title: KD MoYPD1 RA6

city: Thrissur

first: Varsha

middle: C

last: Mohanan

state: Kerala

address: St.Mary's College road, Chembukavu

department: Department of Biotechnology

country: India

institute: St.Mary's College, Thrissur

data_processing:
sequence reads were trimmed (Q>30) using the FASTX tool kit
pre-processed reads were aligned to the reference M. oryzae genome and a gene model was downloaded from Ensembl database (Genome version MG8, strain 70-15)
alignment was performed using the Tophat program (version 2.0.8) with default parameters
The aligned reads were used for estimating expression of the genes and transcripts using Cuffdiff program of Cufflinks package (version 2.0.2) with default  settings
The differentially expressed genes (fold change >log2) were classified into different groups on the basis of their functional domains

organism: Pyricularia oryzae

source_name: Fungal vegetative hyphae

growth_protocol: For total RNA isolation, M. oryzae biomass of KD mutant RA6 and WT B157 was grown for 72 hr in 30 ml liquid complete medium (pH-6.8) at 28oC by shaking at 200 rpm under 12 hr light / dark cycle. Fungal biomass was harvested by filtration. The fungal biomass was weighed, quick frozen in liquid nitrogen and stored at -80 oC freezer

extract_protocol:
The fungal biomass was weighed, quick frozen in liquid nitrogen and stored at -80 oC freezer. Total RNA was isolated from 1 g of fungal biomass using TRIZOL reagent (Invitrogen Life Technologies, California, USA) according to the manufacturer’s instructions. For removal of DNA contamination, extracted RNA was treated  with DNase as recommended by the manufacturer.
Total RNA from KD mutant RA6 and WT biomass was used to generate cDNA using AmpliSeq cDNA synthesis kit as recommended by Illumina standard protocols. Total RNA was eluted in 500 µl RNase-free water and checked for its integrity and quantity on an Agilent Bioanalyzer. Purification of poly-A containing mRNA molecules was done using oligo-(dT) anchored magnetic beads (Sigma-Aldrich). 1ug of total RNA in 50uL was used as starting  material. Following purification, the RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments werre copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNAsynthesis using DNA Polymerase I and RNase H. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR of 12 cycles to create the final cDNA library. The quality of prepped libraries were checked on the BioAnalyser (Agilent Technologies) using the Agilent 1000 or High Sensitivity Chip. The libraries were then quantified by qPCR (KapaBiosystems), normalized, pooled and sequenced in the HiSeq 1000system, usually paired-end 100 cycles run.

value: vegetative hyphae

tag: genetic modification

value: RNAi of MoYPD1

tag: genotype/variation

value: RNAi mutant of histidine phosphotransferase MoYPD1


title: R21 ctr IgG ChIP-seq

status: Public on Feb 09 2022

type: SRA

city: Berkeley

first: Robert

last: Tjian

state: CA

address: LKS

country: USA

institute: UC Berkeley/HHMI

library_source: genomic

data_processing:
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq, ChIP-seq pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32. For Micro-C, Bowtie 2.3.0 with ‘very-sensitive-local’ mode was used.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools. For Micro-C, pairs with multiple hits, low MAPQ, singleton, dangling end, self-circle,PCR duplicates and contacts shorter than 200bp (unligated mono-nucleosomes)  were discarded
ATAC-seq, ChIP-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter.
For Micro-C, contact matrices were then normalized by using iterative correction (IC) in COOL files (Imakaev et al., 2012) or Knight-Ruiz (KR) (Knight and Ruiz, 2013) in HIC files. Regions with low mappability and high noise were blocked before matrix normalization. We expect that matrix balancing normalization corrects systematic biases such as nucleosome occupancy, sequence uniqueness, GC content, or crosslinking effects as reported in Imakaev et al. 2012 and Rao et al. 2014.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw), hic, mcool

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: JM8.N4 mouse ESCs from the C57BL/6N strain and their genome edited derivatives were cultured on 0.1% gelatin coated plates without feeders at 37°C and 5% CO2. The ESC medium was composed of the knockout DMEM(1X) optimized for ESCs (Thermo Fisher Scientific 10829-018), 15% ESC qualified Fetal Bovine Serum (ATCC SCRR-30-2020), 1 mM GlutaMAX (Thermo Fisher Scientific 35050-061), 0.1 mM MEM nonessential amino acids (Thermo Fisher Scientific 11140-50), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific 21985-023),1000 units of Leukemia inhibitory factor (LIF) (Millipore) and Antibiotic-Antimycotic (Thermo Fisher Scientific 15240-062).

extract_protocol:
ChIP-seq: Cells were cross-linked for 10 min at room temperature with 1% methanol-free paraformaldehyde in PBS and quenched with 0.125 M glycine. Cells were scraped and resuspended in cold cell lysis buffer (5 mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40) and incubated for 10 min on ice. After centrifuging, nuclear pellets were resuspended in at least 6 vol of sonication buffer (50 mM Tris-HCl at pH 8.1, 10 mM EDTA, 0.1% SDS), incubated for 10 min on ice, and sonicated using the Covaris S220 sonicator to obtain an average fragment length of ∼500 bp examined by electrophoresis. Sonicated chromatin was diluted in RIPA buffer, aliquoted, and incubated with Protein G Dynabeads that were prebound with individual antibodies for at least 1 h at room temperature. Immunoprecipitation was performed overnight at 4°C with 2–4 µg of antibodies. Ten percent of the chromatin was saved as input. Immunoprecipitated and input DNA was introduced with sequencing adaptors as described previously (Schmidl et al., 2015), washed extensively with RIPA buffer (low salt and high salt) and LiCl buffer, digested with proteinase K and RNase A, reverse-cross-linked at 60oC overnight followed by purification with the AmpureX beads. We also added the spike-in chromatin (active motif, 53083) and spike-in antibody (active motif, 61686) following the manufacturer’s instructions.
Micro-C: 5M ESC cells were resuspended by trypsin, fixed by freshly made 1% formaldehyde at room temperature for 10 min and quenched by adding Tris buffer (pH = 7.5) to the final 0.75 M at room temperature. Fixed cells were washed twice with 1X PBS and then were subjected to the second crosslinking reaction by 3 mM disuccinimidyl glutarate (DSG) (Thermo Fisher # 20593)  for 45 min at room temperature. The DSG solution was freshly made at a 300-mM concentration in DMSO and diluted to 3 mM in 1X PBS before use. The crosslinking reaction was quenched by 0.75 M Tris buffer and washed twice with 1X PBS. Crosslinked cells were snap-frozen in liquid nitrogen and stored at −80°C.  We performed chromatin fragmentation by the micrococcal nuclease (MNase) and optimize the MNase digestion level to have about 80 to 90% of mononucleosomes and 10 to 20% of di-nucleosomes. We typically use ∼20 units MNase for 1 million of JM8.N4 mESCs. Intact nuclei were extracted by treating cells with Micro-C Buffer #1 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 5 mM MgCl2, 1M CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) for 20 min on ice. Chromatin was digested with a pre-titrated MNase concentration (Worthington Biochem #LS004798) at 37°C for 10 min. MNase digestion was stopped by adding 4 mM EGTA and completely inactivated by incubating at 65°C for 10 min. Digested chromatin was washed twice with ice-cold Micro-C Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2).MNase digested chromatin was subjected to multiple steps of biochemical enzyme reactions to generate compatible ends for ligation of adapters for sequencing. Chromatin was incubated with T4 PNK (New England BioLabs # M0201)  in Micro-C end-repair buffer (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2, 100 ug/mL BSA, 2 mM ATP, 5 mM DTT) at 37°C for 15 mi. We then incubate chromatin with Klenow Fragment in the Micro-C end-repair buffer with no dNTPs at 37°C for 15 min. The blunting and labeling reaction was triggered upon adding biotin-dATP (Jena Bioscience # NU-835-BIO14), biotin-dCTP (Jena Bioscience # NU-809-BIOX), dGTP, and dTTP to a final concentration of 66 mM each at room temperature for 45 min. The reaction was inactivated by adding 30 mM EDTA and incubating at 65°C for 20 min. Biotin-labeled chromatin was washed once by ice-cold Micro-C Buffer #3 (50 mM Tris-HCl pH = 7.5, 10 mM MgCl2). The crosslinked nucleosomes were then ligated by T4 DNA Ligase (New England BioLabs #M0202) in 500 μL solution at room temperature for at least 2 h, followed by exonuclease III (New England BioLabs #M0206) treatment to remove biotin-dNTPs on un-ligated ends by incubating ligated chromatin at 37°C for at least 15 min.To specifically extract the ligated di-nucleosomal DNA, the deproteinized chromatin was purified and separated on a low-melting agarose gel (Lonza #50081). A band at the size of 250 to 400 bp corresponding to the ligated dimers was gel-extracted for library preparation. The purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne Streptavidin C1 (Thermo Fisher Scientific #65001). Standard Illumina library preparation protocol including end-repair, A-tailing, and adaptor ligation was performed on beads with the NEBnext Ultra II kit (New England BioLabs # E7645). An optimal PCR cycle for final library amplification was determined by quantification PCR (KAPA Biosystems #KK4602), typically between 5–10 cycles for the input cell number from 5M. The sequencing library was amplified by Kapa HiFi PCR enzyme (KAPA Biosystems #KK2601) with the lowest possible cycles to reduce PCR duplicates.
RNA-seq: Total RNA was isolated according to the manufacturer’s instruction, quantified by Nanodrop (Thermo Fisher Scientific) and diluted to 1 ng/µl in nuclease-free water.  A total of 1 ng of RNA was added to 2.5 µl of cell lysis buffer (nuclease-free water with 0.2 % v/v Triton X-100 and 0.1 U/µl RNase inhibitor), and subjected to cDNA synthesis and amplification as described before (Cembrowski et al., 2018). Libraries were prepared using a modified Nextera XT DNA protocol (Illumina, San Diego, CA) where 5 µM P5NEXTPT5 was substituted for the i5 primers in the kit. Libraries were quantified by qPCR (Roche), normalized to 2 nM, then pooled and sequenced on a NextSeq550 flowcell with 25 bases in read 1, 8 bases in the i7 index read, and 50 bases in read 2. The control library phiX (Illumina) was spiked in at a final concentration of 15% to improve color balance in read 1.
ATAC-seq: we performed ATAC-seq on 50,000 cells which were trypsinized, washed with PBS on ice, and resuspended in the reaction mix (25 μL of 2× TD buffer, 2.5 μL of transposase, 22.5 μL of nuclease-free H2O) for 30 min at 37°C. Following transposition, genomic DNA was purified and amplified by 10-14 cycles of PCR.Both ATAC-seq samples were sequenced in Illumina HiSeq 2500 or Nextseq with 150cycle paired-end sequencing

