title: Cultured normal human epidermal keratinocytes at 35 degrees C (miRNA)

description: cells are cultured at 35 degrees C

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The expression of known and unique miRNAs in each sample are statistically analyzed and normalized by TPM (Zhou et al., 2010).
Assembly: Homo Sapiens(GRCh38)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells were cultured with 3T3J2 feeder cells in cFAD medium at each temprature (32, 35, 36, 37 and 38 degrees C)

value: epidermis

tag: cell

value: keratinocytes (YF29)


title: Cultured normal human epidermal keratinocytes at 38 degrees C (miRNA)

status: Public on May 29 2023

type: SRA

city: Singapore

first: Jun-Ichi

last: Sakabe

address: Blk4 Lv3, Outram Rd

department: Plastic Reconstructive and Aesthetic Surgery

country: Singapore

institute: Singapore General Hospital (SGH)

description: cells are cultured at 38 degrees C

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Epidermis

extract_protocol:
Followed a protocol of miRNAeasy mini kit (QIAGEN)
RNA libraries were prepared for sequencing by using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technology, CA, USA) in Novogen Experimental Department

treatment_protocol: 100 nM Rapamycin was added into medium which are inchubated at 37 degrees C from day0 to end of cell culture

tag: tissue


title: Cultured normal human epidermal keratinocytes at 36 degrees C (miRNA)

description: cells are cultured at 36 degrees C


title: Cultured normal human epidermal keratinocytes at 37 degrees C (miRNA)

description: cells are cultured at 37 degrees C


title: Cultured normal human epidermal keratinocytes with 100 nM Rapamycin at 37 degrees C (miRNA)

description: cells are cultured at 37 degrees C

tag: treatment

value: 100 nM Rapamycin


title: Cultured normal human epidermal keratinocytes at 36 degrees C (mRNA)

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and pairedend clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other nonsplice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Assembly: Homo Sapiens(GRCh38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol:
cells are cultured at 36 degrees C
Cells were cultured with 3T3J2 feeder cells in cFAD medium at each temperature (32, 35, 36, 37 and 38 degrees C)

tag: cell type

value: keratinocytes

tag: cell line

value: 36 degrees C


title: WT_GNP4_c

type: RNA

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Equal amounts of Cy3-labelled samples were hybridized onto Whole Human Genome 4 × 44 K one-color oligonucleotide arrays (G4112F, Agilent Technologies) for 17 h in a Tecan  HS 4800TM Pro hybridization Station.

scan_protocol: The arrays were scanned on an Agilent G2565BA microarray scanner and further processed using Agilent Feature Extraction Software (version 10.7.3.1). For each feature (or spot) on the array, the feature extraction output file contains the Cy3 fluorescence signal, together with feature quality and gene information.

data_processing: Fluorescence signals were log2-transformed, quantile normalized, and filtered with regard to reliability of the feature. Reliable features were defined as features: (1) of which the intensity was higher than the feature noise level, (2) of which the intensity was below the feature saturation level, (3) that were not a population outlier, (4) that were uniform spots, and (5) that were not a control feature.

source_name: THP-1 monocytes

label_protocol: Labelled RNA was prepared and hybridized for each of the eight test conditions. This was performed for three biological replicates, resulting in 24 samples. Fluorescently labelled samples were obtained using the Quick Amp Labelling kit (Agilent). Briefly, 1 µg of total RNA was reverse transcribed into complementary DNA (cDNA) using a T7-promotor primer and MMLV reverse transcrip_x0002_tase. The cDNA was transcribed into complementary RNA (cRNA), during which, it was fluorescently labelled by incorporation of Cy3-CTP. After purification using the RNeasy mini kit (Qiagen), cRNA yield and specific activity were determined using a NanoDrop spectrophotometer.

growth_protocol: THP-1 cells (ATCC TIB-202), THP1-defASC cells, and THP1-defNLRP3 cells (Invivo_x0002_Gen, Toulouse, France) were used in this study. The cells were cultured in CCM (RPMI 1640 (Gibco) supplemented with foetal calf serum (10% v/v, Greiner-Bio), penicillin (100 U/mL), and streptomycin (100 µg/mL) (Gibco)). Additionally, the ASC- and NLRP3-deficient THP-1 cells were cultured in CCM supplemented with HygroGold (200 µg/mL, InvivoGen) to maintain the siRNA responsible for suppression of ASC or NLRP3. All cell lines were sub-cultured twice per week, seeded to a cell density of 2 × 10^5 cells/mL, and not allowed to grow to a density greater than 1 × 10^6 cells/mL. Cells were not cultured beyond twenty passages to prevent genetic divergence. The wildtype, ASC-deficient, and NLRP3-deficient THP-1 cells were differentiated into macrophage-like cells by culturing for 3 h in the presence of 100 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma) in 96-well format at a cell density of 5 × 10^5 cells/mL, 100 µL/well. After this incubation, the cells were adherent. The medium was replaced with fresh culture medium without PMA and the plates were incubated for 24 h at standard conditions (humidified incubator at 37°C, 5% CO2). After this incubation period, the cells were exposed to a two-fold dilution series of gold nanoparticles (GNPs), at 0.05 nM for 48 h at standard conditions.

extract_protocol: For each exposure condition, the cell lysates of two replicate wells were pooled to obtain sufficient RNA. Total RNA was isolated using the miniRNeasy RNA isolation kit, according to the specifications of Qiagen. The RNA concentration was determined using a NanoDrop Spectrophotometer. RNA integrity was analysed using the Agilent 2100 Bioanalyzer. Samples showing an RNA Integrity Number value above 7 were qualified for microarray analysis. RNA was stored in RNase-free water (Qiagen) at −80°C until further use.

treatment_protocol: After centrifugation of the plates and taking off the supernatants, 120 µL consisting of 5 parts RNAprotect Cell Reagent (Qiagen) and 1 part PBS (Gibco) was added to each well. The cell lysates were frozen at −80°C until further use.

tag: genotype

value: wild type

tag: particle

value: GNP4 (spheres)

tag: date

value: THP-1 monocytes


title: ASCdef_GNP6_b

value: ASC deficient

value: GNP6 (rods)


title: NLRP3def_GNP6_b

value: NLRP3 deficient


title: NLRP3def_con_b

value: Control


title: 196_muscle

city: barcelona

first: aintzane

last: rueda

state: Choose State

address: C/ del Dr. Trueta, 179, 08005 Barcelona

country: Spain

institute: Sequentia Biotech SL.

data_processing:
RNA-seq read quality control (QC) analyses and filtering of high-quality reads were executed using FastQC and BBDuk (Bushnell et al. 2017) by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were aligned to the mouse genome reference (GRCm38/Ensembl release 101) with STAR 2.7.3a (Dobin et al. 2012), while FeatureCounts 1.6.3 package (Liao et al. 2014) was used to assign reads to genes.
Genes with low, constant levels of raw counts across one or more experimental conditions were filtered to eliminate the “uninformative” genes using HTSFilter 1.30.1 (Rau et al. 2013). Filtered gene data was further processed with the DESeq2 package v3.16 (Love et al., 2014) to normalize (Trimmed Mean of M-values, TMM, method) the raw counts.
Assembly: GRCm38/Ensembl release 101
Supplementary files format and content: tab-delimited text files that include FPKM values for every gene and every sample for the liver tissue
Supplementary files format and content: tab-delimited text files that include raw gene counts for every gene and every sample for the liver tissue
Supplementary files format and content: tab-delimited text files that include FPKM values for every gene and every sample for the muscle tissue
Supplementary files format and content: tab-delimited text files that include raw gene counts for every gene and every sample for the muscle tissue

organism: Mus musculus

source_name: Skeletal muscle

extract_protocol: Snap frozen muscle samples were trizol extracted then RNA purified using Zymo Direct-Zol extraction columns. Snap frozen liver samples were extracted using RNeasy columns (Qiagen)

value: Skeletal muscle

value: lmre nf 16-4


title: WT_GNP1_c

value: GNP1 (stars)


title: WT_GNP6_c


title: 195_muscle

value: lmre nf 16-3


title: ASCdef_con_c


title: 194_muscle

value: lmre nf 16-2


title: 193_muscle

value: lmre nf 16-1


title: NLRP3def_con_a


title: WT_GNP4_b


title: Cultured normal human epidermal keratinocytes at 32 degrees C (miRNA)

description: cells are cultured at 32 degrees C

value: epidermis

value: keratinocytes (YF29)


title: 192_muscle

value: lmre nf4-4


title: 188_muscle

value: mre nf16-4


title: 190_muscle

value: lmre nf4-2


title: 191_muscle

value: lmre nf4-3


title: NLRP3def_GNP6_a

value: THP-1 monocytes


title: 189_muscle

value: lmre nf4-1


title: RNA-seq.neuron.WT_15days_rep2

first: Zhenhua

last: hu

state: singapore

address: 31 Biopolis drive

institute: IMCB, A*STAR

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases using Trim_Galore (v0.4.2_dev).
For RNA-seq, paired-end raw sequencing reads were trimmed with Trim Galore with parameters: --trim-n --paired. Cleaned reads were either mapped to the mouse mm10 (mESC and mESC-derived neurons) or hg19 (293T cells) reference genome, guided by the corresponding gene models. Both reference genomes and gene models were obtained from Illumina iGenome website. Gene expression quantification were carried out by RSEM pipeline. Differential gene expression was called using DESeq2 with default parameters except that normalization was based on ERCC spike-in if included, and that biological replicates were used as covariant.
For ChIP-seq, single- and paired-end raw sequencing reads were trimmed with Trim Galore with parameters: --trim-n (single-end) or --trim-n --paired (paired-end). Cleaned reads were then mapped to mm10 reference genome obtained from Illumina iGenome website  by Bowtie2 (v.2.2.9) with parameters: -N 1 -L 25 --no-mixed --no-discordant for paired-end and -N 1 -L 25 for single-end sequencing respectively. PCR duplicates were removed using SAMtools (v1.4). Biological replicate alignment files were merged. Bigwig coverage were generated using “bamCompare” function from deepTools package with parameters “-bl mm10-blacklist.bed --ratio subtract -bs 20 --smoothLength 100 –normalizeUsing RPKM -b1 IP.bam -b2 input.bam --extendReads 200” for single-end, and “-bl mm10-blacklist.bed --ratio subtract -bs 20 --smoothLength 100 -p 6 –normalizeUsing RPKM -b1 IP.bam -b2 input.bam –extendReads” for paired-end sequencing, respectively. Blacklist region file “mm10-blacklist.bed” was obtained from https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz. Metaplots were generated using “computeMatrix” and “plotProfile” functions from deepTools package with default parameter settings.
Assembly: mm10, hg19
Supplementary files format and content: " RNA-seq.xlsx.gz" EXCEL file contains DESeq2 differential gene expression analysis results; "geneCount_byRSEM.zip" contains all the gene count files by RSEM pipeline ending with ".genes.results"; ChIP-seq signal files, normalized by input and ending with ".bw"
Supplementary files format and content: ChIP-seq signal files, normalized against input by deeptools

source_name: mESCs

growth_protocol: 293T cells were cultured in DMEM containing 15% fetal bovine serum (Hyclone), GlutaMax (Gibco) and non-essential amino acids.  mESCs were cultured in KnockOut DMEM containing 15% fetal bovine serum (ES-certified, Gibco), L-glutamine, non-essential amino acids, penicillin/streptomycin,2-mercaptoethanol, LIF, 1 µM PD0325901 and 3 µM CHIR99021 (2i) on 0.1% gelatin-coated tissue culture dishes. Neurons were derived from mESCs as described in the paper and matured in Neurobasal Plus supplemented with B27 Plus (Thermofisher Cat #: A3653401), 1.5mM GlutaMAX, 5ng/mL BDNF (Miltenyi Cat #: 130-093-811).

