title: G369_4_t1_exp

description:
G369_4_t1_exp
pilocarpine seizure replicate 2

source_name: 1 hour seizure_2


title: C1 kidney2

status: Public on Dec 31 2023

type: SRA

city: Valhalla

first: Sudhir

last: Jain

state: New York

address: 15 Dana Rd

department: Pathology, Microbiology and Immunology

country: USA

institute: New York Medical Collage

library_source: transcriptomic

data_processing:
Kallisto pseudo-alignment was used with Ensembl mouse transcriptome reference GRCm38
DESeq2 was used for differential gene expression
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM for gene expression level in a csv file

molecule: total RNA

organism: Mus musculus

source_name: Kidney tissue

extract_protocol:
RNA was extracted using Qiagen RNAeasy Kit
Illumina TruSeq Stranded Total RNA Library Preparation using the polyadenylated mRNA pull-down.

tag: strain

tag: group

value: Haplotype-II adult+western diet

tag: tissue

value: kidney


title: B5L19

city: Houston

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

library_source: genomic

data_processing:
Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg38  genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted into gene body regions of RefSeq genes using featureCounts.
Assembly: hg38
Supplementary files format and content: txt file for all sample with raw reads count summarised to gene body regions of Refseq genes.

molecule: genomic DNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).
nano-hmC-Seal

tag: diagnosis

value: Acute myeloid leukemia

tag: age

tag: gender (1 = male, 2 = female)


title: DN-701_Well_F07

city: Ede

first: Alphonsus

middle: Chinedu

last: Ugwu

state: osun state

address: redeemers' university ede osun state

department: Biological Sciences

country: Nigeria

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

data_processing:
Sequence data were analysed using the Seven Bridges Genomics bioinformatics platform (BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0). This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
A cell was considered to be infected if there was at least one GFP sequence read count. This information was then used to define the groups to compare in EdgeR. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05).
Precise WTA Sample Demultiplexing:Paired-end reads are demultiplexed per well based on the sequence of the sample index. This sample index is found in the first 8 bases of Read 01. The Molecular Index is found in Read 01, in positions 8 to 16. The demultiplexing process also includes a structure filtering step. After filtering, the final step in this process stores the Molecular Index in the demultiplexed FASTQ files by appending the index to the sequence headers of Read 02 FASTQ files. The Read 02s from each well are trimmed by Flexbar to remove any Illumina adapter contaminants and mapped to the reference genome using STAR.
Precise WTA Alignment Quantification: After Read 02s are aligned using STAR, the alignments are assigned to gene counts using a custom implementation of HTSeq-count. The number of reads mapping to each gene is generated in the DBEC Read Mapping Report. The unique counts for molecular indices are calculated in the DBEC Molecular Index Mapping Report
Genome_build: mm9
Supplementary_files_format_and_content: text document (after removal of Molecular indices error using Recursive Substitution Error Correction™ (RSEC) and Distribution-Based Error Correction™ (DBEC))

source_name: Bone marrow derived APC

growth_protocol: BM derived cells were generated by incubating bone marrow stem cells with growth factor (GM-CSF/ IL-4) for 6 days in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10 % foetal calf serum (FCS), 100 U penicillin/ml, 0.1 mg streptomycin/ml and 50 M 2-mercaptoethanol. Differentiated cells were harvested and sorted into the three BM geoups by flow cytometry before infection with LCMV or stimulation with poly (I:C).

extract_protocol:
The cells are collected in WTA single cell encoding plate, RNA secondary structure is done at 65C for 3 minutes (hold at 4C), mastermix containing BD customised RT enzymes is added (PN 650000041) and run at 42C for 30 minutes, heat inactivated at 80C for 5 minutes before holding at 4C. The samples is pooled and purify before library prep.
Libraries of the cellular RNA were made using the BD WTA single cell kit and sequenced using MiSeq V2 from Illumina (BM-DC, BM-M, DN).

treatment_protocol: Sorted CD11c+MHC class II+ bone marrow derived cell populations (dendritic cells [BMDC], macrophages [BM-M], double negative cells [DN]) were infected with LCMV clone 13 expressing GFP, as previously described for 12 and 48hr for single cell (from the 12 h culture) sorting into customised BD WTA single cell encoding plates for RNA extraction and reverse transcription (primary infection) according to manufacturer’s instructions (PN 910000014 Rev. 03). Furthermore, a subset of infected cells (from the 48 h culture) were stimulated with 100 µg poly (I:C)/ml and incubated for another 6hr before single cell sorting as above.

tag: cell type

value: Bone marrow derived APC

tag: treatment

value: 12hr infection with LCMV Cl 13


title: B5L64


title: DN-701_Well_F06


title: G369_3_t1_cont

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

description:
G369_3_t1_cont
controls  replicate2

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0) allowing no mismatches in the index read. For mRNA-seq, BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (release 67: "Mus_musculus.Ensembl.NCBIM37.67.gtf"). For microRNA-seq, sequencing reads were subjected to quality filtering, quality trimming and adapter trimming by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit), conducted by fastq_quality_filter function, fastq_quality_trimmer function, and fastq_clipper function, respectively, 4 bases were trimmed from both 5’ and 3’ ends of the sequencing reads by fastq_trimmer function. Oasis 2.0 suite (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2047-z) was used to align and count raw reads of all expressed small RNAs.
Assembly: mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)
Supplementary files format and content: csv file containing raw read counts for each sample ("EG_merged.HTSeq.out.csv" for mRNA-seq, "EGmicro.out.csv" for microRNA-seq)

molecule: polyA RNA

source_name: 1 hour_cont_2

growth_protocol: Mice were purchased from Jackson laboratory and housed in a room with an ambient temperature of 25 C, 30–70% humidity, a 12-h light–dark cycle, and ad libitum access to rodent chow

extract_protocol:
Animal was sacrificed, decapitated and brain was removed from skull. Hippocampus isolation was done  in PBS, right and left halves of hippocampus were flash frozen.Total RNA isolation waswere carried out from the leftfrom left hippocampus with Trizol reagent (15596018, Ambion, Carlsbad, CA, USA) as described in the vendor’s manual. The quality of RNA was assessed on an Agilent Bioanalyzer and confirmed fof their samples with RNA integrity numbers were between greater than 7.9.
For mRNA-seq, the libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (IDT® for Illumina® RNA UD Indexes Set A, Ligation, Illumina) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). For microRNA-seq, the libraries were prepared using the NEXTflexTM Small RNA Library Prep Kit v3 (BioO Scientific) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The denatured libraries were loaded onto an S1 flow cell on a NovaSeq 6000 or a Rapid flow cell on a HiSeq2500 (Illumina) and run for 2X53 cycles (for mRNA-seq) or for 1X49-65 cycles (for microRNA-seq) according to the manufacturer's instructions.

treatment_protocol: C57BL/6j male and female mice 6-7weeks old   injected intraperitoneal  with pilocarpine (350 mg/kg) or vehicle (0.9% bacteriostatic sodium chloride)

value: adult 6-7 weeks

value: hippocampus

tag: molecule subtype

value: mRNA

tag: time

tag: batch


title: S12 kidney1

value: C57 adult


title: B5L14


title: S11 kidney1


title: B5L61


title: G511_04_t1_cont

description:
G511_04_t1_cont
controls  replicate1

source_name: 1 hour_cont_1


title: DN-701_Well_F05


title: DN-701_Well_F04


title: M_WC_3

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. R2 reads were generated as UMI sequences that were later used to extract PCR duplicates. R1 and R3 reads were used as paired sequencing reads. To assess the read quality, FastQC was run, and low quality reads were removed using sickle with default setting. BBDuk version 36_49  was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome GRCh38 was done using HISAT2 version 2.1.0 applying --no-mixed and --no-discordant options. UMI specific workflow that was developed and distributed by Tecan Genomics was used to extract reads that are free from PCR artifacts i.e., deduplication. The resulting deduplicated reads were summarized to each gene using HTseq-count version 0.11.2 by supplementing Ensembl gene annotation GRCh38.78 and ERCC spike-in genes.
Genome_build: GRCh38
Genome_build: mm9
Supplementary_files_format_and_content: Raw read counts are provided in TS_LC_WC_NC.txt and MouseAB_Rawcount.txt files, respectively.
paired-end (R1 and R3, R2 is UMI)

source_name: layer V single pyramidal neurons

growth_protocol:
Coverslips Fisher Scientific, 12-545-80 were coated with Poly-L-Lysine PLL by incubation in PLL solution 0.01% for 30 minutes at 37°C. TOV-21G ATCC, CRL-11730 cells were grown for 48 hours on cover slips in the Complete Growth Medium [a 1:1 mixture of MCDB 105 1.5 g/L sodium bicarbonate and MCDB 199 2.2 g/L sodium bicarbonate added with fetal bovine serum at a final concentration of 15%] for RNA collection.
Mice were deeply anesthetized with isoflurane Halocarbon. A block of brain containing motor cortex MCx was removed and coronal slices 300 μm thick were cut on a vibrating microtome Leica in ice-cold physiological solution ACSF. The solution contained the following in mM: 130 NaCl, 3 KCl, 1.25 KH2PO4, 20 NaHCO3, 10 glucose, 1.3 MgSO4, 2.5 CaCl2 pH 7.35-7.4, in 95% O2-5% CO2. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Slices were incubated for 1 hour at 30°C, then kept at room temperature. For electrophysiological extraction of RNA, slices were held in a chamber on a motorized stage microscope Olympus BX61WI, Gibraltar Burleigh and superfused with ACSF. The location of motor cortex MCx was identified by 1.5-2.0 mm rostral to the start of the hippocampus.