tag: cell type

value: embryonic stem cell line

tag: strain

tag: treatment

value: Control IgG ChIP


title: PBMC-C3: PBMC ctrl rep3

city: Xi'an

first: Yue

last: Yin

state: Shaanxi

address: No. 76, Yanta West Road

department: Histology and Embryology

country: China

institute: Guilin Medical University

description: Subcutaneous injection of 100 μl HBSS, pooled sample of 5

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts (Novogene, China).
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for platelet samples
Supplementary_files_format_and_content: Matrix table with raw gene counts for PBMC samples

molecule: total RNA

source_name: PBMC

extract_protocol:
Blood samples were collected from retro-orbital sinuses of C57BL/6 mice. Blood is collected into a tube containing the anti-coagulant EDTA. Anti-coagulated blood was centrifuged at 180 g at room temperature for 10 min, resulting in platelet-rich plasma. Platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 10 min at 1,250 g, after which the platelet pellet was lysed in TRIzol Reagent (Invitrogen, ThermoFisher) and frozen at -80 °C for further use. The bottom layer of the first centrifuged blood sample was further used for peripheral blood mononuclear cell (PBMC) isolation via mouse PBMC isolation kit (TBD science, Tianjin) following the manufacturer’s instructions. The final PBMC pellet was resuspended and lysed in TRIzol and kept in -80 °C for further use. Total RNAs were extracted according to TRIzol manual instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B16F10 cells suspended in 100 μl HBSS or HBSS control saline were injected under the right flank subcutaneously using a 30G needle.

tag: tissue

value: Blood

tag: tumor stage

value: Control

value: PBMC


title: IPHA

city: Tianjin

first: shengnan

last: yuan

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2(version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets.
Genome_build: ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: bw files and raw files
Supplementary_files_format_and_content: peaks excel files

organism: Homo sapiens

source_name: Human cell line

growth_protocol: K562 cells (HA-PHF6-overexpression or HA-overexpression) were cultured in 1640 medium with 10% fetal bovine serum (FBS)

extract_protocol:
The ChIP assay was performed with a ChIP assay kit (Cell Signaling Technology, Boston, MA, USA) according to the manufacturer’s recommendations. Briefly, chromatin from cross-linked HA-PHF6 OE K562 cells or control cells was sheared using an ultrasonicator (Covaris, S220, ABI, New York, USA) to obtain DNA in the size range of 100–400 bp. Immunoprecipitation was conducted with ChIP-grade HA tag antibody (Abcam, ab9110, Cambridge, UK)
The purified DNA was used for ChIP-seq library preparation. The library was constructed by the Novogene Corporation (Beijing, China). Subsequently, paired-end sequencing of the sample was performed on an Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Untreated

value: K562 leukemia cell

value: Human cell line

tag: chip antibody

value: HA antibody (Abcam, ab9110, Cambridge, UK)

value: untreated

tag: cell line


title: B157

value: Control Wildtype sample


title: Control B4 RNA-seq

value: untreated for the Brd4-degron background


title: PBMC-C2: PBMC ctrl rep2


title: Brd2 dep 6h RNA-seq

value: Brd2 depletion 6 hour


title: PBMC-C1: PBMC ctrl rep1


title: R21 ctr Brd3 ChIP-seq

value: Control Brd3 ChIP


title: SiREV1#2-3

city: Wuhan

first: hua

middle: xiao

last: jie

state: Hubei

address: Xinhua Road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
The RNA integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies).
Paired-end libraries sequencing20 with Illumina MGISEQ-2000 were prepared with the mRNA-seq sample prep kit (Illumina) according to the manufacturer’s specifications.
Illumina data analysis pipeline was then used for sequence analysis. All samples were allocated to lanes and processed in blinded fashion to keep bias to a minimum
Analysis description: Calculate the expression read count using the Stringtie-1.3.3b software. Then, the gene and transcript FPKM were calculated. In this process we simply filtered the expression:1）Remove genes or transcripts with length less than 100 bp. ;2）If the FPKM of a gene or transcript is less than 0.0001, it is considered to be expressed as 0. Remove genes with a table of 0 in all samples.
Genome_build: hg38
Supplementary_files_format_and_content: abundance measurements

growth_protocol: All the cells were cultured in DMEM medium containing 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: A549 cells transfected with Scrambled or SiRNAs targeting REV1 for 48 hours.

value: Human lung adenocarcinoma cells

tag: genotype


title: Control B2 RNA-seq

value: untreated for the Brd2-degron background


title: SiREV1#2-2


title: PBMC-A5: PBMC large tumor rep5

description: Subcutaneous injection of 1 × 10^5 B16F10 cells per mouse, pooled sample of 5

value: Late


title: Rad21 dep B42 Micro-C

data_processing:
Library strategy: Micro-C
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq, ChIP-seq pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32. For Micro-C, Bowtie 2.3.0 with ‘very-sensitive-local’ mode was used.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools. For Micro-C, pairs with multiple hits, low MAPQ, singleton, dangling end, self-circle,PCR duplicates and contacts shorter than 200bp (unligated mono-nucleosomes)  were discarded
ATAC-seq, ChIP-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter.
For Micro-C, contact matrices were then normalized by using iterative correction (IC) in COOL files (Imakaev et al., 2012) or Knight-Ruiz (KR) (Knight and Ruiz, 2013) in HIC files. Regions with low mappability and high noise were blocked before matrix normalization. We expect that matrix balancing normalization corrects systematic biases such as nucleosome occupancy, sequence uniqueness, GC content, or crosslinking effects as reported in Imakaev et al. 2012 and Rao et al. 2014.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw), hic, mcool

value: auxin, 6hour, depleting RAD21, for B42 background


title: PBMC-A4: PBMC large tumor rep4

description: Subcutaneous injection of 1 × 10^5 B16F10 cells per mouse, pooled sample of 3


title: Liver, T5

city: Shanghai

first: He

last: Huang

address: 555 Zuchongzhi Rd

institute: Shanghai Institute of Materia Medica

data_processing:
All reads were mapped to the reference genome of Mesocricetus auratus using HISAT2 v.2.2.1 as instructed. RNA counts were generated from feature Counts (v.2.0.0).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using using edgeR package. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mesocricetus auratus
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mesocricetus auratus

source_name: Liver

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

tag: diet

value: high-fat diet (HFD)

value: Liver


title: Liver, T6


title: Liver, T4


title: SiREV1#1-3


title: Control B42 Micro-C

value: embryonic stem cell line

value: untreated for the B42 background


title: Liver, T3


title: SiREV1#1-2


title: SiREV1#2-1


title: PBMC-A3: PBMC large tumor rep3

value: Blood

value: PBMC


title: Liver, T2


title: Brd4 dep 6h RNA-seq

value: Brd4 depletion 6 hour


title: Liver, T7


title: Liver, T1


title: PBMC-A1: PBMC large tumor rep1


title: Scramble-3

value: Scramble


title: SiREV1#1-1


title: Scramble-2


title: Liver, C6

value: control


title: VF_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BM

extract_protocol:
BM cells were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Massachusetts，USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BM

tag: age

value: post transplantation day 100

value: Phf8 KO


title: Brd4 Rad21 double dep Micro-C

value: auxin 6hour, dTAG13 6 hour


title: VF_2

value: Phf7 KO


title: Scramble-1

value: Human lung adenocarcinoma cells


title: Brd4 Brd2 double dep Micro-C

value: dTAG13, 6hour, depleting BRD4 and BRD2


title: VF_1

value: Phf6 KO


title: Liver, C5

value: high-fat diet (HFD)


title: Liver, C4

value: Liver


title: Brd2 Rad21 double dep Micro-C

value: embryonic stem cell line


title: Brd4 Brd2 Rad21 triple dep Micro-C


title: Liver, C3


title: Rad21 dep B2 Micro-C

value: auxin, 6hour, depleting RAD21


title: Brd2 dep Micro-C

value: dTAG13, 6hour, depleting BRD2


title: F_Y_2

value: Phf7 WT


title: F_Y_3

value: Phf8 WT


title: Liver, C2


title: Control B2 Micro-C

value: untreated


title: F_Y_1

value: Phf6 WT


title: Liver, C1

value: control


title: Liver, C7


title: Brd4 dep Micro-C

value: dTAG13, 6hour, depleting BRD4


title: Pyocyanin

status: Public on Feb 08 2022

type: RNA

city: Winston-Salem

first: Ethan

last: Shelkey

address: 391 Technology Way NE

institute: Wake Forest Institute for Regenerative Medicine

description: organoids treated with pyocyanin

data_processing:
Data was processed automatically using the qiagen geneglobe website and software
Housekeeping genes were averages of B2M, GUSB, HSP90AB1, and ACTB
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control (i.e., PYO+ICB/CTL) ratios.

label: SYBR Green

source_name: Organoid

label_protocol: used rt2 first strand kit for cDNA, rt2 Mouse Cancer Inflammation & Immunity Crosstalk plate for qPCR with RT² SYBR Green ROX™ FAST MasterMix for detection

growth_protocol: 100,000 4T1 cells and 300,000 splenocytes were grown in 10ul organoids for 5 days

extract_protocol: RT2 first strand kit protocol followed

treatment_protocol: organoids treated with bacterial metabolites were treated for all 5 days, organoids treated with ICB had ICB exposure for the last 3 days

value: 4T1 TNBC+ splenocytes


title: Hippurate+ICB

description: organoids treated with hippurate+icb


title: Pyocyanin+ICB

description: organoids treated with pyocyanin+icb


title: Hippurate

description: organoids treated with hippurate


title: CTL

description: untreated organoids


title: CTL+ICB

description: organoids treated with ICB


title: CK_48h_IP_2

city: wuhan

first: dong

last: chen

address: GaoXin 2nd Road

institute: ablife

data_processing:
library strategy: m6A-seq
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions on genome using “ABLIRC” strategy.
Genome_build: PekingDuck_PBH1.5
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

organism: Anas platyrhynchos

source_name: liver tissue of duckling liver collected at 48h after being infected by attenuated vaccine DHAV-1 CH60 (CK)

growth_protocol: One-day-old Cherry Valley ducks were purchased from the poultry farm of Sichuan Agricultural University and were raised in isolators