extract_protocol:
RNA-seq: Total RNA was extracted using TRI-reagent and purified using the Direct-zol RNA MiniPrep Kit (Zymo). For TOP1-ChIP, mESCs were harvested and double-crosslinked in suspension with 2mM DSG in PBS for 45 minutes at room temperature, washed with PBS thrice, and incubated with 1% formaldehyde (FA) in PBS for 10 minutes at room temperature. Crosslinking was quenched by addition of glycine to final concentration of 500mM and incubated at room temperature for 5 min. Cells were washed in PBS and snap frozen for storage at -80degC until ChIP was performed. For RNAP2(S2P) ChIPs, mESCs were subjected to crosslinking in 1% FA for 10 minutes at room temperature. Fixed cells were then subjected to standard ChIP lysis protocol to release chromatin. Released chromatin was sonicated to obtain fragments between 100-300bp, pre-cleared and used for IP with antibody-Dynabead complex. Captured fragments were subjected to several rounds of washes before elution with SDS buffer. DNA was purified using SPRI method.
RNA-seq in 293T and mESC: Equal volumes of RNA preparations (extracted from equal number of cells) from each sample were each mixed with 1 microl of 1:100 diluted Mix 1 of ERCC RNA Spike-In (Life Technologies Cat.# 4456739). The mixture is subjected to ribosomal RNA depletion using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB Cat# E6310) and library construction using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB Cat# E7760), according to manufacturer’s protocol. RNA-seq in neurons: Equal amounts of RNA were directly used in rRNA depletion and library construction. ChIP-seq: Eluted DNA and DNA from relevant input materials was purified and made into libraries using NEBNext Ultra II DNA kit (NEB Cat #: E7645). For both RNA-seq and ChIP-seq libraries, average fragment size was determined on Agilent High Sensitivity DNA and D1000 Screentape system (Agilent Cat #:5067-4626, 5067-5582), quantified using Qubit High Sensitivity DNA system (Life Tech Cat# Q32854), and pooled in equimolar. Pooled libraries were sequenced on the Illumina NextSeq or HiSeq platform.

treatment_protocol: For RNA-seq from 293T overexpressing TOP1 variant,  cells were transfected with pLVX-N’Flag-TOP1 (WT, 4K-A, or R546Q variant)-IRES-GFP constructs, harvested at 70 hours post transfection, and sorted for GFP positive cells. For retinoic acid stimulation, mESCs were treated with 2 microM of retinoic acid for 6 hours.

tag: condition

value: Wildtype

value: differentiation from mESCs

tag: chip antibody


title: WT_GNP1_b

value: wild type


title: ASCdef_GNP6_a

value: ASC deficient

value: GNP6 (rods)


title: WT_GNP6_b


title: ASCdef_con_b

value: Control


title: RNA-seq.neuron.WT_15days_rep1


title: 187_muscle

value: Skeletal muscle

value: mre nf16-3


title: 186_muscle

value: mre nf16-2


title: WT_con_b


title: ASCdef_con_a


title: WT_GNP4_a

value: GNP4 (spheres)


title: WT_GNP1_a

value: GNP1 (stars)


title: RNA-seq.neuron.Mut.2_15days_rep2

value: Top1(R548Q) homozygous


title: WT_GNP6_a


title: 182_muscle

value: mre nf4-2


title: 183_muscle

value: mre nf4-3


title: 181_muscle

value: mre nf4-1


title: 180_muscle

value: livre nf new round 16-2


title: RNA-seq.neuron.Mut.2_15days_rep1


title: RNA-seq.neuron.Mut.1_15days_rep1


title: RNA-seq.neuron.Mut.1_15days_rep2


title: WT_con_a

value: THP-1 monocytes


title: 178_muscle

value: livre nf16-4


title: 176_muscle

value: livre nf4-4


title: 175_muscle

value: livre nf new round 4-1


title: 184_muscle

value: mre nf4-5


title: 174_muscle

value: livre nf4-3


title: 173_muscle

value: livre nf4-2


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.2_IP

description: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.2.bw

library_source: genomic

molecule: genomic DNA

value: Wildtype

value: TOP1 (Bethyl Laboratories, A302-590A)


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.2_input


title: 172_muscle

value: Skeletal muscle

value: livre nf4-1


title: UT-12, 23b OE5

city: Uppsala

first: Andor

last: pivarcsi

state: Uppland

country: Sweden

institute: Uppsala University

description: Gene expression of cSCC cell line transduced with shMIMIC lentiviral microRNAs to over express miR-23b-p

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities. https://www.thermofisher.com/se/en/home/life-science/microarray-analysis.html

data_processing: Data were normalized (log2) and analyzed using Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) using SST-RMA algorithm and annotated on exon/gene level with the library for Clariom D Array (human). Transcripts with fold-change greater than 1.5 and False Discovery Rate (FDR) < 0.05 were differentially expressed.

label: biotin

source_name: UT-SCC-12a expressing miR-23b

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: UT-SCC-12awere cultured in DMEM containing 10% heat inactivated fetal bovine serum, 1% HEPES, 1% non-essential amino acids 1% streptomycin and penicillinCell cultures were maintained in a humidified 5% CO2 incubator at 37°C

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

treatment_protocol: Stable miR-23b-3p or scrambled RNA-overexpressing cSCC cell lines were established by lentiviral transduction with shMIMIC Lentiviral microRNAs in accordance witht he manufactors instructions.

value: cSCC cell

value: transduced with shMIMIC lentiviral microRNAs to over-express miR-23b-p

value: MiR-23b overexpression


title: UT-12, 23b OE4


title: 179_muscle

value: livre nf16-5


title: 171_muscle

value: ko nf newround 16-1


title: 170_muscle

value: ko nf16-4


title: 177_muscle

value: livre nf16-3


title: UT-12, 23b OE3


title: 169_muscle

value: ko nf16-3


title: 168_muscle

value: ko nf16-2


title: S97_L__JacobSmith_RNA_Seq_Directional_S24_R1_001

value: Muscle sample Gastro KO NF4-2


title: 166_muscle

value: ko nf new round 4-2


title: ChIP-seq.mESC.TOP1_Mut.2_input

value: Top1(R548Q) homozygous


title: ChIP-seq.mESC.TOP1_Mut.2_IP


title: 165_muscle

value: ko nf4-4


title: ChIP-seq.mESC.RNAP2S2P_WT_rep2_IP

value: Wildtype

value: RNA polymerase II CTD repeat YSPTSPS (PhosphoS2) (Abcam ab5095)


title: ChIP-seq.mESC.RNAP2S2P_WT_rep2_input


title: 164_muscle

value: Skeletal muscle

value: ko nf4-3


title: ChIP-seq.mESC.RNAP2S2P_WT_rep1_IP

description: ChIP-seq.mESC.RP2S2P_WT_rep12.bw;ChIP-seq.mESC.RP2S2P_WT_rep1.bw


title: 162_muscle

value: ko nf 4-1


title: 161_muscle

value: wt dub nf16-3


title: ChIP-seq.mESC.RNAP2S2P_WT_rep1_input


title: 167_muscle

value: ko nf16-1


title: UT-12, 23b OE2

value: cSCC cell

value: transduced with shMIMIC lentiviral microRNAs to over-express miR-23b-p

value: MiR-23b overexpression


title: 160_muscle

value: wt dub nf16-2


title: UT-12, 23b OE1


title: UT-12, Ctl4

description: Gene expression of cSCC cell line transduced with constructs containing a scrambled RNA to act as a control

source_name: UT-SCC-12a Scrambled RNA

value: control


title: 159_muscle

value: wt hsa nf16-3


title: 158_muscle

value: wt hsa nf16-2


title: 157_muscle

value: wt alf nf16-4


title: ChIP-seq.mESC.RNAP2S2P_Mut.2_rep1_IP

value: Top1(R548Q) homozygous


title: UT-12, Ctl5

value: transduced with constructs containing a scrambled RNA to act as a control


title: 156_muscle

value: wt alf nf16-3


title: UT-12, Ctl2


title: 155_muscle

value: wt dub nf4-4


title: ChIP-seq.mESC.RNAP2S2P_Mut.2_rep1_input


title: UT-12, Ctl1


title: 154_muscle

value: Skeletal muscle

value: wt dub nf4-3


title: 153_muscle

value: wt hsa nf4-3


title: TB model group treated with mycobacterium vaccae, replicate 2

city: beijing

first: yourong

last: yang

state: bj

address: No. 17, Heishanhu, Haidian District, Beijing

country: China

institute: Tuberculosis Institute, Eighth Medical Center of the General Hospital of the Chinese People's Liberation Army

description: Gene expression in Mus musculus blood

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers with Agilent’s hyb protocol

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 11.5.1.

data_processing: Data analysis was performed using Agilent GeneSpring GX 11.5.1 software. Results were provided in the Gene Expression Profiling Data.xls file and Data Analysis Folder

source_name: Peripheral Blood, TB model treated with mycobacterium vaccae

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent Quick Amp Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total RNA was extracted from PBMCs using TRIzol reagent (Life Biotechnology, Shanghai, China). The total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: blood samples were collected in potassium ethylenediaminetetraacetic acid (EDTA) anticoagulant tubes. Peripheral blood mononuclear cells (PBMCs) were isolated using a mouse PBMC separation kit (Haoyang Biological Products Technology, Tianjin, China)

value: whole blood

tag: gender

value: female

tag: age


title: 152_muscle

value: wt hsa nf4-2


title: UT-12, Ctl3

value: cSCC cell


title: ChIP-seq.mESC.RNAP2S2P_Mut.1_rep2_IP

value: RNA polymerase II CTD repeat YSPTSPS (PhosphoS2) (Abcam ab5095)


title: TB model group treated with mycobacterium vaccae, replicate 3

description: Gene expression in Mus musculus blood


title: TB model group treated with high-dose NBXH, replicate 2

description: Gene expression in Mus musculus blood

source_name: Peripheral Blood, TB model treated with high-dose NBXH


title: 151_muscle

value: wtalf nf4-4


title: ChIP-seq.mESC.RNAP2S2P_Mut.1_rep1_IP


title: TB model group treated with high-dose NBXH, replicate 3

description: Gene expression in Mus musculus blood


title: 150_muscle

value: wtalf nf4-3


title: TB model group treated with mycobacterium vaccae, replicate 1

description: Gene expression in Mus musculus blood


title: TB model group treated with high-dose NBXH, replicate 1

description: Gene expression in Mus musculus blood


title: S47_L__JacobSmith_RNA_Seq_Directional_S21_R1

source_name: Liver

value: Liver


title: ChIP-seq.mESC.RNAP2S2P_Mut.1_rep1_input


title: ChIP-seq.mESC.RNAP2S2P_Mut.1_rep2_input


title: TB model group treated with middle-dose NBXH, replicate 3

description: Gene expression in Mus musculus blood

source_name: Peripheral Blood, TB model treated with middle-dose NBXH


title: ZRSR2_KO_P5

first: Pushkar

last: Dakle

address: 14 Medical Dr

institute: Cancer Science Institute of Singapore

data_processing:
MSI (mis-splicing index) values were calculated for each intron
Only those introns with a coverage of at least one read at each of their junctions and with total coverage of the two junctions being higher than 4 were considered. Also, introns which did not have a coverage of at least 1 for 95% of their length were filtered out.
To identify differentially spliced introns, differences in MSI values (ΔMSI) were calculated as ΔMSI=MSIknockout−MSIwildtype. Significance of this difference was computed using Fisher's test and the obtained p-values were corrected for multiple testing.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited output files – intronwise mis-splicing index

