title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A4B)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A5A)

status: Public on Mar 02 2022

type: SRA

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

country: Germany

institute: EMBL Heidelberg

description:
bulk RNA-seq
Spatial_SM.RDS

library_source: transcriptomic

data_processing:
10xGenomics' Cellranger software package (v3.0.2) was used for all preprocessing steps for 10xGenomics data.
The basecaller "freeIbis" was used for SmartSeq2 samples (Bioinformatics. 2013 May 1;29(9):1208-9) and "leeHom" was used to trim adapters and merge Illumina sequencing reads afterwards (Nucleic Acids Res. 2014 Oct;42(18):e141). "deML" was used for robust demultiplexing of Illumina sequences for SmartSeq2 samples (Bioinformatics. 2015 Mar 1;31(5):770-2).
Sequencing reads were mapped against the Physarum polycephalum reference transcriptome (Glockner & Marwan 2017 Sci Rep) using STAR with either Cellranger's built in function for 10xGenomics samples or with a local STAR installation for SmartSeq2 samples (Dobin et al. 2013 Bioinformatics).
Gene expression levels were estimated by custom Perl scripts as TPM values for SmartSeq2 samples or based on UMI counts for 10x Genomics samples, respectively.
Genes without an UniProt annotation (Glockner & Marwan 2017 Sci Rep) were removed from all sample/gene matrices and final data sets were loaded and analyzed using Seurat (Stuart et al. 2019 Cell).
Genome_build: Physarum polycephalum transcriptome (Glockner & Marwan 2017 Sci Rep)
Supplementary_files_format_and_content: Matrix and tsv files are cellranger outputs ready to be loaded by Seurat (Stuart et al. 2019 Cell)
Supplementary_files_format_and_content: RDS files are Seurat objects containing all relevant information for Spatial Transcriptomics data files.

molecule: total RNA

organism: Badhamia polycephala

source_name: Plasmodium pieces

growth_protocol: Physarum polycephalum was cultivated as Microplasmodia in a liquid culture and 100-500 uL of microplasmodia suspension was placed on Agar to induce plasmodium network formation as recently described (Bauerle et al. 2017 Journal of Physics D: Applied Physics).

extract_protocol:
SmartSeq2 (Wollny et al. 2016 bioRxiv / Picelli et al. 2013 Nat Methods)
Illumina Nextera

tag: life cycle stage

value: Plasmodium

tag: individual


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A3B)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A3A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A8A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A6A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_B6A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_B2A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A4A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A2A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A2B)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A1B)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A12B)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A1A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_B12A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A11B)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A11A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A10B)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A10A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: Jonagold-3

city: Yangling

first: Zhengyang

last: Zhao

address: Taocheng Road

country: China

institute: Northwest A&F university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Malus domestica

source_name: pulp of Jonagold apple

extract_protocol:
pulps of apple, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Jonagold apple

tag: skin color

value: red

tag: tissue

value: pulp

tag: treatment

value: unbagged


title: Jonagold-1


title: Granny Smith-3

source_name: pulp of Granny Smith apple

value: Granny Smith apple

value: green


title: Granny Smith-1


title: Granny Smith-2


title: Jonagold-2


title: P7F-2_H3K9me3_CUT&Tag

city: Paris

first: Vanessa

last: Ribes

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod

description: CUT&Tag H3K9me3 on human foreskin fibroblasts expressing P7F-Line2

library_source: genomic

data_processing:
Library strategy: CUT&Tag
hg19
CUT&Tag: Trimmomatic (v0.39), BBmap clumpify (v38.87), Bowtie2 (v2.4.1) on hg19 reference genome
CUT&Tag: Peaks were called using SEACR (v1.3) with the parameters: relaxed (threshold 0,000001)
RNAseq: 3' adapter trimming with Trimmomatic: 0.32 (Bolger et al 2014), mapping with bowtie 2.0.5 and Tophat 2.0.6 on NCBI hg38 or hg19 (specified in the SAMPLES section above)
RNAseq: Pairwise differential analysis of RNAseq data was performed using Cufflinks (Fasteris). Genes with a q-value <0.05 after Bengamini-Hochberg correction for multiple-testing were considered to be significant
Genome_build: hg19 or hg38 (specified above)
Supplementary_files_format_and_content: For CUT&Tag, processed files are in bigWig format; for RNAseq, there is two matrix with RPKM for all samples and genes

molecule: genomic DNA

organism: Homo sapiens

source_name: human foreskin fibroblasts

growth_protocol: DMEM, 10% serum, non essential amino acids, penicillin/streptomycin

extract_protocol:
Extraction was performed as in Kaya-Okur et al, following the procedure described in “Bench top CUT&Tag V.2” available on protocols.io (Henikoff lab)
Libraries were prepared as in Kaya-Okur et al, following the procedure described in “Bench top CUT&Tag V.2” available on protocols.io (Henikoff lab)

tag: antibody

value: H3K9me3 Diagenode C15410193

value: Doxycycline for 48 hours


title: HFF_H3K9me3_CUT&Tag

description: CUT&Tag H3K9me3 on human foreskin fibroblasts


title: P3F-3_H3K9me3_CUT&Tag

description: CUT&Tag H3K9me3 on human foreskin fibroblasts expressing P3F-Line3


title: P3F-1_H3K9me3_CUT&Tag

description: CUT&Tag H3K9me3 on human foreskin fibroblasts expressing P3F-Line1


title: P7F-1_H3K9me3_CUT&Tag

description: CUT&Tag H3K9me3 on human foreskin fibroblasts expressing P7F-Line1


title: P7F-3_H3K9me3_CUT&Tag

description: CUT&Tag H3K9me3 on human foreskin fibroblasts expressing P7F-Line3


title: P3F-2_H3K9me3_CUT&Tag

description: CUT&Tag H3K9me3 on human foreskin fibroblasts expressing P3F-Line2


title: Spatial Transcriptomics 384 well plate (Spatial_SM_GER063_A12A)

description:
bulk RNA-seq
Spatial_SM.RDS


title: P7F-1_H3K27me3_CUT&Tag

description: CUT&Tag H3K27me3 on human foreskin fibroblasts expressing P7F-Line1

value: H3K27me3 Diagenode C15410195


title: P7F-3_H3K27me3_CUT&Tag

description: CUT&Tag H3K27me3 on human foreskin fibroblasts expressing P7F-Line3


title: HFF_H3K27me3_CUT&Tag

description: CUT&Tag H3K27me3 on human foreskin fibroblasts


title: P7F-2_H3K27me3_CUT&Tag

description: CUT&Tag H3K27me3 on human foreskin fibroblasts expressing P7F-Line2


title: P3F-3_H3K27me3_CUT&Tag

description: CUT&Tag H3K27me3 on human foreskin fibroblasts expressing P3F-Line3


title: P3F-2_H3K27me3_CUT&Tag

description: CUT&Tag H3K27me3 on human foreskin fibroblasts expressing P3F-Line2


title: RIF,biological rep4

type: RNA

city: Beijing

first: Feiyan

state: Beijing

address: Yaojiayuan Road No.251

institute: Beijing Obstetrics and Gynecology Hospital, Capital Medical University

description: Gene expression data of endometrium from RIF patients

hyb_protocol: Following purification, 10 ug of cRNA were hybridized for  65°C for 17 hours on Arraystar Human LncRNA Microarray. GeneChips were washed and stained in the Slide-staining dish, with slide rack (Thermo Shandon p/n 121).

scan_protocol: GeneChips were scanned using the Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: The data were analyzed with Agilent Feature Extraction Software using Agilent default analysis settings and global scaling as normalization method.

source_name: endometrium from RIF patients

label_protocol: Cyanine-3 cRNA were prepared according to Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)

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

tag: disease state

value: RIF

value: uterus (endometrium)


title: P3F-1_H3K27me3_CUT&Tag

description: CUT&Tag H3K27me3 on human foreskin fibroblasts expressing P3F-Line1


title: RIF,biological rep5


title: control, biological rep2

description: Gene expression data of endometrium from normal women

source_name: endometrium from normal women

value: normal


title: RIF,biological rep2


title: control, biological rep5


title: RIF,biological rep3


title: control, biological rep3


title: mouse_liver_150d_WT_rep3

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

description: Gene expression in liver of mice with Wild type was detected after 150 days

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE V2.0 Microarray(8*60K)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The backgroup correction and scale normalization were performed by functions in the limma package.

organism: Mus musculus

label_protocol: Labeling was performed according to manufacturer's standard protocol.

extract_protocol: Total RNA was extracted from liver by Trizol (Invitrogen, Life Technologies, USA) method following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HBx fragments (WT/M3/Ct) or empty vector were delivered into Fah deficient mice with Sleeping Beauty transposon system at 8-10 weeks of age . After 150 days, the mice were anesthetized with carbon dioxide and sacrificed. All the RNA from their liver or tumor are extracted for gene expression chips.

value: Wild type

value: Liver tissue


title: mouse_liver_150d_M3_rep2

description: Gene expression in liver of mice with mutat 3 was detected after 150 days

source_name: liver of mice with mutant 3 was detected after 150 days

value: mutant 3

value: Liver tumor


title: mouse_liver_150d_WT_rep2

source_name: liver of mice with Wild type was detected after 150 days


title: mouse_liver_150d_WT_rep1


title: RIF,biological rep1


title: mouse_liver_150d_Vector_rep3

description: Gene expression in liver of mice with vector was detected after 150 days

value: vector


title: mouse_liver_150d_M3_rep1


title: control, biological rep1


title: mouse_liver_150d_M3_rep3


title: mouse_liver_150d_Ct_rep2

description: Gene expression in liver of mice with C-terminal truncated mutation was detected after 150 days

value: C-terminal truncated mutation


title: control, biological rep4


title: mouse_liver_150d_Ct_rep3

source_name: liver of mice with C-terminal truncated mutation was detected after 150 days


title: TEC71/knockin#3 (GE1_2_3)

city: WASHINTON

first: IN-KYU

last: KIM

state: DC

address: 3970 RESERVOIR RD NW, New Research Bldg E212

department: Oncology

country: USA

institute: Georgetown University Medical Center

description: Gtf2i T1211A mutated clone #3

hyb_protocol: The cRNA was fragmented and hybridized with G3 Mouse GE 8X60K microarray (Agilent) at 65º C degree for 17 hours

scan_protocol: The Array was washed and scan using the Agilent DNA Microarray Scanner, Model # G2505C following the One-Color Microarray-Based Gene Expression Analysis protocol

data_processing: The data was extracted using Agilent Feature Extraction Software v11.5.11

source_name: Thymic epithelial cell line

label_protocol: 200 ng of total RNA was used to generate fluorescent cRNA using the Agilent Low Input Quick Amp labeling Kit, One-Color

growth_protocol: Cells were cultivated as mono-layer in RPMI-1640 with 10% FBS and 2% penicillin-streptomycin at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared using the RNeasy Plus Mini Kit (QIAGEN) according to manufacturer’s protocol. RNA quality was examined with the Agilent 2100 Bioanalyzer.