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Ambion) following the manufacturer’s instructions, and mRNA were then purified by GenElute™ mRNA Miniprep Kit (sigma, MRN10).
The polyadenylated mRNAs isolated from total RNA using GenElute™ mRNA Miniprep Kit (sigma, MRN10) were fragmented into 100 nt length by using RNA Fragmentation buffer (0.1M Tris-HCL PH 7.0, 0.1M ZnCl2). Then, 50 and 100 ng fragmented mRNAs were incubated for 2 hours at 4 °C with 12.5 μg of anti-m6A antibody (sysy, 202003) in IP buffer (0.05M Tris-HCL pH 7.4, 0.375M NaCl, 0.5% Igepal CA-630). The mixture was then subjected to immunoprecipitation by incubation with Pierce™ ChIP-grade Protein A/G Magnetic Beads (Thermo, 26162) at 4 °C for 2 hours. After sufficient washing, m6A antibody-bound RNA was eluted from the beads with Elution buffer (1×IP buffer, 7mM m6A, RNase inhibitor), and then ethanol-precipitated. The eluted RNA was resuspended in H2O and used to generate the cDNA library according to RNA-Seq Library Preparation Kit for Transcriptome Discovery–Illumina Compatible, which was then sequenced using the HiSeq 2000 system (Illumina) according to the manufacturer’s instructions.

treatment_protocol: After one week, the ducks were randomly divided into three groups of 15 and raised in separate isolators. The ducks in the first group received 0.40 ml of the DHAV-CH strain (107.88copies/ml) via intramuscular injection, the ducks in the second group received 0.25 ml of the DHAV-CH60 strain (108.07cop-ies/ml) via intramuscular injection, and ducks in the last group were injected with 0.25 ml of 0.75% physiological normal saline (NS) as a negative control. Three ducklings from each group were killed at 12, 24, 36, 48, 60 and 72 hpi, and their livers and blood were collected

tag: infection

value: attenuated vaccine DHAV-1 CH60 (CK)

tag: time

value: 48h after being infected

value: liver

tag: rip antibody

value: m6A Antibody (Synaptic systems; catalog# 202003)


title: CK_48h_IP_3


title: CK_48h_IP_1


title: CK_48h_input_1


title: CK_48h_input_2


title: CK_36h_IP_2

source_name: liver tissue of duckling liver collected at 36h after being infected by attenuated vaccine DHAV-1 CH60 (CK)

value: 36h after being infected


title: CK_36h_IP_1


title: CK_36h_IP_3


title: CK_48h_input_3


title: CK_36h_input_2


title: CK_24h_IP_1

source_name: liver tissue of duckling liver collected at 24h after being infected by attenuated vaccine DHAV-1 CH60 (CK)

value: 24h after being infected


title: CK_36h_input_3


title: CK_24h_input_3


title: Negative-Control (Li-7)

city: Kyoto

first: Hirotaka

last: Furuke

state: Japan

address: 465 Kajii-cho, Kamigyo-ku, Kyoto, 60285

department: Division of digestive surgery

country: Japan

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46
The data of the chp files were further analyzed with Transcriptome Analysis Console (TAC) software using Affymetrix default analysis settings and global scaling as normalization method. The data processed by comparison between negative control and miR-4730 mimic transfection were included in the *data_matrix.txt

label: biotin

source_name: Total RNA of Li-7 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Li-7 cells were cultured in RPMI-1640 (Nacalai Tesque, Kyoto, Japan) and 10% fetal bovine serum (FBS) at 37℃ in a 5% CO2 incubator. HEP-G2 cells were cultured in DMEM (Nacalai Tesque, Kyoto, Japan) and 10% fetal bovine serum (FBS) at 37℃ in a 5% CO2 incubator.

extract_protocol: We extracted total RNA by using an miRNeasy Mini Kit (Qiagen, Hamburg, Germany)

treatment_protocol: miR-4730 mimic was transfected 24 h after seeding using Lipofectamine RNAiMAX reagent (Invitrogen, Carlsbad, CA, USA) with a final concentration of 3nM as described by the manufacturer. miR-4730 mimic (assay ID: MC21609) and control vector (negative control #1) were obtained from Thermo Fisher Scientific.

value: Negative-Control


title: CK_24h_IP_3


title: CK_24h_IP_2


title: Negative-Control (HEP-G2)

source_name: Total RNA of HEP-G2 cells


title: CK_24h_input_1


title: miR-4730 mimic (Li-7)

value: miR-4730 mimic


title: CK_12h_IP_3

source_name: liver tissue of duckling liver collected at 12h after being infected by attenuated vaccine DHAV-1 CH60 (CK)

value: 12h after being infected


title: CK_12h_IP_1


title: CK_36h_input_1


title: CK_12h_input_3


title: CK_12h_input_2


title: CH_48h_IP_2

source_name: liver tissue of duckling liver collected at 48h after being infected by virulent DHAV-1 CH (CH)

value: virulent DHAV-1 CH (CH)


title: CH_48h_IP_3


title: CH_48h_IP_1


title: CK_24h_input_2


title: CH_36h_input_3

source_name: liver tissue of duckling liver collected at 36h after being infected by virulent DHAV-1 CH (CH)


title: CH_48h_input_1


title: CH_36h_IP_1


title: CH_36h_IP_3


title: CH_36h_IP_2


title: CH_36h_input_1


title: CH_24h_IP_3

source_name: liver tissue of duckling liver collected at 24h after being infected by virulent DHAV-1 CH (CH)


title: miR-4730 mimic (HEP-G2)


title: CH_48h_input_2


title: CH_24h_input_2


title: CH_24h_IP_1


title: CH_24h_input_3


title: CH_24h_IP_2


title: CH_12h_IP_2

source_name: liver tissue of duckling liver collected at 12h after being infected by virulent DHAV-1 CH (CH)


title: CK_12h_input_1


title: CH_24h_input_1


title: CH_12h_IP_1


title: CH_36h_input_2


title: CK_12h_IP_2


title: CH_12h_IP_3


title: CH_48h_input_3


title: CH_12h_input_2


title: CH_12h_input_1


title: CH_12h_input_3


title: Upper jaw of oral lamina adjacent to replacement teeth

city: Atlanta

first: Larry

last: Young

state: GA

address: 954 Gatewood Rd NE

department: Department of Psychiatry

institute: Emory University

data_processing:
FASTQ files processed with Cell Ranger version 3.1.0
Cellranger aggr used to aggregate the upper jaw (UJ) and lower jaw (LJ) samples
Genome_build: M_zebra_UMD2a
Supplementary_files_format_and_content: Cellranger output files (in barcodes.tsv, BC-1 corresponds to LJ, BC-2 corresponds to UJ)

organism: Maylandia zebra

source_name: Oral lamina (Upper jaw) adjacent to replacement teeth

extract_protocol:
Nuclei preparation methods were based on the 10x Genomics Demonstrated Protocol for lysis and washing of single nuclei. To this protocol the following modifications were made: 1x HBSS was used in place of HEB; tissues were placed in lysis buffer for 10 minutes (to account for a smaller tissue mass) and then homogenized with disposable pellet pestles (Sigma-Aldrich Z359947) before halting lysis with HBSS; the tissue was suspended in 300 µL of wash buffer and passed through a 30μm MACS SmartStrainer once before proceeding to FACS. Filtered samples were stained with DAPI at a concentration of 0.1 μL DAPI per 100 μL of suspension and sorted using the BD FACSAria Fusion. Gates were set conservatively to collect DAPI+ singlet nuclei (Supplemental Figure 2) and nuclei were sorted into 200 µL of wash buffer. Total volume in each collection tube was recorded, collected nuclei were centrifuged at 300 rcf, 4°C for 10 minutes and supernatant was removed, leaving nuclei suspended in 50 µL of wash buffer. Event counts registered during sorting were used to estimate final cell suspension concentrations: from upper jaw soft tissue, 20668 nuclei were collected for a final concentration of 413 nuclei/µL; from lower jaw soft tissue, 20181 nuclei were collected for a final concentration of 403 nuclei/µL; from regenerating teeth 14700 nuclei were collected for a final concentration of 294 nuclei/µL.
Libraries were prepared for sequencing by the Genome Analysis Core at Georgia Tech using the 10x Chromium V3 Single Cell Gene Expression Solution protocol and reagent kit (10x Genomics 1000092) with a targeted cell recovery of 3,000 nuclei per sample.
NextSeq 500 (Illumina SY-415-1001)


title: Replacement teeth

data_processing:
FASTQ files processed with Cell Ranger version 3.1.0
Genome_build: M_zebra_UMD2a
Supplementary_files_format_and_content: Cellranger output files

source_name: ~300 replacement teeth

extract_protocol:
Nuclei preparation methods were based on the 10x Genomics Demonstrated Protocol for lysis and washing of single nuclei. To this protocol the following modifications were made: 1x HBSS was used in place of HEB; tissues were placed in lysis buffer for 10 minutes (to account for a smaller tissue mass) and then homogenized with disposable pellet pestles (Sigma_Aldrich Z359947) before halting lysis with HBSS; the tissue was suspended in 300 µL of wash buffer and passed through a 30μm MACS SmartStrainer once before proceeding to FACS. Filtered samples were stained with DAPI at a concentration of 0.1 μL DAPI per 100 μL of suspension and sorted using the BD FACSAria Fusion. Gates were set conservatively to collect DAPI+ singlet nuclei (Supplemental Figure 2) and nuclei were sorted into 200 µL of wash buffer. Total volume in each collection tube was recorded, collected nuclei were centrifuged at 300 rcf, 4°C for 10 minutes and supernatant was removed, leaving nuclei suspended in 50 µL of wash buffer. Event counts registered during sorting were used to estimate final cell suspension concentrations: from upper jaw soft tissue, 20668 nuclei were collected for a final concentration of 413 nuclei/µL; from lower jaw soft tissue, 20181 nuclei were collected for a final concentration of 403 nuclei/µL; from regenerating teeth 14700 nuclei were collected for a final concentration of 294 nuclei/µL.
Libraries were prepared for sequencing by the Genome Analysis Core at Georgia Tech using the 10x Chromium V3 Single Cell Gene Expression Solution protocol and reagent kit (10x Genomics 1000092) with a targeted cell recovery of 3,000 nuclei per sample.
NextSeq 500 (Illumina SY_415_1001)

value: ~300 replacement teeth


title: NonNeoplasticSample-Patient0010-TemporalLobeResection

city: Tucson

first: Christopher

middle: Michael

last: Morrison

state: AZ

address: 3838 N Campbell Ave, Bldg #2

department: Radiation Oncology

institute: University of Arizona Cancer Center

hyb_protocol: Isolation and binding of hybridized probes to an optical cartridge was performed on an automated NanoString’s nCounter Prep Station.