source_name: ES cells

extract_protocol:
Total RNA was extracted from ES cells using RNeasy Mini Kits (Qiagen)
polyA-selected RNA was used to prepare libraries using either TruSeq sample preparation kit


title: S46_L__JacobSmith_RNA_Seq_Directional_S20_R1


title: S45_L__JacobSmith_RNA_Seq_Directional_S19_R1


title: ZRSR2_KO_P3


title: S42_L__JacobSmith_RNA_Seq_Directional_S16_R1


title: S43_L__JacobSmith_RNA_Seq_Directional_S17_R1


title: S41_L__JacobSmith_RNA_Seq_Directional_S15_R1


title: ZRSR2_KO_P2


title: WT_ES_P5


title: S40_L__JacobSmith_RNA_Seq_Directional_S14_R1


title: S48_L__JacobSmith_RNA_Seq_Directional_S22_R1


title: WT_ES_P3


title: TB model group treated with middle-dose NBXH, replicate 2

description: Gene expression in Mus musculus blood


title: S44_L__JacobSmith_RNA_Seq_Directional_S18_R1


title: S39_L__JacobSmith_RNA_Seq_Directional_S13_R1


title: WT_ES_P2


title: TB model group treated with middle-dose NBXH, replicate 1

description: Gene expression in Mus musculus blood


title: TB model group treated with low-dose NBXH, replicate 3

description: Gene expression in Mus musculus blood

source_name: Peripheral Blood, TB model treated with low-dose NBXH


title: S38_L__JacobSmith_RNA_Seq_Directional_S12_R1


title: S37_L__JacobSmith_RNA_Seq_Directional_S11_R1


title: RNA-seq.293T-OE.WT_rep2

value: Wildtype

value: transfection with plasmid


title: RNA-seq.293T-OE.WT_rep1


title: NSC_siSCR_Chd4_ChIP_Seq

city: shanghai

first: Ximing

last: Nian

state: Shanghai

address: Chongqing Nanlu 227

institute: Shanghai Jiao Tong University

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie2 alignment programs in two ways: only uniquely aligned reads were kept or both uniquely aligned reads and the sequencing reads that align to repetitive regions were kept for downstream analysis (if a read aligns to multiple genome locations, only one location is arbitrarily chosen).
The multiple reads were collapsed in order to reduce the PCR biases. The aligned reads were used for peak finding with HOMER
Peaks were identified by searching locations of high read density using a 200-bp sliding window. Regions of maximal density exceeding a given threshold were called as peaks, and we required adjacent peaks to be at least 500 bp away to avoid redundant detection
Peaks from separate experiments were considered equivalent/co-bound if their peak centers were located within 200 bp of each other. Read density heat maps were created by first using HOMER to generate read densities and then visualized using Java TreeView
Assembly: hg38
Supplementary files format and content: xls, bigWig (except for Input sample)

source_name: Brain

growth_protocol: Cortical mouse NPCs were cultured using P0 mouse cortex in laminin and poly-L-ornithine-coated plates and maintained in DMEM/F12 (11320033, Thermo) containing 1% penicillin/streptomycin, 1% l-glutamine, 1% N-2 supplement, 1% B27,1×Glutamax (10565-042, Life technologies)，5 mM Hepes, 0.06% Glucose, 50 μM beta-mercaptoethanol, 20 ng/ml EGFand 20 ng/ml bFGF

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the  KAPA HyperPrep Kits (Roche, 07962347001) following manufacturer's protocols..

value: Brain

value: primary neural stem cell

value: wild type

value: growth medium


title: NSC_iKO_Chd4_ChIP_Seq

value: mutant

value: 4-OH-TAM in growth medium


title: NSC_Ctrl_Seh1-1_ChIP_Seq


title: S35_L__JacobSmith_RNA_Seq_Directional_S10_R1


title: NSC_siSeh1_Chd4_ChIP_Seq


title: TB model group treated with low-dose NBXH, replicate 2

description: Gene expression in Mus musculus blood


title: RNA-seq.293T-OE.vector_rep2


title: NSC_iKO_Seh1_flag_ChIP_Seq


title: TB model group treated with isoniazide, replicate 2

description: Gene expression in Mus musculus blood

source_name: Peripheral Blood, TB model treated with isoniazide


title: S34_L__JacobSmith_RNA_Seq_Directional_S9_R1


title: TB model group treated with low-dose NBXH, replicate 1

description: Gene expression in Mus musculus blood


title: TB model group treated with isoniazide, replicate 1

description: Gene expression in Mus musculus blood


title: TB model group, replicate 3

description: Gene expression in Mus musculus blood

source_name: Peripheral Blood, TB model,without treated


title: RNA-seq.293T-OE.vector_rep1


title: NSC_Ctrl_Chd4_ChIP_Seq


title: HUVEC cells, miR-409-3p Mimic-3

city: BOSTON

first: BASAK

last: ICLI

state: MA

address: 800 Washington St Box 80

department: MOLECULAR CARDIOLOGY RESEARCH INSTITUTE

country: USA

institute: TUFTS MEDICAL SCHOOL

description: Biological Replicate 3

data_processing:
instrument model: Illumina NextSeq500/550
Qiagen RNA-Seq Analysis Portal
First, all annotated transcripts are extracted (using anmRNAtrack). If there are several annotated splice variants, they are all extracted.
Next, the reads are mapped against all the transcripts plus to the whole genome. From this mapping, the reads are categorized and assigned to the genes using the EM estimation algorithm , and expression values for each gene and each transcript are calculated.
Each gene is modeled by a separate Generalized Linear Model (GLM) assuming that the read counts follow a Negative Binomial distribution.
The final GLM fit and dispersion used to calculate the total likelihood of the model given the data, and the uncertainty on each fitted coefficient. The two statistical tests, Wald test and Likelihood Ratio test, each make use of one of these values.
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: Tab-delimited text (.txt) files include Identifier (Ensembl ID numbers) and TPM (Transcript per Million) values for each gene

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (Lonza, CC-2519) passaged three times were used for all experiments and cultured in growth media EGM®-2 (Lonza, cc-3162)

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen, #74104). 500ng of total RNA was used for the construction of sequencing libraries.
From 500ng starting material, the mRNA was enriched and fragmented using enzymatic fragmentation. After first and second strand synthesis, the cDNA was end-repaired and 3’ adenylated. Sequencing adapters were ligated to the overhangs.
Adapted molecules were enriched using by 13 cycles or PCR and purified by a bead based cleanup. The libraries size distribution was validated and quality inspected on a TapeStation (Agilent Technologies). High quality libraries are pooled based in equimolar concentrations based on the Bioanalyzer automated electrophoresis system (Agilent Technologies).
The library pool(s) were quantified using qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on a NextSeq500/550 instrument (1x75 cycles) according to the manufacturer instructions (Illumina Inc.).

treatment_protocol:
For transfection studies, HUVECs plated at 50,000 cells/ml were cultured overnight before being transfected with Lipofectamine™ 2000 transfection reagent (Invitrogen, 52887) and either 50nM miR-409-3p mimic (Thermo Scientific, 4464066) or non-specific control (Thermo Scientific, 4464058) in accordance with manufacturer’s instructions.
100uM sodium palmitate (Sigma) for 16 hours prior to harvest of RNA.

value: Human Umbilical Vein Endothelial Cells

value: WT

tag: transfection

value: miR-409-3p mimic

tag: time

value: 48 hours

value: Palmitate

value: 16 hours


title: HO3

city: Shanghai

first: Cunyi

last: Fan

state: China

address: Yishan Road NO.600, Xuhui district, Shanghai

institute: Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai Jiao Tong University

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences.
In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered.
Trimmomatic[1] software was first used for adpter removing, And then low-quality   bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using hisat2[2] to align clean reads to the reference genome of the experimental specie, thesample should be assessed by genomic and gene alignment.
Assembly: GRCm38.p6
Supplementary files format and content: read counts values for all samples
Supplementary files format and content: FPKM values for all samples

source_name: Achilles tendon

extract_protocol:
mirVana™ miRNA ISOlation Kit，Ambion-1561
TruSeq Stranded Total RNA with Ribo-Zero Gold

value: Achilles tendon

value: Achilles tendon amputation


title: RNA-seq.293T-OE.R546Q_rep2


title: HO2


title: TB model group treated with isoniazide, replicate 3

description: Gene expression in Mus musculus blood

value: whole blood

value: female


title: HUVEC cells, miR-409-3p Mimic-1

description: Biological Replicate 1


title: S32_L__JacobSmith_RNA_Seq_Directional_S7_R1

value: Liver


title: RNA-seq.293T-OE.R546Q_rep1

value: Wildtype

value: transfection with plasmid


title: HO1


title: HUVEC cells, Non-Specific Control-3

description: Biological Replicate 3

value: non-specific control


title: S31_L__JacobSmith_RNA_Seq_Directional_S6_R1


title: Control3

value: sham


title: HUVEC cells, Non-Specific Control-2

description: Biological Replicate 2


title: RNA-seq.293T-OE.4K-A_rep2


title: S30_L__JacobSmith_RNA_Seq_Directional_S5_R1


title: Control2


title: RNA-seq.293T-OE.4K-A_rep1


title: HUVEC cells, Non-Specific Control-1

description: Biological Replicate 1


title: HUVEC cells, miR-409-3p Mimic-2

description: Biological Replicate 2


title: S33_L__JacobSmith_RNA_Seq_Directional_S8_R1


title: S29_L__JacobSmith_RNA_Seq_Directional_S4_R1


title: Normal control group, replicate 3

description: Gene expression in Mus musculus blood

source_name: Peripheral Blood, Normal control,without treated


title: Control1


title: dsrct patient

city: Milano

first: Stefano

last: Percio

address: VIa Amadeo 42

country: Italy

institute: Istituto Nazionale dei Tumori

data_processing:
Sequence reads were checked for quality using fastQC
Sequence reads mapping to GrCh37/hg19 and count extration were performed using STAR with default parameters
Assembly: hg19
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: dsrct patient

growth_protocol: From 6 to 8 week-old female SCID mice were implanted into the right flank with the PDX. When xenografts were approximately 500 mm3 was explanted and frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from frozen DSRCT specimen and PDX with an RNeasy mini kit (Qiagen) in accordance with the manufacture's protocol.
cDNA libraries were synthesized from 200 ng total RNA with RNA Prep kit with Tagmentation (Illumina), following manufacturers’ instructions. Libraries were quantified by Qubit assay (Thermo Fisher Scientific Inc) and quality was assessed by the High Sensitivity kit on the 4200TapeStation (Agilent)

