title: ATAC-Seq PHD-fl/fl_CD4cre Acetate Rep2

data_processing:
FastQC (v0.11.5) was used to assess the quality control of raw reads (Andrews, S., 2010). Alignment and mapping to generate BAM files were performed with BWA (v.0.7.16a) (Li et al., 2009). The mouse reference genome used for mapping was GRCm38 release 102 downloaded from GENCODE (https://www.gencodegenes.org/).
The Picard tool (v2.10.9) (Adams et al., 2000) was used to validate BAM files. Genrich (https://github.com/jsh58/Genrich) was used for peak calling with parameters “-r -m 30 -j -a 200 -g 15 -l 15 -d 50” to remove PCR duplicates and include only reads with mapping quality of at least 30. This approach also achieved a minimum AUC for a peak of 200 bp, a maximum distance between significant sites of 15 bp, a minimum length of a peak of 15 bp, and cut sites to 50 bp.
Differentially accessible regions were detected using DiffBind (3.6.1) (Stark and Brown, 2022) in R (4.2.0). Briefly, peaks from all samples have been overlapped and merged resulting into 132759 unique regions. Then, a blacklist region obtained from the ENCODE (Amemiya, Kundaje and Boyle, 2019) project was applied to filter out problematic regions resulting into 116364 peaks that were identified in at least two samples and constituted the peakset. Then, the number of mapped reads was calculated for each peak included in the peakset and background normalization was performed. Finally, differential analysis was performed using DESeq2 resulting into 39647 significant regions with differentially opened chromatin between the PDHfl/fl and PDHfl/fl CD4 Cre+ untreated conditions using an adjusted p-value of 0.05.
ATAC-seq tracks were generated using the bamCoverage command from deepTools (3.5.1) (Ramírez et al., 2016) with the –scaleFactor setting enabled and being equaled to the normalization factors as calculated by DESeq2 for each sample.
Assembly: Genecode v.M27
Supplementary files format and content: CSV reporting normalized abundance measurements pf the DBS from DESeq
Supplementary files format and content: Bigwig files reporting the ATAC-seq tracks normalised with scale factors.

extract_protocol:
ATAC-seq was performed using OMNI-ATAC supplementary protocol 1 as described (Corces et al., 2017) with some modifications. Viable cells (1x105) were resuspended in 50 μL cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin, and lysed for 3 min on ice. Lysates were washed with 1 mL cold ATAC-RSB containing 0.1% Tween-20 but no NP40 or digitonin. Samples were centrifuged for 10 min at 500×g at 4°C, the supernatants removed, and the pellets resuspended in 50 μL transposition mix (Tagment DNA buffer from Illumina, #15027866) containing 2.5 μL Tagment DNA TDE1 Enzyme (Illumina #15027865). After 45 min incubation at 37°C and 1000 rpm in an Eppendorf ThermoMixer, chromatin fragments were isolated using the Zymo Research DNA Clean & Concentrator kit (ZymoResearch ZY-D4013).
For pre-amplification of transposed fragments, 5 PCR cycles were run using primers Ad1 and Ad2.x (Buenrostro et al., 2015). The remaining cycles of library amplification were determined by qPCR (Adams et al., 2000). Another clean-up was performed using the Zymo Research DNA Clean & Concentrator kit (21 µL elution volume) followed by size selection using AMPure XP beads (Beckman Coulter #A63880), with samples adjusted to 100 µL plus 55 µL of beads to remove large fragments. Samples were incubated for 5 min before bead separation using a magnetic stand and transfer of the supernatant to a new tube. Another 225 µL of beads were added followed by incubation for 10 min and separation on a magnetic stand. After washing with 80% ethanol, beads were resuspended in 20 μL elution buffer and incubated for 5 min. After separation on a magnetic stand, the eluate was transferred to a new tube

value: 10 mM Acetate


title: PVN_HT+EA3 [circRNA]

status: Public on Mar 02 2023

type: SRA

city: Shanghai

first: Wei

last: Hu

address: Dongan Road 130

country: China

institute: Fudan university

library_source: transcriptomic

data_processing:
The insert size of the library was examined using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and only effective concentrations >2 nM were used for sequencing.
The raw reads were filtered to obtain the clean reads after removing adapter-related reads, reads containing uncertain bases, and low-quality reads with base quality phred score ≤ 20.
The clean reads were then mapped to the human reference genome (GRCh38/HG38) using HISAT2 algorithms and were quantitatively analyzed using the featureCounts software.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Total RNA was extracted from tissue samples of the PVN and CEA, and the preparation of the cDNA library and the sequencing were performed by Novo Gene Biotech Co. Ltd. (Beijing, China).
A strand-specific library strategy was used to construct the mRNA and circRNA libraries. Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA).

tag: tissue

value: Brain

tag: treatment

value: Hepatectomy + electroacupuncture


title: E14-MYT1L-KO-2

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

country: USA

institute: Washington University of St. Louis

library_source: genomic

data_processing:
Adapator trimming using Trimmomatic
Reads were filtered by samtools and Picard
Reads alignment using Bowtie2 to mm10
Peak calling using MASC2 with q<0.05
Assembly: mm10
Supplementary files format and content: bam file
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

source_name: E14 CTX

extract_protocol:
Nuclei was extracted by Sigma Nuclei EZ Prep kit from mouse brain tissues
CUT&RUN libraries were generated using Roche KAPA HyperPrep Kits

tag: cell line

value: E14 CTX

tag: chip antibody

value: MYT1L (Millipore, ABE2915)


title: E14-IgG-WT-3

value: Rb IgG (Jackson Immuno 011-000-002)


title: s1056

city: New York

first: Aya

last: Osman

state: NY

address: 109 east 102nd street, apartment 3c

department: Neurology

institute: Icahn School of Medicine Mount Sinai

data_processing:
raw sequened data (.bcl filed) generated by illumina were converted to fastq files. One mismatch was allowed for index sequence identification.
raw RNA seq reads for each sample were aligned and read counts generated using BioJupies software package.
non specific filtering required more than 1 million counts per milliom in at least 3 samples
filtered raw counts were then subjected to voom normalisation
voom normalized data were inspected for outlying samples using unsupervised clustering of samples
Assembly: BioJupies
Supplementary files format and content: tab-delimited text files include VOOM normalized values for each Sample

source_name: mPFC

extract_protocol:
Total RNA was isolated from mPFC punches using Rneasy mini kits from Qiagen (74106)
The RNA seq library was generated using NEBNext Ultra II Directional RNAlibrary Prep Kit for Illumina (New England BioLABS, iPSWICH, MS, USA)
Sequencing library was validated on the Aligent TapeStation and quantified by using Qubit 2.0 Flurometer as well as quantitative PCR. Libraries were subsequently multiplexed and sequenced on Illumina HiSeq 4000 using a 2x150bp paired-end configuration.

value: mPFC

tag: cell type

value: Bulk tissue

tag: genotype

value: WT

value: acetate

tag: Sex

value: m

tag: rin value


title: s1053


title: ATAC-Seq PHD-fl/fl_CD4cre Acetate Rep1

city: Esch-sur-Alzette

last: Longworth

state: Luxembourg

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: LIH

source_name: TH17 cells

growth_protocol: Naïve CD4+ T cells were isolated from PDHfl/fl and PDHfl/fl CD4 Cre+ mouse spleen and lymph nodes by magnetic bead sorting  using the Naïve CD4+ T cell isolation kit according to the manufacturer’s protocol. Sorting was performed using an autoMACS® pro-Separator . Sorted cells were seeded at 2x10e6 cells/mL in complete medium consisting of IMDM supplemented with 10% FBS , 55μM 2-mercaptoethanol and 1% penicillin/streptomycin , and incubated for 3 days in the presence of the appropriate Th subset-specific antibody and cytokine mix (5 μg/mL anti-CD3 (plate-bound), 1 μg/mL anti-CD28, 30 ng/mL IL-6, 5 μg/mL anti-IFNγ, 2 ng/mL TGFβ)

treatment_protocol: For acetate-treated cells, in vitro Th cell differentiation was performed in the presence of 10 mM sodium acetate diluted in culture medium

value: TH17 cells

value: PDH knockout


title: E14-MYT1L-KO-1


title: s384


title: E14-IgG-WT-2


title: ATAC-Seq PHD-fl/fl Acetate Rep2


title: ATAC-Seq PHD-fl/fl Acetate Rep1


title: E14-IgG-WT-1


title: s438


title: ATAC-Seq PHD-fl/fl Untreated Rep3

value: Untretated


title: Screen-Experiment3-CD44-high

city: Chicago

first: Adam

last: Williams

state: Ilinois

address: 240 East Huron

department: Department of Medicine, Allergy and Immunology

institute: Northwestern University

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 50X representation, CD44 high, replicate3
Exp3-Top-Sam6

data_processing:
The sgRNA library was obtained from Juong et al . 2017 https://doi.org/10.1038/nature23451
Sequencing was performed on Illumina platform generating paired end reads of 80 bps.
Fragments were trimmed using trim galore software (https://github.com/FelixKrueger/TrimGalore) and reads with quality <20 were filtered out.
Guide counts were calculated using count_spacers.py script from Juong et al. 2017 https://doi.org/10.1038/nprot.2017.016 The significant genes from the screen were identified with MAGeCK software. Any gRNAs targeting more than one lncRNA were excluded from analysis.
Supplementary files format and content: XLSX file containing counts.
Library strategy: Genowide CRISPR-activation screen

organism: Homo sapiens

growth_protocol: Mycoplasma tested HBEC3–KT were cultured at 37°C in a humidified atmosphere with 5 % CO2 in culture ware pre-coated with 0.1 % pig skin gelatin (Sigma Aldrich, Cat# G1890). Briefly, when cultures were about 70-80% confluent, spent medium was removed and discarded. Dulbecco’s Phosphate Buffered Saline, was used to rinse off dead cells. One mL of Trypsin-EDTA Primary Cells (ATCC) / 25 cm2 was added and incubated at 37°C for 4-6 min (until 90% of the cells have detached). 2% FBS in DPBS at 1 mL / 25 cm2 was added to neutralize the trypsin. Cell suspensions were centrifuged at 1000rpm for 5 min at room temperature. 4.0 x 103 to 6.0 x 103 viable cells/cm2 were suspended in Airway Epithelial Cell Basal Medium (ATCC) supplemented with Bronchial Epithelial Cell Growth Kit (ATCC) and seeded to new culture ware pre-coated with 0.1 % pig skin gelatin.