scan_protocol: The cartridge was then scanned by means of the nCounter Digital Analyzer to obtain gene-specific probe counts.

data_processing: Raw data was analyzed by means of NanoString Technologies’ nSolver Analysis (version 4.0) software, using the Advanced Analytics package (version 2.0). Data was normalized against internal positive and negative controls, as well as 40 housekeeping genes, using the geNorm algorithm  per the manufacturer’s instructions.

label: NanoString

source_name: temporal lobe resection

label_protocol: Purified RNA, 300 ng of from FFPE tissue or 100 ng from frozen non-neoplastic tissue, was hybridized with the gene expression code set probes of an nCounter PanCancer Human Pathways panel (NanoString Technologies, Seattle, WA).

extract_protocol: RNA was isolated using a Roche HighPure FFPET RNA Isolation spin-column kit from de-paraffinized FFPE GBM tissue. Frozen non-neoplastic temporal lobe tissue (archived in RNAlater storage reagent) was lysed and homogenized, and RNA was isolated by organic extraction and then purified using a Qiagen RNeasy spin-column kit.

tag: sample type


title: NonNeoplasticSample-Patient0011-TemporalLobeResection


title: NeoplasticSample-Patient0034-TumorResection

source_name: brain tumor resection

tag: gender

value: M

value: FALSE

value: TRUE

tag: kps

value: STR


title: NeoplasticSample-Patient0029-TumorResection

value: F


title: NeoplasticSample-Patient0024-TumorResection


title: NeoplasticSample-Patient0023-TumorResection


title: NeoplasticSample-Patient0027-TumorResection

value: GTR


title: NeoplasticSample-Patient0025-TumorResection


title: NeoplasticSample-Patient0022-TumorResection


title: Lower jaw of oral lamina adjacent to replacement teeth

source_name: Oral lamina (Lower jaw) adjacent to replacement teeth


title: NeoplasticSample-Patient0019-TumorResection


title: NeoplasticSample-Patient0033-TumorResection


title: NonNeoplasticSample-Patient0004-TemporalLobeResection

value: control


title: NeoplasticSample-Patient0030-TumorResection


title: NonNeoplasticSample-Patient0005-TemporalLobeResection


title: NonNeoplasticSample-Patient0012-TemporalLobeResection


title: NonNeoplasticSample-Patient0006-TemporalLobeResection


title: NonNeoplasticSample-Patient0001-TemporalLobeResection


title: NeoplasticSample-Patient0032-TumorResection


title: NonNeoplasticSample-Patient0003-TemporalLobeResection


title: NonNeoplasticSample-Patient0008-TemporalLobeResection


title: NonNeoplasticSample-Patient0007-TemporalLobeResection


title: NeoplasticSample-Patient0031-TumorResection


title: NonNeoplasticSample-Patient0002-TemporalLobeResection


title: NonNeoplasticSample-Patient0009-TemporalLobeResection


title: NeoplasticSample-Patient0012-TumorResection


title: NeoplasticSample-Patient0016-TumorResection


title: NeoplasticSample-Patient0009-TumorResection


title: NeoplasticSample-Patient0010-TumorResection


title: PBMC-A2: PBMC large tumor rep2

description: Subcutaneous injection of 1 × 10^5 B16F10 cells per mouse, pooled sample of 4

source_name: PBMC

value: Blood

value: Late

value: PBMC


title: NeoplasticSample-Patient0017-TumorResection


title: WT_Platelet-2

city: Houston

first: Rebecca

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads were aligned to mm10 genome assembly using STAR aligner.
Differentially expressed genes were identified using DeSeq2.
Gene ontology analysis was done with GOStats.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated file includes FPKM values for each sample

molecule: polyA RNA

source_name: Peripehral blood

growth_protocol: Mice were housed in AAALAC-accredited, specific-pathogen-free animal care facilities at Baylor College of Medicine (BCM) with 12-hour light-dark cycle and received standard chow ad libitum. All procedures were approved by the BCM (protocol #AN-5858) Institutional Animal Care and Use Committees.

extract_protocol:
Platelets  were sorted into Trizol and RNA purified according to the manufacturer's instructions. DNase I-treated RNA samples were purified using the QIAGEN MinElute kit before cDNA was made and amplified with a SMART-Seq2 kit.
The cDNA was then fragmented and barcoded for sequencing using a Nextera XT kit.

tag: strain background

value: WT

value: Peripheral blood platelets


title: AML_Platelet-2

value: AML

tag: cell type


title: a7-KO Nicotine S4

city: New Orleans

first: Xinping

last: Yue

state: Louisiana

address: 1901 Perdido Street, MEB 7205

institute: LOUISIANA STATE UNIVERSITY HEALTH SCIENCES CENTER - N.O.

data_processing:
Fastq data were processed at Illumina BaseSpace.
Sequenced reads were trimmed for adaptor sequence.
RNA sequencing data were analyzed using Python
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq analysis output in excel files
Supplementary_files_format_and_content: counts, log2FoldChange

source_name: Thoracic aorta

extract_protocol:
Thoracic aortas were removed, cleaned of fat tissue, flash frozen in liquid nitrogen, and RNA was harvested using RNeasy Plus mini kit. Library preparation was performed using SMART-Seq v4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and alpha7-nAChR KO mice at 5-month of age were exposed to nicotine vapor or room air for a total of 12 weeks.

tag: strain

value: Thoracic aorta

value: alpha7-nAChR knockout

value: inhaled nicotine


title: NeoplasticSample-Patient0003-TumorResection


title: NeoplasticSample-Patient0004-TumorResection


title: NeoplasticSample-Patient0006-TumorResection


title: AML_Platelet-1


title: NeoplasticSample-Patient0001-TumorResection


title: NeoplasticSample-Patient0020-TumorResection


title: WT_Platelet-3


title: WT Air S10

value: wild type

tag: treatment

value: air control


title: a7-KO Air S1

tag: tissue


title: WT Nicotine S6


title: a7-KO Nicotine S3


title: WT Air S9


title: WT_Platelet-1


title: WT Nicotine S11


title: WT Nicotine S12


title: a7-KO Air S2


title: 2163 CbAtg JIB-04_rep_3

city: Dallas

first: Elisabeth

last: Martinez

address: 6000 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to human genome using TopHat (v2.0.12)
Duplicates were marked using picard-tools (v1.127)
Read counts were generated using featureCounts (subread) for coding genes from gencode (v19)
Normalized read counts generated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: heart

extract_protocol:
RNA were extract using Trizol.
Library was generated using TruSeq Stranded mRNA Library Preparation kits (Ilumina, RS-122-2101, RS-122-2102) according to manufacturer’s protocol.

treatment_protocol: Mice were treated with vehicle or JIB-04 starting from 4 weeks of age at 50 mg/Kg, 3 times per week, and hearts were collected at indicated age.

value: heart

value: post natal day 158

value: calcineurin transgenic

tag: animal reference


title: 2158 CnAtg JIB-04: rep_1


title: a7-KO Nicotine S5


title: WT Air S8


title: 2161 CnAtg Ve_rep_1

value: Vehicle


title: JEGS-Minus-Sall4-D6

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S45/SvJaeJ female mice.

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: reprogramming cells

growth_protocol: MEFs infected with 4 factorsretrovirus for 48 hours and then change the medium to iCD3 plus Rock inhibitor and induction for 7 days

extract_protocol:
Total RNAs were prepared with TRIzol. VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme) was used for library constructions and sequencing done with NextSeq500 Mid output 150 cycles (FC-404-2001, Illumina) for RNA-seq.
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

value: Mouse Enbryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 72 hours before digested for sequencing.

tag: passages

tag: day of reprogramming


title: JEGS-Minus-Sall4-D7

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S46/SvJaeJ female mice.


title: JEGS-Minus-Sall4-D5

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S44/SvJaeJ female mice.


title: 2160 CnAtg JIB-04_rep_2

tag: genotype


title: JEGS-Minus-Sall4-D1

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S40/SvJaeJ female mice.


title: JEGS-Minus-Sall4-D0

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S39/SvJaeJ female mice.


title: JEGS-Minus-Jdp2-D7

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S38/SvJaeJ female mice.


title: JEGS-Minus-Sall4-D3

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S42/SvJaeJ female mice.


title: JEGS-Minus-Jdp2-D0

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S31/SvJaeJ female mice.


title: JEGS-Minus-Jdp2-D1

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S32/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D6

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S29/SvJaeJ female mice.


title: JEGS-Minus-Jdp2-D4

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S35/SvJaeJ female mice.


title: JEGS-Minus-Sall4-D4

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S43/SvJaeJ female mice.


title: a7-KO Air S7


title: NeoplasticSample-Patient0007-TumorResection

value: M

value: FALSE

value: STR


title: JEGS-Minus-Jdp2-D5

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S36/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D5

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S28/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D3

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S26/SvJaeJ female mice.


title: JEGS-Minus-Sall4-D2

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S41/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D1

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S24/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D2

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S25/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D0

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S23/SvJaeJ female mice.


title: JEGS-Minus-Jdp2-D3

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S34/SvJaeJ female mice.


title: 2162 CnAtg Ve_rep_2


title: JEGS-Minus-Esrrb-D7

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S22/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D7

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S30/SvJaeJ female mice.