extract_protocol:
For RNA extraction, cultures and slices were held separately in a chamber on a motorized stage on a motorized microscope Olympus BX61WI, Gibraltar Burleigh Thorlabs. Cultures were superfused 2-4 ml/min in a bath solution of in mM: 145 N-methylglucamine NMG, 2 CaCl2, 1 MgCl2, 10 HEPES, 60 glucose pH 7.3, osmolality 300, in 95% O2-5% CO2 . All procedures were performed with a Multiclamp 700B patch-clamp amplifier Molecular Devices, LLC and using borosilicate glass pipettes with filament, OD 1.5 mm, ID 1.10 mm, Sutter and the input resistance was in the range of 3-9 MΩ. RNA was extracted with a 1440A Digidata AD board Molecular Devices, LLC under pClamp v10. Electrodes pipettes were filled with in mM: 100 KCl, 35 N-methylglucamine NMG, 10 EGTA, 1 CaCl2, 4 MgCl2, and 10 HEPES pH 7.3, 290 mOsm for the RNA extraction from the TOV-21G cells. Electrodes were filled with in mM: 130 K-gluconate, 10 KCl, 10 HEPES, 10 EGTA, 2 MgCl2, 2 Na-ATP, 0.2 Na-GTP, and 5 glutathione pH 7.3, 280-290 mOsm for the RNA extraction from the Thy1-YFP L5 neurons. For the RNA extraction from the Thy1-GCaMP6f L2/3 neurons, electrodes were filled with in mM: 110 K-gluconate, 4 KCl, 4 NaCl, 0.2 CaCl2, 10 HEPES, 1.1 EGTA, 2 Mg-ATP, 1 MgCl2, and 5 glutathione pH 7.2-7.3, 300 mOsm. Membrane voltages were corrected for an estimated liquid junction potential of about 10 mV. Perforation was performed using -escin antibiotics 50 M from a stock solution 25 mM respective for each cellular population. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Lucifer yellow 50 mM was added to the electrode intracellular working solution for all cellular populations. The intercellular working solution including the antibiotics and dye was prepared fresh daily and used at room temperature and were backfilled into the electrodes for the patch-clamp experiments. Holding potentials for TOV-21G cells and cortical neurons were -80 mV and -70 mV, respectively. Electrodes were made by a PP-830 Narishige puller and positive pressure was applied as the pipettes were advanced to the cell of interest. The leak current Ilk was then used for the holding current in the current-clamp protocol and it was noted before and after the current was injected in all cellular populations. Seven current injection steps of 5 pA each was applied for a duration of 500 ms per step for the RNA extraction. Following RNA extraction, electrodes were slowly retracted while leaving the cell intact in its native environment, and the pipette solution was collected for sequencing. Each sample tube was prefilled with 2 µL of IGEPAL working mixture per tube, and positive pressure was applied to eject the internal contents of the electrode into a sample tube. The IGEPAL working mixture contained 65 µL nuclease-free de-ionized water Ambion, AM9938, 25 µL RNaseOUT™ Recombinant Ribonuclease Inhibitor ThermoFisher, 10 µL IGEPAL CA-630 Alfa Aesar, J61055 and was stored in 4°C for up two weeks. RNA was collected in 0.5 mL tubes Protein LoBind Tube 0.5 mL, Eppendorf, 022431064. After RNA extraction, samples were transferred on dry ice and stored at -80°C. After each RNA extraction, the electrode holder and silver-chloride recording electrode were cleaned with 70% ethanol. Cytosolic extraction for all cellular populations was performed by first doing whole-cell patch-clamp, then applying negative pressure light suction to harvest cellular content into IGEPAL working mixture.
The cDNA libraries were prepared using Ovation SoLo RNA-Seq System Tecan Genomics.  UMIs are used to eliminate possible PCR duplicates in sequencing datasets and facilitate unbiased gene expression profiling. For some experiments, ERCC RNA Spike-In Mix Thermo Fisher Scientific was included in the library preparation. The processed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent Technologies. The libraries were pooled and loaded onto a TruSeq SBS v3 flow cells on an Illumina HiSeq 2500 Illumina or an S1 flow cell on an Illumina NovaSeq 6000 Illumina , and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq version 2.18.0.12 allowing no mismatches in the index read.

treatment_protocol: For some experiments, TOV-21G cells were cultured in the Complete Growth Medium added with a IκB kinase IKK inhibitor, IKK-16 IKK Inhibitor VII Sigma-Aldrich at 1 µM for 72 hours before RNA collection.

tag: collection

value: WC-seq


title: S10 kidney1


title: DN-701_Well_F03


title: B5L9


title: S9 kidney1


title: DN-701_Well_F02


title: S8 kidney1

value: Haplotype-I aged


title: B5L39


title: M_WC_1


title: B5L2


title: S6 kidney1


title: M_LC_3

value: LC-seq


title: DN-701_Well_E11


title: B5L41


title: B5L4


title: DN-701_Well_E12


title: M_LC_2


title: S7 kidney1


title: DN-701_Well_F01


title: M_LC_1


title: DN-701_Well_E10


title: 18312X14 KO4-15 months

city: salt lake city

first: Sihem

last: Boudina

state: Utah

department: Nutrition and Integrative Physiology

institute: University of Utah

data_processing:
Mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 100
Reference database was created using STAR version 2.7.3a with splice junctions optimized for 150 base pair reads
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: whole heart tissue

growth_protocol: whole tissue

extract_protocol: Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold (human, mouse, rat, etc.)

treatment_protocol: untreated

tag: genotype/variation

value: cardiac-specific p62 KO mice (Myh6-Cre-Sqstm1fl/fl)

tag: Sex

value: Male

value: 15 months

value: whole heart tissue


title: G369_2_t1_exp

description:
G369_2_t1_exp
pilocarpine seizure replicate 1

source_name: 1 hour seizure_1

value: Pilocarpine


title: S5 kidney1


title: B5L18


title: S4 kidney1

value: Haplotype-I adults


title: M_WC_2


title: S3 kidney1

value: kidney


title: B5L48

value: Acute myeloid leukemia


title: 18312X13 KO3-15 months


title: B5L69


title: G317_2_t8_cont

description:
G317_2_t8_cont
controls  replicate2

source_name: 8 hour_cont_2


title: S2 kidney1


title: 18312X12 KO2-15 months


title: B5L68


title: DN-701_Well_E09

value: Bone marrow derived APC


title: DN-701_Well_E07

value: 12hr infection with LCMV Cl 13


title: S1 kidney1


title: 18312X11 KO1-15 months


title: DN-701_Well_E06


title: C4 kidney1

value: Haplotype-II adult+western diet


title: B5L65


title: B5L63


title: C3 kidney1


title: B5L60


title: 18312X10 WT3-15 months

value: wildtype


title: C2 kidney1


title: B5L59


title: 18312X7 WT1-15 months


title: B4 kidney1

value: Haplotype-I aged+western diet


title: DN-701_Well_E04


title: DN-701_Well_E03


title: DN-701_Well_E08


title: DN-701_Well_E02


title: 18312X8 WT2-15 months


title: DN-701_Well_E05


title: C1 kidney1


title: 18312X6 KO3-2 months

value: 2 months


title: DN-701_Well_E01


title: B5L51


title: B3 kidney1


title: 18312X5 KO2-2 months


title: 18312X9 WT4-15 months


title: B5L49


title: DN-701_Well_D12


title: B2 kidney1


title: DN-701_Well_D11


title: 18312X4 KO1-2 months


title: B1 kidney1


title: DN-701_Well_D10


title: 18312X3 WT3-2 months


title: A4 kidney1

value: Haplotype-I adult+western diet


title: B5L38


title: A3 kidney1


title: DN-701_Well_D09


title: DN-701_Well_D08


title: B5L30


title: 18312X1 WT1-2 months


title: B5L29


title: B5L25


title: DN-701_Well_D06


title: A1 kidney1


title: A2 kidney1


title: B5L53


title: B16 heart2

source_name: Heart tissue

value: Haplotype-II aged+western diet

value: heart


title: B5L24


title: DN-701_Well_D05


title: B5L15


title: DN-701_Well_D04


title: B5L8


title: B15 heart2


title: 18312X2 WT2-2 months


title: B14 heart2


title: B5L1


title: DN-701_Well_D03


title: B13 heart2


title: DN-701_Well_D02


title: DN-701_Well_D07


title: DN-701_Well_D01


title: 786-O, TEAD,ChIP

city: Jinan

first: Tianwei

last: Jia

state: Shandong

address: 天桥区

country: China

institute: Shandong university

data_processing:
fastp software was used to remove the splicer sequence of the sequencing read segment
ChIP-Seq reads were aligned to the hg19 genome using Bowtie2 version2.4.5
narrowPeak files were generated using MACS2 callpeak with the significance cut-off q-value<=0.01.
bigWig files were generated using bedGraphToBigWig.
Getting the normalized bigwig file.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: Clear cell renal

growth_protocol: RPMI-1640, 10% FBS, 1%penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2

extract_protocol:
Cells were cross-linked by 1% warm formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using a water bath sonicator (Diagenode bioruptor).
We use 1x107 cells for one ChIP reaction. DNA was purified using the ChIP DNA Clean & Concentrator kit (D5205, Zymo Reasearch), and then subjected to Illumina ChIP-Seq library construction using Thru-PLEX DNA-seq kit (Rubicon Genomics).Post amplification libraries we're size selected at 300-700 bp in length using AMPure XP breads from Beckman Coulter. Libraries were validated using the Aglient 2100 Bioanalyzer.

value: Clear cell renal

tag: cell line

value: carcinoma cell line

tag: antibody

value: TEAD


title: B7 heart2

value: Haplotype-II aged


title: 786-O, Input,ChIP

value: input


title: B6 heart2


title: B5 heart2


title: B26 heart1

value: Haplotype-I adults+western diet


title: 786-O, H3K27ac,ChIP


title: Normal-4

city: Taiyuan

first: Ziyang

address: 56 South Xinjian Street

institute: Shanxi Medical University

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. 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.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.13.5 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. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs between two groups, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: GRCh38
Supplementary files format and content: FileincludeFPKM/TPMvaluesforeachsample

source_name: Blood

extract_protocol:
Peripheral blood was obtained from 4 patients who had heart failure with atrial fibrillation (HF /AF group) and 4 matched healthy subjects (control group) who excluded HF and AF by ethylenediaminetetraacetic acid disodium salt (EDTA) tubes. The diagnosis of HF and AF were in accordance with the 2022 AHA/ACC/HFSA Guideline for the Management of Heart Failure and Atrial fibrillation: Current understanding and Treatment Recommendations (2021) respectively. According to the Declaration of Helsinki, ethical approval was accepted by the Ethics Committee of First Hospital of Shanxi Medical University and all participants had written informed consent. The patients of the HF/AF group were excluded from hypertension, coronary heart disease, OSA, diabetes, rheumatic disease, valvular heart disease, infectious disease, tumor as well as the dysfunction of the liver and renal. The matched participants of control had sinus rhythm and were in good condition. The HF/AF group was higher than the control group in NT-proBNP. The HF/AF group was significantly lower than the control group in the aspect of ejection fraction (EF). There was no statistical difference in the aspects of age, gender, smoking status and obesity.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Blood

value: PBMC

value: Normal


title: DN-701_Well_C10

value: Bone marrow derived APC

value: 12hr treatment with Phosphate buffer saline (PBS)


title: Normal-3


title: DN-701_Well_C11


title: B25 heart1


title: Normal-2


title: B24 heart1


title: DN-701_Well_C08


title: DN-701_Well_C07


title: B23 heart1


title: B8 heart2


title: HF/AF-4

value: HF /AF group


title: DN-701_Well_C06


title: HF/AF-3


title: DN-701_Well_C12


title: DN-701_Well_C05


title: HF/AF-2


title: B20 heart1

value: Haplotype-I aged+western diet


title: DN-701_Well_C09


title: DN-701_Well_C03


title: DN-701_Well_C04


title: KMI169 biol rep 3

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

country: Germany

institute: Uniklinik-Freiburg

data_processing:
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).
We aligned these reads to the hg19  of the human genome using STAR
The aligned reads were counted with the homer software (analyzeRNA) and edgeR
Assembly: hg19
Supplementary files format and content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

source_name: prostate

growth_protocol: PC-3M prostate tumour cells were cultured in RPMI1640, 10%FCS, Pen/Strep

extract_protocol:
RNA was extracted using RNAeasy mini plus kit.
2 µg RNA (40 ng/µl) were used to construct the libraries.