extract_protocol:
CRISPRa-sgRNA containing cells were harvested and processed for CD44+ sorting. Note, for cell sorting using BD FACSAria II sorter, 120-micron tip was used to let free flow of large mesenchymal-like cells.  We sorted ~50X representation of the library from CD44-low (bottom 10% of the peak) and CD44-high (top 10% of the peak) cells.
Genomic DNA were harvested from CD44 sorted populations using the Quick-DNA plus (Zymo Research) according to the manufacturer’s protocol. To determine distribution of the sgRNA, the spectrophotometer quantified gDNA product was sequenced using primers (listed in Supplementary file 1 of this paper) in Illumina MiSeq (80 cycles of read 1 (forward) and 8 cycles of index 1 with a 5% PhiX control to improve library diversity in order to cover >50 reads per sgRNA in the library).

treatment_protocol: Mycoplasma tested HBEC3–KT were seeded (50,000 cells/cm2) suspended in complete Airway Epithelial Cell Basal Medium supplemented  with 10ng/ml of TGFβ1 (R&D) or PBS. Cells were harvested 72hrs after seeding for various experimentations.

value: bronchial immortalized epithelial cell


title: Screen-Experiment2-CD44-low

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 50X representation, CD44 low, replicate2
Exp2-Bot-Sam3


title: Screen-Experiment2-CD44-high

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 50X representation, CD44 high, replicate2
Exp2-Top-Sam4


title: Screen-Experiment1-CD44-high

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 50X representation, CD44 high, replicate1
Exp1-Top-Sam2


title: Screen-Experiment3-CD44-low

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 50X representation, CD44 low, replicate3
Exp3-Bot-Sam5


title: E14-MYT1L-WT-3


title: s408

value: KO

value: control

value: f


title: ATAC-Seq PHD-fl/fl Untreated Rep1


title: s1077


title: KO-VP-rep3

city: wuhan

first: jianhong

last: zhao

address: 115 Donghu Road, Wuhan, Hubei, China

institute: wuhan university

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer(2×150bp read length)
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
The clean reads were separately aligned to reference genome with orientation modeusing HISAT2 software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: CRC tumor tissue

extract_protocol:
Colons were flushed with PBS to clear feces and slit open longitudinally. Tumors were homogenized in 1 ml of TRIzol (Invitrogen). Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Life Technology) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: CRC tumor tissue


title: E14-MYT1L-WT-1


title: E14-MYT1L-WT-2


title: KO-VP-rep1


title: ATAC-Seq PHD-fl/fl Untreated Rep2


title: ATAC-Seq PHD-fl/fl_CD4cre Untreated Rep1


title: s1209


title: ATAC-Seq PHD-fl/fl_CD4cre Untreated Rep3


title: immune cells, no tumor, scRNAseq [S0096_Praj_HGG]

first: Yang

address: 1305 York Avenue Y-1322

institute: Weill Cornell Medicine

description:
metadata.xlsx
S0096_Praj_HGG
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cells (n= 14,125) were identified as HGG (n=4468), LGG (n=5844), and no tumor (NT) (n=3813). Seurat v.4 and ShinyCell packages were utilized to evaluate gene expression analysis in R
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain’s right hemisphere

extract_protocol:
Tumor or similar-sized normal tissue was excised from the brain’s right hemisphere, where the cells had been injected. The tissue was minced, triturated, and digested with 20 U of Papain for 20 minutes at 37°C. After digested tissue was triturated and passed through a 70 µm cell strainer, CD45+ cells were isolated with a Miltenyi positive selection kit, according to the manufacturer’s instructions.
Cells were run on a Chromium controller (10x Genomics). Sequencing results were mapped to the mm10 mouse genome reference build and quantified using the CellRanger v3.0.2 (10xGenomics).

value: brain’s right hemisphere

value: immune cells

tag: age

value: 6-8 weeks old


title: ATAC-Seq PHD-fl/fl_CD4cre Untreated Rep2


title: s1066


title: Screen-library-100X-1

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 100X library representation, replicate 1
100x-lib1-Sam7


title: WT-Trp53fl/fl-rep3


title: KO-VP-rep2


title: Screen-library-100X-2

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 100X library representation, replicate 2
100x-lib2-Sam8


title: WT-Trp53fl/fl-rep2


title: s1180


title: s1076


title: s1078


title: Screen-Experiment1-CD44-low

description:
HBEC3KT cells, transduced with dCAS9-VP64, P65, and entire SAM library of sgRNAs, 50X representation, CD44 low, replicate1
Exp1-Bot-Sam1


title: immune cells, Low grade gliomas, scRNAseq [S0088_Praj_LGG]

description:
metadata.xlsx
S0088_Praj_LGG
10x Genomics

value: 3-4 weeks old


title: WT-Trp53fl/fl-rep1


title: immune cells, no tumor, scRNAseq [S0087_Praj_nl]

description:
metadata.xlsx
S0087_Praj_nl
10x Genomics

value: 0-2 weeks old


title: s1069

value: mPFC

value: Bulk tissue


title: s347

value: WT


title: s1177

value: m


title: Ms_M_NS_GFPpos

city: Boston

first: Allan

middle: M

last: Goldstein

state: MA

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

data_processing:
Sequencing performed using Illumina NextSeq or NovaSeq platforms
Genome alignment and counts matrices generated using 10X Genomics Cell Ranger pipeline

source_name: 2 M mice pooled, age 12 weeks

extract_protocol:
Single cells (scRNAseq) or single nuclei (multiomic)
10X Genomics Cell Ranger pipeline

value: 3D culture

value: Plp1-positive glia from 3D culture

value: C57BL/6 Plp1::GFP

value: 12 weeks


title: FDGplus_rep3

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
Samples were processed starting from stranded, single ended 75bp-long sequencing reads
The overall quality of sequencing reads was evaluated using a variety of tools, namely FastQC, RSeQC, AfterQC and Qualimap. Sequence alignments to the reference mouse genome (GRCm38) was performed using STAR (v.2.5.2a). Gene-expression was quantified at gene level by using the comprehensive annotations made available by Gencode. Specifically, we used v20 release of the Gene Transfer File (GTF).
Raw counts were further processed in the R Statistical environment and downstream differential expression analysis was performed using the DESeq2 pipeline.  Genes characterized by zero expression were removed and genes with low mean normalized counts were filtered out by the Independent Filtering feature embedded in DESeq243 (alpha = 0.05).
two different runs were performed and to remove the batch effect, removeBatchEffect of limma package was used
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: Matrix table with  gene counts after removebatcheffect function

molecule: polyA RNA

source_name: MDSCs

growth_protocol: GR1+ CD11B + CD45+ cells were sorted from Pten pc-/- prostate cancer mouse model and divided  based on C12FDG staining.

extract_protocol:
RNA was then extracted using TRIzol RNA isolation reagent (Invitrogel, Cat n=15596026) and RNase-Free DNase set (Qiagen, Cat n=79254) treatment was performed following manufacturers’ guidelines.
RNA integrity was checked with Agilent 2100 Bioanalyzer system. Protocol used was NEBNext poly(A) mRNA magnetic isolation module (“NEB #E7490”). Sequencing of the libraries was performed using the NextSeq 500 with the NextSeq 500/550 High Output Kit v2 (75 cycles; Illumina).

value: in vivo sorted MDSCs

value: Pten pc -/-

tag: antibody


title: FDGplus_rep2


title: FDGneg_rep2


title: 11-4891-Tm_S150

city: Washington

first: Chunling

last: Yi

state: DC

address: 3700 O St NW

department: Oncology

institute: Georgetown University

data_processing:
Read trimming: Bbduk from bbmap suite
Read Alignment/Mappng: STAR Aligner
Read Counting: HTSeq-Count
Assembly: mm10
Supplementary files format and content: Text File; Output from HTSeq-Count for each individual File

source_name: Murine Primary PDAC Cells

extract_protocol:
RNAeasy Mini kit from Qiagen
Lexogen QuantSeq 3' Fwd

tag: tissues

value: Pancreas

tag: mouse number

value: Murine Primary PDAC Cells

value: KPYYF


title: 13-4938-Tm_S151


title: Ms_F_NS_GFPpos

source_name: 2 F mice pooled, age 12 weeks


title: 7-4449-Tm_S146


title: FDGneg_rep2_old


title: NS ATAC

source_name: 3 M mice pooled, age 12 weeks


title: 5-4515-GFP_S144

value: KPF


title: 6-4601-GFP_S145


title: glia3 ATAC

source_name: 3 M mice pooled, P16-18

value: Small intestine

value: Plp1-positive myenteric plexus glia


title: FDGplus_rep2_old


title: NS RNA


title: FDGneg_rep1_old


title: FDGneg_rep1


title: HCT116_L2HG

type: RNA

city: Suita

first: Sho

last: Tabata

state: Osaka

address: 3-2 Yamadaoka

department: Institute for Protein Research,ces

country: Japan

institute: Osaka University

description:
Gene expression in HCT116 cells treated with OC-L2HG for 24 h
AR1833_03_HCT116_L2HG

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  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 SureScan Microarray Scanner (G2600D)  using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1（11.5.1.1）（10.10.1.1） (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor.

source_name: cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: HCT116 and HT29 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer's protocol, including on-column DNase I incubation for 15 min at room temperature to reduce genomic DNA contamination. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HCT116 and HT29 cells were treated with 500 μM OC-D2HG or 500 μM OC-L2HG for 24 h.

tag: source gender

value: male

tag: source age


title: 4-4504s-GFP_S143


title: HT29_L2HG

description:
Gene expression in HT29 cells treated with OC-L2HG for 24 h
AR1833_06_HT29_L2HG

value: Female


title: HCT116_D2HG

description:
Gene expression in HCT116 cells treated with OC-D2HG for 24 h
AR1833_02_HCT116_D2HG


title: HT29_D2HG

description:
Gene expression in HT29 cells treated with OC-D2HG for 24 h
AR1833_05_HT29_D2HG


title: FDGplus_rep1_old


title: FDGplus_rep1


title: HCT116_DMSO

description:
Gene expression in HCT116 cells treated with vehicle for 24 h
AR1833_01_HCT116_DMSO

value: control


title: HT29_DMSO

description:
Gene expression in HT29 cells treated with vehicle for 24 h
AR1833_04_HT29_DMSO


title: 2-4435-GFP_S141


title: 3-4504h-GFP_S142


title: glia2 ATAC


title: WT3

source_name: Individual mouse P14


title: glia1 RNA


title: PBMC_ACLF7_HSA_rep1

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Single-stranded-cDNAs were hybridized for 17 hours at 45ºC on the GeneChip Human gene 2.1ST 24 - array plates, using the automated GeneTitan System, which includes the hybridization oven, the fluidic station and the scanner.

scan_protocol: Affymetrix array plate was hybridized, washed, stained and scanned using an Affymetrix Genetitan 4C device.