title: JEGS-Minus-Esrrb-D5

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S20/SvJaeJ female mice.


title: JEGS-Minus-Glis1-D4

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S27/SvJaeJ female mice.


title: JEGS-Minus-Esrrb-D6

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S21/SvJaeJ female mice.


title: JEGS-Minus-Esrrb-D4

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S19/SvJaeJ female mice.


title: JEGS-D6

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S14/SvJaeJ female mice.


title: JEGS-Minus-Esrrb-D2

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S17/SvJaeJ female mice.


title: JEGS-Minus-Esrrb-D0

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S15/SvJaeJ female mice.


title: JEGS-D4

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S12/SvJaeJ female mice.


title: StageII-0618 WGBS

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
The human reference genome hg19 and lambda genome were transformed into fully bisulfite-converted forward (C>T) and reverse (G>A conversion of the forward strand) versions using the script bismark_genome_preparation. Sequence reads were similarly transformed and mapped to prepared genomes using Bowtie2 with parameters set by Bismark.
The alignments to the same position in the genome from the Bismark mapping output were removed using the script deduplicate_bismark.
The methylation information of every single C were extracted using the script bismark_methylation_extractor with parameter ‘-p --no_overlap --ignore 5 --ignore_r2 5 --zero_based --CX --buffer_size 50%’. In this way we got the number of reads that supported methylation and the number of reads covering every CpG site, non-CpG sites were not considered in later analysis.
Genome_build: hg19
Supplementary_files_format_and_content: .bw file containing CpG methylation signal intensity of each sample

source_name: human somatic cells during chemical reprogramming stage II

growth_protocol: Human CiPS cells and hES cells (H1 and H9) were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃. Adult human adipose derived mesenchymal stromal cells (hADSCs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Genomic DNA was extracted using EasyPure Genomic DNA Kit (TransGen, EE101-11). DNA were denatured and bisulfite converted using EZ DNA Methylation-GoldTM Kit (Zymo Research, D5005).
Recovered bisulfite-converted DNAs were constructed into sequencing libraries using Accel-NGS Methyl-Seq DNA Library Kit (Swift, 30024) following the manufacturer’s instructions and each libraries were sequenced 90G raw data by using Illumina HiSeq X Ten.

treatment_protocol: Human somatic cells were treated with different small molecule combinations during human chemical reprogramming.

tag: cell line


title: JEGS-Minus-Esrrb-D1

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S16/SvJaeJ female mice.


title: JEGS-Minus-Esrrb-D3

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S18/SvJaeJ female mice.


title: DSSY783_orcb.s.∆_rap1b.s.∆_Rep2

first: Daniel

middle: S

last: Saxton

address: 100 University Ave

department: MCB

institute: University of California Berkeley

data_processing:
Reads aligned to S288C reference genome (GenBank accession number GCA_000146045.2) using bowtie2
Coverage was computed with a custom Python script (Goodnight & Rine, 2021)
Coverage was normalized to the non-heterochromatin genome-wide median using a custom Python script (Goodnight & Rine, 2021)
Coverage was smoothed with a 300bp rolling mean in R
Genome_build: S288C (GenBank accession number GCA_000146045.2)
Supplementary_files_format_and_content: bedgraph

organism: Saccharomyces cerevisiae

source_name: haploid cells

extract_protocol:
Bead beating > Sonication > Clarification of lysate > ChIP with indicated antibody
NEB Ultra II kit

tag: hm locus

tag: chip antibody

value: anti-myc


title: DSSY780_orcb.s.∆_Rep2


title: DSSY786_orcb.s.∆_rap1b.s.∆_abf1b.s.∆_Rep2


title: DSSY784_orcb.s.∆_abf1b.s.∆_Rep2


title: DSSY785_rap1b.s.∆_abf1b.s.∆_Rep2


title: DSSY782_abf1b.s.∆_Rep2


title: JEGS-Minus-Jdp2-D2

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S33/SvJaeJ female mice.


title: DSSY786_orcb.s.∆_rap1b.s.∆_abf1b.s.∆_Rep1


title: DSSY697_sir1∆_Rep2


title: DSSY781_rap1b.s.∆_Rep2


title: StageI-0618 WGBS

source_name: human somatic cells during chemical reprogramming stage I


title: DSSY785_rap1b.s.∆_abf1b.s.∆_Rep1


title: DSSY783_orcb.s.∆_rap1b.s.∆_Rep1


title: StageII-0127 WGBS

value: human somatic cells during chemical reprogramming stage II


title: JEGS-Minus-Jdp2-D6

description: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S37/SvJaeJ female mice.


title: StageII-5azaC-0127 WGBS

source_name: human somatic cells during chemical reprogramming stage II without 5azac


title: JEGS-D2


title: StageII-JNKIN8-0127 WGBS

source_name: human somatic cells during chemical reprogramming stage II without JNKIN8


title: DSSY782_abf1b.s.∆_Rep1


title: StageI-0127 WGBS

value: human somatic cells during chemical reprogramming stage I


title: DSSY695_SIR+_Rep2


title: DSSY784_orcb.s.∆_abf1b.s.∆_Rep1


title: AML_Platelet-3

value: AML

value: Peripheral blood platelets


title: DSSY781_rap1b.s.∆_Rep1


title: NeoplasticSample-Patient0008-TumorResection

tag: age


title: DSSY697_sir1∆_Rep1


title: DSSY695_SIR+_Rep1


title: HEFs-0127 WGBS

source_name: human embryonic fibroblasts

value: human embryonic fibroblasts


title: hCiPSCs-0809-3# WGBS

source_name: human chemically induced pluripotent stem cells


title: hCiPSCs-1117-2# WGBS

value: human chemically induced pluripotent stem cells


title: DSSY740_sir3bah∆_Rep2


title: hCiPSCs-0118-1# WGBS


title: DSSY734_sir2N345Asir1∆_Rep2


title: hADSCs-0809 WGBS

source_name: adult human adipose derived mesenchymal stromal cells


title: DSSY729_sir2N345A_Rep2


title: hADSCs-0618 WGBS

value: adult human adipose derived mesenchymal stromal cells


title: DSSY727_H3K79L_Rep2


title: DSSY726_H4K16Q_Rep2


title: hADSCs-0118 WGBS


title: DSSY694_SIR+_Rep2


title: DSSY696_sir1∆_Rep2


title: H1 WGBS

source_name: hES cells H1

value: hES cells H1


title: DSSY780_orcb.s.∆_Rep1


title: DSSY734_sir2N345Asir1∆_Rep1


title: CRC-SC#1 SPIP 2

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

data_processing:
Fastq files were analyzed with RSEM v. 1.3.1 in order to obtain normalized counts of expressed genes in TPM. RSEM has been launched using STAR aligner 2.7.1a
Reads were aligned against the human GRCh38 / hg38 genome (Ensembl_database)
RSEM was launched with the following parameters –paired-end --strandedness reverse --calc-ci --ci-memory 12288 --estimate-rspd --append-names --paired-end –star
Genome_build: human GRCh38 / hg38 annotated with Homo_sapiens.GRCh38.100.gtf (Ensembl_database)
all.data.matrix.TPM.xlsx = File containing the normalized counts expressed in TPM in all samples obtained by RSEM.

source_name: Colon cancer stem cells

growth_protocol: HCT116 were cultured in DMEM, 10% of FBS. CRC-SC#1 cultured in suspension as colonospheres in stem cell medium (DMEM/F12) supplemented with EGF (10 μg/ml) and FGF (20 μg /ml), B27 and N2 supplements, nicotinamide (1 mmol/L) and 1% antibiotics-antimycotics

extract_protocol:
Extraction of total RNA from CRC-SC#1 and HCT116 cells was performed using the miRNeasy® Mini Kit (Cat No./ID: 217004 QIAGEN) according to the manufacturer’s recommendation.
Libraries were prepared using the Illumina TruSeq Stranded mRNA (Cat. # RS-122-2101) kit according to the manufacturer’s protocol starting with 0,5 μg total RNA derived from cell lines.

treatment_protocol: 500.000 cells were plated and treated with 10 µmol/L spiperone for 20 hours

tag: spiperone treatment

value: yes


title: CRC-SC#1 SPIP 1


title: DSSY740_sir3bah∆_Rep1


title: ZT12

city: Daejeon

first: Moonyoung

last: Kang

address: Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
mkfastq module in Cell Ranger(v3.1.0) demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
From three fastq files, each expression matrix was generated through the Cell Ranger pipeline, by aligning reads to the N. attenuata genome (NIATTr2) using Cell Ranger count command.
We filtered N. attenuata genome to include only protein-coding genes, using Cell Ranger mkref command.
Genome_build: NIATTr2
Supplementary_files_format_and_content: expression matrices generated from CellRanger count, which can be used for downstream analysis (Seurat, Monocle, ...).

organism: Nicotiana attenuata

source_name: flower

extract_protocol:
Corolla limb + throat cup were excised from 1st day N. attenuata flower (fourty flowers for each library), and protoplasted to isolate single cells. After isolation, cells were washed with 10% (w/v) mannitol solution and filtered before the experiment.
Libraries were prepared according to 10X Genomics's instruction accompanying the Single Cell 3' Library & Gel Bead Kit v3 (10X Genomics, USA)

tag: ecotype

value: Utah

value: flower limb and throat cup

tag: Stage

value: 1st day flower

tag: sampling time


title: CRC-SC#1 CTR 2

value: no


title: hCiPSCs-1117-1# WGBS


title: ZT16


title: ZT8


title: CRC-SC#1 CTR 1


title: UM-UC-3 Treated

city: Nanning

first: Aruo

state: Guangxi

address: Guangxi Medical University, Nanning 530021, Guangxi, China

institute: Guangxi Medical University

description: circRNAs expression in human bladder cancer cell line

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 2 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: human bladder cancer cell line, UM-UC-3 cell

label_protocol: Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was isolated from the cells manually using TRIzol reagent (Invitrogen, Grand Island, NY, USA) following the manufacturer's recommendations.

treatment_protocol: The SV-HUC-1 cells were cultured in F-12K (21127-022, Gibco, USA) supplemented with 10% fetal bovine serum (FBS; 1750114, Gibco). The UM-UC-3 cells were cultured in DMEM (11995-065, Gibco, USA) containing 10% FBS. All cells were cultured in a humid environment (5% CO2 and 95% O2) at 37°C.