tag: cell line

value: thymic epithelial cell line TEC71

tag: origin

value: Medullary thymic epithelial cells

tag: genotype

value: knock-in Gtfi2i T1211A mutation


title: TEC100.4/TFII-I-δmt_Doxycycline- (GE1_2_4)

label_protocol: 200 ng of total RNA was used to generate fluorescent cRNA using the Agilent Low Input Quick Amp labeling Kit, One-Color.

treatment_protocol: Cells were treated with/without doxycycline for 24 hours

value: thymic epithelial cell line TEC100.4

value: Cortical thymic epithelial cells

value: TFII-I-{delta}wt expressing


title: mouse_liver_150d_Vector_rep1

source_name: liver of mice with vector was detected after 150 days


title: TEC100.4/TFII-I-βmt_Doxycycline- (GE1_2_2)

value: TFII-I-{beta}wt expressing


title: TEC71/knockin#1 (GE1_2_1)

description: Gtf2i T1211A mutated clone #1


title: TEC71/knockin#3 (GE1_2_4)

description: Gtf2i T1211A mutated clone #3


title: TEC100.4/TFII-I-βmt_Doxycycline+ (GE1_1_2)

value: TFII-I-{beta}mt overexpression


title: mouse_liver_150d_Vector_rep2


title: TEC100.4/TFII-I-δmt_Doxycycline+ (GE1_1_4)

value: TFII-I-{delta}mt overexpression


title: TEC71/knockin#1 (GE1_2_2)

description: Gtf2i T1211A mutated clone #1


title: TEC100.4/TFII-I-δmt_Doxycycline- (GE1_2_3)


title: TEC100.4/TFII-I-δmt_Doxycycline+ (GE1_1_3)


title: TEC71/knockin control (GE1_1_3)

description: Cas9n and one gRNA transfected

value: knockin control


title: TEC100.4/TFII-I-βmt_Doxycycline- (GE1_2_1)


title: TEC71/knockin#1 (GE1_1_4)

description: Gtf2i T1211A mutated clone #1


title: mouse_liver_150d_Ct_rep1


title: Jejunum - Ctrl - Animal 75

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

institute: INRAE

description: re-analysis of GSM2578884

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to GPL19893 microarray (Agilent 8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 38 out of 47 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 45693 spots out of 61625 were selected. Data were then stored in an ExpressionSet object and normalized by the qsmooth method from the qsmooth R library, considering tissues factor levels to normalize by tissue. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 45692 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: Jejunum

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: 12 crossbred weanling piglets housed in floored indoor pens were used in this study. The piglets were weaned at the age of 28 days and transported to the animal facility of the INRA Research Center in Food Toxicology (Toxalim, Toulouse, France).

extract_protocol: Total RNA was extracted in lysing matrix D tubes (MP Biomedicals, Illkirch, France) containing guanidine thiocyanate-acid phenol (Eurobio, Courtaboeuf, France). Quality of these samples was assessed on Bioanalyzer 2100 (Agilent RNA 6000 Nano Kit, Agilent Technologies, Santa Clara, CA). All samples had a RIN over 7.5.

treatment_protocol: Animals were 6 weeks old at the begining of the study. Animals had ad libitum access to water and feed for the duration of the trial. The first group of pigs was fed with the control diet while the second group was fed with control diet artificially contaminated with 10 ppm Fumonisin B1. They were fed during 4 weeks prior to sacrifice. They were cared for in accordance with the National Institute of Health Guide and the French Ministry of Agriculture for the Care and Use of Laboratory Animals. At the conclusion of the experiment, immediately after electrical stunning, the piglets were sacrificed by exsanguination. A portion of the jejunum, liver, spleen and jejunum with Jejunal Peyers' patches were collected from euthanatized animals, flash-frozen in liquid nitrogen, and stored at -80°C until processed for total RNA extraction.

value: Jejunum

value: Ctrl

tag: animal

tag: washbatch


title: Peyer - FB1 - Animal 74

description: re-analysis of GSM2578906

source_name: Peyer

value: Peyer


title: Peyer - Ctrl - Animal 75

description: re-analysis of GSM2578907


title: Peyer - FB1 - Animal 55

description: re-analysis of GSM2578905


title: Peyer - Ctrl - Animal 73

description: re-analysis of GSM2578904


title: Jejunum - FB1 - Animal 74

description: re-analysis of GSM2578883


title: Jejunum - Ctrl - Animal 71

description: re-analysis of GSM2578880


title: TEC71/knockin control (GE1_1_2)

description: Cas9n and one gRNA transfected


title: TEC71/knockin control (GE1_1_1)

description: Cas9n and one gRNA transfected


title: Jejunum - Ctrl - Animal 73

description: re-analysis of GSM2578881


title: Jejunum - FB1 - Animal 55

description: re-analysis of GSM2578882


title: vip6-065364-23C_R2

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and differentially expressed genes were identified using TopHat2-Cufflinks pipeline
Genome_build: TAIR 10
Supplementary_files_format_and_content: FPKM values for each sample, in excel file

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plant were grown either at 10°C or 23°C under long day conditions on 1/2 strength MS

extract_protocol:
Total RNA was extracted using trizol reagent
mRNA libraries were prepared  1 μg of total RNA using Clontech SMARTer Stranded RNA-Seq Kit, according to the manufacturer's instruction.

treatment_protocol: Growth temperature of 10°C or 23°C

tag: age

value: 23 C grown

tag: growth


title: Jejunum - FB1 - Animal 54

description: re-analysis of GSM2578879


title: Jejunum - Ctrl - Animal 70

description: re-analysis of GSM2578877


title: Peyer - Ctrl - Animal 70

description: re-analysis of GSM2578900


title: Jejunum - Ctrl - Animal 69

description: re-analysis of GSM2578876


title: Jejunum - FB1 - Animal 53

description: re-analysis of GSM2578878


title: Peyer - FB1 - Animal 53

description: re-analysis of GSM2578901


title: vip6-065364-10C_R2

value: 10 C grown


title: vip6-065364-23C_R1


title: vip6-065364-10C_R1


title: Jejunum - FB1 - Animal 52

description: re-analysis of GSM2578875


title: Peyer - Ctrl - Animal 69

description: re-analysis of GSM2578899


title: vip5-062223-23C_R2


title: Peyer - FB1 - Animal 51

description: re-analysis of GSM2578897


title: Spleen - FB1 - Animal 74

description: re-analysis of GSM2578916

source_name: Spleen

value: Spleen


title: vip5-062223-23C_R1


title: Jejunum - Ctrl - Animal 68

description: re-analysis of GSM2578873


title: Peyer - FB1 - Animal 52

description: re-analysis of GSM2578898


title: vip5-062223-10C_R1


title: vip5-062223-10C_R2


title: Spleen - Ctrl - Animal 75

description: re-analysis of GSM2578917


title: Liver - Ctrl - Animal 75

description: re-analysis of GSM2578895

source_name: Liver

value: Liver


title: Jejunum - FB1 - Animal 51

description: re-analysis of GSM2578874


title: Spleen - Ctrl - Animal 73

description: re-analysis of GSM2578915


title: Peyer - Ctrl - Animal 68

description: re-analysis of GSM2578896


title: TEC100.4/TFII-I-βmt_Doxycycline+ (GE1_1_1)


title: Spleen - FB1 - Animal 55


title: Liver - FB1 - Animal 55


title: Liver - Ctrl - Animal 73

description: re-analysis of GSM2578893


title: Liver - FB1 - Animal 74

description: re-analysis of GSM2578894


title: Peyer - FB1 - Animal 54

description: re-analysis of GSM2578902


title: vip4-122755-23C_R1


title: Liver - FB1 - Animal 54

description: re-analysis of GSM2578891


title: Liver - Ctrl - Animal 71

description: re-analysis of GSM2578892


title: vip4-122755-10C_R1


title: vip3-083364-23C_R2


title: Spleen - FB1 - Animal 54

description: re-analysis of GSM2578913


title: vip4-122755-10C_R2


title: vip3-083364-10C_R1


title: vip4-122755-23C_R2


title: vip3-083364-23C_R1


title: vip3-083364-10C_R2


title: Spleen - Ctrl - Animal 71

description: re-analysis of GSM2578914


title: php-008357-23C_R1


title: Spleen - FB1 - Animal 53

description: re-analysis of GSM2578912


title: Liver - Ctrl - Animal 70

description: re-analysis of GSM2578889


title: Spleen - Ctrl - Animal 69

description: re-analysis of GSM2578910


title: Spleen - Ctrl - Animal 70

description: re-analysis of GSM2578911


title: Liver - FB1 - Animal 52

description: re-analysis of GSM2578887


title: Liver - FB1 - Animal 53

description: re-analysis of GSM2578890


title: Spleen - FB1 - Animal 52

description: re-analysis of GSM2578909


title: elf7-046605-23C_R2


title: php-008357-10C_R1


title: php-008357-10C_R2


title: elf7-046605-10C_R2


title: Col-0-10C_R2


title: Col-0-23C_R2


title: Col-0-23C_R1


title: elf7-046605-23C_R1


title: LPS

city: Cambridge

first: Catherine

last: Dulac

state: MA

address: 16 Divinity Ave

institute: Harvard

data_processing:
Sequencing reads were aligned to the mouse genome using 10x Genomics CellRanger pipline
Using the "FindVariableGenes" seurat command, 1500 genes from each sample were collected and the intersect was used to perform canonical correlation analysis (CCA) - 50 components.
The "FindClusters" seurat command was used to generate cell clusters (k=15, resolution=2)
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: CellRanger output

source_name: Brain tissue

extract_protocol:
Tissue was dissected and after filtering steps, nuclei were sorted using DAPI expression
Library was constructed using standard protocols for 10x Genomics single cell sequencing

treatment_protocol: Mice were treated with saline or LPS 2 hours before dissection

tag: strain background

tag: brain area

value: ventral medial preoptic area (VMPO) of the hypothalamus

value: LPS

tag: experiment type

value: Single Nucleus RNA-Seq


title: WTNGNOF8

city: Boston

first: Nora

last: Barrett

address: 60 Fenwood Rd

institute: BWH

data_processing:
demultiplexing and aggregating raw reads using Picard pipeline (Broad Institute)
Concatenated FASTQ files across lanes. Broad Institute runs across 4 lanes.
Pseudo-alignment of counts using Kallisto (v46.1)
Genome_build: GRCm39(GCA_000001635.9)
Supplementary_files_format_and_content: .tsv files (abundance)