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

label: Biotin

source_name: PBMC, HSA

label_protocol: fragmentation and labelling of single-stranded-cDNA were prepared according to Affymetrix WT PLUS Reagent Kit user guide in an automated system (Beckman FX robot).

growth_protocol: PBMC were directly isolated form 20ml EDTA tubes of fresh blood

extract_protocol: RNA was isolated using TRIzol reagent. Briefly, chloroform was added to the samples and were centrifugated at 12.000 g for 15 min at 4ªC. Then, aquos layer, were RNA is found, was collected in a new tube and 0,5 ul of Rnase-free glycogen and 500 ml of isopropyl alcohol were added. Aftwr an over night incubation a -20ªC, samples were centrifhugated at 12.000g for 10 min at 4ªC and RNA pellet was washed with 1 ml of EtOH 70%. Finally, RNA was resuspended with 10 ul of DEPC H2O.

treatment_protocol: PBMC were seeded at a density of 1.0x10e6 cells/mL and incubated with HSA (15 mg/ml) for 24 h in the presence of CpG-DNA (4 µM) or vehicle for the last 4 hours.

tag: disease

value: Acute-on-chronic liver failure (ACLF)

value: HSA

value: PBMC


title: PBMC_ACLF7_CPG_rep1

source_name: PBMC, CPG

value: CPG


title: Trem2_mut_MDSCs_rep2

description: RiboZero RNA

data_processing:
Samples were processed starting from stranded, single ended 75bp-long sequencing reads
the overall quality of sequencing reads was evaluated using a variety of tools, namely FastQC, RSeQC, AfterQC and Qualimap. Sequence alignments to the reference mouse genome (GRCm38) was performed using STAR (v.2.5.2a). Gene-expression was quantified at gene level by using the comprehensive annotations made available by Gencode. Specifically, we used v20 release of the Gene Transfer File (GTF).
Raw counts were further processed in the R Statistical environment and downstream differential expression analysis was performed using the DESeq2 pipeline.  Genes characterized by zero expression were removed and genes with low mean normalized counts were filtered out by the Independent Filtering feature embedded in DESeq243 (alpha = 0.05).
Over-representation analysis was performed using egsea.ora function.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts

growth_protocol: Murine MDSCs were differentiated in vitro. Briefly, bone marrow precursors were flushed from the femurs of C57/BL6 or TREM2mut mice with RPMI 1640 medium. Six-week-old NRG males were challenged subcutaneously with TRAMP-C1 cells. After 4 weeks, mice were treated with BM-MDSCs differentiated in vitro from C57/BL6 or TREM2mut mice. Tumour-bearing mice were sacrificed after 6h upon BM-MDSCs injection.

extract_protocol:
RNA was then extracted using TRIzol RNA isolation reagent (Invitrogel, Cat n=15596026) and RNase-Free DNase set (Qiagen, Cat n=79254) treatment was performed following manufacturers’ guidelines.
RNA integrity was checked with Agilent 2100 Bioanalyzer system. Protocol used was NEBNext rRNA depletion KIT (Human\Mouse\Rat) (“NEB #E6310”). Sequencing of the libraries was performed using the NextSeq 500 with the NextSeq 500/550 High Output Kit v2 (75 cycles; Illumina).

treatment_protocol: Tumours were disaggregated and digested in collagenase D and DNAse for 45 minutes at 37°C to obtain single-cell suspension. After neutralization of unspecific binding with αCD16/CD32 (clone 93), single-cell suspensions were stained with specific mAb (primary antibodies directly conjugated). MDSCs were sorted using FACS Aria (BD) as CD45+, CD11B+, GR1+ cells . RNA isolation was performed using TRIzol (Qiagen)


title: glia1 ATAC

value: C57BL/6 Plp1::GFP


title: PBMC_ACLF7_HSA+CPG_rep1

source_name: PBMC, HSA+CPG

value: HSA+CPG


title: PBMC_ACLF6_CPG_rep1


title: WT2


title: 1-4269-GFP_S140


title: Abdominal aorta, CCN2SMC∆ + Saline [CSS54]

city: Atlanta

first: Qian

last: Xu

state: GA

address: 101 Woodruff Circle

institute: Emory University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Abdominal aorta

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 100-400ng of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Abdominal aorta

value: Male

value: Saline mini-osmotic pumps

tag: time

value: Day 7


title: PBMC_ACLF6_HSA+CPG_rep1


title: PBMC_ACLF7_Veh_rep1

source_name: PBMC, Veh

value: Veh


title: Trem2_mut_MDSCs_rep1

description: RiboZero RNA


title: Abdominal aorta, CCN2SMC∆ + Saline [CSS56]

tag: tissue


title: WT1


title: WT_MDSCs_rep2

description: RiboZero RNA

value: WT


title: Abdominal aorta, CCN2SMC∆ + Saline [CSS55]

tag: treatment


title: MDSC_SENE_ROMI_4

data_processing:
Samples were processed starting from stranded, single ended 75bp-long sequencing reads
the overall quality of sequencing reads was evaluated using a variety of tools, namely FastQC, RSeQC, AfterQC and Qualimap. Sequence alignments to the reference mouse genome (GRCm38) was performed using STAR (v.2.5.2a). Gene-expression was quantified at gene level by using the comprehensive annotations made available by Gencode. Specifically, we used v20 release of the Gene Transfer File (GTF).
Raw counts were further processed in the R Statistical environment and downstream differential expression analysis was performed using the DESeq2 pipeline.  Genes characterized by zero expression were removed and genes with low mean normalized counts were filtered out by the Independent Filtering feature embedded in DESeq243 (alpha = 0.05).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts

growth_protocol: Murine MDSCs were differentiated in vitro. Briefly, bone marrow precursors were flushed from the femurs of C57/BL6  mice with RPMI 1640 medium. The cell pellet was resuspended in RPMI 1640 containing 10% heat-inactivated FBS, and the cells were cultured in vitro in the presence of 40 ng/ml GM-CSF and 40 ng/ml IL-6. On day 4, the cells were washed and resuspended with TRAMP-C1 conditioned medium

treatment_protocol: Senescent-like BM-MDSCs were treated or not with Romidepsin (0,5μM for 6 h)

value: BM-derived MDSCs

value: Treated with Romidepsin


title: MDSC_SENE_ROMI_3


title: PBMC_ACLF6_HSA_rep1


title: PBMC_ACLF3_HSA+CPG_rep1


title: PBMC_ACLF6_Veh_rep1


title: WT_MDSCs_rep1

description: RiboZero RNA


title: Abdominal aorta, CCN2SMC∆ + Ang II [CSA03]

value: Angiotensin II mini-osmotic pumps


title: PBMC_ACLF3_HSA_rep1


title: MDSC_SENE_4

value: Untreated


title: PBMC_ACLF3_CPG_rep1


title: Abdominal aorta, CCN2SMC∆ + Ang II [CSA01]


title: Abdominal aorta, CCN2SMC∆ + Ang II [CSA02]


title: Abdominal aorta, CCN2fl/fl + Saline [CFS70]


title: MDSC_SENE_ROMI_2


title: MDSC_SENE_3


title: Abdominal aorta, CCN2fl/fl + Saline [CFS69]


title: MDSC_SENE_2


title: Abdominal aorta, CCN2fl/fl + Saline [CFS68]


title: MDSC_SENE_ROMI_1


title: Abdominal aorta, CCN2fl/fl + Ang II [CFA74]


title: MDSC_SENE_1


title: PBMC_AD5_HSA_rep1

value: acute descompensated cirrhosis (AD)


title: Abdominal aorta, CCN2fl/fl + Ang II [CFA71]


title: PBMC_ACLF3_Veh_rep1

value: Acute-on-chronic liver failure (ACLF)


title: PBMC_AD5_CPG_rep1


title: PBMC_AD5_HSA+CPG_rep1


title: PBMC_AD5_Veh_rep1


title: PBMC_AD4_HSA+CPG_rep1


title: ICSI single embryo t.12h replicate_a

city: Regensburg

first: Xin

last: Lu

address: Universitätsstraße 31

country: Germany

institute: University of Regensburg

description: ICSI single embryo t.12h replicate_a

hyb_protocol: Corning, Schiphol-Rijk, Netherlands) were prehybridized with 5xSSC + 0.1% SDS + 0.1% BSA at 42C and hybridized in an Arraybooster hybsta- tion (Implen, Munich) at 42C overnight. Washing steps following hybridization were at 50C twice in 1x SSC + 0.1% SDS for 10 min, twice in 0.5· SSC + 0.1% SDS for 10 min, and twice in 0.1x SSC for 30 min. Unspecific binding of labelled proteins was blocked with 1% blocking reagent for nucleic acid hybridization (Roche) followed by a staining procedure with anti-Dig-Cy5 and Streptavidin-Cy3 (each 16 mg/ml, Jackson Laboratories). Excess antibody/streptavidin was removed with 4xSSC + 0.2% Tween-20 and slides were scanned on a Genepix 4000A scanner (Axon Instruments, Union City). Experiments shown in Table 2 were performed using human cells hybridized to Human Genome OpArrays version 4. Protocol details are available upon request.

scan_protocol: Slides were scanned on GenePix 4000A scanner Axon Instruments, Union City). Numerical readout of fluorescence intensities (GPR file) was generated using GenePixPro 7 (Molecular Devices)

data_processing: background correction and normalization using limma package in R

label: biotin

source_name: single cell whole transcriptome amplification

label_protocol: Primary cDNA amplification products were labelled in the presence of 3% formamide, 2.4 mM CP2-BGL primer (TCA-GAATTCATGCCGCCCCCCCGGCCC), dNTPs (0.35 mM dATP and dGTP, 0.3 mM dTTP and dCTP) and 0.05 mM labelled nucleotides. Sample cDNA was labelled with digoxygenin-dUTP (Roche) and aminodigoxygenin-dCTP (PerkinElmer, Rodgau-Ju ̈ gesheim), reference cDNA with biotin-dUTP (Roche) and biotin-dCTP (Invitrogen).

growth_protocol: The Oocytes incubated in kalium simplex optimized medium under mineral oil in humidified 5% CO2 (v/v air) at 37°C, until required (Yoshida et al, 2007).

extract_protocol: It was based on isolation of the cellular mRNA by oligo-dT beads, cDNA synthesis using random octamer and oligo-dT primers, poly-dG tailing, and PCR amplification using a single primer under very stringent conditions adequate for CG-rich sequences. The solid-phase capturing of the mRNA enabled depleting the cDNA from free cDNA synthesis pri- mers and abundant dNTPs thus avoiding the subsequent amplification of tailed primers or inefficient tailing. Together with the introduction of random primers (resulting in a fragmentation of the cDNA to a size amplifiable by PCR) the protocol therefore allowed for optimal conditions of all enzymatic reactions such as high concentrations of dNTPs, primer and enzyme, all of which were individually shown to contribute to increased sensitivity. The highest increase of sensitivity (100-fold) over the original Brady procedure was achieved by the use of poly-G tailing instead of poly-A tailing and the subsequent use of a single poly-C-containing primer. Our methods were based on (Hartmann and Klein, 2006) and further improved to apply for extraction of total RNA from mouse single cells.