title: 39

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

data_processing:
24 samples were sequenced using BGISEQ platform
HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to align the clean reads to the reference genes
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Livers were removed,  and RNA was harvested using Qiagen RNA miniprep kit.
RNA libraries were prepared for sequencing using standard BGI protocols

value: 3 week Lieber-DeCarli alcohol feeding

tag: Sex

value: female

tag: aav injection #1

value: AAV-shKdm5b AAV-shKdm5c

tag: aav injection #2

value: AAV-shAhR


title: 37

tag: treatment


title: HEFs-1117 WGBS

tag: cell type


title: DSSY733_H4K16Qsir1∆_Rep2

city: Berkeley

tag: strain

value: anti-myc


title: DSSY729_sir2N345A_Rep1


title: 40


title: DSSY733_H4K16Qsir1∆_Rep1


title: HCT116 SPIP 1

source_name: Colon cancer cells


title: 32

value: AAV-shControl


title: DSSY726_H4K16Q_Rep1


title: 31


title: 35


title: HCT116 CTR 2


title: DSSY694_SIR+_Rep1


title: H9 WGBS

source_name: hES cells H9

value: hES cells H9


title: 18

value: male


title: 17


title: 30


title: DSSY727_H3K79L_Rep1


title: US20_S6_L004

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

description:
total RNA, including miRNA
US20_S6

data_processing:
Bases were called with Illumina Casava bcl2fastq (version 2.15.0.4).
Sequencing reads were trimmed and filtered using trimmomatic (v0.36) with parameters "-phred33, HEADCROP:11 LEADING:20 TRAILING:20 AVGQUAL:20 MINLEN:25". Reads were mapped to the dog reference genome (Ensembl CanFam 3.1) and corresponding gene model annotation (v94) using STAR (v2.5.3) with parameters: "--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts". RSEM (v.1.3.0) was used to quantify gene expression with parameters "--bam --no-bam-output". Finally, for each library, read counts derived from multiple lanes were added together.
Genome_build: Ensembl CanFam 3.1
Supplementary_files_format_and_content: Tab-delimited text including raw gene counts for every gene Ensembl gene identifier

organism: Canis lupus familiaris

growth_protocol: Tissue samples of suspected prostate or bladder carcinomas were collected from ten patient dogs at the Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany between 2003 and 2015 with the consent of the patients’ owners.

extract_protocol:
RNA from cell pellets was isolated using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany), in accordance with the manufacturer’s protocols. For tissue samples, the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen GmbH) was utilized.
Samples with RNA integrity numbers ≥ 5.2 measured with RNA 6000 Nano LabChip on an Agilent Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA) were further processed for library preparation using the NEBNext Ultra RNA preparation kit (New England Biolabs Inc., Ipswich, MA, USA).

treatment_protocol: Each tissue sample was subsequently divided into three parts: The first part (“original tissue”) was fresh frozen in liquid nitrogen and stored at -80°C until RNA isolation. The second part was histopathologically classified into PAC or TCC by a certified and experienced pathologist.

tag: tissue

value: Bladder cancer

tag: breed

value: Labrador Retriever

tag: description

value: 10 years

tag: histopathological classification

value: transitional cell carcinoma

tag: patient id


title: 27


title: DSSY739_sir3bah∆_Rep2

tag: hm locus

tag: chip antibody


title: 14


title: DSSY738_sir2N345Asir1∆_Rep2


title: DSSY724_sir2N345A_Rep2


title: SV-HUC-1 Control

description: circRNAs expression  in human urothelial immortalized cell line

source_name: human urothelial immortalized cell line, SV-HUC-1 cell

tag: cell line


title: 24


title: 9


title: DSSY722_H3K79Lsir1∆_Rep2


title: HCT116 SPIP 2

tag: spiperone treatment

value: yes


title: 19


title: DSSY696_sir1∆_Rep1


title: 23


title: HCT116 CTR 1


title: 25


title: TCC4_S16_L004

description:
total RNA, including miRNA
TCC4_S16

value: German Shepherd

tag: age

value: 8 years


title: US20_S6_L003

description:
total RNA, including miRNA
US20_S6


title: 3


title: DSSY721_H4K16Qsir1∆_Rep2


title: TCC4_S16_L003

description:
total RNA, including miRNA
TCC4_S16


title: 13


title: US20_S6_L002

description:
total RNA, including miRNA
US20_S6


title: SREBP2+EST-3

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong

address: 6699 Qingdao road

department: School of Pharmaceutical Sciences & Institute of Materia Medica

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)   by (1) Removing reads  containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base  quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4) .
Bowtie2 (v2.2.5)   was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Text Document  include Raw and Normalized read counts for each Sample

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 cells were transduced with retrovirus to express active SREBP2 (1-468aa) or empty vector for 24 h

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases  reads were generated on DNBSEQ  platform.

treatment_protocol: treated with Vehicle or β-estradiol (500nM) for 6 h

value: treated with Beta-estradiol

tag: transduction

value: transduced with  active SREBP2

value: Embryonic stem cells


title: DSSY719_H3K79L_Rep2


title: US20_S6_L001

description:
total RNA, including miRNA
US20_S6

value: female


title: 10

value: 3 week Lieber-DeCarli alcohol feeding

tag: Sex


title: SREBP2+EST-2


title: TCC4_S16_L001

description:
total RNA, including miRNA
TCC4_S16


title: 15

tag: aav injection #1

value: AAV-shKdm5b AAV-shKdm5c


title: DSSY718_H4K16Q_Rep2

value: anti-myc


title: 2

value: AAV-shControl

tag: aav injection #2


title: TCC4_S16_L002

description:
total RNA, including miRNA
TCC4_S16


title: 7

tag: treatment

value: AAV-shAhR


title: Vector+EST-2

value: transduced with  empty vector

tag: cell type


title: SREBP2-3

tag: strain

value: untreated


title: DSSY697_spreadexpt_sir1∆_Rep2


title: TCC2_S14_L004

description:
total RNA, including miRNA
TCC2_S14

tag: tissue

value: Bladder cancer

value: Miniature Pinscher

value: female neutered


title: DSSY695_spreadexpt_SIR+_Rep2


title: Vector+EST-3


title: Vector+EST-1


title: TCC2_S14_L003

description:
total RNA, including miRNA
TCC2_S14

tag: breed

value: transitional cell carcinoma


title: SREBP2-2


title: 5

value: male


title: Vector-2


title: DSSY739_sir3bah∆_Rep1


title: DSSY738_sir2N345Asir1∆_Rep1


title: Vector-1


title: SREBP2-1


title: SREBP2+EST-1


title: Vector-3


title: TCC1_S13_L004

description:
total RNA, including miRNA
TCC1_S13

value: Cairn Terrier

tag: description

value: 11 years


title: DSSY724_sir2N345A_Rep1


title: DSSY722_H3K79Lsir1∆_Rep1


title: DSSY721_H4K16Qsir1∆_Rep1


title: TCC1_S13_L003

description:
total RNA, including miRNA
TCC1_S13

tag: histopathological classification


title: TCC1_S13_L002

description:
total RNA, including miRNA
TCC1_S13

tag: patient id


title: DSSY719_H3K79L_Rep1

tag: hm locus


title: TCC2_S14_L002

description:
total RNA, including miRNA
TCC2_S14

value: 8 years


title: TCC1_S13_L001

description:
total RNA, including miRNA
TCC1_S13


title: TCC2_S14_L001

description:
total RNA, including miRNA
TCC2_S14


title: DSSY718_H4K16Q_Rep1

tag: chip antibody


title: DSSY697_spreadexpt_sir1∆_Rep1


title: DSSY695_spreadexpt_SIR+_Rep1


title: Sir4V5_DSSY745_400nM_Rep2


title: Sir4V5_DSSY745_300nM_Rep2


title: 36Ln2_S5_L004

description:
total RNA, including miRNA
36Ln2_S5

value: Metastasis of prostate cancer

value: Dobermann

value: male neutered

value: 6 years

value: metastasis of prostate adenocarcinoma


title: GB2_S2_L003

description:
total RNA, including miRNA
GB2_S2

value: Prostate cancer

value: German Rough-haired Pointer

value: prostate adenocarcinoma


title: GB2_S2_L002

description:
total RNA, including miRNA
GB2_S2


title: healthy control group (C6)

first: Yue

address: 232 Huandong Road, University Town, Guangzhou

institute: Guangzhou University of Chinese Medicine

hyb_protocol: According to Affymetrix’s chip hybridization procedure, the biotin-labeled cRNA was added to the cartridge gene chip, the matching reagent kit was used, and the chip was subjected to hybridization for 16 h in the shaking hybridization oven at 45 °C. After hybridization was completed, the chip was washed in the washing workstation according to the standard operating procedure.

scan_protocol: The chip results were scanned using GeneChip® Scanner 3000DX2, the raw data were read by Command Console Software 3.1, and the data that passed quality control were normalized by Command Console Software 3.1 software.

data_processing:
The Gene level_SST_RMA algorithm was used to perform quality control on the data and issue the data report, and the Transcriptome Analysis Console software was used to perform preliminary analysis on gene differential expression.   The differentially expressed genes with p< 0.05 and fold change ≥ 2 were screened out and enriched using DAVID, and the pathways with p< 0.05 were selected for analysis.
The differentially expressed genes with p< 0.05 and fold change ≥ 2 were screened out and enriched using DAVID, and the pathways with p< 0.05 were selected for analysis.

source_name: healthy control group

label_protocol: At the same time, biotin was used to label cRNA.

growth_protocol: Affymetrix gene expression profiling kit geneChip WT PLUS Reagent Kit was used to carry out in vitro reverse transcription amplification of the mRNA from the samples according to the mhnufacturer's instructions. At the same time, biotin was used to label-cRNA

extract_protocol: The total RNA was extracted from the samples using the TRI Reagent according to the manufacturer’s instructions.  Then, miRNeasy Micro kit and RNase-Free DNase Set were used to purify total RNA.  After examining the quality, the purified total RNA was evaluated for RNA integrity using the Agilent Bioanalyzer 2100 electrophoresis apparatus.

