title: Maize inbred line Q6-21DAP-Grain-rep2


title: Maize inbred line Q7-21DAP-Grain-rep3

status: Public on Oct 01 2022

type: SRA

city: Yangling

first: Zhou

middle: Jian

last: Qu

state: Shaanxi

address: No.3 Taicheng Road

country: China

institute: Northwest A&F University

library_source: transcriptomic

data_processing:
RNA sequencing was performed on an Illumina NovaSeq-PE150 system
Sequencing reads were quality trimmed using Trimmomatic (v0.38; http://www.usadellab.org/cms/?page=trimmomatic)
Sequencing reads were aligned to the maize B73 reference genome (RefGen_v4; ftp://ftp.ensemblgenomes.org/pub/plants/release-41/fasta/zea_mays/dna/) sequences assembly using HISAT2 (version 2.0.5)
The stringtie (version 1.3.5; https://ccb.jhu.edu/software/stringtie/) was used to normalization and estimation of gene expression level in terms of FPKM (fragments per kilobase per million)
Differentially expressed genes in time-series samples were identified using edgeR (Robinson et al., 2010)
Genome_build: Zea mays v4
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Zea mays

source_name: Maize grain

growth_protocol: Eight maize inbred lines were planted during the summer of 2018 at the maize breeding testing ground of the Northwest A&F University in Yangling, Shaanxi Province (NT, 108°02', 34°16'). The field experiment was conducted using a completely randomized design with two replications. Each inbred lines were planted in a 4 m row, with 4.5 m long and a distance of 0.6 m between adjacent rows. The planting density was 75,000 plants/ha, and following standard irrigation and fertilization management throughout the whole developmental period. The ears were bagged prior to silk emergence and then subjected to manual self-pollination.

extract_protocol:
The RNA of three biological replicates of the samples was extracted separately from each sample using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
A total of 2 μg RNA was used for library construction with an Illumina NEBNext® UltraTM RNA Library Prep Kit (Illumina Co, Ltd), according to the manufacturer’s instructions.

tag: tissue

value: Grain

tag: Stage

value: 21 day after pollination (DAP)

tag: inbred line


title: Maize inbred line Q6-21DAP-Grain-rep1


title: Maize inbred line Q6-56DAP-Grain-rep1

value: 56 day after pollination (DAP)


title: Maize inbred line Q6-42DAP-Grain-rep1

value: 42 day after pollination (DAP)


title: Maize inbred line Q5-56DAP-Grain-rep2


title: Maize inbred line Q5-56DAP-Grain-rep3


title: Maize inbred line Q5-56DAP-Grain-rep1


title: Maize inbred line Q5-49DAP-Grain-rep3

value: 49 day after pollination (DAP)


title: Maize inbred line Q5-49DAP-Grain-rep2


title: Maize inbred line Q5-42DAP-Grain-rep1


title: Maize inbred line Q5-42DAP-Grain-rep3


title: Maize inbred line Q5-42DAP-Grain-rep2


title: Maize inbred line Q5-35DAP-Grain-rep2

value: 35 day after pollination (DAP)


title: Maize inbred line Q5-35DAP-Grain-rep3


title: Maize inbred line Q5-21DAP-Grain-rep3


title: Maize inbred line Q5-28DAP-Grain-rep2

value: 28 day after pollination (DAP)


title: Maize inbred line Q4-49DAP-Grain-rep2


title: Maize inbred line Q5-28DAP-Grain-rep3


title: Maize inbred line Q5-21DAP-Grain-rep1


title: Maize inbred line Q5-28DAP-Grain-rep1


title: Maize inbred line Q5-35DAP-Grain-rep1


title: Maize inbred line Q4-49DAP-Grain-rep1


title: Maize inbred line Q4-49DAP-Grain-rep3


title: Maize inbred line Q4-56DAP-Grain-rep2


title: Maize inbred line Q4-42DAP-Grain-rep2


title: Maize inbred line Q5-21DAP-Grain-rep2


title: Maize inbred line Q4-42DAP-Grain-rep3


title: Maize inbred line Q4-56DAP-Grain-rep1


title: Maize inbred line Q4-35DAP-Grain-rep2


title: Maize inbred line Q4-35DAP-Grain-rep3


title: Maize inbred line Q4-28DAP-Grain-rep2


title: Maize inbred line Q4-28DAP-Grain-rep3


title: Maize inbred line Q4-42DAP-Grain-rep1


title: Maize inbred line Q5-49DAP-Grain-rep1


title: Maize inbred line Q4-21DAP-Grain-rep3


title: Maize inbred line Q4-35DAP-Grain-rep1


title: Maize inbred line Q4-28DAP-Grain-rep1


title: Maize inbred line Q4-21DAP-Grain-rep2


title: Maize inbred line Q4-21DAP-Grain-rep1


title: Maize inbred line Q4-56DAP-Grain-rep3


title: Maize inbred line Q3-56DAP-Grain-rep2


title: Maize inbred line Q3-56DAP-Grain-rep3


title: Maize inbred line Q3-49DAP-Grain-rep3


title: Maize inbred line Q3-56DAP-Grain-rep1


title: Maize inbred line Q3-49DAP-Grain-rep1


title: Maize inbred line Q3-42DAP-Grain-rep2


title: Maize inbred line Q3-49DAP-Grain-rep2


title: Maize inbred line Q3-28DAP-Grain-rep3


title: Maize inbred line Q3-42DAP-Grain-rep3


title: Maize inbred line Q3-42DAP-Grain-rep1


title: Maize inbred line Q3-28DAP-Grain-rep2


title: Maize inbred line Q3-28DAP-Grain-rep1


title: Maize inbred line Q3-35DAP-Grain-rep1


title: Maize inbred line Q3-35DAP-Grain-rep2


title: Maize inbred line Q3-21DAP-Grain-rep3


title: Maize inbred line Q2-49DAP-Grain-rep3


title: Maize inbred line Q2-56DAP-Grain-rep3


title: Maize inbred line Q2-56DAP-Grain-rep2


title: Maize inbred line Q3-21DAP-Grain-rep2


title: Maize inbred line Q2-49DAP-Grain-rep1


title: Maize inbred line Q2-42DAP-Grain-rep3


title: Maize inbred line Q3-21DAP-Grain-rep1


title: Maize inbred line Q2-49DAP-Grain-rep2


title: Maize inbred line Q2-42DAP-Grain-rep2


title: Maize inbred line Q2-56DAP-Grain-rep1


title: Maize inbred line Q2-35DAP-Grain-rep3


title: Maize inbred line Q2-35DAP-Grain-rep2


title: Maize inbred line Q2-28DAP-Grain-rep2


title: Maize inbred line Q2-35DAP-Grain-rep1


title: Maize inbred line Q3-35DAP-Grain-rep3


title: Maize inbred line Q2-21DAP-Grain-rep3


title: Maize inbred line Q2-28DAP-Grain-rep1


title: Maize inbred line Q2-21DAP-Grain-rep2


title: Maize inbred line Q2-21DAP-Grain-rep1


title: Maize inbred line Q1-49DAP-Grain-rep2


title: Maize inbred line Q1-56DAP-Grain-rep3


title: Maize inbred line Q1-42DAP-Grain-rep3


title: Maize inbred line Q1-42DAP-Grain-rep2


title: Maize inbred line Q1-49DAP-Grain-rep3


title: Maize inbred line Q2-42DAP-Grain-rep1


title: Maize inbred line Q1-35DAP-Grain-rep3


title: Maize inbred line Q1-56DAP-Grain-rep1


title: Maize inbred line Q1-35DAP-Grain-rep2


title: Maize inbred line Q1-42DAP-Grain-rep1


title: Maize inbred line Q1-49DAP-Grain-rep1


title: Maize inbred line Q1-35DAP-Grain-rep1


title: Maize inbred line Q1-28DAP-Grain-rep3


title: Maize inbred line Q1-28DAP-Grain-rep2


title: Maize inbred line Q1-21DAP-Grain-rep3


title: Blastocyst_C, bovine

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

country: USA

institute: University of Florida

data_processing:
The Salmon tool was applied to quantify the whole-genome gene expression profile from the raw sequencing data, using the bovine reference genome (UMD3.1.1). Transcript per million reads (TPM) was used as the unit of gene expression. The edgeR tool was applied to identify the differentially expressed genes. The TMM algorithm implemented in the edgeR package was applied to normalize the read count and estimate the effective library size. Groupwise differential expression was performed by the likelihood ratio test implemented in the edgeR package.
All the conventional statistical analyses were conducted using the R platform. Spearman’s rank correlation test was performed using the “cor.test” function. A linear model controlling for fractionation was applied to prioritize the polysome occupied genes with gradual increase/decrease in expression across the developmental stages using the “lm” function. If multiple testing should be accounted for, the Bonferroni procedure was applied for P-value correction using the “p.adjust” function. Principal component analysis on the expression data was performed using the “dudi.pca” function within the package “ade4”. All the heatmaps were plotted by the “heatmap.2” function within the package “gplots”. The pathway/gene ontology analysis was performed using the David tool.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: txt, normalized read counts

organism: Bos taurus

source_name: embryos

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

tag: cell type

value: embryos

tag: developmental stage

value: Blastocyst


title: Maize inbred line Q1-21DAP-Grain-rep1


title: Blastocyst_B, bovine


title: Maize inbred line Q1-28DAP-Grain-rep1


title: Maize inbred line Q1-21DAP-Grain-rep2


title: Maize inbred line Q2-28DAP-Grain-rep3


title: Morula_C, bovine

value: Morula


title: Morula_B, bovine


title: Blastocyst_A, bovine


title: Maize inbred line Q1-56DAP-Grain-rep2


title: 8-cell_C, bovine


title: 2-cell_C, bovine


title: 8-cell_B, bovine


title: Morula_A, bovine


title: 2-cell_B, bovine


title: MII_B, bovine

source_name: oocytes

value: oocytes

value: MII


title: MII_C, bovine


title: GV_B, bovine

value: GV


title: GV_A, bovine


title: GV_C, bovine


title: Blastocyst_F10_B, bovine

data_processing:
Library strategy: Ribo-seq
The Salmon tool was applied to quantify the whole-genome gene expression profile from the raw sequencing data, using the bovine reference genome (UMD3.1.1). Transcript per million reads (TPM) was used as the unit of gene expression. The edgeR tool was applied to identify the differentially expressed genes. The TMM algorithm implemented in the edgeR package was applied to normalize the read count and estimate the effective library size. Groupwise differential expression was performed by the likelihood ratio test implemented in the edgeR package.
All the conventional statistical analyses were conducted using the R platform. Spearman’s rank correlation test was performed using the “cor.test” function. A linear model controlling for fractionation was applied to prioritize the polysome occupied genes with gradual increase/decrease in expression across the developmental stages using the “lm” function. If multiple testing should be accounted for, the Bonferroni procedure was applied for P-value correction using the “p.adjust” function. Principal component analysis on the expression data was performed using the “dudi.pca” function within the package “ade4”. All the heatmaps were plotted by the “heatmap.2” function within the package “gplots”. The pathway/gene ontology analysis was performed using the David tool.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: txt, normalized read counts