source_name: Airway Epithelial Cells

extract_protocol:
1000 cells from each group were sorted from naïve murine trache and lysed in 5uL TCL buffer
SmartSeq2 cell population protocol
RNA-Seq, 2x38bp on NextSeq500

tag: epc subset

value: DIFFERENTIATED EPCS

value: WT

tag: batch

tag: Sex

value: F


title: WTNGNOF7


title: WTNGNOF6


title: Liver - FB1 - Animal 51

description: re-analysis of GSM2578886

tag: tissue


title: php-008357-23C_R2

tag: treatment


title: Col-0-10C_R1


title: Saline

value: Saline


title: Spleen - Ctrl - Animal 68


title: Liver - Ctrl - Animal 68

description: re-analysis of GSM2578885


title: WTNGNOF4


title: Liver - Ctrl - Animal 69

description: re-analysis of GSM2578888


title: Spleen - FB1 - Animal 51

description: re-analysis of GSM2578908


title: WTNGNOF3


title: WTNGNOF2


title: WTNGNOF1


title: WTLONOF8

value: BCAM LO


title: elf7-046605-10C_R1


title: WTLONOF7


title: WTLONOF5


title: WTLONOF6


title: WTLONOF4


title: WTLONOF3


title: WTNGNOF5


title: WTLONOF2


title: WTHINOF7

value: BCAM HI


title: WTHINOF8


title: WTHINOF6


title: Lung_ID 152X (validation set)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Primary microarray data were collected using BeadStudio v3 software package. Raw data were log2-transformed and normalized after removal of the Mouse negative control [Mouse Universal RNA Reference; see sample EI29_UMR in non-normalized_data.txt] using the robust spline normalization method, implemented in the lumi R/Bioconductor package.

label: Biotin

source_name: Frozen section_Lungs_MDA-MB-231 orthotopic xenograft_ID 152X

label_protocol: RNA was reverse transcribed, labeled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit (Life Technologies).

growth_protocol: MDA-MB-231 cells were propagated in vitro and injected in the mammary fat pad of immunocompromised female mice.

extract_protocol: CTC/DTC were isolated using immunoaffinity- and size-based enrichment protocols; tumor nodules and organs were explanted after animal sacrifice; parental cells were collected from in vitro cultures. RNA samples were obtained using kits for mRNA isolation (oligo(dT)-coated magnetic particles) or total RNA extraction (paramagnetic bead-based chemistry). Mouse Universal Reference is a commercially available mixture of total RNAs from a collection of adult (female and male) mouse tissues.

treatment_protocol: (Not applicable)

tag: mouse strain

tag: mouse gender

value: female

tag: material sampling conditions

value: OCT-embedded frozen sections

tag: sample class

value: Lung

tag: tissue source

value: Solid lesions

tag: fraction

value: Total RNA


title: Lung_ID 155X (validation set)

source_name: Frozen section_Lungs_MDA-MB-231 orthotopic xenograft_ID 155X


title: Lung (d)_ID 147X (validation set)

source_name: Distal frozen section_Lungs_MDA-MB-231 orthotopic xenograft_ID 147X

value: Lung (d)


title: Axillary Lymph-Node (c)_ID 152X (validation set)

source_name: Frozen section_Controlateral Axillary Lymph-Nodes_MDA-MB-231 orthotopic xenograft_ID 152X

value: Lymph-node

value: Axillary Lymph-Node (c)


title: Inguinal Primary Tumor (d)_ID 155X (validation set)

source_name: Distal frozen section_Inguinal Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 155X

value: Primary tumor

value: Inguinal Primary Tumor (d)


title: Axillary Lymph-Node (c)_ID 147X (validation set)

source_name: Frozen section_Controlateral Axillary Lymph-Node_MDA-MB-231 orthotopic xenograft_ID 147X


title: WTHINOF5

tag: genotype


title: Axillary Primary Tumor (p)_ID 152X (validation set)

source_name: Proximal frozen section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 152X

value: Axillary Primary Tumor (p)


title: Axillary Lymph-Node (h)_ID 152X (validation set)

source_name: Frozen section_Homolateral Axillary Lymph-Node_MDA-MB-231 orthotopic xenograft_ID 152X

value: Axillary Lymph-Node (h)


title: Axillary Lymph-Node (c)_ID 155X (validation set)

source_name: Frozen section_Controlateral Axillary Lymph-Nodes_MDA-MB-231 orthotopic xenograft_ID 155X


title: Axillary Primary Tumor (d)_ID 155X (validation set)

source_name: Distal frozen section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 155X

value: Axillary Primary Tumor (d)


title: Axillary Primary Tumor (p)_ID 155X (validation set)

source_name: Proximal frozen section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 155X


title: WTHINOF2

value: WT

value: F


title: WTHINOF1


title: Axillary Primary Tumor (d)_ID 152X (validation set)

source_name: Distal frozen section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 152X


title: Lung (p)_ID 147X (validation set)

source_name: Proximal frozen section_Lungs_MDA-MB-231 orthotopic xenograft_ID 147X

value: Lung (p)


title: Inguinal Primary Tumor (d)_ID 147X (validation set)

source_name: Distal frozen section_Inguinal Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 147X


title: F1-RNA-48-4-P5-DMSO

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
MouseF1F3E18pTestisRNAseq_filtered_normalized_counts.corrected.2.xlsx
Normalized_mERV_counts_F1_germline.corrected.2.txt

data_processing:
FASTQ files were filtered through trimGalore! to remove low-quality (Q < 30) reads and adaptor sequences.
FASTQ files were mapped using the STAR aligner to obtain BAM files.
R/Bioconductor package Rsubreads was used to count reads on exons of mRNA transcripts.
The mRNA raw counts were normalized by the negative binominal trimmed mean of M-values (TMM) method using R/Bioconductgor package edgeR.
Differentially expressed mRNA transcripts were identified using the generalized linear model likelihood ratio test implemented by edgeR.
mERV counting, normalization, and identification of differentially expressed mERVs from the BAM files were performed using the ERVmap pipeline with modification for the use of the mm10 mouse genome reference sequence.
MBDseq data analysis from the BAM files was performed using the R/Bioconductor package QSEA.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq (mRNA): an EXCEL spreadsheet of normalized mRNA counts.
Supplementary_files_format_and_content: RNAseq (mouse endogenous retroviruses: mERVs): text files of normalized mERV counts.
Supplementary_files_format_and_content: MBDseq: text files of normalized counts of genomic DNA fragments enriched by the MBD precipiation (simialr to ChIP-seq procedure).

source_name: E18.5 fetus

extract_protocol:
Genomic DNA and total RNA were isolated from FACS-enriched germ cells and somatic cells of E18.5 fetal testes using the QIAGEN AllPrep Micro kit.
RNA-seq Illumina libraries were contructed using Takara Bio's SMART-seq mRNA-seq kit, which involve cDNA synthesis using an oligo-dT primer. MBD-seq libraries were constructed using ThermoFisuer MethylMiner kit.
RNA-seq [targeting mRNA and endogenous retrovirus RNA containing poly(A) tail]; MBD-seq [using a Methyl Binding Domain protein to enrich DNA fragments containing methylated CpG dinucleotides]

treatment_protocol: Pregnant F0 dams of the OG2 mouse strain were gestationally exposed to 50 nM tributyltin or DMSO.

tag: strain

tag: cells

value: P5 germ cells

tag: f0 exposure

value: DMSO


title: WTLONOF1

value: BCAM LO


title: Axillary Primary Tumor (p)_ID 147X (validation set)

source_name: Proximal frozen section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 147X

value: female

value: OCT-embedded frozen sections


title: F1-RNA-48-4-P4-DMSO

value: P4 germ cells


title: MDA-MB-231_Passage 36 (validation set)

source_name: MDA-MB-231 in vitro culture_Passage 36

value: Not applicable

value: frozen cell pellet

tag: cell type

value: epithelial, breast cancer cell

value: Parental cell line

value: Total RNA


title: WTHINOF3

source_name: Airway Epithelial Cells

value: BCAM HI


title: F1-RNA-47-5-P5-TBT

value: TBT


title: F1-RNA-47-5-P4-TBT


title: F1-RNA-47-4-P5-TBT


title: F1-RNA-47-4-P4-TBT


title: F1-RNA-47-3-P5-TBT


title: WTHINOF4


title: F1-RNA-47-3-P4-TBT


title: Inguinal Primary Tumor (d)_ID 152X (validation set)

source_name: Distal frozen section_Inguinal Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 152X

value: Primary tumor

value: Inguinal Primary Tumor (d)

value: Solid lesions


title: F1-RNA-47-1-P4-TBT


title: Axillary Primary Tumor (d)_ID 147X (validation set)

source_name: Distal frozen section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 147X

value: Axillary Primary Tumor (d)


title: Circulating Tumor Cells_ID 147X (validation set)

source_name: Blood_ MDA-MB-231 orthotopic xenograft_ID 147X

value: tumor cells isolated from fresh blood

value: CTC

value: Circulating Tumor Cells

value: Disseminated cells

value: mRNA


title: Circulating Tumor Cells_ID 155X (validation set)

source_name: Blood_ MDA-MB-231 orthotopic xenograft_ID 155X

value: female

value: Disseminated Tumor Cells


title: Circulating Tumor Cells_ID 152X (validation set)

source_name: Blood_ MDA-MB-231 orthotopic xenograft_ID 152X


title: F1-RNA-45-5-P5-TBT

value: P5 germ cells


title: F1-RNA-45-5-P4-TBT

value: P4 germ cells


title: PD-GW-4

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

data_processing:
Sequenced reads were sligned to mm10 geome using STAR/2.6.0b.
Reads per gene were counted with HT-Seq/0.11.0.
Read counts were normalized with R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads for the  genes

source_name: pancreatic tissue_KC/PD mice fed GW501516 diet

growth_protocol: The KC and KC/Pd mice on a GW501516 diet (50 mg/kg) were euthanized (n=3 per group). The pancreta were harvested in Trizol and then stored at -80C freezer till further analysis

extract_protocol:
Total RNA was isolated from the mouse pancreatic tissues using the RNeasy Mini/Micro Kit (Qiagen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500ng of total RNA for the construction of sequencing libraries.
Illumina-compatible mRNA libraries were constructed using the TruSeq RNA sample prep kit v2 (Illumina, Inc). 500ng of total RNA were enriched for Poly-A mRNA using Oligo-dT magnetic beads. The resulting Poly-A mRNA was fragmented to a median size of 150 bp using divalent cations. Randomly primed first- and second-strand synthesis was then performed to create double-stranded cDNA. The ends of the double-stranded cDNA fragments were repaired, 5′-phosphorylated, and 3′-A tailed, and then the Illumina-specific Y-shaped indexed adapters were ligated. The adaptor-ligated fragments were then purified and enriched by 7 cycles of PCR amplification. The amplified library was then quantified by quantitative PCR using a library quantification kit (KAPA Biosystems) and assessed for size distribution using the Bioanalyzer system (Agilent Technologies). Eight libraries were multiplexed and sequenced on an Illumina HiSeq3000 instrument using the 75-bp paired-end format. After sequencing, BCL files were converted into “.fastq.gz” files, and individual sample libraries were de-multiplexed using CASAVA 1.8.2 with no mismatches.

