title: RNA W-DL3 rep2

city: Beijing

first: Peng

last: Wang

address: Qing Long Qiao Street

country: China

institute: Chinese Academy of Forestry

data_processing:
The library  was  sequenced on Illumina sequencing platform.
Low quality bases and adapter sequences were trimmed by using trimmomatic. The parameter settings used was “ SLIDINGWINDOW:5:15 HEADCROP:3 AVGQUAL:15 LEADING:5 TRAILING:5 MINLEN:80”.
Quality control of raw reads was performed using FastQC (version 0.11.5).
The cleaned reads were mapped back to reference genome using BSMAP software.The parameter settings used was “-n 0 -v 0.08 -g 1 -p 48”.
The methylation level was calculated based on the methylated cytosine (mC) percentage in the whole genome as site methylation level = 100× (number of sequences with methylated cytosines (mC)/total number of valid sequences).
Assembly: BXYJv5
Supplementary files format and content: tab-delimited text file includes methylation rate for all C-site types for each Sample
Supplementary files format and content: tab-delimited text file includes methylation rate for MergedCG site type for each Sample

organism: Bursaphelenchus xylophilus

source_name: whole organism

growth_protocol: The DL3 were cultured on Botrytis cinerea and placed in a 25℃ incubator without light to obtain different stages of propagative larvae.

extract_protocol: Protease K/phenol extraction for DNA extraction. 1 ug of total DNA was used for the construction of sequencing libraries.

treatment_protocol: Eggs of the pine wood nematode were collected in glass dishes and incubated at 25℃ in the dark for 24 h, then almost all the eggs hatched to L2. The L2 were inoculated on B. cinerea and cultured for 30 h and 54 h to obtain L3 and L4 in turn.

value: whole organism


title: RNA W-L4 rep1

status: Public on Oct 12 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: RNA W-DL3 rep3


title: 30_31393T

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

country: USA

institute: NCI

description: Gene expression data from PDAC tumor

data_processing:
mRNA-Seq samples were pooled and sequenced on NavoSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 51 to 122 million pass filter reads with more than 90% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM_TMM normalized values for each Sample

organism: Homo sapiens

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NovaSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subtype

value: unclassified

tag: tnm

tag: Stage

value: IIB

tag: grading

tag: cohort

tag: serpinb3 expression (high_low)

value: L

tag: month


title: 255_16

type: genomic

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

data_processing:
Import the CEL files into Axiom Analysis Suite, using Best Practices Workflow from the recommendations of the Axiom Genotyping Solution-Data Analysis
Genotype Call (SNP call): AA, AB, BB, NoCall

label: Biotin

molecule: genomic DNA

source_name: peripheral white blood cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

tag: gender

value: male

tag: cell type

value: peripheral white blood cells

tag: disease state

value: HNSqCC patient


title: RNA W-L3 rep3


title: RNA W-L4 rep3


title: RNA W-L4 rep2


title: RNA W-L3 rep2


title: 254_16

scan_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.


title: RNA W-DL3 rep1


title: RNA W-L3 rep1


title: 289_E599T

description: Gene expression data from PDAC tumor

value: classical


title: 253_16


title: 288_E593T

description: Gene expression data from PDAC tumor


title: 252_16


title: RNA W-L2 rep2


title: RNA W-L2 rep3


title: 285_E577T

description: Gene expression data from PDAC tumor


title: 251_16


title: 283_E532T

description: Gene expression data from PDAC tumor

value: IIA


title: WGBS W-L4 rep3

library_source: genomic

extract_protocol:
Protease K/phenol extraction for DNA extraction. 1 ug of total DNA was used for the construction of sequencing libraries.
Prior to library construction, 1µg sample genome DNA mixed with unmethylated lambda DNA was fragmented using a Bioruptor system to a mean size of approximately 250bp. After fragmentation, the purified randomly fragmented DNA was subsequently treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair, blunt and phosphorylate the ends. The bluntDNA fragments were subsequently 3’ adenylated using Klenow Fragment (3’-5’ exo-) and following with ligation to adaptors synthesized with 5’-methylcytosine instead of cytosine using T4 DNA Ligase. After each step, the DNA was purified using QIAquick PCR purificationkit (Qiagen). After that, ZYMO EZ DNA Methylation-Gold Kit™ was employed to convert unmethylated cytosine into uracil according to the instructions. Finally, PCR was carried out in a final reaction volume of 50µl consisting of 20µl adapter ligated DNA, 4µl 2.5mM dNTP, 5µl 10×buffer, 0.5µl JumpStart™ Taq DNA Polymerase, 2µl PCR primers and 18.5µl water and the following thermal cycling program was 94°C 1 min, 10cycles of 94 °C 10s, 62°C 30s, 72°C 30 then prolong with 5min at 72°C and products could be hold at 12°C. The PCR products were purified using QIAquick PCR purification kit (Qiagen). Before analysis with Illumina sequencing platform, the purified library was analyzed by the Bioanalyzer analysis system (Agilent, Santa Clara, USA) and quantified by the real time PCR.


title: WGBS W-L4 rep2


title: WGBS W-L4 rep1


title: 282_E530T

description: Gene expression data from PDAC tumor

value: H


title: WGBS W-DL3 rep3


title: 257_16


title: WGBS W-DL3 rep2


title: 280_E527T

description: Gene expression data from PDAC tumor


title: 250_16


title: 248_16


title: WGBS W-DL3 rep1


title: 244_16


title: 28_31263T

description: Gene expression data from PDAC tumor

value: basal


title: 287_E580T

description: Gene expression data from PDAC tumor


title: 278_E523T

description: Gene expression data from PDAC tumor


title: RNA W-L2 rep1


title: WGBS W-L3 rep2


title: WGBS W-L2 rep2


title: WGBS W-L3 rep1


title: 236_16


title: WGBS W-L3 rep3


title: WGBS W-L2 rep1


title: WGBS W-L2 rep3


title: 275_E505T

description: Gene expression data from PDAC tumor


title: ZP3 Trim-away R2

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

country: Germany

institute: Max Planck Institute Muenster

description:
Pool of 13 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
ZP14

data_processing:
Samples were demultiplexed (bcl convert 3.8.4) to fastq data and quality controlled (FastQC version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimmomatic (PMID 24695404; version 0.38) was used for adapter trimming and read filtering.
Reads were aligned to the reference genome using Hisat2 (PMID 25751142; version: 2.1.0).
Aligned reads were sorted using samtools (PMID 21903627; version 1.9).
Sorted and aligned reads were counted into genes using HTsec (PMID 25260700; version 0.11.1), then these counts were used to calculate the RPKM to normalize for sequencing depth and gene length.
Assembly: Mus musculus Ensembl GRCm39
Supplementary files format and content: Excel file including read counts and reads per kilobase per million mapped reads (RPKM) values for each sample.

organism: Mus musculus

source_name: embryos Theiler stage E0.5

growth_protocol: Pronuclear-stage oocytes (zygotes) produced in vivo (mating after PMG+hCG) were collected from oviducts in Hepes-buffered CZB medium and cultured in KSOM medium containing aminoacids.

extract_protocol:
Ten hours after microinjection, approx.8pm, total RNA was extracted with Quick-RNA MicroPrep (cat. no. R1051, Zymo Research Europe GmbH).
Libraries of the total RNA were prepared with the NEBNext® Single Cell/ Low Input RNA Library Prep Kit for Illumina (NEB #E6420S/L) according to the manufacturer’s instructions.

treatment_protocol: At 15 hours post-hCG zygotes were microinjected with a mixture of mCherry-Trim21 mRNA, oregon green dextran beads and antibody anti-ZP3 (Proteintech 21279-1-AP) or buffer thereof, and returned to culture in KSOM medium containing aminoacids.

tag: background strain

value: B6C3F1 x CD1

tag: genotype

value: wild-type

tag: treatment

value: Trim-away cocktail


title: ZP3 Trim-away R3

description:
Pool of 13 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
ZP15


title: 235_16


title: 230_16


title: ZP3 Trim-away R1

description:
Pool of 13 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
ZP13


title: ZP3 no Trim R3

description:
Pool of 13 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
ZP12

value: non-functional Trim-away cocktail (antibody buffer in lieu of antibody)


title: 270_E494T

description: Gene expression data from PDAC tumor


title: ZP3 no Trim R2

description:
Pool of 13 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
ZP11


title: ZP3 no Trim R1

description:
Pool of 13 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
ZP10


title: 273_E504T

description: Gene expression data from PDAC tumor


title: 227_16


title: 228_16


title: 269_E480T

description: Gene expression data from PDAC tumor


title: 267_E387T

description: Gene expression data from PDAC tumor


title: 220_16


title: Trim21 overexpression r4

data_processing:
Samples were demultiplexed (bcl convert 3.8.4) to fastq data and quality controlled (FastQC version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimmomatic (PMID 24695404; version 0.38) was used for adapter trimming and read filtering.
Reads were aligned to the reference genome using Hisat2 (PMID 25751142; version: 2.1.0).
Aligned reads were sorted using samtools (PMID 21903627; version 1.9).
Sorted and aligned reads were counted into genes using HTsec (PMID 25260700; version 0.11.1), then these counts were used to calculate the RPKM to normalize for sequencing depth and gene length.
Assembly: Mus musculus Ensembl GRCm38
Supplementary files format and content: Excel file including read counts and reads per kilobase per million mapped reads (RPKM) values for each sample.

source_name: embryos Theiler stage E1.5

extract_protocol:
On the day after microinjection, approx.6pm, total RNA was extracted with Quick-RNA MicroPrep (cat. no. R1051, Zymo Research Europe GmbH).
Libraries of the total RNA were prepared with the NEBNext® Single Cell/ Low Input RNA Library Prep Kit for Illumina (NEB #E6420S/L) according to the manufacturer’s instructions.

treatment_protocol: At 15 hours post-hCG zygotes were microinjected with a mixture of mCherry-Trim21 mRNA, oregon green dextran beads and antibody anti-ZP3 (Proteintech 21279-1-AP), and returned to culture in KSOM medium containing aminoacids.