title: 8-cell_A, bovine


title: Blastocyst_F8_A, bovine


title: Blastocyst_F8_B, bovine


title: Blastocyst_F10_A, bovine


title: Blastocyst_F7_A, bovine


title: Blastocyst_F7_B, bovine


title: Blastocyst_F6_B, bovine


title: MII_A, bovine


title: Blastocyst_F9_A, bovine


title: Blastocyst_F6_A, bovine


title: Blastocyst_F4_B, bovine


title: Blastocyst_F5_B, bovine


title: Blastocyst_F5_A, bovine


title: Blastocyst_F4_A, bovine


title: Blastocyst_F3_A, bovine


title: Blastocyst_F3_B, bovine


title: Blastocyst_F2_B, bovine


title: Blastocyst_F2_A, bovine


title: 2-cell_A, bovine


title: Blastocyst_F1_A, bovine


title: Morula_F10_B, bovine


title: Blastocyst_F9_B, bovine


title: Morula_F10_A, bovine


title: Morula_F8_A, bovine


title: Morula_F7_B, bovine


title: Blastocyst_F1_B, bovine


title: Morula_F7_A, bovine


title: Morula_F8_B, bovine


title: Morula_F5_B, bovine


title: Morula_F5_A, bovine


title: Morula_F6_B, bovine


title: Morula_F6_A, bovine


title: Morula_F4_B, bovine


title: Morula_F4_A, bovine


title: Morula_F3_B, bovine


title: Morula_F9_A, bovine


title: Morula_F3_A, bovine


title: Morula_F2_B, bovine


title: Morula_F2_A, bovine


title: Morula_F1_B, bovine


title: Morula_F9_B, bovine


title: Morula_F1_A, bovine


title: 8-cell_F10_A, bovine


title: 8-cell_F9_A, bovine


title: Peripheral blood mononuclear cells_Kidney transplanted patient 1_Time 0_outcome EGF

type: RNA

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

hyb_protocol: Total RNA was hybridized on to the GeneChip Human Genome U133A Array (Affymetrix, Santa Clara, CA) according to the manufacture's instructions

scan_protocol: We used the default settings of GCOS software to scan the chips.

data_processing:
We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values. R 2.0.1 statistical software was used to perform the normalization of the data according to R. A. Irizarryet al, Biostatistics, 2003. Differentially expressed genes were identified using GeneSpring GX software (Agilent, Palo Alto, CA), by applying a moderated t-test with Storey with bootstrapping multiple testing correction.
We selected the differentially expressed genes using a q-value cut-off of 0.05

label: Biotin

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells Time 5

label_protocol: The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.

growth_protocol: Twenty ml of whole blood were harvested from the selected patients at the time of transplantation, before the administration of induction therapy. PBMCs were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen AG, Basel, Switzerland) and qualitatively and quantitatively analyzed through Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with good quality, indicated by a RIN> 8, were used in the microarray experiment.

tag: sample type

value: Male patient, 58 years old, kidney transplantation, outcome EGF


title: Peripheral blood mononuclear cells_Kidney transplanted patient 4_Time 0_outcome EGF

source_name: Peripheral blood mononuclear cells Time 8

value: Male patient, 48 years old, kidney transplantation, outcome EGF


title: 8-cell_F8_A, bovine


title: Peripheral blood mononuclear cells_Kidney transplanted patient 1_Time 0_outcome DGF

source_name: Peripheral blood mononuclear cells Time 0

value: Male patient, 59 years old, kidney transplantation, outcome DGF


title: 8-cell_F8_B, bovine


title: Peripheral blood mononuclear cells_Kidney transplanted patient 2_Time 0_outcome DGF

source_name: Peripheral blood mononuclear cells Time 1

value: Male patient, 30 years old, kidney transplantation, outcome DGF


title: Peripheral blood mononuclear cells_Kidney transplanted patient 5_Time 0_outcome DGF

source_name: Peripheral blood mononuclear cells Time 4

value: Female patient, 66 years old, kidney transplantation, outcome DGF


title: Peripheral blood mononuclear cells_Kidney transplanted patient 5_Time 0_outcome EGF

source_name: Peripheral blood mononuclear cells Time 9

value: Male patient, 54 years old, kidney transplantation, outcome EGF


title: Peripheral blood mononuclear cells_Kidney transplanted patient 3_Time 0_outcome EGF

source_name: Peripheral blood mononuclear cells Time 7

value: Female patient, 54 years old, kidney transplantation, outcome EGF


title: Peripheral blood mononuclear cells_Kidney transplanted patient 2_Time 0_outcome EGF

source_name: Peripheral blood mononuclear cells Time 6


title: Day40 Flyp/lyp Rat fed with a normal cereal diet from age of day21, rep3

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression interrogating 31099 transcripts

hyb_protocol: The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26].  Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor.

label: biotin

organism: Rattus norvegicus

source_name: Healthy control rats with homozygous mutation at LYP locus

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: DRlyp/lyp and Flyp/lyp rats were maintained at The Medical College of Wisconsin (MCW) under specific pathogen-free conditions with standard light/dark cycles.  Rats were provided chow and water ad libitum.  All federal guidelines for use and care of laboratory animals (http://grants1.nih.gov/grants/olaw/references/phspol.htm) were followed.

extract_protocol: Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA).  RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

treatment_protocol: At 21 days of age, DRlyp/lyp rats were weaned onto a normal cereal diet (DRlyp/lyp ND) containing both plant and animal protein sources (LabDiet 5L0D, Purina, St. Louis, MO, USA) or a gluten-free hydrolyzed bovine casein diet (DRlyp/lyp HCD, Modified AIN-93G diet, Dyets Inc., Bethlehem, PA, USA). Subgroups of DRlyp/lyp rats receiving these diets were supplemented with 50 million CFU/gram body weight/day Lp299v (Lactobacillus plantarum 299v; NextFoods, Boulder, CO) by oral gavage from weaning (DRlyp/lyp ND+Lp299v and DRlyp/lyp HCD+Lp299v).  Flyp/lyp rats were weaned at 21 days onto ND and did not receive Lp299v (Flyp/lyp ND). Weight and blood glucose (measured with an Ascensia Elite XL glucometer; Bayer, Tarrytown, New York, USA) were measured from 40 day of age; diabetes was defined as blood glucose levels ≥250mg/dl on two consecutive days.  Blood was collected by heart puncture from rats under isofluorane anesthesia into EDTA vacutainer tubes (Becton-Dickinson, Franklin Lakes, NJ, USA).  Plasma was separated by centrifugation and stored at  -80°C.  All procedures followed The National Institutes of Health Guide for the Care and Use of Laboratory and were approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee (Assurance Number A3102-01).

tag: diet

value: fed with a normal cereal diet

tag: strain

value: healthy Flyp/lyp strain

value: pancreatic islets

tag: age

value: 40 days old


title: Peripheral blood mononuclear cells_Kidney transplanted patient 4_Time 0_outcome DGF

source_name: Peripheral blood mononuclear cells Time 3

value: Male patient, 34 years old, kidney transplantation, outcome DGF


title: 8-cell_F7_A, bovine

value: embryos


title: Day40 DRlyp/lyp Rat fed with a gluten-free hydrolyzed bovine casein diet (HCD) plus Lp299v from age of day21, rep3

source_name: Diabetes prone rats, with homozygous mutation at LYP locus

value: DRlyp/lyp strain (diabetes prone)


title: Day40 DRlyp/lyp Rat fed with a normal cereal diet from age of day21, rep3


title: Peripheral blood mononuclear cells_Kidney transplanted patient 3_Time 0_outcome DGF

source_name: Peripheral blood mononuclear cells Time 2

value: Male patient, 45 years old, kidney transplantation, outcome DGF


title: Day40 DRlyp/lyp Rat fed with a normal cereal diet plus Lp299v from age of day21, rep3


title: Day40 DRlyp/lyp Rat fed with a gluten-free hydrolyzed bovine casein diet (HCD) from age of day21, rep3


title: 8-cell_F9_B, bovine


title: 8-cell_F10_B, bovine


title: Day40 Flyp/lyp Rat fed with a normal cereal diet from age of day21, rep2


title: 8-cell_F6_B, bovine


title: 8-cell_F7_B, bovine


title: 8-cell_F6_A, bovine


title: Day40 DRlyp/lyp Rat fed with a gluten-free hydrolyzed bovine casein diet (HCD) from age of day21, rep2


title: Day40 Flyp/lyp Rat fed with a normal cereal diet from age of day21, rep1


title: 8-cell_F5_A, bovine


title: 8-cell_F4_B, bovine


title: 8-cell_F5_B, bovine


title: 8-cell_F4_A, bovine


title: 8-cell_F3_A, bovine


title: 8-cell_F2_A, bovine


title: Day40 DRlyp/lyp Rat fed with a normal cereal diet plus Lp299v from age of day21, rep2


title: 8-cell_F1_A, bovine


title: 8-cell_F3_B, bovine


title: 8-cell_F1_B, bovine


title: 2-cell_F10_B, bovine


title: Day40 DRlyp/lyp Rat fed with a normal cereal diet from age of day21, rep1


title: Day40 DRlyp/lyp Rat fed with a normal cereal diet plus Lp299v from age of day21, rep1


title: 2-cell_F9_B, bovine


title: 8-cell_F2_B, bovine


title: Day40 DRlyp/lyp Rat fed with a gluten-free hydrolyzed bovine casein diet (HCD) plus Lp299v from age of day21, rep2


title: 2-cell_F10_A, bovine


title: 2-cell_F9_A, bovine


title: Day40 DRlyp/lyp Rat fed with a normal cereal diet from age of day21, rep2


title: S20-23229-COVID-19

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling of lung tissue from fatal COVID-19

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from approximately 2.5 mls of peripheral blood in Paxgene tubes according to manufacturer's protocol under BSL4 conditions.  RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: Peripheral blood was collected from either a patient infected with Ebola virus or healthy volunteers and stored in Paxgene tubes (Qiagen) according to manufacturer's instructions.

value: Lung

tag: disease state


title: Normal 3-Normal

description: Gene expression profiling of normal lung tissue

source_name: Normal 3-Normal

value: Normal


title: Day40 DRlyp/lyp Rat fed with a gluten-free hydrolyzed bovine casein diet (HCD) from age of day21, rep1


title: JWCI-ID30-b-COVID-19


title: JWCI-ID30-a-COVID-19


title: Day40 DRlyp/lyp Rat fed with a gluten-free hydrolyzed bovine casein diet (HCD) plus Lp299v from age of day21, rep1


title: Normal 1-Normal

source_name: Normal 1-Normal


title: 2-cell_F8_B, bovine


title: S20-23231-COVID-19


title: JWCI-ID31-a-COVID-19


title: JWCI-ID31-b-COVID-19


title: JWCI-18-0401-a-COVID-19


title: JWCI-18-0401-b-COVID-19


title: JWCI-ID-29-a-COVID-19


title: 2-cell_F7_B, bovine


title: Normal 2-Normal

source_name: Normal 2-Normal


title: 2-cell_F7_A, bovine

source_name: embryos


title: 2-cell_F6_B, bovine


title: S20-23461-RUL-32-COVID-19


title: 2-cell_F5_B, bovine


title: 2-cell_F6_A, bovine


title: JWCI-ID-29-b-COVID-19


title: S20-23461-LUL-36-COVID-19


title: S20-23461-RUL-33-COVID-19


title: S20-22718-COVID-19


title: S20-22715-COVID-19


title: 2-cell_F8_A, bovine


title: 2-cell_F4_A, bovine


title: JWCI-190401-a-COVID-19


title: 2-cell_F4_B, bovine


title: 2-cell_F5_A, bovine


title: 2-cell_F3_B, bovine


title: 2-cell_F2_A, bovine


title: MII_F10_B, bovine

source_name: oocytes

value: oocytes

value: MII


title: 2-cell_F1_B, bovine


title: 2-cell_F3_A, bovine


title: MII_F10_A, bovine


title: 2-cell_F1_A, bovine


title: MII_F9_B, bovine


title: 2-cell_F2_B, bovine


title: left_ventricle_wt_old_5

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Array data export and quality control were performed with the Genome Studio Software v2011.1 (Illumina). Raw data were imported into the R software v4.0.2 and normalized with the Lumi R/Bioconductor package. Variance stabilizing transformation (VST) was applied and transformed data were then normalized by robust spline normalization (RSN). Probes with a detection P‐value <0.01 in at least 25% of samples were retained.