treatment_protocol: PC-3M were cultured 4 days in presence of DMSO, 360 nM of the KMT9 inhibitor KMI169, or 360 nM of the negative Ctrl compound KMI169 Ctrl prior to analyse the transcriptome.

value: prostate

tag: genotype

value: male

value: 360 nM 169 treated


title: B22 heart1

tag: strain

value: heart


title: KMI169 biol rep 1


title: DN-701_Well_C02


title: B8 heart1

tag: group

value: Haplotype-I aged


title: B18 heart1

tag: tissue


title: Normal-1


title: HF/AF-1


title: KMI169 biol rep 2


title: KMI169Ctrl biol rep 3

value: 360 nM 169Ctrl treated


title: DN-701_Well_C01


title: DN-701_Well_B12

value: 12hr infection with LCMV Cl 13


title: DN-701_Well_B11


title: B6 heart1


title: DN-701_Well_B10


title: KMI169Ctrl biol rep 2


title: DN-701_Well_B09


title: DMSO biol rep 3

value: DMSO treated


title: B3 heart1

value: C57 adult


title: B19 heart1


title: DN-701_Well_B08


title: B2 heart1


title: DMSO  biol rep 2


title: DN-701_Well_B07


title: DN-701_Well_B06


title: DMSO biol rep 1


title: B1 heart1


title: B2x2_H_P3r3

city: Berkeley

first: Dirk

last: Hockemeyer

state: CA

address: 400 Li Ka Shing Center

department: Department of Molecular & Cell Biology

institute: University of California, Berkeley

library_source: other

data_processing:
Raw sequencing files were demultiplexed on Illumina BaseSpace.
Sequencing reads were trimed to 150bp.
Reads were aligned to reference amplicon sequences and quantifiled with CRISPResso2.
Assembly: BRCA2 exon 2 reference sequence,  ttccagcgcttctgagttttacctcagtcacataataaggaatgcatccctgtgtaagtgcattttggtcttctgttttgcagacttatttaccaagcattggaggaatatcgtaggtaaaaatgcctattggatccaaagagaggccaacattttttgaaatttttaagacacgctgcaacaaagcaggtattgacaaattttatataactttataaattacaccgagaaagtgttttctaaaaaatgcttgctaaaaacccagtacgtcaca; BRCA2 exon 27 reference sequence, tgtaaaggggagaaagagattgatgaccaaaagaactgcaaaaagagaagagccttggatttcttgagtagactgcctttacctccacctgttagtcccatttgtacatttgtttctccggctgcacagaaggcatttcagccaccaaggagttgtggcaccaaatacgaaacacccataaagaaaaaagaactgaattctcctcagatgactccatttaaaaaattcaatgaaatttctcttttggaaagtaattcaatagctgacgaagaacttgc
Supplementary files format and content: plain text, aligned allele sequences and quantification
Library strategy: Amplicon sequencing

molecule: other

growth_protocol: Human pluripotent cells were cultured on 4.1x105/cm2 irradiated mouse embryonic fibroblasts (MEF) in hPSC medium (Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12), 20% KnockOut Serum Replacement (KOSR), 1x Non-Essential Amino Acids (NEAA), 1mM Glutamine, 1x penicillin/streptomycin, 0.1mM ß-mercaptoethanol and 4 ng/ml heat-stable basic FGF). The culture medium was changed daily, and cells were passaged with 1mg/ml collagenase IV every 5-7 days. The day before and after passage, the medium was supplemented with 10µM Y27632 (CD0141, Chemdea) to increase cell survival.

extract_protocol:
Phenol-chloroform extraction for genomic DNA
Using primers containing NGS barcode attachment sites (GCTCTTCCGATCT), the mutagenized regio was amplified with GXL DNA polymerase. Amplicons were then purified using an automated SPRI beads purification protocol at the UC Berkeley DNA Sequencing Facility, i5/i7 barcoded and pooled.

treatment_protocol: Drug sensitivity screening was started on day 21 with at least 0.3 million cells were used in each replicate, and cells were collected on day 28.

value: Embryonic stem cells (ESCs)

value: BRCA2 loHAPs

value: Day 21


title: plasma sample 57

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Genome_build: EquCab3.0 (GCA_002863925.1)

organism: Equus caballus

source_name: plasma

extract_protocol: Trilink Cleantag Kit

value: plasma

tag: timepoint

tag: horse

value: extracellular vesicles


title: B2x2_H_P3r2


title: B7 heart1


title: DN-701_Well_B04

value: Bone marrow derived APC


title: plasma sample 61


title: B2x2_H_P3r1


title: DN-701_Well_B03


title: plasma sample 60


title: B5 heart1


title: KMI169Ctrl biol rep 1


title: B2x2_H_P2r3

value: Day 14


title: plasma sample 74


title: DN-701_Well_B02


title: plasma sample 63


title: B2x2_H_P2r1


title: B2x2_H_P2r2


title: plasma sample 55


title: B2x2_H_P1r3

value: Day 7


title: plasma sample 54


title: DN-701_Well_B05


title: B5L40

tag: diagnosis

value: Acute myeloid leukemia

tag: age

tag: gender (1 = male, 2 = female)


title: DN-701_Well_H12

tag: cell type

tag: treatment


title: B2x2_H_P1r2

tag: time


title: DN-701_Well_A12


title: DN-701_Well_A10


title: B2x2_H_P1r1


title: B21 heart1

value: Haplotype-I aged+western diet


title: B2x2_H_Ola_r3

value: Olaparib


title: DN-701_Well_A09


title: plasma sample 67


title: Nkx2-1/mKO2+ cells-Foxe1KO-day22-rep2

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Removal of low-quality bases and Illumina adapter sequences were performed using Trimmomatic software (Bolger et al. 2014) and sequence reads were aligned against the mouse reference genome using HiSat2 software (Kim, 2015). Raw reads were determined with HTSeq software (Anders et al 2015) using the Ensembl genome annotation GrCm38.
Genome_build: Grcm38/mm10
Supplementary_files_format_and_content: Text format file containing raw counts per sample

source_name: mESC-derived differentiated cells

extract_protocol:
Trypsin based dissociation followed by FACS sorting of 10000 Nkx2-1/mKO2+ cells
Ovation Solo RNA-seq Systems (NuGen)

value: Foxe1KO/Nkx2-1-T2a-mKO2 reporter mESC line

value: Nkx2-1/mKO2+ cells


title: plasma sample 66


title: DN-701_Well_A08


title: plasma sample 64


title: DN-701_Well_A07


title: B2x2_H_Ola_r1


title: B2x2_H_Ola_r2


title: Nkx2-1/mKO2+ cells-Foxe1KO-day22-rep1


title: DN-701_Well_B01


title: plasma sample 56


title: DN-701_Well_A11


title: DN-701_Well_A06


title: DN-701_Well_A05


title: B2x2_H_Nira_r3

value: Niraparib


title: plasma sample 53


title: Nkx2-1/mKO2+ cells-Control-day22-rep1

value: Nkx2-1-T2a-mKO2 reporter mESC line

value: Control


title: plasma sample 72


title: DN-701_Well_A04

value: 12hr infection with LCMV Cl 13


title: B2x2_H_Nira_r1

value: Embryonic stem cells (ESCs)


title: plasma sample 73


title: Nkx2-1/mKO2+ cells-Foxe1KO-day10-rep4


title: B2x2_H_Mock_r3

value: BRCA2 loHAPs

value: Mock


title: plasma sample 70

value: plasma


title: plasma sample 77

value: extracellular vesicles


title: B2x2_H_Nira_r2


title: DN-701_Well_A02

value: Bone marrow derived APC


title: Nkx2-1/mKO2+ cells-Foxe1KO-day10-rep3


title: B2x2_H_Mock_r2


title: Nkx2-1/mKO2+ cells-Foxe1KO-day10-rep2


title: Nkx2-1/mKO2+ cells-Foxe1KO-day10-rep1


title: B2x2_H_Mock_r1


title: plasma sample 59


title: DN-701_Well_A01


title: CB11B_P_Well_H12

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Nkx2-1/mKO2+ cells-Control-day22-rep2


title: B2x2_H_IR2_r3

value: Irradiation


title: plasma sample 76


title: Nkx2-1/mKO2+ cells-Control-day10-rep4


title: plasma sample 69


title: B2x2_H_IR2_r2


title: Nkx2-1/mKO2+ cells-Control-day10-rep3


title: CB11B_P_Well_H11


title: DN-701_Well_A03


title: CB11B_P_Well_H10


title: plasma sample 68


title: plasma sample 71


title: Nkx2-1/mKO2+ cells-Control-day10-rep1


title: B2x2_D_P3r2

value: Diploid

value: Day 21


title: plasma sample 58


title: plasma sample 65


title: B2x2_H_IR2_r1


title: CB11B_P_Well_H07


title: CB11B_P_Well_H06


title: Nkx2-1/mKO2+ cells-Control-day10-rep2


title: Foxe1KO mouse ESC-derived cells

data_processing:
The raw sequencing data were then processed with the ‘count’ command of the Cell Ranger software (v.6.0.1) provided by 10x Genomics with the option ‘–expect-cells’ set to 10,000 (all other options were used as per default).
Genome_build: Grcm38/mm10
Supplementary_files_format_and_content: Tab Separated File containing Cell barcodes. Cell barcodes correspond to columns of the matrix.
Supplementary_files_format_and_content: Tab Separated File containing gene names. Gene names correspond to rows of the matrix.
Supplementary_files_format_and_content: Sparse matrix containing counts obtained from Cell Ranger output.