value: dsrct patient


title: S28_L__JacobSmith_RNA_Seq_Directional_S3_R1


title: dsrct PDX

source_name: dsrct PDX

value: dsrct PDX


title: ezh2 ko clone 19, embyonic stemm cell, ezh2 ko bio rep #2

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: North Carolina

address: 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina at Chapel Hill

description:
rip_ezh2ko_ezh2_negative_scaled.wig
rip_ezh2ko_ezh2_positive_scaled.wig
prc2_ezh2peaks_fc

data_processing:
reads were aligned to genome using star/2.5.4b
filtered for reads that passed quality score q30
used subread featureCounts with manually curated peak files to assign sequence reads to features
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: excel file of processed data

source_name: Embryonic Stem Cells

growth_protocol: RMCE embryonic Stem Cells were maintained in DMEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
immunoprecipitated RNA was prepared with Zymo Clean and Concentrator
KAPA RNA Hyperprep Kit with RiboErase, 9uL of IP +1uL ERCC rna spike in sequenced

value: Embryonic Stem Cells

tag: strain

value: CAST/B6 Male Rosa26-RMCE

value: embryonic stem cells

value: ezh2 KO

value: 3 Days Doxycycline induction


title: S49_L__JacobSmith_RNA_Seq_Directional_S23_R1

value: LiverRE NF4-2_diff batch


title: ezh2 ko clone 12, embyonic stemm cell, ezh2 ko bio rep #1


title: S26_L__JacobSmith_RNA_Seq_Directional_S1_R1


title: wt clone 44, embryonic stem cell, wt bio rep #3

description:
rip_wt_ezh2_negative_scaled.wig
rip_wt_ezh2_positive_scaled.wig
ezh2_10kpeaks.bed
ezh2_filtered_peaks.bed
prc2_ezh2peaks_fc

value: WT


title: S25_L__JacobSmith_RNA_Seq_Directional_S25_R1


title: S24_L__JacobSmith_RNA_Seq_Directional_S24_R1


title: TB model group, replicate 2

description: Gene expression in Mus musculus blood


title: S27_L__JacobSmith_RNA_Seq_Directional_S2_R1


title: S23_L__JacobSmith_RNA_Seq_Directional_S23_R1


title: TB model group, replicate 1

description: Gene expression in Mus musculus blood


title: Normal control group, replicate 1

description: Gene expression in Mus musculus blood


title: parent wt, embryonic stem cell, wt bio rep #1


title: safb/2 dko clone 4, embyonic stemm cell, safb/2 dko bio rep #1

description:
rip_dko_ezh2_negative_scaled.wig
rip_dko_ezh2_positive_scaled.wig
prc2_ezh2peaks_fc

value: safb/2 dko


title: wt clone 20, embryonic stem cell, wt bio rep #2


title: S22_L__JacobSmith_RNA_Seq_Directional_S22_R1


title: F6_zygote_B

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Reads were trimmed using Trim Galore v0.4.1 and mapped onto the mouse GRCm38 genome assembly using STAR (2.5.3a) with default parameters. Individual mapped reads were  quantified as fragments per kilobase of exon model per million mapped fragments (FPKM) values with RefSeq genes as reference. Differential expression analysis was performed by a Partek Flow GSA algorithm with default parameters.
Assembly: GRCm38
Supplementary files format and content: txt files include RPKM values for each Sample

source_name: embryo

extract_protocol:
RNA isolation from oocytes and embryos was used Trizol reagent (Sigma).
RNA-seq libraries were prepared using the Smart-seq V4 kit (Clontech) and Illumina Nextera XT DNA library preparation kit.

value: embryo


title: F6_zygote_D


title: F6_zygote_M_C

value: M-phase of meiosis


title: F6_zygote_M_B


title: F6_MII_C

source_name: oocyte

value: oocyte


title: F6_zygote_C


title: F6_zygote_A


title: safb/2 dko clone 13, embyonic stemm cell, safb/2 dko bio rep #1


title: F6_MII_B


title: F6_zygote_M_A


title: Donor 4 dWAT+IgG

city: Miami

first: Carina

last: Nicu

state: Florida

address: 1600 NW 10th Ave RMSB 6157 Locator Code R-250

department: Dr Phillip Frost Dept of Dermatology and Cutaneous Surgery

institute: University of Miami

description: amplified ds cDNA

hyb_protocol: Samples were hybridized as per the Agilent One-Colour Microarray-based Gene Expression Analysis Protocol.

scan_protocol: Slides were scanned using the Agilent Technologies microarray scanner G2505C US84700251

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14) to obtain background subtracted and spatially de-trended Processed Signal intensities – the final data is presented as gProcessed signal.  Filtering and analysis of data was carried out using GeneSpring GX13: data was per sample normalized by percentile shift to the 75th percentile, and baseline transformed to the time matched vehicle control sample from the same donor.

source_name: Scalp skin

label_protocol: Amplified double-stranded cDNA was labelled with Cy3 using the SureTag DNA labelling kit (Agilent, #5190-3399).

growth_protocol: Hair follicles were cultured in William's E media for 24hrs

extract_protocol: 10um thick cryosections were placed on 1.0 PEN NF membrane slides (Zeiss), stained in an alcohol series and hematoxylin, followed by laser-capture microdissection on Zeis PALM MicroBEAM microscope with PALM Robo Software. RNA was extracted using Qiagen RNeasy micro Kit.

treatment_protocol: Hair follicles were cultured either a) dissected of surrounding tissue (HF) b) dissected of dermis but with 3-5 rows of perifollicular dermal adipocytes (HF+dWAT) and c) HF+dWAT+ neutralizing antibody to human HGF (HF+dWAT+IgG)

value: Female


title: Donor 4 dWAT repeat

description: amplified ds cDNA


title: Donor 4 dWAT

description: amplified ds cDNA


title: S19_L__JacobSmith_RNA_Seq_Directional_S19_R1

value: Liver


title: Donor 3 dWAT repeat

description: amplified ds cDNA

value: Male


title: mouse ESC, CS5246 EZH2

data_processing:
aligned to mm10 b6 and cast genomes using bowtie2
filtered for reads that passed q30 quality filter
peaks were called using macs2 callPeak
used bedtools intersect to find peak overlaps
used subread featureCounts to assign sequencing reads to called peaks
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: bam file of aligned and filtered data

source_name: embryonic stem cells

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde
NEB End Repair, purified with AMPure XP Beads, A-Tailing with Klenow Fragment, Ligated 1uM TruSeq Adapters

tag: antibody

value: CS5246 EZH2


title: Normal control group, replicate 2

description: Gene expression in Mus musculus blood

value: whole blood

value: female


title: F6_MII_A


title: Donor 4 CTRL

description: amplified ds cDNA


title: S18_L__JacobSmith_RNA_Seq_Directional_S18_R1

source_name: Liver


title: F6_GV_C


title: F6_GV_B


title: S16_L__JacobSmith_RNA_Seq_Directional_S16_R1


title: RNA-seq.RA_Mut.1vsWT_WT_rep2

source_name: mESCs

value: Wildtype

value: retinoic acid treatment


title: S17_L__JacobSmith_RNA_Seq_Directional_S17_R1


title: RNA-seq.RA_Mut.1vsWT_WT_rep1


title: S21_L__JacobSmith_RNA_Seq_Directional_S21_R1


title: Donor 3 dWAT

description: amplified ds cDNA


title: F6_GV_A


title: RNA-seq.RA_Mut.1vsWT_Mut.1_rep3

value: Top1(R548Q) homozygous


title: S15_L__JacobSmith_RNA_Seq_Directional_S15_R1


title: RNA-seq.RA_Mut.1vsWT_Mut.1_rep2


title: S14_L__JacobSmith_RNA_Seq_Directional_S14_R1


title: RNA-seq.RA_Mut.1vsWT_WT_rep3


title: F6_2cell_M_C


title: F6_2cell_M_B


title: RNA-seq.RA_Mut.1vsWT_Mut.1_rep1


title: Donor 2 CTRL repeat

description: amplified ds cDNA


title: F6_2cell_M_A


title: S13_L__JacobSmith_RNA_Seq_Directional_S13_R1


title: RNA-seq.mESC.Mut.2vsWT_WT_rep3


title: Donor 3 CTRL

description: amplified ds cDNA


title: S11_L__JacobSmith_RNA_Seq_Directional_S11_R1


title: F6_2cell_C


title: S12_L__JacobSmith_RNA_Seq_Directional_S12_R1


title: F6_2cell_B


title: Donor 3 dWAT+IgG

description: amplified ds cDNA


title: S10_L__JacobSmith_RNA_Seq_Directional_S10_R1


title: Donor 2 dWAT+IgG

description: amplified ds cDNA


title: F6_2cell_A


title: RNA-seq.mESC.Mut.2vsWT_Mut.2_rep3


title: Donor 2 dWAT

description: amplified ds cDNA


title: S9_L__JacobSmith_RNA_Seq_Directional_S9_R1


title: F1_zygote_M_C


title: S8_L__JacobSmith_RNA_Seq_Directional_S8_R1


title: F1_zygote_M_B


title: RNA-seq.mESC.Mut.2vsWT_Mut.2_rep2


title: RNA-seq.mESC.Mut.2vsWT_WT_rep2


title: RNA-seq.mESC.Mut.2vsWT_Mut.2_rep1


title: Donor 2 CTRL

description: amplified ds cDNA


title: RNA-seq.mESC.Mut.2vsWT_WT_rep1


title: S7_L__JacobSmith_RNA_Seq_Directional_S7_R1


title: F1_zygote_M_A


title: M136_rep3

city: Guangzhou

first: Hang

last: Zou

address: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University,

institute: Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China

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 STAR (v1.5.1)
The read counts were extracted using HTSeq-count （v0.11.3）
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: splenic CD19+ B cells

extract_protocol:
RNA was extracted using Trizol reagent. mRNA was enriched with oligo(dT)-attach magnetic beads and fragmented into small pieces, cDNA library was generated using random hexamer-primed reverse transcription followed by second-strand cDNA synthesis and sequenced on an MGI 2000 platform (BGI, Shenzhen, China).
RNA libraries were prepared for sequencing using standard BGI 2000 protocols

value: 6-8 week

value: treated with CD40mAb+deltaKdeltaRAB


title: S6_L__JacobSmith_RNA_Seq_Directional_S6_R1


title: M136_rep2


title: F1_zygote_D


title: Donor 1 CTRL repeat

description: amplified ds cDNA


title: S5_L__JacobSmith_RNA_Seq_Directional_S5_R1


title: RNA-seq.mESC.Mut.1vsWT_WT_rep2


title: F1_zygote_C


title: M136_rep1


title: RNA-seq.mESC.Mut.1vsWT_WT_rep1


title: S4_L__JacobSmith_RNA_Seq_Directional_S4_R1


title: Donor 1 dWAT+IgG

description: amplified ds cDNA


title: A327_rep3

value: treated with CD40mAb+ATCC33277


title: S3_L__JacobSmith_RNA_Seq_Directional_S3_R1


title: F1_zygote_A

value: WT


title: RNA-seq.mESC.Mut.1vsWT_Mut.1_rep3


title: RNA-seq.mESC.Mut.1vsWT_WT_rep3


title: RNA-seq.mESC.Mut.1vsWT_Mut.1_rep2


title: S2_L__JacobSmith_RNA_Seq_Directional_S2_R1


title: A327_rep1


title: F1_MII_C


title: S1_L__JacobSmith_RNA_Seq_Directional_S1_R1


title: RNA-seq.mESC.Mut.1vsWT_Mut.1_rep1


title: F1_MII_B


title: Donor 1 CTRL

description: amplified ds cDNA


title: Donor 1 dWAT

description: amplified ds cDNA


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.1_rep3_input


title: A327_rep2


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.1_rep3_IP

description: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.1_rep123.bw

value: TOP1 (Bethyl Laboratories, A302-590A)


title: ctrl_rep2

value: treated with CD40mAb


title: F1_MII_A


title: F1_GV_C


title: F1_zygote_B

value: embryo


title: F1_GV_B

value: oocyte


title: ctrl_rep1


title: Patient 3 HGF

description: Donor 3 HGF

hyb_protocol: Samples were hybridized as per the Agilent One-Colour Microarray-Based Gene Expression Analysis Protocol (version 6.9.1) using Agilent hi-RPM Gene Expression hybridization kit reagents.