organism: Mus musculus

source_name: Mouse heart

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: Total RNA was extracted from the left ventricles of mice of different age groups using miRNeasy kit (Qiagen) and treated with DNase on column to eliminate genomic contamination, following manufacturer’s instructions.

treatment_protocol: After mouse perfusion with phosphate-buffered saline, hearts were dissected and immediately frozen and then stored at -80°C until processing.

tag: gender

value: female

tag: genotype

value: Wild Type

value: left ventricle

value: 21 months


title: left_ventricle_wt_old_2


title: left_ventricle_ko_old_6

value: Rage-/-


title: left_ventricle_wt_old_6


title: left_ventricle_wt_old_3


title: left_ventricle_ko_old_5


title: MII_F8_B, bovine


title: S20-22329-COVID-19


title: S20-22318-COVID-19


title: left_ventricle_wt_old_4


title: MII_F8_A, bovine


title: left_ventricle_ko_MA_4

value: 12 months


title: MII_F7_B, bovine


title: MII_F7_A, bovine


title: S20-22326-COVID-19


title: JWCI-190401-b-COVID-19


title: MII_F6_A, bovine


title: left_ventricle_ko_MA_3


title: MII_F5_A, bovine


title: MII_F5_B, bovine


title: left_ventricle_ko_MA_1


title: left_ventricle_ko_MA_2


title: MII_F6_B, bovine


title: MII_F9_A, bovine


title: left_ventricle_ko_Young_2

value: 10 weeks


title: MII_F4_B, bovine


title: left_ventricle_ko_Young_1


title: MII_F4_A, bovine


title: left_ventricle_wt_Young_4


title: MII_F2_B, bovine


title: MII_F3_B, bovine


title: MII_F3_A, bovine


title: MII_F2_A, bovine


title: left_ventricle_wt_Young_2


title: GV_F10_B, bovine

value: GV


title: MII_F1_A, bovine


title: GV_F10_A, bovine


title: GV_F9_B, bovine


title: left_ventricle_wt_Young_1


title: left_ventricle_wt_MA_2


title: GV_F9_A, bovine


title: left_ventricle_wt_Young_3


title: GV_F8_A, bovine


title: GV_F8_B, bovine


title: left_ventricle_wt_MA_1


title: LX-2 cells treated with conditioned medium from HCT116FGFBP1 cells #2

city: Guangzhou

first: Minfeng

last: Chen

address: Huangpu road 601

institute: Jinan University

data_processing:
The index of the reference genome was built using Hisat2 (v2.0.5), and the paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
For the quantification of gene expression level, FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Analysis of differential expression was performed using the DESeq2 R package (1.16.1)
The differentially expressed mRNAs and genes were selected with statistical significance (P < 0.05) by R package-edgeR.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Servicebio, Wuhan, China) at a ratio of 106 cells per mL of reagent according to the manufacturer’s instructions.
RNA-sequencing libraries were generated using ribosomal RNA depleted RNAs with the NEBNext Ultra II RNA Library Prep Kit (NEB) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the Bioanalyzer 2100 system (Agilent Technologies, CA).

tag: cell line

value: hepatic stellate cells

tag: treatment

value: cultured for 24h


title: left_ventricle_wt_MA_4


title: left_ventricle_ko_Young_3


title: left_ventricle_ko_Young_5


title: left_ventricle_wt_MA_3


title: left_ventricle_ko_old_1


title: MII_F1_B, bovine


title: GV_F6_B, bovine


title: left_ventricle_ko_old_2


title: GV_F7_A, bovine


title: LX-2 cells treated with conditioned medium from HCT116FGFBP1 cells #1


title: left_ventricle_ko_old_4


title: left_ventricle_ko_old_3


title: LX-2 cells treated with conditioned medium from HCT116Vector cells #2


title: left_ventricle_ko_Young_4


title: LX-2 cells treated with conditioned medium from HCT116Vector cells #1


title: LX-2 cells treated with conditioned medium from HCT116FGFBP1 cells #3


title: left_ventricle_wt_Young_5


title: GV_F6_A, bovine


title: GV_F5_B, bovine


title: LX-2 cells treated with conditioned medium from HCT116Vector cells #3


title: GV_F4_B, bovine


title: GV_F5_A, bovine


title: WT29

city: Beijing

first: Yuan

last: Chu

address: No. 38, kexueyuan Road, Changping District

institute: Beijing Institute of Lifeomics

data_processing:
RSEM software was used to calculate FPKM and mm10 genome build was used for read alignment.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: white adipose tissue, fasted

growth_protocol: Male C57BL/6J mice (16-week-old) were raised in the Specific Pathogen Free (SPF) animal room of the Animal Experiment Center at Academy of Military Medical Sciences. Mice were housed at room temperature (21-25 ˚C) with a relative humidity of 45-65%, a 12/12 hours light/dark cycle and access to food and water ad libitum

extract_protocol:
70 mg of white adipose tissue per sample was lysed by Trizol for RNA extraction, followed by protein depletion with chloroform and RNA purification in isopropanol,and finally RNA was dissolved in DEPC H2O
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The 16-week-old mice were divided into two groups, one was normally fed, and the other was starved for 24 hours, and then white adipose tissue from the epididymis of the mice was used to extract RNA for RNAseq

tag: Sex

value: male

value: white adipose tissue

value: WT

value: fasted 24 h


title: 31NC

source_name: white adipose tissue, fed

value: fed


title: WT10


title: GV_F4_A, bovine

value: oocytes


title: 30NC


title: 6NC


title: GV_F3_A, bovine


title: GV_F2_A, bovine


title: total spleen_3mo F1 (2)

city: Athens

first: Αnastasia

last: Filia

address: Soranou Efessiou 4

country: Greece

institute: BRFAA

data_processing:
Sequenced reads were trimmed at the 3' end for adaptor sequence and low-quality sequence (q<30), then mapped to mm10 whole genome using STAR v2.6 and quantified using HtSeq and Gencode v. M19 annotation file.
EdgeR package in R was used to calculate CPM abundance values.
Assembly: mm10
Supplementary files format and content: Excel file includes CPM values for each Sample

source_name: total spleen

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen)
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit v2

value: post natal 3 months

value: lupus pre-autoimmunity stage

value: total spleen


title: GV_F1_B, bovine


title: total spleen_3mo B6 (2)

value: female

value: healthy


title: Sample 4_NME7_knockdown

city: Shanghai

first: Xiaoyu

last: Liu

state: Shanghai

address: 180 Yue-yang road

department: Department of Interventional Radiology

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

data_processing:
The raw fastq data was asessed and trimed using fastp software.
Then the trimed fastq datasets were mapped to human genome (hg19) using hisat2 software.
The gene read counts were identified us HTseq-count software .
The differentailly expressed genes (DEGs) were perfomed using DEseq2 in R environmet.
Further downstream analysis were perfomed using custom script in Linux or R environment.
Genome_build: hg19

source_name: Hepatic cell carcinoma

growth_protocol: PVTT cells were cultured in DMEM medium (5% CO2, 37°)

extract_protocol:
Total RNA was extracted from each sample using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Added 100ng/ml DOX to PVTT and cultured for three days.

value: +DOX (NME7 knockdown)

value: PVTT


title: GV_F2_B, bovine


title: GV_F3_B, bovine


title: total spleen_1mo B6 (3)

value: post natal 1 month


title: GV_F1_A, bovine

value: GV


title: total spleen_3mo F1 (3)


title: total spleen_3mo B6 (1)


title: WT99


title: Sample 3_NME7_knockdown


title: Sample 1_control

value: -DOX


title: Sample 2_control


title: total kidney_3mo F1 (3)

source_name: total kidney

value: total kidney


title: total kidney_3mo F1 (2)


title: total spleen_1mo B6 (1)


title: total spleen_1mo B6 (2)


title: total kidney_3mo B6 (3)


title: total kidney_1mo B6 (3)


title: total kidney_3mo B6 (1)


title: total spleen_3mo F1 (1)


title: total kidney_1mo B6 (2)


title: total brain_3mo B6 (2)

source_name: total brain

value: total brain


title: total brain_3mo F1 (2)


title: total brain_3mo B6 (3)


title: total brain_3mo F1 (1)


title: total brain_1mo B6 (3)


title: total brain_3mo B6 (1)


title: total brain_1mo B6 (2)


title: total kidney_3mo F1 (1)


title: total brain_1mo B6 (1)


title: Seq10-Ver-D1

first: Zemin

last: Hou

address: 320 Yueyang Road

department: Shanghai Institutes of Biochemistry and Cell biology

institute: Chinese Academy of Sciences

data_processing:
The quality control of raw sequence data was evaluated by FastQC (v. 0.11.7).
Quality trimming and adapter clipping by Trimmomatic (v.0.36-5).
Paired-end reads were aligned to the GRCh38.91 human reference genome using hisat2 (v.2-2.1.0).
Using samtools to filter and sort bam.
The gene expression level was quantified by HTSeq (v.0.11.1).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files (*.no) include counts values for each Sample.

molecule: polyA RNA

growth_protocol: VCaP cells were provided by Dr. Jun Qin (SIBS, Shanghai, China) and maintained in  DMEM with 10% FBS.

extract_protocol:
Total RNAs of each sample were extracted by TRIzol reagent (Invitrogen).
VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina (NR611) was used for library construction following the manufacturer’s instructions.

treatment_protocol: Cells were starved for at least 48h with phenol red-free and charcol stripped serum-medium and treated with  DHT ,enzalutamide or DHT plus enzalutamide for 24h.