value: treated, no ZP3 protein degradation


title: Trim21 overexpression r3


title: 219_16


title: 276_E520T

description: Gene expression data from PDAC tumor


title: Trim-away ZP3 r3

value: treated, ZP3 protein degraded


title: 265_E99_Tp1

description: Gene expression data from PDAC tumor

value: III


title: Trim-away ZP3 r2


title: Trim21 overexpression r2


title: 264_E74T

description: Gene expression data from PDAC tumor

value: IA


title: Trim21 overexpression r1


title: 218_16


title: 216_16


title: Trim-away ZP3 r1


title: 262_E60T

description: Gene expression data from PDAC tumor

value: IB


title: 214_16


title: non-manipulated

value: untreated


title: TS-WAT_Poo2

city: Boston

first: Patrick

middle: T

last: Griffin

state: MA

address: 77 Avenue Louis Pasteur

department: Harvard Medical School, Dept. of Genetics

institute: Patrick Griffin

description:
bisulfite converted DNA
TS-WAT_Pool2.tar.gz

data_processing:
https://github.com/patricktgriffin/TIME-Seq
Assembly: mm10,hg19
Supplementary files format and content: bismark.cov
Library strategy: TIME-Seq

source_name: White fat

value: White fat

tag: strain

tag: age

value: various

tag: Sex

value: mixed


title: 261_E501T

description: Gene expression data from PDAC tumor

value: classical

value: L


title: TS-Kidney_Poo1

description:
bisulfite converted DNA
TS-Kidney_AllPools.tar.gz

source_name: Kidney

tag: tissue

value: Kidney


title: 211_16

value: male

value: peripheral white blood cells

value: HNSqCC patient


title: TS-Kidney_Poo2


title: 26_29827T

description: Gene expression data from PDAC tumor

tag: subtype

value: IIB


title: AA_G1812_cage_embryo_rep1

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
For CAGE-seq, only the R1 read were kept to mapping. Cutadaptwas applied to trim 3’ adaptor and 9 bases at the 5’end, used SortMeRNA to remove the reads originating from chloroplast, mitochondria and rRNA. Clean reads were mapped to the IWGSC (version 1.0) for Chinese Spring data or T. urartu genome for G1812 data with Bowtie2 Only unique mapped reads were used for analysis. The 5′ coordinate of R1 reads was considered the position of the transcription start sites.
For ChIP-seq, Bisulfite-seq and RNA-seq, reads were trimmed with the Trim Galore and cutadapt. For RNA-sequencing, clean reads were aligned with HISAT2. SortMeRNA was used to remove the reads originating from chloroplast, mitochondria and rRNA. The featureCount was used to determine the RNA-seq read density of the high-confidence genes in the IWGSC RefSeq genome assembly (version 1.1). For ChIP-seq data, clean reads were aligned with bwa program. The MACS2 was used to identify the peaks.
For Bisulfite-seq data, the clean reads were then aligned by the Bismark program. The extent of the cytosine methylation was determined with the bismark_methylation_extractor implemented in the Bismark program. Next, the methylation ratio of a cytosine was calculated as the number of mCs divided by the number of reads covering the position. Bases covered by fewer than three reads were considered low confidence positions whose methylation ratios were not recorded.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: CAGE-seq signal in each site were provided in bed file.

organism: Triticum urartu

growth_protocol: Common wheat (Triticum aestivum cultivar ‘Chinese Spring’) seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C. The germinated seeds with residual endosperm were transferred to soil (1:1:3 mixture of vermiculite: perlite: peat soil) or Hoagland solution and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.

extract_protocol:
The seedlings (above-ground parts) in soil were harvested after 9-day growth. The root in Hoagland solution were harvested after 9-day growth. The spikelets at booting stage (Feeke 10) were harvested. The fresh immature embryos (14days post anthesis) were isolated and either frozen in liquid nitrogen
For CAGE-seq，total RNA was treated with RQ1 DNase to remove DNA. The total RNA was treated with T4 polynucleotide kinase subsequently digested with Terminator 5´-Phosphate-Dependent Exonuclease to enrich the capped mRNA. Next, reverse transcription was performed with RT primer harboring a 3'-adaptor sequence and randomized hexamer. Subsequently, the 5’adaptor harboring three additional rG at the 3’terminus was added to the RT reaction to allow template switching and tagging of the 5’ adaptor. The cDNAs were treated with Exonuclease I to digest the primers, purified and amplified with PCR primers. The libraries were applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: No treatment applied

tag: cultivar


title: AA_G1812_cage_embryo_rep2

source_name: fresh immature embryos (14days post anthesis)


title: 212_16


title: 210_16


title: 259_E499T

description: Gene expression data from PDAC tumor

tag: tnm

tag: Stage


title: 206_16


title: 257_E488T

description: Gene expression data from PDAC tumor

tag: grading

tag: cohort


title: H18-Cd

first: YinXin

last: Li

address: Nanxin Cun 20th, Xiangshan, Haidian district

institute: Institute of Botany, Chinese Academy of Sciences

data_processing:
The raw data was filtered out aritifact sequences.
Non-redundant sRNAs ranging from 18 to 30 nt were collected and mapped to S.bicolor genomic database using SOAP,according to its default settings.
Genome_build: miRBase (Release 21) sbi.gff3
Supplementary_files_format_and_content: counts + TPM

organism: Sorghum bicolor

source_name: Root

growth_protocol: The plants were grown in a cultivate room with a day/night temperature regime of 25/20 °C, photoperiod of 16 h, and relative humidity of 60 %. The nutrient solution was continuously renewed every 3 days.

extract_protocol:
Total RNAs of four libraries (H18-CK, L69-CK, H18-Cd and L69-Cd) were isolated from whole root tissues. After treated with RNase-free DNase I (Takara, Japan), the quality of total RNA was measured by agarose electrophoresis and the Agilent 2100 Bioanalyzer.
All RNA samples were submitted to Annoroad Gene Technology Co., Ltd (Beijing, China) for high-throughput sequencing using Illumina Hiseq 2500 platform.

treatment_protocol: Two-week-old H18 and L69 seedlings were treated with 10 μM CdCl2, seedlings treated with basal nutrient solution without CdCl2 were used as control. The basal nutrient solution contained 5 mM Ca(NO3)2, 5 mM KNO3, 1 mM KH2PO4, 2 mM MgSO4, 0.02 mM Fe-EDTA, and micronutrients. After 24 h, roots of 8 seedlings were collected.

value: root

value: two-week-old


title: L69-Cd


title: 255_E482T

description: Gene expression data from PDAC tumor

tag: serpinb3 expression (high_low)

tag: month


title: H18-CK


title: L69-CK


title: 201_16

tag: gender

tag: cell type


title: 253_E465T

description: Gene expression data from PDAC tumor

value: basal

value: IIA

value: H


title: 192_16

tag: disease state


title: 189_16


title: 251_E445T

description: Gene expression data from PDAC tumor

value: III


title: 249_E440T

description: Gene expression data from PDAC tumor


title: 188_16


title: 247_E421T

description: Gene expression data from PDAC tumor


title: 196_16


title: 181_16


title: JW1-SR-H3K27me3-rep2

data_processing:
Sequencing reads were cleaned with the fastp (version 0.20.0)55, which eliminated bases with low quality scores (< 25) and irregular GC contents, sequencing adapters, and short reads. The remaining cleaned reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0) with the Burrows–Wheeler Aligner (version 0.7.17-r1188)56 for the wheat ChIP-Sequencing. For spike-in ChIP-seq, cleaned reads were mapped to the merged genome of common wheat (IWGSC) and Arabidopsis thaliana (TAIR10). The HISAT2 program (version 2.2.1)57 was used for mapping the RNA sequencing (RNA-seq) and chromatin-bound RNA (CB-seq) reads to the reference sequences. The MACS (version 2.2.6)58 program was used to identify the read-enriched regions (peaks) of the ChIP-Seq and CB-Seq data with the cutoff P < 1e−10. To quantify gene expression levels, the featureCount program of the Subread package (version 2.0.0)59  was used to determine the RNA-seq read density for the genes. To compare expression levels across samples and genes, the RNA-seq read density of each gene was normalized based on the exon length in the gene and the sequencing depth (i.e., fragments per kilobase of exon model per million mapped reads). To quantify histone markers across genes for the figure prepared with Integrative Genomics Viewer60, the number of reads at each position was normalized against the total number of reads (reads per million mapped reads). For spike-in ChIP-seq, the number of reads at each position was normalized against the total number of reads mapped to A. thaliana (reference-adjuseted reads per million, RRPM). The edgeR program61 was used for detecting differentially expressed genes based on the combined criteria: |log2 fold-change| > 1 and P < 0.05. The MAnorm2 package62 was used for the quantitative comparison of ChIP-Seq and CB-Seq signals between samples with the following criteria: |M value| > 1 and P < 0.05. For spike-in ChIP-seq, the value of RRPM was used to compare signals between samples with the following criteria: |log2 fold-change| > 1 and RRPM > 5. The peaks of CB-Seq overlapped with genes were identified as coding CB RNA. The peaks overlapped with 8 histone modifications (H3K27ac, H3K27me1, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9ac and H3K9me2) and not overlapped with genes were identified as enhancer RNA (eRNA). The remained CB RNA were identified as non-coding other CB RNA (nc-other). The genes with the peaks around their transcription start sites 3 kb were defined as eRNA targeted genes.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: In ChIP-seq, peak files and bigwig files were provided; In mRNA-seq, RPKM for genes (IWGSC RefSeq v1.0) were provided.

organism: Triticum aestivum

source_name: Triticum aestivum 14-days-old seedlings

growth_protocol: Common wheat (Triticum aestivum variety JW1) seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C, after which the germinated seeds with residual endosperm were transferred to soil. The seedlings were cultivated under long-day conditions.

extract_protocol:
Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols.
For RNA-seq, library construction and deep sequencing were performed by Novogene (Beijing, China) using Illumina NovaSeq 6000 system to produce 150-bp paired-end reads.
For ChIP-seq, crosslinked materials were ground into fine power with liquid nitrogen and resuspended in ChIP Lysis Buffer1 (CLB1: 50 mM HEPES [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% Glycerol, 1x inhibitor Cocktail, 0.035% 2-Mercaptoethanol) and incubated for 60 minutes with rotation at 4°C. After incubation, collect the nucleus after filtering the mixture through 40-um strainer, centrifuging at 3000 g for 30 minutes at 4°C in a swinging bucket rotor and removing the supernatant. The nucleus was washed twice with ChIP Lysis Buffer2 (CLB2: 50 mM HEPES [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% Glycerol, 1x inhibitor Cocktail). DNA was sheared by sonication to approximately 300–500-bp fragments. After centrifugation (10 minutes at 13,000 rpm), the supernatant was precleared with 40 μl salmon sperm (SS) DNA/Protein A agarose for 60 minutes at 4°C. After 2 minutes of centrifugation at 500 g, the supernatant was transferred to a siliconized tube, and 10 μl of the appropriate antibody (H3 trimethyl-Lys 27 (ABclonal, A2363), H3 trimethyl-Lys 4 (Abcam, Cambridge, England), and H3 acetyl-Lys 9 (Millipore)) was added. After incubation overnight with rotation, 40 μl SS DNA/Protein A agarose was added and incubation continued for 1 hr. The agarose beads were then washed with 1 ml of each of the following: Low salt buffer (50 mM HEPES [pH 7.5], 150 mM NaCl, 1 mM EDTA), High salt buffer (50 mM HEPES [pH 7.5], 635 mM NaCl, 1 mM EDTA), LiCl wash buffer (0.25M LiCl, 0.5% NP-40, Tris-HCl [pH 8], 1 mM EDTA), and 1× TE (10 mM Tris-HCl [pH 8], 1 mM EDTA). The immunocomplexes were eluted from the beads with 400 μl 1% SDS, 0.1 M NaHCO3. A total of 20 μl 5 M NaCl was then added to each tube, and crosslinks were reversed by incubation at 65°C for 5–6 hours. Residual protein was degraded by the addition of 20 μg Prot K (in 10 mM EDTA and 40 mM Tris [pH 8.0]) at 45°C for 1 hour, followed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Pellets were washed with 70% EtOH and resuspended in 30 μl TE buffer. More than 10 ng ChIP DNA was used to prepare each sequencing sample. Libraries were constructed and sequenced by Novogene (Beijing, China). The libraries were sequenced with the Illumina NovaSeq 6000 system to produce 150-bp paired-end reads.