scan_protocol: Slides were scanned using the Agilent Technologies microarray scanner G2505C US84700251.

label_protocol: Samples were prepared as per the Agilent One-Colour Microarray-Based Gene Expression Analysis Protocol (version 6.9.1) using the Amp Labelling Kit

growth_protocol: Human scalp hair follicles were cultured ex vivo for 6 hours in William's E Media.

extract_protocol: RNA was extracted using Qiagen RNeasy Micro Kit.

treatment_protocol: The hair follicles were grown with/without recombinant human HGF protein.

tag: agent

value: HGF


title: Patient 3 CTRL

description: Donor 3 CTRL


title: Patient 2 CTRL

description: Donor 2 CTRL


title: ctrl_rep3


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.1_rep2_input


title: F1_GV_A


title: RFP+GFP+BFP, replicate 1

city: Eggenstein-Leopoldshafen

first: Kersten

last: Rabe

state: Select a state

address: Building 601

department: Institute for Biological Interfaces - 1

country: Germany

institute: Karlsruhe Institute of Technology

data_processing:
Trim Galore for adapter and quality trimming.
SortMeRNA v4.3.4 for rRNA removal.
STAR aligner v2.7.6a for mapping to E. coli MG1655 (ASM584v2).
FeatureCounts for gene counting.
DESeq2 for normalization and differential expression analysis.
Supplementary files format and content: Comma seperated  file of raw read counts and normalized read counts.

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

source_name: str. K12 substr. MG1655

growth_protocol: The stress assay started by using an aliquot of the seedbank to inoculate two independent cultures (Cult. 1 & Cult. 2) each in 5 ml LB+kan broth and incubated overnight in 180 rpm shaker at 37 °C. The next day, cultures were diluted to 1:250 using fresh LB+kan and incubated again at the same conditions for 5-6 hours. After reaching adequate optical density, the cultures were diluted using fresh LB+kan to adjust the OD600 to 0.4, which is 2X of the final cell density in the assay plate. At the same time, the chemical stressing agents were diluted in LB+kan to 2X of the final required concentration.

extract_protocol:
RNA was extracted using the Direct-Zol RNA Miniprep Kit (Zymo Research Inc.).
RNA libraries were constructed using Zymo-Seq RiboFree® Total RNA Library Kit (Zymo Research Inc.)

treatment_protocol: The stress treatment started by adding 250 µl diluted sensor strain culture to 250 µl LB-stress mixture (or LB containing no stressor as the control culture) to form 500 µl total volume, which had a final cell density of OD600 0.2 and 1X stressor concentration.

value: str. K12 substr. MG1655

tag: facs subpopulation

value: triple RFP-GFP-BFP

value: 2-propanol 2%


title: Patient 2 HGF

description: Donor 2 HGF

value: Male


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.1_rep2_IP


title: Patient 1 CTRL

description: Donor 1 CTRL


title: F1_2cell_M_C

tag: tissue

value: M-phase of meiosis


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.1_rep1_input

value: Wildtype

tag: treatment


title: Patient 1 HGF

description: Donor 1 HGF


title: RFP, replicate 2

value: mono RFP


title: RFP, replicate 1


title: F1_2cell_M_A


title: ChIP-seq.mESC.TOP1_Mut.1_rep3_IP

value: Top1(R548Q) homozygous


title: RFP+GFP+BFP, replicate 2


title: GFP+RFP, replicate 2

value: dual RFP-GFP


title: F1_2cell_C


title: ChIP-seq.mESC.TOP1_WT-matched-to-Mut.1_rep1_IP


title: F1_2cell_B


title: GFP+RFP, replicate 1


title: F1_2cell_A


title: ChIP-seq.mESC.TOP1_Mut.1_rep3_input


title: ChIP-seq.mESC.TOP1_Mut.1_rep2_input


title: ChIP-seq.mESC.TOP1_Mut.1_rep2_IP


title: GFP, replicate 1

value: mono GFP


title: GFP, replicate 2


title: ChIP-seq.mESC.TOP1_Mut.1_rep1_IP


title: 13cRA_3

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

description: Polysomal RNA from CHP134 cells treated with 5 µM 13cRA for 24 hours.

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: CHP134 cells, 13cRA, polysomal RNA, biological replicate 3

growth_protocol: CHP134 cells were purchased from ECACC (Cat. No. 06122002). The cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium 1640 medium supplemented with 10% fetal bovine serum (FBS) and 2 mM glutamine at 37 °C in a humidified atmosphere of 5 % CO2.

extract_protocol: To extract polysomal RNA, the following procedure was applied. CHP134 cells were incubated with 100 μg/ml cycloheximide for 4 minutes, rinsed with phosphate buffer saline and lysed directly in cell-culture vessels [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1 % Triton X-100, 1 % sodium deoxycholate, 100 μg/ml cycloheximide, 0.2 U/μl RNase inhibitor, 1 mM DTT]. The lysate was collected with a cell scraper, pipetted into a microcentrifuge tube and after 5 minutes incubation on ice centrifuged for 10 min at 12000 g at 4 °C. The supernatant was transferred into a new microcentrifuge tube and stored at –80 °C. The lysates were fractionated by ultracentrifugation (Sorvall rotor, 100 min at 180000 g) through 15–50 % linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2.  Polysomal fractions were collected monitoring the absorbance at 254 nm. Polysomal RNA was isolated after proteinase K treatment, phenol–chloroform extraction and isopropanol precipitation and finally resuspended in 50 μl of water. RNA quality was assessed using the Agilent 2100 Bioanalyzer platform.

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with 5 µM 13cRA for 24 hours.

tag: disease

value: neuroblastoma

tag: fraction

value: polysomal RNA

tag: biological replicate


title: ISR&13cRA_2

description: Polysomal RNA from CHP134 cells treated with 15 µM ISRand 5 µM 13cRA for 24 hours.

source_name: CHP134 cells, ISR&13cRA, polysomal RNA, biological replicate 2

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with 15 µM ISRand 5 µM 13cRA for 24 hours.

tag: cell line


title: 13cRA_2

source_name: CHP134 cells, 13cRA, polysomal RNA, biological replicate 2


title: Golden Hamster Lung, Vaccinated Group, 5 day post challenge, Replicate 4

status: Public on May 28 2023

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to BCM_Maur_2.0 genome by using Hisat2
Raw count were calculated by using featurecounts
Assembly: BCM_Maur_2.0
Supplementary files format and content: tab-delimited txt files include raw count and TPM values for each Sample

organism: Mesocricetus auratus

source_name: Lung

extract_protocol:
The hamster lung lobe was removed, shredded into small pieces and stored in RNA Later Solution (Thermo Fisher Scientific) for a maximum of 24 h at 4 °C. Lung tissue was homogenized using TissueLyser II (Qiagen, Hilden, Germany) and RNA extraction was performed according to the manufacturer’s instructions (QIAamp Viral RNA Mini Kit (Qiagen)).
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Lung

value: Vaccinated with dNS1-RBD, then challenged with SARS-CoV-2 Beta Variant

value: Day 5


title: ISR&13cRA_3

source_name: CHP134 cells, ISR&13cRA, polysomal RNA, biological replicate 3


title: F1_2cell_M_B

value: embryo


title: Golden Hamster Lung, Vaccinated Group, 5 day post challenge, Replicate 3


title: Golden Hamster Lung, Vaccinated Group, 5 day post challenge, Replicate 2


title: ISR&13cRA_1

source_name: CHP134 cells, ISR&13cRA, polysomal RNA, biological replicate 1


title: Golden Hamster Lung, Vaccinated Group, 5 day post challenge, Replicate 1


title: 13cRA_1

source_name: CHP134 cells, 13cRA, polysomal RNA, biological replicate 1


title: Golden Hamster Lung, Vaccinated Group, 3 day post challenge, Replicate 2

value: Day 3


title: Golden Hamster Lung, Vaccinated Group, 3 day post challenge, Replicate 3


title: Golden Hamster Lung, Vaccinated Group, 3 day post challenge, Replicate 4


title: Golden Hamster Lung, Vaccinated Group, 1 day post challenge, Replicate 1

value: Day 1


title: ISR_2

description: Polysomal RNA from CHP134 cells treated with 15 µM ISR for 24 hours.

source_name: CHP134 cells, ISR, polysomal RNA, biological replicate 2

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with 15 µM ISR for 24 hours.

value: ISR


title: Golden Hamster Lung, Vaccinated Group, 3 day post challenge, Replicate 1


title: Golden Hamster Lung, Vaccinated Group, 1 day post challenge, Replicate 4


title: Golden Hamster Lung, Vaccinated Group, 1 day post challenge, Replicate 2


title: Golden Hamster Lung, Vaccinated Group, 1 day post challenge, Replicate 3


title: Golden Hamster Lung, Vaccinated Group, Before challenge, Replicate 3

value: Day 0


title: ChIP-seq.mESC.TOP1_Mut.1_rep1_input

extract_protocol:
RNA-seq: Total RNA was extracted using TRI-reagent and purified using the Direct-zol RNA MiniPrep Kit (Zymo). For TOP1-ChIP, mESCs were harvested and double-crosslinked in suspension with 2mM DSG in PBS for 45 minutes at room temperature, washed with PBS thrice, and incubated with 1% formaldehyde (FA) in PBS for 10 minutes at room temperature. Crosslinking was quenched by addition of glycine to final concentration of 500mM and incubated at room temperature for 5 min. Cells were washed in PBS and snap frozen for storage at -80degC until ChIP was performed. For RNAP2(S2P) ChIPs, mESCs were subjected to crosslinking in 1% FA for 10 minutes at room temperature. Fixed cells were then subjected to standard ChIP lysis protocol to release chromatin. Released chromatin was sonicated to obtain fragments between 100-300bp, pre-cleared and used for IP with antibody-Dynabead complex. Captured fragments were subjected to several rounds of washes before elution with SDS buffer. DNA was purified using SPRI method.
RNA-seq in 293T and mESC: Equal volumes of RNA preparations (extracted from equal number of cells) from each sample were each mixed with 1 microl of 1:100 diluted Mix 1 of ERCC RNA Spike-In (Life Technologies Cat.# 4456739). The mixture is subjected to ribosomal RNA depletion using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB Cat# E6310) and library construction using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB Cat# E7760), according to manufacturer’s protocol. RNA-seq in neurons: Equal amounts of RNA were directly used in rRNA depletion and library construction. ChIP-seq: Eluted DNA and DNA from relevant input materials was purified and made into libraries using NEBNext Ultra II DNA kit (NEB Cat #: E7645). For both RNA-seq and ChIP-seq libraries, average fragment size was determined on Agilent High Sensitivity DNA and D1000 Screentape system (Agilent Cat #:5067-4626, 5067-5582), quantified using Qubit High Sensitivity DNA system (Life Tech Cat# Q32854), and pooled in equimolar. Pooled libraries were sequenced on the Illumina NextSeq or HiSeq platform.