treatment_protocol: Venous blood(10 mL) was collected from the median cubital vein into an anticoagulant-tube containing heparin. Peripheral blood monocytes (PBMC) were isolated by Eicoll-density gradient centrifugation method-(Mendez-David-et al.,2013) with lymphocyte-separation solution (absin. China, item No. abs930b). First, suck the lymphocyte layer-to-aclean-centrifuge tube-and add-6ml-PBS to it, gently-blow-to fully mix-the-lymphocyte layer with PBS, then centrifuge the centrifuge tube at 60-100g at-18-20℃for-10 minutes. Remove the upper separation solution, add 6-8ml PBS to the centrifuge-tube, gently blow with a Pasteur pipete to fully mix the lymphocytes, centrifuge for10-minutes at-18--20-Cand-100-×g, and remove the upper separation solution to obtain PBMC and stored in a refrigerator at-80C.

tag: disease state

value: control

tag: tcm syndrome

value: healthy control group

value: Venous blood (10 mL)

value: monocytes


title: healthy control group (C7)


title: healthy control group (C8)


title: healthy control group (C1)


title: healthy control group (C10)


title: healthy control group (C3)


title: GB2_S2_L004

description:
total RNA, including miRNA
GB2_S2

tag: age


title: blood stasis syndrome (XY21)

source_name: blood stasis syndrome

value: Patient with psoriasis

value: stasis syndrome


title: Sir4V5_DSSY745_200nM_Rep2

source_name: haploid cells


title: healthy control group (C4)


title: blood stasis syndrome (XY22)


title: GB2_S2_L001

description:
total RNA, including miRNA
GB2_S2

value: male


title: healthy control group (C9)


title: healthy control group (C2)


title: blood stasis syndrome (XY23)


title: healthy control group (C5)


title: Sir4V5_DSSY745_100nM_Rep2


title: blood stasis syndrome (XY16)


title: 36Ln2_S5_L003

description:
total RNA, including miRNA
36Ln2_S5


title: blood stasis syndrome (XY18)


title: blood stasis syndrome (XY20)


title: blood stasis syndrome (XY17)


title: blood stasis syndrome (XY19)


title: blood stasis syndrome (XY15)


title: blood stasis syndrome (XY13)


title: 36Ln2_S5_L002

description:
total RNA, including miRNA
36Ln2_S5


title: Sir4V5_DSSY745_0nM_Rep2


title: Sir4V5_DSSY745_400nM_Rep1


title: Sir4V5_DSSY745_50nM_Rep2


title: 36Ln1_S4_L004

description:
total RNA, including miRNA
36Ln1_S4


title: Sir4V5_DSSY745_300nM_Rep1


title: 36Ln1_S4_L003

description:
total RNA, including miRNA
36Ln1_S4


title: 36Ln2_S5_L001

description:
total RNA, including miRNA
36Ln2_S5


title: Sir4V5_DSSY745_200nM_Rep1


title: 36Ln1_S4_L001

description:
total RNA, including miRNA
36Ln1_S4


title: 29

value: 3 week Lieber-DeCarli alcohol feeding

value: female

value: AAV-shControl

value: AAV-shAhR


title: 27P1_S1_L004

description:
total RNA, including miRNA
27P1_S1

value: Bolonka Zwetna

value: male neutered

value: 9 years

value: transitional cell carcinoma


title: blood stasis syndrome (XY14)


title: 36Ln1_S4_L002

description:
total RNA, including miRNA
36Ln1_S4

value: Metastasis of prostate cancer

value: Dobermann

value: 6 years

value: metastasis of prostate adenocarcinoma


title: Sir4V5_DSSY745_50nM_Rep1


title: 27P1_S1_L003

description:
total RNA, including miRNA
27P1_S1

value: Prostate cancer


title: A36

city: Uppsala

first: Frauke

last: Augstein

address: Almas Allé 5

department: IOB

country: Sweden

institute: Uppsala University

data_processing:
Mapping to Arabidopsis thaliana reference genome with Hisat2
Generating of Count files with HTSeq
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Seeds were surface sterilized with ethanol, plated on 1/2MS+MES+bactoagar plates on mesh and stratified for 2 days. Seedlings were grown for 5 days in long day conditions, 16h light (22 C) and 8h darkness (20 C) at light intensity of 110µE/m2/s. Per sample 50-100 seedlings were pooled.

extract_protocol:
RNA was extracted using RNAeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using NEBNext®UltraTM RNA Library Prep Kit for Illumina® for paired-end sequencing with read length 150

treatment_protocol: Seedlings were transferred to plates containing 140mM NaCl or mock and treated for 1h or 8h.

value: 5 days

tag: genotype

value: 140mM NaCl

tag: time


title: blood stasis syndrome (XY12)

value: Patient with psoriasis

value: stasis syndrome

value: Venous blood (10 mL)

value: monocytes


title: blood stasis syndrome (XY6)


title: 27P1_S1_L002

description:
total RNA, including miRNA
27P1_S1


title: Sir4V5_DSSY745_0nM_Rep1


title: blood stasis syndrome (XY3)


title: blood stasis syndrome (XY2)


title: blood stasis syndrome (XY1)


title: blood stasis syndrome (XY7)


title: blood stasis syndrome (XY5)


title: A35


title: blood stasis syndrome (XY9)


title: blood stasis syndrome (XY4)


title: Sir4V5_DSSY744_300nM_Rep2


title: Sir4V5_DSSY744_400nM_Rep2


title: A34


title: blood stasis syndrome (XY10)


title: 27P1_S1_L001

description:
total RNA, including miRNA
27P1_S1


title: blood stasis syndrome (XY11)


title: A33_1

value: mock


title: 27Ln3_S12_L004

description:
total RNA, including miRNA
27Ln3_S12

value: metastasis of transitional cell carcinoma


title: blood stasis syndrome (XY8)


title: A32


title: A31


title: A30

value: gai


title: blood heat syndrome group (XR15)

source_name: blood heat syndrome group

value: heat syndrome group


title: blood heat syndrome group (XR14)


title: 27Ln3_S12_L001

description:
total RNA, including miRNA
27Ln3_S12

value: Bolonka Zwetna

value: male neutered

value: 9 years


title: 1511-3-3_S16_L004

description:
passage 87
1511-3-3_S16

source_name: Metadcarc1511.3 rep3

growth_protocol: Culturing conditions were Medium 199 (Life Technologies GmbH, Darmstadt, Germany) containing 10% fetal calf serum (FBS Superior, Biochrom GmbH, Berlin, Germany), 200 IU/ml penicillin and 200 mg/ml streptomycin (Biochrom GmbH) at 37°C in humidified air.

treatment_protocol: Each cell line was seeded in T25 flasks in triplicate beyond passage 60. At 70-80% confluency, cells were detached with TrypLE™Express (Life Technologies GmbH, Darmstadt, Germany), pelleted, fresh frozen in liquid nitrogen and stored at ‑80°C until further use.

tag: cell line

value: Dobermann

tag: cell line short name

tag: original tumor tissue, from which the cell line was established


title: A28

tag: treatment


title: 27Ln3_S12_L003

description:
total RNA, including miRNA
27Ln3_S12

value: Metastasis of prostate cancer


title: blood heat syndrome group (XR13)

tag: cell type


title: Sir4V5_DSSY744_200nM_Rep2

tag: strain


title: Sir4V5_DSSY744_400nM_Rep1


title: Sir4V5_DSSY744_300nM_Rep1


title: 1511-3-3_S16_L002

description:
passage 87
1511-3-3_S16

tag: breed

value: 6 years

value: metastasis of prostate adenocarcinoma


title: Sir4V5_DSSY744_100nM_Rep2


title: 27Ln3_S12_L002

description:
total RNA, including miRNA
27Ln3_S12

tag: tissue

tag: description


title: A29

value: 5 days


title: A27


title: 1511-3-3_S16_L001

description:
passage 87
1511-3-3_S16

tag: histopathological classification

tag: patient id


title: Sir4V5_DSSY744_0nM_Rep2

tag: hm locus

tag: chip antibody


title: Sir4V5_DSSY744_50nM_Rep2


title: Sir4V5_DSSY744_200nM_Rep1


title: A26


title: blood heat syndrome group (XR12)

tag: disease state

tag: tcm syndrome


title: 1511-3-2_S15_L004

description:
passage 86
1511-3-2_S15

source_name: Metadcarc1511.3 rep2

tag: age


title: 1511-3-2_S15_L002

description:
passage 86
1511-3-2_S15


title: blood heat syndrome group (XR11)


title: A25

tag: genotype

tag: time


title: Sir4V5_DSSY744_100nM_Rep1


title: blood heat syndrome group (XR10)


title: Sir4V5_DSSY744_0nM_Rep1


title: A23

value: della quintuple

value: 140mM NaCl


title: blood heat syndrome group (XR9)

value: Patient with psoriasis


title: A24


title: blood heat syndrome group (XR8)

value: Venous blood (10 mL)


title: Sir4V5_DSSY744_50nM_Rep1


title: 1511-3-2_S15_L003

description:
passage 86
1511-3-2_S15

tag: cell line

tag: cell line short name


title: blood heat syndrome group (XR6)

value: monocytes


title: 1511-3-2_S15_L001

description:
passage 86
1511-3-2_S15

tag: original tumor tissue, from which the cell line was established


title: blood heat syndrome group (XR16)

tag: cell type


title: A21

tag: treatment

value: mock


title: 1511-3-1_S5_L004

description:
passage 79
1511-3-1_S5

source_name: Metadcarc1511.3 rep1

tag: breed


title: Sir4V5_DSSY755_Rep2

tag: strain


title: A22


title: blood heat syndrome group (XR5)

tag: tissue


title: blood heat syndrome group (XR7)


title: Sir4V5_DSSY755_Rep1


title: A20


title: blood heat syndrome group (XR4)


title: Sir4V5_DSSY754_Rep2


title: Sir4V5_DSSY754_Rep1


title: H3K79me3_DSSY697_exp_Rep2


title: Sir4V5_DSSY745_100nM_Rep1


title: A19


title: A17

value: Ler


title: A18


title: blood heat syndrome group (XR3)