treatment_protocol: We collected fresh urediospores of Pst race CYR32 from the leaves of wheat cultivar MingXian169. We dispersed the fresh spores in tap water and spread equal contents on the second leaf of control and transgenic wheat plants. The infected plants were incubated in a humid chamber overnight at 16 °C in dark. We transferred the infected plants to a growth chamber (16 °C at 16 h light/8 h dark, 80 % RH) to allow the growth of rust pathogens.

value: 14-days-old seedlings


title: 245_E419T

description: Gene expression data from PDAC tumor


title: 187_16


title: 244_E415T

description: Gene expression data from PDAC tumor

value: unclassified


title: 180_16


title: JW1-H3K27me3-protoplast_rep1


title: Atopic Dermatitis_rep3, Sup

type: RNA

city: Changsha

first: Zeng

last: Jinrong

address: No.138 Tongzipo Rd, Yuelu District, Changsha, Hunan, China, 410013

institute: the Third Xiangya Hospital, Central South University

description:
raw data file: AD3.txt
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Hierarchical clustering heatmap analysis was performed for differentially m6A-methylated RNAs. Differentially m6A-methylated mRNAs were analyzed for GO and pathway enrichment.

source_name: male;34 years old;skin

label_protocol: Total RNAs were immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Collected samples are maintained in liquid nitrogen

extract_protocol: Total RNA extracted using Trizol reagent.The purity and amount of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.

value: Atopic Dermatitis

value: 34 years old

value: skin

tag: molecule subtype

value: Sup RNA


title: JW1-H3K27me3-protoplast_rep2


title: Atopic Dermatitis_rep1, Sup

description:
raw data file: AD1.txt
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: male;31 years old;skin

value: 31 years old


title: Normal skin_rep2, Sup

description:
raw data file: N2.txt
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: female;55 years old;skin

value: Normal skin

value: female

value: 55 years old


title: Normal skin_rep1, Sup

description:
raw data file: N1.txt
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: male;30 years old;skin

value: male

value: 30 years old


title: 242_E409T

description: Gene expression data from PDAC tumor

value: classical

value: IIB

value: L


title: Atopic Dermatitis_rep3, IP

value: IP RNA


title: JW1-LHP1-rep2


title: JW1-SR-rep2


title: Normal skin_rep2, IP


title: Atopic Dermatitis_rep2, Sup

description:
raw data file: AD2.txt
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: female;50 years old;skin

value: 50 years old


title: Normal skin_rep3, Sup

description:
raw data file: N3.txt
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: male;37 years old;skin

value: 37 years old


title: Normal skin_rep3, IP


title: 179_16

value: peripheral white blood cells

value: HNSqCC patient


title: 241_E405T

description: Gene expression data from PDAC tumor

value: unclassified


title: 246_E420T

description: Gene expression data from PDAC tumor

value: basal

value: H


title: 237_E401T

description: Gene expression data from PDAC tumor


title: 174_16


title: XX329_ale_rep1

data_processing:
For ALE-seq data,The sequencing reads were trimmed with the cutadapt , and clean reads were aligned to the IWGSC reference sequence (version 1.0) with Bowtie2(version 2.3.5) . IGV was used to visualize the sequencing data. For the alignment-based approach, the for-ward and reverse reads were merged to yield the full-length fragment sequences and statistic the coverage in the long terminal region of LTR retrotransposon. Only the full-length fragment started from the 5’ of the long terminal region is counted.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: bigwig file for each ALE-seq sample
Library strategy: ALE-seq

source_name: 12-days seedling

extract_protocol:
Total genomic DNA was extracted from the tissue to generate the ALE-seq library.
The first step was to connect an adapter containing the T7 promoter sequence to the end of 5’ end of the eclDNA, followed by in vitro transcription using T7 RNA polymerase. Reverse transcription was then performed using a primer that binds to the transcript of the PBS region, and LTR-RTs showing transposition potential were extracted.

value: 12-days seedling

tag: genotype

value: WT


title: Atopic Dermatitis_rep2, IP

value: Atopic Dermatitis

value: female

value: skin


title: RNAi1_srna_seq

data_processing:
The reads were trimmed with cutadapt to remove Illumina adapters and low-quality bases (quality score < 30). Shortstack was utilized to map the 21-nt and 24-nt clean reads.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: bw files of normalized 21nt and 24nt smRNA signals for each sRNA-seq data to display the smRNA distribution along the chromosomes

source_name: spikelets at booting stage (Feeke 10)

extract_protocol:
The spikelets at booting stage (Feeke 10) were harvested and frozen in liquid nitrogen for  RNA isolation. 4 μg total RNA was used to prepare each sequencing sample.
Libraries were constructed and sequenced by Novogene (Beijing, China) to generate 50-bp single-end reads.

value: Fielder

value: spikelets at booting stage (Feeke 10)


title: RNAi2_srna_seq


title: JW1-CK-rep2

value: 14-days-old seedlings


title: 172_16

value: male


title: Normal skin_rep1, IP

value: Normal skin

value: 30 years old

value: IP RNA


title: 170_16

value: peripheral white blood cells


title: 236_E400T

description: Gene expression data from PDAC tumor

value: IIB


title: 33.1_5_ale_rep1

source_name: spikelets

value: spikelets

value: POL IV mutant


title: F2_2_ale_rep1


title: 166_16

source_name: peripheral white blood cells

value: HNSqCC patient


title: 33.3_6_ale_rep1


title: G1812_seedling_ale_rep1

value: 12-days seedling


title: 160_16


title: 100mix_ale_rep1

value: WT


title: 177_16


title: 230_E370T

description: Gene expression data from PDAC tumor

value: unclassified

value: III

value: L


title: cs_style_ale_rep1

source_name: style

value: Chinses Spring

value: style


title: CK_srna_seq

value: Fielder

value: spikelets at booting stage (Feeke 10)


title: cs_spikelet_I_ale_rep1


title: 157_16

value: male


title: 228_E365T

description: Gene expression data from PDAC tumor


title: 239_E403T

description: Gene expression data from PDAC tumor

value: classical

value: H


title: 153_16

value: peripheral white blood cells


title: TAA_ale_rep1


title: cs_seedling_ale_rep2


title: cs_root_50um_ale_rep1

source_name: 14-days root

value: 14-days root

tag: treatment

value: treat with 50um 5az for 7 days


title: 226_E29T

description: Gene expression data from PDAC tumor

value: basal


title: 33.3_5_ale_rep1

value: spikelets

value: POL IV mutant


title: 143_16

value: HNSqCC patient


title: 234_E394T

description: Gene expression data from PDAC tumor

value: IIB


title: 225_E260T

description: Gene expression data from PDAC tumor

value: IIA


title: cs_endosperm_ale_rep1

source_name: endosperm

value: endosperm

value: WT


title: cs_heat_ale_rep1

source_name: 14-days seedling

value: Chinses Spring

value: 14-days seedling

value: 7-days old seedling transferred to 40°C for 7 days


title: 23_29818T

description: Gene expression data from PDAC tumor

value: L


title: cs_em_ale_rep3

source_name: fresh immature embryos (14days post anthesis)


title: cs_callus_ale_rep1

source_name: callus

value: callus

value: 2,4-D induction for 12 days


title: cs_em_ale_rep2

value: fresh immature embryos (14days post anthesis)


title: cs_anther_ale_rep1

source_name: anther

value: anther


title: 140_16

value: male

value: peripheral white blood cells


title: cs_RNAi4_rnaseq

data_processing:
For RNA-sequencing data, The sequencing reads were trimmed with the Trim Galore(version 0.6.4) and cutadapt ,clean reads were aligned with HISAT2 program(version 2.1.0) . SortMeRNA was used to remove the reads originating from chloroplast, mitochondria and rRNA. The featureCount program of  was used to determine the RNA-seq read density of the high-confidence genes in the IWGSC RefSeq genome assembly(version 1.1).
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each RNA-seq sample

extract_protocol:
The spikelets at booting stage (Feeke 10) were harvested and frozen in liquid nitrogen for  RNA isolation. More than 2 μg total RNA was used to prepare each sequencing sample.
Libraries were constructed and sequenced by Hanyubio Co. Ltd. (Shanghai, China) to produce 150-bp paired-end reads.