tag: genotype


title: Golden Hamster Lung, Vaccinated Group, Before challenge, Replicate 4


title: control, replicate 2

value: str. K12 substr. MG1655

value: control

value: no-treatment


title: control, replicate 1


title: DMSO_3

description: Polysomal RNA from CHP134 cells treated with DMSO for 24 hours.

source_name: CHP134 cells, DMSO, polysomal RNA, biological replicate 3

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with DMSO for 24 hours.

value: DMSO


title: ISR_3

source_name: CHP134 cells, ISR, polysomal RNA, biological replicate 3


title: Golden Hamster Lung, Control Group, 5 day post challenge, Replicate 1

value: Challenged with SARS-CoV-2 Beta Variant


title: Golden Hamster Lung, Control Group, 5 day post challenge, Replicate 3


title: Golden Hamster Lung, Vaccinated Group, Before challenge, Replicate 1


title: Golden Hamster Lung, Vaccinated Group, Before challenge, Replicate 2


title: Golden Hamster Lung, Control Group, 3 day post challenge, Replicate 2


title: Golden Hamster Lung, Control Group, 3 day post challenge, Replicate 3


title: ISR_1

source_name: CHP134 cells, ISR, polysomal RNA, biological replicate 1


title: Golden Hamster Lung, Control Group, 1 day post challenge, Replicate 4


title: Golden Hamster Lung, Control Group, 1 day post challenge, Replicate 2


title: Golden Hamster Lung, Control Group, 1 day post challenge, Replicate 1


title: Golden Hamster Lung, Control Group, Before challenge, Replicate 2


title: Golden Hamster Lung, Control Group, Before challenge, Replicate 1


title: Duodenum organoids from CDK2-cKO mice, DMSO treated, 48 hours, replicate #3

city: Groton

first: Seda

last: Arat

address: 445 Eastern Point Road

institute: Pfizer

data_processing:
Salmon-based preprocessing and alignment
Supplementary files format and content: differentially expressed gnes in xlsx format

molecule: polyA RNA

source_name: Duodenum

growth_protocol: Organoids were grown in domes of 50:50 Matrigel:Mouse Intesticult OGM (50:50), in Mouse Intesicult OGM (StemCell catalog # 06005), and treated with the indicated drugs for the indicated times

extract_protocol:
Cells were harvested by scraping, washed with ice-cold PBS, and RNA was extracted using Qiagen's RNeasy Micro kit (Qiagen catalog # 74034) following manufacturers recommendation
50 ng RNA was used as input for the Lexogen QuantSeq 3’ mRNA-Seq Library Preparation kit for Illumina (FWD) (Lexogen, catalog # 015.96) and libraries were prepared according to the manufacturer’s protocol

value: Duodenum

tag: time point

value: 48 hours

value: HOM CDK2 cKO


title: Duodenum organoids from CDK2-cKO mice, DMSO treated, 24 hours, replicate #3

value: 24 hours


title: Golden Hamster Lung, Control Group, 5 day post challenge, Replicate 2

value: Lung


title: Golden Hamster Lung, Control Group, 1 day post challenge, Replicate 3


title: Duodenum organoids from CDK2-cKO mice, 1 uM 4-OHT treated, 24 hours, replicate #3

value: 1 uM 4-hydroxytamoxifen


title: Duodenum organoids from WT cko mice, DMSO treated, 48 hours, replicate #3

value: WT cKO


title: Duodenum organoids from CDK5-dTAG mice, 250 nM dTAG-13 treated, 24 hours, replicate #3

value: HOM CDK5-dTAG

value: 250 nM dTAG-13


title: Duodenum organoids from WT cko mice, 1 uM 4-OHT treated, 24 hours, replicate #3


title: Duodenum organoids from CDK5-dTAG mice, 250 nM dTAG-13 treated, 6 hours, replicate #3

value: 6 hours


title: Duodenum organoids from CDK5-dTAG mice, DMSO treated, 6 hours, replicate #3


title: Duodenum organoids from CDK5-dTAG mice, DMSO treated, 24 hours, replicate #3


title: Duodenum organoids from CDK2-dTAG mice, 250 nM dTAG-13 treated, 24 hours, replicate #3

value: HOM CDK2-dTAG


title: Golden Hamster Lung, Control Group, 3 day post challenge, Replicate 1

value: Day 3


title: Duodenum organoids from WT cko mice, 1 uM 4-OHT treated, 48 hours, replicate #3


title: Duodenum organoids from CDK2-dTAG mice, DMSO treated, 24 hours, replicate #3


title: Duodenum organoids from WT mice, DMSO treated, 24 hours, replicate #3

value: WT dTAG


title: Duodenum organoids from WT mice, 250 nM dTAG-13 treated, 24 hours, replicate #3


title: Duodenum organoids from CDK2-cKO mice, 1 uM 4-OHT treated, 48 hours, replicate #2


title: Duodenum organoids from WT mice, DMSO treated, 6 hours, replicate #3


title: Duodenum organoids from CDK2-dTAG mice, DMSO treated, 6 hours, replicate #3


title: Duodenum organoids from CDK2-cKO mice, 1 uM 4-OHT treated, 48 hours, replicate #3


title: Duodenum organoids from CDK2-cKO mice, DMSO treated, 48 hours, replicate #2


title: Duodenum organoids from WT mice, 250 nM dTAG-13 treated, 6 hours, replicate #3


title: Duodenum organoids from CDK2-cKO mice, 1 uM 4-OHT treated, 24 hours, replicate #2


title: Golden Hamster Lung, Control Group, Before challenge, Replicate 3

value: Day 0


title: Duodenum organoids from CDK5-dTAG mice, DMSO treated, 24 hours, replicate #2


title: Duodenum organoids from CDK2-cKO mice, DMSO treated, 24 hours, replicate #2


title: Duodenum organoids from WT cko mice, DMSO treated, 48 hours, replicate #2


title: Duodenum organoids from CDK5-dTAG mice, 250 nM dTAG-13 treated, 24 hours, replicate #2


title: Duodenum organoids from WT cko mice, 1 uM 4-OHT treated, 24 hours, replicate #2


title: Duodenum organoids from CDK5-dTAG mice, 250 nM dTAG-13 treated, 6 hours, replicate #2


title: Duodenum organoids from CDK5-dTAG mice, DMSO treated, 6 hours, replicate #2


title: Duodenum organoids from CDK2-dTAG mice, DMSO treated, 24 hours, replicate #2


title: Duodenum organoids from CDK2-dTAG mice, DMSO treated, 6 hours, replicate #2


title: DMSO_1

source_name: CHP134 cells, DMSO, polysomal RNA, biological replicate 1

value: neuroblastoma

value: polysomal RNA


title: Duodenum organoids from WT mice, 250 nM dTAG-13 treated, 24 hours, replicate #2


title: DMSO_2

source_name: CHP134 cells, DMSO, polysomal RNA, biological replicate 2

value: DMSO


title: Duodenum organoids from CDK2-dTAG mice, 250 nM dTAG-13 treated, 6 hours, replicate #3

value: Duodenum


title: Duodenum organoids from WT cko mice, DMSO treated, 24 hours, replicate #2


title: Duodenum organoids from WT cko mice, DMSO treated, 24 hours, replicate #3


title: Duodenum organoids from WT mice, DMSO treated, 24 hours, replicate #2


title: Duodenum organoids from WT mice, 250 nM dTAG-13 treated, 6 hours, replicate #2


title: Duodenum organoids from WT mice, DMSO treated, 6 hours, replicate #2


title: Duodenum organoids from CDK2-dTAG mice, 250 nM dTAG-13 treated, 6 hours, replicate #2


title: Duodenum organoids from CDK2-cKO mice, 1 uM 4-OHT treated, 48 hours, replicate #1

value: 48 hours


title: Duodenum organoids from CDK2-cKO mice, 1 uM 4-OHT treated, 24 hours, replicate #1

value: HOM CDK2 cKO


title: Duodenum organoids from CDK2-cKO mice, DMSO treated, 48 hours, replicate #1


title: Duodenum organoids from WT cko mice, 1 uM 4-OHT treated, 24 hours, replicate #1

value: 24 hours


title: Duodenum organoids from CDK2-dTAG mice, 250 nM dTAG-13 treated, 24 hours, replicate #1


title: Duodenum organoids from CDK5-dTAG mice, DMSO treated, 6 hours, replicate #1


title: Duodenum organoids from WT cko mice, 1 uM 4-OHT treated, 48 hours, replicate #1


title: Duodenum organoids from WT cko mice, DMSO treated, 24 hours, replicate #1


title: Duodenum organoids from WT cko mice, DMSO treated, 48 hours, replicate #1


title: Duodenum organoids from CDK2-cKO mice, DMSO treated, 24 hours, replicate #1


title: Duodenum organoids from CDK5-dTAG mice, DMSO treated, 24 hours, replicate #1


title: Duodenum organoids from CDK2-dTAG mice, DMSO treated, 24 hours, replicate #1


title: Duodenum organoids from WT mice, DMSO treated, 6 hours, replicate #1


title: Duodenum organoids from CDK2-dTAG mice, DMSO treated, 6 hours, replicate #1


title: Duodenum organoids from CDK2-dTAG mice, 250 nM dTAG-13 treated, 6 hours, replicate #1


title: Duodenum organoids from WT mice, DMSO treated, 24 hours, replicate #1


title: Duodenum organoids from CDK5-dTAG mice, 250 nM dTAG-13 treated, 6 hours, replicate #1


title: Duodenum organoids from CDK5-dTAG mice, 250 nM dTAG-13 treated, 24 hours, replicate #1


title: Duodenum organoids from WT mice, 250 nM dTAG-13 treated, 24 hours, replicate #1


title: Duodenum organoids from WT mice, 250 nM dTAG-13 treated, 6 hours, replicate #1


title: Duodenum organoids from CDK2-dTAG mice, 250 nM dTAG-13 treated, 24 hours, replicate #2


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 6 hours, replicate #3

data_processing:
Salmon-based preprocessing and alignment
Supplementary files format and content: differentially expressed genes in xlsx format
Supplementary files format and content: TPM

source_name: Bone marrow

growth_protocol: Bone marrow cells were isolated from mice and used immediately or frozen for immediate use. Bone marrow derived cells were cultured in Stemline II media (Sigma, catalog # S0192-6X500ML), 10% FBS (ThermoFisher, catalog # 26140095) Penicillin-Streptomycin (Fisher, catalog # MT30002CI) and cytokines (50 ng/mL SCF, RnD Systems, catalog # 455-MC-050; 20 ng/mL G-CSF, RnD Systems, catalog # 414-CS-025; 20 ng/mL GM-CSF, RnD Systems, catalog # 415-ML-020; 50 ng/mL FLT3, RnD Systems, catalog # 768-F3-050; 20 ng/mL IL-6, RnD Systems, catalog # 406-ML-200; 10 ng/mL IL-3, RnD Systems, catalog # 403-ML-050; 30 ng/mL TPO, RnD Systems, catalog # 488-TO-200; 1.5 ng/mL EPO, RnD Systems, catalog # 959-ME-010), and then treated with the indicated drug concentrations for the indicated times.

