gene expression


title: WGBS of ZFP57-KO-p20

value: Deletion of  Zfp57


title: TS_XX_GATA2_r1

tag: cell line

tag: target

value: CUT&Tag


title: PDAML5-Rel-MissionProtein

value: Bone marrow mononuclear cells

value: Time of relapse

tag: library type

value: MissionBio cell surface protein


title: RNAseq of TSa2i-14-p47

value: wild-type


title: HL90

value: Hartley

value: liver

tag: time on diet


title: PDAML5-Rel-DNA

value: M

value: Responder

value: MissionBio single-cell DNA


title: WGBS of 2i-O48 transferred to SF/a2i/L for 19 passages

tag: strain

value: Deletions of H19-DMR and IG-DMR


title: WGBS of 2i-O48


title: PDAML5-Rel-ADT

description:
PDAML5_Rel_barcodes.tsv.gz
PDAML5_Rel_features.tsv.gz
PDAML5_Rel_matrix.mtx.gz

tag: cell type

value: 10x 3' cell surface antibody


title: HL93

value: High Fat Low Vitamin C

value: NASH

value: 32 weeks


title: H88

value: High Fat


title: 4NQO

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: 3' sequencing

data_processing:
10x genomics according to the manufacturer protocol
mm10
Supplementary_files_format_and_content: 3 files containing sparse matrix include mRNA molecule filtered  count values for each Sample

source_name: Tongue epithelium

extract_protocol:
After 5 weeks of treatment, the tongue epithelial tissues were collected from 4NQO-treated and naïve control mice. The tissues were processed with Collagenase /DNAse to obtain single-cell suspensions that were further enriched for CD45+ cells using magnetic columns.
10x genomics according to the manufacturer protocol

treatment_protocol: 1 gram of 4NQO (sigma N8141-5G) was dissolved in 200 mL propylene glycol (sigma P4347-500ML) for 3-5 hours (until homogeneous) and aliquots of the stock solution (5 mg/ml) were stored at 4°C. The stock solution was diluted in 250 ml of drinking water to a final concentration of 60 μg/ml. The water was provided in a dark bottle and replaced twice a week.

tag: organ

value: Tongue

tag: selection marker

value: enrichment to CD45+ cells

value: 4NQO in the drinking water

tag: mouse age

value: 12 weeks


title: WGBS of 2i-14 transferred to SF/a2i/L for 10 passages

tag: genotype


title: H47

tag: tissue

tag: diet


title: WGBS of 2i-14-p49


title: Has2+/- KO mice 24 after chronic OVA stimulation 5

city: Tsukuba

first: Takumi

last: Kiwamoto

address: 1-1-1 Tennoudai

department: Pulmonary Medicine

institute: University of Tsukuba

data_processing: FASTQ files were analyzed using CLC Genomics Workbench (Version 10.1.1; Qiagen, Redwood City, CA).

source_name: Whole lung tissue homogenate

extract_protocol:
Lung were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA sequencing (RNA-seq) libraries were prepared using a NEBNext rRNA Depletion Kit (New England Biolabs, Ipswich, MA) and an ENBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions using 500 ng of total RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Balb/c

value: Has2+/- KO

value: treated with intranasal ovalbumin for 8 weeks

value: lung


title: PDAML5-Rel-GEX

value: Bone marrow mononuclear cells

tag: age range

tag: Sex

value: M

tag: disease state

value: refractory or relapsed AML (R-AML)

value: pembrolizumab and decitabine

value: Time of relapse

value: 10x 3' gene expression


title: PDAML1-Day0-ADT

tag: individual

value: Sorted T cells

tag: disease category

value: Responder

tag: treatment

value: Day 0

value: 10x 5' cell surface antibody


title: H14

value: Hartley

value: liver

value: High Fat

value: NASH

value: 32 weeks


title: WGBS of TSa2i-14-p52

value: wild-type


title: PDAML5-D0-ADT

description:
PDAML5_D0_barcodes.tsv.gz
PDAML5_D0_features.tsv.gz
PDAML5_D0_matrix.mtx.gz