value: VCaP

tag: pretreatment

value: treated with 1uM enzalutamide

tag: pretreatment time

value: 4 month


title: Seq10-Ver-E1


title: Seq10-Ver-D-E2


title: total spleen_6mo F1 (3)

data_processing:
Sequenced reads were trimmed at the 3' end for adaptor sequence and low-quality sequence (q<30), then mapped to mm10 whole genome using STAR v2.6 and quantified using HtSeq and Gencode v. M19 annotation file.
EdgeR package in R was used to calculate CPM abundance values.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes CPM values for each Sample

value: post natal 6 months

value: lupus symptomatic nephritic disease

tag: tissue


title: Seq10-Ver-D-E1


title: total spleen_6mo B6 (2)


title: Seq10-Ver-C2

source_name: Ver-control

value: control


title: Seq10-Ver-D2


title: total kidney_3mo B6 (2)

value: post natal 3 months


title: total spleen_6mo F1 (2)

value: total spleen


title: total spleen_6mo F1 (1)

value: female


title: total spleen_6mo B6 (1)

value: healthy


title: total brain_3mo F1 (3)

value: lupus pre-autoimmunity stage


title: total kidney_1mo B6 (1)


title: Seq10-Vc-E2

value: treated with ethanol


title: total spleen_1mo F1 (3)

value: post natal 1 month

value: lupus asymptomatic pre-puberty


title: total spleen_1mo F1 (2)


title: Seq10-Ver-E2


title: Seq10-Vc-D2


title: Seq10-Vc-D1


title: total spleen_1mo F1 (1)


title: total kidney_6mo F1 (3)


title: total kidney_6mo F1 (2)


title: Seq10-Vc-D-E2


title: total kidney_6mo F1 (1)


title: Seq10-Vc-C2

source_name: Vc-control


title: Seq10-Vc-D-E1


title: total kidney_6mo B6 (3)


title: total kidney_6mo B6 (2)


title: Seq10-Vc-C1


title: total kidney_6mo B6 (1)


title: Seq10-Ver-C1


title: total kidney_1mo F1 (3)


title: total kidney_1mo F1 (2)


title: total brain_6mo F1 (3)


title: total kidney_1mo F1 (1)


title: total brain_6mo F1 (2)


title: IMSB_7_5D_TAIL

city: München

first: Roland

last: Rad

address: Ismaninger Strasse 22

department: Institute of Molecular Oncology and Functional Genomics

country: Germany

institute: Technical University of Munich

description: Primary tissue

library_source: genomic

data_processing:
BAM files were generated using illumina2bam.
The transposon-genomic junction was reassembled by concatenating the 12 bp transposon read and Read1.
Read pairs were split into separate FASTQ files for Read1 and Read2.
Mapping of integrations to the mouse genome was performed using the SSAHA2 algorithm.
High-confidence insertion coordinates were exported as BED file.
Assembly: mm10
Supplementary files format and content: SBvsPB.csv: Processed data file contains insertion sites (genomic positions) from both libraries (5' and 3' transposon end), read counts for each insertion and gene annotations. File is in comma-separated format and contain insertions sites for all samples listed here.

molecule: genomic DNA

source_name: TAIL

extract_protocol:
DNA isolation of tissue samples was performed according to manufacturer’s instructions using the Qiagen DNeasy Blood & Tissue Kit.
DNA samples were sheared with a Covaris AFA sonicator to a mean fragment length of 250 bp. The fragmented DNA was then end-repaired, A-tailed and a splinkerette adapter was ligated to each DNA end. For the 5’ and 3’ transposon end, subsequent steps (amplification and sequencing of transposon-genome junctions) were conducted separately.
The specific structure of the splinkerette adapter (Y-shaped design with a template and a hairpin strand) ensures that only transposon-genome junction fragments (and not genomic fragments without transposon insert) can be amplified in the first PCR step (which was conducted with transposon- and splinkerette-specific primers). Afterwards, a second nested PCR step was performed for further amplification, barcoding of samples and extension with Illumina flow cell binding sites P5 and P7. Samples were equimolarly mixed and the library pool was again quantified. Libraries were sequenced on the Illumina MiSeq sequencer (75 bp, paired-end).

value: TAIL

value: IMSB


title: total brain_6mo B6 (3)

value: total brain


title: IMSB_1_4E_TAIL

description: Primary tissue


title: IMSB_1_1B_TAIL

description: Primary tissue


title: total brain_6mo B6 (2)


title: total brain_1mo F1 (3)


title: total brain_1mo F1 (2)


title: total brain_1mo F1 (1)


title: IMPB_9_7D_TAIL

description: Primary tissue

value: IMPB


title: IMSB_8_5F_TAIL

description: Primary tissue


title: IMPB_9_3B_LN_

description: Primary tissue

source_name: LN

value: LN


title: IMPB_9_2G_TAIL

description: Primary tissue


title: IMPB_1_7D_TAIL

description: Primary tissue


title: ZT13 ASIC1a-/- hypothalamus rep4

city: Lausanne

first: zhong

last: peng

state: Vaud

address: Rue du Bugnon 27

department: Department of Biomedical Sciences

country: Switzerland

institute: University of Lausanne

description: mouse sacrifice at Zeitgeber time 13 (20:00, light off at 19:00, GMT+1)

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013). Reads were aligned against Mus musculus.GRCm38.102 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.102 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Reads were also aligned to the Mus musculus.GRCm38.102 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
mm9
Genome_build: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hypothalamus

extract_protocol:
hypothalamus were removed, flash frozen in liquid nitrogen, and RNA was harvested using RNAqueous™ Total RNA Isolation Kit (Thermo Fisher Scientific, AM1931). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hypothalamus

value: post natal 3 month


title: DRGs after PBS treatment, rep 2

city: Guildford

first: Ngan Pan

middle: Bennett

last: Au

state: Surrey

address: Vet School Main Building (VSM), Daphne Jackson Road

country: United Kingdom

institute: University of Surrey

hyb_protocol: Samples were hybridized for 17 hours according to the SOP of GeneChip™ Expression Wash, Stain and Scan For Cartridge Arrays

scan_protocol: GeneChip™ Scanner 3000 7G

data_processing: Data were processed using R software with the ‘expresso’ function and the MAS5 method. Outliers with mean sample correlations more than three standard deviations below average were omitted.

source_name: PBS-treated DRGs

label_protocol: Samples were biotinylated using the GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays

growth_protocol: L4/5 DRGs from adult male wild-type C57BL/6 mice

extract_protocol: L4/5 DRGs were dissected out after 13 consecutive days of LBP oral administration.

treatment_protocol: Mice were received oral administration of LBP for 13 consecutive days.

value: Adult (8-12 weeks old)

value: L4/5 DRGs

value: male

value: PBS-treated mice


title: DRGs after LBP treatment, rep 3

source_name: LBP-treated DRGs

value: LBP-treated mice


title: DRGs after LBP treatment, rep 1


title: DRGs after PBS treatment, rep 1


title: DRGs after PBS treatment, rep 3


title: ZT13 ASIC1a-/- hypothalamus rep3


title: DRGs after LBP treatment, rep 2


title: IMPB_9_2D_TAIL

description: Primary tissue


title: total brain_6mo F1 (1)

value: female

value: post natal 6 months

value: lupus symptomatic nephritic disease


title: ZT13 ASIC1a-/- hypothalamus rep2


title: ZT13 ASIC1a-/- hypothalamus rep1


title: total brain_6mo B6 (1)

value: healthy


title: IMPB_5_5E_TAIL

description: Primary tissue


title: ZT13 WT hypothalamus rep4

value: wild type


title: adPERK2

city: Dallas

first: GUANGYU

last: ZHANG

state: TX

address: 5323 Harry Hines Blvd

department: Cardiology

institute: UTsouthwestern Medical Center

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 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: heart

growth_protocol: H9c2 cells were purchased from ATCC (#CRL-1446), which were derived from embryonic rat myocardium. H9c2 cells were cultured in 75 cm2 flasks with DMEM medium (high glucose), supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using with the Quick-RNA MicroPrep kit (Zymo research). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, the cells were first washed twice with PBS and incubated with freshly made ischemia Esumi buffer (HEPES 4 mM, NaCl 117 mM, CaCl2 0.9 mM, MgCl2 0.49 mM, KCl 12 mM, 2-deoxyglucose 5.6 mM, sodium lactate 20 mM, pH 6.2) (Esumi et al., 1991). The cells were then placed in a modular incubator chamber at 37°C (Billups-Rothenberg, #MIC-101). Mixed gas (95% N2/5% CO2) was used to flush the chamber for 30 min at pressure less than 2 psi. The chamber was then sealed for an additional 1.5-3.5 hours.

value: Stimulated Ischemia Reperfusion

tag: adenovirus

value: adPERK


title: IMPB_8_5H_MES_LN

description: Primary tissue

source_name: MES LN

value: MES LN


title: ZT13 WT hypothalamus rep3


title: adPERK1


title: ZT13 WT hypothalamus rep1


title: ZT13 WT hypothalamus rep2


title: IMPB_8_1C_TAIL

description: Primary tissue

value: TAIL

value: IMPB


title: control3

value: control


title: IMPB_6_3B_MES_MASS

description: Primary tissue

source_name: MES MASS

value: MES MASS


title: ZT1 ASIC1a-/- hypothalamus rep4

description: mouse sacrifice at Zeitgeber time 1 (8:00, light on at 7:00, GMT+1)

value: hypothalamus

value: post natal 3 month


title: ZT1 ASIC1a-/- hypothalamus rep3


title: ZT1 ASIC1a-/- hypothalamus rep1


title: adPERK3


title: control1


title: ZT1 WT hypothalamus rep3


title: ZT1 WT hypothalamus rep4


title: IMPB_5_5F_SPLEEN

description: Primary tissue

source_name: SPLEEN

value: SPLEEN


title: IMPB_5_2F_SPLEEN

description: Primary tissue


title: ZT1 ASIC1a-/- hypothalamus rep2


title: ZT1 WT hypothalamus rep1


title: ZT1 WT hypothalamus rep2


title: IMPB_9_1B_THOR_LN

description: Primary tissue

source_name: THOR LN

value: THOR LN


title: IMPB_4_6C_MES_MASS

description: Primary tissue


title: smax1_2_replicat1

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

data_processing:
Basecalls performed using RTA VN:1.18.61.0.
Sequenced reads were aligned to TAIR10 whole genome using TopHat2 v2.0.14 (Kim et al., 2013).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: TAIR10.
Supplementary_files_format_and_content: Excel files including RPKM values for each Sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis from WT (Col-0) and smxl5-1, smxl4-1 smxl5-1 and smax1-2 genotypes were grown on 1/2 MS plates for 7 days in long day (12h light 12h dark, constant 21°C).

extract_protocol:
15 seedlings were harvested per biological replicate of each genotype and frozen immediately in liquid nitrogen. Total RNA was extracted with Phenol/Chlorophorm according to Mallory, et al. 2001.
Ambion Dynabeads mRNA Purification Kit for poly A RNA enrichment and the NEB RNA Ultra Kit for preparation of the libraries

value: Seedlings

value: 7 days

tag: background ecotype

value: Col


title: smax1_2_replicat3


title: HTG_AP1

first: Guoyong

last: Hu

address: No. 110, Haining Road

institute: Shanghai General Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Remove the 3' linker sequence in the reads, and remove the reads without inserts due to the connector self-ligation. Remove the reads with low-quality sequence and reads containing the unknown base N, too short(<18nt) or too long(> 32 nt).
Useing fastx_tool 0.04 to ffilter the low quality data , and using bowtie version 1.1.1 for genome mapping.
The expression level of each transcript was calculated according to the (FPKM) method. miRDeep2 was used to quantify gene abundances
Differential gene expression analysis was done using R package DEGseq
Genome_build: Mus_musculus.GRCm38.dna
Supplementary_files_format_and_content: excel file include raw counts of sequencing reads and TPM values for each Sample

source_name: mouse pancreatitis tissue

extract_protocol:
RNA was harvested using Trizol reagent.
Labriaries were prepared according to  Illumina's instructions accompanying the NEXTflex™ Small RNA-Seq Kit v3

value: pancreas

tag: condition

value: hypertriglyceridemia


title: smax1_2_replicat2


title: HTG_AP3


title: HTG_AP2


title: CON_AP3


title: control2

tag: cell type


title: CON_AP1


title: smxl4_1smxl5_1_replicat3

value: smxl4-1 smxl5-1


title: CON_AP2


title: IMSB5_3F_TAIL

description: Primary tissue

value: IMSB


title: smxl4_1smxl5_1_replicat2


title: yeast Dcp2-degron, auxin induced, rep2

city: Paris

first: Cosmin

last: Saveanu

address: 25 rue du docteur Roux

department: Genome and Genetic

country: France

institute: Institut Pasteur

data_processing:
Basecalling using guppy (ONT, see sequencing.summary.txt for each sample)
Mapping to the SC288 reference genome Saccer3.fa using minimap2.1 with options -k 14 -ax map-ont –secondary = no and processed with samtools 1.9 (samtools view -b -o).
The poly(A) tail lengths for each read were estimated using the Nanopolish 0.13.2 polya function (Workman, R. E. et al. Nat. Methods 1–9. https://doi.org/10.1038/s41592-019-0617-2 (2019))
Assembly: Saccer3.fa
Supplementary files format and content: Fast5 (raw data)
Supplementary files format and content: Fastq
Supplementary files format and content: sequencin.summary.txt (from basecalling process)