extract_protocol:
Trypsin based dissociation followed by FACS sorting of 15% bvTg/GFP+, 50% Nkx2-1/mKO2+ and 35% Nkx2-1/mKO2- cells
10x Chromium NextGEM SingleCell 5' Kit v2

value: Foxe1KO/Nkx2-1-T2a-mKO2 reporter mESC lines


title: CB11B_P_Well_H08


title: B2x2_D_P3r3


title: B2x2_D_P2r3

value: Day 14


title: plasma sample 62


title: B2x2_D_P2r2


title: synovial fluid (OA) sample 32

source_name: synovial fluid

value: synovial fluid

value: OA


title: CB11B_P_Well_H04


title: B2x2_D_P2r1


title: CB11B_P_Well_H05


title: CB11B_P_Well_H03


title: B2x2_D_P1r3

value: Day 7


title: plasma sample 78


title: B2x2_D_P3r1


title: plasma sample 75


title: CB11B_P_Well_H09


title: CB11B_P_Well_H02


title: B2x2_D_P1r1


title: CB11B_P_Well_H01


title: B2x2_D_P1r2


title: synovial fluid (OA) sample 3


title: CB11B_P_Well_G12


title: Wei1_EN_rep2

type: RNA

city: Potsdam

first: Eva-Theresa

last: Pyl

address: Am Muehlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Background correction and quantile normalization were performed using the ‘preprocessCore’ and ‘affyPLM’ packages (Bioconductor; Gentleman et al. in Genome Biology 2004, 5(10): R80) to calculate RMA signal intensities. To identify probes potentially affected by SFPs in the raw data, a combination of a median polish method, adapted from (Xie et al. in Theoretical and Applied Genetics 2009, 119(1): 151-164), and a one-way ANOVA were used to select individual probes that were significantly altered between accessions (p < 0.01). To identify probes, which showed lower probe signal intensity in an accession compared to Col-0, significant contrasts were subsequently identified in a post-hoc Tukey HSD test (p < 0.01). The list of 21,297 probes with significant signal alterations in any of the accessions compared to Col-0, was combined with 22,297 Cvi sequence SNPs available from the 1,001 genome project. Additional SNPs were added by taking available data for 19 of the 20 accessions (except for Bu-2, Bu-0 used instead) derived from genotyping accessions using a custom Affymetrix SNP chip containing 250K SNPs (Atwell et al. in Nature 2010, 465(7298): 627-631). The final list of potentially SNP containing probes comprised 44,863 SNPs. Joint masking of all these probes led to a removal of 1,481 probe sets that had <6 probes remaining, reducing the number of probe sets to a final number of 21,329.

label: biotin

organism: Arabidopsis thaliana

source_name: Wei1, end of the night

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: 20 A.th. accessions were grown on soil in a 8h light / 16h dark cycle, at a light intensity of 160 µmol m-2 s-1 and a constant temperature of 20°C for 5 weeks.

extract_protocol: Material from a pool of 5 rosettes was snap frozen in liquid nitrogen and stored until further use at -80C or was processed directly as follows. Frozen plant material was homogenized and total RNA was extracted from 50 mg of homogenized plant material using Qiagen RNeasy Plant mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Before and after DNaseI digestion (Turbo DNA-free DNase I; Applied Biosystems/Ambion, Darmstadt, Germany), RNA concentration and integrity were measured using a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA) and an Agilent-2100 Bioanalyzer using RNA 6000 NanoChips (Agilent Technologies, Böblingen, Germany).

treatment_protocol: For each accession, 5 rosettes from 5 week old plants were harvested and pooled in the last hour of the day (ED; ZT8), or the last hour of the night (EN; ZT24), or 6h into an extended night (XN; ZT30).

value: whole rosettes

value: end of the night (EN; ZT24)


title: Wei1_EN_rep1


title: synovial fluid (OA) sample 48


title: CB11B_P_Well_G11


title: synovial fluid (OA) sample 36


title: synovial fluid (OA) sample 47


title: CB11B_P_Well_G10


title: B2x2_D_Ola_r2

value: Embryonic stem cells (ESCs)

value: Olaparib


title: B2x2_D_Ola_r1


title: Wei1_XN_rep2

source_name: Wei1, 6h extended night

value: 6h extended night (XN; ZT30)


title: synovial fluid (OA) sample 43


title: B2x2_D_Nira_r3

value: Niraparib


title: Wei1_XN_rep1


title: Van0_XN_rep1

source_name: Van0, 6h extended night


title: synovial fluid (OA) sample 15

value: extracellular vesicles


title: B2x2_D_Ola_r3


title: CB11B_P_Well_G09

source_name: Bone marrow derived APC

value: Bone marrow derived APC


title: Wei1_ED_rep1

source_name: Wei1, end of the day

value: end of the day (ED; ZT8)


title: Wei1_ED_rep2


title: Van0_XN_rep2


title: Van0_EN_rep2

source_name: Van0, end of the night


title: synovial fluid (OA) sample 4


title: Van0_EN_rep1


title: CB11B_P_Well_G08

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: CB11B_P_Well_G07

value: 6 hr stimulation with poly (I:C)


title: synovial fluid (OA) sample 9


title: Van0_ED_rep2

source_name: Van0, end of the day


title: B2x2_D_Nira_r1

value: Diploid


title: B2x2_D_Nira_r2


title: synovial fluid (OA) sample 34


title: CB11B_P_Well_G06


title: synovial fluid (OA) sample 39


title: B2x2_D_Mock_r2

value: Mock


title: B2x2_D_Mock_r3


title: synovial fluid (OA) sample 31


title: CB11B_P_Well_G05


title: CB11B_P_Well_G04


title: B2x2_D_Mock_r1


title: synovial fluid (OA) sample 27


title: CB11B_P_Well_G03


title: Van0_ED_rep1


title: synovial fluid (OA) sample 52


title: B2x2_D_IR2_r3

value: Irradiation


title: synovial fluid (OA) sample 7

value: synovial fluid


title: B2x2_D_IR2_r2


title: RRS7_EN_rep2

source_name: RRS7, end of the night


title: CB11B_P_Well_G02


title: RRS7_XN_rep1

source_name: RRS7, 6h extended night


title: CB11B_P_Well_G01


title: RRS7_XN_rep2


title: RRS7_EN_rep1


title: synovial fluid (OA) sample 37

value: OA


title: CB11B_P_Well_F12


title: synovial fluid (OA) sample 23


title: RRS7_ED_rep1

source_name: RRS7, end of the day


title: synovial fluid (OA) sample 45


title: RV5: RV1, L-Gln 2mM, 56 mer 50 nM 48h

city: LOS ANGELES

first: Carlos

middle: David

last: Cruz-Hernandez

state: CALIFORNIA

address: 8700 Beverly Blvd #2900A

department: SOCC

institute: Cedars Sinai

data_processing:
The read counts were normalized using the DESeq alghorithm in the platform BIOBOX
Supplementary files format and content: DESeq analyzed values

source_name: Cell line

growth_protocol: C4-2B and RV1 were cultured in free Gln RPMI-1640 supplemented with 5 % FBS

extract_protocol:
Total RNA was extracted and prepared using the RNeasy Mini extraction kit (Qiagen, Germantown, MA) according to the manufacturer’s instructions
Performed by Novogene company

treatment_protocol: Gln studies were performed in Gln-free RPMI 1640 supplemented with indicated concentrations of L-Gln and 56 mer

value: Cell line

value: Prostate cancer

value: WT

value: L-Glutamine, 56 mer


title: RV6: RV1, L-Gln 2mM, 56 mer 50 nM 48h


title: synovial fluid (OA) sample 49


title: CB11B_P_Well_F10


title: RV4: RV1, L-Gln 2mM, 56 mer 50 nM 48h


title: synovial fluid (OA) sample 41


title: RV3: RV1, L-Gln 2mM, 48h

value: L-Glutamine


title: CB11B_P_Well_F09


title: Petergof_XN_rep1

source_name: Petergof, 6h extended night

value: whole rosettes

value: Petergof

value: 6h extended night (XN; ZT30)


title: synovial fluid (OA) sample 5

value: extracellular vesicles


title: CB11B_P_Well_F07

value: Bone marrow derived APC


title: RV2: RV1, L-Gln 2mM, 48h


title: CB11B_P_Well_F08

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: B2x2_D_IR2_r1

value: Embryonic stem cells (ESCs)


title: Petergof_EN_rep2

source_name: Petergof, end of the night

value: end of the night (EN; ZT24)


title: Petergof_EN_rep1


title: Petergof_XN_rep2


title: CB11B_P_Well_F06


title: C46: C42B, L-Gln 2mM, 56 mer 50 nM 48h


title: synovial fluid (OA) sample 40


title: synovial fluid (OA) sample 35


title: CB11B_P_Well_F11


title: Petergof_ED_rep1

source_name: Petergof, end of the day

value: end of the day (ED; ZT8)


title: C45: C42B, L-Gln 2mM, 56 mer 50 nM 48h


title: Petergof_ED_rep2


title: RV1: RV1, L-Gln 2mM, 48h


title: CB11B_P_Well_F05


title: CB11B_P_Well_F04


title: Old1_XN_rep2

source_name: Old1, 6h extended night


title: C44: C42B, L-Gln 2mM, 56 mer 50 nM 48h


title: synovial fluid (OA) sample 13


title: CB11B_P_Well_F03


title: synovial fluid (OA) sample 10


title: Old1_XN_rep1


title: C42: C42B, L-Gln 2mM, 48h


title: synovial fluid (CTRL) sample 26

value: CTRL


title: Old1_EN_rep2

source_name: Old1, end of the night


title: synovial fluid (CTRL) sample 17

source_name: synovial fluid

value: synovial fluid


title: C41: C42B, L-Gln 2mM, 48h


title: CB11B_P_Well_F01


title: CB11B_P_Well_F02


title: synovial fluid (CTRL) sample 11


title: Old1_EN_rep1


title: CB11B_P_Well_E11


title: synovial fluid (OA) sample 18

value: OA


title: Old1_ED_rep2

source_name: Old1, end of the day


title: 24 hr - IFNG + IL17

city: Frederick

first: David

last: Wink

state: MD

address: 1050 Boyles St

department: CCR

institute: NCI

description: 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)
Analysis performed using sequencing facility bioinformatic established in-house single-cell pipeline, which included popular software packages such as Seurat, ClusterPro, and SingleR  R package for QC, clustering, pathway, and cell type analysis.
scRNAseq data were visualized and explored in the Loupe browser v6 which provided by 10x Genomics
scRNAseq data were imported to Partek Flow for DEG detection
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: breast

extract_protocol:
Right after the treatment period ended, MDA-MB-231 cells were trypsinized and then kept in a suspension mode for cell viability assessment and the subsequent library prep using the 10x Genomics Chromium Single Cell V3  3’ capture kit.
The library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, MDA-MB-231 cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse-transcripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriated-sized fragments were selected with SPRIselect reagent for subsequent library construction. The amplified and purified cDNA was prepared and loaded to the automation platform SciClone to finish the single-cell library prep for Illumina sequencing.