treatment_protocol: ICSI using sperm from 8 to 12 weeks old B6D2F1 males was essentially as previsously described (Suzuki et al., 2010).

tag: zygote generation time

tag: developmental stage

value: single cell embryo


title: ICSI single embryo t.10h replicate_b

description: ICSI single embryo t.10h replicate_b


title: TFIIA 3 hour auxin 2

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

description: PRO-seq

data_processing:
Reads were trimmed using cutadapt version 1.18 with options -e 0.10 --minimum-length 15.
Genome alignments using Bowtie version 1.2.2. Reads were aligned  to artificial genome consisting of tRNA and rRNA with option -m 1000 --best --strata. Non-aligned reads were captured using samtools version 1.9 and -f 4 and then aligned to dm3 with option -m 1. Non-aligned reads and multi-aligned reads were captured as before and aligned to hg19 (spike-in) with option -m 1.
Reads were collapsed by Unique Molecular Identifiers to account for PCR duplicates.
Using bedtools version 2.27.1, the bigBed files were transformed to strand-specific bedGraph files reporting only the polymerase associated positions on a single-nucleotide level. The counts were normalized by library size or spike-in count and the replicates were merged to bigWig files.
Assembly: dm3, hg19
Supplementary files format and content: bigWig files reporting polymerase position on a single-nucleotide level.
Library strategy: PRO-seq

organism: Drosophila melanogaster

source_name: TFIIA C-term AID

growth_protocol: S2 cells were maintained in Gibco's Schneider's medium with 10% heat-inactivated FBS. 10 million cells were used per replicate for PRO-seq experiment

extract_protocol:
Nuclei were extracted by permeabilization according to Mahat, DB. et al. Nature Protocols 2016.
Libraries were amplified with Illumina's TruSeq small RNA library kit. Libraries were sequences on an Illumina HiSeq 2500 instrument.

treatment_protocol: 500uM auxin was added for 3, 6, or 12 hours

tag: endogenously tagged aid gene

value: TFIIA

tag: replicate

value: 3 hour auxin

tag: cell type

value: Drosophila S2 cells


title: ICSI single embryo t.12h replicate_d

description: ICSI single embryo t.12h replicate_d


title: PBMC_AD4_HSA_rep1

value: HSA

value: PBMC


title: ICSI single embryo t.10h replicate_d

description: ICSI single embryo t.10h replicate_d


title: PBMC_AD4_Veh_rep1


title: ICSI single embryo t.12h replicate_c

description: ICSI single embryo t.12h replicate_c


title: ICSI single embryo t.10h replicate_a

description: ICSI single embryo t.10h replicate_a


title: PBMC_AD4_CPG_rep1

value: CPG


title: ICSI single embryo t.12h replicate_b

description: ICSI single embryo t.12h replicate_b


title: ICSI single embryo t.8h replicate_c

description: ICSI single embryo t.8h replicate_c


title: Abdominal aorta, CCN2fl/fl + Ang II [CFA72]

value: Abdominal aorta

tag: Sex

value: Male

tag: genotype


title: ICSI single embryo t.10h replicate_c

description: ICSI single embryo t.10h replicate_c

tag: strain


title: ICSI single embryo t.8h replicate_d

description: ICSI single embryo t.8h replicate_d


title: TFIIA 3 hour auxin 1

description:
PRO-seq
TFIIA_3hAuxin_ps.bw  TFIIA_3hAuxin_ns.bw


title: ICSI single embryo t.8h replicate_a

description: ICSI single embryo t.8h replicate_a


title: DREF 6 hour auxin 2

description: DREF

data_processing:
Library strategy: PRO-seq
Reads were trimmed using cutadapt version 1.18 with options -e 0.10 --minimum-length 15.
Genome alignments using Bowtie version 1.2.2. Reads were aligned  to artificial genome consisting of tRNA and rRNA with option -m 1000 --best --strata. Non-aligned reads were captured using samtools version 1.9 and -f 4 and then aligned to dm3 with option -m 1. Non-aligned reads and multi-aligned reads were captured as before and aligned to hg19 (spike-in) with option -m 1.
Reads were collapsed by Unique Molecular Identifiers to account for PCR duplicates.
Using bedtools version 2.27.1, the bigBed files were transformed to strand-specific bedGraph files reporting only the polymerase associated positions on a single-nucleotide level. The counts were normalized by library size or spike-in count (TFIIA) and the replicates were merged to bigWig files.
Genome_build: dm3, hg19
Supplementary_files_format_and_content: bigWig files reporting polymerase position on a single-nucleotide level.

source_name: DREF N-term AID

treatment_protocol: 500uM auxin was added for 6 hours

value: DREF

value: 6 hour auxin


title: DREF 6 hour auxin 1

description: DREF


title: DREF control 2

description: DREF

value: control


title: PBMC_AD3_HSA+CPG_rep1

value: HSA+CPG


title: ICSI single embryo t.6h replicate_d

description: ICSI single embryo t.6h replicate_d


title: UVA_1%FeTiO211nm.10 mg/L_rep3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: whole body

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts (40 organisms)

tag: stage of development

value: Adult organisms with well developed clitellum

tag: exposure

value: 10 mg/L 1%Fe-TiO2 11 nm + UVA radiation, in ISO reconstituted water, for 5 days


title: PBMC_AD3_HSA_rep1

value: acute descompensated cirrhosis (AD)


title: PBMC_AD3_CPG_rep1


title: UVA_1%FeTiO211nm.10 mg/L_rep1


title: TBP 6 hour auxin 2

description: TBP

source_name: TBP N-term AID

value: TBP


title: ICSI single embryo t.6h replicate_b

description: ICSI single embryo t.6h replicate_b

value: single cell embryo


title: UVA_1%FeTiO211nm.1 mg/L_rep3

value: 1 mg/L 1%Fe-TiO2 11 nm + UVA radiation, in ISO reconstituted water, for 5 days


title: WT_42_2 vs delta-bc1009_42_2

city: Wageningen

first: Jeroen

middle: Steven

last: Koomen

address: Bornse Weilanden 9

country: Netherlands

institute: Wageningen University

description: WT 42 degrees C vs delta-bc1009 42 degrees C, biological duplo, 2 of 2

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 150ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: 8 x 15K Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2505C, using the extended dynamic range scan mode and 10 micron scan resolution according to the Agilent protocol.

data_processing:
Images were analyzed and processed with the Agilent Feature Extraction software (version 10.7.3.1). The obtained extracted data files were analyzed using the limma software package [39] in R (R Core Team, 2014). For Agilent-based arrays, global loess normalization was used when the bulk of genes is not differentially expressed. The analysis was based on a 2-color experimental design using a linear modeling approach by lmfit and empirical Bayes statistics [41].
Log 2 of Lowess normalized ratio (wildtype vs mutants)(30 degrees C over 42 degrees C)
Lowess normalized ratio (wildtype vs mutants)(30 degrees C over 42 degrees C)

organism: Bacillus cereus ATCC 14579

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

growth_protocol: Cells are precultured in BHI at 30 degrees C, shaking at 160 rpm, untill an OD600nm reached between 0.4-0.5 before exposure

extract_protocol: RNA was extracted as described by van Schaik et al., 2004

treatment_protocol: The mid log cultures (OD600nm ~0.4-0.5) are exposed, remaining in the same media, for 20 minutes at 30 degrees C (reference temperature) or 20 minutes at 42 degrees C (heat shock)

tag: sample type

value: Bacillus cereus ATCC14579 WT grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 42 degrees C, shaken at 160 rpm

value: Bacillus cereus ATCC14579 delta-bc1009 grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 42 degrees C, shaken at 160 rpm


title: ICSI single embryo t.6h replicate_a

description: ICSI single embryo t.6h replicate_a


title: UVA_PureTiO227nm.10 mg/L_rep2

value: 10 mg/L Pure TiO2 27 nm + UVA radiation, in ISO reconstituted water, for 5 days


title: ICSI single embryo t.4h replicate_d

description: ICSI single embryo t.4h replicate_d


title: WT_30_1 vs delta-bc1009_30_1

description: WT 30 degrees C vs delta-bc1009 30 degrees C, biological duplo, 1 of 2

value: Bacillus cereus ATCC14579 WT grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 30 degrees C, shaken at 160 rpm

value: Bacillus cereus ATCC14579 delta-bc1009 grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 30 degrees C, shaken at 160 rpm


title: WT_42_1 vs delta-bc1009_42_1

description: WT 42 degrees C vs delta-bc1009 42 degrees C, biological duplo, 1 of 2


title: UVA_1%FeTiO211nm.10 mg/L_rep2


title: TBP 6 hour auxin 1

description: TBP

value: Drosophila S2 cells


title: UVA_1%FeTiO211nm.1 mg/L_rep2


title: WT_30_2 vs delta-bc1009_30_2

description: WT 30 degrees C vs delta-bc1009 30 degrees C, biological duplo, 2 of 2


title: ICSI single embryo t.4h replicate_b

description: ICSI single embryo t.4h replicate_b


title: ICSI single embryo t.4h replicate_c

description: ICSI single embryo t.4h replicate_c


title: UVA_1%FeTiO211nm.1 mg/L_rep1


title: delta-bc1009_30_2 vs delta-bc1009_42_2

description: delta-bc1009 30 degrees C vs delta-bc1009 42 degrees C, biological duplo, 2 of 2


title: UVA_PureTiO227nm.10 mg/L_rep3


title: UVA_PureTiO227nm.10 mg/L_rep1


title: ICSI single embryo t.4h replicate_a

description: ICSI single embryo t.4h replicate_a


title: PBMC_AD3_Veh_rep1

value: Veh

value: PBMC


title: DREF control 1

description: DREF

value: DREF

value: control


title: TFIIA 6 hour auxin 1

description: TFIIA

value: TFIIA

value: 6 hour auxin


title: TBP control 2

description: TBP


title: UVA_PureTiO212nm.10 mg/L_rep1

value: Whole body extracts (40 organisms)

value: Adult organisms with well developed clitellum

value: 10 mg/L Pure TiO2 12 nm + UVA radiation, in ISO reconstituted water, for 5 days


title: TFIIA control 1

description: TFIIA


title: WT_30_1 vs WT_42_1 #2

description: WT 30 degrees C vs WT 42 degrees C, biological duplo, 1 of 2


title: ICSI single embryo t.2h replicate_b

description: ICSI single embryo t.2h replicate_b

value: single cell embryo


title: UVA_PureTiO212nm.10 mg/L_rep3


title: UVA_PureTiO212nm.10 mg/L_rep2


title: WT_30_2 vs WT_42_2 #2

description: WT 30 degrees C vs WT 42 degrees C, biological duplo, 2 of 2


title: ICSI single embryo t.2h replicate_a

description: ICSI single embryo t.2h replicate_a


title: ICSI single embryo t.2h replicate_d

description: ICSI single embryo t.2h replicate_d


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and non-targeting sgRNA2, replicate 3