value: Fielder

value: spikelets at booting stage (Feeke 10)


title: 222_E251T

description: Gene expression data from PDAC tumor

value: unclassified


title: cs_root_ale_rep1

source_name: 12-days root

value: 12-days root


title: cs_em_ale_rep1


title: 139_16

value: HNSqCC patient


title: 138_16


title: 22_29164T

description: Gene expression data from PDAC tumor

value: basal

value: IIA

value: H


title: cs_RNAi1_rnaseq


title: 136_16


title: cs_CK3_rnaseq

value: WT


title: 219_E223T

description: Gene expression data from PDAC tumor

value: classical

value: IIB


title: cs_RNAi2_rnaseq


title: 142_16


title: 218_E221T

description: Gene expression data from PDAC tumor


title: 135_16


title: cs_CK1_rnaseq


title: 141_16


title: JW1-LHP1

data_processing:
Sequencing reads were cleaned with the fastp (version 0.20.0)55, which eliminated bases with low quality scores (< 25) and irregular GC contents, sequencing adapters, and short reads. The remaining cleaned reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0) with the Burrows–Wheeler Aligner (version 0.7.17-r1188)56 for the wheat ChIP-Sequencing. For spike-in ChIP-seq, cleaned reads were mapped to the merged genome of common wheat (IWGSC) and Arabidopsis thaliana (TAIR10). The HISAT2 program (version 2.2.1)57 was used for mapping the RNA sequencing (RNA-seq) and chromatin-bound RNA (CB-seq) reads to the reference sequences. The MACS (version 2.2.6)58 program was used to identify the read-enriched regions (peaks) of the ChIP-Seq and CB-Seq data with the cutoff P < 1e−10. To quantify gene expression levels, the featureCount program of the Subread package (version 2.0.0)59  was used to determine the RNA-seq read density for the genes. To compare expression levels across samples and genes, the RNA-seq read density of each gene was normalized based on the exon length in the gene and the sequencing depth (i.e., fragments per kilobase of exon model per million mapped reads). To quantify histone markers across genes for the figure prepared with Integrative Genomics Viewer60, the number of reads at each position was normalized against the total number of reads (reads per million mapped reads). For spike-in ChIP-seq, the number of reads at each position was normalized against the total number of reads mapped to A. thaliana (reference-adjuseted reads per million, RRPM). The edgeR program61 was used for detecting differentially expressed genes based on the combined criteria: |log2 fold-change| > 1 and P < 0.05. The MAnorm2 package62 was used for the quantitative comparison of ChIP-Seq and CB-Seq signals between samples with the following criteria: |M value| > 1 and P < 0.05. For spike-in ChIP-seq, the value of RRPM was used to compare signals between samples with the following criteria: |log2 fold-change| > 1 and RRPM > 5. The peaks of CB-Seq overlapped with genes were identified as coding CB RNA. The peaks overlapped with 8 histone modifications (H3K27ac, H3K27me1, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9ac and H3K9me2) and not overlapped with genes were identified as enhancer RNA (eRNA). The remained CB RNA were identified as non-coding other CB RNA (nc-other). The genes with the peaks around their transcription start sites 3 kb were defined as eRNA targeted genes.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: In ChIP-seq, peak files and bigwig files were provided; In mRNA-seq and CB-seq, RPKM for genes (IWGSC RefSeq v1.0) were provided.

source_name: Triticum aestivum 14-days-old seedlings

extract_protocol:
Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols.
For RNA-seq, library construction and deep sequencing were performed by Novogene (Beijing, China) using Illumina NovaSeq 6000 system to produce 150-bp paired-end reads.
For ChIP-seq, crosslinked materials were ground into fine power with liquid nitrogen and resuspended in ChIP Lysis Buffer1 (CLB1: 50 mM HEPES [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% Glycerol, 1x inhibitor Cocktail, 0.035% 2-Mercaptoethanol) and incubated for 60 minutes with rotation at 4°C. After incubation, collect the nucleus after filtering the mixture through 40-um strainer, centrifuging at 3000 g for 30 minutes at 4°C in a swinging bucket rotor and removing the supernatant. The nucleus was washed twice with ChIP Lysis Buffer2 (CLB2: 50 mM HEPES [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% Glycerol, 1x inhibitor Cocktail). DNA was sheared by sonication to approximately 300–500-bp fragments. After centrifugation (10 minutes at 13,000 rpm), the supernatant was precleared with 40 μl salmon sperm (SS) DNA/Protein A agarose for 60 minutes at 4°C. After 2 minutes of centrifugation at 500 g, the supernatant was transferred to a siliconized tube, and 10 μl of the appropriate antibody (H3 trimethyl-Lys 27 (ABclonal, A2363), H3 trimethyl-Lys 4 (Abcam, Cambridge, England), and H3 acetyl-Lys 9 (Millipore)) was added. After incubation overnight with rotation, 40 μl SS DNA/Protein A agarose was added and incubation continued for 1 hr. The agarose beads were then washed with 1 ml of each of the following: Low salt buffer (50 mM HEPES [pH 7.5], 150 mM NaCl, 1 mM EDTA), High salt buffer (50 mM HEPES [pH 7.5], 635 mM NaCl, 1 mM EDTA), LiCl wash buffer (0.25M LiCl, 0.5% NP-40, Tris-HCl [pH 8], 1 mM EDTA), and 1× TE (10 mM Tris-HCl [pH 8], 1 mM EDTA). The immunocomplexes were eluted from the beads with 400 μl 1% SDS, 0.1 M NaHCO3. A total of 20 μl 5 M NaCl was then added to each tube, and crosslinks were reversed by incubation at 65°C for 5–6 hours. Residual protein was degraded by the addition of 20 μg Prot K (in 10 mM EDTA and 40 mM Tris [pH 8.0]) at 45°C for 1 hour, followed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Pellets were washed with 70% EtOH and resuspended in 30 μl TE buffer. More than 10 ng ChIP DNA was used to prepare each sequencing sample. Libraries were constructed and sequenced by Novogene (Beijing, China). The libraries were sequenced with the Illumina NovaSeq 6000 system to produce 150-bp paired-end reads.
For spike-in ChIP-seq, Arabidopsis chromatin was added into wheat chromatin before immunoprecipitation. Briefly, before performing immunoprecipitation, 40 ul of chromatin was reverse crosslinked, proteinase K digested followed by DNA purification. The concentration of purified DNA was determined using Qubit dsDNA High-Sensitivity Assays (Invitrogen). Meanwhile, chromatins from Arabidopsis were also isolated and determined the concentration with the same method. One percent of Arabidopsis chromatins were mixed with different Wheat samples before immunoprecipitation. The rest procedures are the same as the previous description.
For nascent RNA (chromatin-bound RNA, CB RNA) library preparation, the chromatin RNA extraction was completed as previously described54. After degrading genomic DNA by TURBO DNase (Life Technologies), CB RNA was subjected to rRNA depletion using a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo(dT) beads (NEB, S1419). Both CB RNA and polyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.

value: 14-days-old seedlings

tag: chip antibody


title: 134_16


title: 217_E205T

description: Gene expression data from PDAC tumor

value: L


title: 224_E253T

description: Gene expression data from PDAC tumor


title: JW1-H3K27me3_spike-in


title: L18-H3K27me3_spike-in


title: 133_16


title: 215_E202T

description: Gene expression data from PDAC tumor


title: 214_E197T

description: Gene expression data from PDAC tumor


title: JW1-H3K27me3_rep2


title: JW1-H3K27me3_rep1


title: JW1-SR-H3K27me3


title: 213_E194T

description: Gene expression data from PDAC tumor


title: JW1-H3K9ac


title: 130_16


title: 211_E193T

description: Gene expression data from PDAC tumor


title: JW1-H3K4me3


title: L18-CK


title: L19-H3K27me3_spike-in


title: L19-SR


title: L18-SR


title: 210_E174T

description: Gene expression data from PDAC tumor


title: L19-CK


title: 129_16


title: 131_16


title: JW1-CK


title: 128_16


title: 127_16


title: JW1-SR


title: 209_E172T

description: Gene expression data from PDAC tumor


title: 126_16


title: cs_cage_root_rep2

data_processing:
For CAGE-seq, only the R1 read were kept to mapping. Cutadaptwas applied to trim 3’ adaptor and 9 bases at the 5’end, used SortMeRNA to remove the reads originating from chloroplast, mitochondria and rRNA. Clean reads were mapped to the IWGSC (version 1.0) with Bowtie2 Only unique mapped reads were used for analysis. The 5′ coordinate of R1 reads was considered the position of the transcription start sites.
For ChIP-seq, Bisulfite-seq and RNA-seq, reads were trimmed with the Trim Galore and cutadapt. For RNA-sequencing, clean reads were aligned with HISAT2. SortMeRNA was used to remove the reads originating from chloroplast, mitochondria and rRNA. The featureCount was used to determine the RNA-seq read density of the high-confidence genes in the IWGSC RefSeq genome assembly (version 1.1). For ChIP-seq data, clean reads were aligned with bwa program. The MACS2 was used to identify the peaks.
For Bisulfite-seq data, the clean reads were then aligned by the Bismark program. The extent of the cytosine methylation was determined with the bismark_methylation_extractor implemented in the Bismark program. Next, the methylation ratio of a cytosine was calculated as the number of mCs divided by the number of reads covering the position. Bases covered by fewer than three reads were considered low confidence positions whose methylation ratios were not recorded.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: CAGE-seq signal in each site were provided in bed file.

source_name: Triticum aestivum 12-days-old seedlings

value: 12-days-old seedlings

value: Chinses Spring

tag: age/tissue

value: 9-days root


title: 207_E164T

description: Gene expression data from PDAC tumor


title: cs_cage_root_rep1

tag: tissue


title: 125_16

value: male

value: peripheral white blood cells


title: cs_cage_embryo_rep3

value: fresh immature embryos (14days post anthesis)


title: 208_E169T

description: Gene expression data from PDAC tumor

tag: subtype


title: cs_RNAi3_rnaseq

tag: cultivar

value: Fielder

value: spikelets at booting stage (Feeke 10)


title: 220_E225T

description: Gene expression data from PDAC tumor

tag: tnm


title: 124_16

value: HNSqCC patient


title: cs_cage_embryo_rep1


title: 206_E157T

description: Gene expression data from PDAC tumor

tag: Stage


title: cs_cage_spikelet_I_rep2


title: 205_E151T

description: Gene expression data from PDAC tumor

value: basal

tag: grading


title: cs_cage_spikelet_I_rep1


title: cs_cage_seedling_rep1

value: 9-days seedling


title: cs_cage_seedling_rep4


title: 123_16


title: 203_E122T

description: Gene expression data from PDAC tumor

tag: cohort

value: H


title: cs_cage_seedling_rep3


title: 200_E250_Tp1

description: Gene expression data from PDAC tumor

value: IV

tag: serpinb3 expression (high_low)


title: 122_16


title: Lbr

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

country: Canada

institute: OHRI

description: ATAC-seq on Lbr -expressing rod photoreceptors

data_processing:
Fastq Groomer
Trimmomatic
Bowtie2
Macs2
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: Retina

extract_protocol:
50 000 flow sorted cells were lysed in cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630).
Nextera DNA Flex Library kit (Illumina)

treatment_protocol: In vivo electroporation on P0 mouse retinas

value: Retina

value: sorted rod photoreceptors

value: wild-type CD1

value: Control transfection (EGFP)