value: breast

value: Epithelial

value: 24 hr - IFNG + IL17


title: CB11B_P_Well_E10


title: synovial fluid (CTRL) sample 38


title: 48 hr - IFNG + IL17

description: 10x Genomics

value: 48 hr - IFNG + IL17


title: CB11B_P_Well_E12


title: C43: C42B, L-Gln 2mM, 48h

value: Cell line

value: Prostate cancer

value: WT

value: L-Glutamine


title: Mh1_XN_rep2

source_name: Mh1, 6h extended night

value: whole rosettes

value: 6h extended night (XN; ZT30)


title: Old1_ED_rep1


title: synovial fluid (CTRL) sample 2

value: extracellular vesicles


title: 48 hr - IFNG + LPS

description: 10x Genomics

value: 48 hr - IFNG + LPS


title: 24 hr - IFNG + LPS

description: 10x Genomics

value: 24 hr - IFNG + LPS


title: Mh1_XN_rep1


title: CB11B_P_Well_E09

source_name: Bone marrow derived APC

value: Bone marrow derived APC

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: synovial fluid (CTRL) sample 16

value: synovial fluid

value: CTRL


title: CB11B_P_Well_E08


title: 48 hr - IFNG + TNFA

description: 10x Genomics

value: breast

value: 48 hr - IFNG + TNFA


title: synovial fluid (CTRL) sample 14


title: CB11B_P_Well_E07


title: 24 hr - IFNG + TNFA

description: 10x Genomics

value: Epithelial

value: 24 hr - IFNG + TNFA


title: synovial fluid (CTRL) sample 29


title: CB11B_P_Well_E06


title: Mh1_EN_rep1

source_name: Mh1, end of the night

value: end of the night (EN; ZT24)


title: 48 hr - IFNG + IL1B

description: 10x Genomics

value: 48 hr - IFNG + IL1B


title: synovial fluid (CTRL) sample 33


title: synovial fluid (CTRL) sample 12


title: CB11B_P_Well_E04


title: Mh1_ED_rep2

source_name: Mh1, end of the day

value: end of the day (ED; ZT8)


title: CB11B_P_Well_E03


title: 24 hr - LPS

description: 10x Genomics

value: 24 hr - LPS


title: 48 hr - LPS

description: 10x Genomics

value: 48 hr - LPS


title: synovial fluid (CTRL) sample 46


title: synovial fluid (CTRL) sample 21


title: Lip0_XN_rep2

source_name: Lip0, 6h extended night

value: whole rosettes

value: 6h extended night (XN; ZT30)


title: Mh1_EN_rep2


title: 24 hr - IL17

description: 10x Genomics


title: synovial fluid (CTRL) sample 1

value: extracellular vesicles


title: synovial fluid (CTRL) sample 50


title: Mh1_ED_rep1


title: Lip0_EN_rep2

source_name: Lip0, end of the night


title: CB11B_P_Well_E05


title: CB11B_P_Well_E01


title: Lip0_ED_rep2

source_name: Lip0, end of the day


title: Lip0_EN_rep1


title: 48 hr - TNFA

description: 10x Genomics

value: 48 hr - TNFA


title: synovial fluid (CTRL) sample 19


title: CB11B_P_Well_D12

value: Bone marrow derived APC


title: CB11B_P_Well_D11

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: 24 hr - TNFA

description: 10x Genomics

value: 24 hr - TNFA


title: Lip0_ED_rep1


title: synovial fluid (CTRL) sample 25

value: synovial fluid

value: CTRL


title: 48 hr - IL17

description: 10x Genomics

value: breast


title: CB11B_P_Well_E02


title: Lip0_XN_rep1


title: CB11B_P_Well_D10


title: synovial fluid (CTRL) sample 6


title: 48 hr - IL1B

description: 10x Genomics

value: Epithelial

value: 48 hr - IL1B


title: Kn0_XN_rep2

source_name: Kn0, 6h extended night


title: Kn0_XN_rep1


title: 24 hr - IFNG + IL1B

description: 10x Genomics

value: 24 hr - IFNG + IL1B


title: synovial fluid (CTRL) sample 42


title: synovial fluid (CTRL) sample 22


title: 48 hr - IFNG

description: 10x Genomics

value: 48 hr - IFNG


title: CB11B_P_Well_D08


title: 24 hr - IL1B

description: 10x Genomics

value: 24 hr - IL1B


title: Kn0_EN_rep2

source_name: Kn0, end of the night

value: end of the night (EN; ZT24)


title: 24 hr - IFNG

description: 10x Genomics

value: 24 hr - IFNG


title: CB11B_P_Well_D06


title: 48 hr - Control

description: 10x Genomics

value: 48 hr - Control


title: synovial fluid (CTRL) sample 28


title: Kn0_ED_rep2

source_name: Kn0, end of the day

value: whole rosettes

value: end of the day (ED; ZT8)


title: synovial fluid (CTRL) sample 51

value: extracellular vesicles


title: APC/KRAS/TP53 mutant colonoid leChRO-seq sample  #2

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

department: Biomedical Science

institute: Cornell University

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel,  KRAS G12V mutation, and TP53-/- mutation induced using CRISPR.
ChRO_miR_RLOG-LIMMA_normCount.csv
AKP_DoxRC2

data_processing:
library strategy: Length extension chromatin run-on sequencing (leChRO-seq)
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNA-seq), or proseq2.0 (leChRO).
smRNA- and RNA-seq data was normalized using DESeq2. leChRO-seq data was rlog transformed followed by limma batch correction.
Assembly: leChRO-seq (hg38), RNA-seq (hg38), smRNA-seq (hg19)
Supplementary files format and content: DESeq2 normalized counts, Rlog normalized + limma batch corrected counts

extract_protocol:
Libraries were prepared according to the protocol outlined in Chu, T. et al. Nature Genetics (2018)
RNA was isolated according to the leChRO-seq protocol described in Chu, T. et al. Nature Genetics (2018)

value: Colon

value: APC/KRAS/TP53 mutant colonoid


title: synovial fluid (CTRL) sample 44


title: 24 hr - Control

description: 10x Genomics

value: 24 hr - Control


title: CB11B_P_Well_D04

value: Bone marrow derived APC

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Kn0_ED_rep1


title: CB11B_P_Well_D03


title: synovial fluid (CTRL) sample 8

value: synovial fluid

value: CTRL


title: Kl0_XN_rep2

source_name: Kl0, 6h extended night

value: 6h extended night (XN; ZT30)


title: CB11B_P_Well_D05


title: CB11B_P_Well_D09


title: synovial fluid (CTRL) sample 30


title: APC/KRAS/TP53 mutant colonoid leChRO-seq sample  #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel,  KRAS G12V mutation, and TP53-/- mutation induced using CRISPR.
ChRO_miR_RLOG-LIMMA_normCount.csv
AKP_DoxRC1


title: CB11B_P_Well_D07


title: APC/KRAS mutant colonoid leChRO-seq sample  #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel and KRAS G12V mutation induced using CRISPR.
ChRO_miR_RLOG-LIMMA_normCount.csv
AK_DoxRC2

source_name: APC/KRAS mutant colonoid leChRO-seq

value: APC/KRAS mutant colonoid


title: synovial fluid (CTRL) sample 20


title: Kl0_XN_rep1


title: APC/KRAS mutant colonoid leChRO-seq sample  #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel and KRAS G12V mutation induced using CRISPR.
ChRO_miR_RLOG-LIMMA_normCount.csv
AK_DoxRC1


title: RRS7_ED_rep2

source_name: RRS7, end of the day


title: synovial fluid (CTRL) sample 24


title: Kl0_EN_rep2

source_name: Kl0, end of the night


title: Kn0_EN_rep1


title: APC mutant colonoid leChRO-seq sample  #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel induced using CRISPR.
ChRO_miR_RLOG-LIMMA_normCount.csv
A_DoxRC2

source_name: APC mutant colonoid leChRO-seq

value: APC mutant colonoid


title: CB11B_P_Well_D01

value: 6 hr stimulation with poly (I:C)


title: CB11B_P_Well_C12


title: Kl0_ED_rep2

source_name: Kl0, end of the day


title: Kl0_ED_rep1


title: iGFP dox colonoid leChRO-seq sample  #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
ChRO_miR_RLOG-LIMMA_normCount.csv
iGFP_DoxRC2

source_name: iGFP dox colonoid leChRO-seq

value: iGFP dox colonoid


title: Hl3_XN_rep2

source_name: Hl3, 6h extended night


title: CB11B_P_Well_C11

source_name: Bone marrow derived APC


title: CB11B_P_Well_C10


title: CB11B_P_Well_D02


title: iGFP dox colonoid leChRO-seq sample  #1

description:
Batch 2. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
ChRO_miR_RLOG-LIMMA_normCount.csv
iGFP_DoxR1


title: Kl0_EN_rep1

value: end of the night (EN; ZT24)


title: CB11B_P_Well_C09


title: Liver_PBS-2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

data_processing:
reads were qualty checked with fastqc, but no preprocessig was required
Mapping was performed with STAR 2.7.10a against the sus scrofa 11.1 version of the reference genome using the genequant option and otherwise standard settings to directly obtain counts of reads assigned to features
The DESeq2 R package was used to perfom all data procesing steps and call differentially expressed genes
Assembly: sus scrofa 11.1
Supplementary files format and content: a tab separated count matrix with raw count data for all samples

organism: Sus scrofa

source_name: liver

extract_protocol:
after 15h the pigs were euthanized and samples from the fourth segment liver were isolalated and stored in RNAlater. Total RNA was isolated using the Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions
Library preparation was performed according to the Illumine TruSeq3 stranded library prep protoco

treatment_protocol: a double lumen catheter was surgically placed in the external jugular vein of piglets, and after one day of recovery a continous infusion of ultrapure LPS from Escherichia coli (O111:B4) (Invitrogen, Toulouse, France) over 15h was administered

value: liver

value: WT

value: PBS


title: Liver_PBS-1


title: Hl3_XN_rep1

value: whole rosettes


title: Liver_LPS-3

value: LPS


title: Liver_LPS-2


title: Liver_PBS-3


title: CB11B_P_Well_C07


title: CB11B_P_Well_C08


title: APC mutant colonoid leChRO-seq sample  #1

description:
Batch 2. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel induced using CRISPR.
ChRO_miR_RLOG-LIMMA_normCount.csv
A_DoxR1

value: Colon


title: Hl3_EN_rep1

source_name: Hl3, end of the night


title: Hl3_ED_rep2

source_name: Hl3, end of the day

value: end of the day (ED; ZT8)


title: Pig 3 - Enterococcus faecium + Poly I:C

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Sus Scrofa genome (11.1)
DEG assessed using DeSeq2
Assembly: Sscrofa11.1
Supplementary files format and content: excel file with count data and Ensembl gene ID for each sample

source_name: Alveolar Macrophage

growth_protocol: Macrophages were cultured using standard cell culture techniques for 24 hours