treatment_protocol: The KC and KC/Pd mice at 6-8 weeks were fed a GW diet (50 mg/kg) for 3 days and then euthanized (n=3 per group).

tag: genotype/variation

value: KC/PD

tag: diet

value: GW501516 diet

value: pancreatic tissues


title: PD-GW-3


title: MDA-MB-231_Passage 35 (validation set)

source_name: MDA-MB-231 in vitro culture_Passage 35

value: Not applicable

value: frozen cell pellet

value: epithelial, breast cancer cell

value: Parental cell line


title: Lung_ID 70X (discovery set)

data_processing: Primary microarray data were collected using BeadStudio v3 software package. Raw data were log2-transformed and normalized after removal of the Mouse negative control [Mouse Universal RNA Reference; see sample CG96_UMR in non-normalized_data.txt] using the robust spline normalization method, implemented in the lumi R/Bioconductor package.

source_name: Section_Lungs_MDA-MB-231 orthotopic xenograft_ID 70X

value: OCT-embedded frozen sections

value: Lung

value: Solid lesions

value: Total RNA


title: Lung_ID 69X (discovery set)

source_name: Section_Lungs_MDA-MB-231 orthotopic xenograft_ID 69X


title: Inguinal Lymph-Node (c)_ID 70X (discovery set)

source_name: Section_Controlateral Inguinal Lymph-Node_MDA-MB-231 orthotopic xenograft_ID 70X

value: Lymph-node

value: Inguinal Lymph-Node (c)


title: Lung_ID 68X (discovery set)

source_name: Section_Lungs_MDA-MB-231 orthotopic xenograft_ID 68X

value: female


title: Axillary Lymph-Node (c)_ID 70X (discovery set)

source_name: Section_Controlateral Axillary Lymph-Node_MDA-MB-231 orthotopic xenograft_ID 70X

value: Axillary Lymph-Node (c)


title: MDA-MB-231_Passage 37 (validation set)

source_name: MDA-MB-231 in vitro culture_Passage 37


title: WT-GW-5

source_name: pancreatic tissue_KC mice fed GW501516 diet

value: KC


title: PD-GW-2


title: F1-RNA-45-4-P4-TBT

source_name: E18.5 fetus

value: P4 germ cells

value: TBT


title: Inguinal Primary Tumor (d)_ID 70X (discovery set)

source_name: Distal section_Inguinal Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 70X

value: Primary tumor

value: Inguinal Primary Tumor (d)


title: Inguinal Lymph-Node (c)_ID 68X (discovery set)

source_name: Section_Controlateral Inguinal Lymph-Node_MDA-MB-231 orthotopic xenograft_ID 68X


title: Axillary Lymph-Node (c)_ID 68X (discovery set)

source_name: Section_Controlateral Axillary Lymph-Node_MDA-MB-231 orthotopic xenograft_ID 68X


title: Axillary Primary Tumor (p)_ID 70X (discovery set)

source_name: Proximal section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 70X

value: Axillary Primary Tumor (p)


title: WT-GW-4

value: GW501516 diet

value: pancreatic tissues


title: F1-RNA-45-3-P5-TBT

value: P5 germ cells


title: F1-RNA-45-3-P4-TBT


title: Axillary Primary Tumor (d)_ID 70X (discovery set)

source_name: Distal section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 70X

value: OCT-embedded frozen sections

value: Axillary Primary Tumor (d)


title: F1-RNA-47-1-P5-TBT


title: AEG-1-WT hepatocytes, CP775146-treated rep1

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
All sequencing reads were quality controlled using FastQC v0.11.2. Illumina adapters were trimmed using Cutadapt v1.9.dev2, replicates were merged and aligned with their reference genome (UCSC mouse genome build mm10) using subread-align v1.4.6-p4.
The BAM files from alignment were processed using featureCounts v1.4.6-p4 to obtain the counts per gene in all samples. Mus_musculus.GRCm38.83.gtf gene definition file was used.
The differential expression analysis was performed using edgeR v3.18.1. Genes having counts per million less than 2 in all samples were excluded. Differentially expressed genes were defined using p-value <0.01 and FDR-corrected p-value <0.1 cutoffs
All bioinformatics analyses were conducted in R/Bioconductor computing environment v3.4.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: Hepatocytes

growth_protocol: AEG-1-L24K/L25H mice were created in C57BL/6/J background using CRISPR/Cas9 technology. AEG-1-L24K/L25H heterozygote x heterozygote mating was performed to generate AEG-1-WT and AEG-1-L24K/L25H littermates. Mice were fed regular chow. For high fat diet (HFD) experiments, 8 weeks old mice were fed a high fat and cholesterol containing diet (Harlan; TD. 88137) for 20 weeks. This diet contains 0.2% total cholesterol and 21% total fat by weight which provides 42% kcal (4.5 kcal/gm). All animal studies were approved by the Institutional Animal Care and Use Committee at Virginia Commonwealth University.

extract_protocol:
Total RNA was extracted using the QIAGEN miRNAeasy Mini Kit (QIAGEN, Valencia, CA). cDNA preparation was done using ABI cDNA synthesis kit (Applied Biosystems, Foster City, CA). Real-time polymerase chain reaction (RT-PCR) was performed using an ABI ViiA7 fast real-time PCR system and Taqman gene expression assays according to the manufacturer’s protocol (Applied Biosystems, Foster City, CA)
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and subject to two rounds of sequencing on Illumina HiSeq3000 platform
RNA-Seq libraries were pooled together to aim about 25-40M read passed filtered reads per sample.

treatment_protocol: Primary mouse hepatocytes were isolated and cultured. The hepatocytes were used immediately after isolation in house and were mycoplasma free as detected by Mycoplasma Detection Kit (ThermoFisher). Hepatocytes were treated with a PPAR-agonist CP775146 (2.5 M) for 24 h, with lipopolysaccharide (LPS, 100 ng/mL) for 24 h and with epidermal growth factor (EGF, 50 ng/mL) for 15 min.


title: Axillary Primary Tumor (p)_ID 69X (discovery set)

source_name: Proximal section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 69X

value: Solid lesions


title: F1-RNA-44-3-P4-DMSO

value: DMSO


title: AEG-1-WT hepatocytes, Untreated rep1

value: Untreated


title: F1-RNA-45-4-P5-TBT


title: AEG-1-WT hepatocytes, Untreated rep2


title: WT-GW-2


title: F1-RNA-44-1-P5-DMSO


title: AEG-1-WT hepatocytes, Untreated rep3


title: AEG-1-L24K/L25H hepatocytes, CP775146-treated rep3


title: AEG-1-WT hepatocytes, CP775146-treated rep3


title: Axillary Primary Tumor (d)_ID 69X (discovery set)

source_name: Distal section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 69X

value: Total RNA


title: F1-RNA-44-1-P4-DMSO


title: AEG-1-L24K/L25H hepatocytes, CP775146-treated rep1


title: AEG-1-L24K/L25H hepatocytes, Untreated rep3


title: AEG-1-L24K/L25H hepatocytes, CP775146-treated rep2


title: Inguinal Primary Tumor (d)_ID 69X (discovery set)

source_name: Distal section_Inguinal Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 69X

value: female


title: F1-RNA-43-5-P5-DMSO


title: Inguinal Primary Tumor (d)_ID 68X (discovery set)

source_name: Distal section_Inguinal Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 68X


title: F1-RNA-43-5-P4-DMSO


title: AEG-1-WT hepatocytes, CP775146-treated rep2


title: Axillary Lymph-Node (c)_ID 69X (discovery set)

source_name: Section_Controlateral Axillary Lymph-Nodes_MDA-MB-231 orthotopic xenograft_ID 69X

value: Lymph-node

value: Axillary Lymph-Node (c)


title: Mexosome

city: SEOUL

first: HYOSUK

address: 5, Hwarang-ro 14-gil, Seongbuk-gu

institute: Korea Institute Science and Technology

data_processing:
High-throughput sequences were produced by NextSeq 500 system as way of single-end 75 sequencing (Illumina).
Sequence reads were mapped by Bowtie2 software tool in order to obtain bam file (alignment file).
Read counts mapped on differentially mature miRNA sequence were extracted from the alignment file using Bedtools (v2.25.0) and Bioconductor using R (version 3.2.2) statistical programming language (R development Core Team, 2016).
Read counts were used to determine the expression levels of miRNAs.
For miRNA target study, miRWalk 2.0 was performed.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: Exosome

extract_protocol:
The beating colonies were picked at designated day and total RNA was isolated using Trizol reagent (Thermo Scientific). RNA quality was assessed by the RNA 6000 Pico Chip for exosomal miRNA sequencing (Agilent Technologies).
NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs) was used for exosomal miRNA sequencing according to the manufacturer’s instructions.
exosomal microRNA sequencing

value: Mexosome


title: AEG-1-L24K/L25H hepatocytes, Untreated rep2


title: MEF exo

value: MEF exo


title: AEG-1-L24K/L25H hepatocytes, Untreated rep1


title: F1-RNA-43-4-P4-DMSO

value: P4 germ cells


title: nCMs

data_processing:
High-throughput sequences were produced by NextSeq 500 system as way of single-end 75 sequencing (Illumina).
Sequence reads were mapped by Bowtie2 software tool in order to obtain bam file (alignment file).
Quantile normalization method was used for comparison between samples.
Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Hierarchical cluster analyses were carried out with Euclidean distance correlation as the distance measurement with average linkage. Clusters and heat maps were visualized via MeV 4.9.0.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: neonatal cardiomyocytes

extract_protocol:
The beating colonies were picked at designated day and total RNA was isolated using Trizol reagent (Thermo Scientific). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip for Quan-seq 3’ mRNA sequencing (Agilent Technologies).
For the construction of library, Quant-Seq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) was used for gene expression analysis.
Quant-seq 3’ mRNA sequencing

value: nCMs


title: F3-RNA-9-P6-TBT

value: P6 somatic cells

value: TBT


title: F1-RNA-43-4-P5-DMSO


title: Axillary Primary Tumor (d)_ID 68X (discovery set)

source_name: Distal section_Axillary Tumor Nodule_MDA-MB-231 orthotopic xenograft_ID 68X

value: Primary tumor


title: MDA-MB-231_Passage 37 (discovery set)