title: 1511-3-1_S5_L003

description:
passage 79
1511-3-1_S5

tag: description

tag: histopathological classification


title: 1511-3-1_S5_L002

description:
passage 79
1511-3-1_S5

tag: patient id


title: 1511-3-1_S5_L001

description:
passage 79
1511-3-1_S5


title: H3K79me3_DSSY697_sil_Rep2

tag: hm locus

tag: chip antibody


title: H3K79me3_DSSY697_mix_Rep2


title: H3K79me3_DSSY303_Rep2


title: 1511-2-3_S14_L004

description:
passage 79
1511-2-3_S14

source_name: Metadcarc1511.2 rep3


title: 1511-2-3_S14_L003

description:
passage 79
1511-2-3_S14


title: 1511-3-3_S16_L003

description:
passage 87
1511-3-3_S16


title: A14


title: H3K79me3_DSSY695_Rep2


title: H3K79me3_DSSY697_exp_Rep1


title: H3K79me3_DSSY697_mix_Rep1


title: 1511-2-2_S13_L004

description:
passage 75
1511-2-2_S13

source_name: Metadcarc1511.2 rep2


title: 1511-2-3_S14_L001

description:
passage 79
1511-2-3_S14


title: 1511-2-3_S14_L002

description:
passage 79
1511-2-3_S14


title: blood heat syndrome group (XR2)

tag: disease state

tag: tcm syndrome


title: A13

tag: age

tag: genotype


title: A16

tag: time


title: 1511-2-2_S13_L003

description:
passage 75
1511-2-2_S13

tag: cell line

tag: cell line short name


title: blood dryness syndrome (XZ22)

source_name: blood Dryness syndrome group

value: dryness syndrome

tag: cell type


title: A12

tag: treatment


title: blood heat syndrome group (XR1)

value: heat syndrome group


title: blood dryness syndrome (XZ23)


title: 1511-2-2_S13_L002

description:
passage 75
1511-2-2_S13

tag: breed

tag: original tumor tissue, from which the cell line was established


title: H3K79me3_DSSY697_sil_Rep1

tag: strain


title: A10


title: A11_1


title: 1511-2-2_S13_L001

description:
passage 75
1511-2-2_S13

tag: description


title: H3K79me3_DSSY695_Rep1


title: A15


title: blood dryness syndrome (XZ20)

tag: tissue


title: H3K79me3_DSSY303_Rep1


title: blood dryness syndrome (XZ17)


title: blood dryness syndrome (XZ21)


title: blood dryness syndrome (XZ19)


title: blood dryness syndrome (XZ18)


title: A08


title: blood dryness syndrome (XZ16)


title: 1511-2-1_S4_L004

description:
passage 68
1511-2-1_S4

source_name: Metadcarc1511.2 rep1

tag: histopathological classification

tag: patient id


title: H4K16ac_DSSY697_mix_Rep2

tag: hm locus

tag: chip antibody


title: H4K16ac_DSSY697_exp_Rep2


title: A07


title: 1511-2-1_S4_L002

description:
passage 68
1511-2-1_S4


title: blood dryness syndrome (XZ14)

tag: disease state

tag: tcm syndrome


title: A06

tag: age

tag: genotype


title: 1511-2-1_S4_L003

description:
passage 68
1511-2-1_S4

tag: cell line


title: H4K16ac_DSSY303_Rep2


title: 1511-2-1_S4_L001

description:
passage 68
1511-2-1_S4

tag: cell line short name


title: A09

tag: time


title: A04

tag: treatment


title: H4K16ac_DSSY695_Rep2


title: H4K16ac_DSSY697_exp_Rep1


title: H4K16ac_DSSY697_sil_Rep2


title: 1511-1-3_S12_L003

description:
passage 95
1511-1-3_S12

source_name: Adcarc1511.1 rep3

tag: breed

value: prostate adenocarcinoma


title: A03


title: 1511-1-3_S12_L002

description:
passage 95
1511-1-3_S12

value: male neutered


title: H4K16ac_DSSY697_mix_Rep1


title: A02


title: A05


title: 1511-1-3_S12_L001

description:
passage 95
1511-1-3_S12


title: 1511-1-3_S12_L004

description:
passage 95
1511-1-3_S12


title: blood dryness syndrome (XZ10)

tag: cell type


title: blood dryness syndrome (XZ13)


title: blood dryness syndrome (XZ11)


title: 1511-1-2_S11_L004

description:
passage 94
1511-1-2_S11

source_name: Adcarc1511.1 rep2


title: blood dryness syndrome (XZ15)


title: blood dryness syndrome (XZ8)


title: 1511-1-2_S11_L003

description:
passage 94
1511-1-2_S11


title: A01


title: blood dryness syndrome (XZ9)


title: H4K16ac_DSSY303_Rep1

tag: strain


title: H4_DSSY697_exp_Rep2


title: 1511-1-2_S11_L001

description:
passage 94
1511-1-2_S11

tag: description


title: 1511-1-2_S11_L002

description:
passage 94
1511-1-2_S11


title: H4_DSSY697_mix_Rep2


title: blood dryness syndrome (XZ7)

tag: tissue


title: H4K16ac_DSSY695_Rep1


title: blood dryness syndrome (XZ6)


title: H4_DSSY697_sil_Rep2


title: H4K16ac_DSSY697_sil_Rep1


title: 1511-1-1_S3_L004

description:
passage 88
1511-1-1_S3

source_name: Adcarc1511.1 rep1

tag: histopathological classification


title: blood dryness syndrome (XZ5)


title: 1511-1-1_S3_L003

description:
passage 88
1511-1-1_S3

tag: patient id


title: 1511-1-1_S3_L002

description:
passage 88
1511-1-1_S3


title: H4_DSSY695_Rep2

tag: hm locus


title: H4_DSSY303_Rep2

tag: chip antibody


title: 1511-1-1_S3_L001

description:
passage 88
1511-1-1_S3


title: H4_DSSY697_mix_Rep1


title: H4_DSSY697_exp_Rep1


title: blood dryness syndrome (XZ12)

tag: disease state


title: U87-glial cells_0.22F_rep2

city: Belém

first: Bruna

last: Puty

state: Pará

address: Travessa Honório José dos Santos, 423, Jurunas

department: ICB

country: Brazil

institute: UFPA

description: Gene expression after 10 days

hyb_protocol: Hybridization was performed with 300ng of Cy3-labelled cRNA, 5µL of 10xgene expression blocking agent and 1µl OF 25X fragmentation buffer at 65°C for 17h  and 10rpm on  a SurePrint  G3 Human  Gene Expression 8x60K microarray chip (G4851A). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: A microarray scanner (G4900DA, Agilent) was used  with the following set-up: scan area (61 x  21.6mm); 5µm of resolution; green Chanel.

data_processing: Microarray scan images were obtained by Feature extraction v10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: U87-glial cells, 0.22, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using a Low Input Quick Labelling Kit (Agilent) according to manufacturer’s instruction. cRNA purification was performed using RNAeasy mini-spin kit. cRNA was quantified and analyzed (A260/280) with the NanoDrop Spectrophotometer.

growth_protocol: U87 glial-like cells were grown in T75 flasks containing 20mL of Dulbecco’s Modified Eagle’s Medium supplemented with 10% of fetal bovine serum, penicilin, streptomycin, gentamycin, and amphoterycin B,  at 37˚C in a controlled 5% CO2 atmosphere.

extract_protocol: RNA extraction was performed using the SV total RNA isolation system from Promega, according to manufacturer’s instruction. RNA was diluted on nuclease-free water  and quantification was performed using a Qubit 2.0. RNA integrity  was assessed by a Tapestation with a high sensitivity  RNA screentape. Only samples with RIN>7 were used for downstream analysis.

treatment_protocol: Cells were exposed to F(0.095µg/mL and 0.22µg/mL) or not for 10 days. Throughout the 10-days exposure period,  medium were replaced every two days.

value: U87 glial cells

tag: origin

value: Brain tumor

value: 0.22ug/mL fluoride


title: blood dryness syndrome (XZ3)

tag: tcm syndrome


title: U87-glial cells_0.095F_rep3

description: Gene expression after 10 days

source_name: U87-glial cells, 0.095, replicate 3

value: 0.095ug/mL fluoride


title: 1509-3_S10_L004

description:
passage 85; cell line's former name: DT15/09
1509-3_S10

source_name: TCC1509 rep3

value: Bolonka Zwetna

tag: age

value: 9 years

value: transitional cell carcinoma

tag: original tumor tissue, from which the cell line was established


title: U87-glial cells_0.22F_rep1

description: Gene expression after 10 days

source_name: U87-glial cells, 0.22, replicate 1


title: H4_DSSY697_sil_Rep1

source_name: haploid cells


title: H929_Meayamicin.B_rep2_8h

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

description: H929 Human Myeloma Cell Line_Meayamicin B treated_rep2

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Robust Multichip Average (RMA) processing was applied on raw data, that were annotated based on Clariom_D_Human.r1.na36.hg38.a1.transcript.csv file by means of Transcriptome Analysis Console (TAC 4.0) software. Following Alternative Splicing Analysis was performed using TAC 4.0 software. Alternative Splicing events were identified in Meayamycin B-treated versus untreated MM cells after filtering for transcripts expressed in both conditions, Exon expressed in at least one condition, Exon Splicing Index of at least 2 (< -2 or > 2), Exon p-value < 0.05. Intron Retention, Cassette Exon, Alternative 3’ Acceptor Site, Alternative 5’ Donor Site, Alternative Last Exon or Complex Event were assigned on the 15798 transcripts passing filtering criteria (11.72%) out of 134748 total analyzed transcripts.

source_name: Human Myeloma Cell Line

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA).

growth_protocol: HMCLs were purchased from ATCC or DSMZ. Cell lines were Mycoplasma-free and routinely tested for it. Cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS; GIBCO), 4mM glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin (GIBCO).

extract_protocol: Total RNA was extracted from cells using the RNeasy mini kit (Qiagen, #74134d) according to the manufacturer’s instructions.

treatment_protocol: H929 cells were treated with 3nM Meayamicin B for 8 hours.

tag: cell line

value: Myeloma

value: Meayamicin B


title: 1509-3_S10_L003

tag: cell line short name


title: U87-glial cells_0.095F_rep1

description: Gene expression after 10 days

source_name: U87-glial cells, 0.095, replicate 1

tag: treatment