title: 121_16


title: Control

description: ATAC-seq on control rod photoreceptors


title: Lamin A

description: ATAC-seq on lamin A -expressing rod photoreceptors


title: 117_16


title: cs_cage_embryo_rep2

value: 12-days-old seedlings


title: TS-TissueInt_Pool2

description:
bisulfite converted DNA
TS-TissueInt_AllPools.tar.gz

source_name: Liver

value: Liver

tag: strain

tag: age

value: various

tag: Sex

value: mixed


title: 118_16

tag: gender

value: male

tag: cell type

value: peripheral white blood cells

tag: disease state


title: TS-TissueInt_Pool3


title: 196_E246_Tp1

description: Gene expression data from PDAC tumor

value: IB

tag: month


title: 198_E249_Tp1

description: Gene expression data from PDAC tumor

value: unclassified

value: IIB

value: L


title: 116_16

value: HNSqCC patient


title: TS-TissueInt_Pool1


title: TS-Blood_DietaryInt_Pool1

description:
bisulfite converted DNA
TS-Blood_DietaryInt.tar.gz

source_name: Whole blood

value: Whole blood


title: TS-Blood_DietaryInt_Pool2


title: cs_cage_seedling_rep2

value: Chinses Spring

value: 9-days seedling


title: 194_E245_Tp1

description: Gene expression data from PDAC tumor

value: classical


title: TS-BloodClock_Val_Pool1

description:
bisulfite converted DNA
TS-BloodClock_Val_AllPools.tar.gz


title: 20_29102T

description: Gene expression data from PDAC tumor

value: H


title: TS-BloodClock_Val_Pool2


title: 108_16


title: 192_E234_Tp1

description: Gene expression data from PDAC tumor


title: TS-Blood_TrainTest_Pool5

description:
bisulfite converted DNA
TS-Blood_TrainTest_AllPools.tar.gz


title: TS-Blood_TrainTest_Pool2


title: TS-BloodClock_Benchmarking

description:
bisulfite converted DNA
TS_BloodClock_Benchmarking.tar.gz


title: 190_E229_Tp1

description: Gene expression data from PDAC tumor


title: TS-Blood_TrainTest_Pool4


title: 107_16


title: TS-Blood_TrainTest_Pool3


title: 19_27881T

description: Gene expression data from PDAC tumor


title: 113_16


title: TS-Blood_TrainTest_Pool1


title: 103_16


title: 188_E220_Tp1

description: Gene expression data from PDAC tumor


title: Adult_KO_TEC_ATAC

first: Yongge

last: Zhao

address: 9000 Rockville Pike

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger ATAC software v1.2.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thymus

extract_protocol: Library was performed according to the manufacter’s instructions (single cell ATAC sequencing protocol, 10x Genomics)

value: TEC

value: thymus

tag: genotype

value: Klf6 KO

value: 4-6 weeks old


title: 102_16


title: 184_E209_Tp2

description: Gene expression data from PDAC tumor


title: Adult_WT_TEC_RNA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: WT


title: E15_KO_TEC_RNA

description: 10x Genomics


title: 97_16

value: male


title: 105_16

value: peripheral white blood cells


title: 182_E208_Tp1

description: Gene expression data from PDAC tumor

data_processing:
mRNA-Seq samples were pooled and sequenced on NavoSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 51 to 122 million pass filter reads with more than 90% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM_TMM normalized values for each Sample


title: AT3, STM3006, 48h, rep3

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the mouse reference genome using HiSAT2 and reads were assigned to genes using htseq-count.
Differential expression was calculated using DESeq2
Assembly: mm10
Supplementary files format and content: Raw gene counts from htseq

source_name: Mammary Carcinoma

growth_protocol: DMEM (Gibco) supplemented with 10% FBS, 100 IU/ml penicillin, 100µg/ml streptomycin, 2mM Glutamax, 15mM HEPES and MEM Non-Essential Amino Acids (Gibco)

extract_protocol:
Qiagen RNeasy kit
QuantSeq 3’ mRNA-Seq Library preparation

value: Mammary Carcinoma

tag: cell line

tag: time

value: 48 hours

tag: treatment


title: 101_16

data_processing:
Import the CEL files into Axiom Analysis Suite, using Best Practices Workflow from the recommendations of the Axiom Genotyping Solution-Data Analysis
Genotype Call (SNP call): AA, AB, BB, NoCall


title: AT3, STM3006, 48h, rep1

tag: tissue


title: Adult_KO_TEC_RNA

description: 10x Genomics


title: Adult_WT_TEC_ATAC

description: 10x Genomics


title: 94_16


title: AT3, STM3006, 48h, rep2


title: 178_E186_Tp2

description: Gene expression data from PDAC tumor

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NovaSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subtype

tag: tnm

value: IIB


title: AT3, STM2457, 48h, rep1


title: 180_E203_Tp1

description: Gene expression data from PDAC tumor

value: basal

tag: Stage

value: IV

tag: grading


title: AT3, STM2457, 48h, rep3


title: 186_E218_Tp1

description: Gene expression data from PDAC tumor

tag: cohort

tag: serpinb3 expression (high_low)


title: E15_WT_TEC_RNA

description: 10x Genomics

tag: strain

tag: age


title: AT3, STM2457, 48h, rep2


title: 92_16

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

tag: gender

value: HNSqCC patient


title: 91_16

tag: cell type


title: 176_E182_Tp2

description: Gene expression data from PDAC tumor

value: L


title: AT3, DMSO, 48h, rep3

value: DMSO


title: AT3, DMSO, 48h, rep2


title: AT3, DMSO, 48h, rep1


title: 174_E181_Tp1

description: Gene expression data from PDAC tumor

value: IIA


title: 90_16

tag: disease state


title: AT3, STM3006, 24h, rep3

value: 24 hours


title: 88_16


title: AT3, STM3006, 24h, rep2


title: 172_E179_Tp1

description: Gene expression data from PDAC tumor

value: classical

tag: month


title: 170_E178_Tp1

description: Gene expression data from PDAC tumor

value: H


title: AT3, STM2457, 24h, rep3

tag: genotype


title: AT3, STM3006, 24h, rep1

tag: cell line


title: 85_16


title: AT3, STM2457, 24h, rep2

tag: time


title: 84_16


title: AT3, STM2457, 24h, rep1

tag: treatment


title: AT3, DMSO, 24h, rep3

tag: tissue


title: AT3, DMSO, 24h, rep1


title: 17_27775T

description: Gene expression data from PDAC tumor

tag: subtype


title: cs_CK2_rnaseq

source_name: spikelets at booting stage (Feeke 10)

tag: cultivar

value: Fielder

value: spikelets at booting stage (Feeke 10)


title: pilot_TIME-Seq_rDNABaitsv1_rep2

description:
bisulfite converted DNA
pilot_TIME-Seq_rDNABaitsv1_re2.tar.gz

value: Whole blood

value: various

tag: Sex

value: mixed


title: 168_E165_Tp1

description: Gene expression data from PDAC tumor

tag: tnm

tag: Stage

tag: grading


title: AT3, DMSO, 24h, rep2

value: Mammary Carcinoma

value: WT


title: TS-rDNA-clock_validation_set2

description:
bisulfite converted DNA
TS-rDNA-clock_validation.tar.gz

tag: strain


title: 83_16

source_name: peripheral white blood cells

value: male

value: peripheral white blood cells


title: 166_E162_Tp1

description: Gene expression data from PDAC tumor

value: IIB

tag: cohort

tag: serpinb3 expression (high_low)


title: ShallowTS-Blood_Val_Pool2

description:
bisulfite converted DNA
ShallowTS-Blood_Val_Pool2.tar.gz

tag: age


title: 81_16

tag: gender

tag: cell type

tag: disease state

value: HNSqCC patient


title: TS-rDNA-clock_validation_set1


title: 162_E139_Tp1

description: Gene expression data from PDAC tumor

tag: month


title: pilot_TIME-Seq_rDNABaitsv1_rep1

description:
bisulfite converted DNA
pilot_TIME-Seq_rDNABaitsv1_rep1.tar.gz


title: 164_E152_Tc5

description: Gene expression data from PDAC tumor

value: L


title: 160_E138_Tp1

description: Gene expression data from PDAC tumor


title: 79_16


title: shallowTS_Liver_mouseDiscBaits_Pool1

description:
bisulfite converted DNA
shallowTS_liver_mouseDiscBaits_AllPools.tar.gz


title: shallowTS_Liver_mouseDiscBaits_Pool2


title: 80_16


title: shallowTS_blood_mouseDiscBaits_Pool3

description:
bisulfite converted DNA
shallowTS_blood_mouseDiscBaits_AllPools.tar.gz


title: shallowTS_blood_mouseDiscBaits_Pool2


title: 77_16


title: 78_16


title: 72_16


title: shallowTS_blood_mouseDiscBaits_Pool1


title: ShallowTS-Blood_Val_Pool1

description:
bisulfite converted DNA
ShallowTS-Blood_Val_Pool1.tar.gz


title: Atopic Dermatitis_rep1, IP

description:
raw data file: AD1.txt
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

source_name: male;31 years old;skin

value: Atopic Dermatitis

value: 31 years old

value: skin

tag: molecule subtype

value: IP RNA


title: 158_E136_Tp1

description: Gene expression data from PDAC tumor

value: classical

value: IIA


title: 16_26576T

description: Gene expression data from PDAC tumor

value: unclassified


title: 71_16


title: 156_E133_Tp4

description: Gene expression data from PDAC tumor

value: H


title: 155_E130_Tp1

description: Gene expression data from PDAC tumor


title: TS-rDNA-clock_rDNABaits_Pool2

description:
bisulfite converted DNA
TS-rDNA-clock_rDNABaits.tar.gz

value: Whole blood

value: various


title: 68_16


title: TS-rDNA-clock_rDNABaits_Pool4

value: mixed


title: 151_E120_Tc7

description: Gene expression data from PDAC tumor

value: basal

value: III


title: TS-rDNA-clock_rDNABaits_Pool1


title: 153_E123_Tc7

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control44

city: Sydney

first: Kelly

last: Williams

state: NSW

address: 75 Talavera Road

department: Motor Neuron Disease Centre

institute: Macquarie University

data_processing:
Trimmomatic v0.38 was applied to raw FASTQ files to remove low quality reads and adaptor sequences.
Salmon v1.9.0 was used to build a transcriptome index and to quantify transcripts (default selective alignment with --seqBias and --gcBias flags).
Tximport v1.26.1 was used to convert transcript abundance estimates to gene-level counts with corresponding offset matrix.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file including raw gene counts
Supplementary files format and content: tab delimited text file including tximport-generated offset matrix

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from peripheral blood using the QIASymphony automated liquid handing robot and the PAXgene Blood RNA kit (Qiagen, Hilden, Germany) as per standard protocol.
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA Sample Prep kit (Illumina, CA, USA).