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: 30°C in YPD, exponential phase (OD 600=0,4)

extract_protocol:
Standard hot phenol protocol
Direct RNA sequencing (ONT kit SQK-RNA002)

treatment_protocol: 1H IAA 100µM, ßoestradiol 1µM

value: yeast

value: BY4741 with TAO3_E1493Q/RME1(YGR044c) insert A -308/trp1-1::TRP1-prURA3-Z3EVtf-tURA3-Z3EV-TIR/DCP2(YNL118c)::polyG-3Flag-AID::kanMX, Mat a

value: 1H IAA 100µM, ßoestradiol 1µM

tag: Stage

value: exponential phase


title: yeast Dcp2-degron, auxin induced, rep1


title: IMSB7_4B_MES_MASS

description: Primary tissue


title: smxl4_1smxl5_1_replicat1


title: yeast Ccr4/Pop2-degron, auxin induced, rep1

value: BY4741 with TAO3_E1493Q/RME1(YGR044c) insert A -308/trp1-1::TRP1-prURA3-Z3EVtf-tURA3-Z3EV-TIR/AID-3Flag-CCR4/CAF1(YNR052c)::AID-KanMX6, Mat a


title: yeast Ccr4/Pop2-degron, auxin induced, rep2


title: IMPB_5_2D_MES_LN

description: Primary tissue

value: MES LN

value: IMPB


title: yeast wild-type reference, auxin induced, rep2

value: leu2{delta}0, his3{delta}1, ura3{delta}0, met15{delta}0, Mat a


title: smxl5_1_replicat3


title: IMSB7_3A_TAIL

description: Primary tissue

value: TAIL


title: yeast wild-type reference, auxin induced, rep1


title: IMSB5_2E_MES_LN

description: Primary tissue


title: smxl5_1_replicat2


title: IMSB2_2B_PROX_SI

description: Primary tissue

source_name: PROX SI

value: PROX SI


title: IMPB_4_5G_TAIL

description: Primary tissue


title: smxl5_1_replicat1

value: Seedlings


title: IMSB1_2B_THYMUS

description: Primary tissue

source_name: THYMUS

value: THYMUS


title: WT_replicat3

value: 7 days

value: WT

value: Col


title: IMSB1_1D_LN_SAL_GL

description: Primary tissue

source_name: LN SAL GL

value: LN SAL GL


title: GV_F7_B, bovine

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Library strategy: Ribo-seq
The Salmon tool was applied to quantify the whole-genome gene expression profile from the raw sequencing data, using the bovine reference genome (UMD3.1.1). Transcript per million reads (TPM) was used as the unit of gene expression. The edgeR tool was applied to identify the differentially expressed genes. The TMM algorithm implemented in the edgeR package was applied to normalize the read count and estimate the effective library size. Groupwise differential expression was performed by the likelihood ratio test implemented in the edgeR package.
All the conventional statistical analyses were conducted using the R platform. Spearman’s rank correlation test was performed using the “cor.test” function. A linear model controlling for fractionation was applied to prioritize the polysome occupied genes with gradual increase/decrease in expression across the developmental stages using the “lm” function. If multiple testing should be accounted for, the Bonferroni procedure was applied for P-value correction using the “p.adjust” function. Principal component analysis on the expression data was performed using the “dudi.pca” function within the package “ade4”. All the heatmaps were plotted by the “heatmap.2” function within the package “gplots”. The pathway/gene ontology analysis was performed using the David tool.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: txt, normalized read counts

source_name: oocytes

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

value: oocytes

tag: developmental stage

value: GV


title: IMSB5_1A_SPLEEN

description: Primary tissue

value: SPLEEN

value: IMSB


title: WT_replicat1


title: IMSB2_3F_SPLEEN

description: Primary tissue


title: KT2440 LB (replicate 1)

city: London

first: Jose

last: Jimenez

address: South Kensington Campus

institute: Imperial College London

description:
mRNA
Sequenced by Novogene Ltd
ConR1

data_processing:
not provided
Assembly: not provided
Supplementary files format and content: Selenite.RawCounts.csv

organism: Pseudomonas putida KT2440

source_name: bacterial

growth_protocol: Cells cultured in LB for 1 hour either in the absence or presence of 1 mM selenite.

extract_protocol: Qiagen bacterial RNA extraction kit.

treatment_protocol: 1 hour exposure to 1 mM selenite.

value: bacterial

value: LB


title: KT2440 LB (replicate 2)

description:
mRNA
Sequenced by Novogene Ltd
ConR2


title: KT2440 LB 1 mM selenite (replicate 2)

description:
mRNA
Sequenced by Novogene Ltd
SelR2

value: LB + selenite


title: IMSB4_1J_MES_LN

description: Primary tissue

value: MES LN


title: WT_replicat2


title: IMSB2_3A_TAIL

description: Primary tissue

source_name: TAIL


title: SA_TENT-5_3

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

data_processing:
Illumina bcl2fastq 2.20 software used for basecalling.
Sequence reads from C. elegans experiments were mapped to the WBCel235 genome build (ENSEMBL, release 94) using STAR v. 2.6.1b
Sequence reads from M. musculus were mapped to the GRCm38 mouse genome build (ENSEMBL, release 94) using STAR v. 2.7.6a
Counts for each transcript in C. elegans experiments were collected using featureCounts from Subread package (v. 1.6.3),  with options options -Q 10 -p -B -C -s 2 -g gene_id -t exon and respective annotation gtf file (WBCel235; ENSEMBL; release 94)
Counts for each transcript in M. musculus experiments were collected using featureCounts from Subread package (v. 2.0.1),  with options options -Q 10 -p -B -C -s 2 -g gene_id -t exon and respective annotation gtf file (Gencode, vM25)
Differential expression analysis was performed using DESeq2, with default settings
Genome_build: GRCm38
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized counts for each sample.

organism: Caenorhabditis elegans

source_name: L4 worms

extract_protocol:
Total RNA from C. elegans and BMDM cells was isolated with TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. Before RNA-seq library preparation, total RNA samples were treated with TURBO DNase (Thermo Fisher Scientific) to remove DNA contamination. RNA was then purified by phenol/chloroform extraction and ethanol precipitation.
Ribosomal RNA was removed from samples using a Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat, Epicentre). Strand-specific libraries were prepared using a dUTP protocol (KAPA Stranded RNA-Seq Library Preparation Kit), according to the manufacturer. Library quality was assessed using chip electrophoresis performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: Synchronized wild-type and mutant worms were grown on NGM plates seeded with E. coli HB101 at 25°C until they reached the L4 stage. The infection plates were prepared as described (Visvikis et al., 2014). In brief, TSA plates with 10 μg/ml Nalidixic acid were prepared one week before the experiment and stored at 4°C in the dark. S. aureus was grown in TSB + Nal overnight at 37°C. 500 μl of the overnight S. aureus culture was uniformly spread onto the entire surface of 100 mm TSA + Nal plates and incubated at 37°C for 6 h. L4 worms were washed three times with sterile 50 mM NaCl and seeded onto infection TSA plates that were previously warmed to RT. After 8 h of infection at 25°C, animals were washed off the plates and resuspended in 1ml of TRI Reagent.

tag: strain

value: tent-5(tm3504) I (NBRP)

value: tent-5(tm3504) mutant

value: grown at 25℃ on TSA, infected by S. aureus NCTC8325 for 8h

value: whole worm

tag: replicate


title: SA_TENT-5_2


title: SA_TENT-5_1


title: Seq10-Vc-E1

value: VCaP

value: treated with ethanol

value: 4 month


title: SA_WT_3

value: N2 Bristol (CGC)

value: wild type


title: IMSB12_1B_TAIL

description: Primary tissue

value: TAIL


title: IMSB1_5F_TAIL

description: Primary tissue


title: IMSB1_3G_SPLEEN

description: Primary tissue


title: ChIP-seq GATA6 DE-48h biol rep 1

city: Baltimore

first: Michael

middle: A

last: Beer

state: MD

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

data_processing:
ChIP-seq: Paired-end reads were mapped to hg38 with bowtie2 using default parameters, and peaks were called using macs2 using default parameters.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

extract_protocol:
ChIP-seq: Cells were crosslinked with 1% formaldehyde and then lysed and sonicated. Clear supernatant was collected for chromatin immunoprecipitation, decrosslinking and DNA purification. Sequencing library was generated by using the NEBNext® Ultra II DNA Library Prep Kit (New England Biolabs; E7103S) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs Index Primers Set 1; NEB, E7335S).
ChIP-seq: Samples were pooled and sequenced on Illumina HiSeq 4000 platform.

value: hESC

value: idCas9-KRAB SOX17eGFP/+

value: ESC-DE differentiaion


title: KT2440 LB 1 mM selenite (replicate 1)

description:
mRNA
Sequenced by Novogene Ltd
SelR1

value: bacterial


title: ChIP-seq H3K27ac DE-72h biol rep 2


title: ChIP-seq GATA6 DE-24h biol rep 1


title: ChIP-seq H3K27ac DE-72h biol rep 1


title: IMSB3_1C_MES_MASS

description: Primary tissue

value: MES MASS

value: IMSB


title: ChIP-seq H3K27ac ESC-0h biol rep 2


title: SA_WT_1


title: SA_WT_2


title: HB_TENT-5_2

treatment_protocol: Synchronized wild-type and mutant worms were grown at 25°C on NGM plates seeded with E. coli HB101 until they reached the L4 stage. Worms were washed 3x with 50 mM NaCl and resuspended in 1 ml of TRI Reagent (Sigma-Aldrich)

value: grown at 25℃ on TSA plates seeded with E. coli HB101


title: IMSB1_5C_TAIL

description: Primary tissue


title: HB_TENT-5_3

value: tent-5(tm3504) I (NBRP)


title: IMSB1_1A_SI_MASS

description: Primary tissue

source_name: SI MASS

value: SI MASS


title: HB_TENT-5_1

value: tent-5(tm3504) mutant


title: HB_WT_3

value: whole worm


title: HB_WT_2


title: ChIP-seq H3K27ac ESC-0h biol rep 1


title: IMPB3_5D_MES_MASS

description: Primary tissue

value: IMPB


title: IMSB1_3B_TAIL

description: Primary tissue


title: HB_WT_1


title: gRNA GFP-

data_processing:
gRNA:   Sequencing reads were aligned to the gRNA library sequences and counts were obtained for each gRNA. The read counts were normalized to total reads of that sample to offset differences in read depth. gRNAs with 0 mismatch (MM)=1, 1MM<10, 2MM<30, 3MM<100 were kept for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

extract_protocol:
gRNA: Genomic DNA from sorted cell pellets was extracted using the QIAGEN Blood & Cell Culture DNA Maxi Kit (QIAGEN; 13362) and quantified by Qubit (ThermoScientific; Q32850) following the manufacturer’s guidelines. A quantity of gDNA covering 1000X representation of gRNAs was PCR amplified to add Illumina adapters and multiplexing barcodes.
gRNA: Amplicons were quantified by Qubit and Bioanalyzer (Agilent) and sequenced on the Illumina HiSeq 2500 platform.