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen)
Standard Illumina

treatment_protocol: treated for 24 hours with no treatment, poly I:C, Bacillus subtilis, Enterococcus faecium, or poly I:C combined with either of the bacterial strains

value: Alveolar Macrophage

value: Enterococcus faecium + Poly I:C


title: Liver_LPS-1


title: CB11B_P_Well_C06

data_processing:
Sequence data were analysed using the Seven Bridges Genomics bioinformatics platform (BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0). This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
A cell was considered to be infected if there was at least one GFP sequence read count. This information was then used to define the groups to compare in EdgeR. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05).
Precise WTA Sample Demultiplexing:Paired-end reads are demultiplexed per well based on the sequence of the sample index. This sample index is found in the first 8 bases of Read 01. The Molecular Index is found in Read 01, in positions 8 to 16. The demultiplexing process also includes a structure filtering step. After filtering, the final step in this process stores the Molecular Index in the demultiplexed FASTQ files by appending the index to the sequence headers of Read 02 FASTQ files. The Read 02s from each well are trimmed by Flexbar to remove any Illumina adapter contaminants and mapped to the reference genome using STAR.
Precise WTA Alignment Quantification: After Read 02s are aligned using STAR, the alignments are assigned to gene counts using a custom implementation of HTSeq-count. The number of reads mapping to each gene is generated in the DBEC Read Mapping Report. The unique counts for molecular indices are calculated in the DBEC Molecular Index Mapping Report
Genome_build: mm9
Supplementary_files_format_and_content: text document (after removal of Molecular indices error using Recursive Substitution Error Correction™ (RSEC) and Distribution-Based Error Correction™ (DBEC))

extract_protocol:
The cells are collected in WTA single cell encoding plate, RNA secondary structure is done at 65C for 3 minutes (hold at 4C), mastermix containing BD customised RT enzymes is added (PN 650000041) and run at 42C for 30 minutes, heat inactivated at 80C for 5 minutes before holding at 4C. The samples is pooled and purify before library prep.
Libraries of the cellular RNA were made using the BD WTA single cell kit and sequenced using MiSeq V2 from Illumina (BM-DC, BM-M, DN).

value: Bone marrow derived APC


title: FOXC1 OE

city: Shanghai

first: Bin

address: Jinzun Road

institute: Shanghai jiaotong University

description: FOXC1 overexpression

data_processing:
CUT&Tag-Seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Briefly, 1×105 cells were treated with ConA beads, then incubated with primary antibody overnight at 4℃. Cells were reacted with secondary antibody for 1 h after being washed for three times.
CUT&Tag assay was performed using Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme) as indicated. Samples were incubated with pAG-Tn5 for 1 h. DNA tagmentation was performed at 37 °C for 1h and followed by DNA extraction. PCR was applied to amplify the libraries followed by product purification. Sequencing and data analysis were performed by Novogene Co. Ltd using Novaseq-PE150 (Illumina).

value: HiPSC-derived cardiomyocytes

tag: chip antibody


title: Control

description: Control


title: Pig 2 - Enterococcus faecium + Poly I:C


title: Hl3_ED_rep1


title: Pig 1 - Enterococcus faecium + Poly I:C


title: HepG2 UBR7Sh_ TREATED2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
Basecalls performed using CASAVA version 1.4
NFCORE-RNASEQ was used to identify transcripts from the raw data
Raw read counts were normalized for obtaining FPKM values and Voom package was used to identify differentially expresssed genes
Assembly: GrCH38
Supplementary files format and content: FPKM data with Gene Identifier

source_name: Human Liver cancer cell

extract_protocol:
Total RNA from the sample is extracted, mRNA was purified using oligo-dT beads (TruSeq RNA Sample Preparation Kit, Illumina) taking 1 μg of intact total RNA.
Sequencing libraries were generated using TruSeq RNA Library Prep Kits for Illumina® (NEB, USA) according to the manufacturer’s instructions, and index codes were added to attribute sequences to each sample

treatment_protocol: HepG2 PLKO1 control and UBR7 knockdown cells were transfected with HBV1.3 mer plasmid for 24 hours

value: Human Liver Cancer cell line

value: 1.3 mer transfected

value: UBR7 knockdown


title: Ei2_XN_rep2

source_name: Ei2, 6h extended night

value: 6h extended night (XN; ZT30)


title: iGFP noDox colonoid leChRO-seq sample  #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
ChRO_miR_RLOG-LIMMA_normCount.csv
iGFP_noDoxRC2

source_name: iGFP noDox colonoid leChRO-seq

value: iGFP noDox colonoid


title: CB11B_P_Well_C05

city: Ede

first: Alphonsus

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

value: 6 hr stimulation with poly (I:C)


title: CB11B_P_Well_C04


title: iGFP noDox colonoid leChRO-seq sample  #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
ChRO_miR_RLOG-LIMMA_normCount.csv
iGFP_noDoxRC1


title: Pig 3 - Bacillus subtilis + Poly I:C

value: Bacillus subtilis + Poly I:C


title: CB11B_P_Well_C02

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: HepG2 UBR7Sh_CTRL2

value: UNTREATED


title: Pig 2 - Bacillus subtilis + Poly I:C


title: CB11B_P_Well_C03


title: HepG2 UBR7Sh_ TREATED1


title: Ei2_XN_rep1

value: whole rosettes


title: HepG2 UBR7Sh_CTRL1


title: Pig 1 - Bacillus subtilis + Poly I:C


title: HepG2 PLKO1_ TREATED2

value: control


title: CB11B_P_Well_B12


title: Ei2_EN_rep2

source_name: Ei2, end of the night

value: end of the night (EN; ZT24)


title: Pig 3 - Enterococcus faecium

value: Enterococcus faecium


title: CB11B_P_Well_B11


title: CB11B_P_Well_B10


title: Pig 2 - Enterococcus faecium

value: Alveolar Macrophage


title: HepG2 PLKO1_CTRL2


title: Pig 1 - Enterococcus faecium


title: Da0_XN_rep2

source_name: Da0, 6h extended night


title: HepG2 PLKO1_CTRL1


title: Da0_XN_rep1


title: CB11B_P_Well_C01


title: MV4-11 treated with JOA_3

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: FPKM value

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: incubating with JOA for 48 h

tag: agent


title: Pig 2 - Bacillus subtilis

value: Bacillus subtilis


title: HepG2 PLKO1_ TREATED1


title: MV4-11 treated with JOA_2


title: CB11B_P_Well_B07

address: redeemers' university ede osun state

value: Bone marrow derived APC


title: Ei2_ED_rep1

source_name: Ei2, end of the day

value: end of the day (ED; ZT8)


title: Pig 1 - Bacillus subtilis


title: Da0_EN_rep1

source_name: Da0, end of the night


title: CB11B_P_Well_B06


title: Pig 3 - Poly I:C

value: Poly I:C


title: Ei2_ED_rep2


title: CB11B_P_Well_B09


title: Da0_ED_rep2

source_name: Da0, end of the day


title: Pig 3 - Bacillus subtilis


title: MV4-11 treated with control_3

value: incubating with control for 48 h

value: Control


title: Cvi_XN_rep2

source_name: Cvi, 6h extended night

value: Cvi

value: 6h extended night (XN; ZT30)


title: Pig 2 - Poly I:C


title: MV4-11 treated with control_2


title: CB11B_P_Well_B04


title: Da0_ED_rep1


title: CB11B_P_Well_B08


title: Hl3_EN_rep2


title: CB11B_P_Well_B05


title: Cvi_XN_rep1


title: MV4-11 treated with control_1


title: MV4-11 treated with JOA_1


title: Pig 3 - Control (no treatment)


title: CB11B_P_Well_B03


title: Cvi_EN_rep1

source_name: Cvi, end of the night


title: Pig 2 - Control (no treatment)


title: 15

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

data_processing:
Raw Count Matrix was obtained from the standard workflow used at The McGill University and Génome Québec Innovation Centre
Features with at least one count per million (CPM) were kept prior to transformation.
Raw Counts were transformed into log2-CPM values using the voom method from the limma Bioconductor R package.
Assembly: GRCh37
Supplementary files format and content: Matrix table with features as rows. First column is the feature ID and each subsequent column represent one sample.

source_name: HIV+ART 7

extract_protocol:
All Prep DNA/RNA/miRNA Universal Kit, Qiagen)
cDNA libraries and RNA-seq were performed by The McGill University and Génome Québec Innovation Centre, Montreal, QC. 100 bp paired-end sequencing was performed on an Illumina-NovaSeq(depth was above 150 million reads).
RNA-Seq (rRNA-depleted stranded (HMR))

treatment_protocol: MDM were generated by culturing monocytes in the presence of M-CSF (10 ng/mL; R&D Systems) for 6 days, with media refreshed every 2 days. In parallel, ATRA-MDM were generated by culturing monocytes in the presence of M-CSF and all trans retinoic acid (ATRA; 10 nM, Sigma) for 6 days, with media refreshed every 2 days

value: Monocyte-derived macrophages (MDMs)

tag: barcode

tag: stimulation

value: M-CSF ATRA


title: CB11B_P_Well_B01

last: Ugwu

value: 48hr treatment with Phosphate buffer saline (PBS)


title: 5

source_name: HIV+ART 5

value: M-CSF


title: Pig 1 - Control (no treatment)

value: control


title: Pig 1 - Poly I:C


title: 14

source_name: HIV+ART 6


title: Cvi_ED_rep2

source_name: Cvi, end of the day

value: whole rosettes


title: CB11B_P_Well_A11

source_name: Bone marrow derived APC


title: 3

source_name: HIV+ART 3


title: 13


title: CB11B_P_Well_A10


title: Cvi_ED_rep1


title: Col0_XN_rep2

source_name: Col0, 6h extended night


title: CB11B_P_Well_B02

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: CB11B_P_Well_A09


title: Col0_EN_rep2

source_name: Col0, end of the night

value: end of the night (EN; ZT24)


title: Col0_EN_rep1


title: 2

source_name: HIV+ART 2


title: Da0_EN_rep2


title: CB11B_P_Well_A08


title: CB11B_P_Well_A12


title: CB11B_P_Well_A07


title: Col0_XN_rep1


title: CB11B_P_Well_A06


title: 1

source_name: HIV+ART 1


title: 10


title: 9


title: 11


title: Col0_ED_rep1

source_name: Col0, end of the day


title: 7


title: 6


title: Col0_ED_rep2


title: T98G cells, shSLC1A5 3

city: Xi'an

first: Liying

last: Han

state: Shaanxi Province

address: Xinsi Road No.1

institute: Tangdu Hospital

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens.
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts.
Supplementary files format and content: StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).