tag: time

value: 10x 3' cell surface antibody


title: Has2+/- KO mice 24 after chronic OVA stimulation 3

value: Balb/c

value: Has2+/- KO

value: treated with intranasal ovalbumin for 8 weeks

value: lung


title: PDAML5-D0-GEX

value: Bone marrow mononuclear cells

value: M

value: refractory or relapsed AML (R-AML)

value: pembrolizumab and decitabine

tag: library type


title: Has2+/- KO mice 24 after chronic OVA stimulation 2


title: H6

tag: time on diet


title: PDAML1-Rel-MissionProtein

value: Responder

value: Time of relapse

value: MissionBio cell surface protein


title: WGBS of a2i-8-p58

tag: strain


title: PDAML1-Rel-DNA

tag: cell type

value: MissionBio single-cell DNA


title: Has2+/- KO mice 24 after chronic OVA stimulation 1


title: WGBS of TSa2i-14-p13


title: PDAML1-Rel-ADT

description:
PDAML1_Rel_barcodes.tsv.gz
PDAML1_Rel_features.tsv.gz
PDAML1_Rel_matrix.mtx.gz


title: H1

value: Hartley

value: liver

value: High Fat


title: WGBS of a2i-8-p9

value: wild-type


title: WT mice 24 after chronic OVA stimulation 5

value: WT


title: H61

value: NASH

value: 32 weeks


title: H18


title: PDAML1-Rel-GEX

value: 10x 3' gene expression


title: WGBS of TSa2i-c57-p13


title: WT mice 24 after chronic OVA stimulation 4

value: Balb/c

value: treated with intranasal ovalbumin for 8 weeks

value: lung


title: L5

value: Low Fat

value: Healthy


title: PDAML1-D0-ADT

description:
PDAML1_D0_barcodes.tsv.gz
PDAML1_D0_features.tsv.gz
PDAML1_D0_matrix.mtx.gz

value: Bone marrow mononuclear cells

value: M

value: refractory or relapsed AML (R-AML)

value: Responder

value: pembrolizumab and decitabine

value: Day 0

value: 10x 3' cell surface antibody


title: mEC_batch2_10X

source_name: mouse embryonic cells

value: Body, Head, Limb

tag: development stage


title: WT mice 24 after chronic OVA stimulation 3

value: WT


title: L46

value: Hartley

value: liver


title: WT mice 24 after chronic OVA stimulation 2


title: L79

value: 32 weeks


title: PDAML1-D0-GEX

source_name: Bone marrow mononuclear cells

value: 10x 3' gene expression


title: H9

value: High Fat

value: NASH


title: NK92_HSF1_input

city: New York

first: Kathryn

middle: Grace

last: Hockemeyer

state: New York

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

data_processing:
Reads were aligned to the Mus musculus genome (mm10/GRCm38) using the Bowtie2 aligner (Langmead et al., 2009) (v2.3.4.1).
Duplicate reads were removed using sambamba markdup.
Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm (v1.4.2) with q < 0.05.
Peak annotation was performed using ChipSeeker (Yu et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Bed files of genomic regions of HSF1 peaks and summits
Supplementary_files_format_and_content: Annotated peak files of genomic regions of HSF1 peaks and summits

source_name: NK-92 MI cells

growth_protocol: NK-92 MI were maintained in αMEM without ribonucleosides and deoxyribonucleosides (Gibco) but containing 1.5 g/L sodium bicarbonate, 12.5% (v/v) horse serum (Gibco), 12.5% (v/v) FBS, 1% (v/v) GlutaMAX (Gibco), 0.2 mM inositol (Sigma), 0.1 mM β-mercaptoethanol (Gibco), and 0.02 mM folic acid (Sigma).

extract_protocol:
Cells were washed in 1XPBS and fixed with 1% formaldehyde for 10 min at room temperature. Subsequent steps until elution used 1x protease inhibitor. Nuclei were isolated on ice using nuclei isolation buffer for 5 minutes, with additional 5 min incubation with NP-40 0.3%. The cell pellet was lysed on ice using nuclei lysis buffer. Samples were sonicated using Covaris sonication. Clarified samples were transferred to Eppendorf tubes and diluted 1:10 with IP dilution buffer. Samples were precleared with 25 µl Protein A by rotation at 4°C for 1h. Supernatants were transferred to fresh tubes, and antibody was added and incubated overnight at 4°C. The next day, 25 µl of Protein A Dynabeads were added and samples were rotated at 4°C for 3 hours. After bead captures, beads were washed twice sequentially in each of. The following buffers: low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE. Samples were eluted and treated with RNase at 37°C for 30 minutes. Crosslinks were reversed overnight with the addition of proteinase K 0.5 mg/ml and 0.5% SDS. DNA was isolated using phenol/chloroform extraction followed by precipitation with ethanol and glycogen.
Libraries were prepared using the Swift biosciences DNA low-input library kit