title: Sham-P14 rep1

city: Dublin

first: vikrant

last: singh

state: Ireland

address: 31 York Street

country: Ireland

institute: Royal college of Surgeons in Ireland

description: Total RNA containing micro-RNA

data_processing:
The overall quality of the fastq files were analysed and assured that all sample having a Qscore>30.
The fastq file were processed by the mapper and quantification module miRDEEP2 ver 2.0.0.7 (PMID: 18392026 ) for miRNA expression profiling.
The processed reads were further mapped and quantified to the known miRNA for mouse by using MIRBASE version 21 (http://www.mirbase.org) and miRNA read counts were obtained for all the samples.
Differential miRNA expression analysis was undertaken using Limma bioconductor package.
Supplementary_files_format_and_content: Processed data contains read count and are in tabular format

source_name: Retina

extract_protocol:
The enucleated rat eyes were harvested at given time point and stored in the RNAlater (Qiagen), and retinas were dissected immediately under the dissection microscope. Total RNA and miRNA were isolated from the dissected retina by using a miRNeasy mini kit (Qiagen, Hilden, Germany). One microgram of miRNA samples in triplicate were prepared as per the manufacturers’ instructions (Illumina Inc. San Diego, CA, USA). The libraries of cDNA from the biological samples in triplicate were sequenced by using an Illumina Hiseq-2000 RNA-seq platform as 50 bp single end chemistry.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: Retina

tag: age

value: Post natal day 14

value: Wild type

tag: disease state

value: control


title: Sham-P14 rep2

description: Total RNA containing micro-RNA

tag: genotype


title: OIR-P29 rep3

description: Total RNA containing micro-RNA

value: Post natal day 29

value: oxygen-induced retinopathy


title: IMPB3_5A_MES_MASS

description: Primary tissue


title: Sham-P14 rep3

description: Total RNA containing micro-RNA


title: IMPB4_1D_MES_LN

description: Primary tissue

value: MES LN


title: gRNA GFP+

tag: cell line

value: hESC

value: idCas9-KRAB SOX17eGFP/+

value: ESC-DE differentiaion


title: OIR-P14 rep3

description: Total RNA containing micro-RNA


title: Hep-2 cells

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

country: India

institute: National Institute of Technology

data_processing:
The quality check of the generated raw reads was done using the FASTqc software, and analysis was performed using a data analysis pipeline, which is based on the Tuxedo software package. Hisat2 was used for read mapping to the GRCh37 human reference genome. StringTie and Cuffdiff were used for transcript-level expression analysis including assembling transcripts from reads and differential expression analysis, respectively.
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKMs

source_name: OSCC cell line

extract_protocol:
Three cell lines. H357 KB and Hep-2 were maintained in DMEM-F12, DMEM and MEM growth media respectively, supplemented with 10% FBS and 1% antibiotics Pen-Strep at proper growing conditions. Total RNA of HOK (Cat. No. #2615) was purchased from Science cell research laboratories, USA. For H357, KB, and Hep-2, total RNA was extracted using trizol method. The purity of isolated RNA was evaluated using NanoDrop spectrophotometer (Thermo Scientific) by measuring absorbance at 260 nm and 280 nm. An aliquot of each sample from H357, HOK, KB and Hep-2 was run on an Agilent RNA Bioanalyzer to check RNA integrity number (RIN), which were found to be 10 for all the samples.
The RNA libraries were constructed for sequencing following Illumina HiSeq transcriptome library protocol. 3’ and 5’ adapter ligation was done followed by PCR-amplification. After library construction, pair-end sequencing was done on Illumina Hiseq2500 with 2×150 bp to obtain reads. After the sequencing, RNA-Seq reads were quality checked and processed into FASTQ files.

value: Oral squamous cell carcinoma (OSCC)


title: OIR-P29 rep2

description: Total RNA containing micro-RNA


title: OIR-P14 rep1

description: Total RNA containing micro-RNA


title: IMPB3_3C_SPLEEN

description: Primary tissue

value: SPLEEN


title: IMPB2_4B_MES_MASS

description: Primary tissue

value: MES MASS


title: H357 cells


title: OIR-P14 rep2

description: Total RNA containing micro-RNA


title: IMPB12_3B_MES_LN

description: Primary tissue


title: extracellular DNA replicate 3

city: St. Paul

first: Scott

middle: M.

last: O'Grady

state: Minnesota

address: 480 Haecker Hall, 1364 Eckles Avenue

department: Animal Science

institute: University of Minnesota

description: Extracellular DNA from hBE cells treated with Alternaria extract, replicate 3

data_processing:
Library strategy: DNA-seq
Trimming sequences: Raw fastq files were trimmed of adapters and low quality sequence with Trimmomatric (settings: ILLUMINACLIP:all_illumina_adapters.fa:2:30:10:2:true LEADING:3)  TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
PCR duplicate removal: Duplicates were removed using Picard v2.18.16
Aligning sequences: Trimmed reads were aligned to the Homo sapiens GRCh38 genome using Star 2.7.1a
Peak calling: Enriched read pileups ("peaks")  were called in each sample with Genrich
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: tab-delimited text files for each replicate containing Genrich peak coordinates and scores, bedgraph files

source_name: Primary human bronchial epithelial (hBE) cells

growth_protocol: Cells were grown in human bronchial epithelial cell growth medium with growth factor supplements (PromoCell GmbH, Heidelberg, Germany) at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol:
DNA extraction was accomplished using Quick-DNA Universal Kit (Zymo Research, Irvine CA) and stored in elution buffer (10 mM Tris-HCl, pH 8.5, 0.1 mM EDTA) at a concentration of ~4 ng/ul.
Nextera DNA library prep protocol

treatment_protocol: Cells were treated with Alternaria extract (100 mg/ml) for 4 hours

tag: cell treatment

value: Alternaria extract

tag: source

value: extracellular DNA


title: IMPB2_6E_SPLEEN

description: Primary tissue

value: IMPB


title: HOK cells

source_name: Human oral keratinocytes

value: HOK

value: normal


title: Xenograft shGLO1#1 replicate 2

type: genomic

city: Brussels

first: Gaurav

last: Dube

state: Brussels Capital Region

address: 808 Route de Lennik

department: Faculty of Medicine

country: Belgium

institute: UCRC-ULB

hyb_protocol: Genomic DNA (300–800 ng) was converted with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research), and it was hybridized with the Illumina HumanMethylation850 BeadChip 850K array according to the manufacturer’s protocol.

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

data_processing: Raw Infinium 850k data were preprocessed following the published guidelines: CpG probes of low quality (detection p-value threshold of 0.05) or targeting X and Y-chromosomes were removed from the analysis. Additionally, probes targeting methylation sites located at common single-nucleotide polymorphism as well as cross-reactive probes (i.e. targeting several genomic locations) were filtered out based on the extended annotation of McCartney et al. Beta-values were computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction.

source_name: MDA-MB-231 cells grafted in mouse

label_protocol: Standard Illumina Protocol

growth_protocol: Breast cancer cell line MDA-MB-231 were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Lonza) containing 10% fetal bovine serum (FBS, ThermoFisher Scientific) and 2mM L-glutamine (Lonza). L-carnosine (C9625), aminoguanidine (396494), methylglyoxal (MG, M0252) and 5’Aza-2’Deoxycytidine (A3656) and cycloheximide (C7698) were from Sigma.

extract_protocol: Genomic DNA was extracted with the QIAamp DNA Mini Kit (from QIAGEN) following the manufacturer’s protocol.

treatment_protocol: MDA-MB-231 cells were stably silenced for GLO1 using shRNA

tag: biologicalreplicate

tag: technicalreplicate


title: extracellular DNA replicate 2

description: Extracellular DNA from hBE cells treated with Alternaria extract, replicate 2


title: Xenograft shGLO1#1 replicate 1


title: Xenograft shNT replicate 1

value: TumorshNT


title: rat rep1

description: Total RNA containing micro-RNA

data_processing:
The quality of all the sample were analysed and assured that all sample have Q-score more than 30.
The fastq file were processed by the mapper and quantification module miRDEEP2 ver 2.0.0.7 (PMID: 18392026 ) for miRNA expression profiling.
The processed reads were further mapped to the known miRNA for mouse and rat by using MIRBASE version 21 (http://www.mirbase.org) and miRNA read counts were obtained for all the samples.
Supplementary_files_format_and_content: Processed data contains read count and are in tabular format

extract_protocol:
The enucleated rat eyes were harvested and stored in the RNAlater (Qiagen), and retinas were dissected immediately under a dissection microscope. Total RNAs and miRNAs were isolated from the dissected retina by using a miRNeasy mini kit (Qiagen, Hilden, Germany). One microgram of miRNA samples in triplicate was prepared as per the manufacturers’ instructions (Illumina Inc. San Diego, CA, USA). The libraries of cDNA from the biological samples in triplicate were sequenced by using an Illumina Hiseq-2500 RNA-seq platform as 50 bp single-end chemistry.
miRNA libraries were prepared for sequencing using a standard Illumina protocols

value: Sprague Dawley

tag: tissue

value: Retina

value: 9 weeks

value: Wild type


title: IMPB12_1B_LN_THROAT

description: Primary tissue

data_processing:
BAM files were generated using illumina2bam.
The transposon-genomic junction was reassembled by concatenating the 12 bp transposon read and Read1.
Read pairs were split into separate FASTQ files for Read1 and Read2.
Mapping of integrations to the mouse genome was performed using the SSAHA2 algorithm.
High-confidence insertion coordinates were exported as BED file.
Assembly: mm10
Supplementary files format and content: SBvsPB.csv: Processed data file contains insertion sites (genomic positions) from both libraries (5' and 3' transposon end), read counts for each insertion and gene annotations. File is in comma-separated format and contain insertions sites for all samples listed here.