value: peripheral blood

value: Healthy control


title: shallowTS_Liver_mouseDiscBaits_Pool3

data_processing:
https://github.com/patricktgriffin/TIME-Seq
Assembly: mm10,hg19
Supplementary files format and content: bismark.cov
Library strategy: TIME-Seq


title: 66_16

value: male

value: peripheral white blood cells

value: HNSqCC patient


title: 64_16


title: PeripheralBlood_Control45


title: PeripheralBlood_Control46


title: PeripheralBlood_Control48


title: PeripheralBlood_Control43


title: 15_26172T

description: Gene expression data from PDAC tumor


title: 149_E119_Tc7

description: Gene expression data from PDAC tumor

value: II


title: 63_16


title: TS-rDNA-clock_rDNABaits_Pool3


title: 147_E109_Tp1

description: Gene expression data from PDAC tumor

value: IIB

value: L


title: PeripheralBlood_Control42


title: PeripheralBlood_Control40


title: 61_16


title: PeripheralBlood_Control41


title: 145_E094_Tc7

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control38


title: 67_16


title: PeripheralBlood_Control39


title: PeripheralBlood_Control47


title: PeripheralBlood_Control37


title: 60_16


title: 59_16


title: 143_E088_Tc7

description: Gene expression data from PDAC tumor

value: classical


title: PeripheralBlood_Control36


title: 140_E082_Tp1

description: Gene expression data from PDAC tumor

value: IVB


title: PeripheralBlood_Control35


title: PeripheralBlood_Control34


title: PeripheralBlood_Control33


title: 138_E073_Tc7

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control32


title: PeripheralBlood_Control30


title: PeripheralBlood_Control31


title: 57_16


title: 136_E064_Tp3

description: Gene expression data from PDAC tumor

value: IVA


title: PeripheralBlood_Control29


title: 55_16


title: 134_E058_Tc7

description: Gene expression data from PDAC tumor

value: H


title: PeripheralBlood_Control28


title: PeripheralBlood_Control27


title: PeripheralBlood_Control26


title: 132_E052_Tc7

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control24


title: 54_16


title: PeripheralBlood_Control25


title: PeripheralBlood_Control23


title: 49_16


title: 48_16


title: 50_16


title: PeripheralBlood_Control21


title: 130_E045_Tc7

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control22


title: 131_E048_Tc7

description: Gene expression data from PDAC tumor


title: 56_16


title: 128_E042_Tc10

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control18


title: 13_22506T

description: Gene expression data from PDAC tumor

value: IIA


title: 46_16


title: PeripheralBlood_Control20


title: PeripheralBlood_Control19


title: 45_16


title: 126_E041_Tc7

description: Gene expression data from PDAC tumor


title: 43_16


title: 121_E021_Tc8

description: Gene expression data from PDAC tumor


title: 40_16


title: PeripheralBlood_Control12


title: PeripheralBlood_Control15


title: 124_E033_Tc7

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control14


title: 41_16


title: PeripheralBlood_Control08


title: 118_E005_Tc8

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control13


title: PeripheralBlood_Control07


title: PeripheralBlood_Control06


title: 117_64563

description: Gene expression data from PDAC tumor

value: GX


title: PeripheralBlood_Control17


title: PeripheralBlood_Control11


title: 120_E012_Tp2

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Control10


title: PeripheralBlood_Control09


title: 37_16


title: 35_16


title: 36_16


title: PeripheralBlood_Control03


title: PeripheralBlood_Control16


title: 115_62659

description: Gene expression data from PDAC tumor

value: unclassified


title: PeripheralBlood_Control04


title: 39_16


title: 32_16


title: PeripheralBlood_Control02


title: 34_16


title: 31_16


title: PeripheralBlood_Case94

value: sALS


title: PeripheralBlood_Control01


title: 114_62084

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Case95


title: 113_60425

description: Gene expression data from PDAC tumor


title: 11_19927T

description: Gene expression data from PDAC tumor

value: basal

value: IB


title: 26_16


title: PeripheralBlood_Control05

value: peripheral blood

value: Healthy control


title: 30_16

value: male

value: peripheral white blood cells


title: 116_64550

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Case87


title: 108_56008

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Case91


title: 111_57488

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Case86


title: PeripheralBlood_Case93


title: PeripheralBlood_Case90


title: 27_16

value: HNSqCC patient


title: PeripheralBlood_Case96


title: PeripheralBlood_Case92


title: PeripheralBlood_Case85


title: PeripheralBlood_Case89


title: PeripheralBlood_Case84


title: 25_16


title: PeripheralBlood_Case88


title: 22_16


title: 21_16


title: PeripheralBlood_Case78


title: 106_62660

description: Gene expression data from PDAC tumor


title: PeripheralBlood_Case82


title: PeripheralBlood_Case81


title: 18_16


title: PeripheralBlood_Case76


title: PeripheralBlood_Case75


title: 100_67161

description: Gene expression data from PDAC tumor


title: RXDX-106 treated biol rep 3

city: Ann Arbor

first: Joseph

last: Decker

state: Michigan

address: 1011 N University Avenue

department: Cariology, Restorative Sciences, and Endodontics

institute: University of Michigan

data_processing:
Reads were trimmed using Cutadapt (version 2.3)
Data quality was ensured using FastQC (version 0.11.8)
Fastq was used to screen for contamination
Reads were mapped using STAR (version 2.8.8a)
Assembly: GRCm39 (MertkKO data), CRCh38 (hMSC data)
Supplementary files format and content: tab-deliminted file including TPM values for each transcript

source_name: Alveolar bone mesenchymal stem cell

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen)
RNA libraries were generated using the SMART-Seq v4 PLUS kit per manufacturer protocols (Takara)

value: Alveolar bone mesenchymal stem cell

tag: treatment


title: PeripheralBlood_Case77

tag: tissue


title: PeripheralBlood_Case80


title: 24_16


title: Untreated biol rep 3

value: Untreated


title: 109_57484

description: Gene expression data from PDAC tumor

tag: subtype

value: IIB

value: L


title: PeripheralBlood_Case74


title: PeripheralBlood_Case79


title: 20_16


title: 17_16


title: RXDX-106 treated biol rep 1


title: 16_16


title: Untreated biol rep 2


title: Untreated biol rep 1


title: PeripheralBlood_Case73


title: RXDX-106 treated biol rep 2


title: PeripheralBlood_Case71


title: 14_16


title: 15_16


title: PeripheralBlood_Case69


title: PeripheralBlood_Case83


title: PeripheralBlood_Case68


title: PeripheralBlood_Case66


title: NCI-H660_Romidepsin_Ipata_I

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofilteR (v1.6).
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: NCI-H660 cell line

extract_protocol:
Total RNA was isolated using RNA STAT-60 (Tel-Test).  The isolated RNA was then purified with Qiagen RNeasy Kit (Qiagen Inc.) according to the manufacturer’s protocol utilizing the manufacturer’s recommended DNase digestion (Qiagen).
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

tag: sample type

value: in vitro culture of dissociated prostate tumor patient-derived xenograft (PDX) tumor

value: prostate cancer

value: 1nM Romidepsin 1uM Ipatasertib

tag: timepoint

value: 24 hours


title: NCI-H660_Romidepsin_Ipata_II


title: PeripheralBlood_Case72


title: PeripheralBlood_Case67


title: NCI-H660_Romidepsin_II

value: 1nM Romidepsin


title: 12_16


title: PeripheralBlood_Case63

value: sALS


title: PeripheralBlood_Case64


title: PeripheralBlood_Case65


title: PeripheralBlood_Case62


title: NCI-H660_Romidepsin_I


title: NCI-H660_Ipata_II

value: 1uM Ipatasertib


title: PeripheralBlood_Case61


title: PeripheralBlood_Case60


title: PeripheralBlood_Case58


title: 4_16


title: NCI-H660_Ipata_I


title: PeripheralBlood_Case59


title: PeripheralBlood_Case70


title: 5_16


title: PeripheralBlood_Case56


title: NCI-H660_Fimepinostat_II

value: 25nM Fimepinostat


title: PeripheralBlood_Case57

value: peripheral blood


title: PeripheralBlood_Case55


title: 3_16


title: NCI-H660_Fimepinostat_I


title: PeripheralBlood_Case54


title: 11_16


title: NCI-H660_Control_II

value: vehicle


title: PeripheralBlood_Case53


title: scRNA-seq of cotton leaves 3

city: Shanghai

first: Longxian

last: Chen

address: 300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

description: 10x Genomics

data_processing:
Cell Ranger
Seurat
Assembly: NBI_Gossypium_hirsutum_v1.1

molecule: polyA RNA

organism: Gossypium hirsutum

source_name: leaf

extract_protocol:
RNA of protoplasts isolated from true leaves of G. hirsutum
10x Genomics

value: leaf


title: 9_16

value: male

value: peripheral white blood cells


title: PeripheralBlood_Case52


title: NCI-H660_Control_I


title: PeripheralBlood_Case51


title: scRNA-seq of cotton leaves 2

description: 10x Genomics


title: PeripheralBlood_Case50


title: PeripheralBlood_Case49


title: PeripheralBlood_Case48


title: PeripheralBlood_Case46


title: C4-2B_Romidepsin_II

source_name: LNCaP C4-2B cell line

value: cell line


title: GARR2KO-3

city: Yangzhou

first: Yijun

state: Jiangsu

address: Wenhui

institute: Yangzhou University

data_processing:
Clean reads were aligned to the maize reference genome (AGPv4) with Tophat2.
Aligned reads of single sample were assembled to generate transcripts with Cufflinks.
FPKM (expected fragments per kilobase of transcript per million fragments sequenced) values were evaluated by the Cuffdiff utility embedded in the Cufflinks package.
Genome_build: AGPv4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Zea mays

source_name: 2nd leaf sheath

growth_protocol: Maize plants were grown in normal conditions.

extract_protocol:
Total RNA was extracted with the RNeasy Plant Mini Kit.
RNA libraries were prepared according to standard Illumina protocols.

treatment_protocol: Seedlings were not treated.

tag: genotype

value: 2nd leaf sheath

value: three-leaf stage


title: PeripheralBlood_Case45


title: PeripheralBlood_Case41


title: PeripheralBlood_Case47


title: WT-3

value: WT


title: PeripheralBlood_Case44


title: GARR2KO-2


title: C4-2B_Romidepsin_Ipata_II


title: PeripheralBlood_Case43


title: C4-2B_Ipata_II


title: C4-2B_Romidepsin_Ipata_I


title: PeripheralBlood_Case40


title: PeripheralBlood_Case42


title: PeripheralBlood_Case39


title: C4-2B_Romidepsin_I


title: PeripheralBlood_Case36


title: PeripheralBlood_Case38


title: C4-2B_Fimepinostat_II


title: WT-2


title: WT-1


title: PeripheralBlood_Case37


title: PeripheralBlood_Case35


title: GARR2KO-1


title: 8C_NR5A2_CR_rep3

first: Fangnong

last: Lai

state: Beijing

address: Haidian district

institute: Tsinghua University

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). scRNA-seq reads were mapped to mm9 genome by HISAT2 (version 2.1.0).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig
Library strategy: CUT&RUN

source_name: 8 Cell embryos

growth_protocol: For collection of wildtypes 2 and 8C embryos, 4–6-week-old C57BL/6J female mice were injected with pregnant mare serum gonadotropin (PMSG) followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with PWK/PhJ mice. Fertilized 2C (39-43h) and 8C (68-70h) embryos were flushed out from the oviduct with HEPES-buffered CZB medium.