data_processing:
trim reads for quality with trim galore (-q 20)
quasi mapping with salmon (--numBootstraps 30)
DEG at gene level with R tximport and DESeq2 packages.
Assembly: hg38
Supplementary files format and content: XLS files include TPM values for each Sample

extract_protocol:
Total RNA was extracted using RLT buffer supplemented with Beta-mercaptoethanol according to the manufacturer’s instructions (Qiagen). Isolated RNA was quantified by spectrophotometry, and RNA concentrations were normalized.
1. PolyA-RNA-seq libraries were prepared with KAPA Stranded mRNA-Seq kit (Roche) according to manufacturer’s instruction. RNA samples were normalized to 300 ngs input in total 44ul and 6ul of 1:1000 dilution ERCC (mix 1) (Thermo Fisher) was spiked in to each sample. First, poly A RNA was isolated from total RNA using oligo-dT magnetic beads. Purified RNA was then fragmented at 85C for 6 mins, targeting fragments range 250-300bp. Fragmented RNA is reverse transcribed with an incubation of 25C for 10mins, 42C for 15mins and an inactivation step at 70C for 15mins. This was followed by second strand synthesis at 16C, 60mins. Double stranded cDNA fragments were purified using Ampure XP beads (Beckman). The dscDNA were then A-tailed, and ligated with illumina adaptors (IDT). Adaptor-ligated DNA was purified using Ampure XP beads. This is followed by 10 cycles of PCR amplification. The final library was cleaned up using AMpure XP beads. Quantification of libraries were performed using real-time qPCR (Thermo Fisher). Sequencing was performed on Illumina HiSeq4000 platform generating paired end reads of 75bp.

treatment_protocol:
Mycoplasma tested HBEC3–KT were seeded (50,000 cells/cm2) suspended in complete Airway Epithelial Cell Basal Medium supplemented either with 10ng/ml of TGFβ1 (R&D) or PBS. Cells were harvested 72hrs after seeding for various experimentations.
Polyethylene glycol-6000 precipitated viral particles were mixed with polybrene (8μg/ml) and transduced into Mycoplasma tested HBEC3–KT.

tag: cell line

value: bronchial immortalized epithelial cell

value: WT

value: Non-targetting sgRNA


title: WT_42_1 vs delta-sigB_42_1

description: WT 42 degrees C vs delta-sigB 42 degrees C, biological duplo, 1 of 2

value: Bacillus cereus ATCC14579 WT grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 42 degrees C, shaken at 160 rpm

value: Bacillus cereus ATCC14579 delta-sigB grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 42 degrees C, shaken at 160 rpm


title: delta-bc1009_30_1 vs delta-bc1009_42_1

description: delta-bc1009 30 degrees C vs delta-bc1009 42 degrees C, biological duplo, 1 of 2

value: Bacillus cereus ATCC14579 delta-bc1009 grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 30 degrees C, shaken at 160 rpm

value: Bacillus cereus ATCC14579 delta-bc1009 grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 42 degrees C, shaken at 160 rpm


title: WT_42_2 vs delta-sigB_42_2

description: WT 42 degrees C vs delta-sigB 42 degrees C, biological duplo, 2 of 2


title: UVA_PureTiO212nm.1 mg/L_rep2

value: 1 mg/L Pure TiO2 12 nm + UVA radiation, in ISO reconstituted water, for 5 days


title: UVA_PureTiO212nm.1 mg/L_rep1


title: WT_30_2 vs delta-sigB_30_2

description: WT 30 degrees C vs delta-sigB 30 degrees C, biological duplo, 2 of 2

value: Bacillus cereus ATCC14579 WT grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 30 degrees C, shaken at 160 rpm

value: Bacillus cereus ATCC14579 delta-sigB grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 30 degrees C, shaken at 160 rpm


title: mII oocyte t.0h replicate_a

description: mII oocyte t.0h replicate_a


title: mII oocyte t.0h replicate_c

description: mII oocyte t.0h replicate_c


title: UVA_PureTiO212nm.1 mg/L_rep3


title: mII oocyte t.0h replicate_d

description: mII oocyte t.0h replicate_d


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and non-targeting sgRNA2, replicate 2


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and non-targeting sgRNA2, replicate 1


title: delta-sigB_30_2 vs delta-sigB_42_2

description: delta-sigB 30 degrees C vs delta-sigB 42 degrees C, biological duplo, 2 of 2


title: Control UVA_rep3

value: UVA radiation, in ISO reconstituted water, for 5 days


title: HBEC3KT cells, TGFB1, 72hrs, replicate3


title: delta-sigB_30_1 vs delta-sigB_42_1

description: delta-sigB 30 degrees C vs delta-sigB 42 degrees C, biological duplo, 1 of 2


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-10

description: cRNA Oct4-10

hyb_protocol: Corning, Schiphol-Rijk, Netherlands) were prehybridized with 5xSSC + 0.1% SDS + 0.1% BSA at 42C and hybridized in an Arraybooster hybstation (Implen, Munich) at 42C overnight. Washing steps following hybridization were at 50C twice in 1· SSC + 0.1% SDS for 10 min, twice in 0.5x SSC + 0.1% SDS for 10 min, and twice in 0.1x SSC for 30 min. Unspecific binding of labelled proteins was blocked with 1% blocking reagent for nucleic acid hybridization (Roche) followed by a staining procedure with anti-Dig-Cy5 and Streptavidin-Cy3 (each 16 mg/ml, Jackson Laboratories). Excess antibody/streptavidin was removed with 4x SSC + 0.2% Tween-20 and slides were scanned on a Genepix 4000A scanner (Axon Instruments, Union City). Experiments shown in Table 2 were performed using human cells hybridized to Human Genome OpArrays version 4. Protocol details are available upon request.

value: 13h post ICSI single zygote

tag: injected

value: Oct4A cRNA


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-08

description: cRNA Oct4-08


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-11

description: cRNA Oct4-11


title: HBEC3KT cells, TGFB1, 72hrs, replicate2


title: HBEC3KT cells, PBS, 72hrs, replicate3

value: PBS


title: TFIIA control 2

description: TFIIA

value: TFIIA

value: control

value: Drosophila S2 cells


title: NoUV_2%FeTiO210nm.10 mg/L_rep3

value: Whole body extracts (40 organisms)

value: Adult organisms with well developed clitellum

value: 10 mg/L 2%Fe-TiO2 10 nm , in ISO reconstituted water


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-09

description: cRNA Oct4-09


title: WT_30_1 vs delta-sigB_30_1

description: WT 30 degrees C vs delta-sigB 30 degrees C, biological duplo, 1 of 2


title: NoUV_2%FeTiO210nm.10 mg/L_rep2


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-06

description: cRNA Oct4-06


title: Control UVA_rep2


title: TRF2+TBP control 2

description: PRO-seq

source_name: TRF2+TBP N-term AID


title: WT_30_1 vs WT_42_1 #1

value: Bacillus cereus ATCC14579 WT grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 42 degrees C, shaken at 160 rpm


title: Control UVA_rep1


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-04

description: cRNA Oct4-04


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-07

description: cRNA Oct4-07


title: HBEC3KT cells, TGFB1, 72hrs, replicate1

value: bronchial immortalized epithelial cell

value: WT


title: H9 hESCs treated with siESRG

city: Wenzhou

first: dandan

last: Fan

address: 270 Xueyuan West Road

institute: Wenzhou Medical University

description: Human HT expression beadchip

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Average normalisation

source_name: human embryonic stem cells

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

growth_protocol: siRNAs delivery into H9 hESCs for transient knockdown. 2 hours before cell plating, the H9 hESCs maintained on Matrigel-coated plates were pretreated with 10 mM Y-27632, and then carefully dissociated into single-cell suspension using Accutase. About 2×105 single cells were plated into wells of a six-well plate (coated with Matrigel) and cultured in CM supplemented with 10 mM Y-27632. After 24 h, siRNA(siControl and siESRG) was transfected into H9 hESCs using Lipofectamine RNAiMAX. The transfection complexes of siRNA/Lipofectamine RNAiMAX were prepared according to the manufacturer’s protocol. After recovery in fresh cell culture medium, cells were often transfected again after 24 h. Total RNA was collected 48 h after post-transfection.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: H9 hESCs

value: siESRG


title: HBEC3KT cells, PBS, 72hrs, replicate2


title: TRF2+TBP 12 hour auxin 2

description: PRO-seq

value: 12 hour auxin


title: HBEC3KT cells, PBS, 72hrs, replicate1


title: NoUV_8%FeTiO25nm.10 mg/L_rep1

value: 10 mg/L 8%Fe-TiO2 5 nm , in ISO reconstituted water


title: WT_30_2 vs WT_42_2 #1

value: Bacillus cereus ATCC14579 WT grown in BHI at 30 degrees C up to OD600nm of 0.4-0.5 followed by 20 minutes of growth at 30 degrees C, shaken at 160 rpm


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and non-targeting sgRNA1, replicate 3

data_processing:
trim reads for quality with trim galore (-q 20)
quasi mapping with salmon (--numBootstraps 30)
DEG at gene level with R tximport and DESeq2.
Assembly: hg38
Supplementary files format and content: XLS files include TPM values for each Sample

extract_protocol:
Total RNA was extracted using RLT buffer supplemented with Beta-mercaptoethanol according to the manufacturer’s instructions (Qiagen). Isolated RNA was quantified by spectrophotometry, and RNA concentrations were normalized.
Ribo-depletion-RNA-seq libraries were prepared with KAPA RNA Hyperprep kit with Riboerase (Roche) according to manufacturer’s instruction. RNA samples were normalized to 300 ngs input in total 10ul and 0.6ul of 1:100 dilution ERCC (mix 1) (Thermo Fisher) was spiked in to each sample. First, ribosomal RNA were depleted using RiboErase. Purified RNA was then fragmented at 85°C for 6 mins, targeting fragments range 250-300bp. Fragmented RNA is reverse transcribed with an incubation of 25°C for 10mins, 42°C for 15mins and an inactivation step at 70C for 15mins. This was followed by second strand synthesis and A-tailing at 16C for 30mins and 62C for 10 min. A-tailed, double stranded cDNA fragments were ligated with illumina unique adaptors (Illumina). Adaptor-ligated DNA was purified using Ampure XP beads. This is followed by 10 cycles of PCR amplification. The final library was cleaned up using AMpure XP beads. Quantification of libraries were performed using real-time qPCR (Thermo Fisher). Sequencing was performed on Illumina NovaSeq platform on an S1 flowcell generating paired end reads of 150bp.