tag: antibody


title: Has2+/- KO mice 24 after chronic OVA stimulation 4

value: Balb/c

value: Has2+/- KO

value: treated with intranasal ovalbumin for 8 weeks

value: lung


title: NK92_HSF1_IP


title: WT mice 24 after chronic OVA stimulation 1


title: L27

value: Low Fat

value: Healthy


title: L92


title: Somitoid Day 5

city: Boston

first: Christoph

last: Budjan

state: MA

address: 450 Brookline Ave

department: Data Sciences

institute: Dana-Farber Cancer Institute

description: Single-cell RNA-seq (10x)

data_processing:
Raw reads were demultiplexed, filtered and mapped to the human reference genome (GRCh38) using Cell Ranger 4.0.0 with default settings. The filtered feature-barcode matrices generated by Cell Ranger were used for further analysis.
For the initial QC, we determined the following thresholds for filtering out low-quality cells: UMI counts less than 500, gene counts less than 200, mitochondrial fraction above 0.2 and a complexity score of less than 0.8 (calculated as log10(genes)/log10(UMIs)).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with filtered UMI counts, containing only detected cell-associated barcodes (number of UMIs associated with a feature (row) and a barcode (column)); TSV files contain gene (feature) and cell (barcode) annotations, respectively.

source_name: NCRM1 human IPSC

extract_protocol:
Cell dissociation protocols were optimized to achieve single cell suspensions with >90% viable cells and low number of doublets. Organoids collected at day 1, 2, 3, and 5 of our differentiation protocol were pooled in pre-warmed PBS, transferred to pre-warmed accutase and incubated for 5-7 min at 37°C. For Day 1 organoid cell suspension, 30 organoids were pooled. For Day 2 organoid cell suspension, 15 organoids were pooled. For Day 3 cell suspension, 8 organoids were pooled. For Day 5 cell suspension, 5 organoids were pooled. Organoids were briefly rinsed in PBS, then transferred to 500 µl PBS/0.05% BSA and carefully triturated to generate a single-cell suspension. Cell suspension was run through a cell strainer (Falcon, cat. no. 352235) and transferred to a 1.5 ml tube. Cells were spun down at 250g for 3 min at 4°C. Cell pellet was resuspended in 25 µl PBS/0.05% BSA, cell concentration and viability was measured using an automated cell counter, and cell suspension was further diluted as appropriate to reach the optimal range for 10x (700-1200 cells per µl).
Cells were subjected to single-cell RNA sequencing (10x Genomics, Chromium Single Cell 3’ v3) aiming for the following target cell numbers: Day 1, 3,000 cells; Day 2, 4,000 cells; Day 3, 5,000 cells; Day 5, 6,000 cells. Estimated actual cell numbers collected were: Day 1, 2,930 cells; Day 2, 4,977; Day 3, 5,968 cells; Day 5, 4,841 cells. Single-cell libraries were generated using standard protocols. Libraries were sequenced together on a NovaSeq 6000 system resulting in 800 million reads.

value: Human iPSC in vitro cultures

tag: developmental stage

value: Day 5

value: wild type


title: Has2+/- KO mice saline control 2

tag: genotype

value: treated with intranasal saline for 8 weeks


title: 19N

city: Wuhu

first: xiao

middle: long

last: zhu

state: Anhui

address: 2 Zheshan western road

institute: Yijishan Hospital

description: Gene expression data from adjacent non-tumor tissues

hyb_protocol: Following fragmentation, aRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: adjacent non-tumor tissues

label_protocol: Biotinylated aRNA were prepared according to the GeneChip 3’IVT Express Kit protocol.

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

tag: tissue

value: brain


title: Somitoid Day 3

description: Single-cell RNA-seq (10x)

value: Day 3