value: Bone marrow

value: Primary cell line

tag: cell type

value: Bone marrow dervied cells


title: Bone marrow from CDK2-dTAG mice, DMSO, 24 hours, replicate #3


title: Bone marrow from CDK2-dTAG mice, DMSO, 6 hours, replicate #3


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 2 hours, replicate #3


title: Bone marrow from CDK2-dTAG mice, DMSO, 2 hours, replicate #3


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 24 hours, replicate #2


title: Bone marrow from CDK2-dTAG mice, no treatment, 24 hours, replicate #3

value: No treatment


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 6 hours, replicate #2

value: 250 nM dTAG-13


title: Bone marrow from CDK2-dTAG mice, DMSO, 6 hours, replicate #2


title: Bone marrow from CDK2-dTAG mice, DMSO, 24 hours, replicate #2


title: Bone marrow from CDK2-dTAG mice, DMSO, 24 hours, replicate #1


title: Bone marrow from CDK2-dTAG mice, DMSO, 2 hours, replicate #2


title: Bone marrow from CDK2-dTAG mice, DMSO, 6 hours, replicate #1


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 24 hours, replicate #1


title: Bone marrow from CDK2-dTAG mice, no treatment, 24 hours, replicate #2


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 2 hours, replicate #2


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 2 hours, replicate #1


title: Bone marrow from CDK2-dTAG mice, no treatment, 24 hours, replicate #1


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 6 hours, replicate #1


title: Bone marrow from WT mice, 250 nM dTAG-13, 6 hours, replicate #3

value: WT


title: Bone marrow from CDK2-dTAG mice, DMSO, 2 hours, replicate #1

value: HOM CDK2-dTAG


title: Bone marrow from WT mice, DMSO, 6 hours, replicate #3


title: Bone marrow from WT mice, no treatment, 24 hours, replicate #3


title: Bone marrow from WT mice, DMSO, 2 hours, replicate #3


title: Bone marrow from WT mice, 250 nM dTAG-13, 24 hours, replicate #2


title: Bone marrow from WT mice, 250 nM dTAG-13, 2 hours, replicate #3


title: Bone marrow from WT mice, DMSO, 24 hours, replicate #2


title: Bone marrow from WT mice, 250 nM dTAG-13, 6 hours, replicate #2


title: Bone marrow from WT mice, DMSO, 6 hours, replicate #2


title: Bone marrow from WT mice, 250 nM dTAG-13, 2 hours, replicate #2


title: Bone marrow from WT mice, DMSO, 2 hours, replicate #2


title: Bone marrow from WT mice, no treatment, 24 hours, replicate #2


title: Bone marrow from WT mice, 250 nM dTAG-13, 24 hours, replicate #1


title: Bone marrow from WT mice, 250 nM dTAG-13, 24 hours, replicate #3


title: Bone marrow from WT mice, DMSO, 24 hours, replicate #3


title: Bone marrow from WT mice, DMSO, 2 hours, replicate #1


title: Bone marrow from WT mice, 250 nM dTAG-13, 2 hours, replicate #1


title: Bone marrow from WT mice, 250 nM dTAG-13, 6 hours, replicate #1


title: Bone marrow from WT mice, DMSO, 6 hours, replicate #1


title: Bone marrow from WT mice, DMSO, 24 hours, replicate #1


title: Bone marrow from WT mice, no treatment, 24 hours, replicate #1


title: Duodenum organoids from WT cko mice, 1 uM 4-OHT treated, 48 hours, replicate #2

value: WT cKO

value: 1 uM 4-hydroxytamoxifen


title: YCCEL1 DMSO1

city: Philadelphia

first: Sarah

last: Alp

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: RRBS

data_processing:
Adapter sequences were removed using TrimGalore
RRBS sequence alignment to the human gammaherpesvirus 4 (HHV4) NC_007605.1 was performed by Bismark
CpG counts were performed using bismark_methylation_extractor function and methylation coverage is provided as a processed file.
Assembly: Viral Genome Human gammaherpesvirus 4 NC_007605.1
Supplementary files format and content: bismark.cov.gz

organism: human gammaherpesvirus 4

extract_protocol:
DNA was extracted as follows using the DNeasy Blood & Tissue Kit (Qiagen, ID 69504) according to the manufacturer’s protocol.
genomic DNA was spiked with lambda phage DNA and digested with MspI restriction enzyme. Fragments were ligated with methylated adapters (NEB) to protect adapter sequences from downstream bisulfite treatment. Digested DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo). All libraries were prepared using NEBNext adapters and indexed with i7 primers. These methylation- based libraries were spiked with 25% phiX Illumina library to ensure sequence diversity and sequenced 75bp paired-end on Illumina HiSeq 2500
Genomic DNA was bisulfite treated so that methylated cytosine residues were protected and unmethylated cytosines were converted to T in the final sequencing.

value: Gastric Cancer

value: Decitibine 7.5uM


title: YCCEL1 7.5uM DEC 1

description: RRBS


title: YCCEL1 DMSO2

description: RRBS


title: SNU719 7.5uM DEC 2

description: RRBS


title: SNU719 DMSO 1

description: RRBS


title: YCCEL1 7.5uM DEC 2

description: RRBS


title: SNU719 DMSO 2

description: RRBS


title: SNU719 7.5uM DEC 1

description: RRBS


title: OD_S91

data_processing:
Salmon quasi-mapping (indexing and quantitation)
Genome_build: Ensembl on May 9, 2019 (v.96)
Supplementary_files_format_and_content: raw counts (tab separated txt file)

source_name: Kidney

extract_protocol:
Frozen tissues of approximately 50 mg were homogenized in Qiazol Lysis Reagent (Qiagen, cat# 79306) with a cooled 5 mm stainless steel bead (Qiagen, cat# 69989) using a TissueLyser II (Qiagen, cat# 85300). Downstream RNA isolation was then performed using the Qiagen RNeasy Mini protocol on the Qiacube according to manufacturer’s instruction. After elution, 1 µL of each sample was evaluated for total RNA concentration using standard 260 nm absorbance on a NanoDrop 1000 (Thermo Scientific) UV-Vis spectrophotometer. The quality of the RNA in each sample was assessed using 2 µL of each sample via electrophoresis on the Agilent Tapestation. The remaining sample was stored at -80°C until analysis.
Total RNA from each kidney sample was prepared for sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation Kit (Illumina, cat# 20020595) according to manufacturer’s instructions on the Perkin Elmer Sciclone NGS prep system. 1,000 ng of total RNA was used to prepare the RNA libraries and fifteen cycles of library amplification PCR was performed. After library generation, 2uL of the cleaned cDNA library was used to quantify the library concentration on the ThermoFisher Scientific Qubit 4 Fluorometer (ThermoFisher Scientific, cat# Q33238). Additionally, the quality of each cDNA sample was assessed using 2 µL of each sample via electrophoresis on the Agilent Tapestation. Samples were binned according to Qubit readings to make a library pool for sequencing, which was diluted to 4 nM before denaturing and further dilution prior to loading onto the Nextseq 500. The remaining individual cDNA libraries were stored at -20°C.
Sequencing was performed at 2 x 150 bp, paired end read setting using a 300-cycle sequencing reagent kit & high output flow cell on a NextSeq 500 Sequencing System (Illumina, San Diego, CA). Condensed and quality controlled paired end fastq files were generated for data analysis.

tag: sample group

value: organ donor


title: OD_S90


title: OD_S89


title: OD_S88


title: OD_S86


title: OD_S85


title: OD_S84


title: OD_S74.C


title: Tumor_S67.C

value: kidney tumor


title: Tumor_S69.C


title: NAT_S68.C

value: normal adjacent tissue


title: CAD_S16.C

value: cadaveric


title: NAT_S38.C


title: Tumor_S39.C


title: Bone marrow from CDK2-dTAG mice, 250 nM dTAG-13, 24 hours, replicate #3


title: CAD_S14.C


title: CAD_S13.C


title: OD_S82


title: OD_S87


title: OD_S83


title: OD_S80


title: OD_S81


title: OD_S79


title: OD_S78


title: CAD_S15.C


title: OD_S77


title: OD_S75


title: OD_S76


title: Tumor_S69.B


title: OD_S74.B


title: NAT_S68.B


title: K4

city: Beijing

first: Shuang

last: Li

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

description: Gene expression after 4 weeks after operation

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: K4 CaPO4 abdominal aortic tissues

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Abdominal aortic tissues from WT and SR-A1-/- mice were collected after CaPO4-envoked.

value: abdominal aortic tissues

tag: gender

value: male

tag: age


title: Tumor_S67.B


title: K5

source_name: K5 CaPO4 abdominal aortic tissues


title: Tumor_S39.B


title: W2

source_name: WT2 CaPO4 abdominal aortic tissues

value: Wild Type


title: NAT_S38.B


title: J01_098

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.

data_processing: Probe intensities were normalized with MAS5.

source_name: fresh frozen tumor sample obtained from radical breast cancer surgery

label_protocol: RNA (1 μg; RIN value >6) was used for generation of second-strand cDNA, and cRNA was amplified with the Oligo dT primer, then biotinated and fragmented with One-Cycle Target Labeling and control reagents (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from tumor tissues obtained at the surgery with the aid of the Qiagen RNeasy® mini kit (QIAGEN Sciences, Germantown, MD).

treatment_protocol: The patients agreed to have their research specimens cryopreserved for future use after undergoing radical breast cancer surgery, and also received endocrine therapy following the surgery.

tag: menopause

value: postmenopausal

tag: ct

tag: cn

tag: er

value: Positive

tag: pgr

tag: hg

value: No


title: W3

source_name: WT3 CaPO4 abdominal aortic tissues

tag: tissue


title: J01_103

value: premenopausal

value: Negative


title: J01_102


title: J01_100


title: J01_097


title: CAD_S16.B


title: J01_101


title: J01_096


title: J01_093


title: J01_105


title: J01_104


title: CAD_S14.B


title: CAD_S13.B


title: OD_S74.A


title: J01_099

value: Yes


title: CAD_S15.B


title: Tumor_S73


title: NAT_S70


title: NAT_S72


title: Tumor_S71


title: Tumor_S69.A


title: NAT_S68.A


title: NAT_S66


title: Tumor_S65


title: Tumor_S67.A


title: J01_089


title: NAT_S64


title: J01_090


title: J01_095


title: J01_092


title: J01_094


title: Tumor_S63


title: J01_091


title: NAT_S62


title: J01_088


title: Tumor_S61


title: J01_082


title: NAT_S60


title: J01_087


title: J01_084


title: J01_083


title: Tumor_S59


title: J01_085


title: Tumor_S57


title: NAT_S58


title: J01_078


title: J01_086


title: J01_081


title: J01_074


title: J01_075


title: J01_077


title: NAT_S56


title: J01_080


title: J01_079


title: J01_076


title: Tumor_S55


title: J01_073


title: NAT_S54


title: J01_072


title: Tumor_S53


title: NAT_S52


title: Tumor_S51


title: J01_069


title: J01_071


title: J01_068


title: NAT_S50


title: J01_067


title: J01_065


title: J01_070


title: J01_062


title: J01_066


title: AKR strain, 3wk cigarette smoke, LPS in saline, biological replicate 1

city: Providence

first: Sharon

last: Rounds

state: RI

address: 830 Chalkstone Avenue,, Building 35, Room 216

institute: Brown University

hyb_protocol: The biotinylated complementary RNA (cRNA) was fragmented at 94oC for 35min in fragmentation buffer and hybridized to the microarrays in 200ul of hybridization buffer. Target cRNA was hybridized to oligonucleotide microarrays containing 54,613 mouse gene probes and expressed sequence tags.