source_name: MDA-MB-231 cells_in vitro culture_Passage 37

value: Not applicable

value: frozen cell pellet

value: epithelial, breast cancer cell

value: Parental cell line


title: MDA-MB-231_Passage 36 (discovery set)

source_name: MDA-MB-231 cells_in vitro culture_Passage 36


title: MDA-MB-231_Passage 35 (discovery set)

source_name: MDA-MB-231 cells_ in vitro culture_Passage 35


title: MEF

source_name: mouse embryonic fibroblasts

value: MEF


title: Embryosome

value: Embryosome


title: F3-RNA-9-P4-TBT

source_name: E18.5 fetus


title: F3-RNA-9-P5-TBT

value: P5 germ cells


title: iCMs at day 30

value: iCMs

tag: time point

value: day 30


title: iCMs at day 15

value: day 15


title: mESC exo

value: mESC exo


title: Circulating Tumor Cells_ID 70X (discovery set)

source_name: Blood_ MDA-MB-231 orthotopic xenograft_ID 70X

value: female

value: tumor cells isolated from fresh blood

value: CTC/DTC

value: Circulating Tumor Cells

value: Disseminated cells

value: mRNA


title: MaelKD_Siwi-piRNA_rep2

city: Tokyo

first: Yurika

last: Namba

state: --- Select a state ---

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences, Graduate School of Science

country: Japan

institute: The University of Tokyo

data_processing:
smRNA-seq: Analysis of PIWI-associated small RNA sequences were performed essentially as described previously (Iwasaki et al., 2017) with some modifications. After removal of adaptor sequences by cutadapt (version 3.1) (Martin et al., 2011), 22-35 nt reads were mapped to the genome using bowtie (version 1.3.0) (Langmead et al., 2009) in random and multiple counting methods not allowing mismatch. Genome mapped reads were processed using SAMtools (H. Li et al., 2009) and BEDTools (Quinlan and Hall, 2010) and used for further analysis with normalized by the number of the genome mapped reads. The genome mapped reads were aligned to the transposon library using bowtie in random and multiple counting methods allowing up to two mismatches.
RNA-seq: Analysis of RNA sequences were performed essentially as described previously (Iwasaki et al., 2017) with some modifications. After cleaning and removal of adaptor sequences by using Rcorrector, TranscriptomeAssemblyTools, and TrimGalore, 36- nt reads were mapped to the genome and to the transposon library using STAR (version 2.7.9a) (Dobin et al., 2012) in random and multiple counting methods allowing up to 4% of mismatches relative to read length. Mapped reads were processed using SAMtools (Li et al., 2009) and BEDTools (Quinlan and Hall, 2010).
Genome_build: silkworm reference genome obtained from Silkbase (Genome assembly; Nov. 2016) (Kawamoto et al., 2019)
Supplementary_files_format_and_content: smRNA-seq: Tab-separated text files include normalized count of reads mapped to each transposon sequences in antisense direction.
Supplementary_files_format_and_content: RNA-seq: Tab-separated text files include normalized count of reads mapped to each transposon sequences in sense direction.

organism: Bombyx mori

source_name: BmN4 cells

growth_protocol: BmN4 cells were cultured at 26°C in EX-CELL 420 Serum-Free Medium for Insect cells (Sigma) supplemented 10% fetal bovine serum (FBS) (Equitech-Bio) and penicillin-streptomycin-glutamine (Gibco).

extract_protocol:
Dynabeads Protein G (Invitrogen) and anti-Flag antibodies (Sigma, M2 mouse monoclonal F3165) were incubated in T-PBS containing 0.02% Tween at room temperature. BmN4 cells were lysed at 4°C with immunoprecipitation (IP) buffer [30 mM HEPES-KOH (pH 7.3), 150 mM KOAc, 2 mM Mg(OAc)2, 5 mM DTT, 0.1% NP-40, 2 μg/mL pepstatin, 2 μg/mL leupeptin, and 0.5% aprotinin] containing RNasin Plus Ribonuclease Inhibitor (Promega). After the cell debris was removed by centrifugation, the cell lysates were incubated with antibodies-conjugated beads for 1 h at 4°C. After protein-antibody binding, the beads were washed once with IP buffer containing 500 mM NaCl and then extensively with IP buffer. The protein-bound RNAs were purified from the beads by proteinase K (Roche) treatment, phenol/CHCl3 treatment, and precipitated with ethanol. RNAs of 22–35 nt in length were separated on denaturing (6 M urea) PAGE and used to generate RNA libraries.
PIWI-associated small RNA libraries were prepared from Luc, Mael, and Ago3 KD BmN4 cells with the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) and sequenced using Illumina MiSeq to obtain 51 nt single reads.

treatment_protocol: To knockdown (KD) endogenous proteins, BmN4 cells (1 × 106 cells) were transfected with 500 pmol of siRNA duplex in 100 μL of EP buffer [137 mM NaCl, 5 mM KCl, 0.5 mM Na2HPO4 and 2.1 mM HEPES-KOH (pH 7.1)] using program T-001 of Nucleofector 2b device (Lonza). siRNA transfection was performed again to raise the RNAi effect. After KD, the cells were cultured for total 10 days and harvested. Luciferase (Luc) siRNA was used as a control. The sequences of siRNAs are summarized in Table S1. To exogenously express proteins, BmN4 cells (6 × 105 cells) were transfected with 2-8 μg of plasmids and 5-20 μL of FuGENE HD transfection reagent (Promega) in 100 μL of complete medium without FBS and added 10% FBS into cell medium 3 h later. After transfection, the cells were cultured for 2 days and harvested.

value: Cultured cell derived from ovary

tag: cell line

tag: knockdown

value: siMael

tag: molecule subtype

value: small RNA

tag: rip antibody

value: anti-FLAG


title: MaelKD_Siwi-piRNA_rep1


title: H23_LCS3_6hr_rep2

city: Vancouver

first: William

last: Lockwood

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: BC Cancer

hyb_protocol: Samples were then hybridized onto arrays (Affymetrix), washed, and scanned according to the manufacturer’s instructions at the Microarray Core Facility at National Human Genome Research Institute.

scan_protocol: GeneChips were scanned according to manufacturer's instructions at the Microarray Core Facility at National Human Genome Research Institute.

data_processing: Affymetrix GeneChip Command Console software was used to summarize probe cell intensity data and generate CEL files for subsequent analysis according to the manufacturer's instructions by the Microarray Core Facility at National Human Genome Research Institute.

label: biotin

source_name: H23, LCS3, 6hr

label_protocol: Targets were prepared using the GeneChip WT Terminal Labeling and Controls kit (Affymetrix) combined with the Ambion WT Expression kit (Ambion) according to the manufacturer’s protocols

growth_protocol: H1650 and H23 cells were cultured at 37℃ with 5% CO2 in humidified atmosphere in RPMI-1650 with 10% FBS.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen). Sample quality was assessed using an Agilent Bioanalyzer and subsequent sample preparation, array hybridization, and data acquisition was performed by the National Human Genome Research Institute’s Microarray Core facility.

treatment_protocol: H1650 and H23 cells were grown in six-well plates, treated with 3 μM LCS3 or DMSO in duplicate for 3, 6 or 12 h.

tag: treatment

value: 3uM LCS3

tag: treatment time


title: Disseminated Tumor Cells_ID 69X (discovery set)

source_name: Bone marrow_ MDA-MB-231 orthotopic xenograft_ID 69X

tag: mouse strain

tag: mouse gender

tag: material sampling conditions

value: tumor cells isolated from fresh bone marrow

tag: sample class

value: Disseminated Tumor Cells


title: H23_LCS3_3hr_rep2

source_name: H23, LCS3, 3hr


title: H23_LCS3_6hr_rep1


title: F3-RNA-8-P5-TBT

tag: strain

value: P5 germ cells

value: TBT


title: Circulating Tumor Cells_ID 69X (discovery set)

source_name: Blood_ MDA-MB-231 orthotopic xenograft_ID 69X

tag: tissue source

tag: fraction


title: F3-RNA-8-P4-TBT

tag: cells

value: P4 germ cells

tag: f0 exposure


title: Ago3KD_Siwi-piRNA_rep2

tag: cell type


title: Circulating Tumor Cells_ID 68X (discovery set)

source_name: Blood_ MDA-MB-231 orthotopic xenograft_ID 68X


title: Ago3KD_Siwi-piRNA_rep1


title: F3-RNA-8-P6-TBT

value: P6 somatic cells


title: F3-RNA-7-P5-TBT


title: LucKD_Siwi-piRNA_rep1

value: siLuc


title: H23_DMSO_6hr_rep2

source_name: H23, DMSO, 6hr

value: 0.1% DMSO


title: H23_DMSO_3hr_rep2

source_name: H23, DMSO, 3hr


title: F3-RNA-6-P6-TBT


title: H23_DMSO_3hr_rep1


title: H23_DMSO_6hr_rep1


title: H23_LCS3_3hr_rep1


title: H23_LCS3_12hr_rep1


title: H1650_LCS3_6hr_rep2


title: H1650_LCS3_6hr_rep1


title: F3-RNA-6-P5-TBT


title: F3-RNA-7-P4-TBT


title: F3-RNA-7-P6-TBT


title: F3-RNA-6-P4-TBT


title: H1650_LCS3_12hr_rep2


title: LucKD_Siwi-piRNA_rep2


title: C4-2B-ENZR cell as control, repl3

city: Jinan

first: Fei

middle: fei

last: Sun

state: Shandong

address: WENHUAXI road

institute: Department of Pathology, Qilu Hospital, Shandong University

description:
NC-3
This sample is of C4-2B-ENZR transfected with siRNA of negative control.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RUVBL1.txt: Tab-delimited text file includes FPKM values for each Sample.

growth_protocol: Cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

extract_protocol:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: C4-2B-ENZR cells transfected with siRNA are referred to as C4-2B-ENZR_NC and C4-2B-ENZR_siRUVBL1.

value: prostate cancer cell line

tag: genotype/variation

value: negative control


title: C4-2B-ENZR cell with RUVBL1 knockdown, rep1

description:
siRUVBL1-1
This sample is of C4-2B-ENZR transfected with siRNA of RUVBL1.

tag: cell line

value: RUVBL1 knockdown


title: H1650_LCS3_3hr_rep2


title: C4-2B-ENZR cell with RUVBL1 knockdown, rep3

description:
siRUVBL1-3
This sample is of C4-2B-ENZR transfected with siRNA of RUVBL1.


title: H1650_LCS3_3hr_rep1


title: H23_LCS3_12hr_rep2


title: H1650_LCS3_12hr_rep1


title: H1650_DMSO_6hr_rep2

source_name: H1650, DMSO, 6hr


title: F3-RNA-5-P6-TBT


title: H1650_DMSO_6hr_rep1


title: C4-2B-ENZR cell with RUVBL1 knockdown, rep2

description:
siRUVBL1-2
This sample is of C4-2B-ENZR transfected with siRNA of RUVBL1.