value: Non-targetting sgRNA


title: TRF2+TBP control 1

description:
PRO-seq
TRF2+TBP_control_ps.bw  TRF2+TBP_control_ns.bw


title: NoUV_8%FeTiO25nm.10 mg/L_rep2


title: NoUV_8%FeTiO25nm.10 mg/L_rep3


title: NoUV_2%FeTiO210nm.10 mg/L_rep1


title: 13h post ICSI single zygote injected Oct4A cRNA-replicate-01

description: cRNA Oct4-01

value: 13h post ICSI single zygote

value: Oct4A cRNA


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-12

description: cRNA mCh-12

value: control mcherry cRNA


title: NoUV_PureTiO210nm.100 mg/L_rep3

value: 100 mg/L Pure TiO2 10 nm , in ISO reconstituted water


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and non-targeting sgRNA1, replicate 1


title: TFIIA 6 hour auxin 2

description: TFIIA

value: TFIIA

value: 6 hour auxin

value: Drosophila S2 cells


title: TRF2+TBP 12 hour auxin 1

description:
PRO-seq
TRF2+TBP_12hAuxin_ps.bw  TRF2+TBP_12hAuxin_ns.bw


title: H9 hESCs treated with siControl

description: Human HT expression beadchip

value: siControl


title: NoUV_PureTiO210nm.100 mg/L_rep2

value: Whole body extracts (40 organisms)

value: Adult organisms with well developed clitellum


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and non-targeting sgRNA1, replicate 2

value: bronchial immortalized epithelial cell

value: WT


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and sgRNA targeting SCREEM3 promoter, replicate 3

value: SCREEM locus activated


title: NoUV_PureTiO210nm.100 mg/L_rep1


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-10

description: cRNA mCh-10


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-11

description: cRNA mCh-11


title: TRF2 control 2

description: PRO-seq

source_name: TRF2 N-term AID

value: control


title: TRF2 control 1

description:
PRO-seq
TRF2_control_ps.bw  TRF2_control_ns.bw


title: TRF2 6 hour auxin 2

description: PRO-seq


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and sgRNA targeting SCREEM3 promoter, replicate 2


title: TRF2 6 hour auxin 1

description:
PRO-seq
TRF2_6hAuxin_ps.bw  TRF2_6hAuxin_ns.bw


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and sgRNA targeting SCREEM3 promoter, replicate 1


title: Active colony zooids (biol rep 2)

city: Haifa

first: Julia

last: Panov

address: Aba Hushi Blvd 199  Mount Carmel

country: Israel

institute: Tauber Bioinformatics Research Center

data_processing:
Sequence reads were trimmed for adaptor sequence/ PCR sequence with Trimmomatic.
Trimmed sequence reads were mapped to B.leachii assembled genome using HiSat2.
Expression quantifications were performed using RSEM.
Functional annotation was done using ANISEED database.
Normalisation of expression and differential expression analysis done with DESeq2.
Assembly: https://www.aniseed.cnrs.fr/aniseed/download/?file=data/boleac/Boleac_SBv3_genome_gff3_fasta.zip&module=aniseed&action=download:index
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Botrylloides leachii

source_name: Zooids

growth_protocol: Colonies were individually tied onto 5 x 7.5 cm glass slides with fine cotton threads, then cultured in 25 L standing seawater tanks, following Rinkevich and Shapira (1998) and fed daily with a variety of food types (including freeze dried rotifers and commercial powdered plankton).

extract_protocol:
The RNeasy mini-Kit (QIAGEN) was used on fresh tissues as per manufacture instructions to isolate RNA.
RNA libraries for RNA-seq were prepared using RNA TruSeq Total RNA Library Prep Kit with Ribo-Zero Gold Sequencing (Epicenter) following manufacturer's protocols.

value: Zooids

tag: physiological state

value: Active colony


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-07

description: cRNA mCh-07


title: Active colony  zooids (biol rep 3)


title: Active colony zooids (biol rep 1)


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and sgRNA targeting SCREEM2 promoter, replicate 2


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and sgRNA targeting SCREEM2 promoter, replicate 3


title: NoUV_PureTiO210nm.10 mg/L_rep2

value: 10 mg/L Pure TiO2 10 nm , in ISO reconstituted water


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-04

description: cRNA mCh-04

value: 13h post ICSI single zygote


title: NoUV_PureTiO210nm.10 mg/L_rep1


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-02

description: cRNA mCh-02


title: 13h post ICSI single zygote injected Morpholino Oct4A-replicate-12

description: Morpholino oct4-12

value: Morpholino Oct4A


title: HBEC3KT cells, transduced with dCAS9-VP64, P65, and sgRNA targeting SCREEM2 promoter, replicate 1


title: Active colony ampulla (biol rep 3)

source_name: Ampullae cells

value: Ampullae cells


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-06

description: cRNA mCh-06

value: control mcherry cRNA


title: NoUV_10%FeTiO210nm.1000 mg/L_rep1

value: 1000 mg/L 10%Fe-TiO2 10 nm , in ISO reconstituted water


title: 13h post ICSI single zygote injected control mcherry cRNA-replicate-01

description: cRNA mCh-01


title: SNT8

city: Guangzhou

first: jinghong

last: Chen

address: Panyu

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: ChIP-seq samples: bigwig file for each sample
RNA-seq samples: TXT file contain counts for each sample

growth_protocol: HANK1 and SNT8 were cultured in Artemis medium-2 supplemented with 2% human plasma serum and 1% P/S. 100 IU/ml IL-2 was included into HANK1 growth media and 700 IU/ml IL-2 into SNT8, respectively. SNK6 and NK92 were maintained in RPMI1640 medium supplemented with 10% FBS, 10% horse serum, 1% P/S and 100 IU/ml IL-2. KHYG1 was grown in RPMI1640 medium supplemented with 10% FBS, 1% P/S and 100 IU/ml IL-2. MEC04 was cultured in RPMI1640 medium supplemented with 15% FBS, 1% P/S and 50 IU/ml IL-2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent (Invitrogen).
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240). RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: HANK1 was treated with DMSO, 0.25um tofacitinib or 0.125um ruxolitinib for 24h.

value: Natural Killer/T-cell lymphoma


title: NoUV_PureTiO210nm.10 mg/L_rep3


title: TBP control 1

description: TBP

value: TBP

value: Drosophila S2 cells


title: 13h post ICSI single zygote injected Morpholino Oct4A-replicate-09

description: Morpholino oct4-09


title: 13h post ICSI single zygote injected Morpholino Oct4A-replicate-07

description: Morpholino oct4-07


title: HANK1


title: NoUV_6%FeTiO25nm.10 mg/L_rep3

value: Whole body extracts (40 organisms)

value: 10 mg/L 6%Fe-TiO2 5 nm , in ISO reconstituted water


title: NoUV_10%FeTiO210nm.1000 mg/L_rep2

value: Adult organisms with well developed clitellum


title: Mid torpor colony zooids (biol rep 3)

value: Mid torpor colony


title: NK92


title: NoUV_10%FeTiO210nm.1000 mg/L_rep3


title: Mid torpor colony zooids (biol rep 2)


title: NoUV_6%FeTiO25nm.10 mg/L_rep2


title: 13h post ICSI single zygote injected Morpholino Oct4A-replicate-05

description: Morpholino oct4-05


title: 13h post ICSI single zygote injected Morpholino Oct4A-replicate-08

description: Morpholino oct4-08


title: MEC04


title: Active colony ampulla (biol rep 1)


title: 13h post ICSI single zygote injected Morpholino Oct4A-replicate-02

description: Morpholino oct4-02


title: Mid torpor colony  ampulla (biol rep 3)


title: NoUV_6%FeTiO25nm.10 mg/L_rep1


title: Active colony ampulla (biol rep 2)


title: SNK6


title: NoUV_PureTiO227nm.10 mg/L_rep3

value: 10 mg/L Pure TiO2 27 nm , in ISO reconstituted water


title: KHYG1


title: Mid torpor colony ampulla (biol rep 2)


title: Mid torpor colony ampulla (biol rep 1)


title: Mid torpor colony zooids (biol rep 1)


title: 13h post ICSI single zygote injected Morpholino Oct4A-replicate-04

description: Morpholino oct4-04


title: NoUV_PureTiO227nm.10 mg/L_rep2


title: NoUV_PureTiO212nm.10 mg/L_rep2

value: 10 mg/L Pure TiO2 12 nm , in ISO reconstituted water


title: liver_MCT_rep3

city: Nanjing

first: Lixin

last: Sun

address: 24 Tong Jia Xiang

institute: China Pharmaceutical University

description: Gene expression in colonic tissue of MCT group

hyb_protocol: Total RNA were transcribed to double strand cDNA, then synthesizedinto cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyzearray images to get raw data. Genespring (version 14.8, Agilent Technologies) were employedto finish the basic analysis with the raw data. To begin with, the raw data was normalizedwith the quantile algorithm. The probes that at least 1 conditions out of 2 conditions haveflags in “Detected” were chosen for further data analysis. Differentially expressed geneswere then identified through fold change as well as P value calculated with t-test. Thethreshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.Afterwards, GO analysis and KEGG analysis were applied to determine the roles of thesedifferentially expressed mRNAs. Finally, Hierarchical Clustering was performed to displaythe distinguishable genes' expression pattern among samples.

source_name: liver tissue, MCT, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integritywas assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Rats were fed adaptively for 7 days before the experiment and randomly divided into two groups (Control, MCT). Hepatic sinusoidal obstruction syndrome was induced 12h after monocrotaline treatment, and the Control group was given with normal saline.

value: liver

tag: gender

value: male

tag: age

value: 7-9 weeks

value: SD rats


title: 13h post ICSI single zygote injected Morpholino control-replicate-08

description: Morpholino cont-08

value: 13h post ICSI single zygote

value: Morpholino control


title: 13h post ICSI single zygote injected Morpholino control-replicate-06

description: Morpholino cont-06


title: NoUV_PureTiO212nm.10 mg/L_rep3

tag: tissue


title: liver_Control_rep3

description: Gene expression in colonic tissue of Control group

source_name: liver tissue, Control, replicate 3


title: NoUV_PureTiO227nm.10 mg/L_rep1


title: Fully torpor colony (biol rep 1)

value: Ampullae cells

value: Torpor colony


title: 13h post ICSI single zygote injected Morpholino control-replicate-04

description: Morpholino cont-04


title: NoUV_PureTiO212nm.1 mg/L_rep2

value: 1 mg/L Pure TiO2 12 nm , in ISO reconstituted water


title: NoUV_PureTiO212nm.10 mg/L_rep1


title: NoUV_PureTiO212nm.1 mg/L_rep1


title: liver_MCT_rep2

source_name: liver tissue, MCT, replicate 2


title: liver_Control_rep2

source_name: liver tissue, Control, replicate 2


title: Fully torpor colony (biol rep 2)


title: 13h post ICSI single zygote injected Morpholino control-replicate-02

description: Morpholino cont-02


title: Human PBMC  42

status: Public on Mar 01 2023

first: Anthony

last: Reder

state: IL

address: 5841 S Maryland Ave

institute: University of Chicago Medicine

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)

data_processing: Raw CEL files from arrays were imported, log2-transformed,  and normalized; gene expression was analyzed as described  previously (Feng et al, 2019a). Transcriptome Analysis  Console (TAC) version 4.02 (ThermoFisher) identified differentially expressed genes (DEGs).