growth_protocol: T98G cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent.
RNA was harvested using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: cell line

value: T98G cell line

value: SLC1A5 knockdown


title: CB11B_P_Well_A02

value: Bone marrow derived APC


title: CB11B_P_Well_A03


title: CB11B_P_Well_A05


title: CB11B_P_Well_A04


title: CB11B_P_Well_A01


title: Muscle-invasive bladder cancer 65503

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

country: United Kingdom

institute: University of Bangor

description: Muscle-invasive bladder cancer

hyb_protocol: Sample hybridisation on Clariom S arrays was carried out by Yourgene Health (Manchester, UK). Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RNA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

scan_protocol: standard Affymetrix protocol

data_processing: The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.

source_name: Anonymised

label_protocol: RNA extracted from both sample cohorts were subject to Clariom S analysis. RNA (8 ng/µl in a 9 µl volume) was prepared for gene expression arrays with the Clariom S pico HT human assay (Thermo Fisher Scientific).

extract_protocol: Two 10µm sections from FFPE bladder cancer embodied blocks. RNA was extracted from the two 10 µm sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).

tag: condition

value: Muscle-invasive bladder cancer


title: T98G cells, shSLC1A5 2


title: CD11B-701_Well_H12

tag: strain

value: 12hr infection with LCMV Cl 13


title: T98G cells, shSLC1A5 1


title: Muscle-invasive bladder cancer 59609

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 60501

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 59606

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 61503

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 59506

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 59503

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 60401

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_H11


title: T98G cells, shControl 3


title: C24_XN_rep2

source_name: C24, 6h extended night

tag: genotype


title: C24_ED_rep1

source_name: C24, end of the day

tag: tissue

value: end of the day (ED; ZT8)


title: C24_XN_rep1


title: T98G cells, shControl 2


title: CD11B-701_Well_H10


title: Bu2_XN_rep2

source_name: Bu2, 6h extended night


title: C24_EN_rep1

source_name: C24, end of the night


title: Ei2_EN_rep1

source_name: Ei2, end of the night


title: Muscle-invasive bladder cancer 61202

description: Muscle-invasive bladder cancer


title: T98G cells, shControl 1


title: Muscle-invasive bladder cancer 62101

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_H09


title: CD11B-701_Well_H08


title: Ovary, rep4

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

data_processing:
Raw sequencing files were generated by using bcl2fastq (v2.17.1.14).
Featurecounts was used to make raw counts table.
Differently expressed genes were determined by edgeR and defined by log2 fold change above 2, P-value < 0.01, FDR < 0.01.
Assembly: GRCh38
Supplementary files format and content: bulk_RNAseq_rawcounts.txt: Tab-delimited text file includes raw gene counts for each Sample.

source_name: Ovary

extract_protocol: Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq6000.

value: Ovary

tag: Sex

value: Female


title: Muscle-invasive bladder cancer 57401

description: Muscle-invasive bladder cancer


title: Ovary, rep3


title: Bu2_XN_rep1

value: 6h extended night (XN; ZT30)


title: C24_EN_rep2


title: CD11B-701_Well_H07


title: Muscle-invasive bladder cancer 59604

description: Muscle-invasive bladder cancer


title: Ovary, rep2


title: CD11B-701_Well_H06


title: C24_ED_rep2


title: CD11B-701_Well_H05


title: Ovary, rep1


title: CD11B-701_Well_H04


title: Muscle-invasive bladder cancer 55504

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 55405

description: Muscle-invasive bladder cancer


title: Epithelial ovarian cancer, rep10

source_name: Epithelial ovarian cancer

value: Epithelial ovarian cancer


title: Bu2_ED_rep2

source_name: Bu2, end of the day


title: CD11B-701_Well_H02


title: Muscle-invasive bladder cancer 55606

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 53504

description: Muscle-invasive bladder cancer


title: Epithelial ovarian cancer, rep9


title: Muscle-invasive bladder cancer 55401

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 53605

description: Muscle-invasive bladder cancer


title: Bu2_EN_rep2

source_name: Bu2, end of the night


title: Muscle-invasive bladder cancer 55505

description: Muscle-invasive bladder cancer


title: Bu2_EN_rep1


title: CD11B-701_Well_G12

source_name: Bone marrow derived APC


title: CD11B-701_Well_H01


title: Muscle-invasive bladder cancer 53603

description: Muscle-invasive bladder cancer


title: Epithelial ovarian cancer, rep6


title: Muscle-invasive bladder cancer 53402

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_H03


title: Bsch2_EN_rep2

source_name: Bsch2, end of the night


title: Bu2_ED_rep1


title: Muscle-invasive bladder cancer 53502

description: Muscle-invasive bladder cancer


title: Bsch2_EN_rep1


title: Muscle-invasive bladder cancer 53401

description: Muscle-invasive bladder cancer


title: Epithelial ovarian cancer, rep7


title: Epithelial ovarian cancer, rep8


title: Bsch2_ED_rep1

source_name: Bsch2, end of the day


title: Bsch2_XN_rep2

source_name: Bsch2, 6h extended night


title: Bsch2_XN_rep1


title: Br0_XN_rep2

source_name: Br0, 6h extended night


title: Bsch2_ED_rep2


title: CD11B-701_Well_G11


title: Br0_XN_rep1


title: Muscle-invasive bladder cancer 52503

description: Muscle-invasive bladder cancer


title: Epithelial ovarian cancer, rep5


title: CD11B-701_Well_G10


title: Epithelial ovarian cancer, rep4


title: Muscle-invasive bladder cancer 17403

description: Muscle-invasive bladder cancer


title: Epithelial ovarian cancer, rep3


title: CD11B-701_Well_G09


title: CD11B-701_Well_G08


title: Epithelial ovarian cancer, rep1


title: CD11B-701_Well_G07


title: Epithelial ovarian cancer, rep2


title: CD11B-701_Well_G06


title: Muscle-invasive bladder cancer 17401

description: Muscle-invasive bladder cancer


title: Fimbriae, rep4

source_name: Fallopian tube (fimbriae)

value: Fallopian tube (fimbriae)


title: Fimbriae, rep3


title: Muscle-invasive bladder cancer 17102

description: Muscle-invasive bladder cancer


title: Br0_EN_rep2

source_name: Br0, end of the night


title: CD11B-701_Well_G05


title: Br0_EN_rep1


title: Fimbriae, rep2


title: CD11B-701_Well_G04


title: Muscle-invasive bladder cancer 16401

description: Muscle-invasive bladder cancer

source_name: Anonymised


title: Muscle-invasive bladder cancer 16402

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_G03


title: CD11B-701_Well_G02


title: Br0_ED_rep2

source_name: Br0, end of the day


title: Fimbriae, rep1


title: Ampulla, rep4

source_name: Fallopian tube (ampulla)

value: Fallopian tube (ampulla)


title: Muscle-invasive bladder cancer 16101

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 15301

description: Muscle-invasive bladder cancer


title: Bla11_XN_rep2

source_name: Bla11, 6h extended night


title: CD11B-701_Well_G01


title: Bla11_EN_rep2

source_name: Bla11, end of the night


title: CD11B-701_Well_F12


title: Muscle-invasive bladder cancer 15403

description: Muscle-invasive bladder cancer


title: Ampulla, rep2


title: Ampulla, rep3


title: Br0_ED_rep1


title: Ampulla, rep1


title: Bla11_EN_rep1


title: Bla11_XN_rep1


title: Bla11_ED_rep2

source_name: Bla11, end of the day


title: Bla11_ED_rep1


title: Muscle-invasive bladder cancer 15111

description: Muscle-invasive bladder cancer


title: Isthmus, rep4

source_name: Fallopian tube (isthmus)

value: Fallopian tube (isthmus)


title: Muscle-invasive bladder cancer 15113

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_F11


title: Isthmus, rep3


title: Muscle-invasive bladder cancer 15110

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_F10


title: Ang0_XN_rep2

source_name: Ang0, 6h extended night


title: Muscle-invasive bladder cancer 15108

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 15109

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 14408

description: Muscle-invasive bladder cancer


title: Isthmus, rep2


title: Ang0_XN_rep1


title: CD11B-701_Well_F09


title: Isthmus, rep1


title: CD11B-701_Well_F07


title: CD11B-701_Well_F08


title: Ang0_EN_rep2

source_name: Ang0, end of the night


title: CD11B-701_Well_F06


title: Ang0_ED_rep2

source_name: Ang0, end of the day


title: Homo_PC9_NC_rep2

city: luzhou

first: Yan

last: Li

address: No. 25 Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

description: Gene expression data from non-small cell lung cancer

hyb_protocol: sample was hybridized to the Affymetrix Clariom S Assay,human (Cat No 902926) for 16-18 h at 45°C. Following hybridization, the microarrays were washed and stained with Streptavidin Phycoerythrin on the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G.

data_processing:
The data were analyzed with the robust multichip analysis (RMA) algorithm using default analysis settings and global scaling as a normalization method Values are presented according to log2 RMA signal intensity
We defined the genes with a fold-change of more than 1.5 or less than −1.5 and a p-value of less than 0.05 as different expression genes, which were selected to undergo basic analysis

label_protocol: sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT)

growth_protocol: The cells were cultured in Dulbecco's modified eagle medium (Gibco)for PC9 or F-12K(Gibco Laboratories, USA) for A549 supplemented with 10% fetal bovine serum (Gibco) at 37℃ in 5% CO2.

extract_protocol: Total RNA was extracted by Trizol (Invitrogen, Carlsbad, CA, USA), and a total of 500 ng RNA was used for cDNA synthesis

treatment_protocol: EN2 or control Neo retroviral supernatants collected from 293FT packaging cell was used to infect PC9 and A549 cells. The stable cells were selected by genemycin.