title: F3-RNA-5-P5-TBT


title: H1650_DMSO_3hr_rep2

source_name: H1650, DMSO, 3hr


title: H1650_DMSO_3hr_rep1


title: NCU10K control siRNA repeat 3

city: Adelaide

first: Quenten

last: Schwarz

state: South Australia

address: Bradley Building, North Terrace

country: Australia

institute: University of South Australia

hyb_protocol: Standard protocols for Affymetrix GeneChip® Mouse Gene 1.0 ST Array. Arrays were hybridised 17 hours at 45C, then stained using the Affymetrix GeneChip™ Fluidics Station 450.

scan_protocol: Standard protocols for Affymetrix GeneChip3000 7G slide scanner

data_processing: Data processed using Partek Genomics Suite 6.5 (RMA method with quantile normalisation and mean probeset summarisation

source_name: Neural crest cell line NCU10K treated with control siRNA

label_protocol: cDNA was prepared from 300ng total RNA using Affymetrix GeneChip WT cDNA Synthesis and Amplification Kit. Biotin labelling was performed using Affymetrix GeneChip WT Terminal Labelling Kit.

growth_protocol: Grown in DMEM + 10% FCS + penicillin / streptomycin

extract_protocol: Total RNAs prepared using Qiagen Rneasy microcolumns

treatment_protocol: siRNA transfected with RNAimax

value: control siRNA


title: NCU10K control siRNA repeat 2


title: F3-RNA-4-P5-DMSO

value: DMSO


title: C4-2B-ENZR cell as control, repl2

description:
NC-2
This sample is of C4-2B-ENZR transfected with siRNA of negative control.


title: NCU10K Nedd4 siRNA repeat 3

source_name: Neural crest cell line NCU10K treated with Nedd4 siRNA

value: Nedd4 siRNA


title: NCU10K Nedd4 siRNA repeat 2


title: F3-RNA-5-P4-TBT


title: C

city: Harbin

first: shang

last: haitao

address: Haping road

department: ultrasound department

institute: Harbin Medical University Cancer Hospital

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data(clean reads) were obtained by removing reads  containing adapter, reads on containing ploy-N and low quality reads from raw data.  At the same time, Q20, Q30 and GC content of the clean data were calculated. All the  down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using bowtie2 v2.2.8 and  paired-end clean reads were aligned to the reference genome using HISAT2(Langmead,  B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set  as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela  Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow  algorithm as well as an optional de novo assembly step to assemble and quantitate full-  length transcripts representing multiple splice variants for each gene locus.
CNCI (Coding-Non-Coding-Index) (v2) profiles adjoining nucleotide triplets to  effectively distinguish protein-coding and non-coding sequences independent of  known annotations (Sun et al. 2013). We use CNCI with default parameters.
CPC (Coding Potential Calculator) (0.9-r2) mainly through assess the extent and  quality of the ORF in a transcript and search the sequences with known protein  sequence database to clarify the coding and non-coding transcripts (Kong et al.  2007). We used the NCBI eukaryotes' protein database and set the e-value ‘1e-10’  in our analysis.
Phast (v1.3) is a software package contains much of statistical programs, most used in  phylogenetic analysis (Siepel, et al. 2005), and phastCons is a conservation scoring and  identificating program of conserved elements. We used phyloFit to compute  phylogenetic models for conserved and non-conserved regions among species and then  gave the model and HMM transition parameters to phyloP to compute a set of  conservation scores of lncRNA and coding genes.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in  each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the  FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of  exon per million fragments mapped, calculated based on the length of the fragments  and reads count mapped to this fragment.
The Ballgown suite includes functions for interactive exploration of the transcriptome  assembly, visualization of transcript structures and feature-specific abundances for  each locus, and post-hoc annotation of assembled features to annotated features(Alyssa  C. Frazee et al.2014). Transcripts with an P-adjust <0.05 were assigned as differentially  expressed. Cuffdiff provides statistical routines for determining differential expression in digital  transcript or gene expression data using a model based on the negative binomial  distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned  as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes or lncRNA  target genes were implemented by the GOseq R package, in which gene length bias  was corrected(Young, M. D.et al.2010). GO terms with corrected Pvalue less than 0.05  were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the  biological system(Kanehisa, M.et al.2008), such as the cell, the organism and the  ecosystem, from molecular-level information, especially large-scale molecular datasets  generated by genome sequencing and other high-throughput experimental technologies  (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical  enrichment of differential expression genes or lncRNA target genes in KEGG  pathways(Mao, X.et al.1995).
PPI analysis of differentially expressed genes was based on the STRING database,  which known and predicted Protein-Protein Interactions. For the species existing in the  database, we construct the networks by extract the target gene list from the database;  Otherwise, Blastx (v2.2.28) was used to align the target gene sequences to the selected  reference protein sequences, and then the networks was built according to the known  interaction of selected reference species.
Genome_build: homo_sapiens_Ensembl_94
Supplementary_files_format_and_content: NOT PROVIDED

source_name: Huh7 cells

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample  preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA  Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol  precipitation.
Subsequently, sequencing libraries were generated using the rRNA-  depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®  (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was  carried out using divalent cations under elevated temperature in NEBNext First Strand  Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random  hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA  synthesis was subsequently performed using DNA Polymerase I and RNase H. In the  reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated  to prepare for hybridization. In order to select cDNA fragments of preferentially  150~200 bp in length, the library fragments were purified with AMPure XP system  (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used  with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at  95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were  purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.

value: hepatocellular carcinoma


title: C4-2B-ENZR cell as control, repl1

description:
NC-1
This sample is of C4-2B-ENZR transfected with siRNA of negative control.


title: A98V_aTc0_2

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

institute: Hokkaido University

data_processing:
The reads were mapped on a reference genome comprised of E. coli ER2796 (GenBank accession no. CP009644.1) and lambda DNA (GenBank accession no. J02459) using BMap (34). From the methylation level of the lambda DNA, the bisulfite conversion efficiency was calculated to be 99% for each sample. For detection of target recognition sequence of BatIM, cytosines mapped with more than 20 reads and detected with equal to or more than 80% of reads methylated were assumed as methylated.
Supplementary_files_format_and_content: Tab delimited files with columns of replicon ID, nucleotide position, strand, number of methylated read, and number of mapped reads.

organism: Escherichia coli

source_name: Lab culture of Escherichia coli

growth_protocol: O/N culture of each strain in LB medium were 100 fold diluted in fresh LB medium. After three hours of growth, anhydrotetracycline (aTc) were added in vairous concentration and grew for an hour before genomic DNA extraction.

extract_protocol:
Genomic DNA were extracted by QIAamp PowerFecal DNA Kit (QIAGEN).
The preparation of libraries for shotgun bisulfite sequencing was conducted based on the post-bisulfite adaptor tagging (PBAT) strategy (33) using a modified protocol described recently (tPBAT protocol version 1.0) (34). First, genomic DNA spiked with unmethylated lambda DNA was bisulfite-treated, and random priming using the DNA as a template was performed. After purification of the product DNA with solid-phase reversible immobilization (SPRI) using AMPure XP (Beckman Coulter), the DNA was served for adaptor tagging with TACS-ligation (34). The library structure was completed with two rounds of primer extension using universal and indexing primers. The library was purified with SPRI again, then the molar concentration of the library was determined with a real-time PCR-based method.

tag: genotype

value: ER2796 pZE31-tetR-batIM (A98V)

value: aTc 0 ng/ml, 1 hour


title: D

source_name: Huh7 was treated using targeted nanobubbles mediated LND with sonodynamic therapy


title: WT_aTc100_2

value: ER2796 pZE31-tetR-batIM (WT)

value: aTc 100 ng/ml, 1 hour


title: A98V_aTc0_1


title: WT_aTc100_1


title: F3-RNA-4-P6-DMSO

source_name: E18.5 fetus


title: WT_aTc100_3


title: A98V_aTc100_1


title: F3-RNA-3-P5-DMSO

value: P5 germ cells


title: NCU10K control siRNA repeat 1


title: NCU10K Nedd4 siRNA repeat 1


title: A98V_aTc0_3


title: A

source_name: HepG2 cells


title: A98V_aTc100_2


title: WT_aTc1_3

value: aTc 1 ng/ml, 1 hour


title: F3-RNA-4-P4-DMSO

value: P4 germ cells


title: D25 organoid with RA

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

institute: MCRI

data_processing:
10x library demultiplexing.
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output files: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Human iPSC kidney organoid

growth_protocol: Takasato et al., 2015 (PMID: 26444236) kidney organoid protocol, modified to use E6 base media as in Howden et al., 2019 (PMID: 30858339).

extract_protocol:
Organoids were harvested by pooling 3 organoids, cutting into small pieces with a scalpel blade and dissociating in 1mL Accutase at 37 degrees Celsius, pipetting every 3 minutes. The incubation was stopped after 15 minutes by placing on ice. The cell solution was passed through a 40um cell strainer into a FACS tube and then washed with 2mL E6 (room temperature). FACS tubes were spun (1500 rpm, 3 minutes) and resuspended in 500uL of E6 media. Samples were cell counted and tested for viability and diluted to the required density for the sequencing protocol (300-1000 cells per uL) in E6 media. The cells were then transported to the sequencing facility on ice (30 minutes total).
Chromium Single Cell Library kit V2.
Illumina HiSeq HT chemistry - 100bp paired end sequencing.

treatment_protocol: Kidney organoids generated as per above protocols, with the addition of 5uM all-trans retinoic acid at day 12 (day 7+5) which continued until the end of organoid culture.