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or  NovaSeq (Illumina) according to the manufacturer’s protocol.

value: 8 Cell embryos

value: wild type

value: C57BL/6J x  PWK/PhJ

tag: chip antibody

value: NR5A2 (antiLRH-1/NR5A2, H2325, R&D)


title: scRNA-seq of cotton leaves 1

description: 10x Genomics


title: C4-2B_Fimepinostat_I

value: prostate cancer

value: 24 hours


title: 2C_NR5A2_CR_rep2

source_name: 2 Cell embryos

value: 2 Cell embryos


title: PeripheralBlood_Case33

value: sALS


title: PeripheralBlood_Case32

value: peripheral blood


title: C4-2B_Control_II

value: vehicle


title: PeripheralBlood_Case26


title: PeripheralBlood_Case29


title: NCI-H660_1nM_Romidepsin_A_14

value: in vitro culture of dissociated prostate tumor patient-derived xenograft (PDX) tumor

value: 1nM Romidepsin


title: PeripheralBlood_Case31


title: C4-2B_Ipata_I

value: male

value: 1uM Ipatasertib


title: NCI-H660_1nM_Romidepsin_B_16


title: PeripheralBlood_Case27


title: PeripheralBlood_Case30


title: C4-2B_Control_I

value: cell line


title: PeripheralBlood_Case34


title: NC3

first: Wei

last: Jin

address: 197 Ruijin 2nd Road,

institute: Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: all.counts.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: hearts

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: PeripheralBlood_Case28


title: PeripheralBlood_Case23


title: NCI-H660_control_A_13


title: PeripheralBlood_Case22


title: NC1

description: all.counts.txt


title: PeripheralBlood_Case20


title: C4-2B_1nM_Romidepsin_B_20


title: NC4

description: all.counts.txt


title: 2C_NR5A2_CR_rep1

tag: strain


title: PeripheralBlood_Case25


title: NCI-H660_control_B_15


title: PeripheralBlood_Case19


title: C4-2B_1nM_Romidepsin_A_18


title: STAT3cKO91

description: all.counts.txt


title: C4-2B_control_A_17


title: PeripheralBlood_Case14


title: PeripheralBlood_Case15


title: 2C_NR5A2_CR_rep3


title: PeripheralBlood_Case13


title: 208.1_control_10

source_name: LuCaP 208.1 PDX

value: 96 hours


title: PeripheralBlood_Case24


title: Control 09

city: Heidelberg

first: Javier

last: Vázquez-Marín

state: Baden-Württemberg

address: Im Neuenheimer Feld 230, 5th floor

department: Centre for Organismal Studies (COS)

institute: Heidelberg University

data_processing:
Raw sequencing data in FASTQ format were processed using Space Ranger software (version 1.3.0) for demultiplexing, genome alignment, UMI counting, and spatial alignment.
Loupe Browser (version 5.0) was used to stablish a manual fiducial alignment and therefore an accurate tissue boundary selection on every image. The resulting JSON file containing the coordinates of every spot labelled as part of the tissue and their corresponding scaling factors that converts pixel positions from full-resolution to downsampled images were used in combination with its corresponding image in TIFF format and the FASTQ files obtained after sequencing to map every read to the mouse reference genome (mm10-2020-A) by using spaceranger count.
The resulting four output CLOUPE files were merged into one single dataset by using spaceranger aggr. This new file was then imported into Loupe Browser for gene expression analysis and manual clustering.
Assembly: mm10-2020-A
Supplementary files format and content: .cloupe flie: provides a user friendly interface for customized data exploration when opened with Loupe Browser (10x Genomics). The four WT replicates are included in the same file. Besides the original clustering performed by Space Ranger, it also includes an additional unsupervised cluster category for DEGs comparisons between anatomical regions previously characterized.
Supplementary files format and content: .h5 file: contains a matrix of raw expression data (UMI counts) per gene and tissue-associated barcode that can be used for further processing in R or Python.
Supplementary files format and content: .json file: contains scale factors relating pixels in tissue_hires_image.png to original full resolution tissue image.
Supplementary files format and content: .png file: downsampled version of the image provided for the data analysis.
Supplementary files format and content: .csv file: contains spatial coordinates for every tissue barcode.
Library strategy: Spatial Transcriptomics

source_name: Brain (E13.5)

extract_protocol:
E13.5 mouse embryonic heads were snap-frozen on dry ice immediately after dissection and stored at -80°C until use. Subsequently, the fresh frozen brains were embedded in ice-cold Tissue-Tek O.C.T. (Leica) and sectioned by a cryo-microtome (Leica CM1950). Ten µm thick cryosections were collected on Visium Spatial Gene Expression slides (Visium Spatial Gene Expression Slide & Reagents Kit, 10xGenomics, 1000187). Each section was collected into a 6,5 x 6,5 mm capture area surrounded by a fiducial frame of 8 x 8 mm. A total of 4 sections from 4 different embryonic brains were used. After collection, brain slices were fixed in -20°C methanol and stained following the manufacturer’s instructions (10x Genomics).  The following primary antibodies were used as markers: anti-phosphorylated histone H3 (PH3 mouse, 1:500, Abcam, ab14955), anti-Nestin (chicken, 1:200, NOVUS, NB100-1604), anti-CD31 (rat 1:200, BD Pharmingen, 550274), and DAPI (1:1000, Invitrogen, D1306). Brightfield imaging - to capture the section within the fiducial frame - and immunofluorescent imaging - to detect protein expression - were obtained with Tissue scanner Olympus VS200. Both type of pictures were subsequently used for spatial mapping and tissue reconstruction.
After imaging, the tissue was then processed for permeabilization and cDNA synthesis as described in 10x Genomics Visium Spatial Gene Expression Kit. Briefly, the tissue was permeabilized in order to release mRNA from the cells that subsequently was bound with spatially barcoded oligonucleotides attached in the capture area. A tissue optimization step was performed beforehand and a permeabilization time of 10 min was established.  Barcoded cDNA was then obtained from captured mRNA and subjected to cDNA amplification and library construction. The Visium Spatial Gene Expression library was sequenced by Illumina NovaSeq 6000.

value: Brain (E13.5)

value: WT


title: PeripheralBlood_Case12


title: C4-2B_control_B_19


title: PeripheralBlood_Case11


title: Control 06


title: 93_control_7

source_name: LuCaP 93 PDX


title: PeripheralBlood_Case10


title: Control 05


title: PeripheralBlood_Case18


title: 8C_NR5A2_CR_rep2

value: 8 Cell embryos

value: wild type


title: PeripheralBlood_Case09


title: PeripheralBlood_Case08


title: 49_control_4

source_name: LuCaP 49 PDX


title: PeripheralBlood_Case16


title: Control 02


title: NCI-H660_control_1


title: PeripheralBlood_Case06


title: PeripheralBlood_Case21


title: VC_D12_KO_D25

city: Durham

first: Meng

last: Jiao

address: 905 S lasalle St

institute: Duke University

description: Included 3 VC_D12 samples and 3 COMT-KO_D25 samples

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using SevenBridge Pipeline provided by BD Rhapsody (https://www.sevenbridges.com).
Assembly: mm10
Supplementary files format and content: CSV (comma-separated values)
Supplementary files format and content: multiplexing labels and expression matrix

source_name: brain tumor

growth_protocol: Vector control and COMT-KO CT2A cells were intrancranially injected into C57BL/6J brain for tumor growth.

extract_protocol:
After sorting, single cells were captured using BD Rhapsody platform.
cDNA was generated using BD Rhapsody cDNA library kit and amplified using BD Rhapsody™ Whole Transcriptome Analysis Amplification Kit. Single cell mulitplexing index library was  also generated according to BD Rhapsody manufacture's instructions.

value: brain tumor

tag: cell line

value: glioblastoma

value: vector control

tag: sample tag_information

value: VC_D12 (SampleTag07_mm; SampleTag08_mm; SampleTag09_mm); KO_D25 (SampleTag10_mm; SampleTag11_mm; SampleTag12_mm)


title: PeripheralBlood_Case02

value: sALS


title: Sox2CreER;LSL-Nrf2E79Q/+ esophageal epithelium, PYR-3

city: Camden

first: Xiaoxin

middle: Luke

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

data_processing:
The data quality was assessed with FastQC (version 0.11.5), low-quality reads were removed, and remaining adapter sequences were hard clipped with cutadapt (version 1.12) whenever applicable.
The quality filtered reads were aligned with STAR (version 2.6.90c) to reference genome with its respective RefSeq annotation.
The expression levels of genes were obtained with FeatureCounts (version 1.5.1)
Assembly: mm10

source_name: esophageal epithelium

extract_protocol:
Total RNA was extracted from mouse esophagus using RNeasy Kit (Qiagen; Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: esophageal epithelium

value: PYR


title: PeripheralBlood_Case03

value: peripheral blood


title: VC_D12_KO_D12

description: Included 4 VC_D12 samples and 3 COMT-KO_D12 samples

value: VC_D12 (SampleTag01_mm; SampleTag02_mm; SampleTag03_mm; SampleTag010_mm); KO_D12 (SampleTag04_mm; SampleTag05_mm; SampleTag06_mm)


title: PeripheralBlood_Case05


title: C4-2B_control

value: male

value: prostate cancer

value: vehicle


title: 22RV1_control

source_name: 22Rv1 cell line

value: cell line

value: 96 hours


title: PeripheralBlood_Case04


title: 35CR_control

source_name: LuCaP 35CR PDX

value: in vitro culture of dissociated prostate tumor patient-derived xenograft (PDX) tumor


title: STAT3cKO3

description: all.counts.txt


title: Sox2CreER;LSL-Nrf2E79Q/+ esophageal epithelium, PYR-2


title: P293T_CC

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

data_processing:
data was processed by using the STAR software package based on the published paper.
Genome_build: hg38
Supplementary_files_format_and_content: excel

source_name: human embryonic kidneys

growth_protocol: HEK-293T, HUVEC, and LO2 cells were maintained in DMEM/HIGH GLUCOSE medium with 4500 mg/L Glucose and 4.0 mM L-Glutamine (HyCloneTM, USA), supplemented with 10% fetal bovine serum (LONSERA, Uruguay), and 1% penicillin and streptomycin (HyCloneTM, USA). The cells were incubated in 37°C, 5% CO2, with medium changes every other day.