source_name: LN THROAT

extract_protocol:
DNA isolation of tissue samples was performed according to manufacturer’s instructions using the Qiagen DNeasy Blood & Tissue Kit.
DNA samples were sheared with a Covaris AFA sonicator to a mean fragment length of 250 bp. The fragmented DNA was then end-repaired, A-tailed and a splinkerette adapter was ligated to each DNA end. For the 5’ and 3’ transposon end, subsequent steps (amplification and sequencing of transposon-genome junctions) were conducted separately.
The specific structure of the splinkerette adapter (Y-shaped design with a template and a hairpin strand) ensures that only transposon-genome junction fragments (and not genomic fragments without transposon insert) can be amplified in the first PCR step (which was conducted with transposon- and splinkerette-specific primers). Afterwards, a second nested PCR step was performed for further amplification, barcoding of samples and extension with Illumina flow cell binding sites P5 and P7. Samples were equimolarly mixed and the library pool was again quantified. Libraries were sequenced on the Illumina MiSeq sequencer (75 bp, paired-end).

value: LN THROAT


title: rat rep3

description: Total RNA containing micro-RNA


title: extracellular DNA replicate 1

description: Extracellular DNA from hBE cells treated with Alternaria extract, replicate 1


title: MDA231 shGLO1#1 replicate 2

source_name: MDA-MB-231 cells


title: Hep-2

data_processing:
The reads obtained from the sequencing were quality checked and Phred scores were calculated, which were found to be around 40 for each sample. The reads were trimmed for adapter sequence using Cutadapt tool followed by subsequent analysis predicting piRNAs, miRNAs and their expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of annotated piRNAs and miRNAs predicted for each sample.

extract_protocol:
Three cell lines, H357, KB, and Hep-2 were procured and grown in DMEM-F12, DMEM, and MEM growth media respectively, supplemented with 10% FBS and 1% antibiotics Pen-Strep under optimal conditions. Total RNA was extracted from the cell lines using the trizol method, yielding 37280ng (from H357), 54800ng (from KB), 1620ng (from HOK), and more than 5000ng (in Hep-2). The purity of isolated RNA was determined using a NanoDrop spectrophotometer and absorbance measurements at 260 and 280 nm. Total RNA of HOK were procured directly from ScienCell Research Laboratories, USA. An aliquot of each sample isolated from these cell lines were also tested on an Agilent RNA Bioanalyzer chip for RNA integrity number (RIN), which was found to be 10 for all cell lines, indicating intactness of the isolated RNA.
The RNA libraries were constructed for sequencing following NEB Next Small RNA Sample Preparation protocol. After library preparation, they were sequenced on Illumina HiSeq 2500 with a 1x50 bp read size to obtain 60-85 million reads. Following the sequencing, the Illumina small RNA-Seq data was processed to create FASTQ files.

tag: cell lines

value: cancer


title: MDA231 shGLO1#1 replicate 1


title: Xenograft shGLO1#2 replicate 2


title: KB cells

value: KB


title: IMPB1_5F_TAIL

description: Primary tissue

value: TAIL


title: Cells arrested in Cdc15 (cdc15-2) Mcd1-6HA replicate 1

first: Jonay

last: Garcia-Luis

state: London

address: Du Cane Road

department: London Institute of Medical Sciences

institute: UKRI

description: Sample_190329JG14731_1_IP_S17_L001_R1_001

data_processing:
HiC: Alignment of the reads and processing of the contact data was done with Hicstuff using the S288C reference genome (Matthey-Doret et al. 2020, 10.5281/zenodo.4066351). Hicstuff pipeline was launched with the following parameters: filter out spurious 3C events, filter out PCR duplicates based on read positions. The “view” mode of Hicstuff ICE function was used to generate normalized contact maps as described in Imakaev et al. 2012, 10.1038/nmeth.2148).
ChIP-seq: Calibrated Chip-seq: The quality of the raw sequence data was assessed using FastQC (version 0.11.5). The reads were mapped to the S. cerevisiae genome (sacCer3) as the experimental genome or C. glabrata genome (CBS138) as the calibration genome using Bowtie 2 (version 2.3.4) with default parameters. To generate an alignment in which all the sequences exclusively map to the sacCer3 genome, the whole reads were first mapped to CBS138 genome and the unmapped reads were retrieved as a separate Fastq file. Subsequently, these unmapped reads were re-aligned to sacCer3 genome and the generated aligned BAM file therefore contained reads that were unique to sacCer3. The same method was used to generate alignments unique to CBS138. The occupancy ratio (ORi) was calculated as in Hu, B. et al.2015 (DOI: 10.1093/nar/gkv670). For each sample, the alignment BAM file was converted to Wig format using bedtools (version 2.27.1). To obtain a calibrated version, the Wig file with the conventional ChIP-seq profile was multiplied by the OR corresponding to each sample. Subsequently, these calibrated BigWig files were used to generate average profile plots for regions in ±10 kb of centromeres for 16 chromosomes in the sacCer3 genome
Genome_build: S288C reference genome
Supplementary_files_format_and_content: HiC: .cool   ChIP-seq: .bw

extract_protocol: 100 ml of culture at OD600=1 were mixed with 30 ml OD600=1 of C. glabrata cells and fixed for 15 minutes at 25 °C, and quenched with glycine (final concentration 125 mM) for 7 minutes before cells were harvested by centrifugation at 4,000 r.p.m. for 1 minute. The cell pellets were washed in PBS and transferred to a screw cap tube and frozen on dry ice. The pellets were stored at -80 °C. Pellets were resuspended in 300 μl of IP buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, NP-40 (0.05% v/v), Triton® X-100 (1% v/v)) containing phenylmethanesulfonyl fluoride (PMSF, final concentration 1 mM) and Complete protease inhibitor cocktail (without EDTA, from Roche). 500 μl of glass beads were added to the tubes. Cells were broken in a FastPrep® FP120 (BIO101) by 3 repetitions of a 20 seconds cycle, power setting 5.5. Cells were maintained on ice for 2 minutes after each cycle. The tubes were pierced with a hot needle and placed into new eppendorf and spun at 2000 r.p.m. for 2 minutes to collect the lysate. 100 μl of IP buffer containing PMSF and protease inhibitors were then added and tubes spun again at 2000 r.p.m. for 1 minute. The cell lysate was spun down for 10 minutes at 15,000 r.p.m at 4 °C. This pellet was resuspended in 1ml of IP buffer containing PMSF and protease inhibitors, and sonicated for 1 hour (30 seconds on, 30 seconds off) at high power at 4 °C in a Diagenode Bioruptor. After sonication samples were spun down for 10 minutes at 15,000 r.p.m. and the supernatant taken. 100 μl of the sonicated chromatin were taken as “input” and 200 μl was incubated with 20 μg of HA antibody (anti-HA 12CA5 from Roche) in a sonicator at low power for 30 minutes (30 seconds on, 30 seconds off). The “input” DNA was precipitated with 0.3 M sodium acetate and 2.5 volumes of cold ethanol and spun down at 15,000 r.p.m. for 30 minutes, and the supernatant removed. The pellet was washed with 70 % ethanol and air dried. After antibody binding the IP sample was spun down at 13,000 r.p.m for 5 minutes and the supernatant added to 30 μl of Dynabeads protein G (Invitrogen) previously equilibrated with IP buffer. Then the samples were incubated for 2 hours at 4 °C in a rotating wheel and washed 5 times with IP buffer using a magnetic separator rack. Finally “input” samples and IP samples were resuspended in de-crosslinking buffer (TE 1X, 1 % SDS,  10 μg/ml RNase A , 1 mg/ml proteinase K) and incubated at 65 °C overnight. Samples were purified using ChIP DNA Clean & Concentrator kit (Zymoresearch) according to the manufacturer instructions. Samples were eluted in 30 μl of water.  For each ChIP tagged and untagged strains were used to eliminate background and non-specific enrichment.

tag: treatment

value: Overnigth culture growing in YPD at 25⁰C was diluted to OD600=0.7. Cells were arrested in late anaphase (cdc15-2) by shifting the temperature to 37⁰C for 3 hours


title: Cells arrested in Cdc15 (cdc15-2) Untagged replicate 2

description: Sample_190329JG1835_2_IP_S19_L001_R1_001


title: IMPB1_2E_TAIL

description: Primary tissue


title: Cells arrested in Cdc15 (cdc15-2) Untagged replicate 1

description: Sample_190329JG1835_1_IP_S15_L001_R1_001


title: KB


title: H357


title: MDA231 shNT replicate 3


title: Silenz_I_Exp_R1

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk 37.31
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with RSEM 1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts

source_name: Ctrl- mouse endothelial cells

growth_protocol: Immortalised mouse endothelial cells (ECs) were cultured in D-MEM with Glutamax supplemented with 20% FBS and 1% penicillin (100 U/ml) and streptomycin (100 μg/ml) (Thermo Fisher Scientific, USA) and grown in a 5% CO2 incubator at 37° C

extract_protocol:
Total RNA was extracted using mini RNase kit reagent (Qiagen, Tübingen, Germany).
Poly-A enriched library were generated with the TruSeq RNA-Seq Library Preparation Kit v2 (#RS-122-2001, Illumina) according to the manufacturer’s instructions. Library quality control was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Indexed libraries were sequenced at CRS4 Next Generation Sequencing facility with the HiSeq 3000 instrument to generate ~40M 50bp single-end reads per sample.

treatment_protocol: Stealth RNAi duplexes designed against mouse Pdcd10 (Thermo Fisher Scientific, USA, PDCD10HSS174173; PDCD10HSS117454; PDCD10HSS117455) or stealth RNAi negative control (Thermo Fisher Scientific, USA, cat#12935115) were transfected in ECs cells (siPdcd10-ECs and Ctrl-ECs respectively) using Lipofectamine RNAiMAX (Thermo Fisher Scientific, USA) according to the manufacturer's protocol.

tag: condition

value: Ctrl-Silenced

value: Immortalised aortic endothelial cells


title: Cells arrested in Cdc15 (cdc15-2) Mcd1-6HA replicate 2

description: Sample_190329JG14731_2_IP_S21_L001_R1_001


title: Silenz_II_Exp_R1

tag: cell type


title: Xenograft shNT replicate 2


title: HOK


title: Xenograft shGLO1#1 replicate 3


title: Silenz_III_Exp_R1


title: JQ1-siBRD4

city: houston

first: Ming-Jer

last: Tsai

state: Texas

address: One Baylor Plaza

institute: baylor college of medicine

data_processing:
Read preparation and QC through EA | Q² Solutions developed tool, fastq-mcf
Alignment and Quantification using STAR version 2.4 and RNA-Seq quantification software RSEM, version 1.2.14
Post-quantification analysis using the SAMPLE.star.bam
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: prostate cancer cell line LNCaP

growth_protocol: LNCaP cells were cultured in PRMI1640 medium supplemented with 10% FBS

extract_protocol:
Cells wer flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were transfected with siRNA, and treated with 200nM JQ1 for 72 hours.

value: prostate cancer

value: LNCaP


title: MDA231 shGLO1#2 replicate 1


title: MDA231 shGLO1#1 replicate 3


title: rat rep2

description: Total RNA containing micro-RNA


title: OIR-P29 rep1

description: Total RNA containing micro-RNA

value: Post natal day 29

value: oxygen-induced retinopathy


title: IMPB10_6B_TAIL

first: Roland

last: Rad

address: Ismaninger Strasse 22

institute: Technical University of Munich

description: Primary tissue

value: IMPB


title: MDA231 shGLO1#2 replicate 3


title: Xenograft shGLO1#2 replicate 1


title: CTRL_I_Exp_R1

source_name: Pdcd10-silenced mouse endothelial cells


title: MDA231 shGLO1#2 replicate 2


title: IMPB11_1B_MES_LN

description: Primary tissue

source_name: MES LN

value: MES LN


title: Xenograft shGLO1#2 replicate 3


title: MDA231 shNT replicate 2


title: MDA231 shNT replicate 1


title: JQ1-siCon


title: Xenograft shNT replicate 3

value: TumorshNT


title: CTRL_II_Exp_R1


title: CTRL_III_Exp_R1


title: DMSO-siBRD4


title: DMSO-siCon

value: DMSO-siCon


title: IMPB10_4B_MES_LN

description: Primary tissue


title: Cells arrested in Cdc15 (cdc15-as) and depleted for Mcd1-AID and Smc3-AID by addition of 6mM IAA