value: non-small cell lung cancer cell line


title: CD11B-701_Well_F02

source_name: Bone marrow derived APC


title: CD11B-701_Well_F05


title: CD11B-701_Well_F04


title: Ang0_ED_rep1

value: whole rosettes


title: CD11B-701_Well_F03


title: Homo_PC9_NC_rep1


title: Muscle-invasive bladder cancer 14403

description: Muscle-invasive bladder cancer


title: 3_GW15

city: BeiJing

first: hao

last: dong

address: Datun Rd

institute: ibp

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: hg19
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Visium spatial

source_name: spinal cord

extract_protocol:
Freshly collected tissue processed as 10x protocal
Library was performed according to the single cell 3’ v2,v3 protocol, and Visium protocal of 10x Genomics.

value: spinal cord

tag: time point


title: Muscle-invasive bladder cancer 11401

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 14407

description: Muscle-invasive bladder cancer


title: Homo_A549_NC_rep2


title: Muscle-invasive bladder cancer 11202

description: Muscle-invasive bladder cancer


title: Homo_PC9_EN2_rep1


title: 7_GW27

description: 10x Genomics


title: Muscle-invasive bladder cancer 11503

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_F01


title: 4_GW13

description: 10x Genomics


title: CD11B-701_Well_E12


title: Tailbud single cells at 16 hpf

city: Irvine

first: Thomas

middle: F

last: Schilling

address: 4462 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California Irvine

data_processing:
FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger.
Further processing was performed using Seurat v3 in R
Low quality cells and doublets were excluded based on thresholds for number of genes detected (>1500; <4000)
Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected (<4%)
Genome_build: GRCz11
Supplementary_files_format_and_content: .csv file contains counts matrix for each cell that met quality thresholds

organism: Danio rerio

source_name: Dissociated tailbuds from 30 16 hpf embryos

extract_protocol:
Tailbuds were manually dissected and then dissociated using collagenase P and trypsin
Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7, which used chemistry v3

tag: transgenic

value: AB wildtypes

value: 16 hpf embryo

value: dissociated tailbuds


title: Ang0_EN_rep1

city: Potsdam

first: Eva-Theresa

address: Am Muehlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

data_processing: Background correction and quantile normalization were performed using the ‘preprocessCore’ and ‘affyPLM’ packages (Bioconductor; Gentleman et al. in Genome Biology 2004, 5(10): R80) to calculate RMA signal intensities. To identify probes potentially affected by SFPs in the raw data, a combination of a median polish method, adapted from (Xie et al. in Theoretical and Applied Genetics 2009, 119(1): 151-164), and a one-way ANOVA were used to select individual probes that were significantly altered between accessions (p < 0.01). To identify probes, which showed lower probe signal intensity in an accession compared to Col-0, significant contrasts were subsequently identified in a post-hoc Tukey HSD test (p < 0.01). The list of 21,297 probes with significant signal alterations in any of the accessions compared to Col-0, was combined with 22,297 Cvi sequence SNPs available from the 1,001 genome project. Additional SNPs were added by taking available data for 19 of the 20 accessions (except for Bu-2, Bu-0 used instead) derived from genotyping accessions using a custom Affymetrix SNP chip containing 250K SNPs (Atwell et al. in Nature 2010, 465(7298): 627-631). The final list of potentially SNP containing probes comprised 44,863 SNPs. Joint masking of all these probes led to a removal of 1,481 probe sets that had <6 probes remaining, reducing the number of probe sets to a final number of 21,329.

extract_protocol: Material from a pool of 5 rosettes was snap frozen in liquid nitrogen and stored until further use at -80C or was processed directly as follows. Frozen plant material was homogenized and total RNA was extracted from 50 mg of homogenized plant material using Qiagen RNeasy Plant mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Before and after DNaseI digestion (Turbo DNA-free DNase I; Applied Biosystems/Ambion, Darmstadt, Germany), RNA concentration and integrity were measured using a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA) and an Agilent-2100 Bioanalyzer using RNA 6000 NanoChips (Agilent Technologies, Böblingen, Germany).

value: end of the night (EN; ZT24)


title: Muscle-invasive bladder cancer 15105

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Total cells Control day4 rep2

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

institute: Université Libre de Bruxelles

data_processing:
For main steps of pre-processing and mapping of ATACseq data, a local installation of Galaxy platform was used (use.galaxu.eu; Afgan et al 2018). Briefly, adapter sequences were removed with Trim Galore, using default parameters. ATACseq paired-end reads were  aligned to mouse genome Grcm38/mm10 with Bowtie2 (v.2.3.4.3), modifying default parameters to include fragments of up 1000bp, allowing dovetailing and using a “very sensitive option” preset. Subsequently, mitochondrial genes, bad quality mapped sequences and PCR  duplicates were removed. Peak calling was performed for each sample using MACS2(v.2.1.1.20160309.6), with parameters setting of -q 0.05 and -- shift 0. Peaks from all samples were merged for downstream analysis. Scaling of bam files generated by MACS2 were performed using BAMscale and used for visualization of data tracks with Integrative Genomics Viewer  (IGV).
Genome_build: Grcm38/mm10
Supplementary_files_format_and_content: Coverage ATAC-seq sample (bigwig format)

source_name: mESC-derived differentiated cells

extract_protocol:
Trypsin based dissociation followed by FACS sorting of 50000 cells
Nextera DNA sample preparation kit, Illumina

value: Nkx2-1-T2a-mKO2 reporter mESC line

value: day 4


title: 1_GW15

description: 10x Genomics


title: Homo_PC9_EN2_rep2


title: Muscle-invasive bladder cancer 11201

description: Muscle-invasive bladder cancer


title: Homo_A549_EN2_rep2


title: CD11B-701_Well_E11

value: Bone marrow derived APC

value: 12hr infection with LCMV Cl 13


title: Homo_A549_NC_rep1


title: CD11B-701_Well_E10


title: Homo_A549_EN2_rep1


title: 5_GW27

description: 10x Genomics


title: 8_GW13

description: 10x Genomics


title: Muscle-invasive bladder cancer 7503

description: Muscle-invasive bladder cancer


title: Total cells Foxe1KO day7 rep1

value: Foxe1KO/Nkx2-1-T2a-mKO2 reporter mESC line

value: day 7


title: CD11B-701_Well_E09


title: Total cells Foxe1KO day7 rep2


title: CD11B-701_Well_E08


title: 2_GW15

description: 10x Genomics


title: Muscle-invasive bladder cancer 6428

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_E07


title: Muscle-invasive bladder cancer 7501

description: Muscle-invasive bladder cancer


title: 6_GW27

description: 10x Genomics


title: Total cells Control day7 rep1


title: CD11B-701_Well_E06


title: Total cells Control day7 rep2


title: Muscle-invasive bladder cancer 11103

description: Muscle-invasive bladder cancer


title: 20minGW8B

description: 10x Genomics


title: Muscle-invasive bladder cancer 6421

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6426

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6433

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_E05


title: Nkx2 1/mKO2+ cells Foxe1KO day22 rep2

value: day 22


title: Nkx2 1/mKO2+ cells Foxe1KO day22 rep1


title: CD11B-701_Well_E03


title: 15minGW9C

description: 10x Genomics


title: Nkx2 1/mKO2+ cells Control day22 rep2


title: CD11B-701_Well_E02


title: Muscle-invasive bladder cancer 6420

description: Muscle-invasive bladder cancer


title: 15minGW9B

description: 10x Genomics


title: 18minGW8D

description: 10x Genomics


title: CD11B-701_Well_E01


title: 15minGW8A

description: 10x Genomics


title: Total cells Control day4 rep1


title: CD11B-701_Well_D12


title: 12minGW9D

description: 10x Genomics


title: CD11B-701_Well_E04


title: Nkx2 1/mKO2+ cells Foxe1KO day17 rep1

value: day 17


title: CD11B-701_Well_D11


title: Muscle-invasive bladder cancer 6414

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6418

description: Muscle-invasive bladder cancer


title: GW9D

description: 10x Genomics


title: Muscle-invasive bladder cancer 6413

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 7201

description: Muscle-invasive bladder cancer


title: Nkx2 1/mKO2+ cells Control day22 rep1


title: Nkx2 1/mKO2+ cells Control day17 rep2


title: Muscle-invasive bladder cancer 6416

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_D10


title: CD11B-701_Well_D09


title: GW8B

description: 10x Genomics


title: Nkx2 1/mKO2+ cells Foxe1KO day10 rep1

value: day 10


title: Muscle-invasive bladder cancer 5201

description: Muscle-invasive bladder cancer


title: Nkx2 1/mKO2+ cells Foxe1KO day17 rep2


title: TSM-3

city: Beijing

first: Yue

last: Wang

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: Institute of zoology, Chinese Academy of Sciences

data_processing:
OmicStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using RSeQC 4.0.0.
Trimmed sequence reads were mapped to GRCh38.p7 using Hisat2 2.2.1.
Read count extraction and normalization were performed using Hisat2 2.2.1. and StringTie 2.1.6 with Fragments Per Kilobase Million value.
Assembly: GRCh38.p7
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hTSC

growth_protocol: hTSCs are cultured in DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin,0.3% BSA, 1% ITS-X supplement, 1.5 mg/mL L-ascorbic acid, 50 ng/mL EGF, 2 mM CHIR99021, 1 mM SB431542, 0.5 mM A83-01, 0.0125% VPA, and 5 µM Y27632 in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using TRIzol (Invitrogen,15596018), and 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Invitrogen SuperScriptTM II Reverse Transcriptase following manufacturer's protocols.

treatment_protocol:
For the drug treatment, we cultured hTSCs in the medium contained 0.5 µM ISRIB and 10 µM Y27652, after removing CHIR99021, A83-01, SB431542 for 6 days.
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: hTSC

value: trophoblast stem cells

value: WT

tag: growth conditions

value: none (original medium)

value: Day 6


title: Muscle-invasive bladder cancer 6412

description: Muscle-invasive bladder cancer


title: Nkx2 1/mKO2+ cells Control day10 rep2


title: Nkx2 1/mKO2+ cells Foxe1KO day10 rep2


title: TSM-2


title: Nkx2 1/mKO2+ cells Control day17 rep1


title: Muscle-invasive bladder cancer 1205

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_D07


title: GW8C

description: 10x Genomics

value: spinal cord


title: CD11B-701_Well_D06


title: CD11B-701_Well_D08


title: 20minGW8A

description: 10x Genomics


title: Muscle-invasive bladder cancer 67101

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_D05


title: Muscle-invasive bladder cancer 1110

description: Muscle-invasive bladder cancer