extract_protocol:
RNA was extracted from cells with BEI-BEI BIOTECH Total RNA Isolation Kit (Zhengzhou, China) and reverse-transcribed by TIANGEN FastKing cDNA Kit (Beijing, China) according to the manufacture’s instructions.
library was prepared by Novogene company.

treatment_protocol: siRNAs were synthesized by Sangon Biotech (Shanghai, China) and transfected with Lipofectamine RNAiMAX (Life Technologies, USA) following the manufacture’s protocols.

value: endothelial cell


title: STAT3cKO6

description: all.counts.txt


title: PeripheralBlood_Case17

source_name: peripheral blood


title: P293T_NC

value: siNC


title: PeripheralBlood_Case07


title: 173.1_control

source_name: LuCaP 173.1 PDX


title: PeripheralBlood_Case01


title: LO2_NC

source_name: human normal liver cells


title: Sox2CreER;LSL-Nrf2E79Q/+ esophageal epithelium, PYR-1


title: LO2_CC


title: 136CR_control

source_name: LuCaP 136CR PDX


title: Sox2CreER;LSL-Nrf2E79Q/+ esophageal epithelium, Vehicle-4

value: Vehicle


title: HUVEC_CC

source_name: human-umbilical-vein-endothelial-cells


title: HASMC,TGF-β,sample 4

first: wu

last: hao

state: shanghai

address: No. 650 Xin Songjiang Road

department: Precision Research Center for Refractory Diseases, Institute for Clinical Research

institute: Shanghai General Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence sequence using porechop
Trimmed sequence reads were mapped to GRCh38 using minimap2
Transcript extraction and normalization were performed using FLAIR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: HASMC

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

extract_protocol:
miR-221 was transfected 24h after HASMC adherence and incubated for 48h
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Differentiation was induced by treatment of 2-day post HASMC cells with 10ug/ml TGF-β or 10ug/ml PDGF (Sigma),

value: HASMC

value: Human Aortic Smooth Muscle Cells

value: WT


title: 208.1_500pM_Romidepsin_11

value: 500pM Romidepsin


title: Sox2CreER;LSL-Nrf2E79Q/+ esophageal epithelium, Vehicle-3

value: esophageal epithelium


title: HASMC,TGF-β,sample 3


title: HUVEC_NC


title: HASMC,TGF-β,sample 2


title: 93_500pM_Romidepsin_8


title: Sox2CreER;LSL-Nrf2E79Q/+ esophageal epithelium, Vehicle-2


title: Sox2CreER;LSL-Nrf2E79Q/+ esophageal epithelium, Vehicle-1


title: HASMC,TGF-β,sample 1


title: HASMC,PDGF,sample 4


title: RNA-Seq_6-3-21-WT-4-PECAM_S10

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and ChIP-Seq reads were mapped using bowtie2
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
ATAC-Seq peak calling was performed using MACS2
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Assembly: mm10
Supplementary files format and content: BigWig (coverage for mapped reads)

source_name: heart

extract_protocol:
RNAs were extracted from isolated cells using the RNeasy Mini kit (Qiagen).
Sequencing libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina).
Samples were sequenced 50 bp paired-ended at 10 million to 20 million reads per replicate on an Illumina HiSeq. 2500 instrument. Library preparation and sequencing were performed at New York University School of Medicine Genome Technology Center. All the reads were mapped to the mouse reference genome (mm10) using the STAR aligner (v2.5.0c)69. Alignments were guided by a Gene Transfer File (GTF, version GRCm38.74) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard/). The read count tables were generated using HTSeq (v0.6.0)70and normalized based on their library size factors using DESeq. 2 (v3.0)71 and differential expression analysis was performed. The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0)72 and bedGraphToBigWig tool (v4), and downstream statistical analyses and generating plots were performed in R environment (v3.1.1) (http://www.r-project.org/).

value: heart

value: cardiac


title: Sox2CreER esophageal epithelium, Vehicle-3


title: HASMC,PDGF,sample 2


title: RNA-Seq_6-3-21-KO-5-PECAM_S14

value: KO


title: Sox2CreER esophageal epithelium, Vehicle-4


title: Sox2CreER esophageal epithelium, Vehicle-2


title: RNA-Seq_6-3-21-WT-4-TMRM_S9


title: RNA-Seq_6-3-21-KO-5-TMRM_S13


title: HASMC,PDGF,sample 3


title: 35CR_1nM_Romidepsin

value: male

value: 1nM Romidepsin


title: C4-2B_1nM_Romidepsin

source_name: LNCaP C4-2B cell line

value: prostate cancer


title: RNA-Seq_6-3-21-KO-1-TMRM_S11


title: 22RV1_1nM_Romidepsin

value: cell line


title: HASMC,PDGF,sample 1


title: RNA-Seq_6-3-21-KO-1-PECAM_S12


title: HASMC,NC mimic, sample 4

value: NC mimic,48h


title: 173.1_500pM_Romidepsin

value: in vitro culture of dissociated prostate tumor patient-derived xenograft (PDX) tumor

value: 96 hours


title: RNA-Seq_5-25-21-WT-2-TMRM_S5


title: 49_500pM_Romidepsin_5


title: Com3

city: Xian

first: Wangyou

last: Feng

address: 169 Changle Western Road

institute: Air Force Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork tab-delimited text file includes raw counts for each Sample
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for RPKM values for each Sample

source_name: ovarian cancer

extract_protocol:
Total RNAs were extracted from tumor tissue of mice using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al. 2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model. (DOI:10.1006/abio.1987.9999).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

value: ovarian cancer

value: CDK4/6i+PD3 antibody


title: NCI-H660_1nM_Romidepsin_2

source_name: NCI-H660 cell line


title: HASMC,NC mimic, sample 3

value: HASMC


title: Com2

value: CDK4/6i+PD2 antibody


title: RNA-Seq_5-25-21-WT-2-PECAM_S6

value: WT


title: 12_153981, PDAC xenografts, AsPC-1_control

city: Bethesda

first: Stefan

last: Ambs

address: Building 37, Room 3050B

institute: NCI

data_processing:
12 mRNA-Seq samples were pooled and sequenced on NovaSeq 6000 SP using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 133 to 164 million pass filter reads with more than 88% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: PDAC cell line xenograft

extract_protocol:
RNA isolation was done using the RNeasy Plus Mini Kit (QIAGEN). Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NovaSeq 6000 SP machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

value: Empty vector (control)


title: HASMC,NC mimic, sample 2

value: Human Aortic Smooth Muscle Cells


title: Com1

value: CDK4/6i+PD1 antibody


title: RNA-Seq_5-25-21-KO-11-TMRM_S7

value: heart

value: cardiac


title: HASMC,NC mimic, sample 1


title: 11_153980, PDAC xenografts, AsPC-1_control


title: a_PD_1_2

value: PD1 antibody


title: a_PD_1_1


title: RNA-Seq_5-25-21-KO-11-PECAM_S8

value: KO


title: HASMC,miR-221 mimic, sample 4

value: miR-221 mimic,48h


title: 10_153977, PDAC xenografts, AsPC-1_control


title: RNA-Seq_5-14-21-WT-6-TMRM_S3


title: Abmea3


title: HASMC,miR-221 mimic, sample 3


title: RNA-Seq_5-14-21-WT-6-PECAM_S4


title: 9_153971, PDAC xenografts, AsPC-1_control


title: Sox2CreER esophageal epithelium, Vehicle-1

value: esophageal epithelium

value: Vehicle


title: HASMC,miR-221 mimic, sample 2


title: 8_153970, PDAC xenografts, AsPC-1_control


title: 7_153968, PDAC xenografts, AsPC-1_control


title: Abmea2


title: 136CR_1nM_Romidepsin

tag: gender

value: male

value: in vitro culture of dissociated prostate tumor patient-derived xenograft (PDX) tumor

value: prostate cancer

value: 1nM Romidepsin


title: RNA-Seq_5-14-21-WT-3-TMRM_S1

tag: cell type


title: HASMC,miR-221 mimic, sample 1

value: HASMC


title: Abmea1

value: ovarian cancer


title: RNA-Seq_5-14-21-WT-3-PECAM_S2

value: WT


title: 6_153975, PDAC xenografts, AsPC-1_SB3

value: SERPINB3-overexpressing transgene


title: PBS2

value: PBS


title: ATAC-Seq_Ebf1_E13-5_WT_6


title: sis2_Delta_A

city: Illkirch-Graffenstaden

first: David

last: Moreno Fortuno

state: Bas Rhin

address: 1 Rue Laurent Fries

country: France

institute: INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE

description: sis2Δ yeast cells

data_processing:
adaptor sequences were trimmed from reads with Cutadapt (Version 3.7), setting a minimum read length of 20nt, as well as a quality cutoff of 20
reads were mapped to reference genome with RNA STAR (Version 2.7.8a)
read counts per gene were summarized with featureCounts (Version 2.0.1), indicating that the RNAseq library was stranded (reverse)
differential gene expression was calculated using limma (Version 3.48.0), using the limma-voom method, filtering lowly expressed genes (less than 0.5 CPM), contrasting sis2_Delta libraries vs BY4741 libraries
Assembly: Saccharomyces cerevisiae genome assembly R64 (sacCer3)
Supplementary files format and content: raw_counts_sis2_rnaseq.tabular: tabular file containing the raw counts corresponding to each gene in each of the libraries
Supplementary files format and content: limma-voom_sis2d-wt.tabular: tabular file containing the limma-voom output of the sis2-wt comparison, including logFC and adjusted pvalue for each gene

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were grown in 15ml of Synthetic complete media with 2% glucose until mid-log phase

extract_protocol:
80 million cells were pelleted and total RNA was extracted with the rYeast total RNA kit (IBI), following the manufacturer instructions
stranded RNA-seq libraries were prepared with the KAPA mRNA HyperPrep Kit, following the manufacturer instructions

value: yeast cells

value: BY4741 sis2_delta::kanMX

value: Synthetic complete media 2% glucose


title: PBS1


title: ATAC-Seq_Ebf1_E13-5_WT_3

value: heart

value: cardiac


title: 4_153966, PDAC xenografts, AsPC-1_SB3


title: BY4741_B

description: BY4741 yeast cells

value: BY4741 wt


title: ATAC-Seq_Ebf1_E13-5_WT_1