value: iPSC-derived kidney organoid

value: retinoic acid at day 12

tag: day of differentiation


title: F3-RNA-3-P6-DMSO

value: P6 somatic cells


title: WT_aTc1_1


title: F3-RNA-3-P4-DMSO


title: WT_aTc0_2


title: F3-RNA-2-P6-DMSO


title: WT_aTc1_2


title: alys-1

city: Shanghai

first: Chen

last: Zhu

address: 300 Feng Lin Road, Shanghai 200032, China

institute: CAS Center for Excellence in Molecular Plant Sciences

description: For mRNA-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample(mRNA-seq)

source_name: Arabidopsis seedling

extract_protocol:
Total RNA was extracted from each tissue using  TRIzol® Reagent (Plant RNA Purification Reagent for  plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library.
Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library

tag: tissue

value: seedling

tag: developmental stage

value: 12 day

tag: eco-type

value: Columbia

value: alys


title: WT_aTc0_1

tag: treatment


title: alys-2

description: For mRNA-seq


title: Control_aTc100_2

value: ER2796 pZE31-tetR


title: A98V_aTc100_3


title: SSR1-2

description: For mRNA-seq

value: SSR1 overexpression


title: B

source_name: HepG2 was treated using targeted nanobubbles mediated LND with sonodynamic therapy

value: hepatocellular carcinoma


title: Control_aTc100_1


title: Control_aTc1_3


title: Col-1

description: For mRNA-seq

value: WT


title: WT_aTc0_3

value: aTc 0 ng/ml, 1 hour


title: Control_aTc100_3


title: Control_aTc1_1


title: Control_aTc1_2


title: F3-RNA-1-P6-DMSO

value: DMSO


title: Col-2

description: For mRNA-seq


title: F3-RNA-1-P5-DMSO


title: F3-MBD-8-P6-TBT

data_processing:
Library strategy: MBD-seq
FASTQ files were filtered through trimGalore! to remove low-quality (Q < 30) reads and adaptor sequences.
FASTQ files were mapped using the STAR aligner to obtain BAM files.
R/Bioconductor package Rsubreads was used to count reads on exons of mRNA transcripts.
The mRNA raw counts were normalized by the negative binominal trimmed mean of M-values (TMM) method using R/Bioconductgor package edgeR.
Differentially expressed mRNA transcripts were identified using the generalized linear model likelihood ratio test implemented by edgeR.
mERV counting, normalization, and identification of differentially expressed mERVs from the BAM files were performed using the ERVmap pipeline with modification for the use of the mm10 mouse genome reference sequence.
MBDseq data analysis from the BAM files was performed using the R/Bioconductor package QSEA.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq (mRNA): an EXCEL spreadsheet of normalized mRNA counts.
Supplementary_files_format_and_content: RNAseq (mouse endogenous retroviruses: mERVs): text files of normalized mERV counts.
Supplementary_files_format_and_content: MBDseq: text files of normalized counts of genomic DNA fragments enriched by the MBD precipiation (simialr to ChIP-seq procedure).

value: TBT


title: F3-RNA-1-P4-DMSO


title: Control_aTc0_1


title: Control_aTc0_3


title: SSR1-1

description: For mRNA-seq


title: F3-MBD-9-P6-TBT


title: F3-RNA-2-P4-DMSO


title: F3-RNA-2-P5-DMSO

value: P5 germ cells


title: F3-MBD-6-P6-TBT


title: Control_aTc0_2


title: F3-MBD-7-P6-TBT


title: F3-MBD-5-P6-DMSO


title: F3-MBD-4-P6-DMSO


title: nmCAF-rep3

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

institute: CHA Bundang Medical Center

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1. gProcessedSignal has been used as gProcessedSignal has been used as normalized signal intensity.normalized signal intensity

source_name: Cancer-associated fibroblasts

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: RNA of CAF was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: CAF from metastatic ovarian cancer (mCAF) or CAF from non-metastatic ovarian cancer (nmCAF)

tag: disease

value: ovarian serous carcinoma tissue

tag: group

value: non-metastatic


title: mCAF-rep3

value: metastatic


title: PDGFb KO_  4wk post-MI

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Data were analyzed using CellRanger software 6.1.2 and a pipeline that produces sparse numerical matrices for each sample, with gene-level counts of unique molecular identifiers (UMI) identified for all single cells passing default quality control metrics.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger output filtered_feature_bc_matrix in .tar

source_name: Single nuclei derived from MI tissues, 4 week post-MI surgery

extract_protocol:
Mice were euthanized and perfused with PBS supplemented with EDTA, and hearts were harvested. Infarcted tissue was dissected under a stereomicroscope.  The nuclei was released by homogenization with Pestle A and B (Sigma #D8938-1SET). Nuclei suspension was washed with PBS-0.01% BSA and filtered with series of 40 um strainers.
Cells were treated and analyzed following a manufacturer 3' GEX library protocol (10x Genomics) and single-cell RNA-seq.
single nuclei RNA-Seq

treatment_protocol: MI was induced by ligation of left anterior descending (LAD) coronary artery (6-8 weeks old). MI tissue were collected 2 or 4 weeks after MI surgery.

value: Cdh5-Cre; PDGFRb fl/fl

tag: stress

value: myocardial infarction (MI)

value: Heart

value: myocardial infarction (MI)-associated cells

tag: time

value: nuclei RNA


title: F3-MBD-3-P6-DMSO

tag: strain

value: P6 somatic cells


title: WT_  4wk post-MI

value: PDGFRb fl/fl

tag: fraction


title: nmCAF-rep1


title: F3-MBD-2-P6-DMSO

tag: cells


title: nmCAF-rep2


title: mCAF-rep2


title: WT_  2wk post-MI

source_name: Single nuclei derived from MI tissues, 2 week post-MI surgery


title: F3-MBD-12-P6-TBT

tag: f0 exposure


title: mCAF-rep1


title: PDGFb KO_  2wk post-MI

tag: cell type


title: F3-MBD-11-P6-TBT


title: F3-MBD-10-P6-TBT


title: 49_R270H_Homo

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: 5 Gy-irradiated mouse

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software (HCS) HD 3.4.0 and Real-Time Analysis (RTA) v2.7.7 software. The bcl2fastq conversion software was used for sample demultiplexing and FASTQ conversion.
RNA-seq data was analyzed using a HISAT-Cufflinks pipeline. De-multiplexed raw sequence reads (FASTQ format) were mapped to the reference mouse genome assembly (GRCm/mm10) using HISAT ((hierarchical indexing for spliced alignment of transcripts). Mapped reads were then passed onto Cufflinks for transcript assembly and quantitation of gene- and transcript isoform expression as FPKM (fragments per kilobase of transcript per million mapped fragments). Subsequently, FPKM expression values were normalized with Cufflinks tools (e.g., Cuffquant, Cuffnorm).
Processed data are Cufflinks-Cufffnorm output files and contain Gene_Symbol, Ensembl ID, FPKM values, and FPKM status.
Genome_build: Dec. 2011, GRCm/mm10
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol, Ensembl ID, FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

source_name: prostate gland

extract_protocol:
Total cellular RNA was isolated from mouse prostate samples using the TRIzol Reagent (Invitrogen) and a modified protocol that incorporates an additional extraction with phenol/chloroform/isoamyl alcohol (25:24:1, pH 4.3) followed by an additional clean-up step with an RNeasy spin column (Qiagen).
Indexed, directional RNA-Seq libraries were prepared from 100 ng total RNA using the TruSeq Stranded mRNA (Illumina, San Diego, CA) according to the manufacturer’s standard protocol.

treatment_protocol: Wild type, heterozygous, and homozygous Trp53 R270H mice that were ~3 months old were exposed to 5 Gy whole body irradiation to activate and stabilize p53, consequently increasing its expression. Mouse prostates were harvested 6 hours post-irradiation and snap-frozen for subsequent RNA extraction and transcriptome profiling with RNA-Sequencing (RNA-Seq) analysis. All animal procedures were reviewed and approved by the UC Davis Institutional Animal Care and Use Committee (IACUC).

tag: mouse model

value: Trp53 R270H

tag: trp53 genotype

value: homozygous

value: 5 Gy irradiation


title: 47_R270H_Homo

description: 5 Gy-irradiated mouse

tag: genotype


title: F3-MBD-1-P6-DMSO


title: F1-RNA-9-P6-TBT

data_processing:
FASTQ files were filtered through trimGalore! to remove low-quality (Q < 30) reads and adaptor sequences.
FASTQ files were mapped using the STAR aligner to obtain BAM files.
R/Bioconductor package Rsubreads was used to count reads on exons of mRNA transcripts.
The mRNA raw counts were normalized by the negative binominal trimmed mean of M-values (TMM) method using R/Bioconductgor package edgeR.
Differentially expressed mRNA transcripts were identified using the generalized linear model likelihood ratio test implemented by edgeR.
mERV counting, normalization, and identification of differentially expressed mERVs from the BAM files were performed using the ERVmap pipeline with modification for the use of the mm10 mouse genome reference sequence.
MBDseq data analysis from the BAM files was performed using the R/Bioconductor package QSEA.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq (mRNA): an EXCEL spreadsheet of normalized mRNA counts.
Supplementary_files_format_and_content: RNAseq (mouse endogenous retroviruses: mERVs): text files of normalized mERV counts.
Supplementary_files_format_and_content: MBDseq: text files of normalized counts of genomic DNA fragments enriched by the MBD precipiation (simialr to ChIP-seq procedure).


title: FF10_Sample1_008LCM481_FPKM

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar St

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale School of Medicine

description: FFPE tissues

data_processing:
Basecalls using Torrent Suite Software Version 5.0.5
mRNA-seq reads were aligned to hg19 using a two stage mapping strategy. In the first stage, tophat version 2.0.12 was used with annotation and the --b2-very-sensitive option. In the second stage, bowtie 2.0.5 was used with local alignment and the --very-sensitive option.
Cufflinks was used to calculate Fragments per Kilobase of exon per Million (FPKM) values.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with FPKM gene counts for every gene and every sample

source_name: lung

extract_protocol:
Laser capture microdissection was performed upon formalin fixed paraffin embedded (FFPE) control non-fibrotic lung tissue (alveolar septae (n=10)) and UIP/IPF FFPE lung tissue (myofibroblast foci, (n=10) and adjacent non-affected alveolar septae (n=10)).
Regions of interest (non-fibrotic control lung tissue alveolar septae, IPF lung tissue fibroblast foci or adjacent non-affected alveolar septae) were selected using a drawing tool on the Leica Laser Microdissection software, and then cut with a laser beam into separate RNase-free tubes containing RecoverAll Total Nucleic Acid digestion buffer (Ambion). RNA isolation was performed using Micro Filter Cartridges from RNAqueous-Micro Total RNA Isolation Kit (Invitrogen) according to the manufacturer’s instructions.
15ng of total RNA was used to make cDNA libraries using Ion Ampli‐Seq‐transcriptome human gene expression kit (Ion Torrent, Life Technologies).
An Ion Torrent Proton Sequencer (RNA-Seq) was used to produce ~20 million single-end ~100bp reads/sample.

value: IPF fibrobalst foci

value: IPF lung


title: FF5_010Chip7_FPKM

description: FFPE tissues


title: 37_R270H_Het

description: 5 Gy-irradiated mouse

value: heterozygous


title: FF8_Sample4_006LCM480_FPKM

description: FFPE tissues


title: 40_R270H_Het

description: 5 Gy-irradiated mouse


title: FF1_008Chip6_FPKM

description: FFPE tissues


title: FF2_009Chip6_FPKM

description: FFPE tissues


title: Donor2_Mix_G1_1000X_rep2

type: genomic

city: Uppsala

first: Polina

last: Lizunkova

address: Norbyvägen 18A

department: Organismal Biology

country: Sweden

institute: Uppsala University

hyb_protocol: Standard Illumina EPIC Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio normalised
The Matrix signal intensities_GEO.txt contains Unmethylated and methylated signal intensities

label: Cy3 - Cy5

source_name: genomic DNA from donor 2 hMSCs

label_protocol: Standard Illumina EPIC Protocol

growth_protocol: The cells were cultured in growth media consisting of DMEM (Gibco) supplemented with 10 % Fetal Bovine Serum (FBS; Gibco), 1 % penicillin-streptomycin (Gibco), and 2 % L-glutamine (Gibco) at 37 °C in an incubator with 5% (v/v) CO2.