source_name: MS Patient

growth_protocol: PBMC were isolated by density gradient centrifugation (Lympholyte, Cedarlane Laboratories, Burlington, NC) within 1–4 h of phlebotomy. Cell lysates were stored at -80!C  in ‘‘buffer RLT plus’’ (Qiagen) for <12 months.

extract_protocol: Total RNA was purified using RNeasy (Qiagen).

treatment_protocol: Six were treated with IFN-b-1a (IM weekly) for ‡7 months, and 10 with  PEG-IFN-b-1a (SQ biweekly) for 1 and 7 months.

value: F

tag: induction time (hours)

tag: ifn-type

value: Plegridy

tag: ms-type

value: RRMS

tag: ms-state

value: stable

tag: therapy duration

value: 7 months


title: Human PBMC  34

scan_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)

tag: Sex

value: M

value: 1 month


title: Human PBMC  39

label_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)


title: Human PBMC  40


title: 13h post ICSI single zygote injected Morpholino control-replicate-05

description: Morpholino cont-05

tag: developmental stage


title: Fully torpor colony (biol rep 3)

tag: cell type


title: 13h post ICSI single zygote injected Morpholino control-replicate-07

description: Morpholino cont-07

tag: strain


title: Human PBMC  30


title: Human PBMC  33


title: Human PBMC  32


title: Human PBMC  41


title: Human PBMC  28


title: Human PBMC  29


title: Human PBMC  27


title: NoUV_PureTiO212nm.1 mg/L_rep3

value: Whole body extracts (40 organisms)

tag: stage of development

value: Adult organisms with well developed clitellum

tag: exposure


title: liver_MCT_rep1

source_name: liver tissue, MCT, replicate 1

value: liver

value: male


title: Human PBMC  24


title: liver_Control_rep1

source_name: liver tissue, Control, replicate 1

value: 7-9 weeks

value: SD rats


title: 13h post ICSI single zygote injected Morpholino control-replicate-03

description: Morpholino cont-03

source_name: single cell whole transcriptome amplification

value: 13h post ICSI single zygote

value: Morpholino control


title: Human PBMC  22


title: Human PBMC  38


title: Human PBMC  37


title: Human PBMC  36

value: Avonex


title: Human PBMC  35


title: 13h post ICSI single zygote injected Morpholino control-replicate 01

description: Morpholino cont-01


title: Human PBMC  31


title: Human PBMC  26


title: Human PBMC  25


title: Human PBMC  20

value: SPMS

value: active


title: Human PBMC  18

value: F

value: Plegridy


title: Human PBMC  11

value: RRMS

value: stable


title: Human PBMC  19

value: 7 months


title: Human PBMC  17


title: Human PBMC  16


title: Human PBMC  15


title: Human PBMC  10

value: 1 month


title: Human PBMC  9


title: Human PBMC  23


title: Human PBMC  21


title: Human PBMC  8


title: Human PBMC  2


title: Human PBMC  5


title: Human PBMC  7


title: Human PBMC  1


title: Human PBMC  3


title: Human PBMC  6


title: Human PBMC  14


title: Human PBMC  12


title: Human PBMC  13


title: Human PBMC  4


title: Human PBMC  87


title: Human PBMC  88


title: Tumor_IL2-IL12_OneDose_2d_B

city: Cambridge

first: K

middle: Dane

last: Wittrup

state: Massachusetts

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

description: Nanostring Canine IO nCounter panel (XT-CIO-12)

hyb_protocol: Hybridization of RNA to the Canine IO nCounter panel probe set (Nanostring) was performed according to manufacturer's instructions for 23 hours at 65C. Hybridized RNA was loaded into the analysis cartridge using Nanostring PrepStation.

scan_protocol: Scanning of analysis cartridge was performed on Nanostring Digital Analyzer under maximum resolution.

data_processing: Nanostring nSolver software was used to process count data, beginning with batch correction between cartridge scans using a panel standard control. Background thresholding was performed using the mean of 8 negative control probes. Normalization was performed in nSolver prior to analysis of differential gene expression and pathway analysis between cohorts.

organism: Canis lupus familiaris

source_name: Tumor

growth_protocol: n/a - client-owned dogs with spontaneous soft tissue sarcomas

extract_protocol: RNA was extracted from FFPE tissue scrolls (10um) using Qiagen FFPE RNEasy kit following manufacturer's protocol. Samples were QC'd for concentration and fragment analysis on Bioanalyzer (Agilent) prior to hybridization to the nCounter panel probe set.

treatment_protocol: Dogs with soft-tissue sarcoma were enrolled into three treatment cohorts to receive intratumoral collagen-binding cytokines IL-2 and IL-12 two days prior to surgical excision (cohort 1; n=3), eight days prior to excision (cohort 2; n=3), or two doses of cytokines (day 0 and day 6) with surgical excision of tumor two days after the second dose (cohort 3; n=4). Archived tissue from untreated soft tissue sarcomas were used as controls for gene expression analysis.

tag: sarcoma type

value: Myxosarcoma

tag: treatment

value: Intratumoral IL-2 and IL-12

tag: cohort

value: Cohort 1


title: Tumor_IL2-IL12_OneDose_8d_A

value: Perivascular wall tumor

value: Cohort 2


title: Tumor_IL2-IL12_TwoDose_2d_C

value: Peripheral nerve sheath tumor

value: Cohort 3


title: Tumor_IL2-IL12_OneDose_8d_C


title: Tumor_IL2-IL12_OneDose_2d_C


title: Tumor_IL2-IL12_TwoDose_2d_A


title: Tumor_IL2-IL12_OneDose_8d_B


title: Tumor_Untreated_A

value: No treatment

value: Untreated


title: Tumor_IL2-IL12_OneDose_2d_A


title: Tumor_Untreated_B


title: Tumor_IL2-IL12_TwoDose_2d_D

value: Fibrosarcoma


title: Tumor_Untreated_D


title: Human PBMC  83

city: Chicago


title: Human PBMC  81


title: Human PBMC  84


title: Human PBMC  82


title: Human PBMC  85


title: Tumor_Untreated_G


title: Human PBMC  86


title: Tumor_Untreated_E


title: Tumor_Untreated_F


title: Human PBMC  79

value: Avonex


title: Human PBMC  89

value: F

value: active


title: Human PBMC  80

value: RRMS


title: Human PBMC  78

value: stable


title: Tumor_Untreated_C


title: Human PBMC  77

value: 7 months


title: Human PBMC  76


title: Human PBMC  75


title: Human PBMC  73

value: Plegridy


title: Tumor_IL2-IL12_TwoDose_2d_B


title: Human PBMC  72


title: Human PBMC  56


title: Human PBMC  64

value: 1 month


title: Human PBMC  69

value: SPMS


title: Human PBMC  57


title: Human PBMC  59


title: Human PBMC  54


title: Human PBMC  55


title: Human PBMC  68


title: Human PBMC  67


title: Human PBMC  62


title: Human PBMC  58


title: Human PBMC  66


title: Human PBMC  71


title: Human PBMC  53


title: Human PBMC  52


title: Human PBMC  61


title: Human PBMC  70


title: Human PBMC  51


title: Human PBMC  50


title: Human PBMC  49


title: Human PBMC  47


title: Human PBMC  48


title: Human PBMC  63


title: Human PBMC  45


title: Human PBMC  65


title: Human PBMC  44


title: Human PBMC  46


title: Human PBMC  74


title: Human PBMC  60


title: Human PBMC  43


title: Escherichia coli MG1655 NCM3416 + tobramycin, biol rep 3

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

institute: Institut Pasteur

data_processing:
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.01 were considered differentially expressed.
Assembly: Escherichia coli K12 accession numbers U00096.2
Supplementary files format and content: Excel files containing number of reads and differencial expression for all the conditions
Supplementary files format and content: MH vs tob (Escherichia coli MG1655 WT non treated vs treated with tobramycin. NCM MH vc tob (Escherichia coli NCM3416 non treated vs treated with tobramycin) and MH vs NCM MH (Escherichia coli K12 WT non treated vs NCM3416 non treated)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria

growth_protocol: Overnight cultures were diluted 1000X in MH medium. Cells were grown until OD600nm of 0.4.

extract_protocol:
Cultures were centrifuged, and RNA was purified using using the RNAeasy kit (Thermofischer Scientific), according to the manufacturer instruction (protocole 2 and 4). Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: Cultures were supplemented or not with 0.25 ug/ml of tobramycin.

value: bacteria

tag: genotype

value: rph+

value: tobramycin


title: Escherichia coli MG1655 NCM3416 biol rep 3


title: Escherichia coli MG1655 NCM3416 + tobramycin, biol rep 2


title: Escherichia coli MG1655 WT + tobramycin, biol rep 3

value: wt


title: Escherichia coli MG1655 WT + tobramycin, biol rep 2


title: Escherichia coli MG1655 WT, biol rep 2


title: Escherichia coli MG1655 WT, biol rep 1


title: Escherichia coli MG1655 WT + tobramycin, biol rep 1


title: Escherichia coli MG1655 WT, biol rep 3


title: Escherichia coli MG1655 NCM3416 biol rep 2


title: Escherichia coli MG1655 NCM3416 + tobramycin, biol rep 1


title: Day 10 of hFOB differentiation replicate 2 [t10b]