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
AT391

extract_protocol:
Cells were fixed with 3% formaldehyde (Sigma-Aldrich, F8775) as detailed in Dauban et al. 2020 (DOI: 10.1016/j.molcel.2020.01.019). Formaldehyde was quenched with 300 mM of glycine at room temperature for 20 min.Hi-C  experiments  were performed  with  a  Hi-C  kit  (Arima  Genomics)  involving  a double DpnII + HinfI restriction digestion.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was done with Collibri™ ES DNA Library Prep Kit for Illumina Systems (Thermo Fisher, A38605024).

value: Cells were first arrested in alpha factor. After release from alpha factor cells were treated with 10µM of 1-NM-PP1 for 1 hour 45 min


title: IMPB10_4C_MES_MASS

description: Primary tissue

source_name: MES MASS

value: MES MASS


title: IMPB10_4A_MES_MASS

description: Primary tissue


title: Cells arrested in Cdc15  (cdc15-as) and depleted for Mcd1-AID by addition of 6mM IAA

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
AT390


title: Cells arrested in Cdc15 (cdc15-as) WT

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
AT389

source_name: Cells arrested in Cdc15 (cdc15-as) WT


title: Bone Marrow, T-ALL Control, rep8 [sample.081417_aavs1]

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

data_processing:
Partek Flow 10.0.22.0524
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek flow
Trimmed raw RNA-seq reads were aligned to the Ensembl release hg38 (Human) using STAR version 2.7.3a
Read count extraction and normalization were performed using Partek flow
Assembly: Ensembl release hg38 (Human)
Supplementary files format and content: Excel files include CPM values for each Sample

source_name: Bone Marrow

extract_protocol:
RNA was harvested using NucleoSpin RNA XS kit (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using SMARTer Ultra Low RNA kit (Clontech) following manufacturer's protocols.

value: Bone Marrow

value: T-ALL blast

value: KDM6B wild type


title: Bone Marrow, T-ALL KO, rep15 [sample.081417_18d]

value: KDM6B knock-out


title: Bone Marrow, T-ALL KO, rep14 [sample.1315818_18d]


title: RNA_X2_cells_Proximal_polyadenylation sites_Rep2

city: Bangalore

first: Dasaradhi

last: Palakodeti

state: Karnataka

address: GKVK Campus, Bellary road

department: TAS

institute: inStem, NCBS

description: We isolated RNA from FACS sorted cells and gene expression analysis was done.

hyb_protocol: Agilent’s In situ Hybridzation kit 5190-6420 was used for hybridization

scan_protocol: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 072436_D_F_20150113) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.Background detrend ( On(FeatNCRange, LoPass)), saturation value 65526.

data_processing: The images were manually verified and found to be devoid of uneven hybridization, streaks, blobs and other artifacts. Hybridization across the slide was good based on number of feature that were “g is PosAndSignif” which indicates feature is positive and significantly above background.The microarray images were overall clean, uniform intensity and with very low background noise.

organism: Schmidtea mediterranea

source_name: X2 cells, Proximal peaks

label_protocol: OligodT primer with T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis).Agilent’s Quick-Amp labeling Kit (p/n:5190-0442) was used for labelling

extract_protocol: We isolated mRNA through oligodT probes from different samples and used as input for the microarray experiment. Qiagen’s RNeasy minikit Cat#74106 was used.

treatment_protocol: No specific treatment was done to isolated RNA

value: X2 (Progenitor cells)

value: Sexual


title: RNA_X1_cells_Proximal_polyadenylation sites_Rep2

source_name: X1 cells, Proximal peaks

value: X1 (Stem cells)


title: RNA_X1_cells_Proximal_polyadenylation sites_Rep1


title: Bone Marrow, T-ALL Control, rep7 [sample.1315818_aavs1]


title: RNA_X2_cells_Proximal_polyadenylation sites_Rep1


title: IMPB1_6D_TAIL

city: München

description: Primary tissue

source_name: TAIL

value: TAIL


title: IMPB11_1A_MES_MASS

description: Primary tissue


title: RNA_Xins_cells_Proximal_polyadenylation sites_Rep1

source_name: Xins cells, Proximal peaks

value: Xins (Differentiated cells)


title: Cells arrested in Cdc20 metaphase

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB60

source_name: Cells arrested in Cdc20 metaphase

value: To arrest cells in metaphase (Cdc20), cells carrying the CDC20 gene under methionine repressible promoter MET3 (MET3-CDC20) were grown overnight in minimal media lacking methionine. The day after cells were arrested by washing the cells and resuspending them in rich media containing 5mM methionine for 3 hours at 23⁰C


title: Bone Marrow, T-ALL KO, rep13 [sample.1315818_18a]


title: Bone Marrow, T-ALL KO, rep11 [sample.1229314_18a]


title: Bone Marrow, T-ALL KO, rep12 [sample.1229314_18d]


title: Cells arrested in Cdc20 metaphase and Mcd1 degraded using AID auxin degron replicate 2

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB57

value: To arrest cells in metaphase (Cdc20), cells carrying the CDC20 gene under methionine repressible promoter MET3 (MET3-CDC20) were grown overnight in minimal media lacking methionine. The day after cells were arrested by washing the cells and resuspending them in rich media containing 5mM methionine for 3 hours at 23⁰C. IAA was added and samples for HiC were collected after 60 minutes


title: RNA_Xins_cells_Proximal_polyadenylation sites_Rep2


title: Cells arrested in Cdc20 metaphase and Mcd1 degraded using AID auxin degron replicate 1

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB56_b


title: IMPB1_5C_LN

description: Primary tissue

source_name: LN

value: LN

value: IMPB


title: IMPB1_5B_CERV_LN

description: Primary tissue

source_name: CERV LN

value: CERV LN


title: Bone Marrow, T-ALL Control, rep6 [sample.1229314_aavs1]


title: Bone Marrow, T-ALL KO, rep10 [sample.1224099_18d]


title: Cells arrested in Cdc20 metaphase and Mcd1 cleaved with TEV protease replicate 2

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB55_b

value: To arrest cells in metaphase (Cdc20), cells carrying the CDC20 gene under methionine repressible promoter MET3 (MET3-CDC20) were grown overnight in minimal media lacking methionine and raffinose 2%. The day after, cells were arrested by washing the cells and resuspending them in rich media containing 5mM methionine for 3 hours at 23⁰C. Galactose 2% was added to the media and samples for HiC were collected after 90 minutes


title: Bone Marrow, T-ALL Control, rep5 [sample.1224099_aavs1]


title: Bone Marrow, T-ALL KO, rep9 [sample.1224099_18a]


title: IMPB10_3D_LN

description: Primary tissue


title: IMPB1_5A_TAIL

description: Primary tissue


title: IMPB10_3C_LN

description: Primary tissue


title: Bone Marrow, T-ALL KO, rep8 [sample.k424_18d]


title: IMPB1_4E_SPLEEN

description: Primary tissue

source_name: SPLEEN

value: SPLEEN


title: Bone Marrow, T-ALL KO, rep7 [sample.k424_18a]


title: Bone Marrow, T-ALL Control, rep4 [sample.k424_aavs1]


title: Cells arrested in Cdc20 metaphase and Mcd1 cleaved with TEV protease replicate 1

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB54_b


title: Bone Marrow, T-ALL KO, rep6 [sample.670_18d]


title: IMPB1_4A_LN

description: Primary tissue


title: Bone Marrow, T-ALL KO, rep5 [sample.670_18a]


title: IMPB1_3A_SPLEEN

description: Primary tissue


title: Bone Marrow, T-ALL KO, rep4 [sample.452_18d]


title: ChIP-seq H3K27ac DE-24h biol rep 2

value: hESC

value: idCas9-KRAB SOX17eGFP/+

value: ESC-DE differentiaion


title: Bone Marrow, T-ALL Control, rep2 [sample.452_aavs1]

value: Bone Marrow

value: T-ALL blast

value: KDM6B wild type


title: Bone Marrow, T-ALL KO, rep3 [sample.452_18a]

value: KDM6B knock-out


title: ChIP-seq H3K27ac DE-24h biol rep 1


title: Bone Marrow, T-ALL KO, rep2 [sample.315_18d]


title: ChIP-seq H3K27ac DE-48h biol rep 2


title: ChIP-seq H3K27ac DE-48h biol rep 1


title: IMPB1_2A_MES_MASS

description: Primary tissue

value: MES MASS


title: IMPB1_2D_CERV_MASS

description: Primary tissue

source_name: CERV MASS

value: CERV MASS


title: ChIP-seq CTCF DE-72h biol rep 2


title: Bone Marrow, T-ALL KO, rep1 [sample.315_18a]


title: Bone Marrow, T-ALL Control, rep3 [sample.670_aavs1]


title: ChIP-seq CTCF DE-72h biol rep 1


title: SOX9KO Huh-7 cells-3

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
We use "FDR ≤0.001 and the absolute value of log2Ratio ≥1" as the threshold to judge the significance of gene expression difference.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count and normalized RPKM values for each Sample

source_name: Huh-7 cells

growth_protocol: Huh-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (foreukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random.  hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End  reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR  amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: SOX9 knockout (SOX9KO)Huh-7 cells were established by crisper-cas9 system. Then 1✖106 Huh-7 and SOX9KO Huh-7 cells  were seeded in 35mm dish and cultured for 48 hours.

value: Huh-7 cells

value: Hapatocarcinoma cells

value: SOX9 knockout


title: SOX9KO Huh-7 cells-2


title: SOX9KO Huh-7 cells-1


title: ChIP-seq CTCF DE-48h biol rep 2


title: ChIP-seq CTCF DE-48h biol rep 1


title: Huh-7 cells-1

value: WT


title: T47D DMSO 24h BioRep 3

city: Atlanta

first: Jennifer

middle: Marie

last: Spangle

state: Georgia

address: 1365C Clifton Rd NE

institute: Emory University

data_processing:
Illumina Dragen 3.7.5 was used to map align and perform quantification (salmon) of transcript expression
Quantification was mapped to hg38 (GrCh38p13/gencode.v36)
Assembly: GrCh38p13
Supplementary files format and content: quant.sf file containing read counts

source_name: not applicable

growth_protocol: T47D were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using the Qiagen RNeasy kit with on-column DNaseI digestion. 1.5ug total RNA was used to construct sequencing libraries
Libraries were constructed by Novogene

treatment_protocol: T47D were treated with 4uM MI503 or DMSO for 24h

value: not applicable

value: Hormone receptor + breast cancer

value: DMSO 24h


title: T47D 4uM MI503 24h BioRep 3


title: T47D DMSO 24h BioRep 2