scan_protocol: The signals were further enhanced by staining for 5 min with streptavidin-phycoerythrin conjugate and scanning with the chip scanner. The hybridization intensity of the transcript was then determined using GeneChip Operating Software.

data_processing: The probe set measurements representing mouse genes were generated by Affymetrix image (.CEL) files using the Robust Multichip Average 21 involving background correction, quartile normalization, and log-2 transformation

source_name: Lung tissue

label_protocol: standard Affymetrix Protocol

tag: Sex

value: 6 wk

tag: strain

value: AKR

tag: treatment

value: cigarette smoke followed by intratracheal instillation of LPS


title: AKR strain, 3wk room air, LPS in saline, biological replicate 1

extract_protocol: The biotinylated complementary RNA (cRNA) was fragmented at 94oC for 35min in fragmentation buffer

value: room air followed by intratracheal instillation of LPS


title: AKR strain, 3 wk cigarette smoke, normal saline, biological replicate 3

value: cigarette smoke followed by intratracheal instillation of normal saline


title: AKR strain, 3 wk cigarette smoke, LPS in saline, biological replicate 2


title: Tumor_S49

value: kidney tumor


title: J01_063


title: J01_064


title: NAT_S48

value: normal adjacent tissue


title: AKR strain, 3 wk room air, LPS in saline, biological replicate 3


title: J01_061


title: AKR strain, 3 wk room air, normal saline, biological replicate 3

value: room air followed by intratracheal instillation of normal saline


title: AKR strain, 3wk cigarette smoke, normal saline, biological replicate 1


title: Tumor_S47


title: AKR strain, 3 wk cigarette smoke, normal saline, biological replicate 2


title: AKR strain, 3 wk room air, LPS in saline, biological replicate 2


title: NAT_S46


title: Tumor_S45


title: J01_060


title: NAT_S44


title: Tumor_S43


title: AKR strain, 3wk room air, normal saline, biological replicate 1


title: C57 strain, 3 wk cigarette smoke, LPS in saline, biological replicate 3


title: J01_058


title: J01_055


title: AKR strain, 3 wk room air, normal saline, biological replicate 2


title: J01_054


title: LTF treatment Replicate 3

type: genomic

first: chongxiang

last: xue

address: No.5 BeiXianGe Street, Xicheng District, Beijing

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sci-ences

description:
LY3
Biological replicate 3 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

hyb_protocol: Samples were then ready for hybridization and analysis by microarray (Hybridization System-Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Scanned on an Agilent Scanner-G2505C

data_processing: Median-centering, quantile normalization and linear smoothing were performed in this analysis process by Bioconductor packages Ringo, limma, and MEDME.

organism: Rattus norvegicus

source_name: methylated DNA immunoprecipitation (MeDIP) - DNA

label_protocol: DNA labelling was performed using the NimbleGen Dual-Color DNA Labeling Kit (Nimblegen Systems, Inc., Madison, WI, USA). And the labeled DNA was purified by isopropanol/ethanol precipitation

growth_protocol: Male Sprague-Dawley (SD) rats (8 weeks old, weighing 20–25 g) were purchased from HFK Bio-Technology.co., LTD (Beijing, China) and housed in a specific-pathogen-free (SPF) facility, with climate-controlled rooms maintained at 22±2◦C, 40-60% relative humidity, and controlled 12h light/dark cycles. All rats were allowed access to standard food and water ad libitum. Subsequently, experimental rats were injected with streptozotocin [STZ, 45 mg/kg, body weight (BW), 0.1 mol/L citric buffer, pH 0.5] intravenously, while the normal control rats were injected with the same volume of citric buffer. 72 h after STZ injection, animals were declared diabetic if their blood glucose exceeded 13.9 mmol/l (250 mg/dl) for 3 consecutive days.

extract_protocol: Then after a 12-h fasting period, all rats were sacrificed and blood samples were collected.

treatment_protocol: Thirty experimental rats were randomly assigned to three groups (n=10): (1) model (Mod.) group: administered distilled water by oral gavage; (2) calcium dobesilate (CaD.) group: administered CaD [0.25 g/kg, body weight (BW)/day)] by oral gavage and insulin (1.5 IU/time/day) by intravenous injection; and (3) LTF (LTF.) group: administered LTF [2 g/kg, herb weight/body weight (BW)/day] by oral gavage and insulin (1.5 IU/time/day) by intravenous injection. Besides, 10 normal control rats mentioned above belonged to the control (Con.) group, conventionally raised with distilled water.

value: Sprague Dawley

value: 20 weeks old

value: peripheral blood

value: DR model SD rats treated with LTF

source_name: input DNA


title: J01_057

value: postmenopausal

value: Positive


title: LTF treatment Replicate 2

description:
LY2
Biological replicate 2 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray


title: J01_053

value: No


title: J01_059

value: premenopausal

value: Negative


title: LTF treatment Replicate 1

description:
LY1
Biological replicate 1 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray


title: J01_056


title: C57 strain, 3 wk room air, LPS in saline, biological replicate 2

value: male

value: 6 wk


title: C57 strain, 3 wk cigarette smoke, LPS in saline, biological replicate 2

value: cigarette smoke followed by intratracheal instillation of LPS


title: C57 strain, 3wk cigarette smoke, LPS in saline, biological replicate 1


title: NAT_S42


title: another Chinse formula  treatment Replicate 3

description:
FY3
Biological replicate 3 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

value: DR model SD rats treated with another Chinse formula


title: CaD treatment Replicate 3

description:
DY3
Biological replicate 3 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

value: DR model SD rats treated with CaD


title: another Chinse formula  treatment Replicate 1

description:
FY1
Biological replicate 1 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray


title: NAT_S40


title: C57 strain, 3wk room air, LPS in saline, biological replicate 1

value: room air followed by intratracheal instillation of LPS


title: J01_052


title: C57 strain, 3 wk room air, LPS in saline, biological replicate 3


title: Tumor_S41

value: kidney tumor


title: NAT_S38.A

value: normal adjacent tissue


title: Tumor_S39.A


title: another Chinse formula  treatment Replicate 2

description:
FY2
Biological replicate 2 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

value: Sprague Dawley


title: CaD treatment Replicate 2

description:
DY2
Biological replicate 2 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

value: 20 weeks old


title: J01_050


title: Tumor_S37


title: C57 strain, 3 wk cigarette smoke, normal saline, biological replicate 3

value: cigarette smoke followed by intratracheal instillation of normal saline


title: C57 strain, 3 wk cigarette smoke, normal saline, biological replicate 2


title: DR model Replicate 3

description:
M3
Biological replicate 3 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

value: peripheral blood

value: DR model SD rats


title: NAT_S36


title: J01_051

value: postmenopausal

value: Positive


title: Gls1_CamkIIaCre_3,BulkRNAseq

first: Jialin

middle: C.

last: Zheng

address: Xincun Road 389

institute: Tongji Hospital Affiliated to Tongji University School of Medicine

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork.
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: prefrontal cortex

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: prefrontal cortex

value: all cells

value: Gls1 in CamKII{alpha}-positive neurons


title: CaD treatment Replicate 1

description:
DY1
Biological replicate 1 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray


title: Gls1_CamkIIaCre_2,BulkRNAseq


title: Tumor_S35


title: C57 strain, 3 wk room air, normal saline, biological replicate 3

value: male

value: 6 wk

value: room air followed by intratracheal instillation of normal saline


title: C57 strain, 3wk cigarette smoke, normal saline, biological replicate 1


title: C57 strain, 3 wk room air, normal saline, biological replicate 2


title: Gls1_CamkIIaCre_1,BulkRNAseq


title: NAT_S34


title: control_3,BulkRNAseq

value: WT


title: DR model Replicate 2

description:
M2
Biological replicate 2 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray


title: C57 strain, 3wk room air, normal saline, biological replicate 1


title: J01_049

value: Negative

value: No


title: J01_046

value: Yes


title: control_2,BulkRNAseq


title: AKR strain, 6wk room air, biological replicate 2

value: AKR

value: room air


title: NAT_S32

value: normal adjacent tissue


title: Tumor_S33

value: kidney tumor


title: DR model Replicate 1

description:
M1
Biological replicate 1 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

value: Sprague Dawley

value: 20 weeks old

value: peripheral blood

value: DR model SD rats


title: J01_048

value: premenopausal

value: Positive


title: J01_047


title: CAD_S31

value: cadaveric


title: AKR strain, 6wk room air, biological replicate 1

value: male

value: 6 wk


title: J01_044

value: postmenopausal


title: Control SD rats Replicate 3

description:
C3
Biological replicate 3 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray

value: Control SD rats


title: AKR strain, 3 wk room air, biological replicate 2


title: CAD_S30


title: AKR strain, 6wk room air, biological replicate 3


title: CAD_S29


title: J01_045

value: Negative

value: No


title: Control SD rats Replicate 2

description:
C2
Biological replicate 2 of 3. Purified MeDIP DNA samples, then hybridized and analyzed by microarray


title: CAD_S28


title: J01_043


title: HCT116 WT, 0.1 % FBS, 72 hr, rep3

city: Seoul

first: Soomin

last: Son

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Low-quality reads (phred quality <20 in 90% of nucleotides) were discarded with FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
TruSeq 3′ adapter sequence was removed, and then 4 nt-long degenerate sequences at the 3′ and 5′ ends were trimmed using cutadapt (Martin 2011). Reads shorter than 18 nt or longer than 26 nt were filtered out.
Preprocessed reads were aligned to the spike-in sequences by STAR (Dobin et al. 2013). Reads mapped to spike-in sequences with at most a single mismatch were considered reliable spike-in reads. The remaining reads were mapped to the hg38 genome using STAR (STAR --outFilterMultimapNmax 20 --outFilterMismatchNmax 0 --alignIntronMax 1).
Reads were classified into annotations from mirBase release 21 by BEDTools and used for further analysis (Kozomara and Griffiths-Jones 2014; Quinlan and Hall 2010).
Assembly: hg38
Supplementary files format and content: Tab-separated BEDTools intersect -c output

extract_protocol:
Total RNAs were isolated using TRIzol (Thermo Fisher Scientific) and treated with DNase I (Takara Bio).
Sequencing libraries were generated as previously described (Kim et al. 2019). In brief, we mixed 20 µg of total RNAs with 10 nmole of 30 equimolar spike-in RNAs described in our previous study (Kim et al. 2019). Small RNAs were enriched by size fractionation by 15% urea-polyacrylamide gel electrophoresis and ligated to the randomized adaptor at the 3′ and 5′ ends. The ligated RNAs were reverse-transcribed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific), amplified using Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific), and subjected to high-throughput sequencing on the MiSeq platform (Illumina).

tag: cell line

value: human colon cancer cells

value: Cultured under serum-starvation with 0.1 % FBS


title: C57 strain, 6 wk room air, biological replicate 3

value: room air


title: CAD_S27