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
samples were demultiplexed using Lime
refinement and clustering using Isoseq V3
samples were CPM normalized within DEseq2
Assembly: GRCh38
Supplementary files format and content: tab delimieted CPM counts

source_name: hFOB 1.19

growth_protocol: hFOB 1.19 cells (American Type Culture Collection [ATCC], Manassas, VA, USA; #CRL-11372) were cultured at 34C and differentiated at 39.5C as recommended with the following modifications. Growth media: minimal essential media (MEM; Gibco, Grand Island, NY, USA; 10370-021) supplemented with 10% fetal bovine serum (FBS; Atlantic Biologicals, Morrisville, NC, USA; S12450), 1% Glutamax (Gibco; 35050-061), 1% Pen Strep (Gibco; 15140-122). Differentiation media: MEM alpha (Gibco; 12571-063) supplemented with 10% FBS, 1% Glutamax, 1% Pen Strep, 50 μg/μL Ascorbic Acid (Sigma-Aldrich, St. Louis, MO, USA; A4544-25G), 10mM beta-Glycerophosphate (Sigma-Aldrich; G9422-100G), 10nM Dexamethasone (Sigma-Aldrich; D4902-25MG). RNA was isolated from ~0.5 × 106 cells at days 0, 2, 4, and 10 of differentiation as recommended (RNAeasy Minikit; QIAGEN, Valencia, CA, USA; 74106). Mineralized nodule formation was measured by staining cultures with Alizarin Red (40mM, pH 5.6; Sigma-Aldrich; A5533-25G). Reported results were obtained from three biological replicate experiments for days 2,4 and 10, and two biological replicates for day 0 of differentiation

extract_protocol:
RNA was extracted from 3 biological replicates of hFOB cells at days (0,2,4, and 10) using Qiagen RNeasy mini kit. Extracted RNA was  used to create full length cDNA using the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification kit (New England Biolabs Ipswich MA Lot#10078130). Following the PacBio Isoseq protocol, first and second strand cDNA were synthesized using NEB dT oligo and the PacBio Template Switching Oligo. For the cDNA amplification 14 cycles of PCR were performed followed by a Pronex bead cleanup (Promega Corporation Madison WI, Lot #NG103A). The amplified and purified cDNA were QCed using the Bioanalyzer DNA 12000 kit
Approximately 300 ng of cDNA was converted into a SMRTbell library using the Iso-Seq Express Kit SMRT Bell Express Template prep kit 2.0 (Pacific Biosciences). This protocol employs bead-based size selection to remove low mass cDNA, specifically using an 86:100 bead-to-sample ratio (Pronex Beads, Promega). Library preparations were performed in technical duplicate. We sequenced libraries using 11 SMRT cells on the Sequel II system using polymerase v2.1 with a loading concentration of 85pM. A 2-h extension and 30-h movie collection time was used for data collection. The “ccs” command from the PacBio SMRTLink suite (SMRTLink version 9) was used to convert raw reads (~22  million) into Circular Consensus Sequence (CCS) reads. CCS reads with a minimum of three full passes and a 99% minimum predicted accuracy (QV20) were kept for further analysis.

tag: cell line

value: hFOB 1.19

value: Human fetal osteoblasts


title: Day 10 of hFOB differentiation replicate 3 [t10c]


title: Day 10 of hFOB differentiation replicate 1 [t10a]


title: Day 4 of hFOB differentiation replicate 1 [t4a]


title: Day 4 of hFOB differentiation replicate 2 [t4b]


title: Escherichia coli MG1655 NCM3416 biol rep 1


title: Day 2 of hFOB differentiation replicate 3 [t2c]


title: Day 2 of hFOB differentiation replicate 1 [t2a]


title: Day 4 of hFOB differentiation replicate 3 [t4c]


title: Day 0 of hFOB differentiation replicate 2 [t0c]


title: Day 2 of hFOB differentiation replicate 2 [t2b]


title: Day 0 of hFOB differentiation replicate 1 [t0a]


title: Ileum_134_NF

city: Illkirch

first: Gérard

last: Gradwohl

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and BCL Convert version 3.8.4.
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20), reads shorter than 40 bases were discarded for further analysis.
Reads mapping to rRNA were discarded (this mapping was performed using bowtie version 2.2.8).
Reads were mapped onto the mm39 assembly of mouse genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 104.
Assembly: mm39
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: Ileum

growth_protocol: RNA sequencing was carried out on the duodenum and ileum from adult Neurog3f/f; Villin-CreERT2 and control males (n=4/genotype) fed with a high fat diet, collected 5 weeks after tamoxifen administration.

extract_protocol:
NucleoSpin RNA Plus, Mini Kit (Macherey-Nagel)
Total RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, USA) following manufacturers' instructions except at the step of ribodepletion for which we used the riboPOOL kit targeting HMR ribosomal rRNA (siTOOLs Biotech, Planegg/Martinsried, DE) in replacement of the rRNA Removal Mix-Gold from Illumina. Following clean up on RNAClean xp beads, depleted RNAs were fragmented into small pieces using divalent cations at 94°C for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: tissue

value: Ileum

value: Male

tag: diet

value: High fat diet


title: Ileum_154_NF


title: Ileum_151_NF


title: Ileum_136_NFVCT

value: Neurog3f/f; Villin-CreERT2


title: Ileum_177_NFVCT


title: Ileum_168_NFVCT


title: Ileum_167_NFVCT


title: Ileum_133_NF


title: Duo_177_NFVCT

source_name: Duodenum

value: Duodenum


title: Duo_154_NF


title: Duo_167_NFVCT


title: Duo_168_NFVCT


title: Duo_151_NF


title: Duo_133_NF


title: Luminal labelled mouse 2

city: Lebanon

first: Diwakar

last: Pattabiraman

state: New Hampshire

address: 1 Medical Center Drive

department: Molecular systems biology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Raw sequencing data were demultiplexed to create individual FASTQ files using Cell Ranger (v.6.0.1) mkfastq (10X Genomics)
Cell Ranger count was used to map sequence reads to the reference genome (mm10-2020-A) and construct a matrix of raw read counts
Expression data were processed for downstream analysis using R-package Seurat v.4.0.3
Doublets were identified and removed using the simulation-based approach implemented by function scDblFinder from R-package scDblFinder, with the doublet rate argument (dbr) set based on the number of recovered cells from each experiment
Cells with ≤ 500 UMIs or ≤ 200 detected features were removed from further analyses
Outlier cells based of proportion of reads mapping to mitochonrial features were identified using function isOutlier from R-package scater v.1.18.6, and excluded from downstream analysis
Assembly: mm10-2020-A
Supplementary files format and content: raw gene expression counts are provided for each sample in the matrix.mtx.gz file (in Market exchange format for sparse matrices). These files contain cell associated barcodes provided by the 'filtered' output from the CellRanger software
Supplementary files format and content: barcode and feature tsv files provide column names (cells) and gene names rows, respectively, for the associated gene expression matrix file (matrix.mtx.gz)
Supplementary files format and content: raw_counts.mtx.zip provides raw counts for all samples aggregated into a single expression matrix (In Market exchange format). Note that only cells included in downstream analyses are included, therefore raw_counts.mtx.zip represents a subset of the cells present in K8_Tumor_397B_matrix.mtx.gz & K8_Tumor_440B_matrix.mtx.gz
Supplementary files format and content: gene_names.txt provides row names for raw_counts.mtx.zip
Supplementary files format and content: cell_IDs.txt provides column names for raw_counts.mtx.zip
Supplementary files format and content: cell_annotations.txt provides annotation data for individual cells, including assigned clusters
Supplementary files format and content: cell_anotation_dictionary.xlsx provides description for variables in cell_annotations.txt

source_name: Mouse MMTV-PyMT tumor

growth_protocol: Animals were maintained under approved IACUC protocols

extract_protocol:
Tumors were harvested once tumor volume reached 1.5cm3. Tumors were digested in Collagenase and hyaluronidase in DMEM for 2 hours, and strained through 70um and 40um filters
Chromium Single Cell 3’ v3.1 kit (10x Genomics)
RNA-seq, paired-end (read 1: 28bp, read 2: 90bp)

treatment_protocol: Mice were treated with 150mg/kg Tamoxifen dissolved in corn oil for 3 days at 5 weeks and 3 days at 6 weeks, for a total of 6 days

value: Mammary epithelial carcinoma

value: Primary tumor cell


title: Bgn KO NB 2

city: Bethesda

first: Marian

last: Young

state: MD

address: Building 30, Room 5A509

institute: NIH

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v5.0.0 using default settings.
Genome_build: mm10-2020-A (10X Genomics)
Supplementary_files_format_and_content: CellRanger v5.0.0 standard output gene count matrices.

source_name: bone cells

extract_protocol: scRNA-Seq

tag: age


title: Duo_134_NF


title: WT NB 2


title: Bgn KO NB 1


title: Duo_136_NFVCT


title: Bgn KO 2


title: LTC_HepG2_MonoCal_FA.rep1

city: Higashi-Osaka

first: Kei

last: IIDA

address: Kowakae 3-4-1

institute: Kindai University

description: mRNA-seq (polyA+) data from HepG2 cells with treatments of free fatty acids (1 mM), replicate 1

data_processing:
The seuqence data was mapped to the genome sequence with minimap2 ver. 2.22.
Assembly: GRCh38.fa
Supplementary files format and content: Expression values of Ensemble GRCh38.98 gene models were counted with bam files.

source_name: Hep G2 Cell Line

growth_protocol: CaCO2 and HepG2 cells were maintained a microfluidic device with Dulbecco’s modified Eagle medium, supplemented with 10%(v/v) fetal bovine serum, 1%(v/v) non-essential amino acids and 1%(v/v) penicillin/streptomycin in a humidified incubator at 37°C with 5%(v/v) CO2.

extract_protocol:
Total RNA was extracted from differentiated primary myoblasts using the RNeasy mini kit (QIAGEN).
PCR-cDNA Barcoding Kit ( Oxford NANOPORE Technologies )

treatment_protocol: Free fatty acids (total 1 mM of palmitic acid and oleic acid with 1:2 molecular ratio) in Dulbecco’s modified Eagle medium supplemented with 1% BSA-fatty acid free, 1% P/S, and 1 mM nonessential amino acids and subjected to sample preparation after 1 day.

tag: condition

value: Treatments with free fatty acid (1 mM)

tag: derived tissue

value: Human hepatocellular carcinoma


title: LTC_HepG2_MonoCal_Cont.rep1

description: mRNA-seq (polyA+) data from HepG2 cells without treatments of free fatty acids, replicate 1

value: No treatments with free fatty acid


title: LTC_HepG2_MonoCal_FA.rep2

description: mRNA-seq (polyA+) data from HepG2 cells with treatments of free fatty acids (1 mM), replicate 2


title: LTC_HepG2_CoCal_Cont.rep2

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells without treatments of free fatty acids, replicate 2

value: Co-cultured with CaCO2 cells. No treatments with free fatty acid


title: LTC_HepG2_CoCal_FA.rep2

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells with treatments of free fatty acids (1 mM), replicate 2

value: Co-cultured with CaCO2 cells. Treatment with free fatty acid (1 mM)


title: LTC_HepG2_CoCal_Cont.rep1

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells without treatments of free fatty acids, replicate 1


title: LTC_HepG2_MonoCal_Cont.rep2

description: mRNA-seq (polyA+) data from HepG2 cells without treatments of free fatty acids, replicate 2


title: LTC_Caco2_MonoCal_FA.rep2

description: mRNA-seq (polyA+) data from CaCO2 cells with treatments of free fatty acids (1 mM), replicate 2

source_name: Caco-2  Cell Line

value: Human intestine


title: LTC_Caco2_MonoCal_FA.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells with treatments of free fatty acids (1 mM), replicate 1


title: LTC_HepG2_CoCal_FA.rep1

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells with treatments of free fatty acids (1 mM), replicate 1