extract_protocol: The DNA was extracted from hMSCs cultured in 6-well plates using AllPrep DNA/RNA micro kit (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: The hMSCs were seeded in 6 well-plates (VWR 734-2323). Growth media was replaced by treatment media (TM) consisting of DMEM supplemented with 10 % charcoal stripped FBS (DCC, Gibco), 1 % penicillin-streptomycin (Gibco), and 2% L-glutamine (Gibco) two-three days before treatment start (day 0). On day 0, the treatments started and continued for 21 days. The Mix G1 exposure media (EM) consisted of TM supplement-ed with Mix G1 in DMSO at 10 nM (0.1X), 100 nM (1X), 1 µM (10X), 10 µM (100X), and 100 µM (1000X). Control medium (CM) contained TM supplemented with DMSO in a ratio of 1:1000.  As positive control, adipogenic induction media (AIM), consisting of TM supplemented with 1 ug/mL insulin (Sigma-Aldrich), 0.25 uM dexamethasone (Sigma-Aldrich) and 0.5 mM 3-isobutyl-1-methylxanthine (IBMX, Sigma-Aldrich), was used.  EM/CM/AIM were changed twice a week

tag: donor

value: Human mesenchymal stem cells


title: Donor2_Mix_G1_10X_rep3


title: Donor1_Mix_G1_1000X_rep3

source_name: genomic DNA from donor 1 hMSCs


title: 39_WT

description: 5 Gy-irradiated mouse

value: wild type


title: FF3_012Chip7_FPKM

description: FFPE tissues

tag: tissue


title: Donor2_Mix_G1_1000X_rep1


title: Donor2_Mix_G1_1X_rep1


title: F1-RNA-7-P6-TBT

city: Charlestown

first: Toshihiro

address: Building 149 - 7th Floor, 13th Street

institute: MGH Cancer Center

extract_protocol:
Genomic DNA and total RNA were isolated from FACS-enriched germ cells and somatic cells of E18.5 fetal testes using the QIAGEN AllPrep Micro kit.
RNA-seq Illumina libraries were contructed using Takara Bio's SMART-seq mRNA-seq kit, which involve cDNA synthesis using an oligo-dT primer. MBD-seq libraries were constructed using ThermoFisuer MethylMiner kit.
RNA-seq [targeting mRNA and endogenous retrovirus RNA containing poly(A) tail]; MBD-seq [using a Methyl Binding Domain protein to enrich DNA fragments containing methylated CpG dinucleotides]

value: TBT


title: Donor2_Mix_G1_1000X_rep3


title: FF16_008Chip4_FPKM

description: FFPE tissues


title: Donor2_Control_rep1

value: control sample


title: F1-RNA-8-P6-TBT


title: Donor2_Mix_G1_1X_rep3


title: M1218e9h-Rbfox2CKO-2

city: Galveston

first: Muge

middle: N

last: Kuyumcu-Martinez

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

data_processing:
Illumina bcl2fastq2-v2.20 was used for base calling
Reads aligned to the mouse GRCm38 genome using STAR version 2.5.4 and the 2-pass mapping method following the STAR manual guidelines
Read counts obtained from the STAR quantMode GeneCounts feature using the Gencode vM16 annotation file.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited file of raw read counts output by the STAR aligner

source_name: Mouse embryonic heart tissue

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Strand specific RNA polyA+ libraries were prepared from 1 ug of total RNA using Illumina's True_Seq RNA kit using standard protocols
RNA-Seq, paired end 75 bases on an Illumina NextSeq 550.

tag: phenotype

value: Rbfox2 homozygous knock-out using Nkx2-5 cre


title: FF14_006Chip3_FPKM

description: FFPE tissues


title: M1218e8h-Rbfox2CKO-1


title: E10_Sample3_012LCM481_FPKM

description: FFPE tissues

value: IPF alveolar septae


title: Donor2_Mix_G1_10X_rep1


title: Donor2_Mix_G1_1X_rep2


title: Donor2_Control_rep3


title: Donor2_Mix_G1_10X_rep2


title: F1-RNA-4-P6-DMSO

last: Shioda

value: DMSO


title: Donor1_Mix_G1_1X_rep2


title: E8_Sample2_010LCM481_FPKM

description: FFPE tissues


title: M1218e6h-Rbfox2HetCKO-2

value: Rbfox2 heterozygous knock-out using Nkx2-5 cre


title: Donor1_Mix_G1_1000X_rep2


title: E5_016Chip8_FPKM

description: FFPE tissues


title: F1-RNA-6-P6-TBT


title: Donor1_Mix_G1_1X_rep3


title: F1-RNA-3-P6-DMSO


title: M1218e5h-Rbfox2HetCKO-1


title: E1_011Chip6_FPKM

description: FFPE tissues


title: M1218e3h-Control-2

value: Control


title: Donor1_Mix_G1_10X_rep3


title: Donor2_Control_rep2


title: Donor1_Mix_G1_1000X_rep1


title: E2_013Chip6_FPKM

description: FFPE tissues


title: Donor1_Mix_G1_10X_rep1


title: E18_015Chip5_FPKM

description: FFPE tissues


title: E3_015Chip8_FPKM

description: FFPE tissues


title: E15_012Chip4_FPKM

description: FFPE tissues


title: E16_013Chip5_FPKM

description: FFPE tissues


title: Donor1_Mix_G1_10X_rep2


title: FF18_010Chip5_FPKM

description: FFPE tissues


title: F1-RNA-2-P6-DMSO

value: P6 somatic cells


title: F1-RNA-11-P6-TBT


title: Donor1_Control_rep3


title: M1218e2h-Control-1


title: Donor1_Mix_G1_1X_rep1


title: Donor1_Control_rep1


title: F1-RNA-10-P6-TBT


title: E14_011Chip4_FPKM

description: FFPE tissues


title: C18_Sample3_003LCM480_FPKM

description: FFPE tissues

value: control alveolar septae

value: control lung


title: Donor1_Control_rep2


title: C16_Sample1_001LCM480_FPKM

description: FFPE tissues


title: F1-RNA-1-P6-DMSO


title: C17_Sample2_002LCM480_FPKM

description: FFPE tissues


title: C31_Sample4_002LCM481_FPKM

description: FFPE tissues


title: C33_004Chip3_FPKM

description: FFPE tissues


title: F1-RNA-12-P6-DMSO


title: C32_003Chip3_FPKM

description: FFPE tissues


title: 41_WT

description: 5 Gy-irradiated mouse

value: Trp53 R270H


title: 131_VD_17

city: Canyon

first: Matthew

middle: Adam

last: Scott

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

description:
mRNA count data
AWO22587-0156-131-VD-17

hyb_protocol: NanoString nCounter PrepStation

scan_protocol: NanoString SPRINT Profiler set to high resolution (550)

data_processing: NanoString nSolver Analysis Software v4.0 was utilized for quality assessment and raw gene count accession. Four housekeeping, six positive spike-in, and eight negative control genes were used for intersample count normalization.

organism: Bos taurus

source_name: Whole blood

label_protocol: NanoString nCounter mRNA Bovine Custom Panel

extract_protocol: Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit

tag: treatment group

value: Healthy

tag: study

tag: location

value: MS

tag: animal info

value: Steer

tag: vaccinated

tag: dewormed


title: 112_PS_19

description:
mRNA count data
AWO22587-0157-112-PS-19

value: Bull


title: 136_MH_19

description:
mRNA count data
AWO22587-0155-136-MH-19


title: C14_014Chip8_FPKM

description: FFPE tissues

tag: disease


title: 146_VD_17

description:
mRNA count data
AWO22587-0154-146-VD-17


title: F1-MBD-6-TBT

tag: strain


title: C13_013Chip7_FPKM

description: FFPE tissues


title: F1-MBD-5-TBT

tag: cells


title: C11_011Chip7_FPKM

description: FFPE tissues


title: F1-MBD-4-TBT

tag: f0 exposure


title: 159_VD_17

description:
mRNA count data
AWO22587-0151-159-VD-17


title: 183_VD_17

description:
mRNA count data
AWO22587-0153-183-VD-17


title: 163_VD_17

description:
mRNA count data
AWO22587-0152-163-VD-17


title: F1-MBD-3-DMSO


title: F1-MBD-2-DMSO


title: 257_TA_20

description:
mRNA count data
AWO22587-0149-257-TA-20

value: Heifer


title: F1-MBD-7-TBT


title: HCT116 cells - transfected with empty vector_rep3

city: Kunming

first: Li

middle: ru

last: hong

address: 245 Huancheng East Road

institute: Yan 'an Hospital affiliated to Kunming Medical University

data_processing:
removing reads containing adapters
removing reads containing polyA and polyG
removing reads containing more than 5% of unknown nucleotides (N)
removing low quality reads containing more than 20% of low quality (Q-value≤20) bases
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced
Genome_build: We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome
Supplementary_files_format_and_content: clean Data and Gene FPKM value

source_name: Human colon cancer cell

growth_protocol: Human colon cancer cell HCT116 was purchased from the Culture bank of Chinese Academy of Sciences (Shanghai).  Briefly, the HCT116 cell line was maintained in McCoy's 5A medium (iCell, China) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin and streptomycin (Gibco).  Cell lines were placed in a humidified incubator containing 5% CO2 and cultured at 37℃.

extract_protocol:
The total RNA of NC group and overEXP group was extracted with TRIzol reagent (Invitrogen, CA, USA) following the manufacturer’s instructions.
RNA sequencing was performed on an Illumina NovaSeq 6000 system of LC Sciences (USA).

treatment_protocol: In simple terms, NC group consisted of normal cultured HCT116 cells, and overEXP group consisted of constructed HCT116 cells stably transfected with EPHX2

tag: cell line

tag: treatment

value: untreated


title: HCT116 cells -  stably transfected with overexpressed EPHX2_rep1


title: HCT116 cells - transfected with empty vector_rep1


title: HCT116 cells -  stably transfected with overexpressed EPHX2_rep3


title: HCT116 cells -  stably transfected with overexpressed EPHX2_rep2


title: FF15_007Chip3_FPKM

description: FFPE tissues

value: IPF fibrobalst foci

value: IPF lung


title: 150_VD_17

description:
mRNA count data
AWO22587-0150-150-VD-17


title: F1-MBD-1-DMSO